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Sample records for secondary structure improves

  1. Computational RNA secondary structure design: empirical complexity and improved methods

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    Condon Anne

    2007-01-01

    Full Text Available Abstract Background We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various classes of RNA structures as the size of the target structure is increased. The purpose of this work is to understand better the factors that make RNA structures hard to design for existing, high-performance algorithms. Such understanding provides the basis for improving the performance of one of the best algorithms for this problem, RNA-SSD, and for characterising its limitations. Results To gain insights into the practical complexity of the problem, we present a scaling analysis on random and biologically motivated structures using an improved version of the RNA-SSD algorithm, and also the RNAinverse algorithm from the Vienna package. Since primary structure constraints are relevant for designing RNA structures, we also investigate the correlation between the number and the location of the primary structure constraints when designing structures and the performance of the RNA-SSD algorithm. The scaling analysis on random and biologically motivated structures supports the hypothesis that the running time of both algorithms scales polynomially with the size of the structure. We also found that the algorithms are in general faster when constraints are placed only on paired bases in the structure. Furthermore, we prove that, according to the standard thermodynamic model, for some structures that the RNA-SSD algorithm was unable to design, there exists no sequence whose minimum free energy structure is the target structure. Conclusion Our analysis helps to better understand the strengths and limitations of both the RNA-SSD and RNAinverse algorithms, and suggests ways in which the performance of these algorithms can be further improved.

  2. Improving the accuracy of protein secondary structure prediction using structural alignment

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    Gallin Warren J

    2006-06-01

    Full Text Available Abstract Background The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3 of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences, the probability of a newly identified sequence having a structural homologue is actually quite high. Results We have developed a method that performs structure-based sequence alignments as part of the secondary structure prediction process. By mapping the structure of a known homologue (sequence ID >25% onto the query protein's sequence, it is possible to predict at least a portion of that query protein's secondary structure. By integrating this structural alignment approach with conventional (sequence-based secondary structure methods and then combining it with a "jury-of-experts" system to generate a consensus result, it is possible to attain very high prediction accuracy. Using a sequence-unique test set of 1644 proteins from EVA, this new method achieves an average Q3 score of 81.3%. Extensive testing indicates this is approximately 4–5% better than any other method currently available. Assessments using non sequence-unique test sets (typical of those used in proteome annotation or structural genomics indicate that this new method can achieve a Q3 score approaching 88%. Conclusion By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible at http://wishart.biology.ualberta.ca/proteus. For high throughput or batch sequence analyses, the PROTEUS programs

  3. Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts.

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    Adhikari, Badri; Cheng, Jianlin

    2017-08-29

    Residue-residue contacts are key features for accurate de novo protein structure prediction. For the optimal utilization of these predicted contacts in folding proteins accurately, it is important to study the challenges of reconstructing protein structures using true contacts. Because contact-guided protein modeling approach is valuable for predicting the folds of proteins that do not have structural templates, it is necessary for reconstruction studies to focus on hard-to-predict protein structures. Using a data set consisting of 496 structural domains released in recent CASP experiments and a dataset of 150 representative protein structures, in this work, we discuss three techniques to improve the reconstruction accuracy using true contacts - adding secondary structures, increasing contact distance thresholds, and adding non-contacts. We find that reconstruction using secondary structures and contacts can deliver accuracy higher than using full contact maps. Similarly, we demonstrate that non-contacts can improve reconstruction accuracy not only when the used non-contacts are true but also when they are predicted. On the dataset consisting of 150 proteins, we find that by simply using low ranked predicted contacts as non-contacts and adding them as additional restraints, can increase the reconstruction accuracy by 5% when the reconstructed models are evaluated using TM-score. Our findings suggest that secondary structures are invaluable companions of contacts for accurate reconstruction. Confirming some earlier findings, we also find that larger distance thresholds are useful for folding many protein structures which cannot be folded using the standard definition of contacts. Our findings also suggest that for more accurate reconstruction using predicted contacts it is useful to predict contacts at higher distance thresholds (beyond 8 Å) and predict non-contacts.

  4. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees.

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    Keller, Alexander; Förster, Frank; Müller, Tobias; Dandekar, Thomas; Schultz, Jörg; Wolf, Matthias

    2010-01-15

    In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.

  5. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

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    Dandekar Thomas

    2010-01-01

    Full Text Available Abstract Background In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber and Eugene V. Koonin. Open peer review Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.

  6. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

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    Lees Jonathan G

    2008-01-01

    Full Text Available Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

  7. ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus

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    Wolf Matthias

    2009-12-01

    mitochondrial marker COI . Compensatory base changes are very rare within Polyommatini and cannot be used for species delimitation. The implementation of secondary structure information into character-based phylogenetic methods is suggested to further improve the versatility of this marker in phylogenetic studies.

  8. A folding algorithm for extended RNA secondary structures.

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    Höner zu Siederdissen, Christian; Bernhart, Stephan H; Stadler, Peter F; Hofacker, Ivo L

    2011-07-01

    RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction. All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.

  9. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

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    Andronescu Mirela

    2008-08-01

    Full Text Available Abstract Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

  10. Secondary Products (Markets, Competition, and Technological Improvements)

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    Philip A. Araman

    1988-01-01

    Competitiveness, imports, exports, and technological improvements--these are issues facing secondary wood-product manufacturers. The major problems focus on increasing foreign imports and the inability of U.S. industries to repell the imports. How and where should we, as researchers, allocate our efforts to enhance the competitiveness of secondary forest industries in...

  11. Nucleic acid secondary structure prediction and display.

    OpenAIRE

    Stüber, K

    1986-01-01

    A set of programs has been developed for the prediction and display of nucleic acid secondary structures. Information from experimental data can be used to restrict or enforce secondary structural elements. The predictions can be displayed either on normal line printers or on graphic devices like plotters or graphic terminals.

  12. Amino acid code of protein secondary structure.

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    Shestopalov, B V

    2003-01-01

    The calculation of protein three-dimensional structure from the amino acid sequence is a fundamental problem to be solved. This paper presents principles of the code theory of protein secondary structure, and their consequence--the amino acid code of protein secondary structure. The doublet code model of protein secondary structure, developed earlier by the author (Shestopalov, 1990), is part of this theory. The theory basis are: 1) the name secondary structure is assigned to the conformation, stabilized only by the nearest (intraresidual) and middle-range (at a distance no more than that between residues i and i + 5) interactions; 2) the secondary structure consists of regular (alpha-helical and beta-structural) and irregular (coil) segments; 3) the alpha-helices, beta-strands and coil segments are encoded, respectively, by residue pairs (i, i + 4), (i, i + 2), (i, i = 1), according to the numbers of residues per period, 3.6, 2, 1; 4) all such pairs in the amino acid sequence are codons for elementary structural elements, or structurons; 5) the codons are divided into 21 types depending on their strength, i.e. their encoding capability; 6) overlappings of structurons of one and the same structure generate the longer segments of this structure; 7) overlapping of structurons of different structures is forbidden, and therefore selection of codons is required, the codon selection is hierarchic; 8) the code theory of protein secondary structure generates six variants of the amino acid code of protein secondary structure. There are two possible kinds of model construction based on the theory: the physical one using physical properties of amino acid residues, and the statistical one using results of statistical analysis of a great body of structural data. Some evident consequences of the theory are: a) the theory can be used for calculating the secondary structure from the amino acid sequence as a partial solution of the problem of calculation of protein three

  13. Strong eukaryotic IRESs have weak secondary structure.

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    Xuhua Xia

    Full Text Available BACKGROUND: The objective of this work was to investigate the hypothesis that eukaryotic Internal Ribosome Entry Sites (IRES lack secondary structure and to examine the generality of the hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: IRESs of the yeast and the fruit fly are located in the 5'UTR immediately upstream of the initiation codon. The minimum folding energy (MFE of 60 nt RNA segments immediately upstream of the initiation codons was calculated as a proxy of secondary structure stability. MFE of the reverse complements of these 60 nt segments was also calculated. The relationship between MFE and empirically determined IRES activity was investigated to test the hypothesis that strong IRES activity is associated with weak secondary structure. We show that IRES activity in the yeast and the fruit fly correlates strongly with the structural stability, with highest IRES activity found in RNA segments that exhibit the weakest secondary structure. CONCLUSIONS: We found that a subset of eukaryotic IRESs exhibits very low secondary structure in the 5'-UTR sequences immediately upstream of the initiation codon. The consistency in results between the yeast and the fruit fly suggests a possible shared mechanism of cap-independent translation initiation that relies on an unstructured RNA segment.

  14. Protein secondary structure: category assignment and predictability

    DEFF Research Database (Denmark)

    Andersen, Claus A.; Bohr, Henrik; Brunak, Søren

    2001-01-01

    In the last decade, the prediction of protein secondary structure has been optimized using essentially one and the same assignment scheme known as DSSP. We present here a different scheme, which is more predictable. This scheme predicts directly the hydrogen bonds, which stabilize the secondary......-forward neural network with one hidden layer on a data set identical to the one used in earlier work....

  15. Prediction of RNA secondary structure using generalized centroid estimators.

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    Hamada, Michiaki; Kiryu, Hisanori; Sato, Kengo; Mituyama, Toutai; Asai, Kiyoshi

    2009-02-15

    Recent studies have shown that the methods for predicting secondary structures of RNAs on the basis of posterior decoding of the base-pairing probabilities has an advantage with respect to prediction accuracy over the conventionally utilized minimum free energy methods. However, there is room for improvement in the objective functions presented in previous studies, which are maximized in the posterior decoding with respect to the accuracy measures for secondary structures. We propose novel estimators which improve the accuracy of secondary structure prediction of RNAs. The proposed estimators maximize an objective function which is the weighted sum of the expected number of the true positives and that of the true negatives of the base pairs. The proposed estimators are also improved versions of the ones used in previous works, namely CONTRAfold for secondary structure prediction from a single RNA sequence and McCaskill-MEA for common secondary structure prediction from multiple alignments of RNA sequences. We clarify the relations between the proposed estimators and the estimators presented in previous works, and theoretically show that the previous estimators include additional unnecessary terms in the evaluation measures with respect to the accuracy. Furthermore, computational experiments confirm the theoretical analysis by indicating improvement in the empirical accuracy. The proposed estimators represent extensions of the centroid estimators proposed in Ding et al. and Carvalho and Lawrence, and are applicable to a wide variety of problems in bioinformatics. Supporting information and the CentroidFold software are available online at: http://www.ncrna.org/software/centroidfold/.

  16. A Kernel for Protein Secondary Structure Prediction

    OpenAIRE

    Guermeur , Yann; Lifchitz , Alain; Vert , Régis

    2004-01-01

    http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=10338&mode=toc; International audience; Multi-class support vector machines have already proved efficient in protein secondary structure prediction as ensemble methods, to combine the outputs of sets of classifiers based on different principles. In this chapter, their implementation as basic prediction methods, processing the primary structure or the profile of multiple alignments, is investigated. A kernel devoted to the task is in...

  17. Structure elucidation of secondary natural products

    International Nuclear Information System (INIS)

    Seger, C.

    2001-06-01

    The presented thesis deals with the structure elucidation of secondary natural products. Most of the compounds under investigation were terpenes, especially triterpenes, alkaloids and stilbenoids. Besides characterizing a multitude of already known and also new compounds, it was possible to detect and correct wrongly assigned literature data. The methodological aspect of this thesis lies - beside in the utilization of modern 2D NMR spectroscopy - in the evaluation of computer assisted structure elucidation (CASE) techniques in the course of spectroscopy supported structure elucidation processes. (author)

  18. RNA secondary structure prediction using soft computing.

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    Ray, Shubhra Sankar; Pal, Sankar K

    2013-01-01

    Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned.

  19. Ensemble-based prediction of RNA secondary structures.

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    Aghaeepour, Nima; Hoos, Holger H

    2013-04-24

    Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile approaches, and improved methods for this task have received much attention over the past five years. Despite the impressive progress that as been achieved in this area, existing evaluations of the prediction accuracy achieved by various algorithms do not provide a comprehensive, statistically sound assessment. Furthermore, while there is increasing evidence that no prediction algorithm consistently outperforms all others, no work has been done to exploit the complementary strengths of multiple approaches. In this work, we present two contributions to the area of RNA secondary structure prediction. Firstly, we use state-of-the-art, resampling-based statistical methods together with a previously published and increasingly widely used dataset of high-quality RNA structures to conduct a comprehensive evaluation of existing RNA secondary structure prediction procedures. The results from this evaluation clarify the performance relationship between ten well-known existing energy-based pseudoknot-free RNA secondary structure prediction methods and clearly demonstrate the progress that has been achieved in recent years. Secondly, we introduce AveRNA, a generic and powerful method for combining a set of existing secondary structure prediction procedures into an ensemble-based method that achieves significantly higher prediction accuracies than obtained from any of its component procedures. Our new, ensemble-based method, AveRNA, improves the state of the art for energy-based, pseudoknot-free RNA secondary structure prediction by exploiting the complementary strengths of multiple existing prediction procedures, as demonstrated using a state-of-the-art statistical resampling approach. In addition, AveRNA allows an intuitive and effective control of the trade-off between

  20. Predicting Protein Secondary Structure with Markov Models

    DEFF Research Database (Denmark)

    Fischer, Paul; Larsen, Simon; Thomsen, Claus

    2004-01-01

    we are considering here, is to predict the secondary structure from the primary one. To this end we train a Markov model on training data and then use it to classify parts of unknown protein sequences as sheets, helices or coils. We show how to exploit the directional information contained...... in the Markov model for this task. Classifications that are purely based on statistical models might not always be biologically meaningful. We present combinatorial methods to incorporate biological background knowledge to enhance the prediction performance....

  1. A semi-supervised learning approach for RNA secondary structure prediction.

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    Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

    2015-08-01

    RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. RNA-SSPT: RNA Secondary Structure Prediction Tools.

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    Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

    2013-01-01

    The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

  3. Cascaded bidirectional recurrent neural networks for protein secondary structure prediction.

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    Chen, Jinmiao; Chaudhari, Narendra

    2007-01-01

    Protein secondary structure (PSS) prediction is an important topic in bioinformatics. Our study on a large set of non-homologous proteins shows that long-range interactions commonly exist and negatively affect PSS prediction. Besides, we also reveal strong correlations between secondary structure (SS) elements. In order to take into account the long-range interactions and SS-SS correlations, we propose a novel prediction system based on cascaded bidirectional recurrent neural network (BRNN). We compare the cascaded BRNN against another two BRNN architectures, namely the original BRNN architecture used for speech recognition as well as Pollastri's BRNN that was proposed for PSS prediction. Our cascaded BRNN achieves an overall three state accuracy Q3 of 74.38\\%, and reaches a high Segment OVerlap (SOV) of 66.0455. It outperforms the original BRNN and Pollastri's BRNN in both Q3 and SOV. Specifically, it improves the SOV score by 4-6%.

  4. Integrating chemical footprinting data into RNA secondary structure prediction.

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    Kourosh Zarringhalam

    Full Text Available Chemical and enzymatic footprinting experiments, such as shape (selective 2'-hydroxyl acylation analyzed by primer extension, yield important information about RNA secondary structure. Indeed, since the [Formula: see text]-hydroxyl is reactive at flexible (loop regions, but unreactive at base-paired regions, shape yields quantitative data about which RNA nucleotides are base-paired. Recently, low error rates in secondary structure prediction have been reported for three RNAs of moderate size, by including base stacking pseudo-energy terms derived from shape data into the computation of minimum free energy secondary structure. Here, we describe a novel method, RNAsc (RNA soft constraints, which includes pseudo-energy terms for each nucleotide position, rather than only for base stacking positions. We prove that RNAsc is self-consistent, in the sense that the nucleotide-specific probabilities of being unpaired in the low energy Boltzmann ensemble always become more closely correlated with the input shape data after application of RNAsc. From this mathematical perspective, the secondary structure predicted by RNAsc should be 'correct', in as much as the shape data is 'correct'. We benchmark RNAsc against the previously mentioned method for eight RNAs, for which both shape data and native structures are known, to find the same accuracy in 7 out of 8 cases, and an improvement of 25% in one case. Furthermore, we present what appears to be the first direct comparison of shape data and in-line probing data, by comparing yeast asp-tRNA shape data from the literature with data from in-line probing experiments we have recently performed. With respect to several criteria, we find that shape data appear to be more robust than in-line probing data, at least in the case of asp-tRNA.

  5. Prediction of the Secondary Structure of HIV-1 gp120

    DEFF Research Database (Denmark)

    Hansen, Jan; Lund, Ole; Nielsen, Jens O.

    1996-01-01

    Fourier transform infrared spectroscopy. The predicted secondary structure of gp120 compared well with data from NMR analysis of synthetic peptides from the V3 loop and the C4 region. As a first step towards modeling the tertiary structure of gp120, the predicted secondary structure may guide the design......The secondary structure of HIV-1 gp120 was predicted using multiple alignment and a combination of two independent methods based on neural network and nearest-neighbor algorithms. The methods agreed on the secondary structure for 80% of the residues in BH10 gp120. Six helices were predicted in HIV...

  6. Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility.

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    Heffernan, Rhys; Yang, Yuedong; Paliwal, Kuldip; Zhou, Yaoqi

    2017-09-15

    The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some 'short to intermediate' non-local interactions. Here, we employed Long Short-Term Memory (LSTM) Bidirectional Recurrent Neural Networks (BRNNs) which are capable of capturing long range interactions without using a window. We showed that the application of LSTM-BRNN to the prediction of protein structural properties makes the most significant improvement for residues with the most long-range contacts (|i-j| >19) over a previous window-based, deep-learning method SPIDER2. Capturing long-range interactions allows the accuracy of three-state secondary structure prediction to reach 84% and the correlation coefficient between predicted and actual solvent accessible surface areas to reach 0.80, plus a reduction of 5%, 10%, 5% and 10% in the mean absolute error for backbone ϕ , ψ , θ and τ angles, respectively, from SPIDER2. More significantly, 27% of 182724 40-residue models directly constructed from predicted C α atom-based θ and τ have similar structures to their corresponding native structures (6Å RMSD or less), which is 3% better than models built by ϕ and ψ angles. We expect the method to be useful for assisting protein structure and function prediction. The method is available as a SPIDER3 server and standalone package at http://sparks-lab.org . yaoqi.zhou@griffith.edu.au or yuedong.yang@griffith.edu.au. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email

  7. On infrared spectroscopic analysis of transfer RNA secondary structure

    Energy Technology Data Exchange (ETDEWEB)

    Semenov, M A; Starikov, E B

    1987-07-14

    Various techniques of IR spectroscopy in the 1550-1750 cm/sup -1/ region employed to analyse the tRNA secondary structure are discussed and a novel improved method is proposed. The main novel features of this method are the approximation of tRNA helical region spectra by catalogue carbonyl absorption bands and approximation of tRNA nonhelical region spectra by those of homopolyribonucleotides. The IR spectra of tRNA/sub yeast//sup phe/ and tRNA/sub E.coli//sup fmet/ in the carbonyl vibration region are explained on the basis of calculated transition moment coupling.

  8. Strategies for measuring evolutionary conservation of RNA secondary structures

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    Hofacker Ivo L

    2008-02-01

    Full Text Available Abstract Background Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential. Results We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons. Conclusion Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.

  9. ncRNA consensus secondary structure derivation using grammar strings.

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    Achawanantakun, Rujira; Sun, Yanni; Takyar, Seyedeh Shohreh

    2011-04-01

    Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is an important issue in today's RNA research. The state-of-the-art structure annotation tools are based on comparative analysis, which derives consensus structure of homologous ncRNAs. Despite promising results from existing ncRNA aligning and consensus structure derivation tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods. In this work, we introduce a consensus structure derivation approach based on grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar (CFG) and a full RNA grammar including pseudoknots. Being a string defined on a special alphabet constructed from a grammar, grammar string converts ncRNA alignment into sequence alignment. We derive consensus secondary structures from hundreds of ncRNA families from BraliBase 2.1 and 25 families containing pseudoknots using grammar string alignment. Our experiments have shown that grammar string-based structure derivation competes favorably in consensus structure quality with Murlet and RNASampler. Source code and experimental data are available at http://www.cse.msu.edu/~yannisun/grammar-string.

  10. PCI-SS: MISO dynamic nonlinear protein secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Aboul-Magd Mohammed O

    2009-07-01

    protein sequence data and also to encode the resulting structure prediction in a machine-readable format. To our knowledge, this represents the only publicly available SOAP-interface for a protein secondary structure prediction service with published WSDL interface definition. Conclusion Relative to the 9 contemporary methods included in the comparison cascaded PCI classifiers perform well, however PCI finds greatest application as a consensus classifier. When PCI is used to combine a sequence-to-structure PCI-based classifier with the current leading ANN-based method, PSIPRED, the overall error rate (Q3 is maintained while the rate of occurrence of a particularly detrimental error is reduced by up to 25%. This improvement in BAD score, combined with the machine-readable SOAP web service interface makes PCI-SS particularly useful for inclusion in a tertiary structure prediction pipeline.

  11. Secondary Education in the European Union: Structures, Organisation and Administration.

    Science.gov (United States)

    EURYDICE European Unit, Brussels (Belgium).

    This study examines the existing secondary education structures of the European Union member nations, the organization of education, teacher training, and the way in which secondary education is managed in Europe today. The three European Free Trade Association/European Economic Area (EFTA/EEC) countries (Iceland, Liechtenstein, and Norway) also…

  12. Original Paper Floristic and structural changes in secondary forests ...

    African Journals Online (AJOL)

    Data from the first inventory in secondary and old-growth forests were ... Structural changes in secondary forests are less known in West Africa, and ... temporal succession from one time spatial ..... s = number of species sampled per hectare; S = species richness of the whole forest; NF = the number of taxonomic families,.

  13. A method for rapid similarity analysis of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Liu Na

    2006-11-01

    Full Text Available Abstract Background Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures. Results Three sets of real data have been used as input for the example applications. Set I includes the structures from 5S rRNAs. Set II includes the secondary structures from RNase P and RNase MRP. Set III includes the structures from 16S rRNAs. Reasonable phylogenetic trees are derived for these three sets of data by using our method. Moreover, our program runs faster as compared to some existing ones. Conclusion The famous Lempel-Ziv algorithm can efficiently extract the information on repeated patterns encoded in RNA secondary structures and makes our method an alternative to analyze the similarity of RNA secondary structures. This method will also be useful to researchers who are interested in evolutionary analysis.

  14. Rapid NMR screening of RNA secondary structure and binding

    International Nuclear Information System (INIS)

    Helmling, Christina; Keyhani, Sara; Sochor, Florian; Fürtig, Boris; Hengesbach, Martin; Schwalbe, Harald

    2015-01-01

    Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3′ end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields μmol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA

  15. Rapid NMR screening of RNA secondary structure and binding

    Energy Technology Data Exchange (ETDEWEB)

    Helmling, Christina; Keyhani, Sara; Sochor, Florian; Fürtig, Boris; Hengesbach, Martin; Schwalbe, Harald, E-mail: schwalbe@nmr.uni-frankfurt.de [Johann Wolfgang Goethe-Universität, Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ) (Germany)

    2015-09-15

    Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3′ end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields μmol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA.

  16. Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics

    Science.gov (United States)

    Hata, Hiroaki; Kitajima, Tetsuro

    2018-01-01

    Abstract Nucleic acid secondary structure plays an important role in nucleic acid–nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not be ignored in DNA hybridization kinetics, especially under isothermal conditions. Here, we report that positive ΔG° secondary structures can change the hybridization rate by two-orders of magnitude, despite the fact that their hybridization obeyed second-order reaction kinetics. The temperature dependence of hybridization rates showed non-Arrhenius behavior; thus, their hybridization is considered to be nucleation limited. We derived a model describing how ΔG° positive secondary structures affect hybridization kinetics in stopped-flow experiments with 47 pairs of oligonucleotides. The calculated hybridization rates, which were based on the model, quantitatively agreed with the experimental rate constant. PMID:29220504

  17. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.

    Science.gov (United States)

    Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

    2016-01-11

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.

