Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

Science.gov (United States)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

Highly conserved non-coding sequences are associated with vertebrate development.

Directory of Open Access Journals (Sweden)

Adam Woolfe

2005-01-01

Full Text Available In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH, in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development

An Auto sequence Code to Integrate a Neutron Unfolding Code with thePC-MCA Accuspec

International Nuclear Information System (INIS)

Darsono

2000-01-01

In a neutron spectrometry using proton recoil method, the neutronunfolding code is needed to unfold the measured proton spectrum to become theneutron spectrum. The process of the unfolding neutron in the existingneutron spectrometry which was successfully installed last year was doneseparately. This manuscript reports that the auto sequence code to integratethe neutron unfolding code UNFSPEC.EXE with the software facility of thePC-MCA Accuspec has been made and run successfully so that the new neutronspectrometry become compact. The auto sequence code was written based on therules in application program facility of PC-MCA Accuspec and then it wascompiled using AC-EXE. Result of the test of the auto sequence code showedthat for binning width 20, 30, and 40 giving a little different spectrumshape. The binning width around 30 gives a better spectrum in mean of givingsmall error compared to the others. (author)

Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes

Directory of Open Access Journals (Sweden)

Maggi Giorgio P

2008-06-01

Full Text Available Abstract Background The accurate detection of genes and the identification of functional regions is still an open issue in the annotation of genomic sequences. This problem affects new genomes but also those of very well studied organisms such as human and mouse where, despite the great efforts, the inventory of genes and regulatory regions is far from complete. Comparative genomics is an effective approach to address this problem. Unfortunately it is limited by the computational requirements needed to perform genome-wide comparisons and by the problem of discriminating between conserved coding and non-coding sequences. This discrimination is often based (thus dependent on the availability of annotated proteins. Results In this paper we present the results of a comprehensive comparison of human and mouse genomes performed with a new high throughput grid-based system which allows the rapid detection of conserved sequences and accurate assessment of their coding potential. By detecting clusters of coding conserved sequences the system is also suitable to accurately identify potential gene loci. Following this analysis we created a collection of human-mouse conserved sequence tags and carefully compared our results to reliable annotations in order to benchmark the reliability of our classifications. Strikingly we were able to detect several potential gene loci supported by EST sequences but not corresponding to as yet annotated genes. Conclusion Here we present a new system which allows comprehensive comparison of genomes to detect conserved coding and non-coding sequences and the identification of potential gene loci. Our system does not require the availability of any annotated sequence thus is suitable for the analysis of new or poorly annotated genomes.

Performance Analysis for Cooperative Communication System with QC-LDPC Codes Constructed with Integer Sequences

Directory of Open Access Journals (Sweden)

Yan Zhang

2015-01-01

Full Text Available This paper presents four different integer sequences to construct quasi-cyclic low-density parity-check (QC-LDPC codes with mathematical theory. The paper introduces the procedure of the coding principle and coding. Four different integer sequences constructing QC-LDPC code are compared with LDPC codes by using PEG algorithm, array codes, and the Mackey codes, respectively. Then, the integer sequence QC-LDPC codes are used in coded cooperative communication. Simulation results show that the integer sequence constructed QC-LDPC codes are effective, and overall performance is better than that of other types of LDPC codes in the coded cooperative communication. The performance of Dayan integer sequence constructed QC-LDPC is the most excellent performance.

GenProBiS: web server for mapping of sequence variants to protein binding sites.

Science.gov (United States)

Konc, Janez; Skrlj, Blaz; Erzen, Nika; Kunej, Tanja; Janezic, Dusanka

2017-07-03

Discovery of potentially deleterious sequence variants is important and has wide implications for research and generation of new hypotheses in human and veterinary medicine, and drug discovery. The GenProBiS web server maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein-protein, protein-nucleic acid, protein-compound, and protein-metal ion binding sites. The concept of a protein-compound binding site is understood in the broadest sense, which includes glycosylation and other post-translational modification sites. Binding sites were defined by local structural comparisons of whole protein structures using the Protein Binding Sites (ProBiS) algorithm and transposition of ligands from the similar binding sites found to the query protein using the ProBiS-ligands approach with new improvements introduced in GenProBiS. Binding site surfaces were generated as three-dimensional grids encompassing the space occupied by predicted ligands. The server allows intuitive visual exploration of comprehensively mapped variants, such as human somatic mis-sense mutations related to cancer and non-synonymous single nucleotide polymorphisms from 21 species, within the predicted binding sites regions for about 80 000 PDB protein structures using fast WebGL graphics. The GenProBiS web server is open and free to all users at http://genprobis.insilab.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Machine-Checked Sequencer for Critical Embedded Code Generator

Science.gov (United States)

Izerrouken, Nassima; Pantel, Marc; Thirioux, Xavier

This paper presents the development of a correct-by-construction block sequencer for GeneAuto a qualifiable (according to DO178B/ED12B recommendation) automatic code generator. It transforms Simulink models to MISRA C code for safety critical systems. Our approach which combines classical development process and formal specification and verification using proof-assistants, led to preliminary fruitful exchanges with certification authorities. We present parts of the classical user and tools requirements and derived formal specifications, implementation and verification for the correctness and termination of the block sequencer. This sequencer has been successfully applied to real-size industrial use cases from various transportation domain partners and led to requirement errors detection and a correct-by-construction implementation.

A nonlinear bi-level programming approach for product portfolio management.

Science.gov (United States)

Ma, Shuang

2016-01-01

Product portfolio management (PPM) is a critical decision-making for companies across various industries in today's competitive environment. Traditional studies on PPM problem have been motivated toward engineering feasibilities and marketing which relatively pay less attention to other competitors' actions and the competitive relations, especially in mathematical optimization domain. The key challenge lies in that how to construct a mathematical optimization model to describe this Stackelberg game-based leader-follower PPM problem and the competitive relations between them. The primary work of this paper is the representation of a decision framework and the optimization model to leverage the PPM problem of leader and follower. A nonlinear, integer bi-level programming model is developed based on the decision framework. Furthermore, a bi-level nested genetic algorithm is put forward to solve this nonlinear bi-level programming model for leader-follower PPM problem. A case study of notebook computer product portfolio optimization is reported. Results and analyses reveal that the leader-follower bi-level optimization model is robust and can empower product portfolio optimization.

Modelling of blackout sequence at Atucha-1 using the MARCH3 code

International Nuclear Information System (INIS)

Baron, J.; Bastianelli, B.

1997-01-01

This paper presents the modelling of a complete blackout at the Atucha-1 NPP as preliminary phase for a Level II safety probabilistic analysis. The MARCH3 code of the STCP (Source Term Code Package) is used, based on a plant model made in accordance with particularities of the plant design. The analysis covers all the severe accident phases. The results allow to view the time sequence of the events, and provide the basis for source term studies. (author). 6 refs., 2 figs

DNA watermarks in non-coding regulatory sequences

Directory of Open Access Journals (Sweden)

Pyka Martin

2009-07-01

Full Text Available Abstract Background DNA watermarks can be applied to identify the unauthorized use of genetically modified organisms. It has been shown that coding regions can be used to encrypt information into living organisms by using the DNA-Crypt algorithm. Yet, if the sequence of interest presents a non-coding DNA sequence, either the function of a resulting functional RNA molecule or a regulatory sequence, such as a promoter, could be affected. For our studies we used the small cytoplasmic RNA 1 in yeast and the lac promoter region of Escherichia coli. Findings The lac promoter was deactivated by the integrated watermark. In addition, the RNA molecules displayed altered configurations after introducing a watermark, but surprisingly were functionally intact, which has been verified by analyzing the growth characteristics of both wild type and watermarked scR1 transformed yeast cells. In a third approach we introduced a second overlapping watermark into the lac promoter, which did not affect the promoter activity. Conclusion Even though the watermarked RNA and one of the watermarked promoters did not show any significant differences compared to the wild type RNA and wild type promoter region, respectively, it cannot be generalized that other RNA molecules or regulatory sequences behave accordingly. Therefore, we do not recommend integrating watermark sequences into regulatory regions.

Comparison of Danish dichotomous and BI-RADS classifications of mammographic density.

Science.gov (United States)

Hodge, Rebecca; Hellmann, Sophie Sell; von Euler-Chelpin, My; Vejborg, Ilse; Andersen, Zorana Jovanovic

2014-06-01

In the Copenhagen mammography screening program from 1991 to 2001, mammographic density was classified either as fatty or mixed/dense. This dichotomous mammographic density classification system is unique internationally, and has not been validated before. To compare the Danish dichotomous mammographic density classification system from 1991 to 2001 with the density BI-RADS classifications, in an attempt to validate the Danish classification system. The study sample consisted of 120 mammograms taken in Copenhagen in 1991-2001, which tested false positive, and which were in 2012 re-assessed and classified according to the BI-RADS classification system. We calculated inter-rater agreement between the Danish dichotomous mammographic classification as fatty or mixed/dense and the four-level BI-RADS classification by the linear weighted Kappa statistic. Of the 120 women, 32 (26.7%) were classified as having fatty and 88 (73.3%) as mixed/dense mammographic density, according to Danish dichotomous classification. According to BI-RADS density classification, 12 (10.0%) women were classified as having predominantly fatty (BI-RADS code 1), 46 (38.3%) as having scattered fibroglandular (BI-RADS code 2), 57 (47.5%) as having heterogeneously dense (BI-RADS 3), and five (4.2%) as having extremely dense (BI-RADS code 4) mammographic density. The inter-rater variability assessed by weighted kappa statistic showed a substantial agreement (0.75). The dichotomous mammographic density classification system utilized in early years of Copenhagen's mammographic screening program (1991-2001) agreed well with the BI-RADS density classification system.

Golay sequences coded coherent optical OFDM for long-haul transmission

Science.gov (United States)

Qin, Cui; Ma, Xiangrong; Hua, Tao; Zhao, Jing; Yu, Huilong; Zhang, Jian

2017-09-01

We propose to use binary Golay sequences in coherent optical orthogonal frequency division multiplexing (CO-OFDM) to improve the long-haul transmission performance. The Golay sequences are generated by binary Reed-Muller codes, which have low peak-to-average power ratio and certain error correction capability. A low-complexity decoding algorithm for the Golay sequences is then proposed to recover the signal. Under same spectral efficiency, the QPSK modulated OFDM with binary Golay sequences coding with and without discrete Fourier transform (DFT) spreading (DFTS-QPSK-GOFDM and QPSK-GOFDM) are compared with the normal BPSK modulated OFDM with and without DFT spreading (DFTS-BPSK-OFDM and BPSK-OFDM) after long-haul transmission. At a 7% forward error correction code threshold (Q2 factor of 8.5 dB), it is shown that DFTS-QPSK-GOFDM outperforms DFTS-BPSK-OFDM by extending the transmission distance by 29% and 18%, in non-dispersion managed and dispersion managed links, respectively.

Fast comparison of IS radar code sequences for lag profile inversion

Directory of Open Access Journals (Sweden)

M. S. Lehtinen

2008-08-01

Full Text Available A fast method for theoretically comparing the posteriori variances produced by different phase code sequences in incoherent scatter radar (ISR experiments is introduced. Alternating codes of types 1 and 2 are known to be optimal for selected range resolutions, but the code sets are inconveniently long for many purposes like ground clutter estimation and in cases where coherent echoes from lower ionospheric layers are to be analyzed in addition to standard F-layer spectra.

The method is used in practice for searching binary code quads that have estimation accuracy almost equal to that of much longer alternating code sets. Though the code sequences can consist of as few as four different transmission envelopes, the lag profile estimation variances are near to the theoretical minimum. Thus the short code sequence is equally good as a full cycle of alternating codes with the same pulse length and bit length. The short code groups cannot be directly decoded, but the decoding is done in connection with more computationally expensive lag profile inversion in data analysis.

The actual code searches as well as the analysis and real data results from the found short code searches are explained in other papers sent to the same issue of this journal. We also discuss interesting subtle differences found between the different alternating codes by this method. We assume that thermal noise dominates the incoherent scatter signal.

Sequence Coding and Search System for licensee event reports: code listings. Volume 2

International Nuclear Information System (INIS)

Gallaher, R.B.; Guymon, R.H.; Mays, G.T.; Poore, W.P.; Cagle, R.J.; Harrington, K.H.; Johnson, M.P.

1985-04-01

Operating experience data from nuclear power plants are essential for safety and reliability analyses, especially analyses of trends and patterns. The licensee event reports (LERs) that are submitted to the Nuclear Regulatory Commission (NRC) by the nuclear power plant utilities contain much of this data. The NRC's Office for Analysis and Evaluation of Operational Data (AEOD) has developed, under contract with NSIC, a system for codifying the events reported in the LERs. The primary objective of the Sequence Coding and Search System (SCSS) is to reduce the descriptive text of the LERs to coded sequences that are both computer-readable and computer-searchable. This system provides a structured format for detailed coding of component, system, and unit effects as well as personnel errors. The database contains all current LERs submitted by nuclear power plant utilities for events occurring since 1981 and is updated on a continual basis. Volume 2 contains all valid and acceptable codes used for searching and encoding the LER data. This volume contains updated material through amendment 1 to revision 1 of the working version of ORNL/NSIC-223, Vol. 2

RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

DEFF Research Database (Denmark)

Wernersson, Rasmus; Pedersen, Anders Gorm

2003-01-01

The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...... proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...

Solving bi-level optimization problems in engineering design using kriging models

Science.gov (United States)

Xia, Yi; Liu, Xiaojie; Du, Gang

2018-05-01

Stackelberg game-theoretic approaches are applied extensively in engineering design to handle distributed collaboration decisions. Bi-level genetic algorithms (BLGAs) and response surfaces have been used to solve the corresponding bi-level programming models. However, the computational costs for BLGAs often increase rapidly with the complexity of lower-level programs, and optimal solution functions sometimes cannot be approximated by response surfaces. This article proposes a new method, namely the optimal solution function approximation by kriging model (OSFAKM), in which kriging models are used to approximate the optimal solution functions. A detailed example demonstrates that OSFAKM can obtain better solutions than BLGAs and response surface-based methods, and at the same time reduce the workload of computation remarkably. Five benchmark problems and a case study of the optimal design of a thin-walled pressure vessel are also presented to illustrate the feasibility and potential of the proposed method for bi-level optimization in engineering design.

Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralogs in Arabidopsis thaliana

Science.gov (United States)

Richardson, Dale N.; Wiehe, Thomas

Whole genome duplication (WGD) has catalyzed the formation of new species, genes with novel functions, altered expression patterns, complexified signaling pathways and has provided organisms a level of genetic robustness. We studied the long-term evolution and interrelationships of 5’ upstream regulatory sequences (URSs), protein coding sequences (CDSs) and expression correlations (EC) of duplicated gene pairs in Arabidopsis. Three distinct methods revealed significant evolutionary conservation between paralogous URSs and were highly correlated with microarray-based expression correlation of the respective gene pairs. Positional information on exact matches between sequences unveiled the contribution of micro-chromosomal rearrangements on expression divergence. A three-way rank analysis of URS similarity, CDS divergence and EC uncovered specific gene functional biases. Transcription factor activity was associated with gene pairs exhibiting conserved URSs and divergent CDSs, whereas a broad array of metabolic enzymes was found to be associated with gene pairs showing diverged URSs but conserved CDSs.

FOURTH SEMINAR TO THE MEMORY OF D.N. KLYSHKO: Algebraic solution of the synthesis problem for coded sequences

Science.gov (United States)

Leukhin, Anatolii N.

2005-08-01

The algebraic solution of a 'complex' problem of synthesis of phase-coded (PC) sequences with the zero level of side lobes of the cyclic autocorrelation function (ACF) is proposed. It is shown that the solution of the synthesis problem is connected with the existence of difference sets for a given code dimension. The problem of estimating the number of possible code combinations for a given code dimension is solved. It is pointed out that the problem of synthesis of PC sequences is related to the fundamental problems of discrete mathematics and, first of all, to a number of combinatorial problems, which can be solved, as the number factorisation problem, by algebraic methods by using the theory of Galois fields and groups.

Bayesian Group Bridge for Bi-level Variable Selection.

Science.gov (United States)

Mallick, Himel; Yi, Nengjun

2017-06-01

A Bayesian bi-level variable selection method (BAGB: Bayesian Analysis of Group Bridge) is developed for regularized regression and classification. This new development is motivated by grouped data, where generic variables can be divided into multiple groups, with variables in the same group being mechanistically related or statistically correlated. As an alternative to frequentist group variable selection methods, BAGB incorporates structural information among predictors through a group-wise shrinkage prior. Posterior computation proceeds via an efficient MCMC algorithm. In addition to the usual ease-of-interpretation of hierarchical linear models, the Bayesian formulation produces valid standard errors, a feature that is notably absent in the frequentist framework. Empirical evidence of the attractiveness of the method is illustrated by extensive Monte Carlo simulations and real data analysis. Finally, several extensions of this new approach are presented, providing a unified framework for bi-level variable selection in general models with flexible penalties.

Halftone Coding with JBIG2

DEFF Research Database (Denmark)

Martins, Bo; Forchhammer, Søren

2000-01-01

of a halftone pattern dictionary.The decoder first decodes the gray-scale image. Then for each gray-scale pixel looks up the corresponding halftonepattern in the dictionary and places it in the reconstruction bitmap at the position corresponding to the gray-scale pixel. The coding method is inherently lossy......The emerging international standard for compression of bilevel images and bi-level documents, JBIG2,provides a mode dedicated for lossy coding of halftones. The encoding procedure involves descreening of the bi-levelimage into gray-scale, encoding of the gray-scale image, and construction...... and care must be taken to avoid introducing artifacts in the reconstructed image. We describe how to apply this coding method for halftones created by periodic ordered dithering, by clustered dot screening (offset printing), and by techniques which in effect dithers with blue noise, e.g., error diffusion...

Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions

DEFF Research Database (Denmark)

Lavstsen, Thomas; Salanti, Ali; Jensen, Anja T R

2003-01-01

and organization of the 3D7 PfEMP1 repertoire was investigated on the basis of the complete genome sequence. METHODS: Using two tree-building methods we analysed the coding and non-coding sequences of 3D7 var and rif genes as well as var genes of other parasite strains. RESULTS: var genes can be sub...

Two-terminal video coding.

Science.gov (United States)

Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

2009-03-01

Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

A Novel Approach toward Fuzzy Generalized Bi-Ideals in Ordered Semigroups

Directory of Open Access Journals (Sweden)

Faiz Muhammad Khan

2014-01-01

Full Text Available In several advanced fields like control engineering, computer science, fuzzy automata, finite state machine, and error correcting codes, the use of fuzzified algebraic structures especially ordered semigroups plays a central role. In this paper, we introduced a new and advanced generalization of fuzzy generalized bi-ideals of ordered semigroups. These new concepts are supported by suitable examples. These new notions are the generalizations of ordinary fuzzy generalized bi-ideals of ordered semigroups. Several fundamental theorems of ordered semigroups are investigated by the properties of these newly defined fuzzy generalized bi-ideals. Further, using level sets, ordinary fuzzy generalized bi-ideals are linked with these newly defined ideals which is the most significant part of this paper.

An application of data mining classification and bi-level programming for optimal credit allocation

Directory of Open Access Journals (Sweden)

Seyed Mahdi Sadatrasou

2015-01-01

Full Text Available This paper investigates credit allocation policy making and its effect on economic development using bi-level programming. There are two challenging problems in bi-level credit allocation; at the first level government/public related institutes must allocate the credit strategically concerning sustainable development to regions and industrial sectors. At the second level, there are agent banks, which should allocate the credit tactically to individual applicants based on their own profitability and risk using their credit scoring models. There is a conflict of interest between these two stakeholders but the cooperation is inevitable. In this paper, a new bi-level programming formulation of the leader-follower game in association with sustainable development theory in the first level and data mining classifier at the second level is used to mathematically model the problem. The model is applied to a national development fund (NDF as a government related organization and one of its agent banks. A new algorithm called Bi-level Genetic fuzzy apriori Algorithm (BGFAA is introduced to solve the bilateral model. Experimental results are presented and compared with a unilateral policy making scenario by the leader. Findings show that although the objective functions of the leader are worse in the bilateral scenario but agent banks collaboration is attracted and guaranteed.

Watt-Level Continuous-Wave Emission from a Bi-Functional Quantum Cascade Laser/Detector

Science.gov (United States)

2017-04-18

cally authorized by the U.S. Government may violate any copyrights that exist in this work. Watt-level continuous- wave emission from a bi- functional ... wave bi- functional devices, opens the perspective of on-chip dual comb spectroscopy. Also for discrete sens- ing setups, one can switch to lasers...seas.harvard.edu Abstract Bi- functional active regions, capable of light generation and detection at the same wavelength, allow a straightforward realization of

IdentiCS – Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence

Directory of Open Access Journals (Sweden)

Zeng An-Ping

2004-08-01

Full Text Available Abstract Background A necessary step for a genome level analysis of the cellular metabolism is the in silico reconstruction of the metabolic network from genome sequences. The available methods are mainly based on the annotation of genome sequences including two successive steps, the prediction of coding sequences (CDS and their function assignment. The annotation process takes time. The available methods often encounter difficulties when dealing with unfinished error-containing genomic sequence. Results In this work a fast method is proposed to use unannotated genome sequence for predicting CDSs and for an in silico reconstruction of metabolic networks. Instead of using predicted genes or CDSs to query public databases, entries from public DNA or protein databases are used as queries to search a local database of the unannotated genome sequence to predict CDSs. Functions are assigned to the predicted CDSs simultaneously. The well-annotated genome of Salmonella typhimurium LT2 is used as an example to demonstrate the applicability of the method. 97.7% of the CDSs in the original annotation are correctly identified. The use of SWISS-PROT-TrEMBL databases resulted in an identification of 98.9% of CDSs that have EC-numbers in the published annotation. Furthermore, two versions of sequences of the bacterium Klebsiella pneumoniae with different genome coverage (3.9 and 7.9 fold, respectively are examined. The results suggest that a 3.9-fold coverage of the bacterial genome could be sufficiently used for the in silico reconstruction of the metabolic network. Compared to other gene finding methods such as CRITICA our method is more suitable for exploiting sequences of low genome coverage. Based on the new method, a program called IdentiCS (Identification of Coding Sequences from Unfinished Genome Sequences is delivered that combines the identification of CDSs with the reconstruction, comparison and visualization of metabolic networks (free to download

Comparisons between Arabidopsis thaliana and Drosophila melanogaster in relation to Coding and Noncoding Sequence Length and Gene Expression

Directory of Open Access Journals (Sweden)

Rachel Caldwell

2015-01-01

Full Text Available There is a continuing interest in the analysis of gene architecture and gene expression to determine the relationship that may exist. Advances in high-quality sequencing technologies and large-scale resource datasets have increased the understanding of relationships and cross-referencing of expression data to the large genome data. Although a negative correlation between expression level and gene (especially transcript length has been generally accepted, there have been some conflicting results arising from the literature concerning the impacts of different regions of genes, and the underlying reason is not well understood. The research aims to apply quantile regression techniques for statistical analysis of coding and noncoding sequence length and gene expression data in the plant, Arabidopsis thaliana, and fruit fly, Drosophila melanogaster, to determine if a relationship exists and if there is any variation or similarities between these species. The quantile regression analysis found that the coding sequence length and gene expression correlations varied, and similarities emerged for the noncoding sequence length (5′ and 3′ UTRs between animal and plant species. In conclusion, the information described in this study provides the basis for further exploration into gene regulation with regard to coding and noncoding sequence length.

Content layer progressive coding of digital maps

DEFF Research Database (Denmark)

Forchhammer, Søren; Jensen, Ole Riis

2000-01-01

A new lossless context based method is presented for content progressive coding of limited bits/pixel images, such as maps, company logos, etc., common on the WWW. Progressive encoding is achieved by separating the image into content layers based on other predefined information. Information from...... already coded layers are used when coding subsequent layers. This approach is combined with efficient template based context bi-level coding, context collapsing methods for multi-level images and arithmetic coding. Relative pixel patterns are used to collapse contexts. The number of contexts are analyzed....... The new methods outperform existing coding schemes coding digital maps and in addition provide progressive coding. Compared to the state-of-the-art PWC coder, the compressed size is reduced to 60-70% on our layered test images....

Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence

Science.gov (United States)

Gordon, Kacy L.; Arthur, Robert K.; Ruvinsky, Ilya

2015-01-01

Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements. PMID:26020930

Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence.

Directory of Open Access Journals (Sweden)

Kacy L Gordon

2015-05-01

Full Text Available Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2 from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements.

Stability of multi-objective bi-level linear programming problems under fuzziness

Directory of Open Access Journals (Sweden)

Abo-Sinna Mahmoud A.

2013-01-01

Full Text Available This paper deals with multi-objective bi-level linear programming problems under fuzzy environment. In the proposed method, tentative solutions are obtained and evaluated by using the partial information on preference of the decision-makers at each level. The existing results concerning the qualitative analysis of some basic notions in parametric linear programming problems are reformulated to study the stability of multi-objective bi-level linear programming problems. An algorithm for obtaining any subset of the parametric space, which has the same corresponding Pareto optimal solution, is presented. Also, this paper established the model for the supply-demand interaction in the age of electronic commerce (EC. First of all, the study uses the individual objectives of both parties as the foundation of the supply-demand interaction. Subsequently, it divides the interaction, in the age of electronic commerce, into the following two classifications: (i Market transactions, with the primary focus on the supply demand relationship in the marketplace; and (ii Information service, with the primary focus on the provider and the user of information service. By applying the bi-level programming technique of interaction process, the study will develop an analytical process to explain how supply-demand interaction achieves a compromise or why the process fails. Finally, a numerical example of information service is provided for the sake of illustration.

Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics

Science.gov (United States)

Mantegna, R. N.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Peng, C. K.; Simons, M.; Stanley, H. E.

1995-01-01

We compare the statistical properties of coding and noncoding regions in eukaryotic and viral DNA sequences by adapting two tests developed for the analysis of natural languages and symbolic sequences. The data set comprises all 30 sequences of length above 50 000 base pairs in GenBank Release No. 81.0, as well as the recently published sequences of C. elegans chromosome III (2.2 Mbp) and yeast chromosome XI (661 Kbp). We find that for the three chromosomes we studied the statistical properties of noncoding regions appear to be closer to those observed in natural languages than those of coding regions. In particular, (i) a n-tuple Zipf analysis of noncoding regions reveals a regime close to power-law behavior while the coding regions show logarithmic behavior over a wide interval, while (ii) an n-gram entropy measurement shows that the noncoding regions have a lower n-gram entropy (and hence a larger "n-gram redundancy") than the coding regions. In contrast to the three chromosomes, we find that for vertebrates such as primates and rodents and for viral DNA, the difference between the statistical properties of coding and noncoding regions is not pronounced and therefore the results of the analyses of the investigated sequences are less conclusive. After noting the intrinsic limitations of the n-gram redundancy analysis, we also briefly discuss the failure of the zeroth- and first-order Markovian models or simple nucleotide repeats to account fully for these "linguistic" features of DNA. Finally, we emphasize that our results by no means prove the existence of a "language" in noncoding DNA.

Coding patient emotional cues and concerns in medical consultations: the Verona coding definitions of emotional sequences (VR-CoDES).

NARCIS (Netherlands)

Zimmermann, C.; Piccolo, L. del; Bensing, J.; Bergvik, S.; Haes, H. de; Eide, H.; Fletcher, I.; Goss, C.; Heaven, C.; Humphris, G.; Young-Mi, K.; Langewitz, W.; Meeuwesen, L.; Nuebling, M.; Rimondini, M.; Salmon, P.; Dulmen, S. van; Wissow, L.; Zandbelt, L.; Finset, A.

2011-01-01

Objective: To present the Verona Coding Definitions of Emotional Sequences (VR-CoDES CC), a consensus based system for coding patient expressions of emotional distress in medical consultations, defined as Cues or Concerns. Methods: The system was developed by an international group of communication

Prevalence of transcription promoters within archaeal operons and coding sequences.

Science.gov (United States)

Koide, Tie; Reiss, David J; Bare, J Christopher; Pang, Wyming Lee; Facciotti, Marc T; Schmid, Amy K; Pan, Min; Marzolf, Bruz; Van, Phu T; Lo, Fang-Yin; Pratap, Abhishek; Deutsch, Eric W; Peterson, Amelia; Martin, Dan; Baliga, Nitin S

2009-01-01

Despite the knowledge of complex prokaryotic-transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have had a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of approximately 64% of all genes, including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction data sets showed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes-events usually considered spurious or non-functional. Using experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements.

Detecting Source Code Plagiarism on .NET Programming Languages using Low-level Representation and Adaptive Local Alignment

Directory of Open Access Journals (Sweden)

Oscar Karnalim

2017-01-01

Full Text Available Even though there are various source code plagiarism detection approaches, only a few works which are focused on low-level representation for deducting similarity. Most of them are only focused on lexical token sequence extracted from source code. In our point of view, low-level representation is more beneficial than lexical token since its form is more compact than the source code itself. It only considers semantic-preserving instructions and ignores many source code delimiter tokens. This paper proposes a source code plagiarism detection which rely on low-level representation. For a case study, we focus our work on .NET programming languages with Common Intermediate Language as its low-level representation. In addition, we also incorporate Adaptive Local Alignment for detecting similarity. According to Lim et al, this algorithm outperforms code similarity state-of-the-art algorithm (i.e. Greedy String Tiling in term of effectiveness. According to our evaluation which involves various plagiarism attacks, our approach is more effective and efficient when compared with standard lexical-token approach.

PATACSDB—the database of polyA translational attenuators in coding sequences

Directory of Open Access Journals (Sweden)

Malgorzata Habich

2016-02-01

Full Text Available Recent additions to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA tracks encoding for poly-lysine runs in protein sequences. Such tracks stall the translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such, they substantially influence the stability of mRNA and the amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance; this makes each of these sequences a potentially interesting case study for the effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present PATACSDB, a resource that contain a comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on the Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A’s allowing for one mismatched base. The PATACSDB database is accessible at: http://sysbio.ibb.waw.pl/patacsdb. The source code is available at http://github.com/habich/PATACSDB, and it includes the scripts with which the database can be recreated.

Bi2Se3/CdS/TiO2 hybrid photoelectrode and its band-edge levels

International Nuclear Information System (INIS)

Zhang, Qi; Su, Jun; Zhang, Xianghui; Li, Jian; Zhang, Aiqing; Gao, Yihua

2012-01-01

Highlights: ► CVD synthesis of Bi 2 Se 3 nanoparticles. ► Bi 2 Se 3 and CdS co-sensitized TiO 2 nanorod arrays electrode was assembled by CVD. ► Direct physical contact heterojunctions were formed at the interfaces of electrode. ► Cascade structure of band-edge levels was formed in Bi 2 Se 3 /CdS/TiO 2 electrode. - Abstract: Bismuth selenide (Bi 2 Se 3 ) was chosen as the sensitizer to TiO 2 nanorod (NR) arrays photoelectrode to harvest infrared (IR) light for its narrow band gap. For utilizing more amount of IR solar energy, Bi 2 Se 3 nanoparticles (NPs) were grown up to a relative larger grain size. And, a cadmium sulfide (CdS) NPs intermediate layer was introduced to help, to coordinate, the structure of band-edge levels in Bi 2 Se 3 /CdS/TiO 2 electrode. Here, a chemical vapor deposition (CVD) strategy was introduced to assemble this kind of composite photoelectrode. And a cascade structure of band-edge levels constructed in it when achieving electrostatic equilibrium in Na 2 S/Na 2 SO 3 aqueous solution electrolyte revealed by electrochemical analysis method, which will facilitate the hydrogen generation.

Bi-Level Optimization for Available Transfer Capability Evaluation in Deregulated Electricity Market

Directory of Open Access Journals (Sweden)

Beibei Wang

2015-11-01

Full Text Available Available transfer capability (ATC is the transfer capability remaining in the physical transmission network for further commercial activity over and above already committed uses which needs to be posted in the electricity market to facilitate competition. ATC evaluation is a complicated task including the determination of total transfer capability (TTC and existing transfer capability (ETC. In the deregulated electricity market, ETC is decided by the independent system operator’s (ISO’s economic dispatch (ED. TTC can then be obtained by a continuation power flow (CPF method or by an optimal power flow (OPF method, based on the given ED solutions as well as the ETC. In this paper, a bi-level optimization framework for the ATC evaluation is proposed in which ATC results can be obtained simultaneously with the ED and ETC results in the deregulated electricity market. In this bi-level optimization model, ATC evaluation is formulated as the upper level problem and the ISO’s ED is the lower level problem. The bi-level model is first converted to a mathematic program with equilibrium constraints (MPEC by recasting the lower level problem as its Karush-Kuhn-Tucher (KKT optimality condition. Then, the MPEC is transformed into a mixed-integer linear programming (MILP problem, which can be solved with the help of available optimization software. In addition, case studies on PJM 5-bus, IEEE 30-bus, and IEEE 118-bus systems are presented to demonstrate the proposed methodology.

Level 1 - level 2 interface

International Nuclear Information System (INIS)

Boneham, P.

2003-01-01

The Plant Damage States (PDS) are the starting point for the level 2 analysis. A PDS is group of core damage sequences that are expected to have similar severe accident progressions. In this paper an overview of Level 1/Level 2 interface, example PDS parameters, example PDS definitions using codes and example Bridge Tree are presented. PDS frequency calculation (identification of sequences for each PDS in level 1,split some CD sequences which have different level 2 progressions), code calculations providing support for grouping decisions and timings as well as PDS frequencies and definitions input to level 2 are also discussed

Modeling compositional dynamics based on GC and purine contents of protein-coding sequences

KAUST Repository

Zhang, Zhang

2010-11-08

Background: Understanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge.Results: To model the compositional dynamics of protein-coding sequences, we propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, with no prerequisite of homologous sequences or their alignments. We evaluated the two models by quantifying theoretical compositions of a large collection of protein-coding sequences (including 46 of Archaea, 686 of Bacteria, and 826 of Eukarya), yielding consistent theoretical compositions across all the collected sequences.Conclusions: We show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms.Reviewers: This article was reviewed by Zhaolei Zhang (nominated by Mark Gerstein), Guruprasad Ananda (nominated by Kateryna Makova), and Daniel Haft. 2010 Zhang and Yu; licensee BioMed Central Ltd.

Modeling compositional dynamics based on GC and purine contents of protein-coding sequences

KAUST Repository

Zhang, Zhang; Yu, Jun

2010-01-01

Background: Understanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge.Results: To model the compositional dynamics of protein-coding sequences, we propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, with no prerequisite of homologous sequences or their alignments. We evaluated the two models by quantifying theoretical compositions of a large collection of protein-coding sequences (including 46 of Archaea, 686 of Bacteria, and 826 of Eukarya), yielding consistent theoretical compositions across all the collected sequences.Conclusions: We show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms.Reviewers: This article was reviewed by Zhaolei Zhang (nominated by Mark Gerstein), Guruprasad Ananda (nominated by Kateryna Makova), and Daniel Haft. 2010 Zhang and Yu; licensee BioMed Central Ltd.

Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer.

Science.gov (United States)

Wojcik, Sylwia E; Rossi, Simona; Shimizu, Masayoshi; Nicoloso, Milena S; Cimmino, Amelia; Alder, Hansjuerg; Herlea, Vlad; Rassenti, Laura Z; Rai, Kanti R; Kipps, Thomas J; Keating, Michael J; Croce, Carlo M; Calin, George A

2010-02-01

Cancer is a genetic disease in which the interplay between alterations in protein-coding genes and non-coding RNAs (ncRNAs) plays a fundamental role. In recent years, the full coding component of the human genome was sequenced in various cancers, whereas such attempts related to ncRNAs are still fragmentary. We screened genomic DNAs for sequence variations in 148 microRNAs (miRNAs) and ultraconserved regions (UCRs) loci in patients with chronic lymphocytic leukemia (CLL) or colorectal cancer (CRC) by Sanger technique and further tried to elucidate the functional consequences of some of these variations. We found sequence variations in miRNAs in both sporadic and familial CLL cases, mutations of UCRs in CLLs and CRCs and, in certain instances, detected functional effects of these variations. Furthermore, by integrating our data with previously published data on miRNA sequence variations, we have created a catalog of DNA sequence variations in miRNAs/ultraconserved genes in human cancers. These findings argue that ncRNAs are targeted by both germ line and somatic mutations as well as by single-nucleotide polymorphisms with functional significance for human tumorigenesis. Sequence variations in ncRNA loci are frequent and some have functional and biological significance. Such information can be exploited to further investigate on a genome-wide scale the frequency of genetic variations in ncRNAs and their functional meaning, as well as for the development of new diagnostic and prognostic markers for leukemias and carcinomas.

Optical orthogonal code-division multiple-access system - Part 2: Multibits/sequence-period OOCDMA

Science.gov (United States)

Kwon, Hyuck M.

1994-08-01

In a recently proposed optical orthogonal code division multiple-access (OOCDMA) system, one bit of user's data is transmitted per sequence-period, and a threshold is employed for the final bit decision. In this paper, a system that can transmit multibits per sequence-period is introduced, and avalanche photodiode (APD) noise, thermal noise, and interference, are included. This system, derived by exploiting orthogonal properties of the OOCDMA code sequence and using a maximum search (instead of a threshold) in the final decision, is log(sub 2) F times higher in throughput, where F is sequence-period. For example, four orders of magnitude are better in bit error probability at - 56 dBW received laser power, with F = 1000 chips, 10 'marks' in a sequence, and 10 users of 30 Mb/s data rate for one-bit/sequence-period and 270 Mb/s data rate for multibits/sequence-period system. Furthermore, an exact analysis is performed for the log(sub 2)F bits/sequence-period system with a hard-limiter placed before the receiver, and its performance is compared to the performance without hard-limiter, for the chip-synchronous case. The improvement from using a hard-limiter is significant in the log(sub 2)F bits/sequence-period OCCDMA system.

Power Grid Construction Project Portfolio Optimization Based on Bi-level programming model

Science.gov (United States)

Zhao, Erdong; Li, Shangqi

2017-08-01

As the main body of power grid operation, county-level power supply enterprises undertake an important emission to guarantee the security of power grid operation and safeguard social power using order. The optimization of grid construction projects has been a key issue of power supply capacity and service level of grid enterprises. According to the actual situation of power grid construction project optimization of county-level power enterprises, on the basis of qualitative analysis of the projects, this paper builds a Bi-level programming model based on quantitative analysis. The upper layer of the model is the target restriction of the optimal portfolio; the lower layer of the model is enterprises’ financial restrictions on the size of the enterprise project portfolio. Finally, using a real example to illustrate operation proceeding and the optimization result of the model. Through qualitative analysis and quantitative analysis, the bi-level programming model improves the accuracy and normative standardization of power grid enterprises projects.

SEAPATH: A microcomputer code for evaluating physical security effectiveness using adversary sequence diagrams

International Nuclear Information System (INIS)

Darby, J.L.

1986-01-01

The Adversary Sequence Diagram (ASD) concept was developed by Sandia National Laboratories (SNL) to examine physical security system effectiveness. Sandia also developed a mainframe computer code, PANL, to analyze the ASD. The authors have developed a microcomputer code, SEAPATH, which also analyzes ASD's. The Authors are supporting SNL in software development of the SAVI code; SAVI utilizes the SEAPATH algorithm to identify and quantify paths

The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape.

Science.gov (United States)

Yousaf, Aisha; Sohail Raza, Muhammad; Ali Abbasi, Amir

2015-08-06

Enhancers lie at the heart of transcriptional and developmental gene regulation. Therefore, changes in enhancer sequences usually disrupt the target gene expression and result in disease phenotypes. Despite the well-established role of enhancers in development and disease, evolutionary sequence studies are lacking. The current study attempts to unravel the puzzle of bony vertebrates' conserved noncoding elements (CNE) enhancer evolution. Bayesian phylogenetics of enhancer sequences spotlights promising interordinal relationships among placental mammals, proposing a closer relationship between humans and laurasiatherians while placing rodents at the basal position. Clock-based estimates of enhancer evolution provided a dynamic picture of interspecific rate changes across the bony vertebrate lineage. Moreover, coelacanth in the study augmented our appreciation of the vertebrate cis-regulatory evolution during water-land transition. Intriguingly, we observed a pronounced upsurge in enhancer evolution in land-dwelling vertebrates. These novel findings triggered us to further investigate the evolutionary trend of coding as well as CNE nonenhancer repertoires, to highlight the relative evolutionary dynamics of diverse genomic landscapes. Surprisingly, the evolutionary rates of enhancer sequences were clearly at odds with those of the coding and the CNE nonenhancer sequences during vertebrate adaptation to land, with land vertebrates exhibiting significantly reduced rates of coding sequence evolution in comparison to their fast evolving regulatory landscape. The observed variation in tetrapod cis-regulatory elements caused the fine-tuning of associated gene regulatory networks. Therefore, the increased evolutionary rate of tetrapods' enhancer sequences might be responsible for the variation in developmental regulatory circuits during the process of vertebrate adaptation to land. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for

Solid-state dewetting of Au-Ni bi-layer films mediated through individual layer thickness and stacking sequence

Science.gov (United States)

Herz, Andreas; Theska, Felix; Rossberg, Diana; Kups, Thomas; Wang, Dong; Schaaf, Peter

2018-06-01

In the present work, the solid-state dewetting of Au-Ni bi-layer thin films deposited on SiO2/Si is systematically studied with respect to individual layer thickness and stacking sequence. For this purpose, a rapid heat treatment at medium temperatures is applied in order to examine void formation at the early stages of the dewetting. Compositional variations are realized by changing the thickness ratio of the bi-layer films, while the total thickness is maintained at 20 nm throughout the study. In the event of Au/Ni films annealed at 500 °C, crystal voids exposing the substrate are missing regardless of chemical composition. In reverse order, the number of voids per unit area in two-phase Au-Ni thin films is found to be governed by the amount of Au-rich material. At higher temperatures up to 650 °C, a decreased probability of nucleation comes at the expense of a major portion of cavities, resulting in the formation of bubbles in 15 nm Ni/5 nm Au bi-layers. Film buckling predominantly occurred at phase boundaries crossing the bubbles.

SRComp: short read sequence compression using burstsort and Elias omega coding.

Directory of Open Access Journals (Sweden)

Jeremy John Selva

Full Text Available Next-generation sequencing (NGS technologies permit the rapid production of vast amounts of data at low cost. Economical data storage and transmission hence becomes an increasingly important challenge for NGS experiments. In this paper, we introduce a new non-reference based read sequence compression tool called SRComp. It works by first employing a fast string-sorting algorithm called burstsort to sort read sequences in lexicographical order and then Elias omega-based integer coding to encode the sorted read sequences. SRComp has been benchmarked on four large NGS datasets, where experimental results show that it can run 5-35 times faster than current state-of-the-art read sequence compression tools such as BEETL and SCALCE, while retaining comparable compression efficiency for large collections of short read sequences. SRComp is a read sequence compression tool that is particularly valuable in certain applications where compression time is of major concern.

Bottom-up-then-up-down Route for Multi-level Construction of Hierarchical Bi2S3 Superstructures with Magnetism Alteration

Science.gov (United States)

Wei, Chengzhen; Wang, Lanfang; Dang, Liyun; Chen, Qun; Lu, Qingyi; Gao, Feng

2015-01-01

A bottom-up-then-up-down route was proposed to construct multi-level Bi2S3 hierarchical architectures assembled by two-dimensional (2D) Bi2S3 sheet-like networks. BiOCOOH hollow spheres and flower-like structures, which are both assembled by 2D BiOCOOH nanosheets, were prepared first by a “bottom-up” route through a “quasi-emulsion” mechanism. Then the BiOCOOH hierarchical structures were transferred to hierarchical Bi2S3 architectures through an “up-down” route by an ion exchange method. The obtained Bi2S3 nanostructures remain hollow-spherical and flower-like structures of the precursors but the constructing blocks are changed to 2D sheet-like networks interweaving by Bi2S3 nanowires. The close matching of crystal lattices between Bi2S3 and BiOCOOH was believed to be the key reason for the topotactic transformation from BiOCOOH nanosheets to 2D Bi2S3 sheet-like nanowire networks. Magnetism studies reveal that unlike diamagnetism of comparative Bi2S3 nanostructures, the obtained multi-level Bi2S3 structures display S-type hysteresis and ferromagnetism at low field which might result from ordered structure of 2D networks. PMID:26028331

The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences as well as the Most Conserved Pmp Protein Differ within and across Chlamydia Species.

Science.gov (United States)

Van Lent, Sarah; Creasy, Heather Huot; Myers, Garry S A; Vanrompay, Daisy

2016-01-01

Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of pmp coding sequences differs between Chlamydia species, but it is unknown whether the number of pmp coding sequences is constant within a Chlamydia species. The level of conservation of the Pmp proteins has previously only been determined for Chlamydia trachomatis. As different Pmp proteins might be indispensible for the pathogenesis of different Chlamydia species, this study investigated the conservation of Pmp proteins both within and across C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci. The pmp coding sequences were annotated in 16 C. trachomatis, 6 C. pneumoniae, 2 C. abortus, and 16 C. psittaci genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed Chlamydia species. The length of coding sequences of pmpA,pmpB, and pmpH was conserved among all analyzed genomes, while the length of pmpE/F and pmpG, and remarkably also of the subtype pmpD, differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci, respectively. PmpB was the most conserved Pmp across the 4 analyzed Chlamydia species. © 2016 S. Karger AG, Basel.

Multi-level trellis coded modulation and multi-stage decoding

Science.gov (United States)

Costello, Daniel J., Jr.; Wu, Jiantian; Lin, Shu

1990-01-01

Several constructions for multi-level trellis codes are presented and many codes with better performance than previously known codes are found. These codes provide a flexible trade-off between coding gain, decoding complexity, and decoding delay. New multi-level trellis coded modulation schemes using generalized set partitioning methods are developed for Quadrature Amplitude Modulation (QAM) and Phase Shift Keying (PSK) signal sets. New rotationally invariant multi-level trellis codes which can be combined with differential encoding to resolve phase ambiguity are presented.

A linear bi-level multi-objective program for optimal allocation of water resources.

Directory of Open Access Journals (Sweden)

Ijaz Ahmad

Full Text Available This paper presents a simple bi-level multi-objective linear program (BLMOLP with a hierarchical structure consisting of reservoir managers and several water use sectors under a multi-objective framework for the optimal allocation of limited water resources. Being the upper level decision makers (i.e., leader in the hierarchy, the reservoir managers control the water allocation system and tend to create a balance among the competing water users thereby maximizing the total benefits to the society. On the other hand, the competing water use sectors, being the lower level decision makers (i.e., followers in the hierarchy, aim only to maximize individual sectoral benefits. This multi-objective bi-level optimization problem can be solved using the simultaneous compromise constraint (SICCON technique which creates a compromise between upper and lower level decision makers (DMs, and transforms the multi-objective function into a single decision-making problem. The bi-level model developed in this study has been applied to the Swat River basin in Pakistan for the optimal allocation of water resources among competing water demand sectors and different scenarios have been developed. The application of the model in this study shows that the SICCON is a simple, applicable and feasible approach to solve the BLMOLP problem. Finally, the comparisons of the model results show that the optimization model is practical and efficient when it is applied to different conditions with priorities assigned to various water users.

On decoding of multi-level MPSK modulation codes

Science.gov (United States)

Lin, Shu; Gupta, Alok Kumar

1990-01-01

The decoding problem of multi-level block modulation codes is investigated. The hardware design of soft-decision Viterbi decoder for some short length 8-PSK block modulation codes is presented. An effective way to reduce the hardware complexity of the decoder by reducing the branch metric and path metric, using a non-uniform floating-point to integer mapping scheme, is proposed and discussed. The simulation results of the design are presented. The multi-stage decoding (MSD) of multi-level modulation codes is also investigated. The cases of soft-decision and hard-decision MSD are considered and their performance are evaluated for several codes of different lengths and different minimum squared Euclidean distances. It is shown that the soft-decision MSD reduces the decoding complexity drastically and it is suboptimum. The hard-decision MSD further simplifies the decoding while still maintaining a reasonable coding gain over the uncoded system, if the component codes are chosen properly. Finally, some basic 3-level 8-PSK modulation codes using BCH codes as component codes are constructed and their coding gains are found for hard decision multistage decoding.

Multiple Access Interference Reduction Using Received Response Code Sequence for DS-CDMA UWB System

Science.gov (United States)

Toh, Keat Beng; Tachikawa, Shin'ichi

This paper proposes a combination of novel Received Response (RR) sequence at the transmitter and a Matched Filter-RAKE (MF-RAKE) combining scheme receiver system for the Direct Sequence-Code Division Multiple Access Ultra Wideband (DS-CDMA UWB) multipath channel model. This paper also demonstrates the effectiveness of the RR sequence in Multiple Access Interference (MAI) reduction for the DS-CDMA UWB system. It suggests that by using conventional binary code sequence such as the M sequence or the Gold sequence, there is a possibility of generating extra MAI in the UWB system. Therefore, it is quite difficult to collect the energy efficiently although the RAKE reception method is applied at the receiver. The main purpose of the proposed system is to overcome the performance degradation for UWB transmission due to the occurrence of MAI during multiple accessing in the DS-CDMA UWB system. The proposed system improves the system performance by improving the RAKE reception performance using the RR sequence which can reduce the MAI effect significantly. Simulation results verify that significant improvement can be obtained by the proposed system in the UWB multipath channel models.

Thermoelectric Properties in Fermi Level Tuned Topological Materials (Bi1-xSnx)2Te3

Science.gov (United States)

Lin, Chan-Chieh; Shon, Won Hyuk; Rathnam, Lydia; Rhyee, Jong-Soo

2018-03-01

We investigated the thermoelectric properties of Sn-doped (Bi1-xSnx)2Te3 (x = 0, 0.1, 0.3, 0.5, and 0.7%) compounds, which is known as topological insulators. Fermi level tuning by Sn-doping can be justified by the n- to p-type transition with increasing Sn-doping concentration, as confirmed by Seebeck coefficient and Hall coefficient. Near x = 0.3 and 0.5%, the Fermi level resides inside the bulk band gap, resulting in a low Seebeck coefficient and increase of electrical resistivity. The magnetoconductivity with applying magnetic field showed weak antilocalization (WAL) effect for pristine Bi2Te3 while Sn-doped compounds do not follow the WAL behavior of magneto-conductivity, implying that the topological surface Dirac band contribution in magneto-conductivity is suppressed with decreasing the Fermi level by Sn-doping. This research can be applied to the topological composite of p-type/n-type topological materials by Fermi level tuning via Sn-doping in Bi2Te3 compounds.

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences.

LENUS (Irish Health Repository)

Ivanov, Ivaylo P

2011-05-01

In eukaryotes, it is generally assumed that translation initiation occurs at the AUG codon closest to the messenger RNA 5\\' cap. However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG, UUG, GUG, ACG, AUA and AUU. While non-AUG initiation has been experimentally verified for a handful of human genes, the full extent to which this phenomenon is utilized--both for increased coding capacity and potentially also for novel regulatory mechanisms--remains unclear. To address this issue, and hence to improve the quality of existing coding sequence annotations, we developed a methodology based on phylogenetic analysis of predicted 5\\' untranslated regions from orthologous genes. We use evolutionary signatures of protein-coding sequences as an indicator of translation initiation upstream of annotated coding sequences. Our search identified novel conserved potential non-AUG-initiated N-terminal extensions in 42 human genes including VANGL2, FGFR1, KCNN4, TRPV6, HDGF, CITED2, EIF4G3 and NTF3, and also affirmed the conservation of known non-AUG-initiated extensions in 17 other genes. In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data.

Reconfigurable, Bi-Directional Flexfet Level Shifter for Low-Power, Rad-Hard Integration

Science.gov (United States)

DeGregorio, Kelly; Wilson, Dale G.