  18. Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

    Science.gov (United States)

    Lorenz, William A.; Clote, Peter

    2011-01-01

    An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server

  19. Computing the partition function for kinetically trapped RNA secondary structures.

    Directory of Open Access Journals (Sweden)

    William A Lorenz

    Full Text Available An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in O(n3 time and O(n2 space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1 the number of locally optimal structures is far fewer than the total number of structures--indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2 the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3 the (modified maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected

  20. Combining neural networks for protein secondary structure prediction

    DEFF Research Database (Denmark)

    Riis, Søren Kamaric

    1995-01-01

    In this paper structured neural networks are applied to the problem of predicting the secondary structure of proteins. A hierarchical approach is used where specialized neural networks are designed for each structural class and then combined using another neural network. The submodels are designed...... by using a priori knowledge of the mapping between protein building blocks and the secondary structure and by using weight sharing. Since none of the individual networks have more than 600 adjustable weights over-fitting is avoided. When ensembles of specialized experts are combined the performance...

  1. RNAstructure: software for RNA secondary structure prediction and analysis.

    Science.gov (United States)

    Reuter, Jessica S; Mathews, David H

    2010-03-15

    To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.

  2. Secondary structural analyses of ITS1 in Paramecium.

    Science.gov (United States)

    Hoshina, Ryo

    2010-01-01

    The nuclear ribosomal RNA gene operon is interrupted by internal transcribed spacer (ITS) 1 and ITS2. Although the secondary structure of ITS2 has been widely investigated, less is known about ITS1 and its structure. In this study, the secondary structure of ITS1 sequences for Paramecium and other ciliates was predicted. Each Paramecium ITS1 forms an open loop with three helices, A through C. Helix B was highly conserved among Paramecium, and similar helices were found in other ciliates. A phylogenetic analysis using the ITS1 sequences showed high-resolution, implying that ITS1 is a good tool for species-level analyses.

  3. RNA secondary structure diagrams for very large molecules: RNAfdl

    DEFF Research Database (Denmark)

    Hecker, Nikolai; Wiegels, Tim; Torda, Andrew E.

    2013-01-01

    There are many programs that can read the secondary structure of an RNA molecule and draw a diagram, but hardly any that can cope with 10 3 bases. RNAfdl is slow but capable of producing intersection-free diagrams for ribosome-sized structures, has a graphical user interface for adjustments...

  4. RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model.

    Science.gov (United States)

    Jabbari, Hosna; Wark, Ian; Montemagno, Carlo

    2018-01-01

    RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design. Since experimental structure determination is time-consuming and expensive, accurate computational prediction of RNA structure is of great importance. Prediction of RNA secondary structure is relatively simpler than its tertiary structure and provides information about its tertiary structure, therefore, RNA secondary structure prediction has received attention in the past decades. Numerous methods with different folding approaches have been developed for RNA secondary structure prediction. While methods for prediction of RNA pseudoknot-free structure (structures with no crossing base pairs) have greatly improved in terms of their accuracy, methods for prediction of RNA pseudoknotted secondary structure (structures with crossing base pairs) still have room for improvement. A long-standing question for improving the prediction accuracy of RNA pseudoknotted secondary structure is whether to focus on the prediction algorithm or the underlying energy model, as there is a trade-off on computational cost of the prediction algorithm versus the generality of the method. The aim of this work is to argue when comparing different methods for RNA pseudoknotted structure prediction, the combination of algorithm and energy model should be considered and a method should not be considered superior or inferior to others if they do not use the same scoring model. We demonstrate that while the folding approach is important in structure prediction, it is not the only important factor in prediction accuracy of a given method as the underlying energy model is also as of great value. Therefore we encourage researchers to pay particular attention in comparing methods with different energy models.

  5. Nuclear fuel assembly incorporating primary and secondary structural support members

    International Nuclear Information System (INIS)

    Carlson, W.R.; Gjertsen, R.K.; Miller, J.V.

    1987-01-01

    A nuclear fuel assembly, comprising: (a) an upper end structure; (b) a lower end structure; (c) elongated primary structural members extending longitudinally between and rigidly interconnecting the upper and lower end structures, the upper and lower end structures and primary structural members together forming a rigid structural skeleton of the fuel assembly; (d) transverse grids supported on the primary structural members at axially spaced locations therealong between the upper and lower end structures; (e) fuel rods extending through and supported by the grids between the upper and lower end structures so as to extend in generally side-by-side spaced relation to one another and to the primary structural members; and (f) elongated secondary structural members extending longitudinally between but unconnected with the upper and lower end structures, the secondary structural members extending through and rigidly interconnected with the grids to extend in generally side-by-side spaced relation to one another, to the fuel rods and to the primary structural members so as to bolster the stiffness of the structural skeleton of the fuel assembly

  6. PFC Performance Improvement of Ultra-supercritical Secondary Reheat Unit

    Directory of Open Access Journals (Sweden)

    Li Jun

    2018-01-01

    Full Text Available Ultra-supercritical secondary reheat unit has been widely used in the world because of its advantages of large capacity, low consumption and high efficiency etc., but rapid load change ability of the turbines to be weakened which caused by its system organization, cannot meet the requirements of power grid frequency modulation. Based on the analysis of the control characteristics of ultra-supercritical once-through reheat unit, the primary frequency control based on feed-water flow overshoot compensation is proposed. The main steam pressure generated by the feed-water is changed to improve the primary frequency control capability. The relevant control strategy has been applied to the 1000MW secondary reheating unit. The results show that the technology is feasible and has high economical efficiency.

  7. RNA secondary structure image - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us fRNAdb RNA secondary structure image Data detail Data name RNA secondary structure image DOI... 10.18908/lsdba.nbdc00452-005 Description of data contents RNA secondary structure images - png.zip: RNA secondary structure image...s (PNG) - pdf.zip: RNA secondary structure images (PDF) - thumbnail.zip: Thumbnails of... RNA secondary structure images Data file File name: RNA_secondary_structure_image... File URL: ftp://ftp.biosciencedbc.jp/archive/frnadb/LATEST/RNA_secondary_structure_image File size: 9.6 GB

  8. Approaches to link RNA secondary structures with splicing regulation

    DEFF Research Database (Denmark)

    Plass, Mireya; Eyras, Eduardo

    2014-01-01

    In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either by facilitat...... describes the steps in the analysis of the secondary structure of the pre-mRNA and its possible relation to splicing. As a working example, we use the case of yeast and the problem of the recognition of the 3' splice site (3'ss).......In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either...

  9. Use of secondary structural information and Cα-Cα distance ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    2007-06-21

    Jun 21, 2007 ... Model evolution; protein modelling; residue contact prediction; secondary structure prediction. Abbreviations used: ... set of sequence data (NR) and calculated conservation index of each ... evaluators (Moult et al 2003) to evaluate these model ... (Siew et al 2000), is a measure aims at identifying the largest.

  10. General enumeration of RNA secondary structures based on new ...

    African Journals Online (AJOL)

    Crick base pairs between AU and GC. Based on the new representation, this paper also computes the number of various types of constrained secondary structures taking the minimum stack length 1 and minimum size m for each bonding loop as ...

  11. A combinatorial enumeration problem of RNA secondary structures

    African Journals Online (AJOL)

    use

    2011-12-21

    Dec 21, 2011 ... connection between Discrete Mathematics and Compu- tational Molecular Biology (Chen et al, 2005; Hofacker et ... in Computational Molecular Biology. An RNA molecule is described by its sequences of bases ... Here, a mathematical definition of secondary structure is given (Stein and Waterman 1978).

  12. A combinatorial enumeration problem of RNA secondary structures

    African Journals Online (AJOL)

    use

    2011-12-21

    Dec 21, 2011 ... interesting combinatorial questions (Chen et al., 2005;. Liu, 2006; Schmitt and Waterman 1994; Stein and. Waterman 1978). The research on the enumeration of. RNA secondary structures becomes one of the hot topics in Computational Molecular Biology. An RNA molecule is described by its sequences of.

  13. Improving ultrasound for appendicitis through standardized reporting of secondary signs.

    Science.gov (United States)

    Partain, Kristin N; Patel, Adarsh U; Travers, Curtis; Short, Heather L; Braithwaite, Kiery; Loewen, Jonathan; Heiss, Kurt F; Raval, Mehul V

    2017-08-01

    Our aim was to implement a standardized US report that included secondary signs of appendicitis (SS) to facilitate accurate diagnosis of appendicitis and decrease the use of computed tomography (CT) and admissions for observation. A multidisciplinary team implemented a quality improvement (QI) intervention in the form of a standardized US report and provided stakeholders with monthly feedback. Outcomes including report compliance, CT use, and observation admissions were compared pretemplate and posttemplate. We identified 387 patients in the pretemplate period and 483 patients in the posttemplate period. In the posttemplate period, the reporting of SS increased from 5.4% to 79.5% (pappendicitis also improved in the posttemplate period. A focused QI initiative led to high compliance rates of utilizing the standardized US report and resulted in lower CT use and fewer admissions for observation. Study of a Diagnostic Test Level of Evidence: 1. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Quantitative DMS mapping for automated RNA secondary structure inference

    OpenAIRE

    Cordero, Pablo; Kladwang, Wipapat; VanLang, Christopher C.; Das, Rhiju

    2012-01-01

    For decades, dimethyl sulfate (DMS) mapping has informed manual modeling of RNA structure in vitro and in vivo. Here, we incorporate DMS data into automated secondary structure inference using a pseudo-energy framework developed for 2'-OH acylation (SHAPE) mapping. On six non-coding RNAs with crystallographic models, DMS- guided modeling achieves overall false negative and false discovery rates of 9.5% and 11.6%, comparable or better than SHAPE-guided modeling; and non-parametric bootstrappin...

  15. Structuring diabetes care in general practices: many improvements, remaining challenges.

    LENUS (Irish Health Repository)

    Jennings, S

    2009-08-07

    BACKGROUND: For people with type 2 diabetes to enjoy improved longevity and quality of life, care needs to be organised in a systematic way. AIM: To test if processes and intermediate outcomes for patients with type 2 diabetes changed with the move to structured care in general practice shared with secondary care. METHODS: An audit of process and intermediate outcomes for patients with type 2 diabetes before and after the change to structured care in 10 Dublin general practices shared with secondary care four years on. RESULTS: Structured diabetes care in general practice has led to more dedicated clinics improved processes of care and increased access to multidisciplinary expertise. Improvement in blood pressure control, the use of aspirin and the use of lipid lowering agents indicate a significant decrease in absolute risk of vascular events for this population. CONCLUSIONS: Structured care in general practice improves intermediate outcomes for people with type 2 diabetes. Further improvements need to be made to reach international targets.

  16. A phase transition in energy-filtered RNA secondary structures

    DEFF Research Database (Denmark)

    Han, Hillary Siwei; reidys, Christian

    2012-01-01

    In this paper we study the effect of energy parameters on minimum free energy (mfe) RNA secondary structures. Employing a simplified combinatorial energy model, that is only dependent on the diagram representation and that is not sequence specific, we prove the following dichotomy result. Mfe...... this phase transition from a discrete limit to a central limit distribution and subsequently put our result into the context of quantifying the effect of sparsification of the folding of these respective mfe-structures. We show that the sparsification of realistic mfe-structures leads to a constant time...

  17. Protein Secondary Structure Prediction Using AutoEncoder Network and Bayes Classifier

    Science.gov (United States)

    Wang, Leilei; Cheng, Jinyong

    2018-03-01

    Protein secondary structure prediction is belong to bioinformatics,and it's important in research area. In this paper, we propose a new prediction way of protein using bayes classifier and autoEncoder network. Our experiments show some algorithms including the construction of the model, the classification of parameters and so on. The data set is a typical CB513 data set for protein. In terms of accuracy, the method is the cross validation based on the 3-fold. Then we can get the Q3 accuracy. Paper results illustrate that the autoencoder network improved the prediction accuracy of protein secondary structure.

  18. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

    Science.gov (United States)

    Hajdin, Christine E; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W; Mathews, David H; Weeks, Kevin M

    2013-04-02

    A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.

  19. Random generation of RNA secondary structures according to native distributions

    Directory of Open Access Journals (Sweden)

    Nebel Markus E

    2011-10-01

    Full Text Available Abstract Background Random biological sequences are a topic of great interest in genome analysis since, according to a powerful paradigm, they represent the background noise from which the actual biological information must differentiate. Accordingly, the generation of random sequences has been investigated for a long time. Similarly, random object of a more complicated structure like RNA molecules or proteins are of interest. Results In this article, we present a new general framework for deriving algorithms for the non-uniform random generation of combinatorial objects according to the encoding and probability distribution implied by a stochastic context-free grammar. Briefly, the framework extends on the well-known recursive method for (uniform random generation and uses the popular framework of admissible specifications of combinatorial classes, introducing weighted combinatorial classes to allow for the non-uniform generation by means of unranking. This framework is used to derive an algorithm for the generation of RNA secondary structures of a given fixed size. We address the random generation of these structures according to a realistic distribution obtained from real-life data by using a very detailed context-free grammar (that models the class of RNA secondary structures by distinguishing between all known motifs in RNA structure. Compared to well-known sampling approaches used in several structure prediction tools (such as SFold ours has two major advantages: Firstly, after a preprocessing step in time O(n2 for the computation of all weighted class sizes needed, with our approach a set of m random secondary structures of a given structure size n can be computed in worst-case time complexity Om⋅n⋅ log(n while other algorithms typically have a runtime in O(m⋅n2. Secondly, our approach works with integer arithmetic only which is faster and saves us from all the discomforting details of using floating point arithmetic with

  20. RNA secondary structures of the bacteriophage phi6 packaging regions.

    OpenAIRE

    Pirttimaa, M J; Bamford, D H

    2000-01-01

    Bacteriophage phi6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only phi6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for phi6, and the packaging signals (pac sites) have been mapped to the 5' ends of the RNA segments. In this study, we propose secondary structure models ...

  1. STUDYING THE SECONDARY STRUCTURE OF ACCESSION NUMBER USING CETD MATRIX

    Directory of Open Access Journals (Sweden)

    Anamika Dutta

    2016-10-01

    Full Text Available This paper, we have tried to analyze about the Secondary Structure of nucleotide sequences of rice. The data have been collected from NCBI (National Centre for Biotechnology Information using Nucleotide as data base. All the programs were developed using R programming language using “sequinr” package. Here, we have used CETD matrix method to study the prediction. The conclusions are drawn accordingly.

  2. Evolutionary rate variation and RNA secondary structure prediction

    DEFF Research Database (Denmark)

    Knudsen, B.; Andersen, E.S.; Damgaard, C.

    2004-01-01

    Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type...... by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions...

  3. Methods and compositions for improving secondary recovery of oil

    Energy Technology Data Exchange (ETDEWEB)

    Marlowe, B.; Raymond, R.L.; Douros, J.D. Jr.

    1964-12-22

    In a waterflood process, the waterflood is improved by incorporating with it a microorganism growth-inhibiting amount of a di-substituted naphthalene of the structure: wherein R and R's are substituents selected from the group consisting of (1) hydroxy, (2) hydroxyalkyl, (3) carboxy, (4) the salts of carboxy, and (5) the oxides of hydroxynaphthalene (the hydroxyalkyl and carboxy substituents each having from 1 to 6 carbon atoms). (7 claims)

  4. Global Analysis of RNA Secondary Structure in Two Metazoans

    Directory of Open Access Journals (Sweden)

    Fan Li

    2012-01-01

    Full Text Available The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA] and unpaired (single-stranded RNA [ssRNA] components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals.

  5. RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

    Science.gov (United States)

    Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

    2009-01-01

    The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

  6. Improved fluid-structure coupling

    International Nuclear Information System (INIS)

    McMaster, W.H.; Gong, E.Y.; Landram, C.S.

    1981-01-01

    In the computer code PELE-IC, an incompressible Eulerian hydrodynamic algorithm was coupled to a Lagrangian finite element shell algorithm for the analysis of pressure suppression in boiling water reactors. This effort also required the development of a free surface algorithm capable of handling expanding gas bubbles. These algorithms have been improved to strengthen the coupling and to add the capability for following the more complex free surfaces resulting from steam condensation. These improvements have also permitted more economical 2D calculations and have made it feasible to develop a 3D version. A compressible option using the acoustic approximation has also been added, furthering the usefulness of the code. The coupling improvements were made in three areas which are identified as (1) preferential coupling, (2) merged cell coupling, and (3) free surface-structure coupling, and are described. These algorithms have been additionally implemented in a three dimensional version of the code called PELE3D. This version has a free surface capability to follow expanding and contracting bubbles and is coupled to a curved rigid surface

  7. RNA secondary structures of the bacteriophage phi6 packaging regions.

    Science.gov (United States)

    Pirttimaa, M J; Bamford, D H

    2000-06-01

    Bacteriophage phi6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only phi6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for phi6, and the packaging signals (pac sites) have been mapped to the 5' ends of the RNA segments. In this study, we propose secondary structure models for the pac sites of phi6 single-stranded RNA segments. Our models accommodate data from structure-specific chemical modifications, free energy minimizations, and phylogenetic comparisons. Previously reported pac site deletion studies are also discussed. Each pac site possesses a unique architecture, that, however, contains common structural elements.

  8. Secondary Structure of Rat and Human Amylin across Force Fields.

    Directory of Open Access Journals (Sweden)

    Kyle Quynn Hoffmann

    Full Text Available The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient

  9. Parallel protein secondary structure prediction based on neural networks.

    Science.gov (United States)

    Zhong, Wei; Altun, Gulsah; Tian, Xinmin; Harrison, Robert; Tai, Phang C; Pan, Yi

    2004-01-01

    Protein secondary structure prediction has a fundamental influence on today's bioinformatics research. In this work, binary and tertiary classifiers of protein secondary structure prediction are implemented on Denoeux belief neural network (DBNN) architecture. Hydrophobicity matrix, orthogonal matrix, BLOSUM62 and PSSM (position specific scoring matrix) are experimented separately as the encoding schemes for DBNN. The experimental results contribute to the design of new encoding schemes. New binary classifier for Helix versus not Helix ( approximately H) for DBNN produces prediction accuracy of 87% when PSSM is used for the input profile. The performance of DBNN binary classifier is comparable to other best prediction methods. The good test results for binary classifiers open a new approach for protein structure prediction with neural networks. Due to the time consuming task of training the neural networks, Pthread and OpenMP are employed to parallelize DBNN in the hyperthreading enabled Intel architecture. Speedup for 16 Pthreads is 4.9 and speedup for 16 OpenMP threads is 4 in the 4 processors shared memory architecture. Both speedup performance of OpenMP and Pthread is superior to that of other research. With the new parallel training algorithm, thousands of amino acids can be processed in reasonable amount of time. Our research also shows that hyperthreading technology for Intel architecture is efficient for parallel biological algorithms.

  10. Changes in secondary structure of poliovirus ribonucleic acid

    International Nuclear Information System (INIS)

    Koza, J.

    1975-01-01

    Infectious single-stranded RNA isolated from mature purified poliovirus was separated into three fractions by means of chromatography on an ''evaporated'' calcium phosphate column. RNA molecules with a higher degree of secondary structure were detected in two of the fractions as a result of the chromatography. These RNA molecules (1) were resistant to hydrolysis by pancreatic ribonuclease A, (2) retained unchanged the original infectivity for actinomycin D-pretreated cells, (3) were resistant to ultraviolet-light inactivation and (4) were partially resistant to formaldehyde inactivation

  11. DNA secondary structures: stability and function of G-quadruplex structures

    Science.gov (United States)

    Bochman, Matthew L.; Paeschke, Katrin; Zakian, Virginia A.

    2013-01-01

    In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures. Although many such structures were long thought to be in vitro artefacts, bioinformatics demonstrates that DNA sequences capable of forming these structures are conserved throughout evolution, suggesting the existence of non-B-form DNA in vivo. In addition, genes whose products promote formation or resolution of these structures are found in diverse organisms, and a growing body of work suggests that the resolution of DNA secondary structures is critical for genome integrity. This Review focuses on emerging evidence relating to the characteristics of G-quadruplex structures and the possible influence of such structures on genomic stability and cellular processes, such as transcription. PMID:23032257

  12. RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

    Science.gov (United States)

    Ellington, Roni; Wachira, James; Nkwanta, Asamoah

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses…

  13. Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

    Science.gov (United States)

    Wu, Johnny C; Gardner, David P; Ozer, Stuart; Gutell, Robin R; Ren, Pengyu

    2009-08-28

    The accurate prediction of the secondary and tertiary structure of an RNA with different folding algorithms is dependent on several factors, including the energy functions. However, an RNA higher-order structure cannot be predicted accurately from its sequence based on a limited set of energy parameters. The inter- and intramolecular forces between this RNA and other small molecules and macromolecules, in addition to other factors in the cell such as pH, ionic strength, and temperature, influence the complex dynamics associated with transition of a single stranded RNA to its secondary and tertiary structure. Since all of the factors that affect the formation of an RNAs 3D structure cannot be determined experimentally, statistically derived potential energy has been used in the prediction of protein structure. In the current work, we evaluate the statistical free energy of various secondary structure motifs, including base-pair stacks, hairpin loops, and internal loops, using their statistical frequency obtained from the comparative analysis of more than 50,000 RNA sequences stored in the RNA Comparative Analysis Database (rCAD) at the Comparative RNA Web (CRW) Site. Statistical energy was computed from the structural statistics for several datasets. While the statistical energy for a base-pair stack correlates with experimentally derived free energy values, suggesting a Boltzmann-like distribution, variation is observed between different molecules and their location on the phylogenetic tree of life. Our statistical energy values calculated for several structural elements were utilized in the Mfold RNA-folding algorithm. The combined statistical energy values for base-pair stacks, hairpins and internal loop flanks result in a significant improvement in the accuracy of secondary structure prediction; the hairpin flanks contribute the most.

  14. Secondary structural entropy in RNA switch (Riboswitch) identification.

    Science.gov (United States)

    Manzourolajdad, Amirhossein; Arnold, Jonathan

    2015-04-28

    RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA. Riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. A typical class of riboswitch has its own unique structural and biological complexity, making de novo riboswitch identification a formidable task. Traditionally, riboswitches have been identified through comparative genomics based on sequence and structural homology. The limitations of structural-homology-based approaches, coupled with the assumption that there is a great diversity of undiscovered riboswitches, suggests the need for alternative methods for riboswitch identification, possibly based on features intrinsic to their structure. As of yet, no such reliable method has been proposed. We used structural entropy of riboswitch sequences as a measure of their secondary structural dynamics. Entropy values of a diverse set of riboswitches were compared to that of their mutants, their dinucleotide shuffles, and their reverse complement sequences under different stochastic context-free grammar folding models. Significance of our results was evaluated by comparison to other approaches, such as the base-pairing entropy and energy landscapes dynamics. Classifiers based on structural entropy optimized via sequence and structural features were devised as riboswitch identifiers and tested on Bacillus subtilis, Escherichia coli, and Synechococcus elongatus as an exploration of structural entropy based approaches. The unusually long untranslated region of the cotH in Bacillus subtilis, as well as upstream regions of certain genes, such as the sucC genes were associated with significant structural entropy values in genome-wide examinations. Various tests show that there

  15. Knowledge base and neural network approach for protein secondary structure prediction.

    Science.gov (United States)

    Patel, Maulika S; Mazumdar, Himanshu S

    2014-11-21

    Protein structure prediction is of great relevance given the abundant genomic and proteomic data generated by the genome sequencing projects. Protein secondary structure prediction is addressed as a sub task in determining the protein tertiary structure and function. In this paper, a novel algorithm, KB-PROSSP-NN, which is a combination of knowledge base and modeling of the exceptions in the knowledge base using neural networks for protein secondary structure prediction (PSSP), is proposed. The knowledge base is derived from a proteomic sequence-structure database and consists of the statistics of association between the 5-residue words and corresponding secondary structure. The predicted results obtained using knowledge base are refined with a Backpropogation neural network algorithm. Neural net models the exceptions of the knowledge base. The Q3 accuracy of 90% and 82% is achieved on the RS126 and CB396 test sets respectively which suggest improvement over existing state of art methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Protein secondary structure prediction for a single-sequence using hidden semi-Markov models

    Directory of Open Access Journals (Sweden)

    Borodovsky Mark

    2006-03-01

    Full Text Available Abstract Background The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of prediction algorithms: Single-sequence prediction algorithms imply that information about other (homologous proteins is not available, while algorithms of the second type imply that information about homologous proteins is available, and use it intensively. The single-sequence algorithms could make an important contribution to studies of proteins with no detected homologs, however the accuracy of protein secondary structure prediction from a single-sequence is not as high as when the additional evolutionary information is present. Results In this paper, we further refine and extend the hidden semi-Markov model (HSMM initially considered in the BSPSS algorithm. We introduce an improved residue dependency model by considering the patterns of statistically significant amino acid correlation at structural segment borders. We also derive models that specialize on different sections of the dependency structure and incorporate them into HSMM. In addition, we implement an iterative training method to refine estimates of HSMM parameters. The three-state-per-residue accuracy and other accuracy measures of the new method, IPSSP, are shown to be comparable or better than ones for BSPSS as well as for PSIPRED, tested under the single-sequence condition. Conclusions We have shown that new dependency models and training methods bring further improvements to single-sequence protein secondary structure prediction. The results are obtained under cross-validation conditions using a dataset with no pair of sequences having significant sequence similarity. As new sequences are added to the database it is possible to augment the dependency structure and obtain even higher accuracy. Current and future advances should contribute to the improvement of function prediction for orphan proteins inscrutable

  17. Bi-objective integer programming for RNA secondary structure prediction with pseudoknots.

    Science.gov (United States)

    Legendre, Audrey; Angel, Eric; Tahi, Fariza

    2018-01-15

    RNA structure prediction is an important field in bioinformatics, and numerous methods and tools have been proposed. Pseudoknots are specific motifs of RNA secondary structures that are difficult to predict. Almost all existing methods are based on a single model and return one solution, often missing the real structure. An alternative approach would be to combine different models and return a (small) set of solutions, maximizing its quality and diversity in order to increase the probability that it contains the real structure. We propose here an original method for predicting RNA secondary structures with pseudoknots, based on integer programming. We developed a generic bi-objective integer programming algorithm allowing to return optimal and sub-optimal solutions optimizing simultaneously two models. This algorithm was then applied to the combination of two known models of RNA secondary structure prediction, namely MEA and MFE. The resulting tool, called BiokoP, is compared with the other methods in the literature. The results show that the best solution (structure with the highest F 1 -score) is, in most cases, given by BiokoP. Moreover, the results of BiokoP are homogeneous, regardless of the pseudoknot type or the presence or not of pseudoknots. Indeed, the F 1 -scores are always higher than 70% for any number of solutions returned. The results obtained by BiokoP show that combining the MEA and the MFE models, as well as returning several optimal and several sub-optimal solutions, allow to improve the prediction of secondary structures. One perspective of our work is to combine better mono-criterion models, in particular to combine a model based on the comparative approach with the MEA and the MFE models. This leads to develop in the future a new multi-objective algorithm to combine more than two models. BiokoP is available on the EvryRNA platform: https://EvryRNA.ibisc.univ-evry.fr .