2009-01-01

Two prototype Reconfigurable, Bi-directional Flexfet Level Shifters (ReBiLS) have been developed, where one version is a stand-alone component designed to interface between external low voltage and high voltage, and the other version is an embedded integrated circuit (IC) for interface between internal low-voltage logic and external high-voltage components. Targeting stand-alone and embedded circuits separately allows optimization for these distinct applications. Both ReBiLS designs use the commercially available 180-nm Flex fet Independently Double-Gated (IDG) SOI CMOS (silicon on insulator, complementary metal oxide semiconductor) technology. Embedded ReBiLS circuits were integrated with a Reed-Solomon (RS) encoder using CMOS Ultra-Low-Power Radiation Tolerant (CULPRiT) double-gated digital logic circuits. The scope of the project includes: creation of a new high-voltage process, development of ReBiLS circuit designs, and adjustment of the designs to maximize performance through simulation, layout, and manufacture of prototypes. The primary technical objectives were to develop a high-voltage, thick oxide option for the 180-nm Flexfet process, and to develop a stand-alone ReBiLS IC with two 8-channel I/O busses, 1.8 2.5 I/O on the low-voltage pins, 5.0-V-tolerant input and 3.3-V output I/O on the high-voltage pins, and 100-MHz minimum operation with 10-pF external loads. Another objective was to develop an embedded, rad-hard ReBiLS I/O cell with 0.5-V low-voltage operation for interface with core logic, 5.0-V-tolerant input and 3.3-V output I/O pins, and 100-MHz minimum operation with 10- pF external loads. A third objective was to develop a 0.5- V Reed-Solomon Encoder with embedded ReBilS I/O: Transfer the existing CULPRiT RS encoder from a 0.35-micron bulk-CMOS process to the ASI 180-nm Flexfet, rad-hard SOI Process. 0.5-V low-voltage core logic. 5.0-V-tolerant input and 3.3-V output I/O pins. 100-MHz minimum operation with 10- pF external loads. The stand

Stark broadening of several Bi IV spectral lines of astrophysical interest

Science.gov (United States)

Colón, C.; Moreno-Díaz, C.; de Andrés-García, I.; Alonso-Medina, A.

2017-09-01

The presence of spectral lines of bismuth in stellar atmospheres has been reported in different stars. The anomalous values of the spectral intensities of Bi II and Bi III, compared to the theoretical Local Termodinamic Equilibrium (LTE) standards of Bi I/Bi II/Bi III, have been reported in the spectra obtained with the High Resolution Spectrograph of the Hubble/Goddard Space Telescope in the chemically peculiar stars HgMn stars χ Lupi and HR 7775. Spectral lines of 1436.8, 1902.3, 2630.9 and 2936.7 Å of Bi II and 1423.4 Å of Bi III were reported and their relative intensities were measured in these studies Litzén & Wahlgren 2002. These lines are overlapped with spectral lines of 1437.65, 2630.1 and 2937.1 Å of Bi IV. A study of the Stark broadening parameters of Bi IV spectral lines can help to study these overlaps. In this paper, using the Griem semi-empirical approach, we report calculated values of the Stark parameters for 64 spectral lines of Bi IV. The matrix elements used in these calculations have been determined from 17 configurations of Bi IV. They were calculated using the cowan code including core polarization effects. Data are displayed for an electron density of 1017 cm-3 and temperatures T = 10 000-160 000 K. Also calculated radiative lifetimes for 12 levels with experimental lifetime are presented, in order to test the goodness of our calculations. Theoretical trends of the Stark width and shift parameters versus the temperature for spectral lines of astrophysical interest are displayed.

Multi-stage decoding of multi-level modulation codes

Science.gov (United States)

Lin, Shu; Kasami, Tadao; Costello, Daniel J., Jr.

1991-01-01

Various types of multi-stage decoding for multi-level modulation codes are investigated. It is shown that if the component codes of a multi-level modulation code and types of decoding at various stages are chosen properly, high spectral efficiency and large coding gain can be achieved with reduced decoding complexity. Particularly, it is shown that the difference in performance between the suboptimum multi-stage soft-decision maximum likelihood decoding of a modulation code and the single-stage optimum soft-decision decoding of the code is very small, only a fraction of dB loss in signal to noise ratio at a bit error rate (BER) of 10(exp -6).

[Transposition errors during learning to reproduce a sequence by the right- and the left-hand movements: simulation of positional and movement coding].

Science.gov (United States)

Liakhovetskiĭ, V A; Bobrova, E V; Skopin, G N

2012-01-01

Transposition errors during the reproduction of a hand movement sequence make it possible to receive important information on the internal representation of this sequence in the motor working memory. Analysis of such errors showed that learning to reproduce sequences of the left-hand movements improves the system of positional coding (coding ofpositions), while learning of the right-hand movements improves the system of vector coding (coding of movements). Learning of the right-hand movements after the left-hand performance involved the system of positional coding "imposed" by the left hand. Learning of the left-hand movements after the right-hand performance activated the system of vector coding. Transposition errors during learning to reproduce movement sequences can be explained by neural network using either vector coding or both vector and positional coding.

Analysis of the AD sequence in Zion plant using the March 1.1 code

International Nuclear Information System (INIS)

Oriolo, F.; Paci, S.

1985-01-01

The analyses of the AD sequences for the Zion power plant, made at the Pisa University, in the framework of the participation in the Source Tern Working Group. After a short description of the plant and the sequence under analysis, the model used for the reference computation and the results obtained using the March 1.1 code are shown. Together with the reference computation a series of parametric tests have been also made, concerning some input code variables, in order to ascertain their influence on the transient trend. The results of these analyses are shown in Appendix

Sequence Coding and Search System for licensee event reports: coder's manual. Volume 4

International Nuclear Information System (INIS)

Gallaher, R.B.; Guymon, R.H.; Mays, G.T.; Poore, W.P.; Cagle, R.J.; Harrington, K.H.; Johnson, M.P.

1985-04-01

Operating experience data from nuclear power plants are essential for safety and reliability analyses, especially analyses of trends and patterns. The licensee event reports (LERs) that are submitted to the Nuclear Regulatory Commission (NRC) by the nuclear power plant utilities contain much of this data. The NRC's Office for Analysis and Evaluation of Operational Data (AEOD) has developed, under contract with NSIC, a system for codifying the events reported in the LERs. The primary objective of the Sequence Coding and Search System (SCSS) is to reduce the descriptive text of the LERs to coded sequences that are both computer-readable and computer-searchable. This four volume report documents and describes SCSS in detail. Volume 3 and 4 provide a technical processor, new to SCSS, the information and methodology necessary to capture descriptive data from the LER and to codify that data into a structured format and serve as reference material for the more experienced technical processor, and contains information that is essential for the more advanced user who needs to be familiar with the intricate coding techniques in order to retrieve specific details in a sequence. This volume contains updated material through amendment 1 to revision 1 of the working version of ORNL/NSIC-223, Vol. 4

Sequence Coding and Search System for licensee event reports: coder's manual. Volume 3

International Nuclear Information System (INIS)

Gallaher, R.B.; Guymon, R.H.; Mays, G.T.; Poore, W.P.; Cagle, R.J.; Harrington, K.H.; Johnson, M.P.

1985-04-01

Operating experience data from nuclear power plants are essential for safety and reliability analyses, especially analyses of trends and patterns. The licensee event reports (LERs) that are submitted to the Nuclear Regulatory Commission (NRC) by the nuclear power plant utilities contain much of this data. The NRC's Office for Analysis and Evaluation of Operational Data (AEOD) has developed, under contract with NSIC, a system for codifying the events reported in the LERs. The primary objective of the Sequence Coding and Search System (SCSS) is to reduce the descriptive text of the LERs to coded sequences that are both computer-readable and computer-searchable. This four volume report documents and describes SCSS in detail. Volumes 3 and 4 provide a technical processor, new to SCSS, the information and methodology necessary to capture descriptive data from the LER and to codify that data into a structured format and serve as reference material for the more experienced technical processor, and contains information is essential for the more advanced user who needs to be familiar with the intricate coding techniques in order to retrieve specific details in a sequence. This volume contains updated material through amendment 1 to revision 1 of the working version of ORNL/NSIC-223, Vol. 3

Sequence Coding and Search System Backfit Quality Assurance Program Plan

International Nuclear Information System (INIS)

Lovell, C.J.; Stepina, P.L.

1985-03-01

The Sequence Coding and Search System is a computer-based encoding system for events described in Licensee Event Reports. This data system contains LERs from 1981 to present. Backfit of the data system to include LERs prior to 1981 is required. This report documents the Quality Assurance Program Plan that EG and G Idaho, Inc. will follow while encoding 1980 LERs

Reliability and code level

NARCIS (Netherlands)

Kasperski, M.; Geurts, C.P.W.

2005-01-01

The paper describes the work of the IAWE Working Group WBG - Reliability and Code Level, one of the International Codification Working Groups set up at ICWE10 in Copenhagen. The following topics are covered: sources of uncertainties in the design wind load, appropriate design target values for the

AutoBD: Automated Bi-Level Description for Scalable Fine-Grained Visual Categorization.

Science.gov (United States)

Yao, Hantao; Zhang, Shiliang; Yan, Chenggang; Zhang, Yongdong; Li, Jintao; Tian, Qi

Compared with traditional image classification, fine-grained visual categorization is a more challenging task, because it targets to classify objects belonging to the same species, e.g. , classify hundreds of birds or cars. In the past several years, researchers have made many achievements on this topic. However, most of them are heavily dependent on the artificial annotations, e.g., bounding boxes, part annotations, and so on . The requirement of artificial annotations largely hinders the scalability and application. Motivated to release such dependence, this paper proposes a robust and discriminative visual description named Automated Bi-level Description (AutoBD). "Bi-level" denotes two complementary part-level and object-level visual descriptions, respectively. AutoBD is "automated," because it only requires the image-level labels of training images and does not need any annotations for testing images. Compared with the part annotations labeled by the human, the image-level labels can be easily acquired, which thus makes AutoBD suitable for large-scale visual categorization. Specifically, the part-level description is extracted by identifying the local region saliently representing the visual distinctiveness. The object-level description is extracted from object bounding boxes generated with a co-localization algorithm. Although only using the image-level labels, AutoBD outperforms the recent studies on two public benchmark, i.e. , classification accuracy achieves 81.6% on CUB-200-2011 and 88.9% on Car-196, respectively. On the large-scale Birdsnap data set, AutoBD achieves the accuracy of 68%, which is currently the best performance to the best of our knowledge.Compared with traditional image classification, fine-grained visual categorization is a more challenging task, because it targets to classify objects belonging to the same species, e.g. , classify hundreds of birds or cars. In the past several years, researchers have made many achievements on this topic

Two-Level Semantics and Code Generation

DEFF Research Database (Denmark)

Nielson, Flemming; Nielson, Hanne Riis

1988-01-01

A two-level denotational metalanguage that is suitable for defining the semantics of Pascal-like languages is presented. The two levels allow for an explicit distinction between computations taking place at compile-time and computations taking place at run-time. While this distinction is perhaps...... not absolutely necessary for describing the input-output semantics of programming languages, it is necessary when issues such as data flow analysis and code generation are considered. For an example stack-machine, the authors show how to generate code for the run-time computations and still perform the compile...

Complete coding sequence of Zika virus from Martinique outbreak in 2015

Directory of Open Access Journals (Sweden)

G. Piorkowski

2016-05-01

Full Text Available Zika virus is an Aedes-borne Flavivirus causing fever, arthralgia, myalgia rash, associated with Guillain–Barré syndrome and suspected to induce microcephaly in the fetus. We report here the complete coding sequence of the first characterized Caribbean Zika virus strain, isolated from a patient from Martinique in December, 2015.

In Silico Mining of Microsatellites in Coding Sequences of the Date Palm (Arecaceae Genome, Characterization, and Transferability

Directory of Open Access Journals (Sweden)

Frédérique Aberlenc-Bertossi

2014-01-01

Full Text Available Premise of the study: To complement existing sets of primarily dinucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri- and hexanucleotide microsatellite loci identified within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops, Livistona, and Hyphaene. Methods and Results: Tandem repeat motifs of 3–6 bp were searched using a simple sequence repeat (SSR–pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplification, intraspecific polymorphisms, and stepwise mutation patterns. Conclusions: These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecific gene flow studies in Phoenix and other Coryphoideae genera.

A Stochastic Bi-Level Scheduling Approach for the Participation of EV Aggregators in Competitive Electricity Markets

DEFF Research Database (Denmark)

Rashidizaheh-Kermani, Homa; Vahedipour-Dahraie, Mostafa; Najafi, Hamid Reza

2017-01-01

are modeled via stochastic programming. Therefore, a two-level problem is formulated here, in which the aggregator makes decision in the upper level and the EV clients purchase energy to charge their EVs in the lower level. Then the obtained nonlinear bi-level framework is transformed into a single......This paper proposes a stochastic bi-level decision-making model for an electric vehicle (EV) aggregator in a competitive environment. In this approach, the EV aggregator decides to participate in day-ahead (DA) and balancing markets and provides energy price offers to the EV owners in order...... is assessed in a realistic case study and the results show that the proposed model would be effective for an EV aggregator decision-making problem in a competitive environment....

Personalized Age Progression with Bi-Level Aging Dictionary Learning.

Science.gov (United States)

Shu, Xiangbo; Tang, Jinhui; Li, Zechao; Lai, Hanjiang; Zhang, Liyan; Yan, Shuicheng

2018-04-01

Age progression is defined as aesthetically re-rendering the aging face at any future age for an individual face. In this work, we aim to automatically render aging faces in a personalized way. Basically, for each age group, we learn an aging dictionary to reveal its aging characteristics (e.g., wrinkles), where the dictionary bases corresponding to the same index yet from two neighboring aging dictionaries form a particular aging pattern cross these two age groups, and a linear combination of all these patterns expresses a particular personalized aging process. Moreover, two factors are taken into consideration in the dictionary learning process. First, beyond the aging dictionaries, each person may have extra personalized facial characteristics, e.g., mole, which are invariant in the aging process. Second, it is challenging or even impossible to collect faces of all age groups for a particular person, yet much easier and more practical to get face pairs from neighboring age groups. To this end, we propose a novel Bi-level Dictionary Learning based Personalized Age Progression (BDL-PAP) method. Here, bi-level dictionary learning is formulated to learn the aging dictionaries based on face pairs from neighboring age groups. Extensive experiments well demonstrate the advantages of the proposed BDL-PAP over other state-of-the-arts in term of personalized age progression, as well as the performance gain for cross-age face verification by synthesizing aging faces.

Source coherence impairments in a direct detection direct sequence optical code-division multiple-access system.

Science.gov (United States)

Fsaifes, Ihsan; Lepers, Catherine; Lourdiane, Mounia; Gallion, Philippe; Beugin, Vincent; Guignard, Philippe

2007-02-01

We demonstrate that direct sequence optical code- division multiple-access (DS-OCDMA) encoders and decoders using sampled fiber Bragg gratings (S-FBGs) behave as multipath interferometers. In that case, chip pulses of the prime sequence codes generated by spreading in time-coherent data pulses can result from multiple reflections in the interferometers that can superimpose within a chip time duration. We show that the autocorrelation function has to be considered as the sum of complex amplitudes of the combined chip as the laser source coherence time is much greater than the integration time of the photodetector. To reduce the sensitivity of the DS-OCDMA system to the coherence time of the laser source, we analyze the use of sparse and nonperiodic quadratic congruence and extended quadratic congruence codes.

Source coherence impairments in a direct detection direct sequence optical code-division multiple-access system

Science.gov (United States)

Fsaifes, Ihsan; Lepers, Catherine; Lourdiane, Mounia; Gallion, Philippe; Beugin, Vincent; Guignard, Philippe

2007-02-01

We demonstrate that direct sequence optical code- division multiple-access (DS-OCDMA) encoders and decoders using sampled fiber Bragg gratings (S-FBGs) behave as multipath interferometers. In that case, chip pulses of the prime sequence codes generated by spreading in time-coherent data pulses can result from multiple reflections in the interferometers that can superimpose within a chip time duration. We show that the autocorrelation function has to be considered as the sum of complex amplitudes of the combined chip as the laser source coherence time is much greater than the integration time of the photodetector. To reduce the sensitivity of the DS-OCDMA system to the coherence time of the laser source, we analyze the use of sparse and nonperiodic quadratic congruence and extended quadratic congruence codes.

Lossless compression of waveform data for efficient storage and transmission

International Nuclear Information System (INIS)

Stearns, S.D.; Tan, Li Zhe; Magotra, Neeraj

1993-01-01

Compression of waveform data is significant in many engineering and research areas since it can be used to alleviate data storage and transmission bandwidth. For example, seismic data are widely recorded and transmitted so that analysis can be performed on large amounts of data for numerous applications such as petroleum exploration, determination of the earth's core structure, seismic event detection and discrimination of underground nuclear explosions, etc. This paper describes a technique for lossless wave form data compression. The technique consists of two stages. The first stage is a modified form of linear prediction with discrete coefficients and the second stage is bi-level sequence coding. The linear predictor generates an error or residue sequence in a way such that exact reconstruction of the original data sequence can be accomplished with a simple algorithm. The residue sequence is essentially white Gaussian with seismic or other similar waveform data. Bi-level sequence coding, in which two sample sizes are chosen and the residue sequence is encoded into subsequences that alternate from one level to the other, further compresses the residue sequence. The principal feature of the two-stage data compression algorithm is that it is lossless, that is, it allows exact, bit-for-bit recovery of the original data sequence. The performance of the lossless compression algorithm at each stage is analyzed. The advantages of using bi-level sequence coding in the second stage are its simplicity of implementation, its effectiveness on data with large amplitude variations, and its near-optimal performance in encoding Gaussian sequences. Applications of the two-stage technique to typical seismic data indicates that an average number of compressed bits per sample close to the lower bound is achievable in practical situations

Coding with partially hidden Markov models

DEFF Research Database (Denmark)

Forchhammer, Søren; Rissanen, J.

1995-01-01

Partially hidden Markov models (PHMM) are introduced. They are a variation of the hidden Markov models (HMM) combining the power of explicit conditioning on past observations and the power of using hidden states. (P)HMM may be combined with arithmetic coding for lossless data compression. A general...... 2-part coding scheme for given model order but unknown parameters based on PHMM is presented. A forward-backward reestimation of parameters with a redefined backward variable is given for these models and used for estimating the unknown parameters. Proof of convergence of this reestimation is given....... The PHMM structure and the conditions of the convergence proof allows for application of the PHMM to image coding. Relations between the PHMM and hidden Markov models (HMM) are treated. Results of coding bi-level images with the PHMM coding scheme is given. The results indicate that the PHMM can adapt...

On the electronic structure and thermoelectric properties of BiTeBr and BiTeI single crystals and of BiTeI with the addition of BiI3 and CuI

International Nuclear Information System (INIS)

Kulbachinskii, Vladimir A.; Kytin, Vladimir G.; Kudryashov, Alexey A.; Kuznetsov, Alexei N.; Shevelkov, Andrei V.

2012-01-01

The electronic structures were calculated for BiTeBr and BiTeI using the density-functional theory approach and accounting for the strong spin–orbital interaction. Qualitatively, the band structures for two compounds are similar, showing strong mixing of the p states of all elements in vicinity of the Fermi level, with the band gaps of 0.595 and 0.478 eV for BiTeBr and BiTeI, respectively. The optimized crystal structures show a tendency for the Bi–X (X=Br, I) bond elongation compared to the Bi–Te one. Both compounds are intrinsic n-type semiconductors but display a metallic-like conductivity coupled to rather large thermopower, which is rationalized within the frames of the acoustic phonons scattering model. Because of larger thermopower BiTeBr exhibits a twice higher thermoelectric figure-of-merit near room temperature, ZT=0.17, compared to BiTeI. The addition of 1 mass% of BiI 3 or CuI to BiTeI decreases the mobility of electrons by two orders of magnitude, leading to significantly lower electrical conductivity, but at the same time effectively reduces the thermal conductivity. The prospects of further enhancing the thermoelectric efficiency are briefly discussed. - Graphical abstract: View of the crystal structure of BiTeBr is shown in the figure The optimized crystal structures show a tendency for the Bi–X (X=Br, I) bond elongation compared to the Bi–Te one. The electronic structures were calculated for BiTeBr and BiTeI using the density-functional theory approach and accounting for the strong spin–orbital interaction. Qualitatively, the band structures for two compounds are similar, showing strong mixing of the p states of all elements in vicinity of the Fermi level, with the band gaps of 0.595 and 0.478 eV for BiTeBr and BiTeI, respectively. Both compounds are intrinsic n-type semiconductors but display a metallic-like conductivity coupled to rather large thermopower, which is rationalized within the frames of the acoustic phonons scattering

Magnetic and thermoelectric properties of three different atomic ratio of Bi/Mn in BiMn2O5: DFT approach

International Nuclear Information System (INIS)

Khan, Wilayat; Reshak, A.H.; Rafezi Ahmad, Khairel; Alahmed, Z.A.

2014-01-01

Electronic structure and magnetic properties of the three different samples of BiMn 2 O 5 , are calculated using the density functional theory (DFT). These samples have different Bi/Mn concentration. For simplicity, we suggest to call them as A, B and C. The calculated band structures show half metallicity for all samples, and possess 100% spin polarization at the Fermi level. The spin up/down density of states are calculated using Engel–Vosko generalized gradient approximation (EV-GGA). We have discussed the effect of Mn magnetic moment (μ B ) on the electronic and magnetic properties of the entire samples. The temperature dependent thermoelectric properties like electrical and thermal conductivity, Seebeck coefficient and power factor are also calculated, employing the Boltzmann transport theory under the BoltzTraP code. Our results indicated that these properties are strongly dependent on Bi/Mn concentration. - Highlights: • FPLAPW method used for calculating the electronic Structure. • The band structure shows that the calculated compounds are half metallic. • The magnetic properties have been calculated. • Thermoelectric properties were also calculated using Boltzmann theory. • Calculated power factor shows that sample B are good thermoelectric material

A bi-level programming for multistage co-expansion planning of the integrated gas and electricity system

DEFF Research Database (Denmark)

Zeng, Qing; Zhang, Baohua; Fang, Jiakun

2017-01-01

as the generation capacities, while the lower-level is formulated as an optimal economic dispatch under the operational constraints given by the upper-level decision. To solve the bi-level multi-stage programming problem, a hybrid algorithm is proposed combining the modified binary particle swarm optimization (BPSO...... power systems. The system operation is optimized and embedded in the planning horizon. A bi-level multi-stage programming problem is formulated to minimize the investment cost plus the operational cost. The upper-level optimizes the expansion plan and determines the network topology as well......) and the interior point method (IPM). The BPSO is used for the upper-level sub-problem, and the IPM is adopted for the lower-level sub-problem. Numerical case studies have been carried out on the practical gas and electricity transmission network in western Denmark. Simulation results demonstrate the effectiveness...

Multi-stage decoding for multi-level block modulation codes

Science.gov (United States)

Lin, Shu

1991-01-01

In this paper, we investigate various types of multi-stage decoding for multi-level block modulation codes, in which the decoding of a component code at each stage can be either soft-decision or hard-decision, maximum likelihood or bounded-distance. Error performance of codes is analyzed for a memoryless additive channel based on various types of multi-stage decoding, and upper bounds on the probability of an incorrect decoding are derived. Based on our study and computation results, we find that, if component codes of a multi-level modulation code and types of decoding at various stages are chosen properly, high spectral efficiency and large coding gain can be achieved with reduced decoding complexity. In particular, we find that the difference in performance between the suboptimum multi-stage soft-decision maximum likelihood decoding of a modulation code and the single-stage optimum decoding of the overall code is very small: only a fraction of dB loss in SNR at the probability of an incorrect decoding for a block of 10(exp -6). Multi-stage decoding of multi-level modulation codes really offers a way to achieve the best of three worlds, bandwidth efficiency, coding gain, and decoding complexity.

Licensee Event Report sequence coding and search procedure workshop

International Nuclear Information System (INIS)

Cottrell, W.B.; Gallaher, R.B.

1981-01-01

Since mid-1980, the Office for Analysis and Evaluation of Operational Data (AEOD) of the Nuclear Regulatory Commission (NRC) has been developing procedures for the systematic review and analysis of Licensee Event Reports (LERs). These procedures generally address several areas of concern, including identification of significant trends and patterns, event sequence of occurrences, component failures, and system and plant effects. The AEOD and NSIC conducted a workshop on the new coding procedure at the American Museum of Science and Energy in Oak Ridge, TN, on November 24, 1980

[Influence of "prehistory" of sequential movements of the right and the left hand on reproduction: coding of positions, movements and sequence structure].

Science.gov (United States)

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.

Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction

DEFF Research Database (Denmark)

Mirzadeh, Kiavash; Martinez, Virginia; Toddo, Stephen

2015-01-01

are poorly expressed even when they are codon-optimized and expressed from vectors with powerful genetic elements. In this study, we show that poor expression can be caused by certain nucleotide sequences (e.g., cloning scars) at the junction between the vector and the coding sequence. Since these sequences...

Whole-Exome Sequencing Identifies Rare and Low-Frequency Coding Variants Associated with LDL Cholesterol

Science.gov (United States)

Lange, Leslie A.; Hu, Youna; Zhang, He; Xue, Chenyi; Schmidt, Ellen M.; Tang, Zheng-Zheng; Bizon, Chris; Lange, Ethan M.; Smith, Joshua D.; Turner, Emily H.; Jun, Goo; Kang, Hyun Min; Peloso, Gina; Auer, Paul; Li, Kuo-ping; Flannick, Jason; Zhang, Ji; Fuchsberger, Christian; Gaulton, Kyle; Lindgren, Cecilia; Locke, Adam; Manning, Alisa; Sim, Xueling; Rivas, Manuel A.; Holmen, Oddgeir L.; Gottesman, Omri; Lu, Yingchang; Ruderfer, Douglas; Stahl, Eli A.; Duan, Qing; Li, Yun; Durda, Peter; Jiao, Shuo; Isaacs, Aaron; Hofman, Albert; Bis, Joshua C.; Correa, Adolfo; Griswold, Michael E.; Jakobsdottir, Johanna; Smith, Albert V.; Schreiner, Pamela J.; Feitosa, Mary F.; Zhang, Qunyuan; Huffman, Jennifer E.; Crosby, Jacy; Wassel, Christina L.; Do, Ron; Franceschini, Nora; Martin, Lisa W.; Robinson, Jennifer G.; Assimes, Themistocles L.; Crosslin, David R.; Rosenthal, Elisabeth A.; Tsai, Michael; Rieder, Mark J.; Farlow, Deborah N.; Folsom, Aaron R.; Lumley, Thomas; Fox, Ervin R.; Carlson, Christopher S.; Peters, Ulrike; Jackson, Rebecca D.; van Duijn, Cornelia M.; Uitterlinden, André G.; Levy, Daniel; Rotter, Jerome I.; Taylor, Herman A.; Gudnason, Vilmundur; Siscovick, David S.; Fornage, Myriam; Borecki, Ingrid B.; Hayward, Caroline; Rudan, Igor; Chen, Y. Eugene; Bottinger, Erwin P.; Loos, Ruth J.F.; Sætrom, Pål; Hveem, Kristian; Boehnke, Michael; Groop, Leif; McCarthy, Mark; Meitinger, Thomas; Ballantyne, Christie M.; Gabriel, Stacey B.; O’Donnell, Christopher J.; Post, Wendy S.; North, Kari E.; Reiner, Alexander P.; Boerwinkle, Eric; Psaty, Bruce M.; Altshuler, David; Kathiresan, Sekar; Lin, Dan-Yu; Jarvik, Gail P.; Cupples, L. Adrienne; Kooperberg, Charles; Wilson, James G.; Nickerson, Deborah A.; Abecasis, Goncalo R.; Rich, Stephen S.; Tracy, Russell P.; Willer, Cristen J.; Gabriel, Stacey B.; Altshuler, David M.; Abecasis, Gonçalo R.; Allayee, Hooman; Cresci, Sharon; Daly, Mark J.; de Bakker, Paul I.W.; DePristo, Mark A.; Do, Ron; Donnelly, Peter; Farlow, Deborah N.; Fennell, Tim; Garimella, Kiran; Hazen, Stanley L.; Hu, Youna; Jordan, Daniel M.; Jun, Goo; Kathiresan, Sekar; Kang, Hyun Min; Kiezun, Adam; Lettre, Guillaume; Li, Bingshan; Li, Mingyao; Newton-Cheh, Christopher H.; Padmanabhan, Sandosh; Peloso, Gina; Pulit, Sara; Rader, Daniel J.; Reich, David; Reilly, Muredach P.; Rivas, Manuel A.; Schwartz, Steve; Scott, Laura; Siscovick, David S.; Spertus, John A.; Stitziel, Nathaniel O.; Stoletzki, Nina; Sunyaev, Shamil R.; Voight, Benjamin F.; Willer, Cristen J.; Rich, Stephen S.; Akylbekova, Ermeg; Atwood, Larry D.; Ballantyne, Christie M.; Barbalic, Maja; Barr, R. Graham; Benjamin, Emelia J.; Bis, Joshua; Boerwinkle, Eric; Bowden, Donald W.; Brody, Jennifer; Budoff, Matthew; Burke, Greg; Buxbaum, Sarah; Carr, Jeff; Chen, Donna T.; Chen, Ida Y.; Chen, Wei-Min; Concannon, Pat; Crosby, Jacy; Cupples, L. Adrienne; D’Agostino, Ralph; DeStefano, Anita L.; Dreisbach, Albert; Dupuis, Josée; Durda, J. Peter; Ellis, Jaclyn; Folsom, Aaron R.; Fornage, Myriam; Fox, Caroline S.; Fox, Ervin; Funari, Vincent; Ganesh, Santhi K.; Gardin, Julius; Goff, David; Gordon, Ora; Grody, Wayne; Gross, Myron; Guo, Xiuqing; Hall, Ira M.; Heard-Costa, Nancy L.; Heckbert, Susan R.; Heintz, Nicholas; Herrington, David M.; Hickson, DeMarc; Huang, Jie; Hwang, Shih-Jen; Jacobs, David R.; Jenny, Nancy S.; Johnson, Andrew D.; Johnson, Craig W.; Kawut, Steven; Kronmal, Richard; Kurz, Raluca; Lange, Ethan M.; Lange, Leslie A.; Larson, Martin G.; Lawson, Mark; Lewis, Cora E.; Levy, Daniel; Li, Dalin; Lin, Honghuang; Liu, Chunyu; Liu, Jiankang; Liu, Kiang; Liu, Xiaoming; Liu, Yongmei; Longstreth, William T.; Loria, Cay; Lumley, Thomas; Lunetta, Kathryn; Mackey, Aaron J.; Mackey, Rachel; Manichaikul, Ani; Maxwell, Taylor; McKnight, Barbara; Meigs, James B.; Morrison, Alanna C.; Musani, Solomon K.; Mychaleckyj, Josyf C.; Nettleton, Jennifer A.; North, Kari; O’Donnell, Christopher J.; O’Leary, Daniel; Ong, Frank; Palmas, Walter; Pankow, James S.; Pankratz, Nathan D.; Paul, Shom; Perez, Marco; Person, Sharina D.; Polak, Joseph; Post, Wendy S.; Psaty, Bruce M.; Quinlan, Aaron R.; Raffel, Leslie J.; Ramachandran, Vasan S.; Reiner, Alexander P.; Rice, Kenneth; Rotter, Jerome I.; Sanders, Jill P.; Schreiner, Pamela; Seshadri, Sudha; Shea, Steve; Sidney, Stephen; Silverstein, Kevin; Smith, Nicholas L.; Sotoodehnia, Nona; Srinivasan, Asoke; Taylor, Herman A.; Taylor, Kent; Thomas, Fridtjof; Tracy, Russell P.; Tsai, Michael Y.; Volcik, Kelly A.; Wassel, Chrstina L.; Watson, Karol; Wei, Gina; White, Wendy; Wiggins, Kerri L.; Wilk, Jemma B.; Williams, O. Dale; Wilson, Gregory; Wilson, James G.; Wolf, Phillip; Zakai, Neil A.; Hardy, John; Meschia, James F.; Nalls, Michael; Singleton, Andrew; Worrall, Brad; Bamshad, Michael J.; Barnes, Kathleen C.; Abdulhamid, Ibrahim; Accurso, Frank; Anbar, Ran; Beaty, Terri; Bigham, Abigail; Black, Phillip; Bleecker, Eugene; Buckingham, Kati; Cairns, Anne Marie; Caplan, Daniel; Chatfield, Barbara; Chidekel, Aaron; Cho, Michael; Christiani, David C.; Crapo, James D.; Crouch, Julia; Daley, Denise; Dang, Anthony; Dang, Hong; De Paula, Alicia; DeCelie-Germana, Joan; Drumm, Allen DozorMitch; Dyson, Maynard; Emerson, Julia; Emond, Mary J.; Ferkol, Thomas; Fink, Robert; Foster, Cassandra; Froh, Deborah; Gao, Li; Gershan, William; Gibson, Ronald L.; Godwin, Elizabeth; Gondor, Magdalen; Gutierrez, Hector; Hansel, Nadia N.; Hassoun, Paul M.; Hiatt, Peter; Hokanson, John E.; Howenstine, Michelle; Hummer, Laura K.; Kanga, Jamshed; Kim, Yoonhee; Knowles, Michael R.; Konstan, Michael; Lahiri, Thomas; Laird, Nan; Lange, Christoph; Lin, Lin; Lin, Xihong; Louie, Tin L.; Lynch, David; Make, Barry; Martin, Thomas R.; Mathai, Steve C.; Mathias, Rasika A.; McNamara, John; McNamara, Sharon; Meyers, Deborah; Millard, Susan; Mogayzel, Peter; Moss, Richard; Murray, Tanda; Nielson, Dennis; Noyes, Blakeslee; O’Neal, Wanda; Orenstein, David; O’Sullivan, Brian; Pace, Rhonda; Pare, Peter; Parker, H. Worth; Passero, Mary Ann; Perkett, Elizabeth; Prestridge, Adrienne; Rafaels, Nicholas M.; Ramsey, Bonnie; Regan, Elizabeth; Ren, Clement; Retsch-Bogart, George; Rock, Michael; Rosen, Antony; Rosenfeld, Margaret; Ruczinski, Ingo; Sanford, Andrew; Schaeffer, David; Sell, Cindy; Sheehan, Daniel; Silverman, Edwin K.; Sin, Don; Spencer, Terry; Stonebraker, Jackie; Tabor, Holly K.; Varlotta, Laurie; Vergara, Candelaria I.; Weiss, Robert; Wigley, Fred; Wise, Robert A.; Wright, Fred A.; Wurfel, Mark M.; Zanni, Robert; Zou, Fei; Nickerson, Deborah A.; Rieder, Mark J.; Green, Phil; Shendure, Jay; Akey, Joshua M.; Bustamante, Carlos D.; Crosslin, David R.; Eichler, Evan E.; Fox, P. Keolu; Fu, Wenqing; Gordon, Adam; Gravel, Simon; Jarvik, Gail P.; Johnsen, Jill M.; Kan, Mengyuan; Kenny, Eimear E.; Kidd, Jeffrey M.; Lara-Garduno, Fremiet; Leal, Suzanne M.; Liu, Dajiang J.; McGee, Sean; O’Connor, Timothy D.; Paeper, Bryan; Robertson, Peggy D.; Smith, Joshua D.; Staples, Jeffrey C.; Tennessen, Jacob A.; Turner, Emily H.; Wang, Gao; Yi, Qian; Jackson, Rebecca; Peters, Ulrike; Carlson, Christopher S.; Anderson, Garnet; Anton-Culver, Hoda; Assimes, Themistocles L.; Auer, Paul L.; Beresford, Shirley; Bizon, Chris; Black, Henry; Brunner, Robert; Brzyski, Robert; Burwen, Dale; Caan, Bette; Carty, Cara L.; Chlebowski, Rowan; Cummings, Steven; Curb, J. David; Eaton, Charles B.; Ford, Leslie; Franceschini, Nora; Fullerton, Stephanie M.; Gass, Margery; Geller, Nancy; Heiss, Gerardo; Howard, Barbara V.; Hsu, Li; Hutter, Carolyn M.; Ioannidis, John; Jiao, Shuo; Johnson, Karen C.; Kooperberg, Charles; Kuller, Lewis; LaCroix, Andrea; Lakshminarayan, Kamakshi; Lane, Dorothy; Lasser, Norman; LeBlanc, Erin; Li, Kuo-Ping; Limacher, Marian; Lin, Dan-Yu; Logsdon, Benjamin A.; Ludlam, Shari; Manson, JoAnn E.; Margolis, Karen; Martin, Lisa; McGowan, Joan; Monda, Keri L.; Kotchen, Jane Morley; Nathan, Lauren; Ockene, Judith; O’Sullivan, Mary Jo; Phillips, Lawrence S.; Prentice, Ross L.; Robbins, John; Robinson, Jennifer G.; Rossouw, Jacques E.; Sangi-Haghpeykar, Haleh; Sarto, Gloria E.; Shumaker, Sally; Simon, Michael S.; Stefanick, Marcia L.; Stein, Evan; Tang, Hua; Taylor, Kira C.; Thomson, Cynthia A.; Thornton, Timothy A.; Van Horn, Linda; Vitolins, Mara; Wactawski-Wende, Jean; Wallace, Robert; Wassertheil-Smoller, Sylvia; Zeng, Donglin; Applebaum-Bowden, Deborah; Feolo, Michael; Gan, Weiniu; Paltoo, Dina N.; Sholinsky, Phyliss; Sturcke, Anne

2014-01-01

Elevated low-density lipoprotein cholesterol (LDL-C) is a treatable, heritable risk factor for cardiovascular disease. Genome-wide association studies (GWASs) have identified 157 variants associated with lipid levels but are not well suited to assess the impact of rare and low-frequency variants. To determine whether rare or low-frequency coding variants are associated with LDL-C, we exome sequenced 2,005 individuals, including 554 individuals selected for extreme LDL-C (>98th or <2nd percentile). Follow-up analyses included sequencing of 1,302 additional individuals and genotype-based analysis of 52,221 individuals. We observed significant evidence of association between LDL-C and the burden of rare or low-frequency variants in PNPLA5, encoding a phospholipase-domain-containing protein, and both known and previously unidentified variants in PCSK9, LDLR and APOB, three known lipid-related genes. The effect sizes for the burden of rare variants for each associated gene were substantially higher than those observed for individual SNPs identified from GWASs. We replicated the PNPLA5 signal in an independent large-scale sequencing study of 2,084 individuals. In conclusion, this large whole-exome-sequencing study for LDL-C identified a gene not known to be implicated in LDL-C and provides unique insight into the design and analysis of similar experiments. PMID:24507775

Nasal bi-level positive airway pressure (BiPAP) versus nasal continuous positive airway pressure (CPAP) in preterm infants ≤32 weeks: A retrospective cohort study.

Science.gov (United States)

Rong, Zhi-Hui; Li, Wen-Bin; Liu, Wei; Cai, Bao-Huan; Wang, Jing; Yang, Min; Li, Wei; Chang, Li-Wen

2016-05-01

To investigate whether Bi-level positive airway pressure (BiPAP), compared with nasal continuous positive airway pressure (CPAP), is a more effective therapeutic strategy in preterm infants ≤32 weeks. All inborn infants between 26(+1) and 32(+6) weeks' gestation, admitted to the neonatal intensive care unit (NICU ) of Tongji Medical Hospital between 1 January, 2010 and 31 December, 2011 (the 2010-2011 cohort or CPAP cohort) and between 1 January, 2012 and 31 December, 2013 (the 2012-2013 cohort or BiPAP cohort), were retrospectively identified. The primary outcome was intubation in infants CPAP were subsequently intubated (P CPAP, reduced the need for intubation within the first 72 h of age. © 2016 Paediatrics and Child Health Division (The Royal Australasian College of Physicians).

A Novel Approach for Bi-Level Segmentation of Tuberculosis Bacilli Based on Meta-Heuristic Algorithms

Directory of Open Access Journals (Sweden)

AYAS, S.

2018-02-01

Full Text Available Image thresholding is the most crucial step in microscopic image analysis to distinguish bacilli objects causing of tuberculosis disease. Therefore, several bi-level thresholding algorithms are widely used to increase the bacilli segmentation accuracy. However, bi-level microscopic image thresholding problem has not been solved using optimization algorithms. This paper introduces a novel approach for the segmentation problem using heuristic algorithms and presents visual and quantitative comparisons of heuristic and state-of-art thresholding algorithms. In this study, well-known heuristic algorithms such as Firefly Algorithm, Particle Swarm Optimization, Cuckoo Search, Flower Pollination are used to solve bi-level microscopic image thresholding problem, and the results are compared with the state-of-art thresholding algorithms such as K-Means, Fuzzy C-Means, Fast Marching. Kapur's entropy is chosen as the entropy measure to be maximized. Experiments are performed to make comparisons in terms of evaluation metrics and execution time. The quantitative results are calculated based on ground truth segmentation. According to the visual results, heuristic algorithms have better performance and the quantitative results are in accord with the visual results. Furthermore, experimental time comparisons show the superiority and effectiveness of the heuristic algorithms over traditional thresholding algorithms.

SinEx DB: a database for single exon coding sequences in mammalian genomes.

Science.gov (United States)

Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S

2016-01-01

Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl. © The Author(s) 2016. Published by Oxford University Press.

Generalized bi-quasi-variational inequalities for quasi-semi-monotone and bi-quasi-semi-monotone operators with applications in non-compact settings and minimization problems

Directory of Open Access Journals (Sweden)

Chowdhury Molhammad SR

2000-01-01

Full Text Available Results are obtained on existence theorems of generalized bi-quasi-variational inequalities for quasi-semi-monotone and bi-quasi-semi-monotone operators in both compact and non-compact settings. We shall use the concept of escaping sequences introduced by Border (Fixed Point Theorem with Applications to Economics and Game Theory, Cambridge University Press, Cambridge, 1985 to obtain results in non-compact settings. Existence theorems on non-compact generalized bi-complementarity problems for quasi-semi-monotone and bi-quasi-semi-monotone operators are also obtained. Moreover, as applications of some results of this paper on generalized bi-quasi-variational inequalities, we shall obtain existence of solutions for some kind of minimization problems with quasi- semi-monotone and bi-quasi-semi-monotone operators.

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

Science.gov (United States)

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

2016-06-15

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

Effects of low-level Ag doping on Bi2Sr2CaCu2O8+x

International Nuclear Information System (INIS)

Deis, T.A.; Eror, N.G.; Krishnaraj, P.; Prorok, B.C.; Lelovic, M.; Balachandran, U.

1995-07-01

Bi 2 Sr 2 CaCu 2 O 8 has been doped with silver, up to 10,000 ppm, in three ways: excess additions, substitution of Ag for Bi, and substitution of Ag for Sr. Effects of doping on the c-axis lattice parameter and critical temperature (T c ) were measured. Effects from doing were only observed in slow-cooled [10 degree/hr] oxygen equilibrated samples. Doping by excess additions caused a small decrease in T c and an increase in the c-axis length of the lattice. Doping by substitution, compared to excess Ag additions, caused a larger decrease in T c and higher c-axis values for doping levels up to 1,000 ppm. Doping by substitution at higher levels (1,000--10,000 ppm) caused T c to increase and the c-axis to decrease. Samples with similar substitutional doping levels exhibited comparable T c values and samples with Ag substituted for Sr consistently exhibited higher c-axis values than samples that had equivalent amounts of Ag substituted for Bi

MLED_BI: a new BI Design Approach to Support Multilingualism in Business Intelligence

Directory of Open Access Journals (Sweden)

Nedim Dedić

2017-11-01

Full Text Available Existing approaches to support Multilingualism (ML in Business Intelligence (BI create problems for business users, present a number of challenges from the technical perspective, and lead to issues with logical dependence in the star schema. In this paper, we propose MLED_BI (Multilingual Enabled Design for Business Intelligence, a novel BI design approach to support the application of ML in BI Environment, which overcomes the issues and problems found with existing approaches. The approach is based on a revision of the data warehouse dimensional modelling approach and treats the Star Schema as a higher level entity. This paper describes MLED_BI and the validation and evaluation approach used.

Generation of Efficient High-Level Hardware Code from Dataflow Programs

OpenAIRE

Siret , Nicolas; Wipliez , Matthieu; Nezan , Jean François; Palumbo , Francesca

2012-01-01

High-level synthesis (HLS) aims at reducing the time-to-market by providing an automated design process that interprets and compiles high-level abstraction programs into hardware. However, HLS tools still face limitations regarding the performance of the generated code, due to the difficulties of compiling input imperative languages into efficient hardware code. Moreover the hardware code generated by the HLS tools is usually target-dependant and at a low level of abstraction (i.e. gate-level...

SYMBOL LEVEL DECODING FOR DUO-BINARY TURBO CODES

Directory of Open Access Journals (Sweden)

Yogesh Beeharry

2017-05-01

Full Text Available This paper investigates the performance of three different symbol level decoding algorithms for Duo-Binary Turbo codes. Explicit details of the computations involved in the three decoding techniques, and a computational complexity analysis are given. Simulation results with different couple lengths, code-rates, and QPSK modulation reveal that the symbol level decoding with bit-level information outperforms the symbol level decoding by 0.1 dB on average in the error floor region. Moreover, a complexity analysis reveals that symbol level decoding with bit-level information reduces the decoding complexity by 19.6 % in terms of the total number of computations required for each half-iteration as compared to symbol level decoding.

ATP Synthase β-Chain Overexpression in SR-BI Knockout Mice Increases HDL Uptake and Reduces Plasma HDL Level

Directory of Open Access Journals (Sweden)

Kexiu Song

2014-01-01

Full Text Available HDL cholesterol is known to be inversely correlated with cardiovascular disease due to its diverse antiatherogenic functions. SR-BI mediates the selective uptake of HDL-C. SR-BI knockout diminishes but does not completely block the transport of HDL; other receptors may be involved. Ectopic ATP synthase β-chain in hepatocytes has been previously characterized as an apoA-I receptor, triggering HDL internalization. This study was undertaken to identify the overexpression of ectopic ATP synthase β-chain on DIL-HDL uptake in primary hepatocytes in vitro and on plasma HDL levels in SR-BI knockout mice. Human ATP synthase β-chain cDNA was delivered to the mouse liver by adenovirus and GFP adenovirus as control. The adenovirus-mediated overexpression of β-chain was identified at both mRNA and protein levels on mice liver and validated by its increasing of DiL-HDL uptake in primary hepatocytes. In response to hepatic overexpression of β-chain, plasma HDL-C levels and cholesterol were reduced in SR-BI knockout mice, compared with the control. The present data suggest that ATP synthase β-chain can serve as the endocytic receptor of HDL, and its overexpression can reduce plasma HDL-C.

Continuous-variable quantum erasure correcting code

DEFF Research Database (Denmark)

Lassen, Mikael Østergaard; Sabuncu, Metin; Huck, Alexander

2010-01-01

We experimentally demonstrate a continuous variable quantum erasure-correcting code, which protects coherent states of light against complete erasure. The scheme encodes two coherent states into a bi-party entangled state, and the resulting 4-mode code is conveyed through 4 independent channels...

Overexpression of BiP in tobacco alleviates endoplasmic reticulum stress

NARCIS (Netherlands)

Leborgne-Castel, N.; Jelitto- Dooren, E.P.W.M. van; Crofts, A.J.; Denecke, J.

1999-01-01

To study the role of the lumenal binding protein (BiP) in the transport and secretion of proteins, we have produced plants with altered BiP levels. Transgenic plants overexpressing BiP showed dramatically increased BiP mRNA levels but only a modest increase in BiP protein levels. The presence of

Coding and decoding libraries of sequence-defined functional copolymers synthesized via photoligation.

Science.gov (United States)

Zydziak, Nicolas; Konrad, Waldemar; Feist, Florian; Afonin, Sergii; Weidner, Steffen; Barner-Kowollik, Christopher

2016-11-30

Designing artificial macromolecules with absolute sequence order represents a considerable challenge. Here we report an advanced light-induced avenue to monodisperse sequence-defined functional linear macromolecules up to decamers via a unique photochemical approach. The versatility of the synthetic strategy-combining sequential and modular concepts-enables the synthesis of perfect macromolecules varying in chemical constitution and topology. Specific functions are placed at arbitrary positions along the chain via the successive addition of monomer units and blocks, leading to a library of functional homopolymers, alternating copolymers and block copolymers. The in-depth characterization of each sequence-defined chain confirms the precision nature of the macromolecules. Decoding of the functional information contained in the molecular structure is achieved via tandem mass spectrometry without recourse to their synthetic history, showing that the sequence information can be read. We submit that the presented photochemical strategy is a viable and advanced concept for coding individual monomer units along a macromolecular chain.

Classifying Coding DNA with Nucleotide Statistics

Directory of Open Access Journals (Sweden)

Nicolas Carels

2009-10-01

Full Text Available In this report, we compared the success rate of classification of coding sequences (CDS vs. introns by Codon Structure Factor (CSF and by a method that we called Universal Feature Method (UFM. UFM is based on the scoring of purine bias (Rrr and stop codon frequency. We show that the success rate of CDS/intron classification by UFM is higher than by CSF. UFM classifies ORFs as coding or non-coding through a score based on (i the stop codon distribution, (ii the product of purine probabilities in the three positions of nucleotide triplets, (iii the product of Cytosine (C, Guanine (G, and Adenine (A probabilities in the 1st, 2nd, and 3rd positions of triplets, respectively, (iv the probabilities of G in 1st and 2nd position of triplets and (v the distance of their GC3 vs. GC2 levels to the regression line of the universal correlation. More than 80% of CDSs (true positives of Homo sapiens (>250 bp, Drosophila melanogaster (>250 bp and Arabidopsis thaliana (>200 bp are successfully classified with a false positive rate lower or equal to 5%. The method releases coding sequences in their coding strand and coding frame, which allows their automatic translation into protein sequences with 95% confidence. The method is a natural consequence of the compositional bias of nucleotides in coding sequences.

On Coding Non-Contiguous Letter Combinations

Directory of Open Access Journals (Sweden)

Frédéric eDandurand

2011-06-01

Full Text Available Starting from the hypothesis that printed word identification initially involves the parallel mapping of visual features onto location-specific letter identities, we analyze the type of information that would be involved in optimally mapping this location-specific orthographic code onto a location-invariant lexical code. We assume that some intermediate level of coding exists between individual letters and whole words, and that this involves the representation of letter combinations. We then investigate the nature of this intermediate level of coding given the constraints of optimality. This intermediate level of coding is expected to compress data while retaining as much information as possible about word identity. Information conveyed by letters is a function of how much they constrain word identity and how visible they are. Optimization of this coding is a combination of minimizing resources (using the most compact representations and maximizing information. We show that in a large proportion of cases, non-contiguous letter sequences contain more information than contiguous sequences, while at the same time requiring less precise coding. Moreover, we found that the best predictor of human performance in orthographic priming experiments was within-word ranking of conditional probabilities, rather than average conditional probabilities. We conclude that from an optimality perspective, readers learn to select certain contiguous and non-contiguous letter combinations as information that provides the best cue to word identity.

An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences.

Science.gov (United States)

Pollier, Jacob; González-Guzmán, Miguel; Ardiles-Diaz, Wilson; Geelen, Danny; Goossens, Alain

2011-01-01

cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) is a commonly used technique for genome-wide expression analysis that does not require prior sequence knowledge. Typically, quantitative expression data and sequence information are obtained for a large number of differentially expressed gene tags. However, most of the gene tags do not correspond to full-length (FL) coding sequences, which is a prerequisite for subsequent functional analysis. A medium-throughput screening strategy, based on integration of polymerase chain reaction (PCR) and colony hybridization, was developed that allows in parallel screening of a cDNA library for FL clones corresponding to incomplete cDNAs. The method was applied to screen for the FL open reading frames of a selection of 163 cDNA-AFLP tags from three different medicinal plants, leading to the identification of 109 (67%) FL clones. Furthermore, the protocol allows for the use of multiple probes in a single hybridization event, thus significantly increasing the throughput when screening for rare transcripts. The presented strategy offers an efficient method for the conversion of incomplete expressed sequence tags (ESTs), such as cDNA-AFLP tags, to FL-coding sequences.

An Explicit Construction of a sequence of codes attaining the Tsfasman-Vladut-Zink Bound:The first steps

DEFF Research Database (Denmark)

Høholdt, Tom; Voss, Cornelia

1997-01-01

We present a sequence of codes attaining the Tsfasman-Vladut-Zink bound. The construction is based on the tower of Artin-Schreier extensions described by Garcia and Stichtenoth (1995). We also determine the dual codes. The first steps of the constructions are explicitly given as generator matrices...

Implementation of the - Constraint Method in Special Class of Multi-objective Fuzzy Bi-Level Nonlinear Problems

Directory of Open Access Journals (Sweden)

Azza Hassan Amer

2017-12-01

Full Text Available Geometric programming problem is a powerful tool for solving some special type nonlinear programming problems. In the last few years we have seen a very rapid development on solving multiobjective geometric programming problem. A few mathematical programming methods namely fuzzy programming, goal programming and weighting methods have been applied in the recent past to find the compromise solution. In this paper, -constraint method has been applied in bi-level multiobjective geometric programming problem to find the Pareto optimal solution at each level. The equivalent mathematical programming problems are formulated to find their corresponding value of the objective function based on the duality theorem at eash level. Here, we have developed a new algorithm for fuzzy programming technique to solve bi-level multiobjective geometric programming problems to find an optimal compromise solution. Finally the solution procedure of the fuzzy technique is illustrated by a numerical example

Coding sequence of human rho cDNAs clone 6 and clone 9

Energy Technology Data Exchange (ETDEWEB)

Chardin, P; Madaule, P; Tavitian, A

1988-03-25

The authors have isolated human cDNAs including the complete coding sequence for two rho proteins corresponding to the incomplete isolates previously described as clone 6 and clone 9. The deduced a.a. sequences, when compared to the a.a. sequence deduced from clone 12 cDNA, show that there are in human at least three highly homologous rho genes. They suggest that clone 12 be named rhoA, clone 6 : rhoB and clone 9 : rhoC. RhoA, B and C proteins display approx. 30% a.a. identity with ras proteins,. mainly clustered in four highly homologous internal regions corresponding to the GTP binding site; however at least one significant difference is found; the 3 rho proteins have an Alanine in position corresponding to ras Glycine 13, suggesting that rho and ras proteins might have slightly different biochemical properties.

Application of Melcor code for the calculo of TMLB sequence in PWR with natural circulating into the vessel

International Nuclear Information System (INIS)

Marten-Fuertes, F.

1995-01-01

The use of computer codes to analyze the phenomena of severe accidents is very important to take decisions in Nuclear Safety. This paper presents the MELCOR code used to calculate the TMLB sequence of PWR with natural circulation into the vessels. The main goal of this code is its application for the PSA (probabilistic safety analysis)

Decay of mass-separated 3.0min 195gBi to levels in 195Pb and shape coexistence in the neutron-deficient odd-mass Pb isotopes

International Nuclear Information System (INIS)

Griffin, J.C.; Braga, R.A.; Fink, R.W.; Bingham, C.R.; Coenen, E.; Huyse, M.; Duppen, P. van

1991-01-01

The radioactive decay of mass-separated 3.0 m 195g Bi to 195 Pb has been studied with the UNISOR and LISOL facilities. Time-sequenced spectra of γ-rays, X-rays, and conversion electrons have been obtained, together with γγt, γXt, eγt, and eXt coincidence data. From this information, a decay scheme has been constructed consisting of 23 excited states and 34 transitions in 195 Pb. Transitions with E0 multipole admixtures, indicative of shape coexistence, have been found to de-excite positive-parity levels at 1093, 1329, and 1380 keV. The beta-decay energy of the 195 Bi ground state is deduced to be Q EC =4800 +600 -550 keV based on the measurement of γ-ray-gated K/β + ratios. The excitation energy of the i 13/2 isomer in 195 Pb has been determined to be 203±4 keV from the α-decays of 199m,g Po. (orig.)

Generating Safety-Critical PLC Code From a High-Level Application Software Specification

Science.gov (United States)

2008-01-01

The benefits of automatic-application code generation are widely accepted within the software engineering community. These benefits include raised abstraction level of application programming, shorter product development time, lower maintenance costs, and increased code quality and consistency. Surprisingly, code generation concepts have not yet found wide acceptance and use in the field of programmable logic controller (PLC) software development. Software engineers at Kennedy Space Center recognized the need for PLC code generation while developing the new ground checkout and launch processing system, called the Launch Control System (LCS). Engineers developed a process and a prototype software tool that automatically translates a high-level representation or specification of application software into ladder logic that executes on a PLC. All the computer hardware in the LCS is planned to be commercial off the shelf (COTS), including industrial controllers or PLCs that are connected to the sensors and end items out in the field. Most of the software in LCS is also planned to be COTS, with only small adapter software modules that must be developed in order to interface between the various COTS software products. A domain-specific language (DSL) is a programming language designed to perform tasks and to solve problems in a particular domain, such as ground processing of launch vehicles. The LCS engineers created a DSL for developing test sequences of ground checkout and launch operations of future launch vehicle and spacecraft elements, and they are developing a tabular specification format that uses the DSL keywords and functions familiar to the ground and flight system users. The tabular specification format, or tabular spec, allows most ground and flight system users to document how the application software is intended to function and requires little or no software programming knowledge or experience. A small sample from a prototype tabular spec application is

Fermi-level tuning of the Dirac surface state in (Bi1-x Sb x )2Se3 thin films

Science.gov (United States)

Satake, Yosuke; Shiogai, Junichi; Takane, Daichi; Yamada, Keiko; Fujiwara, Kohei; Souma, Seigo; Sato, Takafumi; Takahashi, Takashi; Tsukazaki, Atsushi

2018-02-01

We report on the electronic states and the transport properties of three-dimensional topological insulator (Bi1-x Sb x )2Se3 ternary alloy thin films grown on an isostructural Bi2Se3 buffer layer on InP substrates. By angle-resolved photoemission spectroscopy, we clearly detected Dirac surface states with a large bulk band gap of 0.2-0.3 eV in the (Bi1-x Sb x )2Se3 film with x  =  0.70. In addition, we observed by Hall effect measurements that the dominant charge carrier converts from electron (n-type) to hole (p-type) at around x  =  0.7, indicating that the Fermi level can be controlled across the Dirac point. Indeed, the carrier transport was shown to be governed by Dirac surface state in 0.63  ⩽  x  ⩽  0.75. These features suggest that Fermi-level tunable (Bi1-x Sb x )2Se3-based heterostructures provide a platform for extracting exotic topological phenomena.

Thermal hydraulic analysis of Pb-Bi cooled HYPER fuel assemblies using SLTHEN code

International Nuclear Information System (INIS)

Tak, Nam Il; Song, Tae Y.; Park, Won S.; Kim, Chang Hyun

2002-12-01

In the present work, the existing SLTHEN code, which had been originally developed for subchannel analysis of sodium cooled fast reactors, was modified and applied to the Pb-Bi cooled HYPER core which consists of 237 fuel assemblies (TRU assemblies). In the analysis of single fuel assembly having chopped cosine power profile, the validation and the assessment of usefulness of the modified SLTHEN were focused. In the quantitative comparison, the results of the modified SLTHEN agreed well with those of analytical calculations and of MATRA. For the qualitative approaches, the sensitivity calculations for intra-assembly gap flow and turbulent mixing parameter were used. The sensitivity analysis results showed that the modified SLTHEN can provide reasonable simulations of subchannel thermal hydraulics. In particular, turbulent mixing parameter which is known as the most uncertain parameter in subchannel analyses did not affect largely the maximum cladding temperature. Therefore, it can be said that the results of single assembly show the usefulness of the modified SLTHEN code for thermal hydraulic analysis and design of HYPER under the conceptual design stage. In order to assess intra-assembly heat transfer, subchannel analyses were implemented for two types of 7 assemblies; 1) artificial 7 fuel assemblies to maximize intra-assembly heat transfer, 2) central 7 fuel assemblies in the HYPER reference core. The results showed that the modified SLTHEN can reasonably simulate intra-heat transfer and the amount of intra-assembly heat transfer is not so large in HYPER conditions. Particularly, intra-heat transfer did not affect the maximum coolant and the maximum cladding temperatures which are major parameters in conceptual core designs. The capability of full core thermal hydraulic analysis was confirmed by the analysis of 45 fuel assemblies in 1/6 HYPER core at the first cycle. The SLTHEN predicted that the reference design parameters are acceptable in terms of thermal

Comparison of bi-level optimization frameworks for sizing and control of a hybrid electric vehicle

NARCIS (Netherlands)

Silvas, E.; Bergshoeff, N.D.; Hofman, T.; Steinbuch, M.

2015-01-01

This paper discusses the integrated design problem related to determining the power specifications of the main subsystems (sizing) and the supervisory control (energy management). Different bi-level optimization methods, with the outer loop using algorithms as Genetic Algorithms, Sequential

Investigations of bi-directional flow behaviour of a large vertical opening in containment

International Nuclear Information System (INIS)

Sharma, Pavan K.; Markandeya, S.G.; Ghosh, A.K.; Kushwaha, H.S.

2002-01-01

Full text: In the complex codes developed for fire analysis and for containment thermal hydraulic analysis. The junction in the multi-compartment geometries are often modeled as uni-directional junctions. However, certain large size junctions are known to depict bi-directional flow behaviour under specific circumstances. Detailed investigations have been carried out to understand the bi-directionality of a junction by analyzing an earlier reported case study of fire in an enclosure. A computer code FDS was used for the analysis. The paper presents the details of the analysis, the results obtained and further studies required to be conducted so that the findings can be applied to the fire/containment thermal hydraulics analysis codes successfully

Implatation of MC2 computer code

International Nuclear Information System (INIS)

Seehusen, J.; Nair, R.P.K.; Becceneri, J.C.

1981-01-01

The implantation of MC2 computer code in the CDC system is presented. The MC2 computer code calculates multigroup cross sections for tipical compositions of fast reactors. The multigroup constants are calculated using solutions of PI or BI approximations for determined buckling value as weighting function. (M.C.K.) [pt

The localized effect of the Bi level on the valence band in the dilute bismuth GaBixAs1-x alloy

Science.gov (United States)

Zhao, Chuan-Zhen; Zhu, Min-Min; Wang, Jun; Wang, Sha-Sha; Lu, Ke-Qing

2018-05-01

The research on the temperature dependence of the band gap energy of the dilute bismuth GaBixAs1-x alloy has been done. It is found that its temperature insensitiveness is due to the enhanced localized character of the valence band state and the small decrease of the temperature coefficient for the conduction band minimum (CBM). The enhanced localized character of the valence band state is the main factor. In order to describe the localized effect of the Bi levels on the valence band, the localized energy is introduced into the Varshni's equation. It is found that the effect of the localized Bi level on the valence band becomes strong with increasing Bi content. In addition, it is found that the pressure dependence of the band gap energy of GaBixAs1-x does not seem to be influenced by the localized Bi levels. It is due to two factors. One is that the pressure dependence of the band gap energy is mainly determined by the D CBM of GaBixAs1-x. The D CBM of GaBixAs1-x is not influenced by the localized Bi levels. The other is that the small variation of the pressure coefficient for the D valence band maximum (VBM) state of GaBixAs1-x can be cancelled by the variation of the pressure coefficient for the D CBM state of GaBixAs1-x.

Episodic sequence memory is supported by a theta-gamma phase code

OpenAIRE

Heusser, Andrew C.; Poeppel, David; Ezzyat, Youssef; Davachi, Lila

2016-01-01

The meaning we derive from our experiences is not a simple static extraction of the elements, but is largely based on the order in which those elements occur. Models propose that sequence encoding is supported by interactions between high and low frequency oscillations, such that elements within an experience are represented by neural cell assemblies firing at higher frequencies (i.e. gamma) and sequential order is coded by the specific timing of firing with respect to a lower frequency oscil...

Deep Sequencing Reveals Uncharted Isoform Heterogeneity of the Protein-Coding Transcriptome in Cerebral Ischemia.

Science.gov (United States)

Bhattarai, Sunil; Aly, Ahmed; Garcia, Kristy; Ruiz, Diandra; Pontarelli, Fabrizio; Dharap, Ashutosh

2018-06-03

Gene expression in cerebral ischemia has been a subject of intense investigations for several years. Studies utilizing probe-based high-throughput methodologies such as microarrays have contributed significantly to our existing knowledge but lacked the capacity to dissect the transcriptome in detail. Genome-wide RNA-sequencing (RNA-seq) enables comprehensive examinations of transcriptomes for attributes such as strandedness, alternative splicing, alternative transcription start/stop sites, and sequence composition, thus providing a very detailed account of gene expression. Leveraging this capability, we conducted an in-depth, genome-wide evaluation of the protein-coding transcriptome of the adult mouse cortex after transient focal ischemia at 6, 12, or 24 h of reperfusion using RNA-seq. We identified a total of 1007 transcripts at 6 h, 1878 transcripts at 12 h, and 1618 transcripts at 24 h of reperfusion that were significantly altered as compared to sham controls. With isoform-level resolution, we identified 23 splice variants arising from 23 genes that were novel mRNA isoforms. For a subset of genes, we detected reperfusion time-point-dependent splice isoform switching, indicating an expression and/or functional switch for these genes. Finally, for 286 genes across all three reperfusion time-points, we discovered multiple, distinct, simultaneously expressed and differentially altered isoforms per gene that were generated via alternative transcription start/stop sites. Of these, 165 isoforms derived from 109 genes were novel mRNAs. Together, our data unravel the protein-coding transcriptome of the cerebral cortex at an unprecedented depth to provide several new insights into the flexibility and complexity of stroke-related gene transcription and transcript organization.

SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level.

Science.gov (United States)

Heinke, Florian; Bittrich, Sebastian; Kaiser, Florian; Labudde, Dirk

2016-01-01

To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasing number of available structures in databases or structure models produced by automated modeling frameworks this process requires assistance from tools that allow automated structure visualization. In this paper a web server and its underlying method for generating graphical sequence representations of molecular structures is presented. The method, called SequenceCEROSENE (color encoding of residues obtained by spatial neighborhood embedding), retrieves the sequence of each amino acid or nucleotide chain in a given structure and produces a color coding for each residue based on three-dimensional structure information. From this, color-highlighted sequences are obtained, where residue coloring represent three-dimensional residue locations in the structure. This color encoding thus provides a one-dimensional representation, from which spatial interactions, proximity and relations between residues or entire chains can be deduced quickly and solely from color similarity. Furthermore, additional heteroatoms and chemical compounds bound to the structure, like ligands or coenzymes, are processed and reported as well. To provide free access to SequenceCEROSENE, a web server has been implemented that allows generating color codings for structures deposited in the Protein Data Bank or structure models uploaded by the user. Besides retrieving visualizations in popular graphic formats, underlying raw data can be downloaded as well. In addition, the server provides user interactivity with generated visualizations and the three-dimensional structure in question. Color encoded sequences generated by SequenceCEROSENE can aid to quickly perceive the general characteristics of a structure of interest (or entire sets of complexes), thus supporting the researcher in the initial

Code-Switching to Know a TL Equivalent of an L1 Word: Request-Provision-Acknowledgement (RPA) Sequence

Science.gov (United States)

Lucero, Edgar

2011-01-01

This article focuses on the learner's use of Code-switching to learn the TL (Target Language) equivalent of an L1 word. The interactional pattern that this situation creates defines the Request-Provision-Acknowledgement (RPA) sequence. The article explains each of the turns of the sequence under the combination of the Ethnomethodological…

Sequence-based heuristics for faster annotation of non-coding RNA families.

Science.gov (United States)

Weinberg, Zasha; Ruzzo, Walter L

2006-01-01

Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM's accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be. In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that--unlike family-specific solutions--can scale to hundreds of ncRNA families. The source code is available under GNU Public License at the supplementary web site.

Evolution and dispersal of emmer wheat (Triticum sp.) from novel haplotypes of Ppd-1 (photoperiod response) genes and their surrounding DNA sequences.

Science.gov (United States)

Takenaka, Shotaro; Kawahara, Taihachi

2012-09-01

The sequence data from 5' UTR, intronic, coding and 3' UTR regions of Ppd-A1 and Ppd-B1 were investigated for a total of 158 accessions of emmer wheat landraces comprising 19 of wild emmer wheat (Triticum dicoccoides), 45 of hulled emmer wheat (T. dicoccum) and 94 of free-threshing (FT) emmer wheat (T. durum etc.). We detected some novel types of deletions in the coding regions from 22 hulled emmer accessions and 20 FT emmer accessions. Emmer wheat accessions with these deletions could produce predicted proteins likely to lack function. We also observed some novel mutations in Ppd-B1. Sixty-seven and forty-one haplotypes were found in Ppd-A1 and Ppd-B1, respectively. Some mutations found in this study have not been known, so they have potential for useful genetic resources for wheat breeding. On the basis of sequence data from the 5' UTR region, both Ppd-A1 and Ppd-B1 haplotypes were divided into two groups (Type AI/AII and Type BI/BII). Types AI and AII of Ppd-A1 suggested gene flow between wild and hulled emmer. On the other hand, Types BI and BII of Ppd-B1 suggested gene flow between wild and FT emmer. More than half of hulled emmer accessions were Type AII/BI but few FT emmer accessions were of this type. Therefore, over half of the hulled emmer did not contribute to evolution of FT emmer.

Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans

Directory of Open Access Journals (Sweden)

Pupko Tal

2008-10-01

Full Text Available Abstract Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif. Reviewers This article was reviewed by Dan Graur and William Martin. For the full reviews, please go to the Reviewers' Reports section.

The Genomic Code: Genome Evolution and Potential Applications

KAUST Repository

Bernardi, Giorgio

2016-01-25

The genome of metazoans is organized according to a genomic code which comprises three laws: 1) Compositional correlations hold between contiguous coding and non-coding sequences, as well as among the three codon positions of protein-coding genes; these correlations are the consequence of the fact that the genomes under consideration consist of fairly homogeneous, long (≥200Kb) sequences, the isochores; 2) Although isochores are defined on the basis of purely compositional properties, GC levels of isochores are correlated with all tested structural and functional properties of the genome; 3) GC levels of isochores are correlated with chromosome architecture from interphase to metaphase; in the case of interphase the correlation concerns isochores and the three-dimensional “topological associated domains” (TADs); in the case of mitotic chromosomes, the correlation concerns isochores and chromosomal bands. Finally, the genomic code is the fourth and last pillar of molecular biology, the first three pillars being 1) the double helix structure of DNA; 2) the regulation of gene expression in prokaryotes; and 3) the genetic code.

Sequence Coding and Search System for licensee event reports: user's guide. Volume 1, Revision 1

International Nuclear Information System (INIS)

Greene, N.M.; Mays, G.T.; Johnson, M.P.

1985-04-01

Operating experience data from nuclear power plants are essential for safety and reliability analyses, especially analyses of trends and patterns. The licensee event reports (LERs) that are submitted to the Nuclear Regulatory Commission (NRC) by the nuclear power plant utilities contain much of this data. The NRC's Office for Analysis and Evaluation of Operational Data (AEOD) has developed, under contract with NSIC, a system for codifying the events reported in the LERs. The primary objective of the Sequence Coding and Search System (SCSS) is to reduce the descriptive text of the LERs to coded sequences that are both computer-readable and computer-searchable. This system provides a structured format for detailed coding of component, system, and unit effects as well as personnel errors. The database contains all current LERs submitted by nuclear power plant utilities for events occurring since 1981 and is updated on a continual basis. This four volume report documents and describes SCSS in detail. Volume 1 is a User's Guide for searching the SCSS database. This volume contains updated material through February 1985 of the working version of ORNL/NSIC-223, Vol. 1

Detection of viral sequence fragments of HIV-1 subfamilies yet unknown

Directory of Open Access Journals (Sweden)

Stanke Mario

2011-04-01

Full Text Available Abstract Background Methods of determining whether or not any particular HIV-1 sequence stems - completely or in part - from some unknown HIV-1 subtype are important for the design of vaccines and molecular detection systems, as well as for epidemiological monitoring. Nevertheless, a single algorithm only, the Branching Index (BI, has been developed for this task so far. Moving along the genome of a query sequence in a sliding window, the BI computes a ratio quantifying how closely the query sequence clusters with a subtype clade. In its current version, however, the BI does not provide predicted boundaries of unknown fragments. Results We have developed Unknown Subtype Finder (USF, an algorithm based on a probabilistic model, which automatically determines which parts of an input sequence originate from a subtype yet unknown. The underlying model is based on a simple profile hidden Markov model (pHMM for each known subtype and an additional pHMM for an unknown subtype. The emission probabilities of the latter are estimated using the emission frequencies of the known subtypes by means of a (position-wise probabilistic model for the emergence of new subtypes. We have applied USF to SIV and HIV-1 sequences formerly classified as having emerged from an unknown subtype. Moreover, we have evaluated its performance on artificial HIV-1 recombinants and non-recombinant HIV-1 sequences. The results have been compared with the corresponding results of the BI. Conclusions Our results demonstrate that USF is suitable for detecting segments in HIV-1 sequences stemming from yet unknown subtypes. Comparing USF with the BI shows that our algorithm performs as good as the BI or better.

Local variation in Bi crystal sites of epitaxial GaAsBi studied by photoelectron spectroscopy and first-principles calculations

Energy Technology Data Exchange (ETDEWEB)

Laukkanen, P., E-mail: pekka.laukkanen@utu.fi [Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland); Punkkinen, M.P.J., E-mail: marko.punkkinen@utu.fi [Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland); Lahti, A. [Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland); Puustinen, J. [Optoelectronics Research Centre, Tampere University of Technology, FI-33101 Tampere (Finland); Tuominen, M. [Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland); Hilska, J. [Optoelectronics Research Centre, Tampere University of Technology, FI-33101 Tampere (Finland); Mäkelä, J.; Dahl, J.; Yasir, M. [Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland); Kuzmin, M. [Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland); Ioffe Physical-Technical Institute, Russian Academy of Sciences, St. Petersburg 194021, Russian Federation (Russian Federation); Osiecki, J.R.; Schulte, K. [The MAX IV laboratory, P. O. Box 118, Lund University, SE-221 00 Lund (Sweden); Guina, M. [Optoelectronics Research Centre, Tampere University of Technology, FI-33101 Tampere (Finland); Kokko, K. [Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland)

2017-02-28

Highlights: • XPS is used to study bulk-like properties of GaAsBi crystals. • Surface effects are removed from XPS signal by an epitaxial AlAs cap film. • Local variation of Bi composition is found. • The result is consistent with photoluminescence and theoretical results. • Ga vacancies and Bi crystallites are suggested to be dominating defects. - Abstract: Epitaxial Bi-containing III–V crystals (III-V{sub 1-x}Bi{sub x}) have attracted increasing interest due to their potential in infrared applications. Atomic-scale characterization and engineering of bulk-like III-V{sub 1-x}Bi{sub x} properties (e.g., Bi incorporation and defect formation) are challenging but relevant to develop applications. Toward that target, we report here that the traditional surface-science measurement of photoelectron spectroscopy (PES) is a potential, non-destructive method to be combined in the studies of bulk-like properties, when surface effects are properly removed. We have investigated epitaxial GaAs{sub 1-x}Bi{sub x} films, capped by epitaxial AlAs layers, with high-resolution photoelectron spectroscopy. The Bi5d core-level spectra of GaAs{sub 1-x}Bi{sub x} together with ab-initio calculations give direct evidence of variation of Bi bonding environment in the lattice sites. The result agrees with photoluminescence (PL) measurement which shows that the studied GaAs{sub 1-x}Bi{sub x} films include local areas with higher Bi content, which contribute to PL but do not readily appear in x-ray diffraction (XRD). The measured and calculated Bi core-level shifts show also that Ga vacancies and Bi clusters are dominant defects.

Nucleotide sequence of the melA gene, coding for alpha-galactosidase in Escherichia coli K-12.

OpenAIRE

Liljeström, P L; Liljeström, P

1987-01-01

Melibiose uptake and hydrolysis in E.coli is performed by the MelB and MelA proteins, respectively. We report the cloning and sequencing of the melA gene. The nucleotide sequence data showed that melA codes for a 450 amino acid long protein with a molecular weight of 50.6 kd. The sequence data also supported the assumption that the mel locus forms an operon with melA in proximal position. A comparison of MelA with alpha-galactosidase proteins from yeast and human origin showed that these prot...

Bi-level positive airway pressure ventilation for treating heart failure with central sleep apnea that is unresponsive to continuous positive airway pressure.

Science.gov (United States)

Dohi, Tomotaka; Kasai, Takatoshi; Narui, Koji; Ishiwata, Sugao; Ohno, Minoru; Yamaguchi, Tetsu; Momomura, Shin-Ichi

2008-07-01

Cheyne-Stokes respiration with central sleep apnea (CSR-CSA) is associated with a poor prognosis in patients with heart failure (HF). However, some patients do not respond to continuous positive airway pressure (CPAP), so other therapeutic modalities should be considered, such as bi-level positive airway pressure (PAP), which also assists respiration and might be effective for such patients. The 20 patients with HF because of left ventricular systolic dysfunction were assessed: 8 had ischemic etiology, and all had severe CSA according to the apnea - hypopnea index (AHI) determined by polysomnography. All diagnosed patients underwent repeat polysomnography using CPAP. The AHI improved significantly in 11 (AHI or=15). Bi-level PAP titration significantly improved the AHI in the latter group. Those who were unresponsive to CPAP had significantly lower PaCO(2), higher plasma brain natriuretic peptide (BNP), longer mean duration of CSR and fewer obstructive episodes than CPAP responders. After 6 months of positive airway support with either CPAP (n=9) or bi-level PAP (n=7), BNP levels significantly decreased and left ventricular ejection fraction significantly increased. Bi-level PAP could be an effective alternative for patients with HF and pure CSR-CSA who are unresponsive to CPAP.

Research on coding and decoding method for digital levels

Energy Technology Data Exchange (ETDEWEB)

Tu Lifen; Zhong Sidong

2011-01-20

A new coding and decoding method for digital levels is proposed. It is based on an area-array CCD sensor and adopts mixed coding technology. By taking advantage of redundant information in a digital image signal, the contradiction that the field of view and image resolution restrict each other in a digital level measurement is overcome, and the geodetic leveling becomes easier. The experimental results demonstrate that the uncertainty of measurement is 1mm when the measuring range is between 2m and 100m, which can meet practical needs.

Research on coding and decoding method for digital levels.

Science.gov (United States)

Tu, Li-fen; Zhong, Si-dong

2011-01-20

A new coding and decoding method for digital levels is proposed. It is based on an area-array CCD sensor and adopts mixed coding technology. By taking advantage of redundant information in a digital image signal, the contradiction that the field of view and image resolution restrict each other in a digital level measurement is overcome, and the geodetic leveling becomes easier. The experimental results demonstrate that the uncertainty of measurement is 1 mm when the measuring range is between 2 m and 100 m, which can meet practical needs.

Partial Safety Factors and Target Reliability Level in Danish Structural Codes

DEFF Research Database (Denmark)

Sørensen, John Dalsgaard; Hansen, J. O.; Nielsen, T. A.

2001-01-01

The partial safety factors in the newly revised Danish structural codes have been derived using a reliability-based calibration. The calibrated partial safety factors result in the same average reliability level as in the previous codes, but a much more uniform reliability level has been obtained....... The paper describes the code format, the stochastic models and the resulting optimised partial safety factors....

Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data.

Science.gov (United States)

Ragan, Chikako; Mowry, Bryan J; Bauer, Denis C

2012-09-01

Recent advances in RNA sequencing technology (RNA-Seq) enables comprehensive profiling of RNAs by producing millions of short sequence reads from size-fractionated RNA libraries. Although conventional tools for detecting and distinguishing non-coding RNAs (ncRNAs) from reference-genome data can be applied to sequence data, ncRNA detection can be improved by harnessing the full information content provided by this new technology. Here we present NorahDesk, the first unbiased and universally applicable method for small ncRNAs detection from RNA-Seq data. NorahDesk utilizes the coverage-distribution of small RNA sequence data as well as thermodynamic assessments of secondary structure to reliably predict and annotate ncRNA classes. Using publicly available mouse sequence data from brain, skeletal muscle, testis and ovary, we evaluated our method with an emphasis on the performance for microRNAs (miRNAs) and piwi-interacting small RNA (piRNA). We compared our method with Dario and mirDeep2 and found that NorahDesk produces longer transcripts with higher read coverage. This feature makes it the first method particularly suitable for the prediction of both known and novel piRNAs.

MicroRNA-200c modulates the expression of MUC4 and MUC16 by directly targeting their coding sequences in human pancreatic cancer.

Directory of Open Access Journals (Sweden)

Prakash Radhakrishnan

Full Text Available Transmembrane mucins, MUC4 and MUC16 are associated with tumor progression and metastatic potential in human pancreatic adenocarcinoma. We discovered that miR-200c interacts with specific sequences within the coding sequence of MUC4 and MUC16 mRNAs, and evaluated the regulatory nature of this association. Pancreatic cancer cell lines S2.028 and T3M-4 transfected with miR-200c showed a 4.18 and 8.50 fold down regulation of MUC4 mRNA, and 4.68 and 4.82 fold down regulation of MUC16 mRNA compared to mock-transfected cells, respectively. A significant reduction of glycoprotein expression was also observed. These results indicate that miR-200c overexpression regulates MUC4 and MUC16 mucins in pancreatic cancer cells by directly targeting the mRNA coding sequence of each, resulting in reduced levels of MUC4 and MUC16 mRNA and protein. These data suggest that, in addition to regulating proteins that modulate EMT, miR-200c influences expression of cell surface mucins in pancreatic cancer.

Implementation of 3D models in the Monte Carlo code MCNP

International Nuclear Information System (INIS)

Lopes, Vivaldo; Millian, Felix M.; Guevara, Maria Victoria M.; Garcia, Fermin; Sena, Isaac; Menezes, Hugo

2009-01-01

On the area of numerical dosimetry Applied to medical physics, the scientific community focuses on the elaboration of new hybrids models based on 3D models. But different steps of the process of simulation with 3D models needed improvement and optimization in order to expedite the calculations and accuracy using this methodology. This project was developed with the aim of optimize the process of introduction of 3D models within the simulation code of radiation transport by Monte Carlo (MCNP). The fast implementation of these models on the simulation code allows the estimation of the dose deposited on the patient organs on a more personalized way, increasing the accuracy with this on the estimates and reducing the risks to health, caused by ionizing radiations. The introduction o these models within the MCNP was made through a input file, that was constructed through a sequence of images, bi-dimensional in the 3D model, generated using the program '3DSMAX', imported by the program 'TOMO M C' and thus, introduced as INPUT FILE of the MCNP code. (author)

Investigation of the electronic structure of the BiSBr and BiSeBr clusters by density functional method

International Nuclear Information System (INIS)

Audzijonis, A.; Gaigalas, G.; Zigas, L.; Pauliukas, A.; Zaltauskas, R.; Kvedaravicius, A.; Cerskus, A.

2008-01-01

The energy levels of valence bands (VB) of the BiSBr and BiSeBr crystals have been calculated for investigation of the photoelectron emission spectra of BiSBr, BiSeBr and BiSI crystals. The molecular model of this crystal has been used for the calculation of VB by the Density Functional Theory (DFT) method. The molecular cluster, consisting of 20 molecules of BiSBr, BiSeBr, has been used for calculations of averaged total density of states, including atom vibrations. The spectra of the averaged total density of states from VB of BiSBr and BiSeBr clusters have been compared with the experimental photoelectron emission spectra from VB of BiSI crystals. The results clarify that the atomic vibrations in A 5 B 6 C 7 type crystals with chain structure create a smoother appearance of the averaged total density of state spectrum and the experimental X-ray photoemission spectra (XPS)

SequenceL: Automated Parallel Algorithms Derived from CSP-NT Computational Laws

Science.gov (United States)

Cooke, Daniel; Rushton, Nelson

2013-01-01

With the introduction of new parallel architectures like the cell and multicore chips from IBM, Intel, AMD, and ARM, as well as the petascale processing available for highend computing, a larger number of programmers will need to write parallel codes. Adding the parallel control structure to the sequence, selection, and iterative control constructs increases the complexity of code development, which often results in increased development costs and decreased reliability. SequenceL is a high-level programming language that is, a programming language that is closer to a human s way of thinking than to a machine s. Historically, high-level languages have resulted in decreased development costs and increased reliability, at the expense of performance. In recent applications at JSC and in industry, SequenceL has demonstrated the usual advantages of high-level programming in terms of low cost and high reliability. SequenceL programs, however, have run at speeds typically comparable with, and in many cases faster than, their counterparts written in C and C++ when run on single-core processors. Moreover, SequenceL is able to generate parallel executables automatically for multicore hardware, gaining parallel speedups without any extra effort from the programmer beyond what is required to write the sequen tial/singlecore code. A SequenceL-to-C++ translator has been developed that automatically renders readable multithreaded C++ from a combination of a SequenceL program and sample data input. The SequenceL language is based on two fundamental computational laws, Consume-Simplify- Produce (CSP) and Normalize-Trans - pose (NT), which enable it to automate the creation of parallel algorithms from high-level code that has no annotations of parallelism whatsoever. In our anecdotal experience, SequenceL development has been in every case less costly than development of the same algorithm in sequential (that is, single-core, single process) C or C++, and an order of magnitude less

Sequencing learning experiences to engage different level learners in the workplace: An interview study with excellent clinical teachers.

Science.gov (United States)

Chen, H Carrie; O'Sullivan, Patricia; Teherani, Arianne; Fogh, Shannon; Kobashi, Brent; ten Cate, Olle

2015-01-01

Learning in the clinical workplace can appear to rely on opportunistic teaching. The cognitive apprenticeship model describes assigning tasks based on learner rather than just workplace needs. This study aimed to determine how excellent clinical teachers select clinical learning experiences to support the workplace participation and development of different level learners. Using a constructivist grounded theory approach, we conducted semi-structured interviews with medical school faculty identified as excellent clinical teachers teaching multiple levels of learners. We explored their approach to teach different level learners and their perceived role in promoting learner development. We performed thematic analysis of the interview transcripts using open and axial coding. We interviewed 19 clinical teachers and identified three themes related to their teaching approach: sequencing of learning experiences, selection of learning activities and teacher responsibilities. All teachers used sequencing as a teaching strategy by varying content, complexity and expectations by learner level. The teachers initially selected learning activities based on learner level and adjusted for individual competencies over time. They identified teacher responsibilities for learner education and patient safety, and used sequencing to promote both. Excellent clinical teachers described strategies for matching available learning opportunities to learners' developmental levels to safely engage learners and improve learning in the clinical workplace.

Bi-level positive pressure ventilation and adaptive servo ventilation in patients with heart failure and Cheyne-Stokes respiration.

Science.gov (United States)

Fietze, Ingo; Blau, Alexander; Glos, Martin; Theres, Heinz; Baumann, Gert; Penzel, Thomas

2008-08-01

Nocturnal positive pressure ventilation (PPV) has been shown to be effective in patients with impaired left ventricular ejection fraction (LVEF) and Cheyne-Stokes respiration (CSR). We investigated the effect of a bi-level PPV and adaptive servo ventilation on LVEF, CSR, and quantitative sleep quality. Thirty-seven patients (New York heart association [NYHA] II-III) with LVEFCSR were investigated by electrocardiography (ECG), echocardiography and polysomnography. The CSR index (CSRI) was 32.3+/-16.2/h. Patients were randomly treated with bi-level PPV using the standard spontaneous/timed (S/T) mode or with adaptive servo ventilation mode (AutoSetCS). After 6 weeks, 30 patients underwent control investigations with ECG, echocardiography, and polysomnography. The CSRI decreased significantly to 13.6+/-13.4/h. LVEF increased significantly after 6 weeks of ventilation (from 25.1+/-8.5 to 28.8+/-9.8%, plevel PPV and adaptive servo ventilation: the CSRI decreased more in the AutoSetCS group while the LVEF increased more in the bi-level PPV group. Administration of PPV can successfully attenuate CSA. Reduced CSA may be associated with improved LVEF; however, this may depend on the mode of PPV. Changed LVEF is evident even in the absence of significant changes in blood pressure.

Specification of a test problem for HYDROCOIN [Hydrologic Code Intercomparison] Level 3 Case 2: Sensitivity analysis for deep disposal in partially saturated, fractured tuff

International Nuclear Information System (INIS)

Prindle, R.W.

1987-08-01

The international Hydrologic Code Intercomparison Project (HYDROCOIN) was formed to evaluate hydrogeologic models and computer codes and their use in performance assessment for high-level radioactive waste repositories. Three principal activities in the HYDROCOIN Project are Level 1, verification and benchmarking of hydrologic codes; Level 2, validation of hydrologic models; and Level 3, sensitivity and uncertainty analyses of the models and codes. This report presents a test case defined for the HYDROCOIN Level 3 activity to explore the feasibility of applying various sensitivity-analysis methodologies to a highly nonlinear model of isothermal, partially saturated flow through fractured tuff, and to develop modeling approaches to implement the methodologies for sensitivity analysis. These analyses involve an idealized representation of a repository sited above the water table in a layered sequence of welded and nonwelded, fractured, volcanic tuffs. The analyses suggested here include one-dimensional, steady flow; one-dimensional, nonsteady flow; and two-dimensional, steady flow. Performance measures to be used to evaluate model sensitivities are also defined; the measures are related to regulatory criteria for containment of high-level radioactive waste. 14 refs., 5 figs., 4 tabs

Anti-Makeup: Learning A Bi-Level Adversarial Network for Makeup-Invariant Face Verification

OpenAIRE

Li, Yi; Song, Lingxiao; Wu, Xiang; He, Ran; Tan, Tieniu

2017-01-01

Makeup is widely used to improve facial attractiveness and is well accepted by the public. However, different makeup styles will result in significant facial appearance changes. It remains a challenging problem to match makeup and non-makeup face images. This paper proposes a learning from generation approach for makeup-invariant face verification by introducing a bi-level adversarial network (BLAN). To alleviate the negative effects from makeup, we first generate non-makeup images from makeu...

ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites

Directory of Open Access Journals (Sweden)

Stafford Phillip

2009-09-01

Full Text Available Abstract Background Restriction enzymes can produce easily definable segments from DNA sequences by using a variety of cut patterns. There are, however, no software tools that can aid in gene building -- that is, modifying wild-type DNA sequences to express the same wild-type amino acid sequences but with enhanced codons, specific cut sites, unique post-translational modifications, and other engineered-in components for recombinant applications. A fast DNA pattern design algorithm, ICRPfinder, is provided in this paper and applied to find or create potential recognition sites in target coding sequences. Results ICRPfinder is applied to find or create restriction enzyme recognition sites by introducing silent mutations. The algorithm is shown capable of mapping existing cut-sites but importantly it also can generate specified new unique cut-sites within a specified region that are guaranteed not to be present elsewhere in the DNA sequence. Conclusion ICRPfinder is a powerful tool for finding or creating specific DNA patterns in a given target coding sequence. ICRPfinder finds or creates patterns, which can include restriction enzyme recognition sites, without changing the translated protein sequence. ICRPfinder is a browser-based JavaScript application and it can run on any platform, in on-line or off-line mode.

Extubation success in premature infants with respiratory distress syndrome treated with bi-level nasal continuous positive airway pressure versus nasal intermittent positive pressure ventilation.

Science.gov (United States)

Thomas, Patricia E; LeFlore, Judy

2013-01-01

Infants born prematurely with respiratory distress syndrome are at high risk for complications from mechanical ventilation. Strategies are needed to minimize their days on the ventilator. The purpose of this study was to compare extubation success rates in infants treated with 2 different types of continuous positive airway pressure devices. A retrospective cohort study design was used. Data were retrieved from electronic medical records for patients in a large, metropolitan, level III neonatal intensive care unit. A sample of 194 premature infants with respiratory distress syndrome was selected, 124 of whom were treated with nasal intermittent positive pressure ventilation and 70 with bi-level variable flow nasal continuous positive airway pressure (bi-level nasal continuous positive airway pressure). Infants in both groups had high extubation success rates (79% of nasal intermittent positive pressure ventilation group and 77% of bi-level nasal continuous positive airway pressure group). Although infants in the bi-level nasal continuous positive airway pressure group were extubated sooner, there was no difference in duration of oxygen therapy between the 2 groups. Promoting early extubation and extubation success is a vital strategy to reduce complications of mechanical ventilation that adversely affect premature infants with respiratory distress syndrome.

Application of MELCOR Code to a French PWR 900 MWe Severe Accident Sequence and Evaluation of Models Performance Focusing on In-Vessel Thermal Hydraulic Results

International Nuclear Information System (INIS)

De Rosa, Felice

2006-01-01

In the ambit of the Severe Accident Network of Excellence Project (SARNET), funded by the European Union, 6. FISA (Fission Safety) Programme, one of the main tasks is the development and validation of the European Accident Source Term Evaluation Code (ASTEC Code). One of the reference codes used to compare ASTEC results, coming from experimental and Reactor Plant applications, is MELCOR. ENEA is a SARNET member and also an ASTEC and MELCOR user. During the first 18 months of this project, we performed a series of MELCOR and ASTEC calculations referring to a French PWR 900 MWe and to the accident sequence of 'Loss of Steam Generator (SG) Feedwater' (known as H2 sequence in the French classification). H2 is an accident sequence substantially equivalent to a Station Blackout scenario, like a TMLB accident, with the only difference that in H2 sequence the scram is forced to occur with a delay of 28 seconds. The main events during the accident sequence are a loss of normal and auxiliary SG feedwater (0 s), followed by a scram when the water level in SG is equal or less than 0.7 m (after 28 seconds). There is also a main coolant pumps trip when ΔTsat < 10 deg. C, a total opening of the three relief valves when Tric (core maximal outlet temperature) is above 603 K (330 deg. C) and accumulators isolation when primary pressure goes below 1.5 MPa (15 bar). Among many other points, it is worth noting that this was the first time that a MELCOR 1.8.5 input deck was available for a French PWR 900. The main ENEA effort in this period was devoted to prepare the MELCOR input deck using the code version v.1.8.5 (build QZ Oct 2000 with the latest patch 185003 Oct 2001). The input deck, completely new, was prepared taking into account structure, data and same conditions as those found inside ASTEC input decks. The main goal of the work presented in this paper is to put in evidence where and when MELCOR provides good enough results and why, in some cases mainly referring to its

An Automatic Instruction-Level Parallelization of Machine Code

Directory of Open Access Journals (Sweden)

MARINKOVIC, V.

2018-02-01

Full Text Available Prevailing multicores and novel manycores have made a great challenge of modern day - parallelization of embedded software that is still written as sequential. In this paper, automatic code parallelization is considered, focusing on developing a parallelization tool at the binary level as well as on the validation of this approach. The novel instruction-level parallelization algorithm for assembly code which uses the register names after SSA to find independent blocks of code and then to schedule independent blocks using METIS to achieve good load balance is developed. The sequential consistency is verified and the validation is done by measuring the program execution time on the target architecture. Great speedup, taken as the performance measure in the validation process, and optimal load balancing are achieved for multicore RISC processors with 2 to 16 cores (e.g. MIPS, MicroBlaze, etc.. In particular, for 16 cores, the average speedup is 7.92x, while in some cases it reaches 14x. An approach to automatic parallelization provided by this paper is useful to researchers and developers in the area of parallelization as the basis for further optimizations, as the back-end of a compiler, or as the code parallelization tool for an embedded system.

Complete coding sequence of the human raf oncogene and the corresponding structure of the c-raf-1 gene

Energy Technology Data Exchange (ETDEWEB)

Bonner, T I; Oppermann, H; Seeburg, P; Kerby, S B; Gunnell, M A; Young, A C; Rapp, U R

1986-01-24

The complete 648 amino acid sequence of the human raf oncogene was deduced from the 2977 nucleotide sequence of a fetal liver cDNA. The cDNA has been used to obtain clones which extend the human c-raf-1 locus by an additional 18.9 kb at the 5' end and contain all the remaining coding exons.

Pixel-Level Decorrelation and BiLinearly Interpolated Subpixel Sensitivity applied to WASP-29b

Science.gov (United States)

Challener, Ryan; Harrington, Joseph; Cubillos, Patricio; Blecic, Jasmina; Deming, Drake

2017-10-01

Measured exoplanet transit and eclipse depths can vary significantly depending on the methodology used, especially at the low S/N levels in Spitzer eclipses. BiLinearly Interpolated Subpixel Sensitivity (BLISS) models a physical, spatial effect, which is independent of any astrophysical effects. Pixel-Level Decorrelation (PLD) uses the relative variations in pixels near the target to correct for flux variations due to telescope motion. PLD is being widely applied to all Spitzer data without a thorough understanding of its behavior. It is a mathematical method derived from a Taylor expansion, and many of its parameters do not have a physical basis. PLD also relies heavily on binning the data to remove short time-scale variations, which can artifically smooth the data. We applied both methods to 4 eclipse observations of WASP-29b, a Saturn-sized planet, which was observed twice with the 3.6 µm and twice with the 4.5 µm channels of Spitzer's IRAC in 2010, 2011 and 2014 (programs 60003, 70084, and 10054, respectively). We compare the resulting eclipse depths and midpoints from each model, assess each method's ability to remove correlated noise, and discuss how to choose or combine the best data analysis methods. We also refined the orbit from eclipse timings, detecting a significant nonzero eccentricity, and we used our Bayesian Atmospheric Radiative Transfer (BART) code to retrieve the planet's atmosphere, which is consistent with a blackbody. Spitzer is operated by the Jet Propulsion Laboratory, California Institute of Technology, under a contract with NASA. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G.

Bi-Level Integrated System Synthesis (BLISS) for Concurrent and Distributed Processing

Science.gov (United States)

Sobieszczanski-Sobieski, Jaroslaw; Altus, Troy D.; Phillips, Matthew; Sandusky, Robert

2002-01-01

The paper introduces a new version of the Bi-Level Integrated System Synthesis (BLISS) methods intended for optimization of engineering systems conducted by distributed specialty groups working concurrently and using a multiprocessor computing environment. The method decomposes the overall optimization task into subtasks associated with disciplines or subsystems where the local design variables are numerous and a single, system-level optimization whose design variables are relatively few. The subtasks are fully autonomous as to their inner operations and decision making. Their purpose is to eliminate the local design variables and generate a wide spectrum of feasible designs whose behavior is represented by Response Surfaces to be accessed by a system-level optimization. It is shown that, if the problem is convex, the solution of the decomposed problem is the same as that obtained without decomposition. A simplified example of an aircraft design shows the method working as intended. The paper includes a discussion of the method merits and demerits and recommendations for further research.

Spectroscopy of 214Bi and systematics of 210,212,214Pb(0+) long->β-210,212,214Bi(0-)

International Nuclear Information System (INIS)

Berant, Z.; Schuhmann, R.B.; Alburger, D.E.; Chou, W.T.; Gill, R.L.; Warburton, E.K.; Wesselborg, C.

1991-01-01

Experiments designed to provide more information on the spectroscopy of 214 Bi, and on 214 Pb(β - ) 214 Bi in particular, were undertaken because of interest in first-forbidden β decay in the lead region. The experiments consisted of γ-γ coincidences and angular correlations, conversion electron measurements, level lifetime determinations, and precision γ-ray energy measurements. The 352-keV level of 214 Bi was found to be a strong candidate (and the only candidate) for the 0 1 - state. Recent additions to the 214 Pb decay scheme are confirmed by γ-γ coincidence measurements. A careful evaluation of the 214 Bi level scheme is made with emphasis on separating experimentally based conclusions from speculations based on systematics and other ''weak'' arguments. Shell-model calculations of the spectroscopy of 210,212 Bi and 210,212 Pb(β - ) 210,212 Bi were performed using a modification of the Kuo-Herling realistic interaction. These calculations and a generalized seniority model provide a basis for an examination of the systematics of the A=210, 212, 214 spectroscopy and β decay. The generalized seniority model is found to be a quite good approximation which provides a quantitative understanding of the 214 Pb decay rates

Bi-Level Decentralized Active Power Control for Large-Scale Wind Farm Cluster

DEFF Research Database (Denmark)

Huang, Shengli; Wu, Qiuwei; Guo, Yifei

2018-01-01

This paper presents a bi-level decentralized active power control (DAPC) for a large-scale wind farm cluster, consisting of several wind farms for better active power dispatch. In the upper level, a distributed active power control scheme based on the distributed consensus is designed to achieve...... fair active power sharing among multiple wind farms, which generates the power reference for each wind farm. A distributed estimator is used to estimate the total available power of all wind farms. In the lower level, a centralized control scheme based on the Model Predictive Control (MPC) is proposed...... to regulate active power outputs of all wind turbines (WTs) within a wind farm, which reduces the fatigue loads of WTs while tracking the power reference obtained from the upper level control. A wind farm cluster with 8 wind farms and totally 160 WTs, was used to test the control performance of the proposed...

De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences.

Directory of Open Access Journals (Sweden)

Josephine A Reinhardt

Full Text Available How non-coding DNA gives rise to new protein-coding genes (de novo genes is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs, while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important.

Unusual interlayer quantum transport behavior caused by the zeroth Landau level in YbMnBi2.

Science.gov (United States)

Liu, J Y; Hu, J; Graf, D; Zou, T; Zhu, M; Shi, Y; Che, S; Radmanesh, S M A; Lau, C N; Spinu, L; Cao, H B; Ke, X; Mao, Z Q

2017-09-21

Relativistic fermions in topological quantum materials are characterized by linear energy-momentum dispersion near band crossing points. Under magnetic fields, relativistic fermions acquire Berry phase of π in cyclotron motion, leading to a zeroth Landau level (LL) at the crossing point, a signature unique to relativistic fermions. Here we report the unusual interlayer quantum transport behavior resulting from the zeroth LL mode observed in the time reversal symmetry breaking type II Weyl semimetal YbMnBi 2 . The interlayer magnetoresistivity and Hall conductivity of this material are found to exhibit surprising angular dependences under high fields, which can be well fitted by a model, which considers the interlayer quantum tunneling transport of the zeroth LL's Weyl fermions. Our results shed light on the unusual role of zeroth LLl mode in transport.The transport behavior of the carriers residing in the lowest Landau level is hard to observe in most topological materials. Here, Liu et al. report a surprising angular dependence of the interlayer magnetoresistivity and Hall conductivity arising from the lowest Landau level under high magnetic field in type II Weyl semimetal YbMnBi 2 .

Pion-induced fission of 209Bi and 119Sn: measurements, calculations, analyses and comparison

International Nuclear Information System (INIS)

Rana, M.A.; Sher, G.; Manzoor, S.; Shehzad, M.I.

2011-01-01

Cross-sections for the π - -induced fission of 209 Bi and 119 Sn have been measured using the most sensitive CR-39 solid-state nuclear track detector. In experiments, target–detector stacks were exposed to negative pions of energy 500, 672, 1068, and 1665 MeV at the Brookhaven National Laboratory, USA. An important aspect of the present paper is the comparison of pion-induced fission fragment spectra of above mentioned nuclei with the spontaneous fission fragment spectra of 252 Cf. This comparison is made in terms of fission fragment track lengths in the CR-39 detectors. Measurement results are compared with calculations of Monte Carlo and statistical weight functions methods using the computer code CEM95. Agreement between measurements and calculations is fairly good for 209 Bi target nuclei whereas it is indigent for the case of 119 Sn. The possibilities of the trustworthy calculations, using the computer code CEM95, comparable with measurements of pion-induced fission in intermediate and heavy nuclei are explored by employing various systematics available in the code. Energy dependence of pion-induced fission in 119 Sn and 209 Bi is analyzed employing a newly defined parameter geometric-size-normalized fission cross-section (χ f g ). It is found that the collective nuclear excitations, which may lead to fission, become more probable for both 209 Bi and 119 Sn nuclei with increasing energy of negative pions from 500 to 1665 MeV. (author)

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.

Science.gov (United States)

Quang, Daniel; Xie, Xiaohui

2016-06-20

Modeling the properties and functions of DNA sequences is an important, but challenging task in the broad field of genomics. This task is particularly difficult for non-coding DNA, the vast majority of which is still poorly understood in terms of function. A powerful predictive model for the function of non-coding DNA can have enormous benefit for both basic science and translational research because over 98% of the human genome is non-coding and 93% of disease-associated variants lie in these regions. To address this need, we propose DanQ, a novel hybrid convolutional and bi-directional long short-term memory recurrent neural network framework for predicting non-coding function de novo from sequence. In the DanQ model, the convolution layer captures regulatory motifs, while the recurrent layer captures long-term dependencies between the motifs in order to learn a regulatory 'grammar' to improve predictions. DanQ improves considerably upon other models across several metrics. For some regulatory markers, DanQ can achieve over a 50% relative improvement in the area under the precision-recall curve metric compared to related models. We have made the source code available at the github repository http://github.com/uci-cbcl/DanQ. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Application of the verona coding definitions of emotional sequences (VR-CoDES) on a pediatric data set.

Science.gov (United States)

Vatne, Torun M; Finset, Arnstein; Ørnes, Knut; Ruland, Cornelia M

2010-09-01

Adult patients present concerns as defined in the Verona Coding Definitions of Emotional Sequences (VR-CoDES), but we do not know how children express their concerns during medical consultations. This study aimed to evaluate the applicability of VR-CoDES to pediatric oncology consultations. Twenty-eight pediatric consultations were coded with the Verona Coding Definitions of Emotional Sequences (VR-CoDES), and the material was also qualitatively analyzed for descriptive purposes. Five consultations were randomly selected for reliability testing and descriptive statistics were computed. Perfect inter-rater reliability for concerns and moderate reliability for cues were obtained. Cues and/or concerns were present in over half of the consultations. Cues were more frequent than concerns, with the majority of cues being verbal hints to hidden concerns or non-verbal cues. Intensity of expressions, limitations in vocabulary, commonality of statements, and complexity of the setting complicated the use of VR-CoDES. Child-specific cues; use of the imperative, cues about past experiences, and use of onomatopoeia were observed. Children with cancer express concerns during medical consultations. VR-CoDES is a reliable tool for coding concerns in pediatric data sets. For future applications in pediatric settings an appendix should be developed to incorporate the child-specific traits. Copyright (c) 2010 Elsevier Ireland Ltd. All rights reserved.