  18. Improving the Utilisation of Management Information Systems in Secondary Schools

    Science.gov (United States)

    Bosker, R. J.; Branderhorst, E. M.; Visscher, A. J.

    2007-01-01

    Although most secondary schools do use management information systems (MISs), these systems tend not to be used to support higher order managerial activities but are currently primarily used for clerical purposes. This situation is unsatisfactory as MISs fully utilised could offer invaluable support to schools, which are increasingly being granted…

  19. Improving the utilisation of management information systems in secondary schools

    NARCIS (Netherlands)

    Bosker, R. J.; Branderhorst, E. M.; Visscher, A. J.

    2007-01-01

    Although most secondary schools do use management information systems (MISs), these systems tend not to be used to support higher order managerial activities but are currently primarily used for clerical purposes. This situation is unsatisfactory as MISs fully utilised could offer invaluable support

  20. Consequential secondary structure alterations and aggregation during prolonged casein glycation.

    Science.gov (United States)

    Jindal, Supriya; Naeem, Aabgeena

    2013-05-01

    Non-enzymatic glycosylation (glycation) of casein is a process used not just to ameliorate the quality of dairy products but also to increase the shelf life of canned foods, including baby milk supplements. Incubation of κ-casein with reducing sugars for 15 days at physiological temperature showed the formation of a molten globule state at day 9 and 12 during fructation and glucation respectively. This state exhibits substantial secondary structure and maximum ANS binding. Later on, glycation resulted in the formation of aggregates at day 12 in presence of fructose and day 15 in presence of glucose. Aggregates possess extensive β-sheet structure as revealed by far-UV CD and FTIR. These aggregates showed altered tryptophan environment, decrease ANS binding relative to molten globule state and increase in Thioflavin T fluorescence. Aggregates were also accompanied by the accumulation of AGEs, indicative of structural damage to the protein and formation of potentially harmful species at the physiological level. Fructose was more reactive than glucose and thus caused early and significant changes in the protein. From our studies, we conclude that controlling the extent of the Maillard reaction in the food industry is essential to counter its negative effects and expand its safety spectrum.

  1. Protein 8-class secondary structure prediction using conditional neural fields.

    Science.gov (United States)

    Wang, Zhiyong; Zhao, Feng; Peng, Jian; Xu, Jinbo

    2011-10-01

    Compared with the protein 3-class secondary structure (SS) prediction, the 8-class prediction gains less attention and is also much more challenging, especially for proteins with few sequence homologs. This paper presents a new probabilistic method for 8-class SS prediction using conditional neural fields (CNFs), a recently invented probabilistic graphical model. This CNF method not only models the complex relationship between sequence features and SS, but also exploits the interdependency among SS types of adjacent residues. In addition to sequence profiles, our method also makes use of non-evolutionary information for SS prediction. Tested on the CB513 and RS126 data sets, our method achieves Q8 accuracy of 64.9 and 64.7%, respectively, which are much better than the SSpro8 web server (51.0 and 48.0%, respectively). Our method can also be used to predict other structure properties (e.g. solvent accessibility) of a protein or the SS of RNA. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction.

    Science.gov (United States)

    Fang, Chao; Shang, Yi; Xu, Dong

    2018-05-01

    Protein secondary structure prediction can provide important information for protein 3D structure prediction and protein functions. Deep learning offers a new opportunity to significantly improve prediction accuracy. In this article, a new deep neural network architecture, named the Deep inception-inside-inception (Deep3I) network, is proposed for protein secondary structure prediction and implemented as a software tool MUFOLD-SS. The input to MUFOLD-SS is a carefully designed feature matrix corresponding to the primary amino acid sequence of a protein, which consists of a rich set of information derived from individual amino acid, as well as the context of the protein sequence. Specifically, the feature matrix is a composition of physio-chemical properties of amino acids, PSI-BLAST profile, and HHBlits profile. MUFOLD-SS is composed of a sequence of nested inception modules and maps the input matrix to either eight states or three states of secondary structures. The architecture of MUFOLD-SS enables effective processing of local and global interactions between amino acids in making accurate prediction. In extensive experiments on multiple datasets, MUFOLD-SS outperformed the best existing methods and other deep neural networks significantly. MUFold-SS can be downloaded from http://dslsrv8.cs.missouri.edu/~cf797/MUFoldSS/download.html. © 2018 Wiley Periodicals, Inc.

  3. A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures

    Science.gov (United States)

    2014-01-01

    Background Improving accuracy and efficiency of computational methods that predict pseudoknotted RNA secondary structures is an ongoing challenge. Existing methods based on free energy minimization tend to be very slow and are limited in the types of pseudoknots that they can predict. Incorporating known structural information can improve prediction accuracy; however, there are not many methods for prediction of pseudoknotted structures that can incorporate structural information as input. There is even less understanding of the relative robustness of these methods with respect to partial information. Results We present a new method, Iterative HFold, for pseudoknotted RNA secondary structure prediction. Iterative HFold takes as input a pseudoknot-free structure, and produces a possibly pseudoknotted structure whose energy is at least as low as that of any (density-2) pseudoknotted structure containing the input structure. Iterative HFold leverages strengths of earlier methods, namely the fast running time of HFold, a method that is based on the hierarchical folding hypothesis, and the energy parameters of HotKnots V2.0. Our experimental evaluation on a large data set shows that Iterative HFold is robust with respect to partial information, with average accuracy on pseudoknotted structures steadily increasing from roughly 54% to 79% as the user provides up to 40% of the input structure. Iterative HFold is much faster than HotKnots V2.0, while having comparable accuracy. Iterative HFold also has significantly better accuracy than IPknot on our HK-PK and IP-pk168 data sets. Conclusions Iterative HFold is a robust method for prediction of pseudoknotted RNA secondary structures, whose accuracy with more than 5% information about true pseudoknot-free structures is better than that of IPknot, and with about 35% information about true pseudoknot-free structures compares well with that of HotKnots V2.0 while being significantly faster. Iterative HFold and all data used in

  4. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  5. Using "get with the guidelines" to improve cardiovascular secondary prevention.

    Science.gov (United States)

    LaBresh, Kenneth A; Gliklich, Richard; Liljestrand, James; Peto, Randolph; Ellrodt, A Gray

    2003-10-01

    "Get With The Guidelines (GWTG)" was developed and piloted by the American Heart Association (AHA), New England Affiliate; MassPRO, Inc.; and other organizations to reduce the gap in the application of secondary prevention guidelines in hospitalized cardiovascular disease patients. Collaborative learning programs and technology solutions were created for the project. The interactive Web-based patient management tool (PMT) was developed using quality measures derived from the AHA/American College of Cardiology secondary prevention guidelines. It provided data entry, embedded reminders and guideline summaries, and online reports of quality measure performance, including comparisons with the aggregate performance of all hospitals. Multidisciplinary teams from 24 hospitals participated in the 2000-2001 pilot. Four collaborative learning sessions and monthly conference calls supported team interaction. Best-practices sharing and the use of an Internet tool enabled hospitals to change systems and collect data on 1,738 patients. The GWTG program, a template of learning sessions with didactic presentations, best-practices sharing, and collaborative multidisciplinary team meetings supported by the Internet-based data collection and reporting system, can be extended to multiple regions without requiring additional development. Following the completion of the pilot, the AHA adopted GWTG as a national program.

  6. Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.

    Science.gov (United States)

    Al-Khatib, Ra'ed M; Rashid, Nur'Aini Abdul; Abdullah, Rosni

    2011-08-01

    The secondary structure of RNA pseudoknots has been extensively inferred and scrutinized by computational approaches. Experimental methods for determining RNA structure are time consuming and tedious; therefore, predictive computational approaches are required. Predicting the most accurate and energy-stable pseudoknot RNA secondary structure has been proven to be an NP-hard problem. In this paper, a new RNA folding approach, termed MSeeker, is presented; it includes KnotSeeker (a heuristic method) and Mfold (a thermodynamic algorithm). The global optimization of this thermodynamic heuristic approach was further enhanced by using a case-based reasoning technique as a local optimization method. MSeeker is a proposed algorithm for predicting RNA pseudoknot structure from individual sequences, especially long ones. This research demonstrates that MSeeker improves the sensitivity and specificity of existing RNA pseudoknot structure predictions. The performance and structural results from this proposed method were evaluated against seven other state-of-the-art pseudoknot prediction methods. The MSeeker method had better sensitivity than the DotKnot, FlexStem, HotKnots, pknotsRG, ILM, NUPACK and pknotsRE methods, with 79% of the predicted pseudoknot base-pairs being correct.

  7. SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

    Science.gov (United States)

    Tong, Jing; Pei, Jimin; Grishin, Nick V

    2015-09-03

    Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

  8. Improving consensus structure by eliminating averaging artifacts

    Directory of Open Access Journals (Sweden)

    KC Dukka B

    2009-03-01

    Full Text Available Abstract Background Common structural biology methods (i.e., NMR and molecular dynamics often produce ensembles of molecular structures. Consequently, averaging of 3D coordinates of molecular structures (proteins and RNA is a frequent approach to obtain a consensus structure that is representative of the ensemble. However, when the structures are averaged, artifacts can result in unrealistic local geometries, including unphysical bond lengths and angles. Results Herein, we describe a method to derive representative structures while limiting the number of artifacts. Our approach is based on a Monte Carlo simulation technique that drives a starting structure (an extended or a 'close-by' structure towards the 'averaged structure' using a harmonic pseudo energy function. To assess the performance of the algorithm, we applied our approach to Cα models of 1364 proteins generated by the TASSER structure prediction algorithm. The average RMSD of the refined model from the native structure for the set becomes worse by a mere 0.08 Å compared to the average RMSD of the averaged structures from the native structure (3.28 Å for refined structures and 3.36 A for the averaged structures. However, the percentage of atoms involved in clashes is greatly reduced (from 63% to 1%; in fact, the majority of the refined proteins had zero clashes. Moreover, a small number (38 of refined structures resulted in lower RMSD to the native protein versus the averaged structure. Finally, compared to PULCHRA 1, our approach produces representative structure of similar RMSD quality, but with much fewer clashes. Conclusion The benchmarking results demonstrate that our approach for removing averaging artifacts can be very beneficial for the structural biology community. Furthermore, the same approach can be applied to almost any problem where averaging of 3D coordinates is performed. Namely, structure averaging is also commonly performed in RNA secondary prediction 2, which

  9. Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

    Science.gov (United States)

    Spanò, M.; Lillo, F.; Miccichè, S.; Mantegna, R. N.

    2008-10-01

    By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups, hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact, we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.

  10. Reviews of National Policies for Education: Improving Lower Secondary Schools in Norway, 2011

    Science.gov (United States)

    OECD Publishing (NJ3), 2011

    2011-01-01

    The report aims to help education authorities in Norway and other OECD (Organisation for Economic Cooperation and Development) countries to understand the importance of lower secondary education and to find approaches to strengthen this key education level. It provides an overview of the structure of lower secondary education and the main…

  11. Improvements to secondary coolant circuits of a liquid metal cooled nuclear reactor

    International Nuclear Information System (INIS)

    Brachet, Alain.

    1981-01-01

    This invention concerns improvements to secondary coolant-systems for sodium cooled nuclear reactors. It further concerns a protective device for a free level mechanical pump which prevents any gas bubbles due to leaks of the working gas of the pump from entering the secondary system of the nuclear reactor [fr

  12. TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

    Directory of Open Access Journals (Sweden)

    Sharma Gaurav

    2011-04-01

    Full Text Available Abstract Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. Results TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold. TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a

  13. 75 FR 7459 - Office of Elementary and Secondary Education; Overview Information; Improving Literacy Through...

    Science.gov (United States)

    2010-02-19

    ... information literacy, information retrieval, and critical-thinking skills of students; facilitating Internet... DEPARTMENT OF EDUCATION Office of Elementary and Secondary Education; Overview Information; Improving Literacy Through School Libraries Program Notice Inviting Applications for New Awards for Fiscal...

  14. JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.

    Science.gov (United States)

    Shi, Jieming; Li, Xi; Dong, Min; Graham, Mitchell; Yadav, Nehul; Liang, Chun

    2017-01-01

    Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html.

  15. JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

    Science.gov (United States)

    Dong, Min; Graham, Mitchell; Yadav, Nehul

    2017-01-01

    Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

  16. JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.

    Directory of Open Access Journals (Sweden)

    Jieming Shi

    Full Text Available Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html.

  17. Secondary antibodies as tools to improve tumor to non tumor ratio at radioimmunolocalisation and radioimmunotherapy

    International Nuclear Information System (INIS)

    Ullen, A.; Riklund Aalstroem, K.; Hietala, S.O.; Nilsson, B.; Aerlestig, L.; Stigbrand, T.

    1996-01-01

    One way of selectively improving the efficiency of radioimmunolocalization and radioimmunotherapy is to eliminate redundant, circulating, non-targeting radiolabeled antibodies after saturation of the target sites. Secondary antibodies of different types have been proposed as clearing agents for such purposes. The conceptually different approaches of the 'secondary antibody' strategy including its advantages and limitations are discussed. This mini-review also presents a model describing the kinetics of the components (the antigen, the primary and secondary antibodies) and approaches required to improve the efficacy of both radioimmunolocalization and radioimmunotherapy. (orig.)

  18. Rtools: a web server for various secondary structural analyses on single RNA sequences.

    Science.gov (United States)

    Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

    2016-07-08

    The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities.

    Science.gov (United States)

    Hagio, Taichi; Sakuraba, Shun; Iwakiri, Junichi; Mori, Ryota; Asai, Kiyoshi

    2018-02-19

    It is known that functional RNAs often switch their functions by forming different secondary structures. Popular tools for RNA secondary structures prediction, however, predict the single 'best' structures, and do not produce alternative structures. There are bioinformatics tools to predict suboptimal structures, but it is difficult to detect which alternative secondary structures are essential. We proposed a new computational method to detect essential alternative secondary structures from RNA sequences by decomposing the base-pairing probability matrix. The decomposition is calculated by a newly implemented software tool, RintW, which efficiently computes the base-pairing probability distributions over the Hamming distance from arbitrary reference secondary structures. The proposed approach has been demonstrated on ROSE element RNA thermometer sequence and Lysine RNA ribo-switch, showing that the proposed approach captures conformational changes in secondary structures. We have shown that alternative secondary structures are captured by decomposing base-paring probabilities over Hamming distance. Source code is available from http://www.ncRNA.org/RintW .

  20. Improving secondary clarifier performance at the Oakville Oil Refinery

    International Nuclear Information System (INIS)

    Edwards, S.M.; Bagley, D.M.

    2002-01-01

    The purpose of this study was threefold: to investigate the relationship between settleability and the physical properties of activated sludge, to correlate settleability and key operational parameters such as chemical oxygen demand (COD) concentration at the aeration basin inlet and to determine potential operational improvements to the Oakville Oil Refinery Wastewater Treatment Plant. Nine separate sets of stirred sludge-settling tests were conducted over a six-month period to measure settleability. The stirred sludge volume index (SSVI), the zone settling constants, and the Zheng-Bagley compression constants were determined. State point analyses were conducted to determine the maximum solids flux of the clarifiers. The concentrations of Al, Mn, Mg, Fe, Ca, Na, and K were determined to identify potential correlations to settling characteristics. Extracellular polymeric substances were extracted from the sludge and analyzed for the same reason. The performance of the clarifiers was highly variable during the period examined. As the refinery process flows and effluent streams changed, influent COD increased, from an average of 180mg/L to 600mg/L. Concurrently the settleability of the sludge decreased from excellent (SSVI = 68mL/g) to very poor (150mL/g), perhaps as the result of under aeration. State point analyses indicated that the clarifiers are under-sized for process upsets of this magnitude. (author)

  1. Improving secondary clarifier performance at the Oakville Oil Refinery

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, S.M.; Bagley, D.M. [Univ. of Toronto, Dept. of Civil Engineering, Toronto, Ontario (Canada)

    2002-06-15

    The purpose of this study was threefold: to investigate the relationship between settleability and the physical properties of activated sludge, to correlate settleability and key operational parameters such as chemical oxygen demand (COD) concentration at the aeration basin inlet and to determine potential operational improvements to the Oakville Oil Refinery Wastewater Treatment Plant. Nine separate sets of stirred sludge-settling tests were conducted over a six-month period to measure settleability. The stirred sludge volume index (SSVI), the zone settling constants, and the Zheng-Bagley compression constants were determined. State point analyses were conducted to determine the maximum solids flux of the clarifiers. The concentrations of Al, Mn, Mg, Fe, Ca, Na, and K were determined to identify potential correlations to settling characteristics. Extracellular polymeric substances were extracted from the sludge and analyzed for the same reason. The performance of the clarifiers was highly variable during the period examined. As the refinery process flows and effluent streams changed, influent COD increased, from an average of 180mg/L to 600mg/L. Concurrently the settleability of the sludge decreased from excellent (SSVI = 68mL/g) to very poor (150mL/g), perhaps as the result of under aeration. State point analyses indicated that the clarifiers are under-sized for process upsets of this magnitude. (author)

  2. Secondary side water chemistry pH control strategy improvements

    International Nuclear Information System (INIS)

    Roumiguiere, Fernando-Mario; Fandrich, Joerg; Ramminger, Ute; Hoffmann-Wankerl, Stephan; Drexler, Andreas

    2012-09-01

    Over the years the PWR plant operators were aware of the need of optimizing the pH control strategy in the water-steam cycle with the focus on improvement of steam generator performance with the main goal of reducing the corrosion product ingress into the steam generators and their consequences: SG fouling, SG tube corrosion beneath deposits. To achieve this goal, it becomes necessary to harmonize three requirements: a. High overall pH along the circuit for suppression of general corrosion, requiring a volatile amine to ensure a suitable distribution in steam areas and condenser, and b. High local pH at the water phase of two-phase flow areas, requiring an either rather low volatile amine to ensure high pH in the wet steam water film, or larger amounts of a volatile amine. c. Sufficient amount of hydrazine to ensure reducing conditions in the steam generators. The basic strategy of AREVA NP GmbH (formerly KWU), successfully applied in German nuclear power plants since the late seventies consisted on the achievement of the necessary pH by means of ammonia, as generated by thermal decomposition of hydrazine. By dosing of hydrazine at the necessary amounts to ensure reducing conditions, also sufficient ammonia is generated to achieve a high overall pH along the cycle, being the target pH (25 deg. C) ≥ 9.8 resulting in < 1 ppb Fe in final feed water. This treatment is known as H-AVT (High pH - All Volatile Treatment). Main prerequisite for its application is to have a copper-free system. Eventually, H-AVT started to be applied later at some other western nuclear power plants. In some units, the high condenser exhaust flow rate applied caused a considerable amount of ammonia being removed from the cycle, resulting in too low ammonia concentrations to maintain a sufficiently high pH, making the addition of ammonia necessary. AREVA NP GmbH together with plant operators investigated the possibility of complementing the applied classical H-AVT by addition of an advanced

  3. Mathematical and Biological Modelling of RNA Secondary Structure and Its Effects on Gene Expression

    Directory of Open Access Journals (Sweden)

    T. A. Hughes

    2006-01-01

    Full Text Available Secondary structures within the 5′ untranslated regions of messenger RNAs can have profound effects on the efficiency of translation of their messages and thereby on gene expression. Consequently they can act as important regulatory motifs in both physiological and pathological settings. Current approaches to predicting the secondary structure of these RNA sequences find the structure with the global-minimum free energy. However, since RNA folds progressively from the 5′ end when synthesised or released from the translational machinery, this may not be the most probable structure. We discuss secondary structure prediction based on local-minimisation of free energy with thermodynamic fluctuations as nucleotides are added to the 3′ end and show that these can result in different secondary structures. We also discuss approaches for studying the extent of the translational inhibition specified by structures within the 5′ untranslated region.

  4. A comparative method for finding and folding RNA secondary structures within protein-coding regions

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Meyer, Irmtraud Margret; Forsberg, Roald

    2004-01-01

    that RNA-DECODER's parameters can be automatically trained to successfully fold known secondary structures within the HCV genome. We scan the genomes of HCV and polio virus for conserved secondary-structure elements, and analyze performance as a function of available evolutionary information. On known...... secondary structures, RNA-DECODER shows a sensitivity similar to the programs MFOLD, PFOLD and RNAALIFOLD. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD....

  5. Deciphering the shape and deformation of secondary structures through local conformation analysis

    Directory of Open Access Journals (Sweden)

    Camproux Anne-Claude

    2011-02-01

    Full Text Available Abstract Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

  6. Deciphering the shape and deformation of secondary structures through local conformation analysis.

    Science.gov (United States)

    Baussand, Julie; Camproux, Anne-Claude

    2011-02-01

    Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

  7. Improved measurements of RNA structure conservation with generalized centroid estimators

    Directory of Open Access Journals (Sweden)

    Yohei eOkada

    2011-08-01

    Full Text Available Identification of non-protein-coding RNAs (ncRNAs in genomes is acrucial task for not only molecular cell biology but alsobioinformatics. Secondary structures of ncRNAs are employed as a keyfeature of ncRNA analysis since biological functions of ncRNAs aredeeply related to their secondary structures. Although the minimumfree energy (MFE structure of an RNA sequence is regarded as the moststable structure, MFE alone could not be an appropriate measure foridentifying ncRNAs since the free energy is heavily biased by thenucleotide composition. Therefore, instead of MFE itself, severalalternative measures for identifying ncRNAs have been proposed such asthe structure conservation index (SCI and the base pair distance(BPD, both of which employ MFE structures. However, thesemeasurements are unfortunately not suitable for identifying ncRNAs insome cases including the genome-wide search and incur high falsediscovery rate. In this study, we propose improved measurements basedon SCI and BPD, applying generalized centroid estimators toincorporate the robustness against low quality multiple alignments.Our experiments show that our proposed methods achieve higher accuracythan the original SCI and BPD for not only human-curated structuralalignments but also low quality alignments produced by CLUSTALW. Furthermore, the centroid-based SCI on CLUSTAL W alignments is moreaccurate than or comparable with that of the original SCI onstructural alignments generated with RAF, a high quality structuralaligner, for which two-fold expensive computational time is requiredon average. We conclude that our methods are more suitable forgenome-wide alignments which are of low quality from the point of viewon secondary structures than the original SCI and BPD.