Generic detection of poleroviruses using an RT-PCR assay targeting the RdRp coding sequence.

Science.gov (United States)

Lotos, Leonidas; Efthimiou, Konstantinos; Maliogka, Varvara I; Katis, Nikolaos I

2014-03-01

In this study a two-step RT-PCR assay was developed for the generic detection of poleroviruses. The RdRp coding region was selected as the primers' target, since it differs significantly from that of other members in the family Luteoviridae and its sequence can be more informative than other regions in the viral genome. Species specific RT-PCR assays targeting the same region were also developed for the detection of the six most widespread poleroviral species (Beet mild yellowing virus, Beet western yellows virus, Cucurbit aphid-borne virus, Carrot red leaf virus, Potato leafroll virus and Turnip yellows virus) in Greece and the collection of isolates. These isolates along with other characterized ones were used for the evaluation of the generic PCR's detection range. The developed assay efficiently amplified a 593bp RdRp fragment from 46 isolates of 10 different Polerovirus species. Phylogenetic analysis using the generic PCR's amplicon sequence showed that although it cannot accurately infer evolutionary relationships within the genus it can differentiate poleroviruses at the species level. Overall, the described generic assay could be applied for the reliable detection of Polerovirus infections and, in combination with the specific PCRs, for the identification of new and uncharacterized species in the genus. Copyright © 2013 Elsevier B.V. All rights reserved.

A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region.

Science.gov (United States)

Kress, W John; Erickson, David L

2007-06-06

A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.

A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

Directory of Open Access Journals (Sweden)

Glass John I

2010-07-01

repeat may be disseminated by HGT and intra-genomic shuffling. Conclusions We describe novel features of PARCELs (Palindromic Amphipathic Repeat Coding ELements, a set of widely distributed repeat protein domains and coding sequences that were likely acquired through HGT by diverse unicellular microbes, further mobilized and diversified within genomes, and co-opted for expression in the membrane proteome of some taxa. Disseminated by multiple gene-centric vehicles, ORFs harboring these elements enhance accessory gene pools as part of the "mobilome" connecting genomes of various clades, in taxa sharing common niches.

ComboCoding: Combined intra-/inter-flow network coding for TCP over disruptive MANETs

Directory of Open Access Journals (Sweden)

Chien-Chia Chen

2011-07-01

Full Text Available TCP over wireless networks is challenging due to random losses and ACK interference. Although network coding schemes have been proposed to improve TCP robustness against extreme random losses, a critical problem still remains of DATA–ACK interference. To address this issue, we use inter-flow coding between DATA and ACK to reduce the number of transmissions among nodes. In addition, we also utilize a “pipeline” random linear coding scheme with adaptive redundancy to overcome high packet loss over unreliable links. The resulting coding scheme, ComboCoding, combines intra-flow and inter-flow coding to provide robust TCP transmission in disruptive wireless networks. The main contributions of our scheme are twofold; the efficient combination of random linear coding and XOR coding on bi-directional streams (DATA and ACK, and the novel redundancy control scheme that adapts to time-varying and space-varying link loss. The adaptive ComboCoding was tested on a variable hop string topology with unstable links and on a multipath MANET with dynamic topology. Simulation results show that TCP with ComboCoding delivers higher throughput than with other coding options in high loss and mobile scenarios, while introducing minimal overhead in normal operation.

High Performance Microaccelerometer with Wafer-level Hermetic Packaged Sensing Element and Continuous-time BiCMOS Interface Circuit

International Nuclear Information System (INIS)

Ko, Hyoungho; Park, Sangjun; Paik, Seung-Joon; Choi, Byoung-doo; Park, Yonghwa; Lee, Sangmin; Kim, Sungwook; Lee, Sang Chul; Lee, Ahra; Yoo, Kwangho; Lim, Jaesang; Cho, Dong-il

2006-01-01

A microaccelerometer with highly reliable, wafer-level packaged MEMS sensing element and fully differential, continuous time, low noise, BiCMOS interface circuit is fabricated. The MEMS sensing element is fabricated on a (111)-oriented SOI wafer by using the SBM (Sacrificial/Bulk Micromachining) process. To protect the silicon structure of the sensing element and enhance the reliability, a wafer level hermetic packaging process is performed by using a silicon-glass anodic bonding process. The interface circuit is fabricated using 0.8 μm BiCMOS process. The capacitance change of the MEMS sensing element is amplified by the continuous-time, fully-differential transconductance input amplifier. A chopper-stabilization architecture is adopted to reduce low-frequency noise including 1/f noise. The fabricated microaccelerometer has the total noise equivalent acceleration of 0.89 μg/√Hz, the bias instability of 490 μg, the input range of ±10 g, and the output nonlinearity of ±0.5 %FSO

In vitro studies of immunoglobulin heavy-chain binding protein (BiP, GRP78). Interactions of BiP with newly synthesized proteins and adenine nucleotides

International Nuclear Information System (INIS)

Kassenbrock, C.K.

1988-01-01

Here we examine the interaction of BiP with newly synthesized polypeptides in an in vitro protein translations-translocation system. We find that BiP forms tight complexes with nonglycosylated yeast invertase and incorrectly disulfide-bonded prolactin but not with glycosylated invertase or correctly disulfide-bonded prolactin. Moreover, BiP associates detectably only with completed chains of prolactin, not with chains undergoing synthesis. We conclude that BiP recognizes and binds with high affinity to aberrantly folded or aberrantly glycosylated polypeptides in vitro, but not to all nascent chains as they are folding. BiP also binds APT and can be purified by APT affinity chromatography. We show that submicromolar levels of ATP or ADP decrease the rate of absorption of 125 I-BiP to nitrocellulose filters coated with protein or nonionic detergents. ATP and ADP also protect portions of BiP from proteolytic degradation. In contrast, micromolar levels of AMP increase the rate of adsorption and the rate of proteolytic degradation of BiP. We also show that an ATPase activity co-purifies with BiP, but its slow turnover number suggests a regulatory, rather than a functional role. The BiP-associated ATPase shares several properties with the related cytoplasmic protein, HSC70/clathrin uncoating ATPase

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

Science.gov (United States)

Pujar, Shashikant; O'Leary, Nuala A; Farrell, Catherine M; Loveland, Jane E; Mudge, Jonathan M; Wallin, Craig; Girón, Carlos G; Diekhans, Mark; Barnes, If; Bennett, Ruth; Berry, Andrew E; Cox, Eric; Davidson, Claire; Goldfarb, Tamara; Gonzalez, Jose M; Hunt, Toby; Jackson, John; Joardar, Vinita; Kay, Mike P; Kodali, Vamsi K; Martin, Fergal J; McAndrews, Monica; McGarvey, Kelly M; Murphy, Michael; Rajput, Bhanu; Rangwala, Sanjida H; Riddick, Lillian D; Seal, Ruth L; Suner, Marie-Marthe; Webb, David; Zhu, Sophia; Aken, Bronwen L; Bruford, Elspeth A; Bult, Carol J; Frankish, Adam; Murphy, Terence; Pruitt, Kim D

2018-01-04

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

Electronic structure of the BiSI cluster

Energy Technology Data Exchange (ETDEWEB)

Audzijonis, A. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Gaigalas, G. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Institute of Theoretical Physics and Astronomy, Vilnius University, A. Gostauto 12, LT-01108 Vilnius (Lithuania); Zigas, L. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania)]. E-mail: kkol@vpu.lt; Pauliukas, A. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Zaltauskas, R. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Cerskus, A. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Narusis, J. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania); Institute of Theoretical Physics and Astronomy, Vilnius University, A. Gostauto 12, LT-01108 Vilnius (Lithuania); Kvedaravicius, A. [Department of Physics, Vilnius Pedagogical University, Studentu 39, LT-08106 Vilnius (Lithuania)

2007-03-15

The energy levels of valence bands (VB) and core levels (CL) of the BiSI crystals have been investigated theoretically. The molecular model of this crystal was used for calculation of VB and CL by the unrestricted Hartree-Fock method using GAMESS program, with Hw and MINI basis set. The molecular cluster consisting of 20 molecules of BiSI was used for calculations of averaged total density of states including atom vibrations. The spectra of averaged total density of states from VB of BiSI cluster has been compared with experimental X-ray photoelectron spectra (XPS) of VB of SbSI crystal. The results clarify that the atomic vibrations is one of possible reasons for the smoother appearance of the experimental XPS. The investigation of vibrational spectrum reveals new experimental information about the reflection spectrum of BiSI crystals. The cluster model calculations have shown that the splitting of the CL in the BiSI may be caused by the photoelectron emission from the atoms at the surface that is in different valence states. The cluster model calculation showed that splitting energy of CL depends on difference of ionic charges of the same atoms at the edges of BiSI cluster.

Electronic structure of the BiSI cluster

International Nuclear Information System (INIS)

Audzijonis, A.; Gaigalas, G.; Zigas, L.; Pauliukas, A.; Zaltauskas, R.; Cerskus, A.; Narusis, J.; Kvedaravicius, A.

2007-01-01

The energy levels of valence bands (VB) and core levels (CL) of the BiSI crystals have been investigated theoretically. The molecular model of this crystal was used for calculation of VB and CL by the unrestricted Hartree-Fock method using GAMESS program, with Hw and MINI basis set. The molecular cluster consisting of 20 molecules of BiSI was used for calculations of averaged total density of states including atom vibrations. The spectra of averaged total density of states from VB of BiSI cluster has been compared with experimental X-ray photoelectron spectra (XPS) of VB of SbSI crystal. The results clarify that the atomic vibrations is one of possible reasons for the smoother appearance of the experimental XPS. The investigation of vibrational spectrum reveals new experimental information about the reflection spectrum of BiSI crystals. The cluster model calculations have shown that the splitting of the CL in the BiSI may be caused by the photoelectron emission from the atoms at the surface that is in different valence states. The cluster model calculation showed that splitting energy of CL depends on difference of ionic charges of the same atoms at the edges of BiSI cluster

An inexact bi-level simulation–optimization model for conjunctive regional renewable energy planning and air pollution control for electric power generation systems

International Nuclear Information System (INIS)

Chen, Yizhong; He, Li; Li, Jing; Cheng, Xi; Lu, Hongwei

2016-01-01

Highlights: • Detailed model developed for power generation and pollutants mitigation. • Dynamic integration of bi-level programming with uncertainty analyses. • Application of the novel bi-level model for EPS in Fengtai District. • Development of renewable energy under different probability levels. - Abstract: In this study, an IBSOM (inexact bi-level simulation–optimization model) is developed for conjunctive regional renewable energy planning and air pollution control for EPS (electric power systems) under uncertainty. The IBSOM integrates techniques of CFMTVW (combined forecasting model with time-varying weights), ILP (interval linear programming), MIP (mixed integer programming), CCP (chance-constrained programming), as well as BLP (bi-level programming) into a general framework. In the IBSOM, uncertainties expressed as interval and stochastic parameters within multi-period and multi-option contexts can be effectively tackled. In addition, a leader-follower decision strategy is incorporated into the optimization process where two non-competitive objectives are sequentially proposed, with the environmental sector dominating the upper-level objective (leader’s one) and the energy sector providing the lower-level objective (follower’s one). To solve the proposed model, an improved bi-level interactive solution algorithm based on satisfactory degree is introduced into the decision-making process for balancing to what extent the constraints are met and the objective reaches its optima. Then, the IBSOM is applied to a real-world case study of EPS in Fengtai District, Beijing, China. Interval solutions associated with renewable energy development, electricity generation, facility-expansion scheme, as well as pollutants mitigation can be obtained under different system-violation risk. Results indicate that a higher violation risk would lead to a decreased strictness of the constraints or an expanded decision space, which results in the decreased system

The management-retrieval code of nuclear level density sub-library (CENPL-NLD)

International Nuclear Information System (INIS)

Ge Zhigang; Su Zongdi; Huang Zhongfu; Dong Liaoyuan

1995-01-01

The management-retrieval code of the Nuclear Level Density (NLD) is presented. It contains two retrieval ways: single nucleus (SN) and neutron reaction (NR). The latter contains four kinds of retrieval types. This code not only can retrieve level density parameter and the data related to the level density, but also can calculate the relevant data by using different level density parameters and do comparison of the calculated results with related data in order to help user to select level density parameters

The sequence coding and search system: An approach for constructing and analyzing event sequences at commercial nuclear power plants

International Nuclear Information System (INIS)

Mays, G.T.

1989-04-01

The US Nuclear Regulatory Commission (NRC) has recognized the importance of the collection, assessment, and feedstock of operating experience data from commercial nuclear power plants and has centralized these activities in the Office for Analysis and Evaluation of Operational Data (AEOD). Such data is essential for performing safety and reliability analyses, especially analyses of trends and patterns to identify undesirable changes in plant performance at the earliest opportunity to implement corrective measures to preclude the occurrences of a more serious event. One of NRC's principal tools for collecting and evaluating operating experience data is the Sequence Coding and Search System (SCSS). The SCSS consists of a methodology for structuring event sequences and the requisite computer system to store and search the data. The source information for SCSS is the Licensee Event Report (LER), which is a legally required document. This paper describes the objective SCSS, the information it contains, and the format and approach for constructuring SCSS event sequences. Examples are presented demonstrating the use SCSS to support the analysis of LER data. The SCSS contains over 30,000 LERs describing events from 1980 through the present. Insights gained from working with a complex data system from the initial developmental stage to the point of a mature operating system are highlighted

LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification.

Science.gov (United States)

Filatov, Gleb; Bauwens, Bruno; Kertész-Farkas, Attila

2018-05-07

Bioinformatics studies often rely on similarity measures between sequence pairs, which often pose a bottleneck in large-scale sequence analysis. Here, we present a new convolutional kernel function for protein sequences called the LZW-Kernel. It is based on code words identified with the Lempel-Ziv-Welch (LZW) universal text compressor. The LZW-Kernel is an alignment-free method, it is always symmetric, is positive, always provides 1.0 for self-similarity and it can directly be used with Support Vector Machines (SVMs) in classification problems, contrary to normalized compression distance (NCD), which often violates the distance metric properties in practice and requires further techniques to be used with SVMs. The LZW-Kernel is a one-pass algorithm, which makes it particularly plausible for big data applications. Our experimental studies on remote protein homology detection and protein classification tasks reveal that the LZW-Kernel closely approaches the performance of the Local Alignment Kernel (LAK) and the SVM-pairwise method combined with Smith-Waterman (SW) scoring at a fraction of the time. Moreover, the LZW-Kernel outperforms the SVM-pairwise method when combined with BLAST scores, which indicates that the LZW code words might be a better basis for similarity measures than local alignment approximations found with BLAST. In addition, the LZW-Kernel outperforms n-gram based mismatch kernels, hidden Markov model based SAM and Fisher kernel, and protein family based PSI-BLAST, among others. Further advantages include the LZW-Kernel's reliance on a simple idea, its ease of implementation, and its high speed, three times faster than BLAST and several magnitudes faster than SW or LAK in our tests. LZW-Kernel is implemented as a standalone C code and is a free open-source program distributed under GPLv3 license and can be downloaded from https://github.com/kfattila/LZW-Kernel. akerteszfarkas@hse.ru. Supplementary data are available at Bioinformatics Online.

A bar coding system for environmental projects

International Nuclear Information System (INIS)

Barber, R.B.; Hunt, B.J.; Burgess, G.M.

1988-01-01

This paper presents BeCode systems, a bar coding system which provides both nuclear and commercial clients with a data capture and custody management program that is accurate, timely, and beneficial to all levels of project operations. Using bar code identifiers is an essentially paperless and error-free method which provides more efficient delivery of data through its menu card-driven structure, which speeds collection of essential data for uploading to a compatible device. The effects of this sequence include real-time information for operator analysis, management review, audits, planning, scheduling, and cost control

Nuclear RNA sequencing of the mouse erythroid cell transcriptome.

Directory of Open Access Journals (Sweden)

Jennifer A Mitchell

Full Text Available In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transcriptional and posttranscriptional mechanisms, and thus do not provide a clear picture of transcriptional output. Here, using deep sequencing of nuclear RNAs (nucRNA-Seq in parallel with chromatin immunoprecipitation sequencing (ChIP-Seq of active RNA polymerase II, we compared the nuclear transcriptome of mouse anemic spleen erythroid cells with polymerase occupancy on a genome-wide scale. We demonstrate that unspliced transcripts quantified by nucRNA-seq correlate with primary transcript frequencies measured by RNA FISH, but differ from steady-state mRNA levels measured by poly(A-enriched RNA-seq. Highly expressed protein coding genes showed good correlation between RNAPII occupancy and transcriptional output; however, genome-wide we observed a poor correlation between transcriptional output and RNAPII association. This poor correlation is due to intergenic regions associated with RNAPII which correspond with transcription factor bound regulatory regions and a group of stable, nuclear-retained long non-coding transcripts. In conclusion, sequencing the nuclear transcriptome provides an opportunity to investigate the transcriptional landscape in a given cell type through quantification of unspliced primary transcripts and the identification of nuclear-retained long non-coding RNAs.

Code meshing: Online bilingual tutoring in Higher Education

Directory of Open Access Journals (Sweden)

Batyi, Thelma Thokozile

2016-12-01

Full Text Available Students’ academic writing literacies are required to express their knowledge, as academic writing is the common mode of assessment in higher education. 28 isiXhosa-speaking first-year diploma students, who failed an academic literacies admission test evaluating the level of their academic writing literacies in the Business faculty, participated once a week over a period of eight months in a course including the practice of code meshing. In the June and November Tourism Communication tests, which also evaluated their academic writing literacies, there was a significant difference in the mean scores when compared to the admission test in the Business faculty. Their academic writing had also improved, according to their assignment marks. The researcher in this project provides evidence that code meshing as a bi/multilingual strategy could be used to improve academic writing literacies in students.

Tl, Bi, and Pb doping in Ba4BiPb2TlO12-δ

International Nuclear Information System (INIS)

Sutto, T.E.; Averill, B.A.

1992-01-01

To determine the effects of different 6s metal concentrations on the superconducting nature of Ba 4 BiPb 2 TlO 12-δ , materials produced via four doping schemes were examined: Ba 4 Bi(Pb, Tl) 3 O 12-δ , Ba 4 -(BiPb) 3 TlO 12-δ , Ba 4 (Bi,Tl) 2 Pb 2 O 12-δ , and Ba 4 Bi x Pb 4-2x Tl x O 12-δ . For the parent compound a value of δ = 0.91 was observed, indicating that approximately 1/4 oxygen atom was missing per cubic subsection of the unit cell. For all samples, the symmetry of the parent compound changed from orthorhombic to tetragonal as the system moved away from the ideal composition. This was usually accompanied by the loss of superconductivity, which exhibited a maximum T c of 10.5 K for the parent compound Ba 4 BiPb 2 TlO 12-δ . Also reported are high-temperature magnetic susceptibility results, which are used to determine the effect of metal substitution on the density of states at the Fermi level. For each set of variants on the parent composition, the onset of superconductivity was accompanied by a significant decrease in the size of the Pauli paramagnetic signal. 16 refs., 6 figs

Computational identification of MoRFs in protein sequences.

Science.gov (United States)

Malhis, Nawar; Gsponer, Jörg

2015-06-01

Intrinsically disordered regions of proteins play an essential role in the regulation of various biological processes. Key to their regulatory function is the binding of molecular recognition features (MoRFs) to globular protein domains in a process known as a disorder-to-order transition. Predicting the location of MoRFs in protein sequences with high accuracy remains an important computational challenge. In this study, we introduce MoRFCHiBi, a new computational approach for fast and accurate prediction of MoRFs in protein sequences. MoRFCHiBi combines the outcomes of two support vector machine (SVM) models that take advantage of two different kernels with high noise tolerance. The first, SVMS, is designed to extract maximal information from the general contrast in amino acid compositions between MoRFs, their surrounding regions (Flanks), and the remainders of the sequences. The second, SVMT, is used to identify similarities between regions in a query sequence and MoRFs of the training set. We evaluated the performance of our predictor by comparing its results with those of two currently available MoRF predictors, MoRFpred and ANCHOR. Using three test sets that have previously been collected and used to evaluate MoRFpred and ANCHOR, we demonstrate that MoRFCHiBi outperforms the other predictors with respect to different evaluation metrics. In addition, MoRFCHiBi is downloadable and fast, which makes it useful as a component in other computational prediction tools. http://www.chibi.ubc.ca/morf/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

LOX: Inferring level of expression from diverse methods of census sequencing

KAUST Repository

Zhang, Zhang

2010-06-10

Summary: We present LOX (Level Of eXpression) that estimates the Level Of gene eXpression from high-throughput-expressed sequence datasets with multiple treatments or samples. Unlike most analyses, LOX incorporates a gene bias model that facilitates integration of diverse transcriptomic sequencing data that arises when transcriptomic data have been produced using diverse experimental methodologies. LOX integrates overall sequence count tallies normalized by total expressed sequence count to provide expression levels for each gene relative to all treatments as well as Bayesian credible intervals. © The Author 2010. Published by Oxford University Press. All rights reserved.

LOX: Inferring level of expression from diverse methods of census sequencing

KAUST Repository

Zhang, Zhang; Ló pez-Girá ldez, Francesc Francisco; Townsend, Jeffrey P.

2010-01-01

Summary: We present LOX (Level Of eXpression) that estimates the Level Of gene eXpression from high-throughput-expressed sequence datasets with multiple treatments or samples. Unlike most analyses, LOX incorporates a gene bias model that facilitates integration of diverse transcriptomic sequencing data that arises when transcriptomic data have been produced using diverse experimental methodologies. LOX integrates overall sequence count tallies normalized by total expressed sequence count to provide expression levels for each gene relative to all treatments as well as Bayesian credible intervals. © The Author 2010. Published by Oxford University Press. All rights reserved.

mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences.

Science.gov (United States)

Links, Matthew G; Chaban, Bonnie; Hemmingsen, Sean M; Muirhead, Kevin; Hill, Janet E

2013-08-15

Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.

Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs.

LENUS (Irish Health Repository)

Weissenmayer, Barbara A

2011-01-01

Second generation sequencing has prompted a number of groups to re-interrogate the transcriptomes of several bacterial and archaeal species. One of the central findings has been the identification of complex networks of small non-coding RNAs that play central roles in transcriptional regulation in all growth conditions and for the pathogen\\'s interaction with and survival within host cells. Legionella pneumophila is a gram-negative facultative intracellular human pathogen with a distinct biphasic lifestyle. One of its primary environmental hosts in the free-living amoeba Acanthamoeba castellanii and its infection by L. pneumophila mimics that seen in human macrophages. Here we present analysis of strand specific sequencing of the transcriptional response of L. pneumophila during exponential and post-exponential broth growth and during the replicative and transmissive phase of infection inside A. castellanii. We extend previous microarray based studies as well as uncovering evidence of a complex regulatory architecture underpinned by numerous non-coding RNAs. Over seventy new non-coding RNAs could be identified; many of them appear to be strain specific and in configurations not previously reported. We discover a family of non-coding RNAs preferentially expressed during infection conditions and identify a second copy of 6S RNA in L. pneumophila. We show that the newly discovered putative 6S RNA as well as a number of other non-coding RNAs show evidence for antisense transcription. The nature and extent of the non-coding RNAs and their expression patterns suggests that these may well play central roles in the regulation of Legionella spp. specific traits and offer clues as to how L. pneumophila adapts to its intracellular niche. The expression profiles outlined in the study have been deposited into Genbank\\'s Gene Expression Omnibus (GEO) database under the series accession GSE27232.

Using machine-coded event data for the micro-level study of political violence

Directory of Open Access Journals (Sweden)

Jesse Hammond

2014-07-01

Full Text Available Machine-coded datasets likely represent the future of event data analysis. We assess the use of one of these datasets—Global Database of Events, Language and Tone (GDELT—for the micro-level study of political violence by comparing it to two hand-coded conflict event datasets. Our findings indicate that GDELT should be used with caution for geo-spatial analyses at the subnational level: its overall correlation with hand-coded data is mediocre, and at the local level major issues of geographic bias exist in how events are reported. Overall, our findings suggest that due to these issues, researchers studying local conflict processes may want to wait for a more reliable geocoding method before relying too heavily on this set of machine-coded data.

Expected frontiers: Incorporating weather uncertainty into a policy analysis using an integrated bi-level multi-objective optimization framework

Science.gov (United States)

Weather is the main driver in both plant use of nutrients and fate and transport of nutrients in the environment. In previous work, we evaluated a green tax for control of agricultural nutrients in a bi-level optimization framework that linked deterministic models. In this study,...

Bi-Force

DEFF Research Database (Denmark)

Sun, Peng; Speicher, Nora K; Röttger, Richard

2014-01-01

of pairwise similarities. We first evaluated the power of Bi-Force to solve dedicated bicluster editing problems by comparing Bi-Force with two existing algorithms in the BiCluE software package. We then followed a biclustering evaluation protocol in a recent review paper from Eren et al. (2013) (A...... comparative analysis of biclustering algorithms for gene expressiondata. Brief. Bioinform., 14:279-292.) and compared Bi-Force against eight existing tools: FABIA, QUBIC, Cheng and Church, Plaid, BiMax, Spectral, xMOTIFs and ISA. To this end, a suite of synthetic datasets as well as nine large gene expression...

A novel bi-level meta-analysis approach: applied to biological pathway analysis.

Science.gov (United States)

Nguyen, Tin; Tagett, Rebecca; Donato, Michele; Mitrea, Cristina; Draghici, Sorin

2016-02-01

The accumulation of high-throughput data in public repositories creates a pressing need for integrative analysis of multiple datasets from independent experiments. However, study heterogeneity, study bias, outliers and the lack of power of available methods present real challenge in integrating genomic data. One practical drawback of many P-value-based meta-analysis methods, including Fisher's, Stouffer's, minP and maxP, is that they are sensitive to outliers. Another drawback is that, because they perform just one statistical test for each individual experiment, they may not fully exploit the potentially large number of samples within each study. We propose a novel bi-level meta-analysis approach that employs the additive method and the Central Limit Theorem within each individual experiment and also across multiple experiments. We prove that the bi-level framework is robust against bias, less sensitive to outliers than other methods, and more sensitive to small changes in signal. For comparative analysis, we demonstrate that the intra-experiment analysis has more power than the equivalent statistical test performed on a single large experiment. For pathway analysis, we compare the proposed framework versus classical meta-analysis approaches (Fisher's, Stouffer's and the additive method) as well as against a dedicated pathway meta-analysis package (MetaPath), using 1252 samples from 21 datasets related to three human diseases, acute myeloid leukemia (9 datasets), type II diabetes (5 datasets) and Alzheimer's disease (7 datasets). Our framework outperforms its competitors to correctly identify pathways relevant to the phenotypes. The framework is sufficiently general to be applied to any type of statistical meta-analysis. The R scripts are available on demand from the authors. sorin@wayne.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e

Self-complementary circular codes in coding theory.

Science.gov (United States)

Fimmel, Elena; Michel, Christian J; Starman, Martin; Strüngmann, Lutz

2018-04-01

Self-complementary circular codes are involved in pairing genetic processes. A maximal [Formula: see text] self-complementary circular code X of trinucleotides was identified in genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel in Life 7(20):1-16 2017, J Theor Biol 380:156-177, 2015; Arquès and Michel in J Theor Biol 182:45-58 1996). In this paper, self-complementary circular codes are investigated using the graph theory approach recently formulated in Fimmel et al. (Philos Trans R Soc A 374:20150058, 2016). A directed graph [Formula: see text] associated with any code X mirrors the properties of the code. In the present paper, we demonstrate a necessary condition for the self-complementarity of an arbitrary code X in terms of the graph theory. The same condition has been proven to be sufficient for codes which are circular and of large size [Formula: see text] trinucleotides, in particular for maximal circular codes ([Formula: see text] trinucleotides). For codes of small-size [Formula: see text] trinucleotides, some very rare counterexamples have been constructed. Furthermore, the length and the structure of the longest paths in the graphs associated with the self-complementary circular codes are investigated. It has been proven that the longest paths in such graphs determine the reading frame for the self-complementary circular codes. By applying this result, the reading frame in any arbitrary sequence of trinucleotides is retrieved after at most 15 nucleotides, i.e., 5 consecutive trinucleotides, from the circular code X identified in genes. Thus, an X motif of a length of at least 15 nucleotides in an arbitrary sequence of trinucleotides (not necessarily all of them belonging to X) uniquely defines the reading (correct) frame, an important criterion for analyzing the X motifs in genes in the future.

A Quasi-Feed-In-Tariff policy formulation in micro-grids: A bi-level multi-period approach

International Nuclear Information System (INIS)

Taha, Ahmad F.; Hachem, Nadim A.; Panchal, Jitesh H.

2014-01-01

A Quasi-Feed-In-Tariff (QFIT) policy formulation is presented for micro-grids that integrates renewable energy generation considering Policy Makers' and Generation Companies' (GENCOs) objectives assuming a bi-level multi-period formulation that integrates physical characteristics of the power-grid. The upper-level problem corresponds to the PM, whereas the lower-level decisions are made by GENCOs. We consider that some GENCOs are green energy producers, while others are black energy producers. Policy makers incentivize green energy producers to generate energy through the payment of optimal time-varying subsidy price. The policy maker's main objective is to maximize an overall social welfare that includes factors such as demand surplus, energy cost, renewable energy subsidy price, and environmental standards. The lower-level problem corresponding to the GENCOs is based on maximizing the players' profits. The proposed QFIT policy differs from the FIT policy in the sense that the subsidy price-based contracts offered to green energy producers dynamically change over time, depending on the physical properties of the grid, demand, and energy price fluctuations. The integrated problem solves for time-varying subsidy price and equilibrium energy quantities that optimize the system welfare under different grid and system conditions. - Highlights: • We present a bi-level optimization problem formulation for Quasi-Feed-In-Tariff (QFIT) policy. • QFIT dictates that subsidy prices dynamically vary over time depending on conditions. • Power grid's physical characteristics affect optimal subsidy prices and energy generation. • To maximize welfare, policy makers ought to increase subsidy prices during the peak-load

The sequence coding and search system: an approach for constructing and analyzing event sequences at commercial nuclear power plants

International Nuclear Information System (INIS)

Mays, G.T.

1990-01-01

The U.S. Nuclear Regulatory Commission (NRC) has recognized the importance of the collection, assessment, and feedback of operating experience data from commercial nuclear power plants and has centralized these activities in the Office for Analysis and Evaluation of Operational Data (AEOD). Such data is essential for performing safety and reliability analyses, especially analyses of trends and patterns to identify undesirable changes in plant performance at the earliest opportunity to implement corrective measures to preclude the occurrence of a more serious event. One of NRC's principal tools for collecting and evaluating operating experience data is the Sequence Coding and Search System (SCSS). The SCSS consists of a methodology for structuring event sequences and the requisite computer system to store and search the data. The source information for SCSS is the Licensee Event Report (LER), which is a legally required document. This paper describes the objectives of SCSS, the information it contains, and the format and approach for constructing SCSS event sequences. Examples are presented demonstrating the use of SCSS to support the analysis of LER data. The SCSS contains over 30,000 LERs describing events from 1980 through the present. Insights gained from working with a complex data system from the initial developmental stage to the point of a mature operating system are highlighted. Considerable experience has been gained in the areas of evolving and changing data requirements, staffing requirements, and quality control and quality assurance procedures for addressing consistency, software/hardware considerations for developing and maintaining a complex system, documentation requirements, and end-user needs. Two other approaches for constructing and evaluating event sequences are examined including the Accident Precursor Program (ASP) where sequences having the potential for core damage are identified and analyzed, and the Significant Event Compilation Tree

Circular codes revisited: a statistical approach.

Science.gov (United States)

Gonzalez, D L; Giannerini, S; Rosa, R

2011-04-21

In 1996 Arquès and Michel [1996. A complementary circular code in the protein coding genes. J. Theor. Biol. 182, 45-58] discovered the existence of a common circular code in eukaryote and prokaryote genomes. Since then, circular code theory has provoked great interest and underwent a rapid development. In this paper we discuss some theoretical issues related to the synchronization properties of coding sequences and circular codes with particular emphasis on the problem of retrieval and maintenance of the reading frame. Motivated by the theoretical discussion, we adopt a rigorous statistical approach in order to try to answer different questions. First, we investigate the covering capability of the whole class of 216 self-complementary, C(3) maximal codes with respect to a large set of coding sequences. The results indicate that, on average, the code proposed by Arquès and Michel has the best covering capability but, still, there exists a great variability among sequences. Second, we focus on such code and explore the role played by the proportion of the bases by means of a hierarchy of permutation tests. The results show the existence of a sort of optimization mechanism such that coding sequences are tailored as to maximize or minimize the coverage of circular codes on specific reading frames. Such optimization clearly relates the function of circular codes with reading frame synchronization. Copyright © 2011 Elsevier Ltd. All rights reserved.

Development of numerical solution techniques in the KIKO3D code

International Nuclear Information System (INIS)

Panka, Istvan; Kereszturi, Andras; Hegedus, Csaba

2005-01-01

The paper describes the numerical methods applied in KIKO3D three-dimensional reactor dynamics code and present a new, more effective method (Bi-CGSTAB) for accelerating the large sparse matrix equation solution. The convergence characteristics were investigated in a given macro time step of a Control Rod Ejection transient. The results obtained by the old GMRES and new Bi-CGSTAB methods are compared. It is concluded that the real relative errors of the solutions obtained by GMRES or Bi - CGSTAB algorithms are in fact closer together than the estimated relative errors. The KIKO3D-Bi-CGSTAB method converges safely and it is 7-12 % faster than the old KIKO3D-GMRES solution (Authors)

Serotype identification and VP1 coding sequence analysis of foot-and-mouth disease virus from outbreaks in Eastern and Northern Uganda in 2008/9

DEFF Research Database (Denmark)

Kasambula, L.; Belsham, Graham; Siegismund, H. R.

2012-01-01

regions, and the presence of FMDV RNA in these samples was determined using a standard diagnostic RT-PCR assay. From the total of 27 positive samples, the VP1 coding region was amplified and sequenced. Each of these sequences showed >99% identity to each other, and just five distinct sequences were...

Phylogenetic analyses of the polyprotein coding sequences of serotype O foot-and-mouth disease viruses in East Africa: evidence for interserotypic recombination

DEFF Research Database (Denmark)

Balinda, Sheila; Siegismund, Hans; Muwanika, Vincent

2010-01-01

from both serotypes A and O. Conclusions Sequences of the VP1 coding region from recent serotype O FMDVs from Kenya and Uganda are all representatives of a specific East African lineage (topotype EA-2), a probable indication that hardly any FMD introductions of this serotype have occurred from outside...... the region in the recent past. Furthermore, evidence for interserotypic recombination, within the non-structural protein coding regions, between FMDVs of serotypes A and O has been obtained. In addition to characterization using the VP1 coding region, analyses involving the non-structural protein coding...

Aspirin and salicylate bind to immunoglobulin heavy chain binding protein (BiP) and inhibit its ATPase activity in human fibroblasts.

Science.gov (United States)

Deng, W G; Ruan, K H; Du, M; Saunders, M A; Wu, K K

2001-11-01

Salicylic acid (SA), an endogenous signaling molecule of plants, possesses anti-inflammatory and anti-neoplastic actions in human. Its derivative, aspirin, is the most commonly used anti-inflammatory and analgesic drug. Aspirin and sodium salicylate (salicylates) have been reported to have multiple pharmacological actions. However, it is unclear whether they bind to a cellular protein. Here, we report for the first time the purification from human fibroblasts of a approximately 78 kDa salicylate binding protein with sequence identity to immunoglobulin heavy chain binding protein (BiP). The Kd values of SA binding to crude extract and to recombinant BiP were 45.2 and 54.6 microM, respectively. BiP is a chaperone protein containing a polypeptide binding site recognizing specific heptapeptide sequence and an ATP binding site. A heptapeptide with the specific sequence displaced SA binding in a concentration-dependent manner whereas a control heptapeptide did not. Salicylates inhibited ATPase activity stimulated by this specific heptapeptide but did not block ATP binding or induce BiP expression. These results indicate that salicylates bind specifically to the polypeptide binding site of BiP in human cells that may interfere with folding and transport of proteins important in inflammation.

Neonatal non-invasive respiratory support: synchronised NIPPV, non-synchronised NIPPV or bi-level CPAP: what is the evidence in 2013?

Science.gov (United States)

Roberts, C T; Davis, P G; Owen, L S

2013-01-01

Nasal continuous positive airway pressure (NCPAP) has proven to be an effective mode of non-invasive respiratory support in preterm infants; however, many infants still require endotracheal ventilation, placing them at an increased risk of morbidities such as bronchopulmonary dysplasia. Several other modes of non-invasive respiratory support beyond NCPAP, including synchronised and non-synchronised nasal intermittent positive pressure ventilation (SNIPPV and nsNIPPV) and bi-level positive airway pressure (BiPAP) are now also available. These techniques require different approaches, and the exact mechanisms by which they act remain unclear. SNIPPV has been shown to reduce the rate of reintubation in comparison to NCPAP when used as post-extubation support, but the evidence for nsNIPPV and BiPAP in this context is less convincing. There is some evidence that NIPPV (whether synchronised or non-synchronised) used as primary respiratory support is beneficial, but the variation in study methodology makes this hard to translate confidently into clinical practice. There is currently no evidence to suggest a reduction in mortality or important morbidities such as bronchopulmonary dysplasia, with NIPPV or BiPAP in comparison to NCPAP, and there is a lack of appropriately designed studies in this area. This review discusses the different approaches and proposed mechanisms of action of SNIPPV, nsNIPPV and BiPAP, the challenges of applying the available evidence for these distinct modalities of non-invasive respiratory support to clinical practice, and possible areas of future research. © 2013 S. Karger AG, Basel.

Bi-induced band gap reduction in epitaxial InSbBi alloys

Energy Technology Data Exchange (ETDEWEB)

Rajpalke, M. K.; Linhart, W. M.; Birkett, M.; Alaria, J.; Veal, T. D., E-mail: T.Veal@liverpool.ac.uk [Stephenson Institute for Renewable Energy and Department of Physics, School of Physical Sciences, University of Liverpool, Liverpool L69 7ZF (United Kingdom); Yu, K. M. [Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720 (United States); Bomphrey, J. J.; Jones, T. S.; Ashwin, M. J., E-mail: M.J.Ashwin@warwick.ac.uk [Department of Chemistry, University of Warwick, Coventry CV4 7AL (United Kingdom); Sallis, S.; Piper, L. F. J. [Materials Science and Engineering, Binghamton University, Binghamton, New York 13902 (United States)

2014-11-24

The properties of molecular beam epitaxy-grown InSb{sub 1−x}Bi{sub x} alloys are investigated. Rutherford backscattering spectrometry shows that the Bi content increases from 0.6% for growth at 350 °C to 2.4% at 200 °C. X-ray diffraction indicates Bi-induced lattice dilation and suggests a zinc-blende InBi lattice parameter of 6.626 Å. Scanning electron microscopy reveals surface InSbBi nanostructures on the InSbBi films for the lowest growth temperatures, Bi droplets at intermediate temperatures, and smooth surfaces for the highest temperature. The room temperature optical absorption edge was found to change from 172 meV (7.2 μm) for InSb to ∼88 meV (14.1 μm) for InSb{sub 0.976}Bi{sub 0.024}, a reduction of ∼35 meV/%Bi.

Accelerating next generation sequencing data analysis with system level optimizations.

Science.gov (United States)

Kathiresan, Nagarajan; Temanni, Ramzi; Almabrazi, Hakeem; Syed, Najeeb; Jithesh, Puthen V; Al-Ali, Rashid

2017-08-22

Next generation sequencing (NGS) data analysis is highly compute intensive. In-memory computing, vectorization, bulk data transfer, CPU frequency scaling are some of the hardware features in the modern computing architectures. To get the best execution time and utilize these hardware features, it is necessary to tune the system level parameters before running the application. We studied the GATK-HaplotypeCaller which is part of common NGS workflows, that consume more than 43% of the total execution time. Multiple GATK 3.x versions were benchmarked and the execution time of HaplotypeCaller was optimized by various system level parameters which included: (i) tuning the parallel garbage collection and kernel shared memory to simulate in-memory computing, (ii) architecture-specific tuning in the PairHMM library for vectorization, (iii) including Java 1.8 features through GATK source code compilation and building a runtime environment for parallel sorting and bulk data transfer (iv) the default 'on-demand' mode of CPU frequency is over-clocked by using 'performance-mode' to accelerate the Java multi-threads. As a result, the HaplotypeCaller execution time was reduced by 82.66% in GATK 3.3 and 42.61% in GATK 3.7. Overall, the execution time of NGS pipeline was reduced to 70.60% and 34.14% for GATK 3.3 and GATK 3.7 respectively.

Dispersion interactions between neighboring Bi atoms in (BiH3 )2 and Te(BiR2 )2.

Science.gov (United States)

Haack, Rebekka; Schulz, Stephan; Jansen, Georg

2018-03-13

Triggered by the observation of a short Bi⋯Bi distance and a BiTeBi bond angle of only 86.6° in the crystal structure of bis(diethylbismuthanyl)tellurane quantum chemical computations on interactions between neighboring Bi atoms in Te(BiR 2 ) 2 molecules (R = H, Me, Et) and in (BiH 3 ) 2 were undertaken. Bi⋯Bi distances atoms were found to significantly shorten upon inclusion of the d shells of the heavy metal atoms into the electron correlation treatment, and it was confirmed that interaction energies from spin component-scaled second-order Møller-Plesset theory (SCS-MP2) agree well with coupled-cluster singles and doubles theory including perturbative triples (CCSD(T)). Density functional theory-based symmetry-adapted perturbation theory (DFT-SAPT) was used to study the anisotropy of the interplay of dispersion attraction and steric repulsion between the Bi atoms. Finally, geometries and relative stabilities of syn-syn and syn-anti conformers of Te(BiR 2 ) 2 (R = H, Me, Et) and interconversion barriers between them were computed. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Improvement of level-1 PSA computer code package

Energy Technology Data Exchange (ETDEWEB)

Kim, Tae Woon; Park, C. K.; Kim, K. Y.; Han, S. H.; Jung, W. D.; Chang, S. C.; Yang, J. E.; Sung, T. Y.; Kang, D. I.; Park, J. H.; Lee, Y. H.; Kim, S. H.; Hwang, M. J.; Choi, S. Y.

1997-07-01

This year the fifth (final) year of the phase-I of the Government-sponsored Mid- and Long-term Nuclear Power Technology Development Project. The scope of this subproject titled on `The improvement of level-1 PSA Computer Codes` is divided into two main activities : (1) improvement of level-1 PSA methodology, (2) development of applications methodology of PSA techniques to operations and maintenance of nuclear power plant. Level-1 PSA code KIRAP is converted to PC-Windows environment. For the improvement of efficiency in performing PSA, the fast cutset generation algorithm and an analytical technique for handling logical loop in fault tree modeling are developed. Using about 30 foreign generic data sources, generic component reliability database (GDB) are developed considering dependency among source data. A computer program which handles dependency among data sources are also developed based on three stage bayesian updating technique. Common cause failure (CCF) analysis methods are reviewed and CCF database are established. Impact vectors can be estimated from this CCF database. A computer code, called MPRIDP, which handles CCF database are also developed. A CCF analysis reflecting plant-specific defensive strategy against CCF event is also performed. A risk monitor computer program, called Risk Monster, are being developed for the application to the operation and maintenance of nuclear power plant. The PSA application technique is applied to review the feasibility study of on-line maintenance and to the prioritization of in-service test (IST) of motor-operated valves (MOV). Finally, the root cause analysis (RCA) and reliability-centered maintenance (RCM) technologies are adopted and applied to the improvement of reliability of emergency diesel generators (EDG) of nuclear power plant. To help RCA and RCM analyses, two software programs are developed, which are EPIS and RAM Pro. (author). 129 refs., 20 tabs., 60 figs.

Improvement of level-1 PSA computer code package

International Nuclear Information System (INIS)

Kim, Tae Woon; Park, C. K.; Kim, K. Y.; Han, S. H.; Jung, W. D.; Chang, S. C.; Yang, J. E.; Sung, T. Y.; Kang, D. I.; Park, J. H.; Lee, Y. H.; Kim, S. H.; Hwang, M. J.; Choi, S. Y.

1997-07-01

This year the fifth (final) year of the phase-I of the Government-sponsored Mid- and Long-term Nuclear Power Technology Development Project. The scope of this subproject titled on 'The improvement of level-1 PSA Computer Codes' is divided into two main activities : 1) improvement of level-1 PSA methodology, 2) development of applications methodology of PSA techniques to operations and maintenance of nuclear power plant. Level-1 PSA code KIRAP is converted to PC-Windows environment. For the improvement of efficiency in performing PSA, the fast cutset generation algorithm and an analytical technique for handling logical loop in fault tree modeling are developed. Using about 30 foreign generic data sources, generic component reliability database (GDB) are developed considering dependency among source data. A computer program which handles dependency among data sources are also developed based on three stage bayesian updating technique. Common cause failure (CCF) analysis methods are reviewed and CCF database are established. Impact vectors can be estimated from this CCF database. A computer code, called MPRIDP, which handles CCF database are also developed. A CCF analysis reflecting plant-specific defensive strategy against CCF event is also performed. A risk monitor computer program, called Risk Monster, are being developed for the application to the operation and maintenance of nuclear power plant. The PSA application technique is applied to review the feasibility study of on-line maintenance and to the prioritization of in-service test (IST) of motor-operated valves (MOV). Finally, the root cause analysis (RCA) and reliability-centered maintenance (RCM) technologies are adopted and applied to the improvement of reliability of emergency diesel generators (EDG) of nuclear power plant. To help RCA and RCM analyses, two software programs are developed, which are EPIS and RAM Pro. (author). 129 refs., 20 tabs., 60 figs

Construction and Analysis of a Novel 2-D Optical Orthogonal Codes Based on Modified One-coincidence Sequence

Science.gov (United States)

Ji, Jianhua; Wang, Yanfen; Wang, Ke; Xu, Ming; Zhang, Zhipeng; Yang, Shuwen

2013-09-01

A new two-dimensional OOC (optical orthogonal codes) named PC/MOCS is constructed, using PC (prime code) for time spreading and MOCS (modified one-coincidence sequence) for wavelength hopping. Compared with PC/PC, the number of wavelengths for PC/MOCS is not limited to a prime number. Compared with PC/OCS, the length of MOCS need not be expanded to the same length of PC. PC/MOCS can be constructed flexibly, and also can use available wavelengths effectively. Theoretical analysis shows that PC/MOCS can reduce the bit error rate (BER) of OCDMA system, and can support more users than PC/PC and PC/OCS.

Deciphering the genetic regulatory code using an inverse error control coding framework.

Energy Technology Data Exchange (ETDEWEB)

Rintoul, Mark Daniel; May, Elebeoba Eni; Brown, William Michael; Johnston, Anna Marie; Watson, Jean-Paul

2005-03-01

We have found that developing a computational framework for reconstructing error control codes for engineered data and ultimately for deciphering genetic regulatory coding sequences is a challenging and uncharted area that will require advances in computational technology for exact solutions. Although exact solutions are desired, computational approaches that yield plausible solutions would be considered sufficient as a proof of concept to the feasibility of reverse engineering error control codes and the possibility of developing a quantitative model for understanding and engineering genetic regulation. Such evidence would help move the idea of reconstructing error control codes for engineered and biological systems from the high risk high payoff realm into the highly probable high payoff domain. Additionally this work will impact biological sensor development and the ability to model and ultimately develop defense mechanisms against bioagents that can be engineered to cause catastrophic damage. Understanding how biological organisms are able to communicate their genetic message efficiently in the presence of noise can improve our current communication protocols, a continuing research interest. Towards this end, project goals include: (1) Develop parameter estimation methods for n for block codes and for n, k, and m for convolutional codes. Use methods to determine error control (EC) code parameters for gene regulatory sequence. (2) Develop an evolutionary computing computational framework for near-optimal solutions to the algebraic code reconstruction problem. Method will be tested on engineered and biological sequences.

An integrated bi-level optimization model for air quality management of Beijing's energy system under uncertainty.

Science.gov (United States)

Jin, S W; Li, Y P; Nie, S

2018-05-15

In this study, an interval chance-constrained bi-level programming (ICBP) method is developed for air quality management of municipal energy system under uncertainty. ICBP can deal with uncertainties presented as interval values and probability distributions as well as examine the risk of violating constraints. Besides, a leader-follower decision strategy is incorporated into the optimization process where two decision makers with different goals and preferences are involved. To solve the proposed model, a bi-level interactive algorithm based on satisfactory degree is introduced into the decision-making processes. Then, an ICBP based energy and environmental systems (ICBP-EES) model is formulated for Beijing, in which air quality index (AQI) is used for evaluating the integrated air quality of multiple pollutants. Result analysis can help different stakeholders adjust their tolerances to achieve the overall satisfaction of EES planning for the study city. Results reveal that natural gas is the main source for electricity-generation and heating that could lead to a potentially increment of imported energy for Beijing in future. Results also disclose that PM 10 is the major contributor to AQI. These findings can help decision makers to identify desired alternatives for EES planning and provide useful information for regional air quality management under uncertainty. Copyright © 2018 Elsevier B.V. All rights reserved.

Verona Coding Definitions of Emotional Sequences (VR-CoDES): Conceptual framework and future directions.

Science.gov (United States)

Piccolo, Lidia Del; Finset, Arnstein; Mellblom, Anneli V; Figueiredo-Braga, Margarida; Korsvold, Live; Zhou, Yuefang; Zimmermann, Christa; Humphris, Gerald

2017-12-01

To discuss the theoretical and empirical framework of VR-CoDES and potential future direction in research based on the coding system. The paper is based on selective review of papers relevant to the construction and application of VR-CoDES. VR-CoDES system is rooted in patient-centered and biopsychosocial model of healthcare consultations and on a functional approach to emotion theory. According to the VR-CoDES, emotional interaction is studied in terms of sequences consisting of an eliciting event, an emotional expression by the patient and the immediate response by the clinician. The rationale for the emphasis on sequences, on detailed classification of cues and concerns, and on the choices of explicit vs. non-explicit responses and providing vs. reducing room for further disclosure, as basic categories of the clinician responses, is described. Results from research on VR-CoDES may help raise awareness of emotional sequences. Future directions in applying VR-CoDES in research may include studies on predicting patient and clinician behavior within the consultation, qualitative analyses of longer sequences including several VR-CoDES triads, and studies of effects of emotional communication on health outcomes. VR-CoDES may be applied to develop interventions to promote good handling of patients' emotions in healthcare encounters. Copyright © 2017 Elsevier B.V. All rights reserved.

Arthropod phylogenetics in light of three novel millipede (myriapoda: diplopoda mitochondrial genomes with comments on the appropriateness of mitochondrial genome sequence data for inferring deep level relationships.

Directory of Open Access Journals (Sweden)

Michael S Brewer

Full Text Available BACKGROUND: Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda. RESULTS: The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly. As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic. CONCLUSIONS: The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic

Arthropod phylogenetics in light of three novel millipede (myriapoda: diplopoda) mitochondrial genomes with comments on the appropriateness of mitochondrial genome sequence data for inferring deep level relationships.

Science.gov (United States)

Brewer, Michael S; Swafford, Lynn; Spruill, Chad L; Bond, Jason E

2013-01-01

Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda. The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly). As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic. The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic signal renders the resulting tree topologies as suspect

The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins.

Science.gov (United States)

Ponce de Leon, Miguel; de Miranda, Antonio Basilio; Alvarez-Valin, Fernando; Carels, Nicolas

2014-01-01

For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a regularity (the codon structure) resulting from physicochemical constraints on proteins and thermodynamic constraints on ribosomal machinery. The physicochemical constraints on proteins mainly come from the hydropathy and molecular weight (MW) of secondary structures as well as the energy cost of amino acid synthesis. These constraints appear through a network of statistical correlations, such as (i) the cost of amino acid synthesis, which is in favor of a higher level of guanine in the first codon position, (ii) the constructive contribution of hydropathy alternation in proteins, (iii) the spatial organization of secondary structure in proteins according to solvent accessibility, (iv) the spatial organization of secondary structure according to amino acid hydropathy, (v) the statistical correlation of MW with protein secondary structures and their overall hydropathy, (vi) the statistical correlation of thymine in the second codon position with hydropathy and the energy cost of amino acid synthesis, and (vii) the statistical correlation of adenine in the second codon position with amino acid complexity and the MW of secondary protein structures. Amino acid physicochemical properties and functional constraints on proteins constitute a code that is translated into a purine bias within the coding DNA via tRNAs. In that sense, the Rrr pattern within coding DNA is the effect of information transfer on nucleotide composition from protein to DNA by selection according to the codon positions. Thus, coding DNA structure and ribosomal machinery co-evolved to minimize the energy cost of protein coding given the functional

Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions.

Science.gov (United States)

Galián, José A; Rosato, Marcela; Rosselló, Josep A

2014-03-01

Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclear 5S rDNA gene family rarely used contiguous 5S coding sequences due to the routine use of head-to-tail polymerase chain reaction primers that are anchored to the coding region. Moreover, the 5S coding sequences have been concatenated with independent, adjacent gene units in many studies, creating simulated chimeric genes as the raw data for evolutionary analysis. This practice is based on the tacitly assumed, but rarely tested, hypothesis that strict intra-locus concerted evolution processes are operating in 5S rDNA genes, without any empirical evidence as to whether it holds for the recovered data. The potential pitfalls of analysing the patterns of molecular evolution and reconstructing phylogenies based on these chimeric genes have not been assessed to date. Here, we compared the sequence integrity and phylogenetic behavior of entire versus concatenated 5S coding regions from a real data set obtained from closely related plant species (Medicago, Fabaceae). Our results suggest that within arrays sequence homogenization is partially operating in the 5S coding region, which is traditionally assumed to be highly conserved. Consequently, concatenating 5S genes increases haplotype diversity, generating novel chimeric genotypes that most likely do not exist within the genome. In addition, the patterns of gene evolution are distorted, leading to incorrect haplotype relationships in some evolutionary reconstructions.

Calculation of levels, transition rates, and lifetimes for the arsenic isoelectronic sequence Sn XVIII-Ba XXIV, W XLII

Science.gov (United States)

Wang, K.; Chen, Z. B.; Chen, C. Y.; Yan, J.; Dang, W.; Zhao, X. H.; Yang, X.

2017-09-01

Multi-configuration Dirac-Fock (MCDF) calculations of energy levels, wavelengths, oscillator strengths, lifetimes, and electric dipole (E1), magnetic dipole (M1), electric quadrupole (E2), magnetic quadrupole (M2) transition rates are reported for the arsenic isoelectronic sequence Sn XVIII-Ba XXIV, W XLII. Results are presented among the 86 levels of the 4s2 4p3, 4 s 4p4, 4p5, 4s2 4p2 4 d, and 4 s 4p3 4 d configurations in each ion. The relativistic atomic structure package GRASP2K is adopted for the calculations, in which the contributions from the correlations within the n ≤ 7 complexes, Breit interaction (BI) and quantum electrodynamics (QED) effects are taking into account. The many-body perturbation theory (MBPT) method is also employed as an independent calculation for comparison purposes, taking W XLII as an example. Calculated results are compared with data from other calculations and the observed values from the Atomic Spectra Database (ASD) of the National Institute of Standards and Technology (NIST). Good agreements are obtained. i.e, the accuracy of our energy levels is assessed to be better than 0.6%. These accurate theoretical data should be useful for diagnostics of hot plasmas in fusion devices.

Confidentiality of 2D Code using Infrared with Cell-level Error Correction

Directory of Open Access Journals (Sweden)

Nobuyuki Teraura

2013-03-01

Full Text Available Optical information media printed on paper use printing materials to absorb visible light. There is a 2D code, which may be encrypted but also can possibly be copied. Hence, we envisage an information medium that cannot possibly be copied and thereby offers high security. At the surface, the normal 2D code is printed. The inner layers consist of 2D codes printed using a variety of materials, which absorb certain distinct wavelengths, to form a multilayered 2D code. Information can be distributed among the 2D codes forming the inner layers of the multiplex. Additionally, error correction at cell level can be introduced.

DNA methylation of miRNA coding sequences putatively associated with childhood obesity.

Science.gov (United States)

Mansego, M L; Garcia-Lacarte, M; Milagro, F I; Marti, A; Martinez, J A

2017-02-01

Epigenetic mechanisms may be involved in obesity onset and its consequences. The aim of the present study was to evaluate whether DNA methylation status in microRNA (miRNA) coding regions is associated with childhood obesity. DNA isolated from white blood cells of 24 children (identification sample: 12 obese and 12 non-obese) from the Grupo Navarro de Obesidad Infantil study was hybridized in a 450 K methylation microarray. Several CpGs whose DNA methylation levels were statistically different between obese and non-obese were validated by MassArray® in 95 children (validation sample) from the same study. Microarray analysis identified 16 differentially methylated CpGs between both groups (6 hypermethylated and 10 hypomethylated). DNA methylation levels in miR-1203, miR-412 and miR-216A coding regions significantly correlated with body mass index standard deviation score (BMI-SDS) and explained up to 40% of the variation of BMI-SDS. The network analysis identified 19 well-defined obesity-relevant biological pathways from the KEGG database. MassArray® validation identified three regions located in or near miR-1203, miR-412 and miR-216A coding regions differentially methylated between obese and non-obese children. The current work identified three CpG sites located in coding regions of three miRNAs (miR-1203, miR-412 and miR-216A) that were differentially methylated between obese and non-obese children, suggesting a role of miRNA epigenetic regulation in childhood obesity. © 2016 World Obesity Federation.

Facile synthesis of Bi/BiOCl composite with selective photocatalytic properties

International Nuclear Information System (INIS)

Chen, Dongling; Zhang, Min; Lu, Qiuju; Chen, Junfang; Liu, Bitao; Wang, Zhaofeng

2015-01-01

This paper presents a novel and facile method to fabricate Bi/BiOCl composites with dominant (001) facets in situ via a microwave reduction route. Different characterization techniques, including X-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), transmission scanning electron microscopy (TEM), UV–vis diffuse reflectance spectrometry (DRS), X-ray photoelectron spectroscopy (XPS), electron spin resonance spectroscopy (ESR), cathodoluminescence spectrum (CL), and lifetime, have been employed to investigate the structure, optical and electrical properties of the Bi/BiOCl composites. The experimental results show that the introduction of Bi particles can efficiently enhance the photocatalytic performance of BiOCl for the degradation of several dyes under ultraviolet (UV) light irradiation, especially for negative charged methyl orange (MO). Unlike the UV photocatalytic performance, such Bi/BiOCl composite shows higher degradation efficiency towards rhodamine B (RhB) than MO and methylene blue (MB) under visible light irradiation. This special photocatalytic performance can be ascribed to the synergistic effect between oxygen vacancies and Bi particles. This work provides new insights about the photodegradation mechanisms of MO, MB and RhB under UV and visible light irradiation, which would be helpful to guide the selection of an appropriate catalyst for other pollutants. - Highlights: • Bi/BiOCl composites were synthesized via a microwave reduction. • Tunable selectivity photocatalytic activity can be achieved. • Photodegradation mechanism under UV and visible light were proposed

Association of Amine-Receptor DNA Sequence Variants with Associative Learning in the Honeybee.

Science.gov (United States)

Lagisz, Malgorzata; Mercer, Alison R; de Mouzon, Charlotte; Santos, Luana L S; Nakagawa, Shinichi

2016-03-01

Octopamine- and dopamine-based neuromodulatory systems play a critical role in learning and learning-related behaviour in insects. To further our understanding of these systems and resulting phenotypes, we quantified DNA sequence variations at six loci coding octopamine-and dopamine-receptors and their association with aversive and appetitive learning traits in a population of honeybees. We identified 79 polymorphic sequence markers (mostly SNPs and a few insertions/deletions) located within or close to six candidate genes. Intriguingly, we found that levels of sequence variation in the protein-coding regions studied were low, indicating that sequence variation in the coding regions of receptor genes critical to learning and memory is strongly selected against. Non-coding and upstream regions of the same genes, however, were less conserved and sequence variations in these regions were weakly associated with between-individual differences in learning-related traits. While these associations do not directly imply a specific molecular mechanism, they suggest that the cross-talk between dopamine and octopamine signalling pathways may influence olfactory learning and memory in the honeybee.

Bismuth-boron multiple bonding in BiB_2O"- and Bi_2B"-

International Nuclear Information System (INIS)

Jian, Tian; Cheung, Ling Fung; Chen, Teng-Teng; Wang, Lai-Sheng

2017-01-01

Despite its electron deficiency, boron is versatile in forming multiple bonds. Transition-metal-boron double bonding is known, but boron-metal triple bonds have been elusive. Two bismuth boron cluster anions, BiB_2O"- and Bi_2B"-, containing triple and double B-Bi bonds are presented. The BiB_2O"- and Bi_2B"- clusters are produced by laser vaporization of a mixed B/Bi target and characterized by photoelectron spectroscopy and ab initio calculations. Well-resolved photoelectron spectra are obtained and interpreted with the help of ab initio calculations, which show that both species are linear. Chemical bonding analyses reveal that Bi forms triple and double bonds with boron in BiB_2O"- ([Bi≡B-B≡O]"-) and Bi_2B"- ([Bi=B=Bi]"-), respectively. The Bi-B double and triple bond strengths are calculated to be 3.21 and 4.70 eV, respectively. This is the first experimental observation of Bi-B double and triple bonds, opening the door to design main-group metal-boron complexes with multiple bonding. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

The modulation and reconstruction of a BiO layer of cuprate Bi2212

International Nuclear Information System (INIS)

Fan Wei; Zeng, Z

2011-01-01

Studies based on ab initio density functional theory show that the modulated structures of BiO surfaces of cuprate Bi2212 superconductors are spontaneously formed and closely related to the reconstructions of BiO surfaces. The reconstructions of BiO layers occur both on the surface and in the bulk, accompanied with the formations of BiO-zigzag chains and Bi 2 O 2 quadrilaterals. The structural modulations of the BiO surface are along the b axis, perpendicular to the BiO-zigzag chains along the a axis. Our calculations provide a unified understanding of the formation of modulating structures in Bi2212. Another interesting result is that electronic structures of BiO surfaces are significantly influenced by the CuO 2 layer beneath because of the structural modulations and reconstructions.

cDNA sequence of human transforming gene hst and identification of the coding sequence required for transforming activity

International Nuclear Information System (INIS)

Taira, M.; Yoshida, T.; Miyagawa, K.; Sakamoto, H.; Terada, M.; Sugimura, T.

1987-01-01

The hst gene was originally identified as a transforming gene in DNAs from human stomach cancers and from a noncancerous portion of stomach mucosa by DNA-mediated transfection assay using NIH3T3 cells. cDNA clones of hst were isolated from the cDNA library constructed from poly(A) + RNA of a secondary transformant induced by the DNA from a stomach cancer. The sequence analysis of the hst cDNA revealed the presence of two open reading frames. When this cDNA was inserted into an expression vector containing the simian virus 40 promoter, it efficiently induced the transformation of NIH3T3 cells upon transfection. It was found that one of the reading frames, which coded for 206 amino acids, was responsible for the transforming activity

Novel Bi/BiOBr/AgBr composite microspheres: Ion exchange synthesis and photocatalytic performance

Science.gov (United States)

Lyu, Jianchang; Li, Zhenlu; Ge, Ming

2018-06-01

Novel Bi/BiOBr/AgBr composite microspheres were prepared by a rational in situ ion exchange reaction between Bi/BiOBr microspheres and AgNO3. The characteristic of the as-obtained ternary microspheres was tested by X-ray diffraction (XRD), energy dispersive X-ray spectrometer (EDS), scanning electron microscope (SEM), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), UV-vis diffuse reflectance spectroscopy (UV-vis DRS) and photoluminescence (PL). Under visible light irradiation, Bi/BiOBr/AgBr microspheres exhibited an excellent photocatalytic efficiency for rhodamine B (RhB) degradation, which was about 1.4 and 4.9 times as high as that of Bi/BiOBr and BiOBr/AgBr, demonstrating that the highest separation efficiency of charge carriers in the heterostructured Bi/BiOBr/AgBr. The photocatalytic activity of Bi/BiOBr/AgBr microspheres just exhibited a slight decrease after three consecutive cycles. The photocatalytic mechanism investigation confirmed that the superoxide radicals (O2•-) were the dominant reactive oxygen species for RhB degradation in Bi/BiOBr/AgBr suspension.

Photocatalytic activity of Bi_2WO_6/Bi_2S_3 heterojunctions: the facilitation of exposed facets of Bi_2WO_6 substrate

International Nuclear Information System (INIS)

Yan, Long; Wang, Yufei; Shen, Huidong; Zhang, Yu; Li, Jian; Wang, Danjun

2017-01-01

Highlights: • Bi_2S_3/Bi_2WO_6 hybrids with exposed (020) Bi_2WO_6 facets have been synthesized. • X-ray photoelectron spectroscopy reveals that a small amount of Bi_2S_3 was formed. • The enhanced photoactivity of hybrids is due to heterojunction and (020) facets. • A possible photocatalytic degradation mechanism is proposed. - Abstract: Bi_2S_3/Bi_2WO_6 hybrid architectures with exposed (020) Bi_2WO_6 facets have been synthesized via a controlled anion exchange approach. X-ray photoelectron spectroscopy (XPS) reveals that a small amount of Bi_2S_3 was formed on the surface of Bi_2WO_6 during the anion exchange process, thus leading to the transformation from the Bi_2WO_6 to Bi_2S_3/Bi_2WO_6. A rhodamine B (RhB) aqueous solution was chosen as model organic pollutants to evaluate the photocatalytic activities of the Bi_2S_3/Bi_2WO_6 catalysts. Under visible light irradiation, the Bi_2S_3/Bi_2WO_6-TAA displayed the excellent visible light photoactivities compared with pure Bi_2S_3, Bi_2WO_6 and other composite photocatalysts. The efficient photocatalytic activity of the Bi_2S_3/Bi_2WO_6-TAA composite microspheres was ascribed to the constructed heterojunctions and the inner electric field caused by the exposed (020) Bi_2WO_6 facets. Active species trapping experiments revealed that h"+ and O_2·"− are the main active species in the photocatalytic process. Furthermore, the as-obtained photocatalysts showed good photocatalytic activity after four recycles. The results presented in this study provide a new concept for the rational design and development of highly efficient photocatalysts.

Heterojunction BiOI/Bi2MoO6 nanocomposite with much enhanced photocatalytic activity

International Nuclear Information System (INIS)

Li, Wen Ting; Zheng, Yi Fan; Yin, Hao Yong; Song, Xu Chun

2015-01-01

BiOI/Bi 2 MoO 6 heterostructures with different amounts of BiOI were successfully prepared via a facile deposition method. The obtained BiOI/Bi 2 MoO 6 photocatalysts exhibited much higher visible light (λ > 420 nm) induced photocatalytic activity compared with single Bi 2 MoO 6 and BiOI photocatalysts. 20 % BiOI/Bi 2 MoO 6 nanocomposite exhibited the highest photocatalytic activity with almost all RhB decomposed within 70 min. However, excess BiOI covering on the surface of Bi 2 MoO 6 can inversely reduce the photocatalytic activity. The enhanced photocatalytic activities could be resulted from the function of the novel p–n heterojunction interface between Bi 2 MoO 6 and BiOI, which could separate photoinduced carriers efficiently. Possible mechanisms on the basis of the relative band positions were also discussed

Multiferroic BiFeO3-BiMnO3 Nanocheckerboard From First Principles

OpenAIRE

Palova, L.; Chandra, P.; Rabe, K. M.

2010-01-01

We present a first principles study of an unusual heterostructure, an atomic-scale checkerboard of BiFeO3-BiMnO3, and compare its properties to the two bulk constituent materials, BiFeO3 and BiMnO3. The "nanocheckerboard" is found to have a multiferroic ground state with the desired properties of each constituent: polar and ferrimagnetic due to BiFeO3 and BiMnO3, respectively. The effect of B-site cation ordering on magnetic ordering in the BiFeO3-BiMnO3 system is studied. The checkerboard ge...

Identification of coding and non-coding mutational hotspots in cancer genomes.

Science.gov (United States)

Piraino, Scott W; Furney, Simon J

2017-01-05

The identification of mutations that play a causal role in tumour development, so called "driver" mutations, is of critical importance for understanding how cancers form and how they might be treated. Several large cancer sequencing projects have identified genes that are recurrently mutated in cancer patients, suggesting a role in tumourigenesis. While the landscape of coding drivers has been extensively studied and many of the most prominent driver genes are well characterised, comparatively less is known about the role of mutations in the non-coding regions of the genome in cancer development. The continuing fall in genome sequencing costs has resulted in a concomitant increase in the number of cancer whole genome sequences being produced, facilitating systematic interrogation of both the coding and non-coding regions of cancer genomes. To examine the mutational landscapes of tumour genomes we have developed a novel method to identify mutational hotspots in tumour genomes using both mutational data and information on evolutionary conservation. We have applied our methodology to over 1300 whole cancer genomes and show that it identifies prominent coding and non-coding regions that are known or highly suspected to play a role in cancer. Importantly, we applied our method to the entire genome, rather than relying on predefined annotations (e.g. promoter regions) and we highlight recurrently mutated regions that may have resulted from increased exposure to mutational processes rather than selection, some of which have been identified previously as targets of selection. Finally, we implicate several pan-cancer and cancer-specific candidate non-coding regions, which could be involved in tumourigenesis. We have developed a framework to identify mutational hotspots in cancer genomes, which is applicable to the entire genome. This framework identifies known and novel coding and non-coding mutional hotspots and can be used to differentiate candidate driver regions from

GRABGAM: A Gamma Analysis Code for Ultra-Low-Level HPGe SPECTRA

Energy Technology Data Exchange (ETDEWEB)

Winn, W.G.

1999-07-28

The GRABGAM code has been developed for analysis of ultra-low-level HPGe gamma spectra. The code employs three different size filters for the peak search, where the largest filter provides best sensitivity for identifying low-level peaks and the smallest filter has the best resolution for distinguishing peaks within a multiplet. GRABGAM basically generates an integral probability F-function for each singlet or multiplet peak analysis, bypassing the usual peak fitting analysis for a differential f-function probability model. Because F is defined by the peak data, statistical limitations for peak fitting are avoided; however, the F-function does provide generic values for peak centroid, full width at half maximum, and tail that are consistent with a Gaussian formalism. GRABGAM has successfully analyzed over 10,000 customer samples, and it interfaces with a variety of supplementary codes for deriving detector efficiencies, backgrounds, and quality checks.

Detecting non-coding selective pressure in coding regions

Directory of Open Access Journals (Sweden)

Blanchette Mathieu

2007-02-01

Full Text Available Abstract Background Comparative genomics approaches, where orthologous DNA regions are compared and inter-species conserved regions are identified, have proven extremely powerful for identifying non-coding regulatory regions located in intergenic or intronic regions. However, non-coding functional elements can also be located within coding region, as is common for exonic splicing enhancers, some transcription factor binding sites, and RNA secondary structure elements affecting mRNA stability, localization, or translation. Since these functional elements are located in regions that are themselves highly conserved because they are coding for a protein, they generally escaped detection by comparative genomics approaches. Results We introduce a comparative genomics approach for detecting non-coding functional elements located within coding regions. Codon evolution is modeled as a mixture of codon substitution models, where each component of the mixture describes the evolution of codons under a specific type of coding selective pressure. We show how to compute the posterior distribution of the entropy and parsimony scores under this null model of codon evolution. The method is applied to a set of growth hormone 1 orthologous mRNA sequences and a known exonic splicing elements is detected. The analysis of a set of CORTBP2 orthologous genes reveals a region of several hundred base pairs under strong non-coding selective pressure whose function remains unknown. Conclusion Non-coding functional elements, in particular those involved in post-transcriptional regulation, are likely to be much more prevalent than is currently known. With the numerous genome sequencing projects underway, comparative genomics approaches like that proposed here are likely to become increasingly powerful at detecting such elements.

Coding Local and Global Binary Visual Features Extracted From Video Sequences

Science.gov (United States)

Baroffio, Luca; Canclini, Antonio; Cesana, Matteo; Redondi, Alessandro; Tagliasacchi, Marco; Tubaro, Stefano

2015-11-01

Binary local features represent an effective alternative to real-valued descriptors, leading to comparable results for many visual analysis tasks, while being characterized by significantly lower computational complexity and memory requirements. When dealing with large collections, a more compact representation based on global features is often preferred, which can be obtained from local features by means of, e.g., the Bag-of-Visual-Word (BoVW) model. Several applications, including for example visual sensor networks and mobile augmented reality, require visual features to be transmitted over a bandwidth-limited network, thus calling for coding techniques that aim at reducing the required bit budget, while attaining a target level of efficiency. In this paper we investigate a coding scheme tailored to both local and global binary features, which aims at exploiting both spatial and temporal redundancy by means of intra- and inter-frame coding. In this respect, the proposed coding scheme can be conveniently adopted to support the Analyze-Then-Compress (ATC) paradigm. That is, visual features are extracted from the acquired content, encoded at remote nodes, and finally transmitted to a central controller that performs visual analysis. This is in contrast with the traditional approach, in which visual content is acquired at a node, compressed and then sent to a central unit for further processing, according to the Compress-Then-Analyze (CTA) paradigm. In this paper we experimentally compare ATC and CTA by means of rate-efficiency curves in the context of two different visual analysis tasks: homography estimation and content-based retrieval. Our results show that the novel ATC paradigm based on the proposed coding primitives can be competitive with CTA, especially in bandwidth limited scenarios.

Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features

Directory of Open Access Journals (Sweden)

Zhang Ya-Nan

2012-05-01

Full Text Available Abstract Background Adenosine-5′-triphosphate (ATP is one of multifunctional nucleotides and plays an important role in cell biology as a coenzyme interacting with proteins. Revealing the binding sites between protein and ATP is significantly important to understand the functionality of the proteins and the mechanisms of protein-ATP complex. Results In this paper, we propose a novel framework for predicting the proteins’ functional residues, through which they can bind with ATP molecules. The new prediction protocol is achieved by combination of sequence evolutional information and bi-profile sampling of multi-view sequential features and the sequence derived structural features. The hypothesis for this strategy is single-view feature can only represent partial target’s knowledge and multiple sources of descriptors can be complementary. Conclusions Prediction performances evaluated by both 5-fold and leave-one-out jackknife cross-validation tests on two benchmark datasets consisting of 168 and 227 non-homologous ATP binding proteins respectively demonstrate the efficacy of the proposed protocol. Our experimental results also reveal that the residue structural characteristics of real protein-ATP binding sites are significant different from those normal ones, for example the binding residues do not show high solvent accessibility propensities, and the bindings prefer to occur at the conjoint points between different secondary structure segments. Furthermore, results also show that performance is affected by the imbalanced training datasets by testing multiple ratios between positive and negative samples in the experiments. Increasing the dataset scale is also demonstrated useful for improving the prediction performances.

ASTEC V2. Overview of code development and application at GRS

International Nuclear Information System (INIS)

Reinke, N.; Nowack, H.; Sonnenkalb, M.

2011-01-01

The integral code ASTEC (Accident Source Term Evaluation Code) commonly developed since 1996 by the French IRSN and the German GRS is a fast running programme, which allows the calculation of entire sequences of severe accidents (SA) in light water reactors from the initiating event up to the release of fission products into the environment, thereby covering all important in-vessel and containment phenomena. Thus, the main ASTEC application fields are intended to be accident sequence studies, uncertainty and sensitivity studies, probabilistic safety analysis level 2 as well as support to experiments. The modular structure of ASTEC allows running each module independently and separately, e.g. for separate effects analyses as well as a combination of multiple modules for coupled effects testing and integral analyses. Subject of this paper is an overview of the new V2 series of the ASTEC code system and presentation of exemplary results for the application to severe accidents sequences at PWRs. (orig.)

Accident sequence precursor analysis level 2/3 model development

International Nuclear Information System (INIS)

Lui, C.H.; Galyean, W.J.; Brownson, D.A.

1997-01-01

The US Nuclear Regulatory Commission's Accident Sequence Precursor (ASP) program currently uses simple Level 1 models to assess the conditional core damage probability for operational events occurring in commercial nuclear power plants (NPP). Since not all accident sequences leading to core damage will result in the same radiological consequences, it is necessary to develop simple Level 2/3 models that can be used to analyze the response of the NPP containment structure in the context of a core damage accident, estimate the magnitude of the resulting radioactive releases to the environment, and calculate the consequences associated with these releases. The simple Level 2/3 model development work was initiated in 1995, and several prototype models have been completed. Once developed, these simple Level 2/3 models are linked to the simple Level 1 models to provide risk perspectives for operational events. This paper describes the methods implemented for the development of these simple Level 2/3 ASP models, and the linkage process to the existing Level 1 models

Genetic Variant of the Scavenger Receptor BI in Humans

NARCIS (Netherlands)

Vergeer, Menno; Korporaal, Suzanne J. A.; Franssen, Remco; Meurs, Illiana; Out, Ruud; Hovingh, G. Kees; Hoekstra, Menno; Sierts, Jeroen A.; Dallinga-Thie, Geesje M.; Motazacker, Mohammad Mahdi; Holleboom, Adriaan G.; van Berkel, Theo J. C.; Kastelein, John J. P.; van Eck, Miranda; Kuivenhoven, Jan Albert

2011-01-01

BACKGROUND In mice, the scavenger receptor class B type I (SR-BI) is essential for the delivery of high-density lipoprotein (HDL) cholesterol to the liver and steroidogenic organs. Paradoxically, elevated HDL cholesterol levels are associated with increased atherosclerosis in SR-BI-knockout mice. It

Genetic variant of the scavenger receptor BI in humans

NARCIS (Netherlands)

Vergeer, Menno; Korporaal, Suzanne J A; Franssen, Remco; Meurs, Illiana; Out, Ruud; Hovingh, G Kees; Hoekstra, Menno; Sierts, Jeroen A; Dallinga-Thie, Geesje M; Motazacker, Mohammad Mahdi; Holleboom, Adriaan G; Van Berkel, Theo J C; Kastelein, John J P; Van Eck, Miranda; Kuivenhoven, Jan Albert

2011-01-01

BACKGROUND: In mice, the scavenger receptor class B type I (SR-BI) is essential for the delivery of high-density lipoprotein (HDL) cholesterol to the liver and steroidogenic organs. Paradoxically, elevated HDL cholesterol levels are associated with increased atherosclerosis in SR-BI-knockout mice.

In-situ synthesis of nanofibers with various ratios of BiOCl{sub x}/BiOBr{sub y}/BiOI{sub z} for effective trichloroethylene photocatalytic degradation

Energy Technology Data Exchange (ETDEWEB)

Zhang, Yifan [Department of Chemistry, Inha University, 100 Inharo, Incheon 402-751 (Korea, Republic of); Park, Mira [Department of Organic Materials and Fiber Engineering, Chonbuk National University, Jeonju 561-756 (Korea, Republic of); Kim, Hak Yong [Department of BIN Convergence Technology, Chonbuk National University, Jeonju, 561-756 (Korea, Republic of); Ding, Bin [College of Textiles, Donghua University, Shanghai 201620 (China); Park, Soo-Jin, E-mail: sjpark@inha.ac.kr [Department of Chemistry, Inha University, 100 Inharo, Incheon 402-751 (Korea, Republic of)

2016-10-30

Highlights: • BiOCl{sub x}/BiOBr{sub y}/BiOI{sub z}/PAN fibers were synthesized by in-situ method. • Photodegradation behavior of BiOCl{sub x}/BiOBr{sub y}/BiOI{sub z}/PAN fibers was measured under solar light irradiation. • BiOCl{sub 0.3}/BiOBr{sub 0.3}/BiOI{sub 0.4}/PAN fibers exhibited the highest photocatalytic activity. • Photocatalytic mechanism was discussed in detail. - Abstract: In this work, BiOCl{sub x}/BiOBr{sub y}/BiOI{sub z} (x + y + z = 1) composite nanofibers were prepared through electrospinning and the sol-gel methods. Photocatalytic degradation of trichloroethylene (TCE) by BiOCl{sub x}/BiOBr{sub y}/BiOI{sub z}/PAN nanofibers was systematically investigated via gas chromatography (GC). Optimum photocatalytic activity was achieved with BiOCl{sub 0.3}/BiOBr{sub 0.3}/BiOI{sub 0.4} fibers under solar light irradiation. X-ray photoelectron spectroscopy (XPS) peaks due to C−O and C=O were observed at 286.0 and 288.3 eV, respectively, it indicated that the BiOCl{sub x}/BiOBr{sub y}/BiOI{sub z} mixture had been successfully doped on the polyacrylonitrile (PAN) fibers. Furthermore, X-ray diffraction (XRD) results also confirmed that we had synthesized the as-prepared composite nanofibers successfully. Photocatalytic activities of BiOCl{sub 0.3}/BiOBr{sub 0.3}/BiOI{sub 0.4} were up to 3 times higher than the pure BiOCl, BiOBr and BiOI samples, respectively.

Bi-exponential T2 analysis of healthy and diseased Achilles tendons: an in vivo preliminary magnetic resonance study and correlation with clinical score.

Science.gov (United States)

Juras, Vladimir; Apprich, Sebastian; Szomolanyi, Pavol; Bieri, Oliver; Deligianni, Xeni; Trattnig, Siegfried

2013-10-01

To compare mono- and bi-exponential T2 analysis in healthy and degenerated Achilles tendons using a recently introduced magnetic resonance variable-echo-time sequence (vTE) for T2 mapping. Ten volunteers and ten patients were included in the study. A variable-echo-time sequence was used with 20 echo times. Images were post-processed with both techniques, mono- and bi-exponential [T2 m, short T2 component (T2 s) and long T2 component (T2 l)]. The number of mono- and bi-exponentially decaying pixels in each region of interest was expressed as a ratio (B/M). Patients were clinically assessed with the Achilles Tendon Rupture Score (ATRS), and these values were correlated with the T2 values. The means for both T2 m and T2 s were statistically significantly different between patients and volunteers; however, for T2 s, the P value was lower. In patients, the Pearson correlation coefficient between ATRS and T2 s was -0.816 (P = 0.007). The proposed variable-echo-time sequence can be successfully used as an alternative method to UTE sequences with some added benefits, such as a short imaging time along with relatively high resolution and minimised blurring artefacts, and minimised susceptibility artefacts and chemical shift artefacts. Bi-exponential T2 calculation is superior to mono-exponential in terms of statistical significance for the diagnosis of Achilles tendinopathy. • Magnetic resonance imaging offers new insight into healthy and diseased Achilles tendons • Bi-exponential T2 calculation in Achilles tendons is more beneficial than mono-exponential • A short T2 component correlates strongly with clinical score • Variable echo time sequences successfully used instead of ultrashort echo time sequences.

Securing optical code-division multiple-access networks with a postswitching coding scheme of signature reconfiguration

Science.gov (United States)

Huang, Jen-Fa; Meng, Sheng-Hui; Lin, Ying-Chen

2014-11-01

The optical code-division multiple-access (OCDMA) technique is considered a good candidate for providing optical layer security. An enhanced OCDMA network security mechanism with a pseudonoise (PN) random digital signals type of maximal-length sequence (M-sequence) code switching to protect against eavesdropping is presented. Signature codes unique to individual OCDMA-network users are reconfigured according to the register state of the controlling electrical shift registers. Examples of signature reconfiguration following state switching of the controlling shift register for both the network user and the eavesdropper are numerically illustrated. Dynamically changing the PN state of the shift register to reconfigure the user signature sequence is shown; this hinders eavesdroppers' efforts to decode correct data sequences. The proposed scheme increases the probability of eavesdroppers committing errors in decoding and thereby substantially enhances the degree of an OCDMA network's confidentiality.

Polarization-multiplexed rate-adaptive non-binary-quasi-cyclic-LDPC-coded multilevel modulation with coherent detection for optical transport networks.

Science.gov (United States)

Arabaci, Murat; Djordjevic, Ivan B; Saunders, Ross; Marcoccia, Roberto M

2010-02-01

In order to achieve high-speed transmission over optical transport networks (OTNs) and maximize its throughput, we propose using a rate-adaptive polarization-multiplexed coded multilevel modulation with coherent detection based on component non-binary quasi-cyclic (QC) LDPC codes. Compared to prior-art bit-interleaved LDPC-coded modulation (BI-LDPC-CM) scheme, the proposed non-binary LDPC-coded modulation (NB-LDPC-CM) scheme not only reduces latency due to symbol- instead of bit-level processing but also provides either impressive reduction in computational complexity or striking improvements in coding gain depending on the constellation size. As the paper presents, compared to its prior-art binary counterpart, the proposed NB-LDPC-CM scheme addresses the needs of future OTNs, which are achieving the target BER performance and providing maximum possible throughput both over the entire lifetime of the OTN, better.

Complete mitochondrial genome sequences from five Eimeria species (Apicomplexa; Coccidia; Eimeriidae) infecting domestic turkeys.

Science.gov (United States)

Ogedengbe, Mosun E; El-Sherry, Shiem; Whale, Julia; Barta, John R

2014-07-17

Clinical and subclinical coccidiosis is cosmopolitan and inflicts significant losses to the poultry industry globally. Seven named Eimeria species are responsible for coccidiosis in turkeys: Eimeria dispersa; Eimeria meleagrimitis; Eimeria gallopavonis; Eimeria meleagridis; Eimeria adenoeides; Eimeria innocua; and, Eimeria subrotunda. Although attempts have been made to characterize these parasites molecularly at the nuclear 18S rDNA and ITS loci, the maternally-derived and mitotically replicating mitochondrial genome may be more suited for species level molecular work; however, only limited sequence data are available for Eimeria spp. infecting turkeys. The purpose of this study was to sequence and annotate the complete mitochondrial genomes from 5 Eimeria species that commonly infect the domestic turkey (Meleagris gallopavo). Six single-oocyst derived cultures of five Eimeria species infecting turkeys were PCR-amplified and sequenced completely prior to detailed annotation. Resulting sequences were aligned and used in phylogenetic analyses (BI, ML, and MP) that included complete mitochondrial genomes from 16 Eimeria species or concatenated CDS sequences from each genome. Complete mitochondrial genome sequences were obtained for Eimeria adenoeides Guelph, 6211 bp; Eimeria dispersa Briston, 6238 bp; Eimeria meleagridis USAR97-01, 6212 bp; Eimeria meleagrimitis USMN08-01, 6165 bp; Eimeria gallopavonis Weybridge, 6215 bp; and Eimeria gallopavonis USKS06-01, 6215 bp). The order, orientation and CDS lengths of the three protein coding genes (COI, COIII and CytB) as well as rDNA fragments encoding ribosomal large and small subunit rRNA were conserved among all sequences. Pairwise sequence identities between species ranged from 88.1% to 98.2%; sequence variability was concentrated within CDS or between rDNA fragments (where indels were common). No phylogenetic reconstruction supported monophyly of Eimeria species infecting turkeys; Eimeria dispersa may have arisen

Confidence level in the calculations of HCDA consequences using large codes

International Nuclear Information System (INIS)

Nguyen, D.H.; Wilburn, N.P.

1979-01-01

The probabilistic approach to nuclear reactor safety is playing an increasingly significant role. For the liquid-metal fast breeder reactor (LMFBR) in particular, the ultimate application of this approach could be to determine the probability of achieving the goal of a specific line-of-assurance (LOA). Meanwhile a more pressing problem is one of quantifying the uncertainty in a calculated consequence for hypothetical core disruptive accident (HCDA) using large codes. Such uncertainty arises from imperfect modeling of phenomenology and/or from inaccuracy in input data. A method is presented to determine the confidence level in consequences calculated by a large computer code due to the known uncertainties in input invariables. A particular application was made to the initial time of pin failure in a transient overpower HCDA calculated by the code MELT-IIIA in order to demonstrate the method. A probability distribution function (pdf) for the time of failure was first constructed, then the confidence level for predicting this failure parameter within a desired range was determined

Facile Fabrication of BiOI/BiOCl Immobilized Films With Improved Visible Light Photocatalytic Performance

Directory of Open Access Journals (Sweden)

Yingxian Zhong

2018-03-01

Full Text Available HIGHLIGHTSA facial method was used to fabricate BiOI/BiOCl film at room temperature.30% BiOI/BiOCl showed an excellent photocatalytic activity and stability.Improvement of photocatalytic activity was owed to expanded visible light absorption and high separation efficiency of charge.Photocatalysis has been considered to be one of the most promising ways to photodegrade organic pollutants. Herein, a series of BiOI/BiOCl films coating on FTO were fabricated through a simple method at room temperature. The photocatalytic efficiency of 30%BiOI/BiOCl could reach more than 99% aiming to degrading RhB and MB after 90 and 120 min, respectively. Compared with BiOCl, 30%BiOI/BiOCl showed 12 times higher efficiency when degrading RhB. In comparison with BiOI, 30%BiOI/BiOCl showed 5 and 6 times higher efficiency when degrading RhB and MB, respectively. These obvious enhancements were attributed to expanded visible light absorption and high separation performance of photoinduced charge. Moreover, the photocatalytic activity of 30%BiOI/BiOCl had no obvious decrease after five recycles, suggesting that it was a promising photocatalyst for the removal of MB and RhB pollutants. Finally, the possible growth process for the BiOI/BiOCl thin films and photocatalysis mechanism were investigated in details. This work would provide insight to the reasonable construction of BiOX heterojunction and the photocatalytic mechanism in degrading organic pollutants.

Evidence for a novel coding sequence overlapping the 5'-terminal ~90 codons of the Gill-associated and Yellow head okavirus envelope glycoprotein gene

Directory of Open Access Journals (Sweden)

Atkins John F

2009-12-01

Full Text Available Abstract The genus Okavirus (order Nidovirales includes a number of viruses that infect crustaceans, causing major losses in the shrimp industry. These viruses have a linear positive-sense ssRNA genome of ~26-27 kb, encoding a large replicase polyprotein that is expressed from the genomic RNA, and several additional proteins that are expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the envelope glycoprotein encoding sequence, ORF3, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF3. We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein.

Influence of photoinduced Bi-related self-doping on the photocatalytic activity of BiOBr nanosheets

Energy Technology Data Exchange (ETDEWEB)

Wu, Dan [School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR (China); Yue, Songtao; Wang, Wei [College of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); An, Tiacheng, E-mail: antc99@gig.ac.cn [Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006 (China); Li, Guiying [Institute of Environmental Health and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006 (China); Ye, Liqun [School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR (China); College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang 473061 (China); Yip, Ho Yin [School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR (China); Wong, Po Keung, E-mail: pkwong@cuhk.edu.hk [School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR (China)

2017-01-01

Highlights: • Bi{sup 5+} self-doped BiOBr nanosheets are achieved under UV irradiation. • Bi{sup 5+} is formed due to the oxidation of surface Bi{sup 3+} by photoexcited h{sup +} of BiOBr. • Two photoinduced h{sup +} mediated oxidation processes happen simultaneously. • Self-doped BiOBr is superior in phenol degradation and bacterial inactivation. • Bi{sup 5+} electron trapping induced photocatalytic enhancement mechanism is proposed. - Abstract: Under UV irradiation, self-doped Bi{sup 5+} is evidenced to be generated on the surface of BiOBr nanosheets, but with well-preserved crystal structure and morphology compared with pure counterpart. Bi{sup 5+} self-doping BiOBr (BiOBr-4) exhibits distinct photocatalytic mode for dyes degradation, as compared with pure BiOBr nanosheets. These photodegradation distinctions are mainly due to the simultaneous occurrence of two photoinduced hole (h{sup +}) mediated oxidation processes on the BiOBr surfaces: (1) a portion of photoexcited h{sup +} participates in the photocatalytic oxidation of dyes, and (2) partial h{sup +} involves the oxidation of Bi{sup 3+} to Bi{sup 5+}. Notably, BiOBr-4 nanosheets comparatively show superior photocatalytic activity for the phenol decomposition as well as the bacterial inactivation. Besides Bi{sup 5+} induced narrowed bandgap and enhanced light adsorption capacity, significantly, the oxidative Bi{sup 5+} acts as electron traps to promote the photoexcited electron-hole separation and accelerate h{sup +} migration, resulting in the considerable photocatalytic enhancement of BiOBr-4 nanosheets. These novel findings will not only give new insights into the photocatalytic mechanism but also explore new route to enhance photocatalytic performance of Bi-based materials.

Transference of particles in the fusion process of 6He + 209Bi

International Nuclear Information System (INIS)

Lizcano, D.; Aguilera, E.F.; Martinez Q, E.

2000-01-01

In a recent work were reported measurements done to energy which was to the Coulomb barrier for the 6 He + 209 Bi system. The fusion excitation function measured for this system shows a strong enhancement with respect to the predictions of the penetration model of unidimensional barrier at minor energies to the Coulombian barrier. In basis with the results obtained for different degrees of freedom it was determined with the CCDEF code, that the transfer of 2 neutrons of 6 He to binding states to 209 Bi, producing 211 Bi, is the mechanism looked as the best candidate for explain the great enhancement in the fusion excitation function of this system at energies under Coulomb barrier. It is corroborated what was affirmed by others authors about the strength value at 1.5 MeV as a typical value for the transference of two particles between the projectile and the target. (Author)

New tools to analyze overlapping coding regions.

Science.gov (United States)

Bayegan, Amir H; Garcia-Martin, Juan Antonio; Clote, Peter

2016-12-13

Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement). We describe a unique computational tool, RNAsampleCDS, designed to compute the number of RNA sequences that code two (or more) peptides p,q in overlapping reading frames, that are identical (or have BLOSUM/PAM similarity that exceeds a user-specified value) to the input peptides p,q. RNAsampleCDS then samples a user-specified number of messenger RNAs that code such peptides; alternatively, RNAsampleCDS can exactly compute the position-specific scoring matrix and codon usage bias for all such RNA sequences. Our software allows the user to stipulate overlapping coding requirements for all 6 possible reading frames simultaneously, even allowing IUPAC constraints on RNA sequences and fixing GC-content. We generalize the notion of codon preference index (CPI) to overlapping reading frames, and use RNAsampleCDS to generate control sequences required in the computation of CPI. Moreover, by applying RNAsampleCDS, we are able to quantify the extent to which the overlapping coding requirement in HIV-1 [resp. HCV] contribute to the formation of the stem-loop [resp. double stem-loop] secondary structure known as the frameshift stimulating signal. Using our software, we confirm that certain experimentally determined deleterious HCV mutations occur in positions for which our software RNAsampleCDS and RNAiFold both indicate a single possible nucleotide. We

Psacoin level 1A intercomparison probabilistic system assessment code (PSAC) user group

International Nuclear Information System (INIS)

Nies, A.; Laurens, J.M.; Galson, D.A.; Webster, S.

1990-01-01

This report describes an international code intercomparison exercise conducted by the NEA Probabilistic System Assessment Code (PSAC) User Group. The PSACOIN Level 1A exercise is the third of a series designed to contribute to the verification of probabilistic codes that may be used in assessing the safety of radioactive waste disposal systems or concepts. Level 1A is based on a more realistic system model than that used in the two previous exercises, and involves deep geological disposal concepts with a relatively complex structure of the repository vault. The report compares results and draws conclusions with regard to the use of different modelling approaches and the possible importance to safety of various processes within and around a deep geological repository. In particular, the relative significance of model uncertainty and data variability is discussed

Bi2(Sr, Ln)2CuOz (Ln = Nd, Sm) phases: stability, crystal growth and superconducting properties

International Nuclear Information System (INIS)

Faqir, H.; Kikuchi, M.; Syono, Y.; Mansori, M.; Satre, P.; Sebaoun, A.; Vacquier, G.

2000-01-01

Bi 2 (Sr,Ln) 2 CuO z (Ln = Nd, Sm) single crystals were successfully grown by a self-flux method from stoichiometric and (Bi, Cu)-rich melts. Thermal analysis and thermogravimetry were used to determine stability and the melting sequence of Bi 2 (Sr,Ln) 2 CuO z phases in air. As-grown crystals of the ideal Bi 2 (Sr,Ln) 2 CuO z phase, of dimensions 1x0.5x0.03 mm 3 , exhibit superconducting behaviour with critical temperature T c = 21 K for the Bi 1.9 Sr 1.6 Nd 0.6 CuO z crystal and Tc = 14 K for the Bi 1.8 Sr 1.6 Sm 0.6 CuO z crystal. The compositions of these crystals were homogeneous and close to the stoichiometric composition. We report on the growth of Bi 2 Sr 2-x Sm x CuO z single crystals of large dimensions 9x3x0.03 mm 3 using Bi 2 Sr 1.5 Sm 0.5 CuO z as precursor and Bi 2 CuO 4 as flux. (author)

System-level hazard analysis using the sequence-tree method

International Nuclear Information System (INIS)

Huang, H.-W.; Shih Chunkuan; Yih Swu; Chen, M.-H.

2008-01-01

A system-level PHA using the sequence-tree method is presented to perform safety-related digital I and C system SSA. The conventional PHA involves brainstorming among experts on various portions of the system to identify hazards through discussions. However, since the conventional PHA is not a systematic technique, the analysis results depend strongly on the experts' subjective opinions. The quality of analysis cannot be appropriately controlled. Therefore, this study presents a system-level sequence tree based PHA, which can clarify the relationship among the major digital I and C systems. This sequence-tree-based technique has two major phases. The first phase adopts a table to analyze each event in SAR Chapter 15 for a specific safety-related I and C system, such as RPS. The second phase adopts a sequence tree to recognize the I and C systems involved in the event, the working of the safety-related systems and how the backup systems can be activated to mitigate the consequence if the primary safety systems fail. The defense-in-depth echelons, namely the Control echelon, Reactor trip echelon, ESFAS echelon and Monitoring and indicator echelon, are arranged to build the sequence-tree structure. All the related I and C systems, including the digital systems and the analog back-up systems, are allocated in their specific echelons. This system-centric sequence-tree analysis not only systematically identifies preliminary hazards, but also vulnerabilities in a nuclear power plant. Hence, an effective simplified D3 evaluation can also be conducted

Final technical position on documentation of computer codes for high-level waste management

International Nuclear Information System (INIS)

Silling, S.A.

1983-06-01

Guidance is given for the content of documentation of computer codes which are used in support of a license application for high-level waste disposal. The guidelines cover theoretical basis, programming, and instructions for use of the code

A Bi-Level Programming Model for the Railway Express Cargo Service Network Design Problem

Directory of Open Access Journals (Sweden)

Boliang Lin

2018-06-01

Full Text Available Service network design is fundamentally crucial for railway express cargo transportation. The main challenge is to strike a balance between two conflicting objectives: low network setup costs and high expected operational incomes. Different configurations of these objectives will have different impacts on the quality of freight transportation services. In this paper, a bi-level programming model for the railway express cargo service network design problem is proposed. The upper-level model forms the optimal decisions in terms of the service characteristics, and the low-level model selects the service arcs for each commodity. The rail express cargo is strictly subject to the service commitment, the capacity restriction, flow balance constraints, and logical relationship constraints among the decisions variables. Moreover, linearization techniques are used to convert the lower-level model to a linear one so that it can be directly solved by a standard optimization solver. Finally, a real-world case study based on the Beijing–Guangzhou Railway Line is carried out to demonstrate the effectiveness and efficiency of the proposed solution approach.

Coding Local and Global Binary Visual Features Extracted From Video Sequences.

Science.gov (United States)

Baroffio, Luca; Canclini, Antonio; Cesana, Matteo; Redondi, Alessandro; Tagliasacchi, Marco; Tubaro, Stefano

2015-11-01

Binary local features represent an effective alternative to real-valued descriptors, leading to comparable results for many visual analysis tasks while being characterized by significantly lower computational complexity and memory requirements. When dealing with large collections, a more compact representation based on global features is often preferred, which can be obtained from local features by means of, e.g., the bag-of-visual word model. Several applications, including, for example, visual sensor networks and mobile augmented reality, require visual features to be transmitted over a bandwidth-limited network, thus calling for coding techniques that aim at reducing the required bit budget while attaining a target level of efficiency. In this paper, we investigate a coding scheme tailored to both local and global binary features, which aims at exploiting both spatial and temporal redundancy by means of intra- and inter-frame coding. In this respect, the proposed coding scheme can conveniently be adopted to support the analyze-then-compress (ATC) paradigm. That is, visual features are extracted from the acquired content, encoded at remote nodes, and finally transmitted to a central controller that performs the visual analysis. This is in contrast with the traditional approach, in which visual content is acquired at a node, compressed and then sent to a central unit for further processing, according to the compress-then-analyze (CTA) paradigm. In this paper, we experimentally compare the ATC and the CTA by means of rate-efficiency curves in the context of two different visual analysis tasks: 1) homography estimation and 2) content-based retrieval. Our results show that the novel ATC paradigm based on the proposed coding primitives can be competitive with the CTA, especially in bandwidth limited scenarios.

Bi3+–Pr3+ energy transfer processes and luminescent properties of LuAG:Bi,Pr and YAG:Bi,Pr single crystalline films

International Nuclear Information System (INIS)

Zorenko, Y.; Gorbenko, V.; Savchyn, V.; Zorenko, T.; Nikl, M.; Mares, J.A.; Beitlerova, A.; Jary, V.

2013-01-01

Absorption, cathodoluminescence, excitation spectra of photoluminescence (PL) and PL decay kinetics were studied at 300 K for the double doped with Bi 3+ –Pr 3+ and separately doped with Bi 3+ and Pr 3+ Lu 3 Al 5 O 12 (LuAG) and Y 3 Al 5 O 12 (YAG) single crystalline film (SCF) phosphors grown by the liquid phase epitaxy method. The emission bands in the UV range arising from the intrinsic radiative transitions of Bi 3+ based centers, and emission bands in the visible range, related to the luminescence of excitons localized around Bi 3+ based centers, were identified both in Bi–Pr and Bi-doped LuAG and YAG SCFs. The energy transfer processes from the host lattice simultaneously to Bi 3+ and Pr 3+ ions and from Bi 3+ to Pr 3+ ions were investigated. Competition between Pr 3+ and Bi 3+ ions in the energy transfer processes from the LuAG and YAG hosts was evidenced. The strong decrease of the intensity of Pr 3+ luminescence both in LuAG:Pr and YAG:Pr SCFs phosphors, grown from Bi 2 O 3 flux, is observed due to the quenching influence of Bi 3+ flux related impurity. Due to overlap of the UV emission band of Bi 3+ centers with the f–d absorption bands of Pr 3+ ions in the UV range and the luminescence of excitons localized around Bi ions with the f–f absorption bands of Pr 3+ ions in the visible range, an effective energy transfer from Bi 3+ ions to Pr 3+ ions takes place in LuAG:Bi,Pr and YAG:Bi,Pr SCFs, resulting in the appearance of slower component in the decay kinetics of the Pr 3+ d–f luminescence. -- Highlights: • Bi and Pr doped film phosphor grown by liquid phase epitaxy method. • Energy transfer from Bi 3+ to Pr 3+ ions. • Strong quenching of the Pr 3+ luminescence by Bi 3+ co-dopant

Facile Fabrication of BiOI/BiOCl Immobilized Films with Improved Visible Light Photocatalytic Performance

Science.gov (United States)

Zhong, Yingxian; Liu, Yuehua; Wu, Shuang; Zhu, Yi; Chen, Hongbin; Yu, Xiang; Zhang, Yuanming

2018-03-01

Photocatalysis has been considered to be one of the most promising ways to photodegrade organic pollutants. Herein, a series of BiOI/BiOCl films coating on FTO were fabricated through a simple method at room temperature. The photocatalytic efficiency of 30%BiOI/BiOCl could reach more than 99% aiming to degrading RhB and MB after 90 and 120 min, respectively. Compared with BiOCl, 30%BiOI/BiOCl showed 12 times higher efficiency when degrading RhB. In comparison with BiOI, 30%BiOI/BiOCl showed 5 and 6 times higher efficiency when degrading RhB and MB, respectively. These obvious enhancements were attributed to expanded visible light absorption and high separation performance of photoinduced charge. Moreover, the photocatalytic activity of 30%BiOI/BiOCl had no obvious decrease after 5 recycles, suggesting that it was a promising photocatalyst for the removal of MB and RhB pollutants. Finally, the possible growth process for the BiOI/BiOCl thin films and photocatalysis mechanism were investigated in details. This work would provide insight to the reasonable construction of BiOX heterojunction and the photocatalytic mechanism in degrading organic pollutants.

Rfam: annotating families of non-coding RNA sequences.

Science.gov (United States)

Daub, Jennifer; Eberhardt, Ruth Y; Tate, John G; Burge, Sarah W

2015-01-01

The primary task of the Rfam database is to collate experimentally validated noncoding RNA (ncRNA) sequences from the published literature and facilitate the prediction and annotation of new homologues in novel nucleotide sequences. We group homologous ncRNA sequences into "families" and related families are further grouped into "clans." We collate and manually curate data cross-references for these families from other databases and external resources. Our Web site offers researchers a simple interface to Rfam and provides tools with which to annotate their own sequences using our covariance models (CMs), through our tools for searching, browsing, and downloading information on Rfam families. In this chapter, we will work through examples of annotating a query sequence, collating family information, and searching for data.