  8. Evolving stochastic context-free grammars for RNA secondary structure prediction

    DEFF Research Database (Denmark)

    Anderson, James WJ; Tataru, Paula Cristina; Stains, Joe

    2012-01-01

    Background Stochastic Context-Free Grammars (SCFGs) were applied successfully to RNA secondary structure prediction in the early 90s, and used in combination with comparative methods in the late 90s. The set of SCFGs potentially useful for RNA secondary structure prediction is very large, but a few...... to structure prediction as has been previously suggested. Results These search techniques were applied to predict RNA secondary structure on a maximal data set and revealed new and interesting grammars, though none are dramatically better than classic grammars. In general, results showed that many grammars...... with quite different structure could have very similar predictive ability. Many ambiguous grammars were found which were at least as effective as the best current unambiguous grammars. Conclusions Overall the method of evolving SCFGs for RNA secondary structure prediction proved effective in finding many...

  9. Visualizing RNA Secondary Structure Base Pair Binding Probabilities using Nested Concave Hulls

    OpenAIRE

    Sansen , Joris; Bourqui , Romain; Thebault , Patricia; Allali , Julien; Auber , David

    2015-01-01

    International audience; The challenge 1 of the BIOVIS 2015 design contest consists in designing an intuitive visual depiction of base pairs binding probabilities for secondary structure of ncRNA. Our representation depicts the potential nucleotide pairs binding using nested concave hulls over the computed MFE ncRNA secondary structure. Thus, it allows to identify regions with a high level of uncertainty in the MFE computation and the structures which seem to match to reality.

  10. Protein secondary structure assignment revisited: a detailed analysis of different assignment methods

    Directory of Open Access Journals (Sweden)

    de Brevern Alexandre G

    2005-09-01

    Full Text Available Abstract Background A number of methods are now available to perform automatic assignment of periodic secondary structures from atomic coordinates, based on different characteristics of the secondary structures. In general these methods exhibit a broad consensus as to the location of most helix and strand core segments in protein structures. However the termini of the segments are often ill-defined and it is difficult to decide unambiguously which residues at the edge of the segments have to be included. In addition, there is a "twilight zone" where secondary structure segments depart significantly from the idealized models of Pauling and Corey. For these segments, one has to decide whether the observed structural variations are merely distorsions or whether they constitute a break in the secondary structure. Methods To address these problems, we have developed a method for secondary structure assignment, called KAKSI. Assignments made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR, as well as secondary structures found in PDB files, on 4 datasets (X-ray structures with different resolution range, NMR structures. Results A detailed comparison of KAKSI assignments with those of STRIDE and PSEA reveals that KAKSI assigns slightly longer helices and strands than STRIDE in case of one-to-one correspondence between the segments. However, KAKSI tends also to favor the assignment of several short helices when STRIDE and PSEA assign longer, kinked, helices. Helices assigned by KAKSI have geometrical characteristics close to those described in the PDB. They are more linear than helices assigned by other methods. The same tendency to split long segments is observed for strands, although less systematically. We present a number of cases of secondary structure assignments that illustrate this behavior. Conclusion Our method provides valuable assignments which favor the regularity of secondary structure segments.

  11. The Globular State of the Single-Stranded RNA: Effect of the Secondary Structure Rearrangements

    Science.gov (United States)

    Grigoryan, Zareh A.; Karapetian, Armen T.

    2015-01-01

    The mutual influence of the slow rearrangements of secondary structure and fast collapse of the long single-stranded RNA (ssRNA) in approximation of coarse-grained model is studied with analytic calculations. It is assumed that the characteristic time of the secondary structure rearrangement is much longer than that for the formation of the tertiary structure. A nonequilibrium phase transition of the 2nd order has been observed. PMID:26345143

  12. The Globular State of the Single-Stranded RNA: Effect of the Secondary Structure Rearrangements

    Directory of Open Access Journals (Sweden)

    Zareh A. Grigoryan

    2015-01-01

    Full Text Available The mutual influence of the slow rearrangements of secondary structure and fast collapse of the long single-stranded RNA (ssRNA in approximation of coarse-grained model is studied with analytic calculations. It is assumed that the characteristic time of the secondary structure rearrangement is much longer than that for the formation of the tertiary structure. A nonequilibrium phase transition of the 2nd order has been observed.

  13. Salient design features of secondary containment structure of Narora Atomic Power Project

    International Nuclear Information System (INIS)

    Rahalkar, B.D.

    1975-01-01

    Design of the secondary containment structure for Narora Atomic Power Project is an improvement over the two earlier structures at of Rajasthan and Kalpakkam wherein Candu-type of reactors are involved. The major improvements envisaged are : to limit the leakage through the double containment envelope to 0.1% of volume of the building per day as against 0.1% per hour achieved for earlier stations; to separate heavy water atmosphere from that of light water for effective heavy water recovery; and better man-rem budgetting by limiting inner containment structure upto boiler room floor level and making boiler room area accessible during normal operation for servicing of light water system equipment. Narora Atomic Power Station is located in the Indo-Gangetic alluvial plains in seismically active zone IV. Comprehensive soil investigation, including dynamic properties of soil is required to be undertaken as the foundation level of the containment structure is 17 M below the ground level. The salient results of this investigation relevant to the foundations as well as type of foundation proposed are presented in brief. Double containment concept similar to that adopted for Kalpakkam station is provided for this station also. However, necessary changes in design to withstand large earthquake forces are required to be made. These design problems are discussed in brief. (author)

  14. Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures.

    Science.gov (United States)

    Kountouris, Petros; Hirst, Jonathan D

    2010-07-31

    Beta-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains. We have developed a novel method that predicts beta-turns and their types using information from multiple sequence alignments, predicted secondary structures and, for the first time, predicted dihedral angles. Our method uses support vector machines, a supervised classification technique, and is trained and tested on three established datasets of 426, 547 and 823 protein chains. We achieve a Matthews correlation coefficient of up to 0.49, when predicting the location of beta-turns, the highest reported value to date. Moreover, the additional dihedral information improves the prediction of beta-turn types I, II, IV, VIII and "non-specific", achieving correlation coefficients up to 0.39, 0.33, 0.27, 0.14 and 0.38, respectively. Our results are more accurate than other methods. We have created an accurate predictor of beta-turns and their types. Our method, called DEBT, is available online at http://comp.chem.nottingham.ac.uk/debt/.

  15. Aerospace structural design process improvement using systematic evolutionary structural modeling

    Science.gov (United States)

    Taylor, Robert Michael

    2000-10-01

    A multidisciplinary team tasked with an aircraft design problem must understand the problem requirements and metrics to produce a successful design. This understanding entails not only knowledge of what these requirements and metrics are, but also how they interact, which are most important (to the customer as well as to aircraft performance), and who in the organization can provide pertinent knowledge for each. In recent years, product development researchers and organizations have developed and successfully applied a variety of tools such as Quality Function Deployment (QFD) to coordinate multidisciplinary team members. The effectiveness of these methods, however, depends on the quality and fidelity of the information that team members can input. In conceptual aircraft design, structural information is of lower quality compared to aerodynamics or performance because it is based on experience rather than theory. This dissertation shows how advanced structural design tools can be used in a multidisciplinary team setting to improve structural information generation and communication through a systematic evolution of structural detail. When applied to conceptual design, finite element-based structural design tools elevate structural information to the same level as other computationally supported disciplines. This improved ability to generate and communicate structural information enables a design team to better identify and meet structural design requirements, consider producibility issues earlier, and evaluate structural concepts. A design process experiment of a wing structural layout in collaboration with an industrial partner illustrates and validates the approach.

  16. Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases

    Directory of Open Access Journals (Sweden)

    Sudha Sharma

    2011-01-01

    Full Text Available In addition to the canonical B-form structure first described by Watson and Crick, DNA can adopt a number of alternative structures. These non-B-form DNA secondary structures form spontaneously on tracts of repeat sequences that are abundant in genomes. In addition, structured forms of DNA with intrastrand pairing may arise on single-stranded DNA produced transiently during various cellular processes. Such secondary structures have a range of biological functions but also induce genetic instability. Increasing evidence suggests that genomic instabilities induced by non-B DNA secondary structures result in predisposition to diseases. Secondary DNA structures also represent a new class of molecular targets for DNA-interactive compounds that might be useful for targeting telomeres and transcriptional control. The equilibrium between the duplex DNA and formation of multistranded non-B-form structures is partly dependent upon the helicases that unwind (resolve these alternate DNA structures. With special focus on tetraplex, triplex, and cruciform, this paper summarizes the incidence of non-B DNA structures and their association with genomic instability and emphasizes the roles of RecQ-like DNA helicases in genome maintenance by resolution of DNA secondary structures. In future, RecQ helicases are anticipated to be additional molecular targets for cancer chemotherapeutics.

  17. Testing Mediation Using Multiple Regression and Structural Equation Modeling Analyses in Secondary Data

    Science.gov (United States)

    Li, Spencer D.

    2011-01-01

    Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the…

  18. Effects of Secondary Hyperparathyroidism Treatment on Improvement in Anemia: Results from the MBD-5D Study.

    Directory of Open Access Journals (Sweden)

    Motoko Tanaka

    Full Text Available Anemia is an important prognostic factor in hemodialysis patients. It has been reported that parathyroidectomy ameliorates anemia and reduces the requirement of postoperative erythropoiesis-stimulating agents. The objective of this study was to assess the effect of cinacalcet, which is considered as a pharmacological parathyroidectomy, on anemia in hemodialysis patients.We used data from a prospective cohort of Japanese hemodialysis patients with secondary hyperparathyroidism; the criteria were: intact parathyroid hormone concentrations ≥ 180 pg/mL or use of an intravenous or oral vitamin D receptor activator. All patients were cinacalcet-naïve at study enrollment. The main outcome measure was achievement of the target hemoglobin level (≥10.0 g/dL, which was measured repeatedly every 6 months. Cinacalcet exposure was defined as cumulative time since initiation. Both conventional longitudinal models and marginal structural models were adjusted for confounding factors.Among 3,201 cinacalcet-naïve individuals at baseline, cinacalcet was initiated in 1,337 individuals during the follow up. Cinacalcet users were slightly younger; included more patients with chronic glomerulonephritis and fewer with diabetes; were more likely to have a history of parathyroidectomy; and were more often on activated vitamin D agents, phosphate binders, and iron supplements. After adjusting for both time-invariant and time-varying potential confounders, including demographics, comorbidities, comedications, and laboratory values, each additional 6-month duration on cinacalcet was associated with a 1.1-fold increase in the odds of achieving the target hemoglobin level.Cinacalcet may improve anemia in chronic hemodialysis patients with secondary hyperparathyroidism, possibly through pathways both within and outside the parathyroid hormone pathways. Further investigations are warranted to delineate the roles of cinacalcet not only in the management of chronic kidney

  19. Generating a Networked Improvement Community to Improve Secondary Mathematics Teacher Preparation: Network Leadership, Organization, and Operation

    Science.gov (United States)

    Martin, W. Gary; Gobstein, Howard

    2015-01-01

    The Mathematics Teacher Education Partnership (MTE-Partnership) was formed to address the undersupply of new secondary mathematics teachers who are well prepared to help their students attain the goals of the Common Core State Standards and other college- and career-ready standards. This national consortium of more than 90 universities and 100…

  20. Sheath structure transition controlled by secondary electron emission

    Science.gov (United States)

    Schweigert, I. V.; Langendorf, S. J.; Walker, M. L. R.; Keidar, M.

    2015-04-01

    In particle-in-cell Monte Carlo collision (PIC MCC) simulations and in an experiment we study sheath formation over an emissive floating Al2O3 plate in a direct current discharge plasma at argon gas pressure 10-4 Torr. The discharge glow is maintained by the beam electrons emitted from a negatively biased hot cathode. We observe three types of sheaths near the floating emissive plate and the transition between them is driven by changing the negative bias. The Debye sheath appears at lower voltages, when secondary electron emission is negligible. With increasing applied voltage, secondary electron emission switches on and a first transition to a new sheath type, beam electron emission (BEE), takes place. For the first time we find this specific regime of sheath operation near the floating emissive surface. In this regime, the potential drop over the plate sheath is about four times larger than the temperature of plasma electrons. The virtual cathode appears near the emissive plate and its modification helps to maintain the BEE regime within some voltage range. Further increase of the applied voltage U initiates the second smooth transition to the plasma electron emission sheath regime and the ratio Δφs/Te tends to unity with increasing U. The oscillatory behavior of the emissive sheath is analyzed in PIC MCC simulations. A plasmoid of slow electrons is formed near the plate and transported to the bulk plasma periodically with a frequency of about 25 kHz.

  1. DCJ-RNA - double cut and join for RNA secondary structures.

    Science.gov (United States)

    Badr, Ghada H; Al-Aqel, Haifa A

    2017-10-16

    Genome rearrangements are essential processes for evolution and are responsible for existing varieties of genome architectures. Many studies have been conducted to obtain an algorithm that identifies the minimum number of inversions that are necessary to transform one genome into another; this allows for genome sequence representation in polynomial time. Studies have not been conducted on the topic of rearranging a genome when it is represented as a secondary structure. Unlike sequences, the secondary structure preserves the functionality of the genome. Sequences can be different, but they all share the same structure and, therefore, the same functionality. This paper proposes a double cut and join for RNA secondary structures (DCJ-RNA) algorithm. This algorithm allows for the description of evolutionary scenarios that are based on secondary structures rather than sequences. The main aim of this paper is to suggest an efficient algorithm that can help researchers compare two ribonucleic acid (RNA) secondary structures based on rearrangement operations. The results, which are based on real datasets, show that the algorithm is able to count the minimum number of rearrangement operations, as well as to report an optimum scenario that can increase the similarity between the two structures. The algorithm calculates the distance between structures and reports a scenario based on the minimum rearrangement operations required to make the given structure similar to the other. DCJ-RNA can also be used to measure the distance between the two structures. This can help identify the common functionalities between different species.

  2. Induction of secondary and tertiary lymphoid structures in the skin.

    NARCIS (Netherlands)

    Cupedo, T.; Jansen, W.; Kraal, G.; Mebius, R.E.

    2004-01-01

    During embryogenesis a developmental program leading to the formation of lymph nodes and Peyer's patches is initiated. We now show that lymph node-like structures as well as tertiary lymphoid structures can ectopically be induced by intradermal injection of newborn lymph node-derived cells.

  3. [Changes in the secondary and tertiary structure of serum albumin in interactions with ligands of various structures].

    Science.gov (United States)

    Trinus, F P; Braver-Chernobul'skaia, B S; Luĭk, A I; Boldeskul, A E; Velichko, A N

    1984-01-01

    High affinity interactions between blood serum albumin and five substances of various chemical structure, exhibiting distinct physiological activity, were accompanied by alterations in the protein tertiary structure, while the albumin secondary structure was involved in conformational transformation after less effective affinity binding.

  4. Composite Dry Structure Cost Improvement Approach

    Science.gov (United States)

    Nettles, Alan; Nettles, Mindy

    2015-01-01

    This effort demonstrates that by focusing only on properties of relevance, composite interstage and shroud structures can be placed on the Space Launch System vehicle that simultaneously reduces cost, improves reliability, and maximizes performance, thus providing the Advanced Development Group with a new methodology of how to utilize composites to reduce weight for composite structures on launch vehicles. Interstage and shroud structures were chosen since both of these structures are simple in configuration and do not experience extreme environments (such as cryogenic or hot gas temperatures) and should represent a good starting point for flying composites on a 'man-rated' vehicle. They are used as an example only. The project involves using polymer matrix composites for launch vehicle structures, and the logic and rationale behind the proposed new methodology.

  5. Inflatable Habitat with Integrated Primary and Secondary Structure, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Paragon Space Development Corp (Paragon) and Thin Red Line Aerospace (TRLA) proposes to explore the utilization of inflatable structures by designing a habitation...

  6. Improving reasoning skills in secondary history education by working memory training

    NARCIS (Netherlands)

    Ariës, R.J.; Groot, W.; Maassen van den Brink, H.

    2015-01-01

    Secondary school pupils underachieve in tests in which reasoning abilities are required. Brain-based training of working memory (WM) may improve reasoning abilities. In this study, we use a brain-based training programme based on historical content to enhance reasoning abilities in history courses.

  7. Improving Reasoning Skills in Secondary History Education by Working Memory Training

    Science.gov (United States)

    Ariës, Roel Jacobus; Groot, Wim; van den Brink, Henriette Maassen

    2015-01-01

    Secondary school pupils underachieve in tests in which reasoning abilities are required. Brain-based training of working memory (WM) may improve reasoning abilities. In this study, we use a brain-based training programme based on historical content to enhance reasoning abilities in history courses. In the first experiment, a combined intervention…

  8. Developing Quality Strategic Plan in Secondary Schools for Successful School Improvement

    Science.gov (United States)

    Chukwumah, Fides Okwukweka

    2015-01-01

    The study examined the extent to which development of quality strategic plans for Anambra State secondary schools' improvement had been done by schools. The research design used was a descriptive survey. Respondents comprised 217 principals. There was no sampling since all the principals were used. Data were collected using "Schools'…

  9. Problems of Implementation of Strategic Plans for Secondary Schools' Improvement in Anambra State

    Science.gov (United States)

    Chukwumah, Fides Okwukweka; Ezeugbor, Carol Obiageli

    2015-01-01

    This study investigated the extent of problems of strategic plans implementation for secondary schools' improvement in Anambra State, Nigeria for quality education provision. The study used a descriptive survey design paradigm. Respondents comprised 217 principals. There was no sampling. All the principals were used. Data were collected using…

  10. Density functional study of molecular interactions in secondary structures of proteins.

    Science.gov (United States)

    Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

    2016-01-01

    Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

  11. Landscape and variation of RNA secondary structure across the human transcriptome.

    OpenAIRE

    Wan, Y; Qu, K; Zhang, QC; Flynn, RA; Manor, O; Ouyang, Z; Zhang, J; Spitale, RC; Snyder, MP; Segal, E; Chang, HY

    2014-01-01

    In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program. However, the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child). This provides a comp...

  12. Improving the submicro determination of vanadium in natural water using primary-secondary wavelength spectrophotometry

    International Nuclear Information System (INIS)

    Khongven Gao

    1999-01-01

    In acidic solution and in the presence of ammonium persulfate, the conventional reaction of vanadium(5) with gallic acid to form an orange complex has been used for the improvement of the determination of trace amounts of vanadium in water by the updated method named primary-secondary wavelength spectrophotometry. The results show that the analytical precision and accuracy were improved and gave higher determination sensitivity than ordinary spectrophotometry. The relative standard deviations were less than 5.6 % [ru

  13. Probing the glycosidic linkage: secondary structures in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Simons, John P; Cristina Stanca-Kaposta, E; Cocinero, Emilio J; Liu, B [Chemistry Department, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (United Kingdom); Davis, Benjamin G; Gamblin, David P [Chemistry Department, Chemical Research Laboratory, 12 Mansfield Road, Oxford OX1 4TA (United Kingdom); Kroemer, Romano T [Sanofi-Aventis, CRVA, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine (France)], E-mail: John.Simons@chem.ox.ac.uk

    2008-10-15

    The functional importance of carbohydrates in biological processes, particularly those involving specific molecular recognition, is immense. Characterizing the three-dimensional (3D) structures of carbohydrates and glycoproteins, and their interactions with other molecules, not least the ubiquitous solvent, water, is a key starting point for understanding these processes. The combination of laser-based electronic and vibrational spectroscopy of mass-selected carbohydrate molecules and their hydrated complexes, conducted under molecular beam conditions, with ab initio computation is providing a uniquely powerful means of characterizing 3D carbohydrate conformations; the structures of their hydrated complexes, the hydrogen-bonded networks they support (or which support them); and the factors that determine their conformational and structural preferences.

  14. Probing the glycosidic linkage: secondary structures in the gas phase

    International Nuclear Information System (INIS)

    Simons, John P; Cristina Stanca-Kaposta, E; Cocinero, Emilio J; Liu, B; Davis, Benjamin G; Gamblin, David P; Kroemer, Romano T

    2008-01-01

    The functional importance of carbohydrates in biological processes, particularly those involving specific molecular recognition, is immense. Characterizing the three-dimensional (3D) structures of carbohydrates and glycoproteins, and their interactions with other molecules, not least the ubiquitous solvent, water, is a key starting point for understanding these processes. The combination of laser-based electronic and vibrational spectroscopy of mass-selected carbohydrate molecules and their hydrated complexes, conducted under molecular beam conditions, with ab initio computation is providing a uniquely powerful means of characterizing 3D carbohydrate conformations; the structures of their hydrated complexes, the hydrogen-bonded networks they support (or which support them); and the factors that determine their conformational and structural preferences.

  15. GC content around splice sites affects splicing through pre-mRNA secondary structures

    Directory of Open Access Journals (Sweden)

    Chen Liang

    2011-01-01

    Full Text Available Abstract Background Alternative splicing increases protein diversity by generating multiple transcript isoforms from a single gene through different combinations of exons or through different selections of splice sites. It has been reported that RNA secondary structures are involved in alternative splicing. Here we perform a genomic study of RNA secondary structures around splice sites in humans (Homo sapiens, mice (Mus musculus, fruit flies (Drosophila melanogaster, and nematodes (Caenorhabditis elegans to further investigate this phenomenon. Results We observe that GC content around splice sites is closely associated with the splice site usage in multiple species. RNA secondary structure is the possible explanation, because the structural stability difference among alternative splice sites, constitutive splice sites, and skipped splice sites can be explained by the GC content difference. Alternative splice sites tend to be GC-enriched and exhibit more stable RNA secondary structures in all of the considered species. In humans and mice, splice sites of first exons and long exons tend to be GC-enriched and hence form more stable structures, indicating the special role of RNA secondary structures in promoter proximal splicing events and the splicing of long exons. In addition, GC-enriched exon-intron junctions tend to be overrepresented in tissue-specific alternative splice sites, indicating the functional consequence of the GC effect. Compared with regions far from splice sites and decoy splice sites, real splice sites are GC-enriched. We also found that the GC-content effect is much stronger than the nucleotide-order effect to form stable secondary structures. Conclusion All of these results indicate that GC content is related to splice site usage and it may mediate the splicing process through RNA secondary structures.

  16. Porous carbonaceous electrode structure and method for secondary electrochemical cell

    Science.gov (United States)

    Kaun, Thomas D.

    1977-03-08

    Positive and negative electrodes are provided as rigid, porous carbonaceous matrices with particulate active material fixedly embedded. Active material such as metal chalcogenides, solid alloys of alkali metal or alkaline earth metals along with other metals and their oxides in particulate form are blended with a thermosetting resin and a solid volatile to form a paste mixture. Various electrically conductive powders or current collector structures can be blended or embedded into the paste mixture which can be molded to the desired electrode shape. The molded paste is heated to a temperature at which the volatile transforms into vapor to impart porosity as the resin begins to cure into a rigid solid structure.

  17. Effects of truncation of the peptide chain on the secondary structure and bioactivities of palmitoylated anoplin.

    Science.gov (United States)

    Salas, Remmer L; Garcia, Jan Kathryne D L; Miranda, Ana Carmela R; Rivera, Windell L; Nellas, Ricky B; Sabido, Portia Mahal G

    2018-06-01

    Anoplin (GLLKRIKTLL-NH 2 ) is of current interest due to its short sequence and specificity towards bacteria. Recent studies on anoplin have shown that truncation and acylation compromises its antimicrobial activity and specificity, respectively. In this study, truncated analogues (pal-ano-9 to pal-ano-5) of palmitoylated anoplin (pal-anoplin) were synthesized to determine the effects of C-truncation on its bioactivities. Moreover, secondary structure of each analogue using circular dichroism (CD) spectroscopy was determined to correlate with bioactivities. Interestingly, pal-anoplin, pal-ano-9 and pal-ano-6 were helical in water, unlike anoplin. In contrast, pal-ano-8, pal-ano-7 and pal-ano-5, with polar amino acid residues at the C-terminus, were random coil in water. Nevertheless, all the peptides folded into helical structures in 30% trifluoroethanol/water (TFE/H 2 O) except for the shortest analogue pal-ano-5. Hydrophobicity played a significant role in the enhancement of activity against bacteria E. coli and S. aureus as all lipopeptides including the random coil pal-ano-5 were more active than the parent anoplin. Meanwhile, the greatest improvement in activity against the fungus C. albicans was observed for pal-anoplin analogues (pal-ano-9 and pal-ano-6) that were helical in water. Although, hydrophobicity is a major factor in the secondary structure and antimicrobial activity, it appears that the nature of amino acids at the C-terminus also influence folding of lipopeptides in water and its antifungal activity. Moreover, the hemolytic activity of the analogues was found to correlate with hydrophobicity, except for the least hemolytic, pal-ano-5. Since most of the analogues are more potent and shorter than anoplin, they are promising drug candidates for further development. Copyright © 2018. Published by Elsevier Inc.