Genomic sequence around butterfly wing development genes: annotation and comparative analysis.

Directory of Open Access Journals (Sweden)

Inês C Conceição

Full Text Available BACKGROUND: Analysis of genomic sequence allows characterization of genome content and organization, and access beyond gene-coding regions for identification of functional elements. BAC libraries, where relatively large genomic regions are made readily available, are especially useful for species without a fully sequenced genome and can increase genomic coverage of phylogenetic and biological diversity. For example, no butterfly genome is yet available despite the unique genetic and biological properties of this group, such as diversified wing color patterns. The evolution and development of these patterns is being studied in a few target species, including Bicyclus anynana, where a whole-genome BAC library allows targeted access to large genomic regions. METHODOLOGY/PRINCIPAL FINDINGS: We characterize ∼1.3 Mb of genomic sequence around 11 selected genes expressed in B. anynana developing wings. Extensive manual curation of in silico predictions, also making use of a large dataset of expressed genes for this species, identified repetitive elements and protein coding sequence, and highlighted an expansion of Alcohol dehydrogenase genes. Comparative analysis with orthologous regions of the lepidopteran reference genome allowed assessment of conservation of fine-scale synteny (with detection of new inversions and translocations and of DNA sequence (with detection of high levels of conservation of non-coding regions around some, but not all, developmental genes. CONCLUSIONS: The general properties and organization of the available B. anynana genomic sequence are similar to the lepidopteran reference, despite the more than 140 MY divergence. Our results lay the groundwork for further studies of new interesting findings in relation to both coding and non-coding sequence: 1 the Alcohol dehydrogenase expansion with higher similarity between the five tandemly-repeated B. anynana paralogs than with the corresponding B. mori orthologs, and 2 the high

Genomic and antigenic relationships between two 'HoBi'-like strains and other members of the Pestivirus genus.

Science.gov (United States)

Mósena, Ana Cristina S; Cibulski, Samuel P; Weber, Matheus N; Silveira, Simone; Silva, Mariana S; Mayer, Fabiana Q; Roehe, Paulo M; Canal, Cláudio W

2017-10-01

'HoBi'-like viruses comprise a putative new species within the genus Pestivirus of the family Flaviviridae. 'HoBi'-like viruses have been detected worldwide in batches of fetal calf serum, in surveillance programs for bovine pestiviruses and from animals presenting clinical signs resembling bovine viral diarrhea virus (BVDV)-associated diseases. To date, few complete genome sequences of 'HoBi'-like viruses are available in public databases. Moreover, detailed analyses of such genomes are still scarce. In an attempt to expand data on the genetic diversity and biology of pestiviruses, two genomes of 'HoBi'-like viruses recovered from Brazilian cattle were described and characterized in this study. Analysis of the whole genome and antigenic properties of these two new 'HoBi'-like isolates suggest that these viruses are genetically close to recognized pestiviruses. The present data provide evidence that 'HoBi'-like viruses are members of the genus Pestivirus and should be formally recognized as a novel species.

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

Science.gov (United States)

Martin, Andrew C R

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

Identification of Natural Infections in Sheep/Goats with HoBi-like Pestiviruses in China.

Science.gov (United States)

Shi, H; Kan, Y; Yao, L; Leng, C; Tang, Q; Ji, J; Sun, S

2016-10-01

The natural infections of HoBi-like pestiviruses in cattle have been reported in South America, Europe and Asia. In China, although the detections of HoBi-like pestivirus have been reported, the epidemiological investigation was limited. From January 2014 to October 2015, several flocks of sheep/goats in Henan province in central China suffered respiratory diseases which were recovered slowly after antibiotics treatment. To test whether it is the HoBi-like pestivirus caused this symptom, 49 serum samples and 22 nasal swabs were then collected for analysis by serology and RT-PCR. Serological result revealed that prevalence of pestivirus in small ruminants was 12.2% (6/49) in central China. Sequence analysis of partial 5'-UTR nucleotides of pestivirus-positive samples suggested that HoBi-like pestivirus might have circulated in sheep/goats of China for a period and have evolved into new genotype clusters. It is apparent that the study provides the molecular evidence of natural infections in goat/sheep species with HoBi-like pestiviruses in China. © 2016 Blackwell Verlag GmbH.

Phaleria macrocarpa Boerl. (Thymelaeaceae Leaves Increase SR-BI Expression and Reduce Cholesterol Levels in Rats Fed a High Cholesterol Diet

Directory of Open Access Journals (Sweden)

Yosie Andriani

2015-03-01

Full Text Available In vitro and in vivo studies of the activity of Phaleria macrocarpa Boerl (Thymelaeaceae leaves against the therapeutic target for hypercholesterolemia were done using the HDL receptor (SR-BI and hypercholesterolemia-induced Sprague Dawley rats. The in vitro study showed that the active fraction (CF6 obtained from the ethyl acetate extract (EMD and its component 2',6',4-trihydroxy-4'-methoxybenzophenone increased the SR-BI expression by 95% and 60%, respectively. The in vivo study has proven the effect of EMD at 0.5 g/kgbw dosage in reducing the total cholesterol level by 224.9% and increasing the HDL cholesterol level by 157% compared to the cholesterol group. In the toxicity study, serum glutamate oxalate transaminase (SGOT and serum glutamate pyruvate transaminase (SGPT activity were observed to be at normal levels. The liver histology also proved no toxicity and abnormalities in any of the treatment groups, so it can be categorized as non-toxic to the rat liver. The findings taken together show that P. macrocarpa leaves are safe and suitable as an alternative control and prevention treatment for hypercholesterolemia in Sprague Dawley rats.

Analysis of the first temperate broad host range brucellaphage (BiPBO1 isolated from B. inopinata

Directory of Open Access Journals (Sweden)

Jens Andre Hammerl

2016-01-01

Full Text Available Brucella species are important human and animal pathogens. Though, only little is known about mobile genetic elements of these highly pathogenic bacteria. To date, neither plasmids nor temperate phages have been described in brucellae. We analysed genomic sequences of various reference and type strains and identified a number of putative prophages residing within the Brucella chromosomes. By induction, phage BiPBO1 was isolated from B. inopinata. BiPBO1 is a siphovirus that infects several Brucella species including B. abortus and B. melitensis. Integration of the phage genome occurs adjacent to a tRNA gene in chromosome 1 (chr 1. The bacterial (attB and phage (attP attachment sites comprise an identical sequence of 46 bp. This sequence exists in many Brucella and Ochrobactrum species. The BiPBO1 genome is composed of a 46,877 bp double-stranded DNA. Eighty-seven putative gene products were determined, of which 32 could be functionally assigned. Strongest similarities were found to a temperate phage residing in the chromosome of Ochrobactrum anthropi ATCC 49188 and to prophages identified in several families belonging to the order rhizobiales. The data suggest that horizontal gene transfer may occur between Brucella and Ochrobactrum and underpin the close relationship of these environmental and pathogenic bacteria.

ParBiBit: Parallel tool for binary biclustering on modern distributed-memory systems.

Science.gov (United States)

González-Domínguez, Jorge; Expósito, Roberto R

2018-01-01

Biclustering techniques are gaining attention in the analysis of large-scale datasets as they identify two-dimensional submatrices where both rows and columns are correlated. In this work we present ParBiBit, a parallel tool to accelerate the search of interesting biclusters on binary datasets, which are very popular on different fields such as genetics, marketing or text mining. It is based on the state-of-the-art sequential Java tool BiBit, which has been proved accurate by several studies, especially on scenarios that result on many large biclusters. ParBiBit uses the same methodology as BiBit (grouping the binary information into patterns) and provides the same results. Nevertheless, our tool significantly improves performance thanks to an efficient implementation based on C++11 that includes support for threads and MPI processes in order to exploit the compute capabilities of modern distributed-memory systems, which provide several multicore CPU nodes interconnected through a network. Our performance evaluation with 18 representative input datasets on two different eight-node systems shows that our tool is significantly faster than the original BiBit. Source code in C++ and MPI running on Linux systems as well as a reference manual are available at https://sourceforge.net/projects/parbibit/.

Cross-sections of (p, xn) nuclear reactions on Pb and Bi by 100 MeV protons

Energy Technology Data Exchange (ETDEWEB)

Oranj, Leila Mokhtari; Jung, Nam Suk; Oh, Joo Hee; Lee, Arim; Kim, Dong Hyun; Bae, Oryun; Lee, Hee Seock [POSTECH, Pohang (Korea, Republic of)

2016-04-15

The development of high-intensity and high-energy accelerator is gaining interest in Korea, in recent years. Rare Isotope Science Project (RISP), Pohang Accelerator Laboratory X-ray Free Electron Laser (PAL-XFEL), Korea Heavy Ion Medical Accelerator (KHIMA) facilities are being designed. In the frame of above projects, for the safety issue and shielding analysis of the accelerator facility, extensive studies including experimental and simulation on the production yields of residual nuclei induced in the accelerator materials such as Pb, Cu and Bi by protons and heavy ions are in progress. In this work, we measured cross-sections of {sup na}'tPb(p,xn){sup 206,205,204,20{sup ,202}}Bi and {sup 209}Bi(p, xn){sup 207,206,205,204},{sup 203}Po nuclear reactions by the 100-MeV protons. The present experimental data are in good agreement with the results of Titarenkoet al. and Gloris et al.. Experimental data were higher than theoretical data. In other words, results of TALYS code and data in TENDL library underestimated the measured crosss sections and library of TALYS code and TENDL need to be improved.

Temporal code-driven stimulation: definition and application to electric fish signaling

Directory of Open Access Journals (Sweden)

Angel Lareo

2016-10-01

Full Text Available Closed-loop activity-dependent stimulation is a powerful methodology to assess information processing in biological systems. In this context, the development of novel protocols, their implementation in bioinformatics toolboxes and their application to different description levels open up a wide range of possibilities in the study of biological systems. We developed a methodology for studying biological signals representing them as temporal sequences of binary events. A specific sequence of these events (code is chosen to deliver a predefined stimulation in a closed-loop manner. The response to this code-driven stimulation can be used to characterize the system. This methodology was implemented in a real time toolbox and tested in the context of electric fish signaling. We show that while there are codes that evoke a response that cannot be distinguished from a control recording without stimulation, other codes evoke a characteristic distinct response. We also compare the code-driven response to open-loop stimulation. The discussed experiments validate the proposed methodology and the software toolbox.

Preparation, characterization and enhanced visible-light photocatalytic activities of BiPO4/BiVO4 composites

International Nuclear Information System (INIS)

Wu, Siyuan; Zheng, Hong; Lian, Youwei; Wu, Yiying

2013-01-01

Graphical abstract: - Highlights: • BiPO 4 /BiVO 4 composites were successfully prepared by the hydrothermal method. • BiPO 4 /BiVO 4 composites exhibited broad absorption in the visible region. • Visible-light photocatalytic activities of BiPO 4 /BiVO 4 composites were enhanced. • P/V molar ratio and pH value of the reaction affect photocatalytic activity. • The mechanism of enhanced visible-light photocatalytic activities was discussed. - Abstract: BiPO 4 /BiVO 4 composites with different P/V molar ratios were prepared by the hydrothermal method and the effect of pH values of hydrothermal reaction on photocatalytic activity of BiPO 4 /BiVO 4 composite was investigated. The photocatalysts were characterized by X-ray diffraction, field emission scanning electron microscopy, energy-dispersive spectroscopy, X-ray photoelectron spectroscopy and UV–vis diffuse reflectance spectroscopy. The photocatalytic property of BiPO 4 /BiVO 4 was evaluated by photocatalytic degradation of Methylene blue under visible light irradiation. The results showed that the photocatalytic activity of the composites was much higher than that of pure BiPO 4 and BiVO 4 . The rate constant of Methylene blue degradation over BiPO 4 /BiVO 4 (P/V molar ratio of 5:1 and hydrothermal reaction pH value of 1.5) is 1.7 times that of pure BiVO 4 . The photocatalytic activity enhancement of BiPO 4 /BiVO 4 composite is closely related to the BiVO 4 functioning as a sensitizer to adsorb visible light and the heterojunction of BiPO 4 /BiVO 4 acting as an active center for hindering the rapid recombination of electron–hole pairs during the photocatalytic reaction

Spatial profile of thermoelectric effects during Peltier pulsing in Bi and Bi/MnBi eutectic

Science.gov (United States)

Silberstein, R. P.; Larson, D. J., Jr.

1987-01-01

The spatial profile of the thermal transients that occur during and following the current pulsing associated with Peltier Interface Demarcation during directional solidification is studied. Results for pure Bi are presented in detail and compared with corresponding results for the Bi/MnBi eutectic. Significant thermal transients occur throughout the sample that can be accounted for by the Peltier effect, the Thomson effect, and Joule heating. These effects are separated and their behavior is studied as a function of time, current density, and position with respect to the solid/liquid interface.

State diagram of Pr-Bi system

International Nuclear Information System (INIS)

Abulkhaev, V.L.; Ganiev, I.N.

1994-01-01

By means of thermal differential analysis, X-ray and microstructural analysis the state diagram of Pr-Bi system was studied. Following intermetallic compounds were defined in the system: Pr 2 Bi, Pr 5 Bi 3 , Pr 4 Bi 3 , Pr Bi, PrBi 2 , Pr 2 Bi, Pr 5 Bi 3 , Pr 4 Bi 3 and PrBi 2 . The data analysis on Ln-Bi diagram allowed to determine the regularity of change of properties of intermetallic compounds in the line of rare earth elements of cerium subgroup.

Transference of particles in the fusion process of {sup 6}He + {sup 209}Bi; Transferencia de particulas en el proceso de fusion de {sup 6}He + {sup 209}Bi

Energy Technology Data Exchange (ETDEWEB)

Lizcano, D.; Aguilera, E.F.; Martinez Q, E. [Instituto Nacional de Investigaciones Nucleares, A.P. 18-1027, 11801 Mexico D.F. (Mexico)

2000-07-01

In a recent work were reported measurements done to energy which was to the Coulomb barrier for the {sup 6} He + {sup 209} Bi system. The fusion excitation function measured for this system shows a strong enhancement with respect to the predictions of the penetration model of unidimensional barrier at minor energies to the Coulombian barrier. In basis with the results obtained for different degrees of freedom it was determined with the CCDEF code, that the transfer of 2 neutrons of {sup 6} He to binding states to {sup 209} Bi, producing {sup 211} Bi, is the mechanism looked as the best candidate for explain the great enhancement in the fusion excitation function of this system at energies under Coulomb barrier. It is corroborated what was affirmed by others authors about the strength value at 1.5 MeV as a typical value for the transference of two particles between the projectile and the target. (Author)

Spectral entropy criteria for structural segmentation in genomic DNA sequences

International Nuclear Information System (INIS)

Chechetkin, V.R.; Lobzin, V.V.

2004-01-01

The spectral entropy is calculated with Fourier structure factors and characterizes the level of structural ordering in a sequence of symbols. It may efficiently be applied to the assessment and reconstruction of the modular structure in genomic DNA sequences. We present the relevant spectral entropy criteria for the local and non-local structural segmentation in DNA sequences. The results are illustrated with the model examples and analysis of intervening exon-intron segments in the protein-coding regions

Ultrafast all-optical code-division multiple-access networks

Science.gov (United States)

Kwong, Wing C.; Prucnal, Paul R.; Liu, Yanming

1992-12-01

In optical code-division multiple access (CDMA), the architecture of optical encoders/decoders is another important factor that needs to be considered, besides the correlation properties of those already extensively studied optical codes. The architecture of optical encoders/decoders affects, for example, the amount of power loss and length of optical delays that are associated with code sequence generation and correlation, which, in turn, affect the power budget, size, and cost of an optical CDMA system. Various CDMA coding architectures are studied in the paper. In contrast to the encoders/decoders used in prime networks (i.e., prime encodes/decoders), which generate, select, and correlate code sequences by a parallel combination of fiber-optic delay-lines, and in 2n networks (i.e., 2n encoders/decoders), which generate and correlate code sequences by a serial combination of 2 X 2 passive couplers and fiber delays with sequence selection performed in a parallel fashion, the modified 2n encoders/decoders generate, select, and correlate code sequences by a serial combination of directional couplers and delays. The power and delay- length requirements of the modified 2n encoders/decoders are compared to that of the prime and 2n encoders/decoders. A 100 Mbit/s optical CDMA experiment in free space demonstrating the feasibility of the all-serial coding architecture using a serial combination of 50/50 beam splitters and retroreflectors at 10 Tchip/s (i.e., 100,000 chip/bit) with 100 fs laser pulses is reported.

Investigation on gamma and neutron radiation shielding parameters for BaO/SrO‒Bi2O3‒B2O3 glasses

Science.gov (United States)

Sayyed, M. I.; Lakshminarayana, G.; Dong, M. G.; Ersundu, M. Çelikbilek; Ersundu, A. E.; Kityk, I. V.

2018-04-01

In this work, mass attenuation coefficients (μ/ρ), effective atomic number (Zeff), electron density (Ne), mean free path (MFP), and half-value layer (HVL) of 20 BaO/SrO‒(x) Bi2O3‒(80‒x) B2O3 glasses (where x=10, 20, 30, 40, 50 and 60 mol%) were calculated using WinXCom program and MCNP5 code. The obtained (μ/ρ) results using both MCNP5 code and WinXCom program were in good agreement. It is found that the addition of Bi2O3 leads to increase the Zeff values in both BaO/SrO‒Bi2O3‒B2O3 glass systems. However, the Zeff values of the BaO‒Bi2O3‒B2O3 glass system are higher than those of the SrO‒Bi2O3‒B2O3 glasses. The fast neutrons effective removal cross sections (ΣR) for 20 SrO‒40 Bi2O3‒40 B2O3 glass is the highest among all studied glasses. The calculated half-value layer values were compared with different glass systems and it was found that the shielding properties of the selected glasses are comparable or even better than other glass systems such as phosphate glasses.

Oblate deformation and intruder configuration in 194,195Bi

International Nuclear Information System (INIS)

Mukherjee, G.; Banerjee, K.; Banerjee, S.R.; Basu, S.K.; Bhattacharya, C.; Bhattacharya, S.; Bhattacharya, Srijit; Bhattacharjee, T.; Chanda, S.; Dey, A.; Gupta, D.; Meena, J.K.; Mukhopadhyay, S.; Rana, T.K.; Bhattacharya, Sudeb; Ganguly, S.; Goswami, A.; Kshetri, R.; Pradhan, M.K.; Raut, R.; Dey, G.

2006-01-01

The experimental information on 194,195 Bi are very scarce compared to its neighbouring isotopes. Only 6 levels above the ground state band of 195 Bi, based on 9/2, are known with tentative spin parity assignments. Only two low energy gamma rays above the 10 isomeric state are known in 194 Bi. It is interesting not only to extend the presently known bands to higher spins, beyond band crossing but also to search for the intruder quasiparticle configurations to get a clear idea about the structure of these nuclei

The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features

Science.gov (United States)

Tu, Shiqi; Yuan, Guo-Cheng; Shao, Zhen

2017-01-01

Recently, long non-coding RNAs (lncRNAs) have emerged as an important class of molecules involved in many cellular processes. One of their primary functions is to shape epigenetic landscape through interactions with chromatin modifying proteins. However, mechanisms contributing to the specificity of such interactions remain poorly understood. Here we took the human and mouse lncRNAs that were experimentally determined to have physical interactions with Polycomb repressive complex 2 (PRC2), and systematically investigated the sequence features of these lncRNAs by developing a new computational pipeline for sequences composition analysis, in which each sequence is considered as a series of transitions between adjacent nucleotides. Through that, PRC2-binding lncRNAs were found to be associated with a set of distinctive and evolutionarily conserved sequence features, which can be utilized to distinguish them from the others with considerable accuracy. We further identified fragments of PRC2-binding lncRNAs that are enriched with these sequence features, and found they show strong PRC2-binding signals and are more highly conserved across species than the other parts, implying their functional importance.

Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs

Directory of Open Access Journals (Sweden)

Vaughn Matthew

2010-11-01

Full Text Available Abstract Background Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories - based on the data structures which they employ. The first class uses an overlap/string graph and the second type uses a de Bruijn graph. However with the recent advances in short read sequencing technology, de Bruijn graph based algorithms seem to play a vital role in practice. Efficient algorithms for building these massive de Bruijn graphs are very essential in large sequencing projects based on short reads. In an earlier work, an O(n/p time parallel algorithm has been given for this problem. Here n is the size of the input and p is the number of processors. This algorithm enumerates all possible bi-directed edges which can overlap with a node and ends up generating Θ(nΣ messages (Σ being the size of the alphabet. Results In this paper we present a Θ(n/p time parallel algorithm with a communication complexity that is equal to that of parallel sorting and is not sensitive to Σ. The generality of our algorithm makes it very easy to extend it even to the out-of-core model and in this case it has an optimal I/O complexity of Θ(nlog(n/BBlog(M/B (M being the main memory size and B being the size of the disk block. We demonstrate the scalability of our parallel algorithm on a SGI/Altix computer. A comparison of our algorithm with the previous approaches reveals that our algorithm is faster - both asymptotically and practically. We demonstrate the scalability of our sequential out-of-core algorithm by comparing it with the algorithm used by VELVET to build the bi-directed de Bruijn graph. Our experiments reveal that our algorithm can build the graph with a constant amount of memory, which clearly outperforms VELVET. We also provide efficient algorithms for the bi-directed chain compaction problem. Conclusions The bi

Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs.

Science.gov (United States)

Kundeti, Vamsi K; Rajasekaran, Sanguthevar; Dinh, Hieu; Vaughn, Matthew; Thapar, Vishal

2010-11-15

Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories - based on the data structures which they employ. The first class uses an overlap/string graph and the second type uses a de Bruijn graph. However with the recent advances in short read sequencing technology, de Bruijn graph based algorithms seem to play a vital role in practice. Efficient algorithms for building these massive de Bruijn graphs are very essential in large sequencing projects based on short reads. In an earlier work, an O(n/p) time parallel algorithm has been given for this problem. Here n is the size of the input and p is the number of processors. This algorithm enumerates all possible bi-directed edges which can overlap with a node and ends up generating Θ(nΣ) messages (Σ being the size of the alphabet). In this paper we present a Θ(n/p) time parallel algorithm with a communication complexity that is equal to that of parallel sorting and is not sensitive to Σ. The generality of our algorithm makes it very easy to extend it even to the out-of-core model and in this case it has an optimal I/O complexity of Θ(nlog(n/B)Blog(M/B)) (M being the main memory size and B being the size of the disk block). We demonstrate the scalability of our parallel algorithm on a SGI/Altix computer. A comparison of our algorithm with the previous approaches reveals that our algorithm is faster--both asymptotically and practically. We demonstrate the scalability of our sequential out-of-core algorithm by comparing it with the algorithm used by VELVET to build the bi-directed de Bruijn graph. Our experiments reveal that our algorithm can build the graph with a constant amount of memory, which clearly outperforms VELVET. We also provide efficient algorithms for the bi-directed chain compaction problem. The bi-directed de Bruijn graph is a fundamental data structure for

Knockdown expression and hepatic deficiency reveal anatheroprotective role for SR-BI in liver and peripheral tissues

Energy Technology Data Exchange (ETDEWEB)

Huby, Thierry; Doucet, Chantal; Dachet, Christiane; Ouzilleau,Betty; Ueda, Yukihiko; Afzal, Veena; Rubin, Edward; Chapman, M. John; Lesnik, Philippe

2006-07-18

Scavenger receptor SR-BI has been implicated inHDL-dependent atheroprotective mechanisms. We report the generation of anSR-BI conditional knockout mouse model in which SR-BI gene targeting byloxP site insertion produced a hypomorphic allele (hypomSR-BI).Attenuated SR-BI expression in hypomSR-BI mice resulted in 2-foldelevation in plasma total cholesterol (TC) levels. Cre-mediated SR-BIgene inactivation of the hypomorphic SR-BI allele in hepatocytes(hypomSR-BI-KOliver) was associated with high plasma TC concentrations,increased plasma free cholesterol/TC (FC/TC) ratio, and alipoprotein-cholesterol profile typical of SR-BI-/- mice. Plasma TClevels were increased 2-fold in hypomSR-BI and control mice fed anatherogenic diet, whereas hypomSR-BI-KOliver and SR-BI-/- mice developedsevere hypercholesterolemia due to accumulation of FC-rich, VLDL-sizedparticles. Atherosclerosis in hypomSR-BI mice was enhanced (2.5-fold)compared with that in controls, but to a much lower degree than inhypomSR-BI-KOliver (32-fold) and SR-BI-/- (48-fold) mice. The lattermodels did not differ in either plasma lipid levels or in the capacity ofVLDL-sized lipoproteins to induce macrophage cholesterol loading.However, reduced atherosclerosis in hypomSR-BI-KOliver mice wasassociated with decreased lesional macrophage content as compared withthat in SR-BI-/- mice. These data imply that, in addition to its majoratheroprotective role in liver, SR-BI may exert an antiatherogenic rolein extrahepatic tissues.

One-step growth of nanosheet-assembled BiOCl/BiOBr microspheres for highly efficient visible photocatalytic performance

Science.gov (United States)

Zhang, Jinfeng; Lv, Jiali; Dai, Kai; Liang, Changhao; Liu, Qi

2018-02-01

In this work, we have developed a simple synthetic approach of nanosheet-assembled BiOCl/BiOBr microspheres by an ethylene glycol (EG)-assisted hydrothermal method. The crystalline form, morphology, chemical composition, optical performance and surface area of BiOCl/BiOBr microspheres were identified using X-ray diffraction (XRD), transmission electron microscopy (TEM), high resolution TEM (HRTEM), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy spectra (EDX), UV-vis diffuse reflectance spectroscopy (DRS) analysis, high resolution X-ray photoelectron spectra (XPS) and N2 adsorption-desorption isotherms. BiOCl/BiOBr microspheres were nanosheet-assembled particles, which possessed visible light absorption under LED light irridation. Additionally, the methylene blue (MB) photodegradation performance of different BiOCl/BiOBr microspheres irradiated under 410 nm LED light arrays were investigated, the results exhibited that as-prepared BiOCl/BiOBr products showed higher catalytic effiency than pure BiOCl or BiOBr. By optimizing the composition ration of the BiOCl and BiOBr, up to 93% degradation rate can be obtained in the 40%BiOCl/BiOBr microspheres. Finally, the photocatalytic mechanism of BiOCl/BiOBr microspheres had been proposed.

A Fuzzy Max–Min Decision Bi-Level Fuzzy Programming Model for Water Resources Optimization Allocation under Uncertainty

Directory of Open Access Journals (Sweden)

Chongfeng Ren

2018-04-01

Full Text Available Water competing conflict among water competing sectors from different levels should be taken under consideration during the optimization allocation of water resources. Furthermore, uncertainties are inevitable in the optimization allocation of water resources. In order to deal with the above problems, this study developed a fuzzy max–min decision bi-level fuzzy programming model. The developed model was then applied to a case study in Wuwei, Gansu Province, China. In this study, the net benefit and yield were regarded as the upper-level and lower-level objectives, respectively. Optimal water resource plans were obtained under different possibility levels of fuzzy parameters, which could deal with water competing conflict between the upper level and the lower level effectively. The obtained results are expected to make great contribution in helping local decision-makers to make decisions on dealing with the water competing conflict between the upper and lower level and the optimal use of water resources under uncertainty.

Selection of bi-level image compression method for reduction of communication energy in wireless visual sensor networks

Science.gov (United States)

Khursheed, Khursheed; Imran, Muhammad; Ahmad, Naeem; O'Nils, Mattias

2012-06-01

Wireless Visual Sensor Network (WVSN) is an emerging field which combines image sensor, on board computation unit, communication component and energy source. Compared to the traditional wireless sensor network, which operates on one dimensional data, such as temperature, pressure values etc., WVSN operates on two dimensional data (images) which requires higher processing power and communication bandwidth. Normally, WVSNs are deployed in areas where installation of wired solutions is not feasible. The energy budget in these networks is limited to the batteries, because of the wireless nature of the application. Due to the limited availability of energy, the processing at Visual Sensor Nodes (VSN) and communication from VSN to server should consume as low energy as possible. Transmission of raw images wirelessly consumes a lot of energy and requires higher communication bandwidth. Data compression methods reduce data efficiently and hence will be effective in reducing communication cost in WVSN. In this paper, we have compared the compression efficiency and complexity of six well known bi-level image compression methods. The focus is to determine the compression algorithms which can efficiently compress bi-level images and their computational complexity is suitable for computational platform used in WVSNs. These results can be used as a road map for selection of compression methods for different sets of constraints in WVSN.

DNA barcode goes two-dimensions: DNA QR code web server.

Science.gov (United States)

Liu, Chang; Shi, Linchun; Xu, Xiaolan; Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

2012-01-01

The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

DNA barcode goes two-dimensions: DNA QR code web server.

Directory of Open Access Journals (Sweden)

Chang Liu

Full Text Available The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

Seven fundamental, unsolved questions in molecular biology. Cooperative storage and bi-directional transfer of biological information by nucleic acids and proteins: an alternative to "central dogma".

Science.gov (United States)

Biro, J C

2004-01-01

The Human Genome Mapping Project provided us a large amount of sequence data. However our understanding of these data did not grow proportionally, because old dogmas still set the limits of our thinking. The gene-centric, reductionistical side of molecular biology is reviewed and seven problems are formulated, each indicating the insufficiency of the "central dogma". The following is concluded and suggested: 1. Genes are located and expressed on both DNA strands; 2. Introns are the source of important biological regulation and diversity; 3. Repeats are the frame of the chromatin structure and participate in the chromatin regulation; 4. The molecular accessibility of the canonical dsDNA structure is poor; 5. The genetic code is co-evolved with the amino acids and there is a stereochemical matching between the codes andamino acids; 6. The flow of information between nucleic acids and proteins is bi-directional and reverse translation might exist; 7. Complex genetic information is always carried and stored by nucleic acids and proteins together.

Improving performance of DS-CDMA systems using chaotic complex Bernoulli spreading codes

Science.gov (United States)

Farzan Sabahi, Mohammad; Dehghanfard, Ali

2014-12-01

The most important goal of spreading spectrum communication system is to protect communication signals against interference and exploitation of information by unintended listeners. In fact, low probability of detection and low probability of intercept are two important parameters to increase the performance of the system. In Direct Sequence Code Division Multiple Access (DS-CDMA) systems, these properties are achieved by multiplying the data information in spreading sequences. Chaotic sequences, with their particular properties, have numerous applications in constructing spreading codes. Using one-dimensional Bernoulli chaotic sequence as spreading code is proposed in literature previously. The main feature of this sequence is its negative auto-correlation at lag of 1, which with proper design, leads to increase in efficiency of the communication system based on these codes. On the other hand, employing the complex chaotic sequences as spreading sequence also has been discussed in several papers. In this paper, use of two-dimensional Bernoulli chaotic sequences is proposed as spreading codes. The performance of a multi-user synchronous and asynchronous DS-CDMA system will be evaluated by applying these sequences under Additive White Gaussian Noise (AWGN) and fading channel. Simulation results indicate improvement of the performance in comparison with conventional spreading codes like Gold codes as well as similar complex chaotic spreading sequences. Similar to one-dimensional Bernoulli chaotic sequences, the proposed sequences also have negative auto-correlation. Besides, construction of complex sequences with lower average cross-correlation is possible with the proposed method.

QR codes: next level of social media.

Science.gov (United States)

Gottesman, Wesley; Baum, Neil

2013-01-01

The OR code, which is short for quick response code, system was invented in Japan for the auto industry. Its purpose was to track vehicles during manufacture; it was designed to allow high-speed component scanning. Now the scanning can be easily accomplished via cell phone, making the technology useful and within reach of your patients. There are numerous applications for OR codes in the contemporary medical practice. This article describes QR codes and how they might be applied for marketing and practice management.

A bi-level integrated generation-transmission planning model incorporating the impacts of demand response by operation simulation

International Nuclear Information System (INIS)

Zhang, Ning; Hu, Zhaoguang; Springer, Cecilia; Li, Yanning; Shen, Bo

2016-01-01

Highlights: • We put forward a novel bi-level integrated power system planning model. • Generation expansion planning and transmission expansion planning are combined. • The effects of two sorts of demand response in reducing peak load are considered. • Operation simulation is conducted to reflect the actual effects of demand response. • The interactions between the two levels can guarantee a reasonably optimal result. - Abstract: If all the resources in power supply side, transmission part, and power demand side are considered together, the optimal expansion scheme from the perspective of the whole system can be achieved. In this paper, generation expansion planning and transmission expansion planning are combined into one model. Moreover, the effects of demand response in reducing peak load are taken into account in the planning model, which can cut back the generation expansion capacity and transmission expansion capacity. Existing approaches to considering demand response for planning tend to overestimate the impacts of demand response on peak load reduction. These approaches usually focus on power reduction at the moment of peak load without considering the situations in which load demand at another moment may unexpectedly become the new peak load due to demand response. These situations are analyzed in this paper. Accordingly, a novel approach to incorporating demand response in a planning model is proposed. A modified unit commitment model with demand response is utilized. The planning model is thereby a bi-level model with interactions between generation-transmission expansion planning and operation simulation to reflect the actual effects of demand response and find the reasonably optimal planning result.

Performance Tuning of x86 OpenMP Codes with MAQAO

Science.gov (United States)

Barthou, Denis; Charif Rubial, Andres; Jalby, William; Koliai, Souad; Valensi, Cédric

Failing to find the best optimization sequence for a given application code can lead to compiler generated codes with poor performances or inappropriate code. It is necessary to analyze performances from the assembly generated code to improve over the compilation process. This paper presents a tool for the performance analysis of multithreaded codes (OpenMP programs support at the moment). MAQAO relies on static performance evaluation to identify compiler optimizations and assess performance of loops. It exploits static binary rewriting for reading and instrumenting object files or executables. Static binary instrumentation allows the insertion of probes at instruction level. Memory accesses can be captured to help tune the code, but such traces require to be compressed. MAQAO can analyze the results and provide hints for tuning the code. We show on some examples how this can help users improve their OpenMP applications.

Valence band structure of InAs(1-x)Bi(x) and InSb(1-x)Bi(x) alloy semiconductors calculated using valence band anticrossing model.

Science.gov (United States)

Samajdar, D P; Dhar, S

2014-01-01

The valence band anticrossing model has been used to calculate the heavy/light hole and spin-orbit split-off energies in InAs(1-x)Bi(x) and InSb(1-x)Bi(x) alloy systems. It is found that both the heavy/light hole, and spin-orbit split E + levels move upwards in energy with an increase in Bi content in the alloy, whereas the split E - energy for the holes shows a reverse trend. The model is also used to calculate the reduction of band gap energy with an increase in Bi mole fraction. The calculated values of band gap variation agree well with the available experimental data.

Impact of the Level of State Tax Code Progressivity on Children's Health Outcomes

Science.gov (United States)

Granruth, Laura Brierton; Shields, Joseph J.

2011-01-01

This research study examines the impact of the level of state tax code progressivity on selected children's health outcomes. Specifically, it examines the degree to which a state's tax code ranking along the progressive-regressive continuum relates to percentage of low birthweight babies, infant and child mortality rates, and percentage of…

Kangaroo – A pattern-matching program for biological sequences

Directory of Open Access Journals (Sweden)

Betel Doron

2002-07-01

Full Text Available Abstract Background Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/. Conclusion A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats.

Capsid coding sequences of foot-and-mouth disease viruses are determinants of pathogenicity in pigs.

Science.gov (United States)

Lohse, Louise; Jackson, Terry; Bøtner, Anette; Belsham, Graham J

2012-05-24

The surface exposed capsid proteins, VP1, VP2 and VP3, of foot-and-mouth disease virus (FMDV) determine its antigenicity and the ability of the virus to interact with host-cell receptors. Hence, modification of these structural proteins may alter the properties of the virus.In the present study we compared the pathogenicity of different FMDVs in young pigs. In total 32 pigs, 7-weeks-old, were exposed to virus, either by direct inoculation or through contact with inoculated pigs, using cell culture adapted (O1K B64), chimeric (O1K/A-TUR and O1K/O-UKG) or field strain (O-UKG/34/2001) viruses. The O1K B64 virus and the two chimeric viruses are identical to each other except for the capsid coding region.Animals exposed to O1K B64 did not exhibit signs of disease, while pigs exposed to each of the other viruses showed typical clinical signs of foot-and-mouth disease (FMD). All pigs infected with the O1K/O-UKG chimera or the field strain (O-UKG/34/2001) developed fulminant disease. Furthermore, 3 of 4 in-contact pigs exposed to the O1K/O-UKG virus died in the acute phase of infection, likely from myocardial infection. However, in the group exposed to the O1K/A-TUR chimeric virus, only 1 pig showed symptoms of disease within the time frame of the experiment (10 days). All pigs that developed clinical disease showed a high level of viral RNA in serum and infected pigs that survived the acute phase of infection developed a serotype specific antibody response. It is concluded that the capsid coding sequences are determinants of FMDV pathogenicity in pigs.

Development of MnBi permanent magnet: Neutron diffraction of MnBi powder

Energy Technology Data Exchange (ETDEWEB)

Cui, J., E-mail: jun.cui@pnnl.gov; Choi, J. P.; Li, G.; Polikarpov, E.; Darsell, J. [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354 (United States); Kramer, M. J.; Zarkevich, N. A.; Wang, L. L.; Johnson, D. D. [Materials Sciences and Engineering Division, Ames Laboratory, Ames, Iowa 50011 (United States); Marinescu, M. [Electron Energy Corporation, Landisville, Pennsylvania 17538 (United States); Huang, Q. Z.; Wu, H. [NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102 (United States); Vuong, N. V.; Liu, J. P. [Department of Physics, University of Texas at Arlington, Arlington, Texas 76019 (United States)

2014-05-07

MnBi attracts great attention in recent years for its great potential as permanent magnet materials. MnBi phase is difficult to obtain because of the rather drastic peritectic reaction between Mn and Bi. In this paper, we report our effort on synthesizing high purity MnBi compound using conventional powder metallurgical approaches. Neutron diffraction was carried out to investigate the crystal and nuclear structure of the obtained powder. The result shows that the purity of the obtained powder is about 91 wt. % at 300 K, and the magnetic moment of the Mn atom in MnBi lattice is 4.424 and 4.013 μ{sub B} at 50 K and 300 K, respectively.

Development of MnBi permanent magnet: Neutron diffraction of MnBi powder

Energy Technology Data Exchange (ETDEWEB)

Cui, J; Choi, JP; Li, G; Polikarpov, E; Darsell, J; Kramer, MJ; Zarkevich, NA; Wang, LL; Johnson, DD; Marinescu, M; Huang, QZ; Wu, H; Vuong, NV; Liu, JP

2014-05-07

MnBi attracts great attention in recent years for its great potential as permanent magnet materials. MnBi phase is difficult to obtain because of the rather drastic peritectic reaction between Mn and Bi. In this paper, we report our effort on synthesizing high purity MnBi compound using conventional powder metallurgical approaches. Neutron diffraction was carried out to investigate the crystal and nuclear structure of the obtained powder. The result shows that the purity of the obtained powder is about 91 wt. % at 300 K, and the magnetic moment of the Mn atom in MnBi lattice is 4.424 and 4.013 mu(B) at 50 K and 300 K, respectively. (C) 2014 AIP Publishing LLC.

Effect of annealing on the structural and optical properties of (3 1 1)B GaAsBi layers

Energy Technology Data Exchange (ETDEWEB)

Rodrigo, J.F., E-mail: juanfrancisco.rodrigo@uca.es [Departamento de Ciencia de los Materiales e I. M. y Q. I., Facultad de Ciencias, Universidad de Cadiz, 11510 Puerto Real, Cadiz (Spain); Sales, D.L. [Departamento de Ciencia de los Materiales e I. M. y Q. I., Facultad de Ciencias, Universidad de Cadiz, 11510 Puerto Real, Cadiz (Spain); Shafi, M. [School of Physics and Astronomy, University of Nottingham, NG7 2RD Nottingham (United Kingdom); Henini, M. [School of Physics and Astronomy, University of Nottingham, NG7 2RD Nottingham (United Kingdom); Nottingham Nanotechnology and Nanoscience Centre, University of Nottingham, NG7 2RD Nottingham (United Kingdom); Turyanska, L.; Novikov, S. [School of Physics and Astronomy, University of Nottingham, NG7 2RD Nottingham (United Kingdom); Molina, S.I. [Departamento de Ciencia de los Materiales e I. M. y Q. I., Facultad de Ciencias, Universidad de Cadiz, 11510 Puerto Real, Cadiz (Spain)

2010-07-01

The influence of post-growth annealing on the microstructure and photoluminescence (PL) of GaAsBi alloys grown on (3 1 1)B GaAs is analyzed. Conventional transmission electron microscopy (TEM) performed on as-grown samples evidence the presence of structural defects and a mosaic structure in the GaAsBi layer. A sequence of stacking faults at regions close to the GaAs/GaAsBi interface are observed in high resolution TEM images. After annealing at 473 K during 3 h the mosaic structure disappears, the presence of defects is reduced and the PL peak intensely enhances.

Effect of annealing on the structural and optical properties of (3 1 1)B GaAsBi layers

International Nuclear Information System (INIS)

Rodrigo, J.F.; Sales, D.L.; Shafi, M.; Henini, M.; Turyanska, L.; Novikov, S.; Molina, S.I.

2010-01-01

The influence of post-growth annealing on the microstructure and photoluminescence (PL) of GaAsBi alloys grown on (3 1 1)B GaAs is analyzed. Conventional transmission electron microscopy (TEM) performed on as-grown samples evidence the presence of structural defects and a mosaic structure in the GaAsBi layer. A sequence of stacking faults at regions close to the GaAs/GaAsBi interface are observed in high resolution TEM images. After annealing at 473 K during 3 h the mosaic structure disappears, the presence of defects is reduced and the PL peak intensely enhances.

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

Directory of Open Access Journals (Sweden)

Cronn Richard

2009-12-01

Full Text Available Abstract Background Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels? Results We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with ≥ 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (ycf1, ycf2, highlighting their unusual evolutionary properties. Conclusion Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling

Global EiBI-monopole

Directory of Open Access Journals (Sweden)

JIN Xinghua

2014-04-01

Full Text Available A global EiBI-monopole problem is studied under EiBI gravitational theory.The equations of global EiBI-monopole are derived in the curved spacetime and the relation between the spacetime metric and auxiliary metric is found.In the case of a very small parameter,an asymptotic form of equations is given.The series solutions of global EiBI-monopole at infinity are found.

Sensitivity analysis and benchmarking of the BLT low-level waste source term code

International Nuclear Information System (INIS)

Suen, C.J.; Sullivan, T.M.

1993-07-01

To evaluate the source term for low-level waste disposal, a comprehensive model had been developed and incorporated into a computer code, called BLT (Breach-Leach-Transport) Since the release of the original version, many new features and improvements had also been added to the Leach model of the code. This report consists of two different studies based on the new version of the BLT code: (1) a series of verification/sensitivity tests; and (2) benchmarking of the BLT code using field data. Based on the results of the verification/sensitivity tests, the authors concluded that the new version represents a significant improvement and it is capable of providing more realistic simulations of the leaching process. Benchmarking work was carried out to provide a reasonable level of confidence in the model predictions. In this study, the experimentally measured release curves for nitrate, technetium-99 and tritium from the saltstone lysimeters operated by Savannah River Laboratory were used. The model results are observed to be in general agreement with the experimental data, within the acceptable limits of uncertainty

A multi-level code for metallurgical effects in metal-forming processes

Energy Technology Data Exchange (ETDEWEB)

Taylor, P.A.; Silling, S.A. [Sandia National Labs., Albuquerque, NM (United States). Computational Physics and Mechanics Dept.; Hughes, D.A.; Bammann, D.J.; Chiesa, M.L. [Sandia National Labs., Livermore, CA (United States)

1997-08-01

The authors present the final report on a Laboratory-Directed Research and Development (LDRD) project, A Multi-level Code for Metallurgical Effects in metal-Forming Processes, performed during the fiscal years 1995 and 1996. The project focused on the development of new modeling capabilities for simulating forging and extrusion processes that typically display phenomenology occurring on two different length scales. In support of model fitting and code validation, ring compression and extrusion experiments were performed on 304L stainless steel, a material of interest in DOE nuclear weapons applications.

TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.

Science.gov (United States)

Fortin, Connor H; Schulze, Katharina V; Babbitt, Gregory A

2015-01-01

It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence logos plots are severely limited in that they convey no explicit information regarding the structural dynamics of DNA backbone, a feature often critical to binding specificity. We present TRX-LOGOS, an R software package and Perl wrapper code that interfaces the JASPAR database for computational regulatory genomics. TRX-LOGOS extends the traditional sequence logo plot to include Shannon information content calculated with regard to the dinucleotide-based BI-BII conformation shifts in phosphate linkages on the DNA backbone, thereby adding a visual measure of intrinsic DNA flexibility that can be critical for many DNA-protein interactions. TRX-LOGOS is available as an R graphics module offered at both SourceForge and as a download supplement at this journal. To demonstrate the general utility of TRX logo plots, we first calculated the information content for 416 Saccharomyces cerevisiae transcription factor binding sites functionally confirmed in the Yeastract database and matched to previously published yeast genomic alignments. We discovered that flanking regions contain significantly elevated information content at phosphate linkages than can be observed at nucleobases. We also examined broader transcription factor classifications defined by the JASPAR database, and discovered that many general signatures of transcription factor binding are locally more information rich at the level of DNA backbone dynamics than nucleobase sequence. We used TRX-logos in combination with MEGA 6.0 software

Conservation patterns in different functional sequence categoriesof divergent Drosophila species

Energy Technology Data Exchange (ETDEWEB)

Papatsenko, Dmitri; Kislyuk, Andrey; Levine, Michael; Dubchak, Inna

2005-10-01

We have explored the distributions of fully conservedungapped blocks in genome-wide pairwise alignments of recently completedspecies of Drosophila: D.yakuba, D.ananassae, D.pseudoobscura, D.virilisand D.mojavensis. Based on these distributions we have found that nearlyevery functional sequence category possesses its own distinctiveconservation pattern, sometimes independent of the overall sequenceconservation level. In the coding and regulatory regions, the ungappedblocks were longer than in introns, UTRs and non-functional sequences. Atthe same time, the blocks in the coding regions carried 3N+2 signaturecharacteristic to synonymic substitutions in the 3rd codon positions.Larger block sizes in transcription regulatory regions can be explainedby the presence of conserved arrays of binding sites for transcriptionfactors. We also have shown that the longest ungapped blocks, or'ultraconserved' sequences, are associated with specific gene groups,including those encoding ion channels and components of the cytoskeleton.We discussed how restrained conservation patterns may help in mappingfunctional sequence categories and improving genomeannotation.

An export coefficient based inexact fuzzy bi-level multi-objective programming model for the management of agricultural nonpoint source pollution under uncertainty

Science.gov (United States)

Cai, Yanpeng; Rong, Qiangqiang; Yang, Zhifeng; Yue, Wencong; Tan, Qian

2018-02-01

In this research, an export coefficient based inexact fuzzy bi-level multi-objective programming (EC-IFBLMOP) model was developed through integrating export coefficient model (ECM), interval parameter programming (IPP) and fuzzy parameter programming (FPP) within a bi-level multi-objective programming framework. The proposed EC-IFBLMOP model can effectively deal with the multiple uncertainties expressed as discrete intervals and fuzzy membership functions. Also, the complexities in agricultural systems, such as the cooperation and gaming relationship between the decision makers at different levels, can be fully considered in the model. The developed model was then applied to identify the optimal land use patterns and BMP implementing levels for agricultural nonpoint source (NPS) pollution management in a subcatchment in the upper stream watershed of the Miyun Reservoir in north China. The results of the model showed that the desired optimal land use patterns and implementing levels of best management of practices (BMPs) would be obtained. It is the gaming result between the upper- and lower-level decision makers, when the allowable discharge amounts of NPS pollutants were limited. Moreover, results corresponding to different decision scenarios could provide a set of decision alternatives for the upper- and lower-level decision makers to identify the most appropriate management strategy. The model has a good applicability and can be effectively utilized for agricultural NPS pollution management.

Interface requirements to couple thermal hydraulics codes to severe accident codes: ICARE/CATHARE

Energy Technology Data Exchange (ETDEWEB)

Camous, F.; Jacq, F.; Chatelard, P. [IPSN/DRS/SEMAR CE-Cadarache, St Paul Lez Durance (France)] [and others

1997-07-01

In order to describe with the same code the whole sequence of severe LWR accidents, up to the vessel failure, the Institute of Protection and Nuclear Safety has performed a coupling of the severe accident code ICARE2 to the thermalhydraulics code CATHARE2. The resulting code, ICARE/CATHARE, is designed to be as pertinent as possible in all the phases of the accident. This paper is mainly devoted to the description of the ICARE2-CATHARE2 coupling.

Adaptive decoding of convolutional codes

Science.gov (United States)

Hueske, K.; Geldmacher, J.; Götze, J.

2007-06-01

Convolutional codes, which are frequently used as error correction codes in digital transmission systems, are generally decoded using the Viterbi Decoder. On the one hand the Viterbi Decoder is an optimum maximum likelihood decoder, i.e. the most probable transmitted code sequence is obtained. On the other hand the mathematical complexity of the algorithm only depends on the used code, not on the number of transmission errors. To reduce the complexity of the decoding process for good transmission conditions, an alternative syndrome based decoder is presented. The reduction of complexity is realized by two different approaches, the syndrome zero sequence deactivation and the path metric equalization. The two approaches enable an easy adaptation of the decoding complexity for different transmission conditions, which results in a trade-off between decoding complexity and error correction performance.

Synthesis, crystal structure, and physical properties of the Gd{sub 3}BiO{sub 3} and Gd{sub 8}Bi{sub 3}O{sub 8} phases

Energy Technology Data Exchange (ETDEWEB)

Forbes, Scott; Yuan, Fang [Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1 (Canada); Kosuda, Kosuke; Kolodiazhnyi, Taras [Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044 (Japan); Mozharivskyj, Yurij, E-mail: mozhar@mcmaster.ca [Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1 (Canada)

2016-01-15

The second and third known rare-earth bismuthide oxides, Gd{sub 3}BiO{sub 3} and Gd{sub 8}Bi{sub 3}O{sub 8}, have been discovered via high temperature reactions at 1300 °C. Like its Gd–Sb–O counterparts, the Gd{sub 3}BiO{sub 3} and Gd{sub 8}Bi{sub 3}O{sub 8} phases crystallize in the monoclinic C2/m space group, with the latter containing disordered Bi atoms along the b direction of the unit cell. Unlike the RE{sub 8}Sb{sub 3}O{sub 8} series, the formation of the Gd{sub 3}BiO{sub 3} phase does not necessarily precede the formation of Gd{sub 8}Bi{sub 3}O{sub 8}, which is likely due to the difficulty of accommodating bismuth in the RE–O framework due to its larger size. Physical property measurements performed on a pure Gd{sub 8}Bi{sub 3}O{sub 8} sample reveal semiconducting behavior. Although electronic structure calculations predict metallic behavior due to an unbalanced electron count, the semiconducting behavior originates from the Anderson localization of the Bi p states near the Fermi level as a result of atomic disorder. - Graphical abstract: Reaction of GdBi and Gd{sub 2}O{sub 3} at high temperatures yields Gd–Bi–O phases. - Highlights: • Gd{sub 3}BiO{sub 3} and Gd{sub 8}Bi{sub 3}O{sub 8}, the second and third rare-earth bismuthide oxides, have been discovered. • Gd{sub 3}BiO{sub 3} and Gd{sub 8}Bi{sub 3}O{sub 8} are isostructural with RE{sub 3}SbO{sub 3} and RE{sub 8}Sb{sub 3}O{sub 8}. • Gd{sub 8}Bi{sub 3}O{sub 8} displays semiconducting behavior despite an unbalanced electron count. • Anderson localization of Bi p states results in semiconducting behavior in Gd{sub 8}Bi{sub 3}O{sub 8}.

The Calculation of Flooding Level using CFX Code

International Nuclear Information System (INIS)

Oh, Seo Bin; Kim, Keon Yeop; Lee, Hyung Ho

2015-01-01

The plant design should consider internal flooding by postulated pipe ruptures, component failures, actuation of spray systems, and improper system alignment. The flooding causes failure of safety-related equipment and affects the integrity of the structure. The safety-related equipment should be installed above the flood level for protection against flooding effects. Conservative estimates of the flood level are important when a DBA occurs. The flooding level can be calculated simply applying Bernoulli's equation. However, in this study, a realistic calculation is performed with ANSYS CFX code. In calculation with CFX, air-core vortex phenomena, and turbulent flow can be simulated, which cannot be calculated analytically. The flooding level is evaluated by analytical calculation and CFX analysis for an assumed condition. The flood level is calculated as 0.71m and 1.1m analytically and with CFX simulation, respectively. Comparing the analytical calculation and simulation, they are similar, but the analytical calculation is not conservative. There are many factors reducing the drainage capacity such as air-core vortex, intake of air, and turbulent flow. Therefore, in case of flood level evaluation by analytical calculation, a sufficient safety margin should be considered

Syndrome-source-coding and its universal generalization. [error correcting codes for data compression

Science.gov (United States)

Ancheta, T. C., Jr.

1976-01-01

A method of using error-correcting codes to obtain data compression, called syndrome-source-coding, is described in which the source sequence is treated as an error pattern whose syndrome forms the compressed data. It is shown that syndrome-source-coding can achieve arbitrarily small distortion with the number of compressed digits per source digit arbitrarily close to the entropy of a binary memoryless source. A 'universal' generalization of syndrome-source-coding is formulated which provides robustly effective distortionless coding of source ensembles. Two examples are given, comparing the performance of noiseless universal syndrome-source-coding to (1) run-length coding and (2) Lynch-Davisson-Schalkwijk-Cover universal coding for an ensemble of binary memoryless sources.

Application of Quaternion in improving the quality of global sequence alignment scores for an ambiguous sequence target in Streptococcus pneumoniae DNA

Science.gov (United States)

Lestari, D.; Bustamam, A.; Novianti, T.; Ardaneswari, G.

2017-07-01

DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (PA, PT, PG, PC), where PA, PT, PG, PC are the probability of A, T, G, C bases that could appear in Q and PA + PT + PG + PC = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

Study on a new meteorological sampling scheme developed for the OSCAAR code system

International Nuclear Information System (INIS)

Liu Xinhe; Tomita, Kenichi; Homma, Toshimitsu

2002-03-01

One important step in Level-3 Probabilistic Safety Assessment is meteorological sequence sampling, on which the previous studies were mainly related to code systems using the straight-line plume model and more efforts are needed for those using the trajectory puff model such as the OSCAAR code system. This report describes the development of a new meteorological sampling scheme for the OSCAAR code system that explicitly considers population distribution. A group of principles set for the development of this new sampling scheme includes completeness, appropriate stratification, optimum allocation, practicability and so on. In this report, discussions are made about the procedures of the new sampling scheme and its application. The calculation results illustrate that although it is quite difficult to optimize stratification of meteorological sequences based on a few environmental parameters the new scheme do gather the most inverse conditions in a single subset of meteorological sequences. The size of this subset may be as small as a few dozens, so that the tail of a complementary cumulative distribution function is possible to remain relatively static in different trials of the probabilistic consequence assessment code. (author)

Motion Vector Sharing and Bitrate Allocation for 3D Video-Plus-Depth Coding

Directory of Open Access Journals (Sweden)

Béatrice Pesquet-Popescu

2008-08-01

Full Text Available The video-plus-depth data representation uses a regular texture video enriched with the so-called depth map, providing the depth distance for each pixel. The compression efficiency is usually higher for smooth, gray level data representing the depth map than for classical video texture. However, improvements of the coding efficiency are still possible, taking into account the fact that the video and the depth map sequences are strongly correlated. Classically, the correlation between the texture motion vectors and the depth map motion vectors is not exploited in the coding process. The aim of this paper is to reduce the amount of information for describing the motion of the texture video and of the depth map sequences by sharing one common motion vector field. Furthermore, in the literature, the bitrate control scheme generally fixes for the depth map sequence a percentage of 20% of the texture stream bitrate. However, this fixed percentage can affect the depth coding efficiency, and it should also depend on the content of each sequence. We propose a new bitrate allocation strategy between the texture and its associated per-pixel depth information. We provide comparative analysis to measure the quality of the resulting 3D+t sequences.

Bi∼3.785Cd∼3.575Cu∼1.5(PO4)3.5O5.5, a new arrangement of double (n=2) and triple (n=3) [M4Bi2n-2O2n]x+ polycationic ribbons in the bismuth-transition metal oxy-phosphate series

International Nuclear Information System (INIS)

Colmont, Marie; Huve, Marielle; Abraham, Francis; Mentre, Olivier

2004-01-01

This work is dedicated to investigation of new disordered bismuth-containing oxy-phosphates compounds with an original structure type. As previously observed in this series, they are formed of [M 4 Bi 2n-2 O 2n ] x+ polycationic ribbons of width n O(Bi,M) 4 tetrahedra, surrounded by PO 4 groups. In the new crystal structure type, double (=D), triple (=T) and tunnels (=t) alternate along a common axis obeying the TtDtTtDt/TTtTTt sequence in respect to a nomenclature previously described and recalled in this work. The existence this new polymorph has first been detected by electron diffraction in a multi-phased sample. Then, the crystal structure type, i.e., the TtDtTtDt/TTtTTt sequence, has been deduced from HREM images help to a contrast-interpreting code available for these series of polycations-formed compounds. The subsequent compounds formulation leads to a number of new materials that verify the general formula: [Bi 2 (Bi,M) 4 O 4 ] 2 [Bi 4 (Bi,M) 4 O 6 ] 6 (PO 4 ) 28 M x , with x= 2+ , Cd 2+ cations. Single crystals of the nominal [O6Bi 4.57 Cd 3.43 ] 4 +8.57 [O 6 Bi 4 Cd 4 ] 2 +8 [O 4 Bi 2 Cd 3.56 Cu 0.44 ] 2 +6 (PO 4 ) 28 Cu 10.86 have been prepared in a further stage and confirms the predicted crystal structure, Bi ∼3.785 Cd ∼3.575 Cu ∼1.5 (PO 4 ) 3.5 O 5.5 , a=11.506(8)A, b=5.416(4)A, c=53.94 (4)A, β=90.10(1) o , RF=0.0835, RwF=0.0993, SG=A2/m, Z=8. As already observed for other elements of this family such as Bi ∼1.2 M ∼1.2 O 1.5 (PO 4 ), Bi ∼6.2 Cu ∼6.2 O 8 (PO 4 ) 5 or Bi ∼3 Cd ∼3.72 M ∼1.28 O 5 (PO 4 ) 3 (M=Cu, Co, Zn), this compound shows an additional example of PO 4 disorder due to the presence of mixed Bi 3+ /M 2+ sites at the edges of ribbons. The origin and consequence of this so-called disorder mostly occurring on PO 4 configurations is intensively discussed and has been characterized by infrared spectroscopy and by neutron diffraction on similar compounds. It is noticeable that the great number of antagonist PO 4

High photocatalytic performance of BiOI/Bi{sub 2}WO{sub 6} toward toluene and Reactive Brilliant Red

Energy Technology Data Exchange (ETDEWEB)

Li Huiquan [School of Chemistry and Chemical Engineering, Fuyang Normal College, Fuyang 236041 (China); Key Laboratory of Mesoscopic Chemistry of MOE, Jiangsu Provincial Key Laboratory of Nanotechnology, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093 (China); Cui Yumin, E-mail: cuiyumin0908@163.com [School of Chemistry and Chemical Engineering, Fuyang Normal College, Fuyang 236041 (China); Hong Wenshan [School of Chemistry and Chemical Engineering, Fuyang Normal College, Fuyang 236041 (China)

2013-01-01

Graphical abstract: When BiOI/Bi{sub 2}WO{sub 6} catalyst was exposed to UV or visible light, the electrons in the valence band of Bi{sub 2}WO{sub 6} would be excited into the conduction band and then injected into the more positive conduction band of BiOI. Therefore, the photoelectrons were generated from Bi{sub 2}WO{sub 6} and transferred across the interface between BiOI and Bi{sub 2}WO{sub 6} to the surface of BiOI, leaving the photogenerated holes in the valence band of Bi{sub 2}WO{sub 6}. In this way, the photoinduced electron-hole pairs were effectively separated. Highlights: Black-Right-Pointing-Pointer BiOI sensitized Bi{sub 2}WO{sub 6} catalysts were successfully prepared by a facile method. Black-Right-Pointing-Pointer The 13.2% BiOI/Bi{sub 2}WO{sub 6} catalyst exhibits higher photoactivities than P25. Black-Right-Pointing-Pointer A possible transfer process of photogenerated carriers was proposed. - Abstract: BiOI sensitized nano-Bi{sub 2}WO{sub 6} photocatalysts with different BiOI contents were successfully synthesized by a facile deposition method at room temperature, and characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) high-resolution transmission electron microscopy (HR-TEM), photoluminescence (PL) spectra, UV-vis diffuse reflection spectroscopy (UV-vis DRS) and Brunauer-Emmett-Teller (BET) surface area measurements. The photocatalytic activity of BiOI/Bi{sub 2}WO{sub 6} was evaluated by the photo-degradation of Reactive Brilliant Red (X-3B) in suspended solution and toluene in gas phase. It has been shown that the BiOI/Bi{sub 2}WO{sub 6} catalysts exhibit a coexistence of both tetragonal BiOI and orthorhombic Bi{sub 2}WO{sub 6} phases. With increasing BiOI content, the absorption intensity of BiOI/Bi{sub 2}WO{sub 6} catalysts increases in the 380-600 nm region and the absorption edge shifts significantly to longer wavelengths as compared to pure Bi{sub 2}WO{sub 6}. The 13.2% BiOI/Bi{sub 2}WO{sub 6} catalyst exhibits

Explaining the Behavioral Intention towards BI Implementation in Public Administrations - A Principal-Agent Theory Approach

Science.gov (United States)

Becker, Jörg; Bergener, Philipp; Lis, Łukasz; Niehaves, Björn

Business Intelligence (BI) is an established instrument to support public administrations in their management tasks by increasing their information level. BI is of special interest in the context of introducing accrual accounting in public administrations as this affects the information level of different stakeholders, leading to a possible decrease for municipal councils. The principal-agent theory can help to explain different behavioral intentions of the stakeholders concerning the introduction of BI. We employ a single qualitative case study to analyze these behavioral intentions. It shows that the introduction of accrual accounting did decrease the information level of the municipal council making the principal-agent problems possible. Furthermore, it shows that BI might be a solution for this problem. Therefore, council members show the behavioral intention to support the BI implementation while administration staff members rather resist it. Based on these finding, we discuss implications for practice and future research.

Mercure IV code application to the external dose computation from low and medium level wastes

International Nuclear Information System (INIS)

Tomassini, T.

1985-01-01

In the present work the external dose from low and medium level wastes is calculated using MERCURE IV code. The code utilizes MONTECARLO method for integrating multigroup line of sight attenuation Kernels

Ga-Bi-Te system

International Nuclear Information System (INIS)

Rustamov, P.G.; Seidova, N.A.; Shakhbazov, M.G.; AN Azerbajdzhanskoj SSR, Baku. Inst. Neorganicheskoj i Fizicheskoj Khimii)

1976-01-01

To elucidate the nature of interaction in the system Ga-Bi-Te, a study has been made of sections GaTe-Bi 2 Te 3 , Ga 2 Te 3 -Bi, GaTe-Bi and Bi 2 Te 3 -Ga. The alloys have been prepared by direct melting of the components or their alloys with subsequent homogenizin.o annealing at 400 deg C. The study has been made by the methods of differential thermal, microstructural analysis and by microhardness measurements. On the basis of literature data and data obtained a projection of the liquidus surface of the phase diagram for the system Ga-Bi-Te has been constructed. In the ternary system there are 17 curves of monovariant equilibrium dividing the liquidus into 10 fields of primary crystallization of phases, 9 points of non-variant equilibrium of which 4 points are triple eutectics and 5 points are triple peritectics

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics.

Science.gov (United States)

Timmermans, M J T N; Dodsworth, S; Culverwell, C L; Bocak, L; Ahrens, D; Littlewood, D T J; Pons, J; Vogler, A P

2010-11-01

Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags ('barcodes'). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three 'bait' sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species 'barcodes' that currently use the cox1 gene only.

Flexible manipulation of terahertz wave reflection using polarization insensitive coding metasurfaces.

Science.gov (United States)

Jiu-Sheng, Li; Ze-Jiang, Zhao; Jian-Quan, Yao

2017-11-27

In order to extend to 3-bit encoding, we propose notched-wheel structures as polarization insensitive coding metasurfaces to control terahertz wave reflection and suppress backward scattering. By using a coding sequence of "00110011…" along x-axis direction and 16 × 16 random coding sequence, we investigate the polarization insensitive properties of the coding metasurfaces. By designing the coding sequences of the basic coding elements, the terahertz wave reflection can be flexibly manipulated. Additionally, radar cross section (RCS) reduction in the backward direction is less than -10dB in a wide band. The present approach can offer application for novel terahertz manipulation devices.

Is a genome a codeword of an error-correcting code?

Directory of Open Access Journals (Sweden)

Luzinete C B Faria

Full Text Available Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction.

HYDROCOIN [HYDROlogic COde INtercomparison] Level 1: Benchmarking and verification test results with CFEST [Coupled Fluid, Energy, and Solute Transport] code: Draft report

International Nuclear Information System (INIS)

Yabusaki, S.; Cole, C.; Monti, A.M.; Gupta, S.K.

1987-04-01

Part of the safety analysis is evaluating groundwater flow through the repository and the host rock to the accessible environment by developing mathematical or analytical models and numerical computer codes describing the flow mechanisms. This need led to the establishment of an international project called HYDROCOIN (HYDROlogic COde INtercomparison) organized by the Swedish Nuclear Power Inspectorate, a forum for discussing techniques and strategies in subsurface hydrologic modeling. The major objective of the present effort, HYDROCOIN Level 1, is determining the numerical accuracy of the computer codes. The definition of each case includes the input parameters, the governing equations, the output specifications, and the format. The Coupled Fluid, Energy, and Solute Transport (CFEST) code was applied to solve cases 1, 2, 4, 5, and 7; the Finite Element Three-Dimensional Groundwater (FE3DGW) Flow Model was used to solve case 6. Case 3 has been ignored because unsaturated flow is not pertinent to SRP. This report presents the Level 1 results furnished by the project teams. The numerical accuracy of the codes is determined by (1) comparing the computational results with analytical solutions for cases that have analytical solutions (namely cases 1 and 4), and (2) intercomparing results from codes for cases which do not have analytical solutions (cases 2, 5, 6, and 7). Cases 1, 2, 6, and 7 relate to flow analyses, whereas cases 4 and 5 require nonlinear solutions. 7 refs., 71 figs., 9 tabs

A Bi-Level Particle Swarm Optimization Algorithm for Solving Unit Commitment Problems with Wind-EVs Coordinated Dispatch

Science.gov (United States)

Song, Lei; Zhang, Bo

2017-07-01

Nowadays, the grid faces much more challenges caused by wind power and the accessing of electric vehicles (EVs). Based on the potentiality of coordinated dispatch, a model of wind-EVs coordinated dispatch was developed. Then, A bi-level particle swarm optimization algorithm for solving the model was proposed in this paper. The application of this algorithm to 10-unit test system carried out that coordinated dispatch can benefit the power system from the following aspects: (1) Reducing operating costs; (2) Improving the utilization of wind power; (3) Stabilizing the peak-valley difference.

A bi-level intervention to improve oral hygiene of older and disabled adults in low-income housing: results of a pilot study.

Science.gov (United States)

Reisine, S; Schensul, J J; Goldblatt, R; Radda, K; Foster-Bey, C; Acosta-Glynn, C; Miron-Carcamo, L; Ioannidou, E

2016-06-01

This paper describes the results of a bi-level intervention, using a cognitive-behavioral theoretical approach, to improve the oral hygiene of older adults and the disabled in community-based low income senior housing. The bi-level pilot intervention consisted of an on-site tailored adapted motivational interviewing (AMI) session and two oral health fairs, supported by a resident campaign committee, to change community norms. All materials were available in English and Spanish. Participants completed a survey consisting of 12 domains that provided the basis for tailoring the AMI and shaping the campaigns. The domains were activities of daily living (ADLs), access to oral health information, oral hygiene status, dental knowledge, hygiene behaviors, importance of oral hygiene, self-efficacy/locus of control, diet, intentions, self-management worries/fears, perceived risk and dry mouth. Each participant received clinical assessments consisting of full-mouth plaque score (PS) and gingival index (GI) before the intervention and at three months. Twenty-seven residents with at least one tooth completed all phases of the study. The mean number of domains requiring attention was 4.5 (SD 1.6) with a range of one to seven. Mean baseline PS was 83% (SD 16%) which improved significantly to 58% (SD 31%); mean baseline GI was 1.15 (SD 0.61) and improved significantly to 0.49 (SD 0.46). This pilot study supports the feasibility and acceptability of a tailored oral hygiene intervention among older and disabled adults living in low income senior housing. Although a small sample, the study demonstrated significant improvements in both plaque and gingival scores three months after the bi-level intervention.

Pionic 4f→3d transition in 181Ta, natural Re, and 209Bi and the strong interaction level shift and the strong interaction level shift and width of the pionic 3d state

International Nuclear Information System (INIS)

Konijn, J.; Panman, J.K.; Koch, J.H.; Doesburg, W. van; Ewan, G.T.; Johansson, T.; Tibell, G.; Fransson, K.; Tauscher, L.

1979-01-01

Owing to a powerful Compton-suppression technique it was possible to observe for the first time the pionic 4f→3d X-ray transition in elements heavier than A=150. The strong interaction monopole shifts epsilon 0 and widths GAMMA 0 as well as the quadrupole splitting of the 3d levels have been measured in Ta, Re and Bi. Thus in addition to the strongly shifted and broadened 5g→4f transitions, a second, strongly affected line is available for these elements. For the pionic 4f levels, standard optical potentials fit the strong interaction shifts and broadenings quite well. The now observed, deeper-lying 3d states in Ta, Re and Bi have shifts and widths that differ by a factor of 2 or more from the standard optical potential predictions. From the observed relative X-ray intensities of the pionic cascade the strong interaction widths of the 5g and 4f levels are also extracted. (Auth.)

Codes and curves

CERN Document Server

Walker, Judy L

2000-01-01

When information is transmitted, errors are likely to occur. Coding theory examines efficient ways of packaging data so that these errors can be detected, or even corrected. The traditional tools of coding theory have come from combinatorics and group theory. Lately, however, coding theorists have added techniques from algebraic geometry to their toolboxes. In particular, by re-interpreting the Reed-Solomon codes, one can see how to define new codes based on divisors on algebraic curves. For instance, using modular curves over finite fields, Tsfasman, Vladut, and Zink showed that one can define a sequence of codes with asymptotically better parameters than any previously known codes. This monograph is based on a series of lectures the author gave as part of the IAS/PCMI program on arithmetic algebraic geometry. Here, the reader is introduced to the exciting field of algebraic geometric coding theory. Presenting the material in the same conversational tone of the lectures, the author covers linear codes, inclu...

Luminescence and excited state dynamics of Bi{sup 3+} centers in Y{sub 2}O{sub 3}

Energy Technology Data Exchange (ETDEWEB)

Babin, V. [Institute of Physics AS CR, Cukrovarnicka 10, 16200 Prague (Czech Republic); Chernenko, K., E-mail: nuclearphys@yandex.ru [Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu (Estonia); Peter the Great Saint-Petersburg Polytechnic University, Polytekhnicheskaya 29, 195251 St. Petersburg (Russian Federation); Lipińska, L. [Institute of Electronic Materials Technology, Wólczyńska 133, 01919 Warsaw (Poland); Mihokova, E.; Nikl, M. [Institute of Physics AS CR, Cukrovarnicka 10, 16200 Prague (Czech Republic); Schulman, L.S. [Physics Department, Clarkson University, Potsdam, NY 13699-5820 (United States); Shalapska, T. [Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu (Estonia); Suchocki, A. [Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw (Poland); Institute of Physics, University of Bydgoszcz, Weyssenhoffa 11, 85072 Bydgoszcz (Poland); Zazubovich, S. [Institute of Physics, University of Tartu, Ravila 14c, 50411 Tartu (Estonia); Zhydachevskii, Ya. [Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw (Poland); Lviv Polytechnic National University, Bandera 12, 79646 Lviv (Ukraine)

2015-11-15

Photoluminescence of Y{sub 2}O{sub 3}:Bi nanopowder synthesized by the modified sol–gel method is studied using time-resolved luminescence spectroscopy in the 4.2–300 K temperature range. Bi{sup 3+} ions are substituted for Y{sup 3+} ions in two different crystal lattice sites, one having S{sub 6} symmetry (Bi(S{sub 6})) and the other C{sub 2} symmetry (Bi(C{sub 2})). The luminescence characteristics of these two centers are found to have strongly different electron–phonon interactions. The luminescence of Bi(S{sub 6}) and Bi(C{sub 2}) centers peak at 3.04 eV and 2.41 eV, respectively, and arise from the radiative decay of the triplet relaxed excited state (RES) of Bi{sup 3+} ions. The model and structure of the RES, responsible for the luminescence of Bi(S{sub 6}) and Bi(C{sub 2}) centers in Y{sub 2}O{sub 3}:Bi, as well as radiative and nonradiative processes, taking place in the excited states of these centers, are investigated. The parameters of the triplet RES (the separation between the metastable and radiative levels and probabilities of radiative and nonradiative transitions from these levels) are determined. Low-temperature quenching of the triplet luminescence of these centers is explained by nonradiative quantum tunneling transitions from the metastable minima of their triplet RES to closely located defect- or exciton-related levels. - Highlights: • Photoluminescence of Bi{sup 3+} centers of two types in Y{sub 2}O{sub 3}:Bi is investigated. • Bi(S{sub 6}) and Bi(C{sub 2}) centers reveal strongly different electron–phonon interaction. • Radiative and nonradiative processes in their triplet excited states are clarified. • Low-temperature luminescence quenching in Bi(S{sub 6}) and Bi(C{sub 2}) centers is studied. • New fast weak ≈2.9 eV emission is suggested to arise from Bi(C{sub 2}) centers.

Electronic structures and stability of Ni/Bi2Te3 and Co/Bi2Te3 interfaces

International Nuclear Information System (INIS)

Xiong Ka; Wang Weichao; Alshareef, Husam N; Gupta, Rahul P; Gnade, Bruce E; Cho, Kyeongjae; White, John B

2010-01-01

We investigate the electronic structures and stability for Ni/Bi 2 Te 3 , NiTe/Bi 2 Te 3 , Co/Bi 2 Te 3 and CoTe 2 /Bi 2 Te 3 interfaces by first-principles calculations. It is found that the surface termination strongly affects the band alignment. Ni and Co are found to form Ohmic contacts to Bi 2 Te 3 . The interface formation energy for Co/Bi 2 Te 3 interfaces is much lower than that of Ni/Bi 2 Te 3 interfaces. Furthermore, we found that NiTe on Bi 2 Te 3 is more stable than Ni, while the formation energies for Co and CoTe 2 on Bi 2 Te 3 are comparable.

A note on {sup 207}Bi in environmental samples

Energy Technology Data Exchange (ETDEWEB)

Bossew, P. [European Commission, DG Joint Research Centre, Institute of Environment and Sustainability, Radioactivity Environmental Monitoring Group. Via Fermi 1, I-21020 Ispra, Vatican City State, Holy See (Italy)]. E-mail: peter.bossew@jrc.it; Lettner, H. [Institute of Physics and Biophysics, University of Salzburg, Hellbrunner Strasse 34, A-5020 Salzburg (Austria)]. E-mail: herbert.lettner@sbg.ac.at; Hubmer, A. [Institute of Physics and Biophysics, University of Salzburg, Hellbrunner Strasse 34, A-5020 Salzburg (Austria)

2006-07-01

Traces of the radionuclide {sup 207}Bi were identified in soil and cryoconite (glacier sediment) samples from Alpine regions of Austria. This nuclide has been produced in thermonuclear explosions mainly in the early 1960s and subsequently dispersed in the atmosphere. Activity concentrations up to 22 Bq/kg d.m. have been found. The ratio {sup 207}Bi:{sup 137}Cs(global fallout) equals (1.70 {+-} 0.12)10{sup -3}, which is in accordance with literature data. When low levels of {sup 207}Bi are assessed by gamma spectrometry, corrections must be made for a gamma line produced in the lead shield by neutron activation due to cosmic neutrons.

Adaptive decoding of convolutional codes

Directory of Open Access Journals (Sweden)

K. Hueske

2007-06-01

Full Text Available Convolutional codes, which are frequently used as error correction codes in digital transmission systems, are generally decoded using the Viterbi Decoder. On the one hand the Viterbi Decoder is an optimum maximum likelihood decoder, i.e. the most probable transmitted code sequence is obtained. On the other hand the mathematical complexity of the algorithm only depends on the used code, not on the number of transmission errors. To reduce the complexity of the decoding process for good transmission conditions, an alternative syndrome based decoder is presented. The reduction of complexity is realized by two different approaches, the syndrome zero sequence deactivation and the path metric equalization. The two approaches enable an easy adaptation of the decoding complexity for different transmission conditions, which results in a trade-off between decoding complexity and error correction performance.

The fuel and channel thermal/mechanical behaviour code FACTAR 2.0 (LOCA)

International Nuclear Information System (INIS)

Westbye, C.J.; Mackinnon, J.C.; Gu, B.W.

1996-01-01

The computer code FACTAR 2.0 (LOCA) models the thermal and mechanical response of components within a single CANDU fuel channel under loss-of-coolant accident conditions. This code version is the successor to the FACTAR 1.x code series, and features many modelling enhancements over its predecessor. In particular, the thermal hydraulic treatment has been extended to model reverse and bi-directional coolant flow, and the axial variation in coolant flow rate. Thermal radiation is calculated by a detailed surface-to-surface model, and the ability to represent a greater range of geometries (including experimental configurations employed in code validation) has been implemented. Details of these new code treatments are described in this paper. (author)

QR-codes as a tool to increase physical activity level among school children during class hours

DEFF Research Database (Denmark)

Christensen, Jeanette Reffstrup; Kristensen, Allan; Bredahl, Thomas Viskum Gjelstrup

the students physical activity level during class hours. Methods: A before-after study was used to examine 12 students physical activity level, measured with pedometers for six lessons. Three lessons of traditional teaching and three lessons, where QR-codes were used to make orienteering in school area...... as old fashioned. The students also felt positive about being physically active in teaching. Discussion and conclusion: QR-codes as a tool for teaching are usable for making students more physically active in teaching. The students were exited for using QR-codes and they experienced a good motivation......QR-codes as a tool to increase physical activity level among school children during class hours Introduction: Danish students are no longer fulfilling recommendations for everyday physical activity. Since August 2014, Danish students in public schools are therefore required to be physically active...

Two human cDNA molecules coding for the Duchenne muscular dystrophy (DMD) locus are highly homologous

Energy Technology Data Exchange (ETDEWEB)

Rosenthal, A.; Speer, A.; Billwitz, H. (Zentralinstitut fuer Molekularbiologie, Berlin-Buch (Germany Democratic Republic)); Cross, G.S.; Forrest, S.M.; Davies, K.E. (Univ. of Oxford (England))

1989-07-11

Recently the complete sequence of the human fetal cDNA coding for the Duchenne muscular dystrophy (DMD) locus was reported and a 3,685 amino acid long, rod-shaped cytoskeletal protein (dystrophin) was predicted as the protein product. Independently, the authors have isolated and sequenced different DMD cDNA molecules from human adult and fetal muscle. The complete 12.5 kb long sequence of all their cDNA clones has now been determined and they report here the nucleotide (nt) and amino acid (aa) differences between the sequences of both groups. The cDNA sequence comprises the whole coding region but lacks the first 110 nt from the 5{prime}-untranslated region and the last 1,417 nt of the 3{prime}-untranslated region. They have found 11 nt differences (approximately 99.9% homology) from which 7 occurred at the aa level.

O 1s core levels in Bi2Sr2CaCu2O8+δ single crystals

International Nuclear Information System (INIS)

Parmigiani, F.; Shen, Z.X.; Mitzi, D.B.; Lindau, I.; Spicer, W.E.; Kapitulnik, A.

1991-01-01

High-quality Bi 2 Sr 2 CaCu 2 O 8+δ superconducting single crystals, annealed at different oxygen partial pressures, have been studied using angular-resolved x-ray photoelectron spectroscopy with a resolution higher than that used in any previous study. Two states of the oxygen, separated by ∼0.7 eV, are unambiguously observed. Examining these components at different angles makes it possible to distinguish bulk from surface components. Using this capability we discover that annealing under lower oxygen partial pressure (1 atm) results in oxygen intercalation beneath the Bi-O surface layer of the crystal, whereas for higher-pressure anneals (12 atm) additional oxygen is found on the Bi-O surfaces. This steplike intercalation mechanism is also confirmed by the changes observed in the Cu and Bi core lines as a function of the annealing oxygen partial pressure

Studies of α-spectra in 221Fr, 217At, 213Bi and 213Po decays

International Nuclear Information System (INIS)

Chumin, V.G.; Fominykh, V.I.; Furyaev, T.A.; Gromov, K.Ya.; Jabber, J.K.; Kalyapkin, K.V.; Kudrya, S.A.; Tsupko-Sitnikov, V.V.

1997-01-01

The alpha-recoil phenomenon is used to gain data on the weak components of the α-spectra of the nuclides from the 225 Ac equilibrium chain. It is established that there is no experimental basis for introducing the 450 keV level of 213 Bi in the 217 At decay and the 868 keV level of 209 Tl in the 213 Bi decay. Excitation of the 759 keV level in the 217 At decay is confirmed. The intensities of the 221 Fr, 217 At and 213 Bi β - -decay are measured

BiCuSeO Thermoelectrics: An Update on Recent Progress and Perspective

Directory of Open Access Journals (Sweden)

Xiaoxuan Zhang

2017-02-01

Full Text Available A BiCuSeO system has been reported as a promising thermoelectric material and has attracted great attention in the thermoelectric community since 2010. Recently, several remarkable studies have been reported and the ZT of BiCuSeO was pushed to a higher level. It motivates us to systematically summarize the recent reports on the BiCuSeO system. In this short review, we start with several attempts to optimize thermoelectric properties of BiCuSeO. Then, we introduce several opinions to explore the origins of low thermal conductivity for BiCuSeO. Several approaches to enhance thermoelectric performance are also summarized, including modulation doping, introducing dual-vacancies, and dual-doping, etc. At last, we propose some possible strategies for enhancing thermoelectric performance of BiCuSeO in future research.

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses.

Science.gov (United States)

Chen, Chih-Yu; Shi, Wenqiang; Balaton, Bradley P; Matthews, Allison M; Li, Yifeng; Arenillas, David J; Mathelier, Anthony; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Brown, Carolyn J; Wasserman, Wyeth W

2016-11-18

Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted in silico analyses of the sexes using human datasets to gain perspectives into such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study suggests a role for YY1 in transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors.

Electronic structures and stability of Ni/Bi2Te3 and Co/Bi2Te3 interfaces

KAUST Repository

Xiong, Ka; Wang, Weichao; Alshareef, Husam N.; Gupta, Rahul P.; White, John B.; Gnade, Bruce E.; Cho, Kyeongjae

2010-01-01

We investigate the electronic structures and stability for Ni/Bi 2Te3, NiTe/Bi2Te3, Co/Bi 2Te3 and CoTe2/Bi2Te3 interfaces by first-principles calculations. It is found that the surface termination strongly affects the band alignment. Ni and Co are found to form Ohmic contacts to Bi2Te3. The interface formation energy for Co/Bi2Te3 interfaces is much lower than that of Ni/Bi2Te3 interfaces. Furthermore, we found that NiTe on Bi2Te3 is more stable than Ni, while the formation energies for Co and CoTe2 on Bi2Te3 are comparable. © 2010 IOP Publishing Ltd.

Electronic structures and stability of Ni/Bi2Te3 and Co/Bi2Te3 interfaces

KAUST Repository

Xiong, Ka

2010-03-04

We investigate the electronic structures and stability for Ni/Bi 2Te3, NiTe/Bi2Te3, Co/Bi 2Te3 and CoTe2/Bi2Te3 interfaces by first-principles calculations. It is found that the surface termination strongly affects the band alignment. Ni and Co are found to form Ohmic contacts to Bi2Te3. The interface formation energy for Co/Bi2Te3 interfaces is much lower than that of Ni/Bi2Te3 interfaces. Furthermore, we found that NiTe on Bi2Te3 is more stable than Ni, while the formation energies for Co and CoTe2 on Bi2Te3 are comparable. © 2010 IOP Publishing Ltd.

Bismuth-boron multiple bonding in BiB{sub 2}O{sup -} and Bi{sub 2}B{sup -}

Energy Technology Data Exchange (ETDEWEB)

Jian, Tian; Cheung, Ling Fung; Chen, Teng-Teng; Wang, Lai-Sheng [Department of Chemistry, Brown University, Providence, RI (United States)

2017-08-01

Despite its electron deficiency, boron is versatile in forming multiple bonds. Transition-metal-boron double bonding is known, but boron-metal triple bonds have been elusive. Two bismuth boron cluster anions, BiB{sub 2}O{sup -} and Bi{sub 2}B{sup -}, containing triple and double B-Bi bonds are presented. The BiB{sub 2}O{sup -} and Bi{sub 2}B{sup -} clusters are produced by laser vaporization of a mixed B/Bi target and characterized by photoelectron spectroscopy and ab initio calculations. Well-resolved photoelectron spectra are obtained and interpreted with the help of ab initio calculations, which show that both species are linear. Chemical bonding analyses reveal that Bi forms triple and double bonds with boron in BiB{sub 2}O{sup -} ([Bi≡B-B≡O]{sup -}) and Bi{sub 2}B{sup -} ([Bi=B=Bi]{sup -}), respectively. The Bi-B double and triple bond strengths are calculated to be 3.21 and 4.70 eV, respectively. This is the first experimental observation of Bi-B double and triple bonds, opening the door to design main-group metal-boron complexes with multiple bonding. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

Microstructure Of MnBi/Bi Eutectic Alloy

Science.gov (United States)

Wilcox, William R.; Eisa, G. F.; Baskaran, B.; Richardson, Donald C.

1988-01-01

Collection of three reports describes studies of directional solidification of MnBi/Bi eutectic alloy. Two of the reports, "Influence of Convection on Lamellar Spacing of Eutectics" and "Influence of Convection on Eutectic Microstructure," establish theoretical foundation for remaining document. Reports seek to quantify effect of convection on concentration field of growing lamellar eutectic. Remaining report, "Study of Eutectic Formation," begins by continuing theoretical developments. New technique under development by one of the authors helps to reveal three-dimensional microstructures of alloys.

Implicit learning of predictable sound sequences modulates human brain responses at different levels of the auditory hierarchy

Directory of Open Access Journals (Sweden)

Françoise eLecaignard

2015-09-01

Full Text Available Deviant stimuli, violating regularities in a sensory environment, elicit the Mismatch Negativity (MMN, largely described in the Event-Related Potential literature. While it is widely accepted that the MMN reflects more than basic change detection, a comprehensive description of mental processes modulating this response is still lacking. Within the framework of predictive coding, deviance processing is part of an inference process where prediction errors (the mismatch between incoming sensations and predictions established through experience are minimized. In this view, the MMN is a measure of prediction error, which yields specific expectations regarding its modulations by various experimental factors. In particular, it predicts that the MMN should decrease as the occurrence of a deviance becomes more predictable. We conducted a passive oddball EEG study and manipulated the predictability of sound sequences by means of different temporal structures. Importantly, our design allows comparing mismatch responses elicited by predictable and unpredictable violations of a simple repetition rule and therefore departs from previous studies that investigate violations of different time-scale regularities. We observed a decrease of the MMN with predictability and interestingly, a similar effect at earlier latencies, within 70 ms after deviance onset. Following these pre-attentive responses, a reduced P3a was measured in the case of predictable deviants. We conclude that early and late deviance responses reflect prediction errors, triggering belief updating within the auditory hierarchy. Beside, in this passive study, such perceptual inference appears to be modulated by higher-level implicit learning of sequence statistical structures. Our findings argue for a hierarchical model of auditory processing where predictive coding enables implicit extraction of environmental regularities.

Photocatalytic activity of Bi{sub 2}WO{sub 6}/Bi{sub 2}S{sub 3} heterojunctions: the facilitation of exposed facets of Bi{sub 2}WO{sub 6} substrate

Energy Technology Data Exchange (ETDEWEB)

Yan, Long [School of Chemistry and Chemical Engineering, Yulin University, Shaanxi Key Laboratory of Low Metamorphic Coal Clean Utilization, Yulin 71900 (China); School of Chemistry and Chemical Engineering, Yan’an University, Shaanxi Key Laboratory of Chemical Reaction Engineering, Yan’an 716000 (China); Wang, Yufei [School of Chemistry and Chemical Engineering, Yulin University, Shaanxi Key Laboratory of Low Metamorphic Coal Clean Utilization, Yulin 71900 (China); Shen, Huidong; Zhang, Yu [School of Chemistry and Chemical Engineering, Yan’an University, Shaanxi Key Laboratory of Chemical Reaction Engineering, Yan’an 716000 (China); Li, Jian [School of Chemistry and Chemical Engineering, Yulin University, Shaanxi Key Laboratory of Low Metamorphic Coal Clean Utilization, Yulin 71900 (China); Wang, Danjun, E-mail: yulyanlong@aliyun.com [School of Chemistry and Chemical Engineering, Yan’an University, Shaanxi Key Laboratory of Chemical Reaction Engineering, Yan’an 716000 (China)

2017-01-30

Highlights: • Bi{sub 2}S{sub 3}/Bi{sub 2}WO{sub 6} hybrids with exposed (020) Bi{sub 2}WO{sub 6} facets have been synthesized. • X-ray photoelectron spectroscopy reveals that a small amount of Bi{sub 2}S{sub 3} was formed. • The enhanced photoactivity of hybrids is due to heterojunction and (020) facets. • A possible photocatalytic degradation mechanism is proposed. - Abstract: Bi{sub 2}S{sub 3}/Bi{sub 2}WO{sub 6} hybrid architectures with exposed (020) Bi{sub 2}WO{sub 6} facets have been synthesized via a controlled anion exchange approach. X-ray photoelectron spectroscopy (XPS) reveals that a small amount of Bi{sub 2}S{sub 3} was formed on the surface of Bi{sub 2}WO{sub 6} during the anion exchange process, thus leading to the transformation from the Bi{sub 2}WO{sub 6} to Bi{sub 2}S{sub 3}/Bi{sub 2}WO{sub 6}. A rhodamine B (RhB) aqueous solution was chosen as model organic pollutants to evaluate the photocatalytic activities of the Bi{sub 2}S{sub 3}/Bi{sub 2}WO{sub 6} catalysts. Under visible light irradiation, the Bi{sub 2}S{sub 3}/Bi{sub 2}WO{sub 6}-TAA displayed the excellent visible light photoactivities compared with pure Bi{sub 2}S{sub 3}, Bi{sub 2}WO{sub 6} and other composite photocatalysts. The efficient photocatalytic activity of the Bi{sub 2}S{sub 3}/Bi{sub 2}WO{sub 6}-TAA composite microspheres was ascribed to the constructed heterojunctions and the inner electric field caused by the exposed (020) Bi{sub 2}WO{sub 6} facets. Active species trapping experiments revealed that h{sup +} and O{sub 2}·{sup −} are the main active species in the photocatalytic process. Furthermore, the as-obtained photocatalysts showed good photocatalytic activity after four recycles. The results presented in this study provide a new concept for the rational design and development of highly efficient photocatalysts.

Noncoding sequence classification based on wavelet transform analysis: part I

Science.gov (United States)

Paredes, O.; Strojnik, M.; Romo-Vázquez, R.; Vélez Pérez, H.; Ranta, R.; Garcia-Torales, G.; Scholl, M. K.; Morales, J. A.

2017-09-01

DNA sequences in human genome can be divided into the coding and noncoding ones. Coding sequences are those that are read during the transcription. The identification of coding sequences has been widely reported in literature due to its much-studied periodicity. Noncoding sequences represent the majority of the human genome. They play an important role in gene regulation and differentiation among the cells. However, noncoding sequences do not exhibit periodicities that correlate to their functions. The ENCODE (Encyclopedia of DNA elements) and Epigenomic Roadmap Project projects have cataloged the human noncoding sequences into specific functions. We study characteristics of noncoding sequences with wavelet analysis of genomic signals.

Doping of (Bi,Pb)-2223 with metal oxides

International Nuclear Information System (INIS)

Goehring, D.; Vogt, M.; Wischert, W.; Kemmler-Sack, S.

1997-01-01

The effect of doping on formation, superconductivity and pinning forces of (Bi,Pb)-2223 was studied for several dopants. They can be subdivided into promoters (Cu, Mn at low doping level of x=0.1 and Rh) and inhibitors (Mg, Al, Sn, Co, Y, Pd and high substitution levels of Mn and Ni) of the transformation of the precursor material into (Bi,Pb)-2223. According to X-ray diffraction (XRD) studies the incorporation of the dopant into the 2223 lattice is restricted to a very low doping level. Higher dopant concentrations are accompanied by a segregation of secondary phases. These segregations are not effective in the process of creating flux pinning centres. A depression of T c is observed for 2223 materials with the dopants Co, Ni and Pd. (orig.)

Optimization of excess Bi doping to enhance ferroic orders of spin casted BiFeO3 thin film

International Nuclear Information System (INIS)

Gupta, Surbhi; Gupta, Vinay; Tomar, Monika; James, A. R.; Pal, Madhuparna; Guo, Ruyan; Bhalla, Amar

2014-01-01

Multiferroic Bismuth Ferrite (BiFeO 3 ) thin films with varying excess bismuth (Bi) concentration were grown by chemical solution deposition technique. Room temperature multiferroic properties (ferromagnetism, ferroelectricity, and piezoelectricity) of the deposited BiFeO 3 thin films have been studied. High resolution X-ray diffraction and Raman spectroscopy studies reveal that the dominant phases formed in the prepared samples change continuously from a mixture of BiFeO 3 and Fe 2 O 3 to pure BiFeO 3 phase and, subsequently, to a mixture of BiFeO 3 and Bi 2 O 3 with increase in the concentration of excess Bi from 0% to 15%. BiFeO 3 thin films having low content (0% and 2%) of excess Bi showed the traces of ferromagnetic phase (γ-Fe 2 O 3 ). Deterioration in ferroic properties of BiFeO 3 thin films is also observed when prepared with higher content (15%) of excess Bi. Single-phased BiFeO 3 thin film prepared with 5% excess Bi concentration exhibited the soft ferromagnetic hysteresis loops and ferroelectric characteristics with remnant polarization 4.2 μC/cm 2 and saturation magnetization 11.66 emu/g. The switching of fine spontaneous domains with applied dc bias has been observed using piezoresponse force microscopy in BiFeO 3 thin films having 5% excess Bi. The results are important to identify optimum excess Bi concentration needed for the formation of single phase BiFeO 3 thin films exhibiting the improved multiferroic properties.

Phylogenetic analyses of the polyprotein coding sequences of serotype O foot-and-mouth disease viruses in East Africa: evidence for interserotypic recombination

Directory of Open Access Journals (Sweden)

Balinda Sheila N

2010-08-01

Full Text Available Abstract Background Foot-and-mouth disease (FMD is endemic in East Africa with the majority of the reported outbreaks attributed to serotype O virus. In this study, phylogenetic analyses of the polyprotein coding region of serotype O FMD viruses from Kenya and Uganda has been undertaken to infer evolutionary relationships and processes responsible for the generation and maintenance of diversity within this serotype. FMD virus RNA was obtained from six samples following virus isolation in cell culture and in one case by direct extraction from an oropharyngeal sample. Following RT-PCR, the single long open reading frame, encoding the polyprotein, was sequenced. Results Phylogenetic comparisons of the VP1 coding region showed that the recent East African viruses belong to one lineage within the EA-2 topotype while an older Kenyan strain, K/52/1992 is a representative of the topotype EA-1. Evolutionary relationships between the coding regions for the leader protease (L, the capsid region and almost the entire coding region are monophyletic except for the K/52/1992 which is distinct. Furthermore, phylogenetic relationships for the P2 and P3 regions suggest that the K/52/1992 is a probable recombinant between serotypes A and O. A bootscan analysis of K/52/1992 with East African FMD serotype A viruses (A21/KEN/1964 and A23/KEN/1965 and serotype O viral isolate (K/117/1999 revealed that the P2 region is probably derived from a serotype A strain while the P3 region appears to be a mosaic derived from both serotypes A and O. Conclusions Sequences of the VP1 coding region from recent serotype O FMDVs from Kenya and Uganda are all representatives of a specific East African lineage (topotype EA-2, a probable indication that hardly any FMD introductions of this serotype have occurred from outside the region in the recent past. Furthermore, evidence for interserotypic recombination, within the non-structural protein coding regions, between FMDVs of serotypes A

Development of the PRO-LOCA Probabilistic Fracture Mechanics Code, MERIT Final Report

International Nuclear Information System (INIS)

Scott, Paul; Kurth, Robert; Cox, Andrew; Olson, Rick; Rudland, Dave

2010-12-01

The MERIT project has been an internationally financed program with the main purpose of developing probabilistic models for piping failure of nuclear components and to include these models in a probabilistic code named PRO-LOCA. The principal objective of the project has been to develop probabilistic models for piping failure of nuclear components and to include these models in a probabilistic code. The MERIT program has produced a code named PRO-LOCA with the following features: - Crack initiation models for fatigue or stress corrosion cracking for previously unflawed material. - Subcritical crack growth models for fatigue and stress corrosion cracking for both initiated and pre-existing circumferential defects. - Models for flaw detection by inspections and leak detection. - Crack stability. The PRO-LOCA code can thus predict the leak or break frequency for the whole sequence of initiation, subcritical crack growth until wall penetration and leakage, instability of the through-wall crack (pipe rupture). The outcome of the PRO-LOCA code are a sequence of failure frequencies which represents the probability of surface crack developing, a through-wall crack developing and six different sizes of crack opening areas corresponding to different leak flow rates or LOCA categories. Note that the level of quality assurance of the PRO-LOCA code is such that the code in its current state of development is considered to be more of a research code than a regulatory tool.

Development of the PRO-LOCA Probabilistic Fracture Mechanics Code, MERIT Final Report

Energy Technology Data Exchange (ETDEWEB)

Scott, Paul; Kurth, Robert; Cox, Andrew; Olson, Rick (Battelle Columbus (United States)); Rudland, Dave (Nuclear Regulatory Commission (United States))

2010-12-15

The MERIT project has been an internationally financed program with the main purpose of developing probabilistic models for piping failure of nuclear components and to include these models in a probabilistic code named PRO-LOCA. The principal objective of the project has been to develop probabilistic models for piping failure of nuclear components and to include these models in a probabilistic code. The MERIT program has produced a code named PRO-LOCA with the following features: - Crack initiation models for fatigue or stress corrosion cracking for previously unflawed material. - Subcritical crack growth models for fatigue and stress corrosion cracking for both initiated and pre-existing circumferential defects. - Models for flaw detection by inspections and leak detection. - Crack stability. The PRO-LOCA code can thus predict the leak or break frequency for the whole sequence of initiation, subcritical crack growth until wall penetration and leakage, instability of the through-wall crack (pipe rupture). The outcome of the PRO-LOCA code are a sequence of failure frequencies which represents the probability of surface crack developing, a through-wall crack developing and six different sizes of crack opening areas corresponding to different leak flow rates or LOCA categories. Note that the level of quality assurance of the PRO-LOCA code is such that the code in its current state of development is considered to be more of a research code than a regulatory tool.

Conceptual design tool development for a Pb-Bi cooled reactor

International Nuclear Information System (INIS)

Lee, K. G.; Chang, S. H.; No, H. C.; Chunm, M. H.

2000-01-01

Conceptual design is generally ill-structured and mysterious problem solving. This leads the experienced experts to be still responsible for the most of synthesis and analysis task, which are not amenable to logical formulations in design problems. Especially because a novel reactor such as a Pb-Bi cooled reactor is going on a conceptual design stage, it will be very meaningful to develop the conceptual design tool. This tool consists of system design module with artificial intelligence, scaling module, and validation module. System design decides the optimal structure and the layout of a Pb-Bi cooled reactor, using design synthesis part and design analysis part. The designed system is scaled to be optimal with desired power level, and then the design basis accidents (Dbase) are analyzed in validation module. Design synthesis part contains the specific data for reactor components and the general data for a Pb-Bi cooled reactor. Design analysis part contains several design constraints for formulation and solution of a design problem. In addition, designer's intention may be externalized through emphasis on design requirements. For the purpose of demonstration, the conceptual design tool is applied to a Pb-Bi cooled reactor with 125 M Wth of power level. The Pb-Bi cooled reactor is a novel reactor concept in which the fission-generated heat is transferred from the primary coolant to the secondary coolant through a reactor vessel wall of a novel design. The Pb-Bi cooled reactor is to deliver 125 M Wth per module for 15 effective full power years without any on-site fuel handling. The conceptual design tool investigated the feasibility of a Pb-Bi cooled reactor. Application of the conceptual design tool will be, in detail, presented in the full paper. (author)

DSAP: deep-sequencing small RNA analysis pipeline.

Science.gov (United States)

Huang, Po-Jung; Liu, Yi-Chung; Lee, Chi-Ching; Lin, Wei-Chen; Gan, Richie Ruei-Chi; Lyu, Ping-Chiang; Tang, Petrus

2010-07-01

DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log(2)-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw.

Decomposing the (seafood vs. meat) evening meal decision-making sequence

DEFF Research Database (Denmark)

Perrea, Toula; Brunsø, Karen; Altintzoglou, Themistoklis

2012-01-01

as the content of the family’s daily food (i.e. seafood and meat-related) decision-making process. Design/methodology/approach – Twenty-four families in Denmark, Norway and Iceland were asked to fill in a one-to-two-week semi-structured diary regarding any thoughts they had about the decision-making sequence...... regarding their evening meals. Data were analysed by means of content analysis so as to gain insight into the main themes and distinctive patterns with respect to the four stages of the decision-making sequence by identifying a number of codes and sub-codes of high and lower abstraction level. Findings...... – The main results were similar across the three countries. Planning was the most important phase of the evening meal decision-making sequence, where Nordic respondents considered practical issues, and engaged in a more rational type of thinking, allowing cognitive aspects to prevail at this particular stage...

Sub-band/transform compression of video sequences

Science.gov (United States)

Sauer, Ken; Bauer, Peter

1992-01-01

The progress on compression of video sequences is discussed. The overall goal of the research was the development of data compression algorithms for high-definition television (HDTV) sequences, but most of our research is general enough to be applicable to much more general problems. We have concentrated on coding algorithms based on both sub-band and transform approaches. Two very fundamental issues arise in designing a sub-band coder. First, the form of the signal decomposition must be chosen to yield band-pass images with characteristics favorable to efficient coding. A second basic consideration, whether coding is to be done in two or three dimensions, is the form of the coders to be applied to each sub-band. Computational simplicity is of essence. We review the first portion of the year, during which we improved and extended some of the previous grant period's results. The pyramid nonrectangular sub-band coder limited to intra-frame application is discussed. Perhaps the most critical component of the sub-band structure is the design of bandsplitting filters. We apply very simple recursive filters, which operate at alternating levels on rectangularly sampled, and quincunx sampled images. We will also cover the techniques we have studied for the coding of the resulting bandpass signals. We discuss adaptive three-dimensional coding which takes advantage of the detection algorithm developed last year. To this point, all the work on this project has been done without the benefit of motion compensation (MC). Motion compensation is included in many proposed codecs, but adds significant computational burden and hardware expense. We have sought to find a lower-cost alternative featuring a simple adaptation to motion in the form of the codec. In sequences of high spatial detail and zooming or panning, it appears that MC will likely be necessary for the proposed quality and bit rates.