  18. An image processing approach to computing distances between RNA secondary structures dot plots

    Directory of Open Access Journals (Sweden)

    Sapiro Guillermo

    2009-02-01

    Full Text Available Abstract Background Computing the distance between two RNA secondary structures can contribute in understanding the functional relationship between them. When used repeatedly, such a procedure may lead to finding a query RNA structure of interest in a database of structures. Several methods are available for computing distances between RNAs represented as strings or graphs, but none utilize the RNA representation with dot plots. Since dot plots are essentially digital images, there is a clear motivation to devise an algorithm for computing the distance between dot plots based on image processing methods. Results We have developed a new metric dubbed 'DoPloCompare', which compares two RNA structures. The method is based on comparing dot plot diagrams that represent the secondary structures. When analyzing two diagrams and motivated by image processing, the distance is based on a combination of histogram correlations and a geometrical distance measure. We introduce, describe, and illustrate the procedure by two applications that utilize this metric on RNA sequences. The first application is the RNA design problem, where the goal is to find the nucleotide sequence for a given secondary structure. Examples where our proposed distance measure outperforms others are given. The second application locates peculiar point mutations that induce significant structural alternations relative to the wild type predicted secondary structure. The approach reported in the past to solve this problem was tested on several RNA sequences with known secondary structures to affirm their prediction, as well as on a data set of ribosomal pieces. These pieces were computationally cut from a ribosome for which an experimentally derived secondary structure is available, and on each piece the prediction conveys similarity to the experimental result. Our newly proposed distance measure shows benefit in this problem as well when compared to standard methods used for assessing

  19. Upper mantle velocity structure beneath Italy from direct and secondary P-wave teleseismic tomography

    Directory of Open Access Journals (Sweden)

    P. De Gori

    1997-06-01

    Full Text Available High-quality teleseismic data digitally recorded by the National Seismic Network during 1988-1995 have been analysed to tomographically reconstruct the aspherical velocity structure of the upper mantle beneath the Italian region. To improve the quality and the reliability of the tomographic images, both direct (P, PKPdf and secondary (pP,sP,PcP,PP,PKPbc,PKPab travel-time data were used in the inversion. Over 7000 relative residuals were computed with respect to the IASP91 Earth velocity model and inverted using a modified version of the ACH technique. Incorporation of data of secondary phases resulted in a significant improvement of the sampling of the target volume and of the spatial resolution of the heterogeneous zones. The tomographic images show that most of the lateral variations in the velocity field are confined in the first ~250 km of depth. Strong low velocity anomalies are found beneath the Po plain, Tuscany and Eastern Sicily in the depth range between 35 and 85 km. High velocity anomalies dominate the upper mantle beneath the Central-Western Alps, Northern-Central Apennines and Southern Tyrrhenian sea at lithospheric depths between 85 and 150 km. At greater depth, positive anomalies are still observed below the northernmost part of the Apenninic chain and Southern Tyrrhenian sea. Deeper anomalies present in the 3D velocity model computed by inverting only the first arrivals dataset, generally appear less pronounced in the new tomographic reconstructions. We interpret this as the result of the ray sampling improvement on the reduction of the vertical smearing effects.

  20. Irradiation effects on secondary structure of protein induced by keV ions

    International Nuclear Information System (INIS)

    Cui, F.Z.; Lin, Y.B.; Zhang, D.M.; Tian, M.B.

    2001-01-01

    Protein secondary structure changes by low-energy ion irradiation are reported for the first time. The selected system is 30 keV N + irradiation on bovine serum albumin (BSA). After irradiation at increasing fluences from 1.0x10 15 to 2.5x10 16 ion/cm 2 , Fourier transform infrared spectra analysis was conducted. It was found that the secondary structures of BSA molecules were very sensitive to ion irradiation. Secondary conformations showed different trends of change during irradiation. With the increase of ion fluence from 0 to 2.5x10 16 ion/cm 2 , the fraction of α-helix and β-turns decreased from 17 to 12%, and from 40 to 31%, respectively, while that of random coil and β-sheet structure increased from 18 to 27%, and from 25 to 30%, respectively. Possible explanations for the secondary conformational changes of protein are proposed. (author)

  1. A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

    Science.gov (United States)

    Rivas, Elena; Lang, Raymond; Eddy, Sean R

    2012-02-01

    The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases.

  2. Tchebichef image moment approach to the prediction of protein secondary structures based on circular dichroism.

    Science.gov (United States)

    Li, Sha Sha; Li, Bao Qiong; Liu, Jin Jin; Lu, Shao Hua; Zhai, Hong Lin

    2018-04-20

    Circular dichroism (CD) spectroscopy is a widely used technique for the evaluation of protein secondary structures that has a significant impact for the understanding of molecular biology. However, the quantitative analysis of protein secondary structures based on CD spectra is still a hard work due to the serious overlap of the spectra corresponding to different structural motifs. Here, Tchebichef image moment (TM) approach is introduced for the first time, which can effectively extract the chemical features in CD spectra for the quantitative analysis of protein secondary structures. The proposed approach was applied to analyze reference set. and the obtained results were evaluated by the strict statistical parameters such as correlation coefficient, cross-validation correlation coefficient and root mean squared error. Compared with several specialized prediction methods, TM approach provided satisfactory results, especially for turns and unordered structures. Our study indicates that TM approach can be regarded as a feasible tool for the analysis of the secondary structures of proteins based on CD spectra. An available TMs package is provided and can be used directly for secondary structures prediction. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

  3. Prediction of backbone dihedral angles and protein secondary structure using support vector machines

    Directory of Open Access Journals (Sweden)

    Hirst Jonathan D

    2009-12-01

    Full Text Available Abstract Background The prediction of the secondary structure of a protein is a critical step in the prediction of its tertiary structure and, potentially, its function. Moreover, the backbone dihedral angles, highly correlated with secondary structures, provide crucial information about the local three-dimensional structure. Results We predict independently both the secondary structure and the backbone dihedral angles and combine the results in a loop to enhance each prediction reciprocally. Support vector machines, a state-of-the-art supervised classification technique, achieve secondary structure predictive accuracy of 80% on a non-redundant set of 513 proteins, significantly higher than other methods on the same dataset. The dihedral angle space is divided into a number of regions using two unsupervised clustering techniques in order to predict the region in which a new residue belongs. The performance of our method is comparable to, and in some cases more accurate than, other multi-class dihedral prediction methods. Conclusions We have created an accurate predictor of backbone dihedral angles and secondary structure. Our method, called DISSPred, is available online at http://comp.chem.nottingham.ac.uk/disspred/.

  4. A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction

    Science.gov (United States)

    Al-Khatib, Ra’ed M.; Abdullah, Rosni; Rashid, Nur’Aini Abdul

    2010-01-01

    RNA molecules have been discovered playing crucial roles in numerous biological and medical procedures and processes. RNA structures determination have become a major problem in the biology context. Recently, computer scientists have empowered the biologists with RNA secondary structures that ease an understanding of the RNA functions and roles. Detecting RNA secondary structure is an NP-hard problem, especially in pseudoknotted RNA structures. The detection process is also time-consuming; as a result, an alternative approach such as using parallel architectures is a desirable option. The main goal in this paper is to do an intensive investigation of parallel methods used in the literature to solve the demanding issues, related to the RNA secondary structure prediction methods. Then, we introduce a new taxonomy for the parallel RNA folding methods. Based on this proposed taxonomy, a systematic and scientific comparison is performed among these existing methods. PMID:20458364

  5. Secondary Structure Adopted by the Gly-Gly-X Repetitive Regions of Dragline Spider Silk

    Directory of Open Access Journals (Sweden)

    Geoffrey M. Gray

    2016-12-01

    Full Text Available Solid-state NMR and molecular dynamics (MD simulations are presented to help elucidate the molecular secondary structure of poly(Gly-Gly-X, which is one of the most common structural repetitive motifs found in orb-weaving dragline spider silk proteins. The combination of NMR and computational experiments provides insight into the molecular secondary structure of poly(Gly-Gly-X segments and provides further support that these regions are disordered and primarily non-β-sheet. Furthermore, the combination of NMR and MD simulations illustrate the possibility for several secondary structural elements in the poly(Gly-Gly-X regions of dragline silks, including β-turns, 310-helicies, and coil structures with a negligible population of α-helix observed.

  6. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

    Science.gov (United States)

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Free energy minimization to predict RNA secondary structures and computational RNA design.

    Science.gov (United States)

    Churkin, Alexander; Weinbrand, Lina; Barash, Danny

    2015-01-01

    Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

  8. Lactobacillus paracasei feeding improves the control of secondary experimental meningococcal infection in flu-infected mice.

    Science.gov (United States)

    Belkacem, Nouria; Bourdet-Sicard, Raphaëlle; Taha, Muhamed-Kkeir

    2018-04-10

    The use of probiotics to improve anti-microbial defence, such as for influenza infections, is increasingly recommended. However, no data are available on the effect of probiotics on flu-associated secondary bacterial infections. There is strong evidence of a spatiotemporal association between influenza virus infection and invasive Neisseria meningitidis. We thus investigated the effect of feeding mice Lactobacillus paracasei CNCM I-1518 in a mouse model of sequential influenza-meningococcal infection. We intranasally infected BALB/c mice with a strain of influenza A virus (IAV) H3N2 that was first adapted to mice. Seven days later, a secondary bacterial infection was induced by intranasal administration of bioluminescent N. meningitidis. During the experiment, mice orally received either L. paracasei CNCM I-1518 or PBS as a control. The effect of L. paracasei administration on secondary bacterial infection by N. meningitidis was evaluated. Oral consumption of L. paracasei CNCM I-1518 reduced the weight loss of infected mice and lowered the bioluminescent signal of infecting meningococci. This improvement was associated with higher recruitment of inflammatory myeloid cells, such as interstitial monocytes and dendritic cells, to the lungs. Our data highlight the role of the gut-lung axis. L. paracasei CNCM I-1518 may boost the defence against IAV infection and secondary bacterial infection, which should be further studied and validated in clinical trials.

  9. Secondary flow structures under stent-induced perturbations for cardiovascular flow in a curved artery model

    International Nuclear Information System (INIS)

    Glenn, Autumn L.; Bulusu, Kartik V.; Shu Fangjun; Plesniak, Michael W.

    2012-01-01

    Secondary flows within curved arteries with unsteady forcing result from amplified centrifugal instabilities and are expected to be driven by the rapid accelerations and decelerations inherent in physiological waveforms. These secondary flows may also affect the function of curved arteries through pro-atherogenic wall shear stresses, platelet residence time and other vascular response mechanisms. Planar PIV measurements were performed under multi-harmonic non-zero-mean and physiological carotid artery waveforms at various locations in a rigid bent-pipe curved artery model. Results revealed symmetric counter-rotating vortex pairs that developed during the acceleration phases of both multi-harmonic and physiological waveforms. An idealized stent model was placed upstream of the bend, which initiated flow perturbations under physiological inflow conditions. Changes in the secondary flow structures were observed during the systolic deceleration phase (t/T ≈ 0.20–0.50). Proper Orthogonal Decomposition (POD) analysis of the flow morphologies under unsteady conditions indicated similarities in the coherent secondary-flow structures and correlation with phase-averaged velocity fields. A regime map was created that characterizes the kaleidoscope of vortical secondary flows with multiple vortex pairs and interesting secondary flow morphologies. This regime map in the curved artery model was created by plotting the secondary Reynolds number against another dimensionless acceleration-based parameter marking numbered regions of vortex pairs.

  10. Secondary flow structures under stent-induced perturbations for cardiovascular flow in a curved artery model

    Energy Technology Data Exchange (ETDEWEB)

    Glenn, Autumn L.; Bulusu, Kartik V. [Department of Mechanical and Aerospace Engineering, George Washington University, 801 22nd Street, NW., Washington, DC 20052 (United States); Shu Fangjun [Department of Mechanical and Aerospace Engineering, New Mexico State University, MSC 3450, P.O. Box 30001, Las Cruces, NM 88003-8001 (United States); Plesniak, Michael W., E-mail: plesniak@gwu.edu [Department of Mechanical and Aerospace Engineering, George Washington University, 801 22nd Street, NW., Washington, DC 20052 (United States)

    2012-06-15

    Secondary flows within curved arteries with unsteady forcing result from amplified centrifugal instabilities and are expected to be driven by the rapid accelerations and decelerations inherent in physiological waveforms. These secondary flows may also affect the function of curved arteries through pro-atherogenic wall shear stresses, platelet residence time and other vascular response mechanisms. Planar PIV measurements were performed under multi-harmonic non-zero-mean and physiological carotid artery waveforms at various locations in a rigid bent-pipe curved artery model. Results revealed symmetric counter-rotating vortex pairs that developed during the acceleration phases of both multi-harmonic and physiological waveforms. An idealized stent model was placed upstream of the bend, which initiated flow perturbations under physiological inflow conditions. Changes in the secondary flow structures were observed during the systolic deceleration phase (t/T Almost-Equal-To 0.20-0.50). Proper Orthogonal Decomposition (POD) analysis of the flow morphologies under unsteady conditions indicated similarities in the coherent secondary-flow structures and correlation with phase-averaged velocity fields. A regime map was created that characterizes the kaleidoscope of vortical secondary flows with multiple vortex pairs and interesting secondary flow morphologies. This regime map in the curved artery model was created by plotting the secondary Reynolds number against another dimensionless acceleration-based parameter marking numbered regions of vortex pairs.

  11. RNA secondary structure prediction by using discrete mathematics: an interdisciplinary research experience for undergraduate students.

    Science.gov (United States)

    Ellington, Roni; Wachira, James; Nkwanta, Asamoah

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems.

  12. SAAS: Short Amino Acid Sequence - A Promising Protein Secondary Structure Prediction Method of Single Sequence

    Directory of Open Access Journals (Sweden)

    Zhou Yuan Wu

    2013-07-01

    Full Text Available In statistical methods of predicting protein secondary structure, many researchers focus on single amino acid frequencies in α-helices, β-sheets, and so on, or the impact near amino acids on an amino acid forming a secondary structure. But the paper considers a short sequence of amino acids (3, 4, 5 or 6 amino acids as integer, and statistics short sequence's probability forming secondary structure. Also, many researchers select low homologous sequences as statistical database. But this paper select whole PDB database. In this paper we propose a strategy to predict protein secondary structure using simple statistical method. Numerical computation shows that, short amino acids sequence as integer to statistics, which can easy see trend of short sequence forming secondary structure, and it will work well to select large statistical database (whole PDB database without considering homologous, and Q3 accuracy is ca. 74% using this paper proposed simple statistical method, but accuracy of others statistical methods is less than 70%.

  13. RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

    Science.gov (United States)

    Ellington, Roni; Wachira, James

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems. PMID:20810968

  14. Detection of secondary structure elements in proteins by hydrophobic cluster analysis.

    Science.gov (United States)

    Woodcock, S; Mornon, J P; Henrissat, B

    1992-10-01

    Hydrophobic cluster analysis (HCA) is a protein sequence comparison method based on alpha-helical representations of the sequences where the size, shape and orientation of the clusters of hydrophobic residues are primarily compared. The effectiveness of HCA has been suggested to originate from its potential ability to focus on the residues forming the hydrophobic core of globular proteins. We have addressed the robustness of the bidimensional representation used for HCA in its ability to detect the regular secondary structure elements of proteins. Various parameters have been studied such as those governing cluster size and limits, the hydrophobic residues constituting the clusters as well as the potential shift of the cluster positions with respect to the position of the regular secondary structure elements. The following results have been found to support the alpha-helical bidimensional representation used in HCA: (i) there is a positive correlation (clearly above background noise) between the hydrophobic clusters and the regular secondary structure elements in proteins; (ii) the hydrophobic clusters are centred on the regular secondary structure elements; (iii) the pitch of the helical representation which gives the best correspondence is that of an alpha-helix. The correspondence between hydrophobic clusters and regular secondary structure elements suggests a way to implement variable gap penalties during the automatic alignment of protein sequences.

  15. Primary and secondary structure of U8 small nuclear RNA

    International Nuclear Information System (INIS)

    Reddy, R.; Henning, D.; Busch, H.

    1985-01-01

    U8 small nuclear RNA is a new, capped, 140 nucleotides long RNA species found in Novikoff hepatoma cells. Its sequence is: m3GpppAmUmCGUCAGGA GGUUAAUCCU UACCUGUCCC UCCUUUCGGA GGGCAGAUAG AAAAUGAUGA UUGGAGCUUG CAUGAUCUGC UGAUUAUAGC AUUUCCGUGU AAUCAGGACC UGACAACAUC CUGAUUGCUU CUAUCUGAUUOH. This RNA is present in approximately 25,000 copies/cell, and it is enriched in nucleolar preparations. Like U1, U2, U4/U6, and U5 RNAs, U8 RNA was also present as a ribonucleoprotein associated with the Sm antigen. The rat U8 RNA was highly homologous (greater than 90%) to a recently characterized 5.4 S RNA from mouse cells infected with spleen focus-forming virus. In addition to the U8 RNA, three other U small nuclear RNAs were found in anti-Sm antibody immunoprecipitates from labeled rat and HeLa cells. Each of these contained a m3GpppAm cap structure; their apparent chain lengths were 60, 130, and 65 nucleotides. These U small nuclear RNAs are designated U7, U9, and U10 RNAs, respectively

  16. The Improvement of Behavior Recognition Accuracy of Micro Inertial Accelerometer by Secondary Recognition Algorithm

    Directory of Open Access Journals (Sweden)

    Yu Liu

    2014-05-01

    Full Text Available Behaviors of “still”, “walking”, “running”, “jumping”, “upstairs” and “downstairs” can be recognized by micro inertial accelerometer of low cost. By using the features as inputs to the well-trained BP artificial neural network which is selected as classifier, those behaviors can be recognized. But the experimental results show that the recognition accuracy is not satisfactory. This paper presents secondary recognition algorithm and combine it with BP artificial neural network to improving the recognition accuracy. The Algorithm is verified by the Android mobile platform, and the recognition accuracy can be improved more than 8 %. Through extensive testing statistic analysis, the recognition accuracy can reach 95 % through BP artificial neural network and the secondary recognition, which is a reasonable good result from practical point of view.

  17. Improvement of illumination uniformity for LED flat panel light by using micro-secondary lens array.

    Science.gov (United States)

    Lee, Hsiao-Wen; Lin, Bor-Shyh

    2012-11-05

    LED flat panel light is an innovative lighting product in recent years. However, current flat panel light products still contain some drawbacks, such as narrow lighting areas and hot spots. In this study, a micro-secondary lens array technique was proposed and applied for the design of the light guide surface to improve the illumination uniformity. By using the micro-secondary lens array, the candela distribution of the LED flat panel light can be adjusted to similar to batwing distribution to improve the illumination uniformity. The experimental results show that the enhancement of the floor illumination uniformity is about 61%, and that of the wall illumination uniformity is about 20.5%.

  18. THE PECULIARITIES OF NICKNAME STRUCTURE IN THE VICINITY OF VELIUONA: SECONDARY NICKNAMES

    Directory of Open Access Journals (Sweden)

    Ilona Mickienė

    2014-10-01

    Full Text Available The paper analyses 782 nicknames that were recorded at Veliuona vicinity during the project of the Institute of the Lithuanian Language “Modern Research of Geolinguistics in Lithuania: Optimisation of Network of Points and Interactive Spread of Dialectal Information”. The paper aims to identify the characteristic attributes of nickname structure. The analysis of the relations in derivation, i. e., tentatively distinguishing the derivation base and formant is the only way to talk about common word derivation. While researching the nicknames it is difficult to find such a universal criterion in derivation which would enable the distribution of nicknames into the primary and the secondary ones due to the fact that when a nickname and its appellative derivation motivation coincides the confusion arises. Thus, the paper invokes the structural analysis of nicknames to find universal criteria that would enable the distinction of nicknames into the primary and the secondary. The article eliminates the primary nicknames that do not differ from the motivational word, 241 secondary nickname is being researched ant structurally analysed. The structural analysis discloses a proper structure and common words being selected for nickname creation. Structurally analysing the secondary nicknames, the nicknames with suffix, inflection, mixed structure, compound, composite and phrasal nicknames were distinguished. It was determined that in vacinity of Veliuona the nicknames with suffix and inflection are mostly used.

  19. A Reference Database for Circular Dichroism Spectroscopy Covering Fold and Secondary Structure Space

    International Nuclear Information System (INIS)

    Lees, J.; Miles, A.; Wien, F.; Wallace, B.

    2006-01-01

    Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined. This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology

  20. Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.

    Science.gov (United States)

    Lin, Luan; McKerrow, Wilson H; Richards, Bryce; Phonsom, Chukiat; Lawrence, Charles E

    2018-03-05

    The nearest neighbor model and associated dynamic programming algorithms allow for the efficient estimation of the RNA secondary structure Boltzmann ensemble. However because a given RNA secondary structure only contains a fraction of the possible helices that could form from a given sequence, the Boltzmann ensemble is multimodal. Several methods exist for clustering structures and finding those modes. However less focus is given to exploring the underlying reasons for this multimodality: the presence of conflicting basepairs. Information theory, or more specifically mutual information, provides a method to identify those basepairs that are key to the secondary structure. To this end we find most informative basepairs and visualize the effect of these basepairs on the secondary structure. Knowing whether a most informative basepair is present tells us not only the status of the particular pair but also provides a large amount of information about which other pairs are present or not present. We find that a few basepairs account for a large amount of the structural uncertainty. The identification of these pairs indicates small changes to sequence or stability that will have a large effect on structure. We provide a novel algorithm that uses mutual information to identify the key basepairs that lead to a multimodal Boltzmann distribution. We then visualize the effect of these pairs on the overall Boltzmann ensemble.

  1. Bayesian Inference using Neural Net Likelihood Models for Protein Secondary Structure Prediction

    Directory of Open Access Journals (Sweden)

    Seong-Gon Kim

    2011-06-01

    Full Text Available Several techniques such as Neural Networks, Genetic Algorithms, Decision Trees and other statistical or heuristic methods have been used to approach the complex non-linear task of predicting Alpha-helicies, Beta-sheets and Turns of a proteins secondary structure in the past. This project introduces a new machine learning method by using an offline trained Multilayered Perceptrons (MLP as the likelihood models within a Bayesian Inference framework to predict secondary structures proteins. Varying window sizes are used to extract neighboring amino acid information and passed back and forth between the Neural Net models and the Bayesian Inference process until there is a convergence of the posterior secondary structure probability.

  2. Fine-grained parallelism accelerating for RNA secondary structure prediction with pseudoknots based on FPGA.

    Science.gov (United States)

    Xia, Fei; Jin, Guoqing

    2014-06-01

    PKNOTS is a most famous benchmark program and has been widely used to predict RNA secondary structure including pseudoknots. It adopts the standard four-dimensional (4D) dynamic programming (DP) method and is the basis of many variants and improved algorithms. Unfortunately, the O(N(6)) computing requirements and complicated data dependency greatly limits the usefulness of PKNOTS package with the explosion in gene database size. In this paper, we present a fine-grained parallel PKNOTS package and prototype system for accelerating RNA folding application based on FPGA chip. We adopted a series of storage optimization strategies to resolve the "Memory Wall" problem. We aggressively exploit parallel computing strategies to improve computational efficiency. We also propose several methods that collectively reduce the storage requirements for FPGA on-chip memory. To the best of our knowledge, our design is the first FPGA implementation for accelerating 4D DP problem for RNA folding application including pseudoknots. The experimental results show a factor of more than 50x average speedup over the PKNOTS-1.08 software running on a PC platform with Intel Core2 Q9400 Quad CPU for input RNA sequences. However, the power consumption of our FPGA accelerator is only about 50% of the general-purpose micro-processors.

  3. QUALITY IMPROVEMENT OF SECONDARY SILUMINS BY USING REFINING-MODIFYING, HEAT AND LASER TREATMENTS

    Directory of Open Access Journals (Sweden)

    I. P. Volchok

    2014-10-01

    Full Text Available Purpose. As a rule secondary silumins are characterized by lower quality than their primary analogues. During manufacture of alloys a large quantity of intermetallides, first of all on the basis of iron, in their structure is ignored. To achieve the optimum level of properties it is necessary to search for ways to adapt refining-modifying, heat and laser treatments to peculiarities of the structure of secondary Al-Si alloys. Methodology. The research was carried out by using standard methods of metallographic analysis, determination of foundry, mechanical and service properties of alloys according to rotatable plans of multifactor experiments. Findings. It was established, that refiningmodifying treatment is a required procedure during manufacture of secondary silumins as it permits to effectively influence the iron-containing phases' segregations by changing their morphology, size and distribution and to increase the effectiveness of further treatment in solid state. It was found that standard modes of heat treatment are not optimal for secondary silumins. Laser treatment has shown high effectiveness in increasing of strength, wear resistance, corrosion and cavitation resistance of secondary Al-Si alloys, and the increased iron content contributed to additional solid solution hardening. Originality. It was established, that after refining-modifying treatment the phase Al5SiFe, which crystallizes in the shape of long stretched plates transformed into phase Al15(FeMn3Si2 in skeletal or polyhedral shape. The relationship between iron content in secondary silumins and holding time during heat treatment that ensures optimum of mechanical properties was obtained. It was proved that the presence of ironcontaining intermetallides Al5SiFe results in the decrease of hardened layer's depth during laser treatment. It was established, that with increasing of iron concentration the corrosion rate of secondary silumins in 3 % NaCl + 0.1 % H2O2 and 10 % HCl

  4. Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments.

    Science.gov (United States)

    Zheng, Ce; Kurgan, Lukasz

    2008-10-10

    beta-turn is a secondary protein structure type that plays significant role in protein folding, stability, and molecular recognition. To date, several methods for prediction of beta-turns from protein sequences were developed, but they are characterized by relatively poor prediction quality. The novelty of the proposed sequence-based beta-turn predictor stems from the usage of a window based information extracted from four predicted three-state secondary structures, which together with a selected set of position specific scoring matrix (PSSM) values serve as an input to the support vector machine (SVM) predictor. We show that (1) all four predicted secondary structures are useful; (2) the most useful information extracted from the predicted secondary structure includes the structure of the predicted residue, secondary structure content in a window around the predicted residue, and features that indicate whether the predicted residue is inside a secondary structure segment; (3) the PSSM values of Asn, Asp, Gly, Ile, Leu, Met, Pro, and Val were among the top ranked features, which corroborates with recent studies. The Asn, Asp, Gly, and Pro indicate potential beta-turns, while the remaining four amino acids are useful to predict non-beta-turns. Empirical evaluation using three nonredundant datasets shows favorable Q total, Q predicted and MCC values when compared with over a dozen of modern competing methods. Our method is the first to break the 80% Q total barrier and achieves Q total = 80.9%, MCC = 0.47, and Q predicted higher by over 6% when compared with the second best method. We use feature selection to reduce the dimensionality of the feature vector used as the input for the proposed prediction method. The applied feature set is smaller by 86, 62 and 37% when compared with the second and two third-best (with respect to MCC) competing methods, respectively. Experiments show that the proposed method constitutes an improvement over the competing prediction

  5. Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments

    Directory of Open Access Journals (Sweden)

    Kurgan Lukasz

    2008-10-01

    Full Text Available Abstract Background β-turn is a secondary protein structure type that plays significant role in protein folding, stability, and molecular recognition. To date, several methods for prediction of β-turns from protein sequences were developed, but they are characterized by relatively poor prediction quality. The novelty of the proposed sequence-based β-turn predictor stems from the usage of a window based information extracted from four predicted three-state secondary structures, which together with a selected set of position specific scoring matrix (PSSM values serve as an input to the support vector machine (SVM predictor. Results We show that (1 all four predicted secondary structures are useful; (2 the most useful information extracted from the predicted secondary structure includes the structure of the predicted residue, secondary structure content in a window around the predicted residue, and features that indicate whether the predicted residue is inside a secondary structure segment; (3 the PSSM values of Asn, Asp, Gly, Ile, Leu, Met, Pro, and Val were among the top ranked features, which corroborates with recent studies. The Asn, Asp, Gly, and Pro indicate potential β-turns, while the remaining four amino acids are useful to predict non-β-turns. Empirical evaluation using three nonredundant datasets shows favorable Qtotal, Qpredicted and MCC values when compared with over a dozen of modern competing methods. Our method is the first to break the 80% Qtotal barrier and achieves Qtotal = 80.9%, MCC = 0.47, and Qpredicted higher by over 6% when compared with the second best method. We use feature selection to reduce the dimensionality of the feature vector used as the input for the proposed prediction method. The applied feature set is smaller by 86, 62 and 37% when compared with the second and two third-best (with respect to MCC competing methods, respectively. Conclusion Experiments show that the proposed method constitutes an

  6. Web-Beagle: a web server for the alignment of RNA secondary structures.

    Science.gov (United States)

    Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2015-07-01

    Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Two-dimensional dynamics of a free molecular chain with a secondary structure

    DEFF Research Database (Denmark)

    Zolotaryuk, Alexander; Christiansen, Peter Leth; Savin, A.V.

    1996-01-01

    A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model of an anharmo......A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model...

  8. Artificial Intelligence in Prediction of Secondary Protein Structure Using CB513 Database

    Science.gov (United States)

    Avdagic, Zikrija; Purisevic, Elvir; Omanovic, Samir; Coralic, Zlatan

    2009-01-01

    In this paper we describe CB513 a non-redundant dataset, suitable for development of algorithms for prediction of secondary protein structure. A program was made in Borland Delphi for transforming data from our dataset to make it suitable for learning of neural network for prediction of secondary protein structure implemented in MATLAB Neural-Network Toolbox. Learning (training and testing) of neural network is researched with different sizes of windows, different number of neurons in the hidden layer and different number of training epochs, while using dataset CB513. PMID:21347158

  9. RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

    Directory of Open Access Journals (Sweden)

    Chen Chun

    2008-03-01

    Full Text Available Abstract Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1 present a robust and effective way for RNA structural data compression; (2 design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool

  10. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    Science.gov (United States)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

  11. FTIR study of secondary structure of bovine serum albumin and ovalbumin

    International Nuclear Information System (INIS)

    Abrosimova, K V; Shulenina, O V; Paston, S V

    2016-01-01

    Proteins structure is the critical factor for their functioning. Fourier transform infrared spectroscopy provides a possibility to obtain information about secondary structure of proteins in different states and also in a whole biological samples. Infrared spectra of egg white from the untreated and hard-boiled hen's egg, and also of chicken ovalbumin and bovine serum albumin in lyophilic form and in aqueous solution were studied. Lyophilization of investigated globular proteins is accompanied by the decrease of a-helix structures and the increase in amount of intermolecular β-sheets. Analysis of infrared spectrum of egg white allowed to make an estimation of OVA secondary structure and to observe α-to-β structural transformation as a result of the heat denaturation. (paper)

  12. Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks.

    Science.gov (United States)

    Babaei, Sepideh; Geranmayeh, Amir; Seyyedsalehi, Seyyed Ali

    2010-12-01

    The supervised learning of recurrent neural networks well-suited for prediction of protein secondary structures from the underlying amino acids sequence is studied. Modular reciprocal recurrent neural networks (MRR-NN) are proposed to model the strong correlations between adjacent secondary structure elements. Besides, a multilayer bidirectional recurrent neural network (MBR-NN) is introduced to capture the long-range intramolecular interactions between amino acids in formation of the secondary structure. The final modular prediction system is devised based on the interactive integration of the MRR-NN and the MBR-NN structures to arbitrarily engage the neighboring effects of the secondary structure types concurrent with memorizing the sequential dependencies of amino acids along the protein chain. The advanced combined network augments the percentage accuracy (Q₃) to 79.36% and boosts the segment overlap (SOV) up to 70.09% when tested on the PSIPRED dataset in three-fold cross-validation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  13. Secondary Data Analysis of National Surveys in Japan Toward Improving Population Health

    Science.gov (United States)

    Ikeda, Nayu

    2016-01-01

    Secondary data analysis of national health surveys of the general population is a standard methodology for health metrics and evaluation; it is used to monitor trends in population health over time and benchmark the performance of health systems. In Japan, the government has established electronic databases of individual records from national surveys of the population’s health. However, the number of publications based on these datasets is small considering the scale and coverage of the surveys. There appear to be two major obstacles to the secondary use of Japanese national health survey data: strict data access control under the Statistics Act and an inadequate interdisciplinary research environment for resolving methodological difficulties encountered when dealing with secondary data. The usefulness of secondary analysis of survey data is evident with examples from the author’s previous studies based on vital records and the National Health and Nutrition Surveys, which showed that (i) tobacco smoking and high blood pressure are the major risk factors for adult mortality from non-communicable diseases in Japan; (ii) the decrease in mean blood pressure in Japan from the late 1980s to the early 2000s was partly attributable to the increased use of antihypertensive medication and reduced dietary salt intake; and (iii) progress in treatment coverage and control of high blood pressure is slower in Japan than in the United States and Britain. National health surveys in Japan are an invaluable asset, and findings from secondary analyses of these surveys would provide important suggestions for improving health in people around the world. PMID:26902170

  14. Improving secondary prevention screening in clinical encounters using mhealth among prelicensure master's entry clinical nursing students.

    Science.gov (United States)

    FitzGerald, Leah Z; Rorie, Anne; Salem, Benissa E

    2015-04-01

    To determine the feasibility and acceptability of a mHealth application among nursing students for health promotion and secondary prevention health recommendations for hospitalized adult patients. A pretest-posttest design with a convenience sample of 169 prelicensure master's entry clinical nursing students in a large urban public university. Survey questions assessed intention to use, perceived usefulness, perceived ease of use, subjective norm, voluntariness, clinical area relevance, output quality, and result demonstrability of the United States Preventive Services Task Force (USPSTF) evidence-based practice guidelines via the mHealth application. Descriptive statistics and frequencies were used to explore sociodemographics; paired t-tests were used to evaluate pre- and posttest differences. Pre- and posttest significant differences (p technology among prelicensure master's entry clinical nursing students in order to engage and foster translational learning and improve dissemination of secondary prevention screening guidelines among hospitalized patients. © 2015 Sigma Theta Tau International.

  15. Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Scheid Anika

    2012-07-01

    -case time requirements of such an SCFG based sampling method without significant accuracy losses. If, on the other hand, the quality of sampled structures can be observed to strongly react to slight disturbances, there is little hope for improving the complexity by heuristic procedures. We hence provide a reliable test for the hypothesis that a heuristic method could be implemented to improve the time scaling of RNA secondary structure prediction in the worst-case – without sacrificing much of the accuracy of the results. Conclusions Our experiments indicate that absolute errors generally lead to the generation of useless sample sets, whereas relative errors seem to have only small negative impact on both the predictive accuracy and the overall quality of resulting structure samples. Based on these observations, we present some useful ideas for developing a time-reduced sampling method guaranteeing an acceptable predictive accuracy. We also discuss some inherent drawbacks that arise in the context of approximation. The key results of this paper are crucial for the design of an efficient and competitive heuristic prediction method based on the increasingly accepted and attractive statistical sampling approach. This has indeed been indicated by the construction of prototype algorithms.

  16. Motor cortex stimulation does not improve dystonia secondary to a focal basal ganglia lesion.

    Science.gov (United States)

    Rieu, Isabelle; Aya Kombo, Magaly; Thobois, Stéphane; Derost, Philippe; Pollak, Pierre; Xie, Jing; Pereira, Bruno; Vidailhet, Marie; Burbaud, Pierre; Lefaucheur, Jean Pascal; Lemaire, Jean Jacques; Mertens, Patrick; Chabardes, Stephan; Broussolle, Emmanuel; Durif, Franck

    2014-01-14

    To assess the efficacy of epidural motor cortex stimulation (MCS) on dystonia, spasticity, pain, and quality of life in patients with dystonia secondary to a focal basal ganglia (BG) lesion. In this double-blind, crossover, multicenter study, 5 patients with dystonia secondary to a focal BG lesion were included. Two quadripolar leads were implanted epidurally over the primary motor (M1) and premotor cortices, contralateral to the most dystonic side. The leads were placed parallel to the central sulcus. Only the posterior lead over M1 was activated in this study. The most lateral or medial contact of the lead (depending on whether the dystonia predominated in the upper or lower limb) was selected as the anode, and the other 3 as cathodes. One month postoperatively, patients were randomly assigned to on- or off-stimulation for 3 months each, with a 1-month washout between the 2 conditions. Voltage, frequency, and pulse width were fixed at 3.8 V, 40 Hz, and 60 μs, respectively. Evaluations of dystonia (Burke-Fahn-Marsden Scale), spasticity (Ashworth score), pain intensity (visual analog scale), and quality of life (36-Item Short Form Health Survey) were performed before surgery and after each period of stimulation. Burke-Fahn-Marsden Scale, Ashworth score, pain intensity, and quality of life were not statistically significantly modified by MCS. Bipolar epidural MCS failed to improve any clinical feature in dystonia secondary to a focal BG lesion. This study provides Class I evidence that bipolar epidural MCS with the anode placed over the motor representation of the most affected limb failed to improve any clinical feature in dystonia secondary to a focal BG lesion.

  17. Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

    Science.gov (United States)

    Sloma, Michael F.; Mathews, David H.

    2016-01-01

    RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. PMID:27852924

  18. Viral IRES prediction system - a web server for prediction of the IRES secondary structure in silico.

    Directory of Open Access Journals (Sweden)

    Jun-Jie Hong

    Full Text Available The internal ribosomal entry site (IRES functions as cap-independent translation initiation sites in eukaryotic cells. IRES elements have been applied as useful tools for bi-cistronic expression vectors. Current RNA structure prediction programs are unable to predict precisely the potential IRES element. We have designed a viral IRES prediction system (VIPS to perform the IRES secondary structure prediction. In order to obtain better results for the IRES prediction, the VIPS can evaluate and predict for all four different groups of IRESs with a higher accuracy. RNA secondary structure prediction, comparison, and pseudoknot prediction programs were implemented to form the three-stage procedure for the VIPS. The backbone of VIPS includes: the RNAL fold program, aimed to predict local RNA secondary structures by minimum free energy method; the RNA Align program, intended to compare predicted structures; and pknotsRG program, used to calculate the pseudoknot structure. VIPS was evaluated by using UTR database, IRES database and Virus database, and the accuracy rate of VIPS was assessed as 98.53%, 90.80%, 82.36% and 80.41% for IRES groups 1, 2, 3, and 4, respectively. This advance useful search approach for IRES structures will facilitate IRES related studies. The VIPS on-line website service is available at http://140.135.61.250/vips/.

  19. Secondary structure of bovine albumin as studied by polarization-sensitive multiplex CARS spectroscopy

    NARCIS (Netherlands)

    Voroshilov, A.; Voroshilov, Artemy; Otto, Cornelis; Greve, Jan

    1996-01-01

    The first application of polarization-sensitive multiplex coherent anti-Stokes Raman spectroscopy (MCARS) in the absence of resonance enhancement to the resolution of the secondary structure of a protein in solution is reported. Polarization MCARS spectra of bovine albumin in D2O were obtained in

  20. Instruction in text-structure as a determinant of senior secondary ...

    African Journals Online (AJOL)

    The study determined the effectiveness of instruction in text-structure on achievement of students in English narrative text. The pretest-posttest control group quasi experimental design was adopted for the study. The participants were 120 students in intact classes from four purposively selected senior secondary schools in ...

  1. Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Réblová, K.; Štěpánek, Václav

    2015-01-01

    Roč. 35, December 2015 (2015), s. 21-38 ISSN 0031-5850 R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 ; RVO:61388971 Keywords : Barbatosphaeria * molecular systematic * ITS secondary structures Subject RIV: EF - Botanics; EE - Microbiology, Virology (MBU-M) Impact factor: 5.725, year: 2015

  2. Interfacial ordering of thermotropic liquid crystals triggered by the secondary structures of oligopeptides.

    Science.gov (United States)

    Wang, Xiaoguang; Yang, Pei; Mondiot, Frederic; Li, Yaoxin; Miller, Daniel S; Chen, Zhan; Abbott, Nicholas L

    2015-12-07

    We report that assemblies formed by eight oligopeptides at phospholipid-decorated interfaces of thermotropic liquid crystals (LCs) trigger changes in ordering of the LCs that are dependent on the secondary structures of the oligopeptides (as characterized in situ using infrared-visible sum-frequency spectroscopy).

  3. A possible contribution of mRNA secondary structure to translation initiation efficiency in Lactococcus lactis

    NARCIS (Netherlands)

    Guchte, Maarten van de; Lende, Ted van der; Kok, Jan; Venema, Gerard

    1991-01-01

    Gene expression signals derived from Lactococcus lactis were linked to lacZ-fused genes with different 5'-nucleotide sequences. Computer predictions of mRNA secondary structure were combined with lacZ expression studies to direct base-substitutions that could possibly influence gene expression.

  4. Glassy transition in a disordered model for the RNA secondary structure

    International Nuclear Information System (INIS)

    Pagnani, A.; Parisi, G.; Ricci-Tersenghi, F.

    2000-04-01

    We numerically study a disordered model for the RNA secondary structure and we find that it undergoes a phase transition, with a breaking of the replica symmetry in the low temperature region (like in spin glasses). Our results are based on the exact evaluation of the partition function. (author)

  5. Tropical rain-forest matrix quality affects bat assemblage structure in secondary forest patches

    NARCIS (Netherlands)

    Vleut, I.; Levy-Tacher, I.; Galindo-Gonzalez, J.; Boer, de W.F.; Ramirez-Marcial, N.

    2012-01-01

    We studied Phyllostomidae bat assemblage structure in patches of secondary forest dominated by the pioneer tree Ochroma pyramidale, largely (.85%) or partially (,35%) surrounded by a matrix of tropical rain forest, to test 3 hypotheses: the highest bat diversity and richness is observed in the

  6. Secondary structures of rRNAs from all three domains of life.

    Directory of Open Access Journals (Sweden)

    Anton S Petrov

    Full Text Available Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2° structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU 23S/28S and small subunit (SSU 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only, Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery. Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision.

  7. Analysis of the secondary structure of ITS transcripts in peritrich ciliates (Ciliophora, Oligohymenophorea): implications for structural evolution and phylogenetic reconstruction.

    Science.gov (United States)

    Sun, Ping; Clamp, John C; Xu, Dapeng

    2010-07-01

    Despite extensive previous morphological work, little agreement has been reached about phylogenetic relationships among peritrich ciliates, making it difficult to study the evolution of the group in a phylogenetic framework. In this study, the nucleotide characteristics and secondary structures of internal transcribed spacers 1 and 2 (ITS1 and ITS2) of 26 peritrich ciliates in 12 genera were analyzed. Information from secondary structures of ITS1 and ITS2 then was used to perform the first systematic study of ITS regions in peritrich ciliates, including one species of Rhabdostyla for which no sequence has been reported previously. Lengths of ITS1 and ITS2 sequences varied relatively little among taxa studied, but their G+C content was highly variable. General secondary structure models of ITS1 and ITS2 were proposed for peritrich ciliates and their reliability was assessed by compensatory base changes. The secondary structure of ITS1 contains three major helices in peritrich ciliates and deviations from this basic structure were found in all taxa examined. The core structure of peritrich ITS2 includes four helices, with helix III as the longest and containing a motif 5'-MAC versus GUK-3' at its apex as well as a YU-UY mismatch in helix II. In addition, the structural motifs of both ITS secondary structures were identified. Phylogenetic analyses using ITS data were performed by means of Bayesian inference, maximum likelihood and neighbor joining methods. Trees had a consistent branching pattern that included the following features: (1) Rhabdostyla always clustered with members of the family Vorticellidae, instead of members of the family Epistylididae, in which it is now classified on the basis of morphology. (2) The systematically questionable genus Ophrydium closely associated with Carchesium, forming a clearly defined, monophyletic group within the Vorticellidae. This supported the hypothesis derived from previous study based on small subunit rRNA gene sequences

  8. Developments in the Curriculum and Structures of Upper-Secondary Education in Australia: The Last Decade.

    Science.gov (United States)

    McKinnon, Ken

    1988-01-01

    Examines the recent influences on and development of upper-secondary Australian education. These influences include youth unemployment, rapid technological and social change, immigration, increasing federal role, and limited entry to tertiary education. Changes include broader curriculum planning to include all students, and improvement of the…

  9. Fold classification based on secondary structure – how much is gained by including loop topology?

    Directory of Open Access Journals (Sweden)

    Przytycka Teresa

    2006-03-01

    Full Text Available Abstract Background It has been proposed that secondary structure information can be used to classify (to some extend protein folds. Since this method utilizes very limited information about the protein structure, it is not surprising that it has a higher error rate than the approaches that use full 3D fold description. On the other hand, the comparing of 3D protein structures is computing intensive. This raises the question to what extend the error rate can be decreased with each new source of information, especially if the new information can still be used with simple alignment algorithms. We consider the question whether the information about closed loops can improve the accuracy of this approach. While the answer appears to be obvious, we had to overcome two challenges. First, how to code and to compare topological information in such a way that local alignment of strings will properly identify similar structures. Second, how to properly measure the effect of new information in a large data sample. We investigate alternative ways of computing and presenting this information. Results We used the set of beta proteins with at most 30% pairwise identity to test the approach; local alignment scores were used to build a tree of clusters which was evaluated using a new log-odd cluster scoring function. In particular, we derive a closed formula for the probability of obtaining a given score by chance.Parameters of local alignment function were optimized using a genetic algorithm. Of 81 folds that had more than one representative in our data set, log-odds scores registered significantly better clustering in 27 cases and significantly worse in 6 cases, and small differences in the remaining cases. Various notions of the significant change or average change were considered and tried, and the results were all pointing in the same direction. Conclusion We found that, on average, properly presented information about the loop topology improves noticeably

  10. Secondary structure classification of amino-acid sequences using state-space modeling

    OpenAIRE

    Brunnert, Marcus; Krahnke, Tillmann; Urfer, Wolfgang

    2001-01-01

    The secondary structure classification of amino acid sequences can be carried out by a statistical analysis of sequence and structure data using state-space models. Aiming at this classification, a modified filter algorithm programmed in S is applied to data of three proteins. The application leads to correct classifications of two proteins even when using relatively simple estimation methods for the parameters of the state-space models. Furthermore, it has been shown that the assumed initial...

  11. Data Use for School Improvement : Knowledge Sharing and Knowledge Brokerage in Network Structures

    NARCIS (Netherlands)

    Hubers, Mireille Desirée; Moolenaar, Nienke; Schildkamp, Kim; Handelzalts, Adam; Pieters, Julius Marie; Daly, A.J.; Daly, Alan J.

    2015-01-01

    Data teams are used in Dutch secondary education to support schools in data use for school improvement. Such teams are likely to be most effective when knowledge is shared between the data team members and brokered throughout the school. Social network structures may play an important role in this.

  12. A study on the efficiency improvement of the plant secondary System in NPP

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Chun Ho; Song Jong Sun [Chosun Univ., Kwangju (Korea, Republic of)

    2012-10-15

    The ultimate objective of the diagnostic test for thermal performance of generation facilities is to assist in making an economic decision on operation optimization of power plants by understanding the degree of heat aging due to operation of relevant facilities and planning on this basis the maintenance and repair. In this thesis, the trend in performance change was analyzed against the acceptance performance test conducted after the replacement of the high pressure turbine in 2007, through thermal performance diagnosis conducted at 100 % reactor thermal output after the 19th planned preventive maintenance of Yonggwang Nuclear Units 1 and 2, and the power plant operation was optimized by acquiring base line data for management of performance record for each major facility of the secondary system and by improving efficiency of unit instruments and peripheral instruments of the secondary system. As a result derived from the thermal performance analysis, the increase in electric output of the power plants was achieved through such operation optimizations of efficiency affecting instruments as optimization of the continuous exhaust flow rate for water supply heaters, vacuum improvement of condensers due to opening the upper/lower screens of heat transfer pipe washing system for condensers during summer, and flow rate optimization of the water vapor supplied to MSR (Moisture Separator Re heater) high pressure re heaters. This improves operation of the existing power plants without additional expense and so requires expert review by responsible personnel for practical application.