Improvement of Level-1 PSA computer code package -A study for nuclear safety improvement-

International Nuclear Information System (INIS)

Park, Chang Kyu; Kim, Tae Woon; Ha, Jae Joo; Han, Sang Hoon; Cho, Yeong Kyun; Jeong, Won Dae; Jang, Seung Cheol; Choi, Young; Seong, Tae Yong; Kang, Dae Il; Hwang, Mi Jeong; Choi, Seon Yeong; An, Kwang Il

1994-07-01

This year is the second year of the Government-sponsored Mid- and Long-Term Nuclear Power Technology Development Project. The scope of this subproject titled on 'The Improvement of Level-1 PSA Computer Codes' is divided into three main activities : (1) Methodology development on the under-developed fields such as risk assessment technology for plant shutdown and external events, (2) Computer code package development for Level-1 PSA, (3) Applications of new technologies to reactor safety assessment. At first, in the area of PSA methodology development, foreign PSA reports on shutdown and external events have been reviewed and various PSA methodologies have been compared. Level-1 PSA code KIRAP and CCF analysis code COCOA are converted from KOS to Windows. Human reliability database has been also established in this year. In the area of new technology applications, fuzzy set theory and entropy theory are used to estimate component life and to develop a new measure of uncertainty importance. Finally, in the field of application study of PSA technique to reactor regulation, a strategic study to develop a dynamic risk management tool PEPSI and the determination of inspection and test priority of motor operated valves based on risk importance worths have been studied. (Author)

Topological Weyl semimetals in Bi1 -xSbx alloys

Science.gov (United States)

Su, Yu-Hsin; Shi, Wujun; Felser, Claudia; Sun, Yan

2018-04-01

We investigated Weyl semimetal (WSM) phases in bismuth antimony (Bi1 -xSbx ) alloys by combination of atomic composition and arrangement. Via first-principles calculations, we found two WSM states with Sb concentrations of x =0.5 and 0.83 with specific inversion-symmetry-broken elemental arrangement. The Weyl points are close to the Fermi level in both of these two WSM states. Therefore, it is likely to obtain Weyl points in Bi-Sb alloy. The WSM phase provides a reasonable explanation for the current transport study of Bi-Sb alloy with the violation of Ohm's law [D. Shin, Y. Lee, M. Sasaki, Y. H. Jeong, F. Weickert, J. B. Betts, H.-J. Kim, K.-S. Kim, and J. Kim, Nat. Mater. 16, 1096 (2017), 10.1038/nmat4965]. This paper shows that the topological phases in Bi-Sb alloys depend on both elemental composition and their specific arrangement.

Experimental Cross Sections for Reactions of Heavy Ions and 208Pb, 209Bi, 238U, and 248Cm Targets

International Nuclear Information System (INIS)

Patin, Joshua B.

2002-01-01

The study of the reactions between heavy ions and 208 Pb, 209 Bi, 238 U, and 248 Cm targets was performed to look at the differences between the cross sections of hot and cold fusion reactions. Experimental cross sections were compared with predictions from statistical computer codes to evaluate the effectiveness of the computer code in predicting production cross sections. Hot fusion reactions were studied with the MG system, catcher foil techniques and the Berkeley Gas-filled Separator (BGS). 3n- and 4n-exit channel production cross sections were obtained for the 238 U( 18 O,xn) 256-x Fm, 238 U( 22 Ne,xn) 260-x No, and 248 Cm( 15 N,xn) 263-x Lr reactions and are similar to previous experimental results. The experimental cross sections were accurately modeled by the predictions of the HIVAP code using the Reisdorf and Schaedel parameters and are consistent with the existing systematics of 4n exit channel reaction products. Cold fusion reactions were examined using the BGS. The 208 Pb( 48 Ca,xn) 256-x No, 208 Pb( 50 Ti,xn) 258-x Rf, 208 Pb( 51 V,xn) 259-x Db, 209 Bi( 50 Ti,xn) 259-x Db, and 209 Bi( 51 V,xn) 260-x Sg reactions were studied. The experimental production cross sections are in agreement with the results observed in previous experiments. It was necessary to slightly alter the Reisdorf and Schaedel parameters for use in the HIVAP code in order to more accurately model the experimental data. The cold fusion experimental results are in agreement with current 1n- and 2n-exit channel systematics

Topotactic synthesis of a new BiS2-based superconductor Bi2(O,F)S2

OpenAIRE

Okada, Tomoyuki; Ogino, Hiraku; Shimoyama, Jun-ichi; Kishio, Kohji

2015-01-01

A new BiS2-based superconductor Bi2(O,F)S2 was discovered. This is a layered compound consisting of alternate stacking structure of rock-salt-type BiS2 superconducting layer and fluorite-type Bi(O,F) blocking layer. Bi2(O,F)S2 was obtained as the main phase by topotactic fluorination of undoped Bi2OS2 using XeF2, which is the first topotactic synthesis of an electron-doped superconductor via reductive fluorination. With increasing F-content, a- and c-axis length increased and decreased, respe...

Overlayer growth and electronic properties of the Bi/GaSb(110) interface

Science.gov (United States)

Gavioli, Luca; Betti, Maria Grazia; Casarini, Paolo; Mariani, Carlo

1995-06-01

The overlayer growth and electronic properties of the Bi/GaSb(110) interface and of the two-dimensional ordered (1×1)- and (1×2)-Bi layers have been investigated by complementary spectroscopic techniques (high-resolution electron-energy-loss, photoemission, and Auger spectroscopy). Bismuth forms an epitaxial monolayer, followed by island formation (Stranski-Krastanov growth mode) covering an average surface area of 40% at a nominal coverage of 4 ML. The (1×2)-symmetry stable structural phase, obtained after annealing at ~220 °C, corresponds to an average nominal Bi coverage of about 0.7 ML, suggesting an atomic geometry different from the epitaxial-continued layer structure. The disposal of Bi atoms in the (1×2) structure should build up an ``open'' layer, as the Ga-related surface exciton quenched in the (1×1) epitaxial monolayer is present in the (1×2) stable phase. The two symmetry phases are characterized by strong absorption features at 1 eV [(1×1)-Bi] and 0.54 eV [(1×2)-Bi], related to interband electronic transitions between Bi-induced electronic states. The major Bi-related occupied electronic levels, present in the valence band of the (1×1)- and (1×2)-Bi layer, have been detected by angle-integrated ultraviolet photoemission spectroscopy. Both the (1×1) and (1×2) phases show a metallic nature, with a low density of electronic states at the Fermi level. Schottky barrier heights of 0.20 and 0.14 eV are estimated for the epitaxial (1×1)- and (1×2)-symmetry stage, respectively, by analyzing the space-charge layer conditions through the study of the dopant-induced free-carrier plasmon in the GaSb substrate.

Adsorbate-induced modification of electronic band structure of epitaxial Bi(111) films

Energy Technology Data Exchange (ETDEWEB)

Matetskiy, A.V., E-mail: mateckij@iacp.dvo.ru [Institute of Automation and Control Processes FEB RAS, 5 Radio Street, 690041 Vladivostok (Russian Federation); Bondarenko, L.V.; Tupchaya, A.Y.; Gruznev, D.V. [Institute of Automation and Control Processes FEB RAS, 5 Radio Street, 690041 Vladivostok (Russian Federation); Eremeev, S.V. [Institute of Strength Physics and Materials Science, 634021 Tomsk (Russian Federation); Tomsk State University, 634050 Tomsk (Russian Federation); Zotov, A.V. [Institute of Automation and Control Processes FEB RAS, 5 Radio Street, 690041 Vladivostok (Russian Federation); School of Natural Sciences, Far Eastern Federal University, 690950 Vladivostok (Russian Federation); Department of Electronics, Vladivostok State University of Economics and Service, 690600 Vladivostok (Russian Federation); Saranin, A.A. [Institute of Automation and Control Processes FEB RAS, 5 Radio Street, 690041 Vladivostok (Russian Federation); School of Natural Sciences, Far Eastern Federal University, 690950 Vladivostok (Russian Federation)

2017-06-01

Highlights: • Modification of electronic properties of ultrathin Bi films by adsorbates is demonstrated. • Due to electron doping from Cs adatoms, surface-state bands shift to higher binding energies. • As a result, only electron pockets are left in the Fermi map. • Tin acts as an acceptor dopant for Bi, shifting Fermi level upward. • As a result, only hole pockets are left in the Fermi map. - Abstract: Changes of the electronic band structure of Bi(111) films on Si(111) induced by Cs and Sn adsorption have been studied using angle-resolved photoemission spectroscopy and density functional theory calculations. It has been found that small amounts of Cs when it presents at the surface in a form of the adatom gas leads to shifting of the surface and quantum well states to the higher binding energies due to the electron donation from adsorbate to the Bi film. In contrast, adsorbed Sn dissolves into the Bi film bulk upon heating and acts as an acceptor dopant, that results in shifting of the surface and quantum well states upward to the lower binding energies. These results pave the way to manipulate with the Bi thin film electron band structure allowing to achieve a certain type of conductivity (electron or hole) with a single spin channel at the Fermi level making the adsorbate-modified Bi a reliable base for prospective spintronics applications.

Performance Analysis of Direct-Sequence Code-Division Multiple-Access Communications with Asymmetric Quadrature Phase-Shift-Keying Modulation

Science.gov (United States)

Wang, C.-W.; Stark, W.

2005-01-01

This article considers a quaternary direct-sequence code-division multiple-access (DS-CDMA) communication system with asymmetric quadrature phase-shift-keying (AQPSK) modulation for unequal error protection (UEP) capability. Both time synchronous and asynchronous cases are investigated. An expression for the probability distribution of the multiple-access interference is derived. The exact bit-error performance and the approximate performance using a Gaussian approximation and random signature sequences are evaluated by extending the techniques used for uniform quadrature phase-shift-keying (QPSK) and binary phase-shift-keying (BPSK) DS-CDMA systems. Finally, a general system model with unequal user power and the near-far problem is considered and analyzed. The results show that, for a system with UEP capability, the less protected data bits are more sensitive to the near-far effect that occurs in a multiple-access environment than are the more protected bits.

Trapping control of phase development in zone melting of Bi-Sr-Ca-Cu-O superconducting fibres

International Nuclear Information System (INIS)

Costa, F M; Carrasco, M F; Silva, R F; Vieira, J M

2003-01-01

Highly-texturized polycrystalline fibres of the Bi-Sr-Ca-Cu-O system have been grown by the laser floating zone technique at seven different pulling rates: (1.1, 2.2, 4.17, 8.3, 16.7, 33.3, 60.5) x 10 -6 m s -1 . The assessment of the cation segregation at the solid/liquid interface allowed us to calculate their equilibrium and effective distribution coefficients. The equilibrium distribution coefficients (k 0,Bi = 0.55, k 0,Sr = 0.97, k 0,Ca = 1.67, k 0,Cu = 1.10) were estimated using the Burton, Primm and Slichter (BPS) theory by taking into account the determined effective values. The effective distribution coefficients tend to unity as long as the pulling rate increases. The composition profiles along the initial transient region of the solidified fibres show a fast approach to the nominal composition as the pulling rate increases. The outstanding effect of the growth speed on superconducting phase type development is explained based on the solute trapping phenomena. The sequence of crystallization for superconducting phases ('2212' → '4413' → '2201') with pulling rate is a spontaneous effect of the system thermodynamics in order to balance the Bi trapping. This phase sequence corresponds to the smallest change of Bi chemical potential from the liquid phase to the solid phase. A diagram of free energy curves of the interdendritic superconducting phases illustrates the partitionless solidification phenomena at the highest growth speed

2D BiOCl/Bi12O17Cl2 nanojunction: Enhanced visible light photocatalytic NO removal and in situ DRIFTS investigation

Science.gov (United States)

Zhang, Wendong; Dong, Xin'an; Jia, Bin; Zhong, Junbo; Sun, Yanjuan; Dong, Fan

2018-02-01

Novel two-dimensional (2D) BiOCl/Bi12O17Cl2 nanojunctions were fabricated by a facile one-pot in situ method at room temperature. The as-prepared samples were analyzed by XRD, SEM, TEM, HRTEM, UV-vis DRS, PL, ESR and BET-BJH measurement in detail. The photocatalytic performance of the samples was evaluated by removal of NO at ppb level under visible-light illumination. The result reveals that the BiOCl/Bi12O17Cl2 nanojunctions manifests conspicuously enhanced photocatalytic efficiency for NO removal. The facilitated performance can be ascribed to the well-matched band structure and relatively high specific surface area. In addition, the in situ diffuse reflectance infrared Fourier transform spectroscopy was applied to investigate the adsorption and photocatalytic NO oxidation processes. The reaction mechanism of photocatalytic NO oxidation was proposed based on the observed intermediates. The present work could pave a way to synthesize novel visible light photocatalysts at room temperature for environmental application.

One step synthesis of Bi@Bi{sub 2}O{sub 3}@carboxylate-rich carbon spheres with enhanced photocatalytic performance

Energy Technology Data Exchange (ETDEWEB)

Qu, Lingling [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China); Luo, Zhijun, E-mail: lzj@ujs.edu.cn [School of the Environment, Jiangsu University, Zhenjiang 212013 (China); State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210093 (China); Tang, Chao [Maple Leaf International High School, Zhenjiang 212013 (China)

2013-11-15

Graphical abstract: Functional groups of sodium gluconate play synergetic roles in the formation of Bi@Bi{sub 2}O{sub 3}@carboxylate-rich carbon core–shell nanosturctures (Bi@Bi{sub 2}O{sub 3}@CRCSs). Bi@Bi{sub 2}O{sub 3}@CRCSs exhibits significant enhanced photocatalytic activity under visible light irradiation. - Highlights: • One step synthesis of Bi@Bi{sub 2}O{sub 3}@carboxylate-rich carbon spheres. • Functional groups of sodium gluconate play synergetic roles in the formation of Bi@Bi{sub 2}O{sub 3}@CRCSs. • Bi@Bi{sub 2}O{sub 3}@CRCSs exhibits enhanced photocatalytic activity under visible light irradiation. - Abstract: Bi@Bi{sub 2}O{sub 3}@carboxylate-rich carbon core-shell nanosturctures (Bi@Bi{sub 2}O{sub 3}@CRCSs) have been synthesized via a one-step method. The core–shell nanosturctures of the as-prepared samples were confirmed by X-ray powder diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), and Raman spectroscopy. The formation of Bi@Bi{sub 2}O{sub 3}@CRCSs core–shell nanosturctures should attribute to the synergetic roles of different functional groups of sodium gluconate. Bi@Bi{sub 2}O{sub 3}@CRCSs exhibits significant enhanced photocatalytic activity under visible light irradiation (λ > 420 nm) and shows an O{sub 2}-dependent feature. According to trapping experiments of radicals and holes, hydroxyl radicals were not the main active oxidative species in the photocatalytic degradation of MB, but O{sub 2}·{sup −} are the main active oxidative species.

Computer codes for level 1 probabilistic safety assessment

International Nuclear Information System (INIS)

1990-06-01

Probabilistic Safety Assessment (PSA) entails several laborious tasks suitable for computer codes assistance. This guide identifies these tasks, presents guidelines for selecting and utilizing computer codes in the conduct of the PSA tasks and for the use of PSA results in safety management and provides information on available codes suggested or applied in performing PSA in nuclear power plants. The guidance is intended for use by nuclear power plant system engineers, safety and operating personnel, and regulators. Large efforts are made today to provide PC-based software systems and PSA processed information in a way to enable their use as a safety management tool by the nuclear power plant overall management. Guidelines on the characteristics of software needed for management to prepare a software that meets their specific needs are also provided. Most of these computer codes are also applicable for PSA of other industrial facilities. The scope of this document is limited to computer codes used for the treatment of internal events. It does not address other codes available mainly for the analysis of external events (e.g. seismic analysis) flood and fire analysis. Codes discussed in the document are those used for probabilistic rather than for phenomenological modelling. It should be also appreciated that these guidelines are not intended to lead the user to selection of one specific code. They provide simply criteria for the selection. Refs and tabs

Functional interrogation of non-coding DNA through CRISPR genome editing.

Science.gov (United States)

Canver, Matthew C; Bauer, Daniel E; Orkin, Stuart H

2017-05-15

Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

Bacillus anthracis genome organization in light of whole transcriptome sequencing

Energy Technology Data Exchange (ETDEWEB)

Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas; Borodovsky, Mark

2010-03-22

Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess correlation of gene expression level with promoter, terminator and RBS scores, codon adaptation index, as well as with a new measure of gene translational efficiency, average translation speed. We compared computational predictions of operon topologies with the transcript borders inferred from RNA-Seq reads. Transcriptome mapping may also improve existing gene annotation. Upon assessment of accuracy of current annotation of protein-coding genes in the B. anthracis genome we have shown that the transcriptome data indicate existence of more than a hundred genes missing in the annotation though predicted by an ab initio gene finder. Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity.

Metal resistance sequences and transgenic plants

Science.gov (United States)

Meagher, Richard Brian; Summers, Anne O.; Rugh, Clayton L.

1999-10-12

The present invention provides nucleic acid sequences encoding a metal ion resistance protein, which are expressible in plant cells. The metal resistance protein provides for the enzymatic reduction of metal ions including but not limited to divalent Cu, divalent mercury, trivalent gold, divalent cadmium, lead ions and monovalent silver ions. Transgenic plants which express these coding sequences exhibit increased resistance to metal ions in the environment as compared with plants which have not been so genetically modified. Transgenic plants with improved resistance to organometals including alkylmercury compounds, among others, are provided by the further inclusion of plant-expressible organometal lyase coding sequences, as specifically exemplified by the plant-expressible merB coding sequence. Furthermore, these transgenic plants which have been genetically modified to express the metal resistance coding sequences of the present invention can participate in the bioremediation of metal contamination via the enzymatic reduction of metal ions. Transgenic plants resistant to organometals can further mediate remediation of organic metal compounds, for example, alkylmetal compounds including but not limited to methyl mercury, methyl lead compounds, methyl cadmium and methyl arsenic compounds, in the environment by causing the freeing of mercuric or other metal ions and the reduction of the ionic mercury or other metal ions to the less toxic elemental mercury or other metals.

Topotactic synthesis of a new BiS2-based superconductor Bi2(O,F)S2

Science.gov (United States)

Okada, Tomoyuki; Ogino, Hiraku; Shimoyama, Jun-ichi; Kishio, Kohji

2015-02-01

A new BiS2-based superconductor, Bi2(O,F)S2, was discovered. It is a layered compound consisting of alternately stacked structure of rock-salt-type BiS2 superconducting layers and fluorite-type Bi(O,F) blocking layers. Bi2(O,F)S2 was obtained as the main phase by topotactic fluorination of undoped Bi2OS2 using XeF2. This is the first topotactic synthesis of an electron-doped superconductor via reductive fluorination. With increasing F-content, a- and c-axis lengths increased and decreased, respectively, and Tc increased to 5.1 K.

Biased Gene Conversion and GC-Content Evolution in the Coding Sequences of Reptiles and Vertebrates

Science.gov (United States)

Figuet, Emeric; Ballenghien, Marion; Romiguier, Jonathan; Galtier, Nicolas

2015-01-01

Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins. PMID:25527834

Reduced-Rank Chip-Level MMSE Equalization for the 3G CDMA Forward Link with Code-Multiplexed Pilot

Directory of Open Access Journals (Sweden)

Goldstein J Scott

2002-01-01

Full Text Available This paper deals with synchronous direct-sequence code-division multiple access (CDMA transmission using orthogonal channel codes in frequency selective multipath, motivated by the forward link in 3G CDMA systems. The chip-level minimum mean square error (MMSE estimate of the (multiuser synchronous sum signal transmitted by the base, followed by a correlate and sum, has been shown to perform very well in saturated systems compared to a Rake receiver. In this paper, we present the reduced-rank, chip-level MMSE estimation based on the multistage nested Wiener filter (MSNWF. We show that, for the case of a known channel, only a small number of stages of the MSNWF is needed to achieve near full-rank MSE performance over a practical single-to-noise ratio (SNR range. This holds true even for an edge-of-cell scenario, where two base stations are contributing near equal-power signals, as well as for the single base station case. We then utilize the code-multiplexed pilot channel to train the MSNWF coefficients and show that adaptive MSNWF operating in a very low rank subspace performs slightly better than full-rank recursive least square (RLS and significantly better than least mean square (LMS. An important advantage of the MSNWF is that it can be implemented in a lattice structure, which involves significantly less computation than RLS. We also present structured MMSE equalizers that exploit the estimate of the multipath arrival times and the underlying channel structure to project the data vector onto a much lower dimensional subspace. Specifically, due to the sparseness of high-speed CDMA multipath channels, the channel vector lies in the subspace spanned by a small number of columns of the pulse shaping filter convolution matrix. We demonstrate that the performance of these structured low-rank equalizers is much superior to unstructured equalizers in terms of convergence speed and error rates.

Sodium citrate-assisted anion exchange strategy for construction of Bi2O2CO3/BiOI photocatalysts

International Nuclear Information System (INIS)

Song, Peng-Yuan; Xu, Ming; Zhang, Wei-De

2015-01-01

Highlights: • Heterostructured Bi 2 O 2 CO 3 /BiOI microspheres were prepared via anion exchange. • Sodium citrate-assisted anion exchange for construction of composite photocatalysts. • Bi 2 O 2 CO 3 /BiOI composites show high visible light photocatalytic activity. - Abstract: Bi 2 O 2 CO 3 /BiOI heterojuncted photocatalysts were constructed through a facile partial anion exchange strategy starting from BiOI microspheres and urea with the assistance of sodium citrate. The content of Bi 2 O 2 CO 3 in the catalysts was regulated by modulating the amount of urea as a precursor, which was decomposed to generate CO 3 2− in the hydrothermal process. Citrate anion plays a key role in controlling the morphology and composition of the products. The Bi 2 O 2 CO 3 /BiOI catalysts display much higher photocatalytic activity than pure BiOI and Bi 2 O 2 CO 3 towards the degradation of rhodamine B (RhB) and bisphenol A (BPA). The enhancement of photocatalytic activity of the heterojuncted catalysts is attributed to the formation of p–n junction between p-BiOI and n-Bi 2 O 2 CO 3 , which is favorable for retarding the recombination of photoinduced electron-hole pairs. Moreover, the holes are demonstrated to be the main active species for the degradation of RhB and BPA

The crystal structure of baliczunicite, Bi₂O(SO₄)₂, a new natural bismuth oxide sulfate

DEFF Research Database (Denmark)

Pinto, Daniela; Garavelli, Anna; Balic Zunic, Tonci

2015-01-01

parallel to the (100) plane. The planes are stacked atom on atom such that Bi always overlays S and vice versa. This structural feature is shared with the known structure of the high-temperature polymorph of the same compound, stable at T >535oC. However, the sequences of Bi and S atoms in the two...

Overexpression of long non-coding RNAs following exposure to xenobiotics in the aquatic midge Chironomus riparius

International Nuclear Information System (INIS)

Martínez-Guitarte, José-Luis; Planelló, Rosario; Morcillo, Gloria

2012-01-01

Non-coding RNAs (ncRNAs) represent an important transcriptional output of eukaryotic genomes. In addition to their functional relevance as housekeeping and regulatory elements, recent studies have suggested their involvement in rather unexpected cellular functions. The aim of this work was to analyse the transcriptional behaviour of non-coding RNAs in the toxic response to pollutants in Chironomus riparius, a reference organism in aquatic toxicology. Three well-characterized long non-coding sequences were studied: telomeric repeats, Cla repetitive elements and the SINE CTRT1. Transcription levels were evaluated by RT-PCR after 24-h exposures to three current aquatic contaminants: bisphenol A (BPA), benzyl butyl phthalate (BBP) and the heavy metal cadmium (Cd). Upregulation of telomeric transcripts was found after BPA treatments. Moreover, BPA significantly activated Cla transcription, which also appeared to be increased by cadmium, whereas BBP did not affect the transcription levels of these sequences. Transcription of SINE CTRT1 was not altered by any of the chemicals tested. These data are discussed in the light of previous studies that have shown a response by long ncRNAS (lncRNAs) to cellular stressors, indicating a relationship with environmental stimuli. Our results demonstrated for the first time the ability of bisphenol A to activate non-coding sequences mainly located at telomeres and centromeres. Overall, this study provides evidence that xenobiotics can induce specific responses in ncRNAs derived from repetitive sequences that could be relevant in the toxic response, and also suggests that ncRNAs could represent a novel class of potential biomarkers in toxicological assessment.

Overexpression of long non-coding RNAs following exposure to xenobiotics in the aquatic midge Chironomus riparius

Energy Technology Data Exchange (ETDEWEB)

Martinez-Guitarte, Jose-Luis, E-mail: jlmartinez@ccia.uned.es [Grupo de Biologia y Toxicologia Ambiental, Facultad de Ciencias, Universidad Nacional de Educacion a Distancia, UNED, Senda del Rey 9, 28040 Madrid (Spain); Planello, Rosario; Morcillo, Gloria [Grupo de Biologia y Toxicologia Ambiental, Facultad de Ciencias, Universidad Nacional de Educacion a Distancia, UNED, Senda del Rey 9, 28040 Madrid (Spain)

2012-04-15

Non-coding RNAs (ncRNAs) represent an important transcriptional output of eukaryotic genomes. In addition to their functional relevance as housekeeping and regulatory elements, recent studies have suggested their involvement in rather unexpected cellular functions. The aim of this work was to analyse the transcriptional behaviour of non-coding RNAs in the toxic response to pollutants in Chironomus riparius, a reference organism in aquatic toxicology. Three well-characterized long non-coding sequences were studied: telomeric repeats, Cla repetitive elements and the SINE CTRT1. Transcription levels were evaluated by RT-PCR after 24-h exposures to three current aquatic contaminants: bisphenol A (BPA), benzyl butyl phthalate (BBP) and the heavy metal cadmium (Cd). Upregulation of telomeric transcripts was found after BPA treatments. Moreover, BPA significantly activated Cla transcription, which also appeared to be increased by cadmium, whereas BBP did not affect the transcription levels of these sequences. Transcription of SINE CTRT1 was not altered by any of the chemicals tested. These data are discussed in the light of previous studies that have shown a response by long ncRNAS (lncRNAs) to cellular stressors, indicating a relationship with environmental stimuli. Our results demonstrated for the first time the ability of bisphenol A to activate non-coding sequences mainly located at telomeres and centromeres. Overall, this study provides evidence that xenobiotics can induce specific responses in ncRNAs derived from repetitive sequences that could be relevant in the toxic response, and also suggests that ncRNAs could represent a novel class of potential biomarkers in toxicological assessment.

Validation uncertainty of MATRA code for subchannel void distributions

Energy Technology Data Exchange (ETDEWEB)

Hwang, Dae-Hyun; Kim, S. J.; Kwon, H.; Seo, K. W. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2014-10-15

To extend code capability to the whole core subchannel analysis, pre-conditioned Krylov matrix solvers such as BiCGSTAB and GMRES are implemented in MATRA code as well as parallel computing algorithms using MPI and OPENMP. It is coded by fortran 90, and has some user friendly features such as graphic user interface. MATRA code was approved by Korean regulation body for design calculation of integral-type PWR named SMART. The major role subchannel code is to evaluate core thermal margin through the hot channel analysis and uncertainty evaluation for CHF predictions. In addition, it is potentially used for the best estimation of core thermal hydraulic field by incorporating into multiphysics and/or multi-scale code systems. In this study we examined a validation process for the subchannel code MATRA specifically in the prediction of subchannel void distributions. The primary objective of validation is to estimate a range within which the simulation modeling error lies. The experimental data for subchannel void distributions at steady state and transient conditions was provided on the framework of OECD/NEA UAM benchmark program. The validation uncertainty of MATRA code was evaluated for a specific experimental condition by comparing the simulation result and experimental data. A validation process should be preceded by code and solution verification. However, quantification of verification uncertainty was not addressed in this study. The validation uncertainty of the MATRA code for predicting subchannel void distribution was evaluated for a single data point of void fraction measurement at a 5x5 PWR test bundle on the framework of OECD UAM benchmark program. The validation standard uncertainties were evaluated as 4.2%, 3.9%, and 2.8% with the Monte-Carlo approach at the axial levels of 2216 mm, 2669 mm, and 3177 mm, respectively. The sensitivity coefficient approach revealed similar results of uncertainties but did not account for the nonlinear effects on the

Investigations of bi-directional flow behaviour in presence of a large vertical opening in a fire compartment

International Nuclear Information System (INIS)

Sharma, Pavan K.; Gera, B.

2011-01-01

In the complex thermal hydraulics codes developed for fire, reactor and containment safety the junctions in the multi-compartment geometries are often modeled as uni-directional junctions and some construct of flow coefficient. However, certain large size junctions are known to depict bi-directional flow behaviour under specific circumstances. The CFD based computer code FDS was used for an earlier reported study of fire in an enclosure on the bidirectional flow behaviour in present of a wall opening. Numerical simulation is directed to monitor the entrainment of the fresh air from outside to the fire compartment and resulting plume deflection due to presence of a big opening. The paper presents the details of the analysis, the results obtained, and comparison with the reported experimental data in terms of plume deflection, entrainment. Detailed investigations have been carried out to understand the bi-directionality of a junction by analyzing studying the outgoing hot air flow and incoming cold air. (orig.)

Optical spectroscopy of Pr3+ in M+Bi(XO4)2, M+ = Li or Na and X = W or Mo, locally disordered single crystals

International Nuclear Information System (INIS)

Mendez-Blas, A; Rico, M; Volkov, V; Cascales, C; Zaldo, C; Coya, C; Kling, A; Alves, L C

2004-01-01

NaBi(WO 4 ) 2 (NBW), NaBi(MoO 4 ) 2 (NBMo) and LiBi(MoO 4 ) 2 (LBMo) single crystals grown by the Czochralski technique have been doped up to a praseodymium concentration of Pr ∼1x10 20 cm -3 in the crystal. 10 K polarized optical absorption and photoluminescence measurements have been used to determine the energy position of 32, 39 and 36 Pr 3+ Stark levels in NBW, NBMo and LBMo crystals, respectively. These energy levels were labelled with the appropriate irreducible representations corresponding to a C 2 local symmetry of an average optical centre. Single-electron Hamiltonians including free-ion and crystal field interactions have been used in the fitting of experimental energy levels and in the simulation of the full sequence of the 4f 2 Pr 3+ configuration. 300 K absorption spectra of different 2S+1 L J Pr 3+ multiplets were determined and used in the context of the Judd-Ofelt theory and for the calculation of the 1 D 2 -related emission cross sections of this average Pr 3+ centre. Non-radiative electron relaxation from the 3 P 0 level feeds the 1 D 2 multiplet. This latter level efficiently decays radiatively to the ground 3 H 4 multiplet but still there is a significant rate of radiative decay to the 1 D → 3 F 3 praseodymium laser channel. For Pr ≥ 2x10 19 cm -3 , non-radiative electric dipole-dipole Pr pair energy transfer limits the radiative yield

Dynamic tracking of prosthetic valve motion and deformation from bi-plane x-ray views: feasibility study

Science.gov (United States)

Hatt, Charles R.; Wagner, Martin; Raval, Amish N.; Speidel, Michael A.

2016-03-01

Transcatheter aortic valve replacement (TAVR) requires navigation and deployment of a prosthetic valve within the aortic annulus under fluoroscopic guidance. To support improved device visualization in this procedure, this study investigates the feasibility of frame-by-frame 3D reconstruction of a moving and expanding prosthetic valve structure from simultaneous bi-plane x-ray views. In the proposed method, a dynamic 3D model of the valve is used in a 2D/3D registration framework to obtain a reconstruction of the valve. For each frame, valve model parameters describing position, orientation, expansion state, and deformation are iteratively adjusted until forward projections of the model match both bi-plane views. Simulated bi-plane imaging of a valve at different signal-difference-to-noise ratio (SDNR) levels was performed to test the approach. 20 image sequences with 50 frames of valve deployment were simulated at each SDNR. The simulation achieved a target registration error (TRE) of the estimated valve model of 0.93 +/- 2.6 mm (mean +/- S.D.) for the lowest SDNR of 2. For higher SDNRs (5 to 50) a TRE of 0.04 mm +/- 0.23 mm was achieved. A tabletop phantom study was then conducted using a TAVR valve. The dynamic 3D model was constructed from high resolution CT scans and a simple expansion model. TRE was 1.22 +/- 0.35 mm for expansion states varying from undeployed to fully deployed, and for moderate amounts of inter-frame motion. Results indicate that it is feasible to use bi-plane imaging to recover the 3D structure of deformable catheter devices.

BiP clustering facilitates protein folding in the endoplasmic reticulum.

Directory of Open Access Journals (Sweden)

Marc Griesemer

2014-07-01

Full Text Available The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER: translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, experimental evidence revealed the spatial heterogeneity of BiP within the nuclear and peripheral ER of S. cerevisiae (commonly referred to as 'clusters'. Here, we developed a model to evaluate the potential advantages of accounting for multiple BiP molecules binding to peptides, while proposing that BiP's spatial heterogeneity may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness of binding multiple chaperone molecules to peptides. Using two metrics: folding efficiency and chaperone cost, we determined that the single binding site model achieves a higher efficiency than models characterized by multiple binding sites, in the absence of cooperativity. Due to entropic pulling, however, multiple chaperones perform in concert to facilitate the resolubilization and ultimate yield of folded proteins. As a result of cooperativity, multiple binding site models used fewer BiP molecules and maintained a higher folding efficiency than the single binding site model. These insilico investigations reveal that clusters of BiP molecules bound to unfolded proteins may enhance folding efficiency through cooperative action via entropic pulling.

Technology for cleaning of Pb-Bi adhering to steel (1). Basic tests

International Nuclear Information System (INIS)

Saito, Shigeru; Sasa, Toshinobu; Umeno, Makoto; Kurata, Yuji; Kikuchi, Kenji; Futakawa, Masatoshi

2004-12-01

The accelerator driven system (ADS) is proposed to transmute minor actinides (MA) in high-level waste from spent fuels of nuclear power reactors. Liquid Pb-Bi alloy is a candidate material for spallation target and coolant of ADS. Pb-Bi cleaning technology is required to reduce radiation exposure during maintenance service and to decontaminate replaced components. In this study, three cleaning methods were tested; silicon oil cleaning at 170degC, mixture of acetic acid and nitric acid cleaning. Specimens were prepared by immersion in melted Pb-Bi. After silicon oil tests, most of Pb-Bi remained on the surface of the specimens. It was found that blushing was needed to remove Pb-Bi effectively. On the other hands, Pb-Bi was easily dissolved and almost removed in the mixed acid and nitric acid. Silicon oil cleaning did not affect on base metals. The surface of base metals was slightly blacked after mixed acid cleaning. F82H base metals were corroded by nitric acid. (author)

Selection of a computer code for Hanford low-level waste engineered-system performance assessment

International Nuclear Information System (INIS)

McGrail, B.P.; Mahoney, L.A.

1995-10-01

Planned performance assessments for the proposed disposal of low-level waste (LLW) glass produced from remediation of wastes stored in underground tanks at Hanford, Washington will require calculations of radionuclide release rates from the subsurface disposal facility. These calculations will be done with the aid of computer codes. Currently available computer codes were ranked in terms of the feature sets implemented in the code that match a set of physical, chemical, numerical, and functional capabilities needed to assess release rates from the engineered system. The needed capabilities were identified from an analysis of the important physical and chemical process expected to affect LLW glass corrosion and the mobility of radionuclides. The highest ranked computer code was found to be the ARES-CT code developed at PNL for the US Department of Energy for evaluation of and land disposal sites

Code Verification Capabilities and Assessments in Support of ASC V&V Level 2 Milestone #6035

Energy Technology Data Exchange (ETDEWEB)

Doebling, Scott William [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Budzien, Joanne Louise [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ferguson, Jim Michael [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Harwell, Megan Louise [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Hickmann, Kyle Scott [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Israel, Daniel M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Magrogan, William Richard III [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Singleton, Jr., Robert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Srinivasan, Gowri [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Walter, Jr, John William [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Woods, Charles Nathan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-09-26

This document provides a summary of the code verification activities supporting the FY17 Level 2 V&V milestone entitled “Deliver a Capability for V&V Assessments of Code Implementations of Physics Models and Numerical Algorithms in Support of Future Predictive Capability Framework Pegposts.” The physics validation activities supporting this milestone are documented separately. The objectives of this portion of the milestone are: 1) Develop software tools to support code verification analysis; 2) Document standard definitions of code verification test problems; and 3) Perform code verification assessments (focusing on error behavior of algorithms). This report and a set of additional standalone documents serve as the compilation of results demonstrating accomplishment of these objectives.

Optimization of excess Bi doping to enhance ferroic orders of spin casted BiFeO{sub 3} thin film

Energy Technology Data Exchange (ETDEWEB)

Gupta, Surbhi; Gupta, Vinay, E-mail: drguptavinay@gmail.com [Department of Physics and Astrophysics, University of Delhi, Delhi (India); Tomar, Monika [Department of Physics, Miranda Housea, University of Delhi, Delhi (India); James, A. R. [Defence Metallurgical Research Laboratory, Hyderabad (India); Pal, Madhuparna; Guo, Ruyan; Bhalla, Amar [Department of Electrical and Computer Engineering, College of Engineering, University of Texas at SanAntonio, San Antonio 78249 (United States)

2014-06-21

Multiferroic Bismuth Ferrite (BiFeO{sub 3}) thin films with varying excess bismuth (Bi) concentration were grown by chemical solution deposition technique. Room temperature multiferroic properties (ferromagnetism, ferroelectricity, and piezoelectricity) of the deposited BiFeO{sub 3} thin films have been studied. High resolution X-ray diffraction and Raman spectroscopy studies reveal that the dominant phases formed in the prepared samples change continuously from a mixture of BiFeO{sub 3} and Fe{sub 2}O{sub 3} to pure BiFeO{sub 3} phase and, subsequently, to a mixture of BiFeO{sub 3} and Bi{sub 2}O{sub 3} with increase in the concentration of excess Bi from 0% to 15%. BiFeO{sub 3} thin films having low content (0% and 2%) of excess Bi showed the traces of ferromagnetic phase (γ-Fe{sub 2}O{sub 3}). Deterioration in ferroic properties of BiFeO{sub 3} thin films is also observed when prepared with higher content (15%) of excess Bi. Single-phased BiFeO{sub 3} thin film prepared with 5% excess Bi concentration exhibited the soft ferromagnetic hysteresis loops and ferroelectric characteristics with remnant polarization 4.2 μC/cm{sup 2} and saturation magnetization 11.66 emu/g. The switching of fine spontaneous domains with applied dc bias has been observed using piezoresponse force microscopy in BiFeO{sub 3} thin films having 5% excess Bi. The results are important to identify optimum excess Bi concentration needed for the formation of single phase BiFeO{sub 3} thin films exhibiting the improved multiferroic properties.

Nucleotide sequence of the gene coding for human factor VII, a vitamin K-dependent protein participating in blood coagulation

International Nuclear Information System (INIS)

O'Hara, P.J.; Grant, F.J.; Haldeman, B.A.; Gray, C.L.; Insley, M.Y.; Hagen, F.S.; Murray, M.J.

1987-01-01

Activated factor VII (factor VIIa) is a vitamin K-dependent plasma serine protease that participates in a cascade of reactions leading to the coagulation of blood. Two overlapping genomic clones containing sequences encoding human factor VII were isolated and characterized. The complete sequence of the gene was determined and found to span about 12.8 kilobases. The mRNA for factor VII as demonstrated by cDNA cloning is polyadenylylated at multiple sites but contains only one AAUAAA poly(A) signal sequence. The mRNA can undergo alternative splicing, forming one transcript containing eight segments as exons and another with an additional exon that encodes a larger prepro leader sequence. The latter transcript has no known counterpart in the other vitamin K-dependent proteins. The positions of the introns with respect to the amino acid sequence encoded by the eight essential exons of factor VII are the same as those present in factor IX, factor X, protein C, and the first three exons of prothrombin. These exons code for domains generally conserved among members of this gene family. The comparable introns in these genes, however, are dissimilar with respect to size and sequence, with the exception of intron C in factor VII and protein C. The gene for factor VII also contains five regions made up of tandem repeats of oligonucleotide monomer elements. More than a quarter of the intron sequences and more than a third of the 3' untranslated portion of the mRNA transcript consist of these minisatellite tandem repeats

Electronic structure of clean and Ag-covered single-crystalline Bi2Sr2CuO6

International Nuclear Information System (INIS)

Lindberg, P.A.P.; Shen, Z.; Wells, B.O.; Mitzi, D.B.; Lindau, I.; Spicer, W.E.; Kapitulnik, A.

1989-01-01

Photoemission studies of single-crystalline samples of Bi 2 Sr 2 CuO 6 show clear resemblance to the corresponding data for single crystals of Bi 2 Sr 2 CaCu 2 O 8 . In particular, a sharp Fermi-level cutoff, giving evidence of metallic conductivity at room temperature, as well as single-component O 1s emission and Cu 2p satellites with a strength amounting to about 50% of that of the main Cu 2p line, are observed. An analysis of the relative core-level photoemission intensities shows that the preferential cleavage plane of single-crystalline Bi 2 Sr 2 CuO 6 is between adjacent Bi-O layers. Deposition of Ag adatoms causes only weak reaction with the Bi and O ions of the Bi 2 Sr 2 CuO 6 substrate, while the Cu states rapidly react with the Ag adatoms, as monitored by a continuous reduction of the Cu 2p satellite intensity as the Ag overlayer becomes thicker

Phase formation in the (1-y)BiFeO{sub 3}-yBiScO{sub 3} system under ambient and high pressure

Energy Technology Data Exchange (ETDEWEB)

Salak, A.N., E-mail: salak@ua.pt [Department of Materials and Ceramic Engineering and CICECO – Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro (Portugal); Khalyavin, D.D., E-mail: dmitry.khalyavin@stfc.ac.uk [ISIS Facility, Rutherford Appleton Laboratory, Chilton, OX11 0QX Didcot (United Kingdom); Pushkarev, A.V.; Radyush, Yu.V.; Olekhnovich, N.M. [Scientific-Practical Materials Research Centre of NAS of Belarus, P. Brovka Street, 19, 220072 Minsk (Belarus); Shilin, A.D.; Rubanik, V.V. [Institute of Technical Acoustics of NAS of Belarus, Lyudnikov Avenue, 13, 210023 Vitebsk (Belarus)

2017-03-15

FeO{sub 3} at ambient pressure is about 15 at%. • R3c → Pnma → C2/c phase sequence in high-pressure prepared BiFe{sub 1-y}Sc{sub y}O{sub 3} ceramics. • The perovskite BiFe{sub 1-y}Sc{sub y}O{sub 3} phases formed under high pressure are metastable.

Statistical properties and fractals of nucleotide clusters in DNA sequences

International Nuclear Information System (INIS)

Sun Tingting; Zhang Linxi; Chen Jin; Jiang Zhouting

2004-01-01

Statistical properties of nucleotide clusters in DNA sequences and their fractals are investigated in this paper. The average size of nucleotide clusters in non-coding sequence is larger than that in coding sequence. We investigate the cluster-size distribution P(S) for human chromosomes 21 and 22, and the results are different from previous works. The cluster-size distribution P(S 1 +S 2 ) with the total size of sequential Pu-cluster and Py-cluster S 1 +S 2 is studied. We observe that P(S 1 +S 2 ) follows an exponential decay both in coding and non-coding sequences. However, we get different results for human chromosomes 21 and 22. The probability distribution P(S 1 ,S 2 ) of nucleotide clusters with the size of sequential Pu-cluster and Py-cluster S 1 and S 2 respectively, is also examined. In the meantime, some of the linear correlations are obtained in the double logarithmic plots of the fluctuation F(l) versus nucleotide cluster distance l along the DNA chain. The power spectrums of nucleotide clusters are also discussed, and it is concluded that the curves are flat and hardly changed and the 1/3 frequency is neither observed in coding sequence nor in non-coding sequence. These investigations can provide some insights into the nucleotide clusters of DNA sequences

Luminescence of Bi3+ ions in Y3Al5O12:Bi single crystalline films

International Nuclear Information System (INIS)

Zorenko, Yu.; Gorbenko, V.; Voznyak, T.; Vistovsky, V.; Nedilko, S.; Nikl, M.

2007-01-01

The absorption and cathodoluminescence spectra of single crystalline films (SCF) of Y 3 Al 5 O 12 :Bi garnet depending on Bi concentration were analyzed. For consideration of the nature of the UV and visible Bi-related emission bands the time-resolved luminescence of Bi 3+ (ns 2 ) ions in YAG:Bi SCF was studied at 10 K under excitation by synchrotron radiation. The difference in the excitation spectra and emission decay of the UV and visible bands has been explained via radiative relaxation from the 3 P 1,0 excited states to the 1 S 0 ground state of the isolated and pair/clustered Bi 3+ emission centers in the garnet lattice, respectively

Response of MnBi-Bi eutectic to freezing rate changes

Science.gov (United States)

Nair, M.; Fu, T.-W.; Wilcox, W. R.; Doddi, K.; Ravishankar, P. S.; Larson, D.

1982-01-01

Reference is made to a study by Fu and Wilcox (1981), which treated theoretically the influence on freezing rate of sudden changes in translation rate in the Bridgman-Stockbarger technique. This treatment is extended here to a linear ramped translation rate and an oscillatory freezing rate. It is found that oscillations above a few hertz are highly damped in small-diameter apparatus. An experimental test is carried out of the theoretical predictions for a sudden change of translation rate. The MnBi-Bi eutectic is solidified with current-induced interface demarcation. The experimental results accord reasonably well with theory if the silica ampoule wall is assumed to either (1) contribute only a resistance to heat exchange between the sample and the furnace wall or (2) transmit heat effectively in the axial direction by radiation. In an attempt to explain the fact that a finer microstructure is obtained in space, MnBi-Bi microstructure is determined when the freezing rate is increased or decreased rapidly. Preliminary results suggest that fiber branching does not occur as readily as fiber termination.

The effect of Bi{sub In} hetero-antisite defects in In{sub 1–x}PBi{sub x} alloy

Energy Technology Data Exchange (ETDEWEB)

Wu, Liyuan [State Key Laboratory of Information Photonics and Optical Communications, Ministry of Education, Beijing University of Posts and Telecommunications, P.O. Box 72, Beijing 100876 (China); Lu, Pengfei, E-mail: photon.bupt@gmail.com [State Key Laboratory of Information Photonics and Optical Communications, Ministry of Education, Beijing University of Posts and Telecommunications, P.O. Box 72, Beijing 100876 (China); State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050 (China); Yang, Chuanghua [School of Physics and Telecommunication Engineering, Shanxi University of Technology (SNUT), Hanzhong 723001, Shaanxi (China); Liang, Dan [State Key Laboratory of Information Photonics and Optical Communications, Ministry of Education, Beijing University of Posts and Telecommunications, P.O. Box 72, Beijing 100876 (China); Zhang, Chunfang [Beijing Computational Science Research Center, Beijing 100094 (China); Wang, Shumin [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050 (China); Photonics Laboratory, Department of Microtechnology and Nanoscience, Chalmers University of Technology, 41296 Gothenburg (Sweden)

2016-07-25

Bi{sub In} hetero-antisite defects in InP:Bi alloy is performed by using first-principle calculations. It is found that the hetero-antisite defect Bi{sub In} is energetically easier than Bi{sub P}. This Bi{sub In} defect is a deep level donor, and the related defect band is introduced by the sp-hybridization mainly between the 6s state of Bi{sub In} and 3p states of the nearest P atoms. The band gap of InP:Bi alloy increases slightly with the increase of Bi compositions, and the relative position of the defect level remains almost unchanged. These results represent that hetero-antisite defect Bi{sub In} does not contribute to the reduction of the band gap of InP:Bi alloy. The calculations of optical properties show that hetero-antisite defect Bi{sub In} can contribute to the red shift phenomena observed in experiment as the Bi composition increases. In addition, the interaction of two Bi{sub In} atoms can result in the split of the impurity band and cause a strong absorption in near-infrared region, indicating it can be a potential candidate for optoelectronics application. - Highlights: • The effects of Bi{sub In} hetero-antisite defects in InP:Bi alloy are studied. • The appearance and origin of Bi{sub In} related impurity band are discovered. • Bi{sub In} defects can contribute to the red shift phenomena observed in experiment. • A strong absorption in near-infrared region caused by two Bi{sub In} atoms is found.

Development of a computer code for low-and intermediate-level radioactive waste disposal safety assessment

International Nuclear Information System (INIS)

Park, J. W.; Kim, C. L.; Lee, E. Y.; Lee, Y. M.; Kang, C. H.; Zhou, W.; Kozak, M. W.

2002-01-01

A safety assessment code, called SAGE (Safety Assessment Groundwater Evaluation), has been developed to describe post-closure radionuclide releases and potential radiological doses for low- and intermediate-level radioactive waste (LILW) disposal in an engineered vault facility in Korea. The conceptual model implemented in the code is focused on the release of radionuclide from a gradually degrading engineered barrier system to an underlying unsaturated zone, thence to a saturated groundwater zone. The radionuclide transport equations are solved by spatially discretizing the disposal system into a series of compartments. Mass transfer between compartments is by diffusion/dispersion and advection. In all compartments, radionuclides are decayed either as a single-member chain or as multi-member chains. The biosphere is represented as a set of steady-state, radionuclide-specific pathway dose conversion factors that are multiplied by the appropriate release rate from the far field for each pathway. The code has the capability to treat input parameters either deterministically or probabilistically. Parameter input is achieved through a user-friendly Graphical User Interface. An application is presented, which is compared against safety assessment results from the other computer codes, to benchmark the reliability of system-level conceptual modeling of the code

Capsid coding sequences of foot-and-mouth disease viruses are determinants of pathogenicity in pigs

DEFF Research Database (Denmark)

Lohse, Louise; Jackson, Terry; Bøtner, Anette

2012-01-01

The surface exposed capsid proteins, VP1, VP2 and VP3, of foot-and-mouth disease virus (FMDV) determine its antigenicity and the ability of the virus to interact with host-cell receptors. Hence, modification of these structural proteins may alter the properties of the virus. In the present study we...... compared the pathogenicity of different FMDVs in young pigs. In total 32 pigs, 7-weeks-old, were exposed to virus, either by direct inoculation or through contact with inoculated pigs, using cell culture adapted (O1K B64), chimeric (O1K/A-TUR and O1K/O-UKG) or field strain (O-UKG/34/2001) viruses. The O1K...... coding sequences are determinants of FMDV pathogenicity in pigs....

Photoreduction of non-noble metal Bi on the surface of Bi{sub 2}WO{sub 6} for enhanced visible light photocatalysis

Energy Technology Data Exchange (ETDEWEB)

Zhang, Xiaojing [State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Southwest Petroleum University, No. 8, Xindu Road, Xindu District, Chengdu 610500 (China); The Center of New Energy Materials and Technology, School of Materials Science and Engineering, Southwest Petroleum University, No. 8, Xindu Road, Xindu District, Chengdu 610500 (China); Yu, Shan; Liu, Yang; Zhang, Qian [The Center of New Energy Materials and Technology, School of Materials Science and Engineering, Southwest Petroleum University, No. 8, Xindu Road, Xindu District, Chengdu 610500 (China); Zhou, Ying, E-mail: yzhou@swpu.edu.cn [State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation, Southwest Petroleum University, No. 8, Xindu Road, Xindu District, Chengdu 610500 (China); The Center of New Energy Materials and Technology, School of Materials Science and Engineering, Southwest Petroleum University, No. 8, Xindu Road, Xindu District, Chengdu 610500 (China)

2017-02-28

Highlights: • Bi{sub 2}WO{sub 6}-Bi composite was synthesized by in situ photoreduction of Bi{sub 2}WO{sub 6}. • Bi{sub 2}WO{sub 6}-Bi exhibits improved photocatalytic efficiency towards degradation of Rhodamine B. • The generation of elemental Bi in Bi{sub 2}WO{sub 6}-Bi induces vacancy and structure distortion of Bi{sub 2}WO{sub 6}. • The surface oxygen adsorption mode changes from hydroxyl group on Bi{sub 2}WO{sub 6} to molecular oxygen on Bi{sub 2}WO{sub 6}-Bi. - Abstract: In this report, Bi{sub 2}WO{sub 6}-Bi composite was prepared through an in situ photoreduction method and was characterized systematically by X-Ray diffraction, transmission electron microscopy, X-Ray photoelectron spectroscopy and UV-vis diffuse reflectance spectroscopy. The as-prepared Bi{sub 2}WO{sub 6}-Bi maintains the same crystal structure with the pristine Bi{sub 2}WO{sub 6} regardless of some surface defects. Nevertheless, these surface defects result in the change of surface oxygen adsorption mode from hydroxyl to molecular oxygen on Bi{sub 2}WO{sub 6}. Photocatalytic activity over Bi{sub 2}WO{sub 6}-Bi is 2.4 times higher than that of Bi{sub 2}WO{sub 6} towards the degradation of organic dye Rhodamine B (RhB) under visible light irradiation (λ > 420 nm). A deep study shows that cleavage of benzene ring is the main pathway for RhB degradation over Bi{sub 2}WO{sub 6}, but both the benzene cleavage and de-ethylation pathway coexist for RhB decomposition in the presence of Bi{sub 2}WO{sub 6}-Bi as the photocatalyst. Photoelectrochemical study including transient photocurrent tests and electrochemical impedance spectroscopy measurements shows that Bi{sub 2}WO{sub 6}-Bi could facilitate the charge transfer process compared to Bi{sub 2}WO{sub 6}. These data above has indicated a new insight into the promotion mechanism based on Bi related heterostructures.

New sparse matrix solver in the KIKO3D 3-dimensional reactor dynamics code