  13. Prediction of guide strand of microRNAs from its sequence and secondary structure

    Directory of Open Access Journals (Sweden)

    Ahmed Firoz

    2009-04-01

    nucleotide sequence and secondary structure. This method will be useful in understanding microRNA processing and can be implemented in RNA silencing technology to improve the biological and clinical research. A web server has been developed based on SVM models described in this study http://crdd.osdd.net:8081/RISCbinder/.

  14. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

    Science.gov (United States)

    Ding, Yiliang; Tang, Yin; Kwok, Chun Kit; Zhang, Yu; Bevilacqua, Philip C; Assmann, Sarah M

    2014-01-30

    RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

  15. Interventions for improving modifiable risk factor control in the secondary prevention of stroke.

    Science.gov (United States)

    Lager, Kate E; Mistri, Amit K; Khunti, Kamlesh; Haunton, Victoria J; Sett, Aung K; Wilson, Andrew D

    2014-05-02

    People with stroke or transient ischaemic attack (TIA) are at increased risk of future stroke and other cardiovascular events. Evidence-based strategies for secondary stroke prevention have been established. However, the implementation of prevention strategies could be improved. To assess the effects of stroke service interventions for implementing secondary stroke prevention strategies on modifiable risk factor control, including patient adherence to prescribed medications, and the occurrence of secondary cardiovascular events. We searched the Cochrane Stroke Group Trials Register (April 2013), the Cochrane Effective Practice and Organisation of Care Group Trials Register (April 2013), CENTRAL (The Cochrane Library 2013, issue 3), MEDLINE (1950 to April 2013), EMBASE (1981 to April 2013) and 10 additional databases. We located further studies by searching reference lists of articles and contacting authors of included studies. We included randomised controlled trials (RCTs) that evaluated the effects of organisational or educational and behavioural interventions (compared with usual care) on modifiable risk factor control for secondary stroke prevention. Two review authors selected studies for inclusion and independently extracted data. One review author assessed the risk of bias for the included studies. We sought missing data from trialists. This review included 26 studies involving 8021 participants. Overall the studies were of reasonable quality, but one study was considered at high risk of bias. Fifteen studies evaluated predominantly organisational interventions and 11 studies evaluated educational and behavioural interventions for patients. Results were pooled where appropriate, although some clinical and methodological heterogeneity was present. The estimated effects of organisational interventions were compatible with improvements and no differences in the modifiable risk factors mean systolic blood pressure (mean difference (MD) -2.57 mmHg; 95% confidence

  16. Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

    DEFF Research Database (Denmark)

    Kato, Yuki; Gorodkin, Jan; Havgaard, Jakob Hull

    2017-01-01

    . Methods: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes...... without alignment. Results: Our computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity. Conclusions: DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs....

  17. Reflection of the energy structure of a tungsten monocrystal nearsurface area in the secondary electron spectrum

    International Nuclear Information System (INIS)

    Artamonov, O.M.; Smirnov, O.M.; Terekhov, A.N.

    1982-01-01

    Formation of secondary electron energy spectrum during emission from the crystal layer near the surface has been considered, at that layer energy structure can be different from volumetric energy structure. Its thickness depends on the predominant mechanism of electron scattering and is determined by corresponding phenomenological parameters. It is shown that the structure in the secondary electron spectrum appears in the case when energy structure of emitting monocrystal layer can not be described in the approximation of almost free electron gas and, as experimental investigations show, approaches energy zone structure of its volume. It is also show that in the case when the energy structure of the emitting layer is satisfactorily described with the model of almost free electron gas, the SE spectrum is characterized with traditional cascade minimum. Experimental investigation of SE energy distribution was carried out for the W monocrystalline face (110). It was established that distinct structure in the SE spectrum appears only after electrochemical polishing of the specimen surface. It is related to the appearance of ''far'' order in the monocrystal emission layer on initially disturbed tungsten surface during such treatment. Disturbance of tungsten monocrystal surface structure on its oxidation in O 2 atmosphere results in the appearance of the cascade maximum and disappearance of distinct peculiarities in the SE spectrum

  18. A contribution to understanding the structure of amphivasal secondary bundles in monocotyledons

    Directory of Open Access Journals (Sweden)

    Joanna Jura-Morawiec

    2014-04-01

    Full Text Available Secondary growth of monocotyledonous plants is connected with the activity of the monocot cambium that accumulates most of the derivatives inner to the cambial cylinder. These derivatives differentiate into (a secondary bundles with the amphivasal arrangement, i.e. xylem composed of tracheids surrounds the phloem cells and (b the parenchymatous secondary conjunctive tissue in which the bundles are embedded. The amphivasal secondary bundles differ in the arrangement of xylem cells as visible on single cross sections through the secondary body of the monocots. Apart from the bundles with typical ring of tracheids also the bundles where tracheids do not quite surround the phloem are present. We aimed to elucidate the cross sectional anatomy of the amphivasal secondary bundles with the use of the serial sectioning method which allowed us to follow very precisely the bundle structure along its length. The studies were carried out with the samples of secondary tissues collected from the stem of Dracaena draco L. growing in the greenhouses of the Polish Academy of Sciences Botanical Garden – CBDC in Powsin and the Adam Mickiewicz University Botanical Garden. The material was fixed in a mixture of glycerol and ethanol (1:1; v/v, dehydrated stepwise with graded ethanol series and finally embedded in epon resin. Afterwards, the material was sectioned with microtome into continuous series of thin (3 μm sections, stained with PAS/toluidine blue and examined under the light microscope. The results, described in details in Jura‑Morawiec & Wiland-Szymańska (2014, revealed novel facts about tracheids arrangement. Each amphivasal bundle is composed of sectors where tracheids form a ring as well as of such where tracheids are separated by vascular parenchyma cells. We hypothesize that strands of vascular parenchyma cells locally separating the tracheids enable radial transport of assimilates from sieve elements of the bundle towards the sink tissues, e

  19. Analysis of energy-based algorithms for RNA secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Hajiaghayi Monir

    2012-02-01

    Full Text Available Abstract Background RNA molecules play critical roles in the cells of organisms, including roles in gene regulation, catalysis, and synthesis of proteins. Since RNA function depends in large part on its folded structures, much effort has been invested in developing accurate methods for prediction of RNA secondary structure from the base sequence. Minimum free energy (MFE predictions are widely used, based on nearest neighbor thermodynamic parameters of Mathews, Turner et al. or those of Andronescu et al. Some recently proposed alternatives that leverage partition function calculations find the structure with maximum expected accuracy (MEA or pseudo-expected accuracy (pseudo-MEA methods. Advances in prediction methods are typically benchmarked using sensitivity, positive predictive value and their harmonic mean, namely F-measure, on datasets of known reference structures. Since such benchmarks document progress in improving accuracy of computational prediction methods, it is important to understand how measures of accuracy vary as a function of the reference datasets and whether advances in algorithms or thermodynamic parameters yield statistically significant improvements. Our work advances such understanding for the MFE and (pseudo-MEA-based methods, with respect to the latest datasets and energy parameters. Results We present three main findings. First, using the bootstrap percentile method, we show that the average F-measure accuracy of the MFE and (pseudo-MEA-based algorithms, as measured on our largest datasets with over 2000 RNAs from diverse families, is a reliable estimate (within a 2% range with high confidence of the accuracy of a population of RNA molecules represented by this set. However, average accuracy on smaller classes of RNAs such as a class of 89 Group I introns used previously in benchmarking algorithm accuracy is not reliable enough to draw meaningful conclusions about the relative merits of the MFE and MEA-based algorithms

  20. Improved data visualization techniques for analyzing macromolecule structural changes.

    Science.gov (United States)

    Kim, Jae Hyun; Iyer, Vidyashankara; Joshi, Sangeeta B; Volkin, David B; Middaugh, C Russell

    2012-10-01

    The empirical phase diagram (EPD) is a colored representation of overall structural integrity and conformational stability of macromolecules in response to various environmental perturbations. Numerous proteins and macromolecular complexes have been analyzed by EPDs to summarize results from large data sets from multiple biophysical techniques. The current EPD method suffers from a number of deficiencies including lack of a meaningful relationship between color and actual molecular features, difficulties in identifying contributions from individual techniques, and a limited ability to be interpreted by color-blind individuals. In this work, three improved data visualization approaches are proposed as techniques complementary to the EPD. The secondary, tertiary, and quaternary structural changes of multiple proteins as a function of environmental stress were first measured using circular dichroism, intrinsic fluorescence spectroscopy, and static light scattering, respectively. Data sets were then visualized as (1) RGB colors using three-index EPDs, (2) equiangular polygons using radar charts, and (3) human facial features using Chernoff face diagrams. Data as a function of temperature and pH for bovine serum albumin, aldolase, and chymotrypsin as well as candidate protein vaccine antigens including a serine threonine kinase protein (SP1732) and surface antigen A (SP1650) from S. pneumoniae and hemagglutinin from an H1N1 influenza virus are used to illustrate the advantages and disadvantages of each type of data visualization technique. Copyright © 2012 The Protein Society.

  1. Protein Phosphorylation and Mineral Binding Affect the Secondary Structure of the Leucine-Rich Amelogenin Peptide

    Directory of Open Access Journals (Sweden)

    Hajime Yamazaki

    2017-06-01

    Full Text Available Previously, we have shown that serine-16 phosphorylation in native full-length porcine amelogenin (P173 and the Leucine-Rich Amelogenin Peptide (LRAP(+P, an alternative amelogenin splice product, affects protein assembly and mineralization in vitro. Notably, P173 and LRAP(+P stabilize amorphous calcium phosphate (ACP and inhibit hydroxyapatite (HA formation, while non-phosphorylated counterparts (rP172, LRAP(−P guide the growth of ordered bundles of HA crystals. Based on these findings, we hypothesize that the phosphorylation of full-length amelogenin and LRAP induces conformational changes that critically affect its capacity to interact with forming calcium phosphate mineral phases. To test this hypothesis, we have utilized Fourier transform infrared spectroscopy (FTIR to determine the secondary structure of LRAP(−P and LRAP(+P in the absence/presence of calcium and selected mineral phases relevant to amelogenesis; i.e., hydroxyapatite (HA: an enamel crystal prototype and (ACP: an enamel crystal precursor phase. Aqueous solutions of LRAP(−P or LRAP(+P were prepared with or without 7.5 mM of CaCl2 at pH 7.4. FTIR spectra of each solution were obtained using attenuated total reflectance, and amide-I peaks were analyzed to provide secondary structure information. Secondary structures of LRAP(+P and LRAP(−P were similarly assessed following incubation with suspensions of HA and pyrophosphate-stabilized ACP. Amide I spectra of LRAP(−P and LRAP(+P were found to be distinct from each other in all cases. Spectra analyses showed that LRAP(−P is comprised mostly of random coil and β-sheet, while LRAP(+P exhibits more β-sheet and α-helix with little random coil. With added Ca, the random coil content increased in LRAP(−P, while LRAP(+P exhibited a decrease in α-helix components. Incubation of LRAP(−P with HA or ACP resulted in comparable increases in β-sheet structure. Notably, however, LRAP(+P secondary structure was more affected by

  2. Control of Helical Chirality of Ferrocene-Dipeptide Conjugates by the Secondary Structure of Dipeptide Chains.

    Science.gov (United States)

    Moriuchi, Toshiyuki; Nishiyama, Taiki; Nobu, Masaki; Hirao, Toshikazu

    2017-09-18

    Controlling helical chirality and creating protein secondary structures in cyclic/acyclic ferrocene-dipeptide bioorganometallic conjugates were achieved by adjusting the conformational flexibility of the dipeptide chains. In systems reported to date, the helical chirality of a conjugate was determined by the absolute configuration of the adjacent amino acid reside. In contrast, it was possible to induce both M- and P-helical chirality, even when the configuration of the adjacent amino acid was the same. It is particularly interesting to note that M-helical chirality was produced in a cyclic ferrocene-dipeptide conjugate composed of the l-Ala-d-Pro-cystamine-d-Pro-l-Ala dipeptide sequence (1), in which a type II β-turn-like secondary structure was established. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

    Science.gov (United States)

    Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

    2012-01-01

    RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

  4. Structure of the spin polarization spectrum of secondary electrons emitted from nickel

    International Nuclear Information System (INIS)

    Helman, J.S.

    1985-01-01

    The main features of the structure observed in the energy resolved spin polarization of secondary electrons emitted from Ni are interpreted in terms of surface and bulk plasmon assisted emission. The model also predicts a measureable shift of the main polarization peak of about 0.3 eV to lower energies as the temperature is raised from room temperature to closely below the Curie temperature. (Author) [pt

  5. An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences

    Czech Academy of Sciences Publication Activity Database

    Pánek, Josef; Modrák, Martin; Schwarz, Marek

    2017-01-01

    Roč. 8, OCT 10 (2017), s. 1-11, č. článku 147. ISSN 1664-8021 R&D Projects: GA ČR GA15-00885S; GA MŠk(CZ) LM2015047 Institutional support: RVO:61388971 Keywords : RNA * secondary structure * homology Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 3.789, year: 2016

  6. CentroidFold: a web server for RNA secondary structure prediction

    OpenAIRE

    Sato, Kengo; Hamada, Michiaki; Asai, Kiyoshi; Mituyama, Toutai

    2009-01-01

    The CentroidFold web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine. The server accepts two kinds of sequence data: a single RNA sequence and a multiple alignment of RNA sequences. It responses with a prediction result shown as a popular base-pair notation and a graph representation. PDF version of the graph representation is also available. For a multiple alignment sequence, the ser...

  7. [Peculiarities of secondary structure of serum albumin of some representatives of the animal kingdom].

    Science.gov (United States)

    Pekhymenko, G V; Kuchmerovskaia, T M

    2011-01-01

    Methods of infrared (IR) spectroscopy and circular dichroism (CD) are suitable techniques for detection of proteins structural changes. These methods were used for determinating peculiarities of the secondary structure of serum albumins in some representatives of two classes of reptiles: Horsfield's tortoise (Testudo horsfieldi), water snake (Natrix tessellata) and grass snake (Natrix natrix) and birds: domestic goose (Anser anser), domestic chicken (Gallus domesticus), domestic duck (Anas platyrhyncha) and dove colored (Columba livia). An analysis of IR spectra and spectra obtained by the method of CD of serum albumins of both classes representatives revealed that beta-folding structure and alpha-helical sections that form the alpha-conformation play an important role in conformational structure formation of polypeptide chain and also disordered sites of molecules of these proteins. It was observed that certain redistribution depending on animals species exists, in the formation of secondary structure of serum albumins of the investigated representatives of reptiles and birds classes between the content of beta-folding structure, alpha-helical sections and disordered sites in molecules of these proteins.

  8. Correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    Science.gov (United States)

    Lundgren, Martin; Niemi, Antti J.

    2012-08-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central Cα carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the Cβ carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the Cα-Cβ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

  9. SVM-PB-Pred: SVM based protein block prediction method using sequence profiles and secondary structures.

    Science.gov (United States)

    Suresh, V; Parthasarathy, S

    2014-01-01

    We developed a support vector machine based web server called SVM-PB-Pred, to predict the Protein Block for any given amino acid sequence. The input features of SVM-PB-Pred include i) sequence profiles (PSSM) and ii) actual secondary structures (SS) from DSSP method or predicted secondary structures from NPS@ and GOR4 methods. There were three combined input features PSSM+SS(DSSP), PSSM+SS(NPS@) and PSSM+SS(GOR4) used to test and train the SVM models. Similarly, four datasets RS90, DB433, LI1264 and SP1577 were used to develop the SVM models. These four SVM models developed were tested using three different benchmarking tests namely; (i) self consistency, (ii) seven fold cross validation test and (iii) independent case test. The maximum possible prediction accuracy of ~70% was observed in self consistency test for the SVM models of both LI1264 and SP1577 datasets, where PSSM+SS(DSSP) input features was used to test. The prediction accuracies were reduced to ~53% for PSSM+SS(NPS@) and ~43% for PSSM+SS(GOR4) in independent case test, for the SVM models of above two same datasets. Using our method, it is possible to predict the protein block letters for any query protein sequence with ~53% accuracy, when the SP1577 dataset and predicted secondary structure from NPS@ server were used. The SVM-PB-Pred server can be freely accessed through http://bioinfo.bdu.ac.in/~svmpbpred.

  10. CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures

    Directory of Open Access Journals (Sweden)

    Hamed Bostan

    2012-01-01

    Full Text Available Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

  11. JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure.

    Science.gov (United States)

    Troshin, Peter V; Procter, James B; Sherstnev, Alexander; Barton, Daniel L; Madeira, Fábio; Barton, Geoffrey J

    2018-06-01

    JABAWS 2.2 is a computational framework that simplifies the deployment of web services for Bioinformatics. In addition to the five multiple sequence alignment (MSA) algorithms in JABAWS 1.0, JABAWS 2.2 includes three additional MSA programs (Clustal Omega, MSAprobs, GLprobs), four protein disorder prediction methods (DisEMBL, IUPred, Ronn, GlobPlot), 18 measures of protein conservation as implemented in AACon, and RNA secondary structure prediction by the RNAalifold program. JABAWS 2.2 can be deployed on a variety of in-house or hosted systems. JABAWS 2.2 web services may be accessed from the Jalview multiple sequence analysis workbench (Version 2.8 and later), as well as directly via the JABAWS command line interface (CLI) client. JABAWS 2.2 can be deployed on a local virtual server as a Virtual Appliance (VA) or simply as a Web Application Archive (WAR) for private use. Improvements in JABAWS 2.2 also include simplified installation and a range of utility tools for usage statistics collection, and web services querying and monitoring. The JABAWS CLI client has been updated to support all the new services and allow integration of JABAWS 2.2 services into conventional scripts. A public JABAWS 2 server has been in production since December 2011 and served over 800 000 analyses for users worldwide. JABAWS 2.2 is made freely available under the Apache 2 license and can be obtained from: http://www.compbio.dundee.ac.uk/jabaws. g.j.barton@dundee.ac.uk.

  12. FT-IR spectroscopic studies of protein secondary structures for breast cancer diagnosis

    International Nuclear Information System (INIS)

    Karamancheva, I; Simonova, D.; Milev, A.

    2013-01-01

    Full text: Roughly 14 million new cancer cases and 8 million cancer deaths have occurred worldwide in 2012. At least 30 % of all cancer cases and 40 % of the cancer deaths should be avoided by improving the early detection. Fourier transform infrared (FT-IR) spectroscopy has shown many advantages as a tool for the detection of cancer over the traditional methods such as histopathological analysis, X-ray transmission, ultrasonic and computer tomography techniques. With the aim to establish the FT-IR spectroscopy as an alternative method for the diagnosis of human cancers, we have made several studies to examine in details the spectroscopic properties of normal and carcinomatous tissues. Human breast tissues were obtained immediately after surgical breast resection with the informed patient's consent. In our studies we made extensive use of Fourier self-deconvolution, second-order derivatization, difference spectra, curve-fitting procedures and quantitative determinations according to Beer's law. Cancer is a multi-step process. Characteristic differences in both the frequencies and the intensity ratios of several bands have been revealed. Considerable differences have been found in the spectral patterns. The most important and informative region in the mid-IR for determination of protein secondary structure is the amide I and amide II region. The bands between 1730 and 1600 cm -1 are highly sensitive to conformational changes. Considerable changes were observed in the A1735/A1652 absorbance ratio, which provides a measure for the content of a- helix and P-sheet domains. Our investigations have shown that the major biomarker peaks are in the amide I and amide II regions. In the so called 'fingerprint region' many molecular constituents such as lipids, phospholipids, proteins, DNA and RNA, carbohydrates and metabolites may overlap and the quantitative interpretation is impossible. The spectrum may therefore reflect only the average biochemical composition.; key words

  13. Improving motor skills of children in secondary school by using means specific to football game

    Directory of Open Access Journals (Sweden)

    Sorin BRÎNDESCU

    2017-03-01

    Full Text Available Football, by tradition is a popular sport, a mass sport, both for those who 32ractici it and for the audience. The game of football becomes the only sport that can be 32racticin by everybody. Its simplicity is expressed by a regulation set which includes few basic rules, logical rules and relatively easy to understand. Football is a game that develops basic motor skills: speed, strength, stamina, specific skills. Use of means specific to the football game in physical education classes at the secondary level aims to improve motor skills and streamline the educational process. The means specific to the football game that are used are simple, clear, suitable for both girls and boys, in order to achieve outstanding results in physical education classes

  14. The Case for Improved Interprofessional Care: Fatal Analgesic Overdose Secondary to Acute Dental Pain during Pregnancy

    Directory of Open Access Journals (Sweden)

    Sarah K. Y. Lee

    2016-01-01

    Full Text Available Prenatal oral health extends beyond the oral cavity, impacting the general well-being of the pregnant patient and her fetus. This case report follows a 19-year-old pregnant female presenting with acute liver failure secondary to acetaminophen overdose for management of dental pain following extensive dental procedures. Through the course of her illness, the patient suffered adverse outcomes including fetal demise, acute kidney injury, spontaneous bacterial peritonitis, and septic shock before eventual death from multiple organ failure. In managing the pregnant patient, healthcare providers, including physicians and dentists, must recognize and optimize the interconnected relationships shared by the health disciplines. An interdisciplinary approach of collaborative and coordinated care, the timing, sequence, and treatment for the pregnant patient can be improved and thereby maximize overall quality of health. Continued efforts toward integrating oral health into general healthcare education through interprofessional education and practice are necessary to enhance the quality of care that will benefit all patients.

  15. Exploiting the Past and the Future in Protein Secondary Structure Prediction

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren; Frasconi, P

    1999-01-01

    predictions based on variable ranges of dependencies. These architectures extend recurrent neural networks, introducing non-causal bidirectional dynamics to capture both upstream and downstream information. The prediction algorithm is completed by the use of mixtures of estimators that leverage evolutionary......Motivation: Predicting the secondary structure of a protein (alpha-helix, beta-sheet, coil) is an important step towards elucidating its three-dimensional structure, as well as its function. Presently, the best predictors are based on machine learning approaches, in particular neural network...

  16. Impact of natalizumab on ambulatory improvement in secondary progressive and disabled relapsing-remitting multiple sclerosis.

    Directory of Open Access Journals (Sweden)

    Diego Cadavid

    Full Text Available There is an unmet need for disease-modifying therapies to improve ambulatory function in disabled subjects with multiple sclerosis.Assess the effects of natalizumab on ambulatory function in disabled subjects with relapsing-remitting multiple sclerosis (RRMS or secondary progressive multiple sclerosis (SPMS.We retrospectively reviewed ambulatory function as measured by timed 25-foot walk (T25FW in clinical trial subjects with an Expanded Disability Status Scale score ≥3.5, including RRMS subjects from the phase 3 AFFIRM and SENTINEL trials, relapsing SPMS subjects from the phase 2 MS231 study, and nonrelapsing SPMS subjects from the phase 1b DELIVER study. For comparison, SPMS subjects from the intramuscular interferon beta-1a (IM IFNβ-1a IMPACT study were also analyzed. Improvement in ambulation was measured using T25FW responder status; response was defined as faster walking times over shorter (6-9-month or longer (24-30-month treatment periods relative to subjects' best predose walking times.There were two to four times more T25FW responders among disabled MS subjects in the natalizumab arms than in the placebo or IM IFNβ-1a arms. Responders walked 25 feet an average of 24%-45% faster than nonresponders.Natalizumab improves ambulatory function in disabled RRMS subjects and may have efficacy in disabled SPMS subjects. Confirmation of the latter finding in a prospective SPMS study is warranted.

  17. Opportunities to improve the conversion of food waste to lactate: Fine-tuning secondary factors.

    Science.gov (United States)

    RedCorn, Raymond; Engelberth, Abigail S

    2017-11-01

    Extensive research has demonstrated the potential for bioconversion of food waste to lactate, with major emphasis on adjusting temperature, pH, and loading rate of the fermentation. Each of these factors has a significant effect on lactate production; however, additional secondary factors have received little attention. Here we investigate three additional factors where opportunities exist for process improvement: freezing of samples during storage, discontinuous pH control, and holdover of fermentation broth between fermentations. Freezing samples prior to fermentation was shown to reduce the production rate of lactate by 8%, indicating freeze-thaw should be avoided in experiments. Prior work indicated a trade-off in pH control strategies, where discontinuous pH control correlated with higher lactate accumulation while continuous pH control correlated with higher production rate. Here we demonstrate that continuous pH control can achieve both higher lactate accumulation and higher production rate. Finally, holding over fermentation broth was shown to be a simple method to improve production rate (by 18%) at high food waste loading rates (>140 g volatile solids L -1 ) but resulted in lower lactate accumulation (by 17%). The results inform continued process improvements within the waste treatment of food waste through fermentation to lactic acid.

  18. CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

    Science.gov (United States)

    Puton, Tomasz; Kozlowski, Lukasz P.; Rother, Kristian M.; Bujnicki, Janusz M.

    2013-01-01

    We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure. According to our tests, on the average, the most accurate predictions obtained by a comparative approach are generated by CentroidAlifold, MXScarna, RNAalifold and TurboFold. On the average, the most accurate predictions obtained by single-sequence analyses are generated by CentroidFold, ContextFold and IPknot. The best comparative methods typically outperform the best single-sequence methods if an alignment of homologous RNA sequences is available. This article presents the results of our benchmarks as of 3 October 2012, whereas the rankings presented online are continuously updated. We will gladly include new prediction methods and new measures of accuracy in the new editions of CompaRNA benchmarks. PMID:23435231

  19. CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction.

    Science.gov (United States)

    Puton, Tomasz; Kozlowski, Lukasz P; Rother, Kristian M; Bujnicki, Janusz M

    2013-04-01

    We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure. According to our tests, on the average, the most accurate predictions obtained by a comparative approach are generated by CentroidAlifold, MXScarna, RNAalifold and TurboFold. On the average, the most accurate predictions obtained by single-sequence analyses are generated by CentroidFold, ContextFold and IPknot. The best comparative methods typically outperform the best single-sequence methods if an alignment of homologous RNA sequences is available. This article presents the results of our benchmarks as of 3 October 2012, whereas the rankings presented online are continuously updated. We will gladly include new prediction methods and new measures of accuracy in the new editions of CompaRNA benchmarks.

  20. Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Cobaugh Christian W

    2004-08-01

    Full Text Available Abstract Background A detailed understanding of an RNA's correct secondary and tertiary structure is crucial to understanding its function and mechanism in the cell. Free energy minimization with energy parameters based on the nearest-neighbor model and comparative analysis are the primary methods for predicting an RNA's secondary structure from its sequence. Version 3.1 of Mfold has been available since 1999. This version contains an expanded sequence dependence of energy parameters and the ability to incorporate coaxial stacking into free energy calculations. We test Mfold 3.1 by performing the largest and most phylogenetically diverse comparison of rRNA and tRNA structures predicted by comparative analysis and Mfold, and we use the results of our tests on 16S and 23S rRNA sequences to assess the improvement between Mfold 2.3 and Mfold 3.1. Results The average prediction accuracy for a 16S or 23S rRNA sequence with Mfold 3.1 is 41%, while the prediction accuracies for the majority of 16S and 23S rRNA structures tested are between 20% and 60%, with some having less than 20% prediction accuracy. The average prediction accuracy was 71% for 5S rRNA and 69% for tRNA. The majority of the 5S rRNA and tRNA sequences have prediction accuracies greater than 60%. The prediction accuracy of 16S rRNA base-pairs decreases exponentially as the number of nucleotides intervening between the 5' and 3' halves of the base-pair increases. Conclusion Our analysis indicates that the current set of nearest-neighbor energy parameters in conjunction with the Mfold folding algorithm are unable to consistently and reliably predict an RNA's correct secondary structure. For 16S or 23S rRNA structure prediction, Mfold 3.1 offers little improvement over Mfold 2.3. However, the nearest-neighbor energy parameters do work well for shorter RNA sequences such as tRNA or 5S rRNA, or for larger rRNAs when the contact distance between the base-pairs is less than 100 nucleotides.

  1. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

    Energy Technology Data Exchange (ETDEWEB)

    Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States); Assadi, Amir [University of Wisconsin-Madison, Mathematics Department (United States); Markley, John L. [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)], E-mail: eghbalni@nmrfam.wisc.edu

    2005-05-15

    We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.

  2. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

    International Nuclear Information System (INIS)

    Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash; Assadi, Amir; Markley, John L.

    2005-01-01

    We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states

  3. Secbase: database module to retrieve secondary structure elements with ligand binding motifs.

    Science.gov (United States)

    Koch, Oliver; Cole, Jason; Block, Peter; Klebe, Gerhard

    2009-10-01

    Secbase is presented as a novel extension module of Relibase. It integrates the information about secondary structure elements into the retrieval facilities of Relibase. The data are accessible via the extended Relibase user interface, and integrated retrieval queries can be addressed using an extended version of Reliscript. The primary information about alpha-helices and beta-sheets is used as provided by the PDB. Furthermore, a uniform classification of all turn families, based on recent clustering methods, and a new helix assignment that is based on this turn classification has been included. Algorithms to analyze the geometric features of helices and beta-strands were also implemented. To demonstrate the performance of the Secbase implementation, some application examples are given. They provide new insights into the involvement of secondary structure elements in ligand binding. A survey of water molecules detected next to the N-terminus of helices is analyzed to show their involvement in ligand binding. Additionally, the parallel oriented NH groups at the alpha-helix N-termini provide special binding motifs to bind particular ligand functional groups with two adjacent oxygen atoms, e.g., as found in negatively charged carboxylate or phosphate groups, respectively. The present study also shows that the specific structure of the first turn of alpha-helices provides a suitable explanation for stabilizing charged structures. The magnitude of the overall helix macrodipole seems to have no or only a minor influence on binding. Furthermore, an overview of the involvement of secondary structure elements with the recognition of some important endogenous ligands such as cofactors shows some distinct preference for particular binding motifs and amino acids.

  4. Effect of Secondary Doping Using Sorbitol on Structure and Transport Properties of PEDOT-PSS Thin Films

    Science.gov (United States)

    Khasim, Syed; Pasha, Apsar; Roy, Aashish S.; Parveen, Ameena; Badi, Nacer

    2017-07-01

    Poly(3,4-ethylene dioxythiophene):poly(styrenesulphonate) (PEDOT-PSS) in the recent past has emerged as one of the most fascinating conducting polymers for many device applications. The unique feature of PEDOT-PSS is its transparency in the entire visible spectrum with excellent thermal stability. The PEDOT-PSS as prepared as an aqueous dispersion has very low conductivity, and it hinders the performance of a device. In this work we report the conductivity enhancement of PEDOT-PSS thin films through secondary doping using a polar organic solvent such as sorbitol. The mechanism of conductivity enhancement was studied through various physical and chemical characterizations. The effect of sorbitol concentration on structure and transport properties of PEDOT-PSS thin films was investigated in detail. The structural and morphological modifications in PEDOT-PSS due to the addition of sorbitol was studied through Fourier transform spectroscopy, Ultra Violet-visible spectroscopy, theromogravimetric analysis, scanning electron microscopy and atomic force microscopy. The interactions resulting from conformational changes of PEDOT chains that changes from coiled to linear structure due to the sorbitol treatment significantly improves the conductivity of PEDOT-PSS films. The secondary doping of sorbitol reduces the energy barrier that facilitates the charge carrier hopping leading to enhanced conductivity. We have observed that the conductivity of PEDOT-PSS thin films was increased by two fold due to sorbitol treatment when compared to conductivity of pure PEDOT-PSS. We have carried out detailed analysis of dielectric parameters of sorbitol-treated PEDOT-PSS films and found that sorbitol treatment has a significant effect on various dielectric attributes of PEDOT-PSS films. Hence, secondary doping using sorbitol could be a useful way to effectively tailor the conductivity and dielectric properties of PEDOT-PSS thin films that can be used as flexible electrodes in

  5. Teaching the foundations of quantum mechanics in secondary school: a proposed conceptual structure

    Directory of Open Access Journals (Sweden)

    Maria de los Angeles Fanaro

    2009-03-01

    Full Text Available This paper is part of a doctoral thesis that investigates Basic Quantum Mechanics (QM teaching in high school. A Conceptual Structure of Reference (CSR based on the Path Integral Method of Feynman (1965 was rebuilt and a Proposed Conceptual Structure for Teaching (PCST (Otero, 2006, 2007 the basics of Quantum Mechanics at secondary school was designed, analysed and carried out. This PCST does not follow the historical route and it is complementary to the canonical formalism. The concepts: probability distribution, quantum system, x(t alternative, amplitude of probability, sum of probability amplitude, action, Planck's constant, and classic-quantum transition were rebuilt with the students. Mathematical formalism was avoided by using simulation software assistance. The Proposed Conceptual Structure for Teaching (PCST is described and some results from the test carried out by the class group are discussed. This information allows the analysis of the Conceptual Structure Effectively Reconstructed (CSER to be initiated with the students.

  6. Validation-driven protein-structure improvement

    NARCIS (Netherlands)

    Touw, W.G.

    2016-01-01

    High-quality protein structure models are essential for many Life Science applications, such as protein engineering, molecular dynamics, drug design, and homology modelling. The WHAT_CHECK model validation project and the PDB_REDO model optimisation project have shown that many structure models in

  7. VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program.

    Science.gov (United States)

    Yahyavi, Masoumeh; Falsafi-Zadeh, Sajad; Karimi, Zahra; Kalatarian, Giti; Galehdari, Hamid

    2014-01-01

    The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features. The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755.

  8. Improved age-diffusion model for low-energy electron transport in solids. II. Application to secondary emission from aluminum

    International Nuclear Information System (INIS)

    Dubus, A.; Devooght, J.; Dehaes, J.C.

    1987-01-01

    The ''improved age-diffusion'' model for secondary-electron transport is applied to aluminum. Electron cross sections for inelastic collisions with the free-electron gas using the Lindhard dielectric function and for elastic collisions with the randomly distributed ionic cores are used in the calculations. The most important characteristics of backward secondary-electron emission induced by low-energy electrons on polycrystalline Al targets are calculated and compared to experimental results and to Monte Carlo calculations. The model appears to predict the electronic yield, the energy spectra, and the spatial dependence of secondary emission with reasonable accuracy

  9. 18 CFR 367.56 - Structures and improvements.

    Science.gov (United States)

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Structures and... ACT Service Company Property Instructions § 367.56 Structures and improvements. (a) The accounts for structures and improvements must include the cost of all buildings and facilities to house, support, or...

  10. Does family structure matter? Comparing the life goals and aspirations of learners in secondary schools

    Directory of Open Access Journals (Sweden)

    Eugene Lee Davids

    2013-01-01

    Full Text Available The aim of this study was to compare the goals and aspirations of learners from single- and two-parent families. The study used a quantitative methodology with a cross-sectional comparative group design. The sample consisted of 853 Grade 11 learners from secondary schools in the Northern, Southern and Metro Central education districts in the Western Cape. The data were collected using the Aspirations Index and a short biographical questionnaire. The results suggest that there was a significant main effect of family structure on certain goals and aspirations of learners in secondary schools. These goals and aspirations included wealth, image, personal growth, relationships, and health. Furthermore, learners in single-parent families placed more emphasis on intrinsic goals.

  11. The Structures of the Alternative Conceptions of Preservice Secondary Teachers on Seasonal Changes

    Directory of Open Access Journals (Sweden)

    Junyoung Oh

    2005-03-01

    Full Text Available This study was to understand the components that influence preservice secondary teachers' conceptions about "seasonal changes". We selected 74 university science education students among whom 23 were in the second, 23 in the third, and 28 in the fourth year. The data collected from the paper-pencil test and individual interview with students. The results of this study show that the students had considerable apparent alternative conceptions, and that the 'distance theory' had most important effects on their alternative conceptions. It can be said that preservice secondary teachers' initial models of the seasonal change have their origin in their belief sets (specific theory related to 'seasonal change', on the basis of which they can interpret their observations and cultural information with the constraints of a naive framework of physics. The structures and possible sources of their alternative conceptions for overcoming these alternative conceptions were also discussed. Implications for preservice science teacher education related to the results were discussed.

  12. A systematic review on popularity, application and characteristics of protein secondary structure prediction tools.

    Science.gov (United States)

    Kashani-Amin, Elaheh; Tabatabaei-Malazy, Ozra; Sakhteman, Amirhossein; Larijani, Bagher; Ebrahim-Habibi, Azadeh

    2018-02-27

    Prediction of proteins' secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple secondary structure prediction (SSP) options is challenging. The current study is an insight onto currently favored methods and tools, within various contexts. A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of 209 studies were finally found eligible to extract data. Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating a SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. This study provides a comprehensive insight about the recent usage of SSP tools which could be helpful for selecting a proper tool's choice. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  13. Prediction of RNA secondary structures: from theory to models and real molecules

    International Nuclear Information System (INIS)

    Schuster, Peter

    2006-01-01

    RNA secondary structures are derived from RNA sequences, which are strings built form the natural four letter nucleotide alphabet, {AUGC}. These coarse-grained structures, in turn, are tantamount to constrained strings over a three letter alphabet. Hence, the secondary structures are discrete objects and the number of sequences always exceeds the number of structures. The sequences built from two letter alphabets form perfect structures when the nucleotides can form a base pair, as is the case with {GC} or {AU}, but the relation between the sequences and structures differs strongly from the four letter alphabet. A comprehensive theory of RNA structure is presented, which is based on the concepts of sequence space and shape space, being a space of structures. It sets the stage for modelling processes in ensembles of RNA molecules like evolutionary optimization or kinetic folding as dynamical phenomena guided by mappings between the two spaces. The number of minimum free energy (mfe) structures is always smaller than the number of sequences, even for two letter alphabets. Folding of RNA molecules into mfe energy structures constitutes a non-invertible mapping from sequence space onto shape space. The preimage of a structure in sequence space is defined as its neutral network. Similarly the set of suboptimal structures is the preimage of a sequence in shape space. This set represents the conformation space of a given sequence. The evolutionary optimization of structures in populations is a process taking place in sequence space, whereas kinetic folding occurs in molecular ensembles that optimize free energy in conformation space. Efficient folding algorithms based on dynamic programming are available for the prediction of secondary structures for given sequences. The inverse problem, the computation of sequences for predefined structures, is an important tool for the design of RNA molecules with tailored properties. Simultaneous folding or cofolding of two or more RNA

  14. CNNH_PSS: protein 8-class secondary structure prediction by convolutional neural network with highway.

    Science.gov (United States)

    Zhou, Jiyun; Wang, Hongpeng; Zhao, Zhishan; Xu, Ruifeng; Lu, Qin

    2018-05-08

    Protein secondary structure is the three dimensional form of local segments of proteins and its prediction is an important problem in protein tertiary structure prediction. Developing computational approaches for protein secondary structure prediction is becoming increasingly urgent. We present a novel deep learning based model, referred to as CNNH_PSS, by using multi-scale CNN with highway. In CNNH_PSS, any two neighbor convolutional layers have a highway to deliver information from current layer to the output of the next one to keep local contexts. As lower layers extract local context while higher layers extract long-range interdependencies, the highways between neighbor layers allow CNNH_PSS to have ability to extract both local contexts and long-range interdependencies. We evaluate CNNH_PSS on two commonly used datasets: CB6133 and CB513. CNNH_PSS outperforms the multi-scale CNN without highway by at least 0.010 Q8 accuracy and also performs better than CNF, DeepCNF and SSpro8, which cannot extract long-range interdependencies, by at least 0.020 Q8 accuracy, demonstrating that both local contexts and long-range interdependencies are indeed useful for prediction. Furthermore, CNNH_PSS also performs better than GSM and DCRNN which need extra complex model to extract long-range interdependencies. It demonstrates that CNNH_PSS not only cost less computer resource, but also achieves better predicting performance. CNNH_PSS have ability to extracts both local contexts and long-range interdependencies by combing multi-scale CNN and highway network. The evaluations on common datasets and comparisons with state-of-the-art methods indicate that CNNH_PSS is an useful and efficient tool for protein secondary structure prediction.

  15. Educational Leadership Based on Social Capital for Improving Quality of Private Secondary School

    Directory of Open Access Journals (Sweden)

    Suwadi

    2017-12-01

    Full Text Available This study aims to explain the leadership pattern of social capital based education for the quality improvement of private schools. The research is conducted at private Junior Secondary Level with a qualitative naturalistic approach. This location is in Sleman District. The subject consists of selected cases purposively. The research procedure is carried out by four steps and methods of obtaining the data through observation, indepth interview, and documentation. Data analysis was carried out by inductive model while the level of trust result of research was undertaken by fulfilling criteria of credibility, transferability, dependability and conformability. The research findings are as follows. First, the concept of leadership of social capital based education rests on the ability of principals to influence school resources to achieve goals through an integrated pattern of trust dimensions, reciprocal relationships and networking. Second, school quality can be improved through a school leadership in recognizing social capital, b school leadership in utilizing social capital, c school leadership in functioning social capital. Third, the utilization of social capital based on leadership in private schools in the form of a bridging stakeholder aspirations both initiated by schools and stakeholders; b bonding stakeholder relations with schools; c following up or responding to stakeholder resources in school programs as a perspective new leadership at school.

  16. Landscape and variation of RNA secondary structure across the human transcriptome.

    Science.gov (United States)

    Wan, Yue; Qu, Kun; Zhang, Qiangfeng Cliff; Flynn, Ryan A; Manor, Ohad; Ouyang, Zhengqing; Zhang, Jiajing; Spitale, Robert C; Snyder, Michael P; Segal, Eran; Chang, Howard Y

    2014-01-30

    In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program. However, the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child). This provides a comprehensive RSS map of human coding and non-coding RNAs. We identify unique RSS signatures that demarcate open reading frames and splicing junctions, and define authentic microRNA-binding sites. Comparison of native deproteinized RNA isolated from cells versus refolded purified RNA suggests that the majority of the RSS information is encoded within RNA sequence. Over 1,900 transcribed single nucleotide variants (approximately 15% of all transcribed single nucleotide variants) alter local RNA structure. We discover simple sequence and spacing rules that determine the ability of point mutations to impact RSSs. Selective depletion of 'riboSNitches' versus structurally synonymous variants at precise locations suggests selection for specific RNA shapes at thousands of sites, including 3' untranslated regions, binding sites of microRNAs and RNA-binding proteins genome-wide. These results highlight the potentially broad contribution of RNA structure and its variation to gene regulation.

  17. Application of nano-structured coatings to mitigate flow-accelerated corrosion in secondary pipe systems of nuclear power plants

    International Nuclear Information System (INIS)

    Kim, Seung Hyun; Kim, Jong Jin; Yoo, Seung Chang; Kim, Ji Hyun

    2014-01-01

    Carbon steel is widely used as a structural material in secondary pipe systems. However, the passivity of carbon steel is not sufficient for protection in secondary water chemistry with a very fast-flowing fluid because of the dissolution of ferrous and magnetite ions and surface friction at the interface of the coolant and pipe surface. There have been many efforts to mitigate flow-accelerated corrosion through adoption of advanced water chemistries such as optimized dissolve oxygen (DO) concentration and temperature, as well as usage of new additives such as monoethanol amine (ETA) to adjust pH. However, these mitigation techniques pose certain challenges relating to the compatibility of new water chemistries with the steam generator, the thermal efficiency of the secondary side, etc. In this study, to improve the passivity of carbon steel, nanostructured coatings especially nanoparticle-enhanced surface coatings were adopted to improve resistance to corrosion and wear. Nanoparticles in the coating matrix help decrease the electrochemical potential compared coatings without nanoparticles, and thus help improve the mechanical properties, especially hardness, through precipitation. In other words, nanoparticle-enhanced surface coatings have the potential to mitigate flow-accelerated corrosion in secondary pipe systems. As candidate coatings, TiO 2 - and SiC-enhanced electrolytic and electroless nickel plating and Fe-Cr-W amorphous metallic coatings (AMC) were selected by acquiring the Pourbaix diagram with thermodynamic calculations. Both TiO 2 and SiC show a stable state in secondary water chemistry, and it is estimated that Fe-Cr-W can be applied to secondary water chemistry because it has a similar chemical composition to carbon steel. Electron microscopic analysis results with scanning electron microscopy (SEM) and tunneling electron microscopy (TEM) show the distribution of TiO 2 nanoparticles in the nickel matrix coating layer, whereas the SiC nanoparticles

  18. Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be.

    KAUST Repository

    Schaefer, Christian

    2010-01-16

    MOTIVATION: The mutation of amino acids often impacts protein function and structure. Mutations without negative effect sustain evolutionary pressure. We study a particular aspect of structural robustness with respect to mutations: regular protein secondary structure and natively unstructured (intrinsically disordered) regions. Is the formation of regular secondary structure an intrinsic feature of amino acid sequences, or is it a feature that is lost upon mutation and is maintained by evolution against the odds? Similarly, is disorder an intrinsic sequence feature or is it difficult to maintain? To tackle these questions, we in silico mutated native protein sequences into random sequence-like ensembles and monitored the change in predicted secondary structure and disorder. RESULTS: We established that by our coarse-grained measures for change, predictions and observations were similar, suggesting that our results were not biased by prediction mistakes. Changes in secondary structure and disorder predictions were linearly proportional to the change in sequence. Surprisingly, neither the content nor the length distribution for the predicted secondary structure changed substantially. Regions with long disorder behaved differently in that significantly fewer such regions were predicted after a few mutation steps. Our findings suggest that the formation of regular secondary structure is an intrinsic feature of random amino acid sequences, while the formation of long-disordered regions is not an intrinsic feature of proteins with disordered regions. Put differently, helices and strands appear to be maintained easily by evolution, whereas maintaining disordered regions appears difficult. Neutral mutations with respect to disorder are therefore very unlikely.

  19. Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be.

    KAUST Repository

    Schaefer, Christian; Schlessinger, Avner; Rost, Burkhard

    2010-01-01

    MOTIVATION: The mutation of amino acids often impacts protein function and structure. Mutations without negative effect sustain evolutionary pressure. We study a particular aspect of structural robustness with respect to mutations: regular protein secondary structure and natively unstructured (intrinsically disordered) regions. Is the formation of regular secondary structure an intrinsic feature of amino acid sequences, or is it a feature that is lost upon mutation and is maintained by evolution against the odds? Similarly, is disorder an intrinsic sequence feature or is it difficult to maintain? To tackle these questions, we in silico mutated native protein sequences into random sequence-like ensembles and monitored the change in predicted secondary structure and disorder. RESULTS: We established that by our coarse-grained measures for change, predictions and observations were similar, suggesting that our results were not biased by prediction mistakes. Changes in secondary structure and disorder predictions were linearly proportional to the change in sequence. Surprisingly, neither the content nor the length distribution for the predicted secondary structure changed substantially. Regions with long disorder behaved differently in that significantly fewer such regions were predicted after a few mutation steps. Our findings suggest that the formation of regular secondary structure is an intrinsic feature of random amino acid sequences, while the formation of long-disordered regions is not an intrinsic feature of proteins with disordered regions. Put differently, helices and strands appear to be maintained easily by evolution, whereas maintaining disordered regions appears difficult. Neutral mutations with respect to disorder are therefore very unlikely.

  20. Mechanical properties of amyloid-like fibrils defined by secondary structures

    Science.gov (United States)

    Bortolini, C.; Jones, N. C.; Hoffmann, S. V.; Wang, C.; Besenbacher, F.; Dong, M.

    2015-04-01

    Amyloid and amyloid-like fibrils represent a generic class of highly ordered nanostructures that are implicated in some of the most fatal neurodegenerative diseases. On the other hand, amyloids, by possessing outstanding mechanical robustness, have also been successfully employed as functional biomaterials. For these reasons, physical and chemical factors driving fibril self-assembly and morphology are extensively studied - among these parameters, the secondary structures and the pH have been revealed to be crucial, since a variation in pH changes the fibril morphology and net chirality during protein aggregation. It is important to quantify the mechanical properties of these fibrils in order to help the design of effective strategies for treating diseases related to the presence of amyloid fibrils. In this work, we show that by changing pH the mechanical properties of amyloid-like fibrils vary as well. In particular, we reveal that these mechanical properties are strongly related to the content of secondary structures. We analysed and estimated the Young's modulus (E) by comparing the persistence length (Lp) - measured from the observation of TEM images by using statistical mechanics arguments - with the mechanical information provided by peak force quantitative nanomechanical property mapping (PF-QNM). The secondary structure content and the chirality are investigated by means of synchrotron radiation circular dichroism (SR-CD). Results arising from this study could be fruitfully used as a protocol to investigate other medical or engineering relevant peptide fibrils.Amyloid and amyloid-like fibrils represent a generic class of highly ordered nanostructures that are implicated in some of the most fatal neurodegenerative diseases. On the other hand, amyloids, by possessing outstanding mechanical robustness, have also been successfully employed as functional biomaterials. For these reasons, physical and chemical factors driving fibril self-assembly and morphology

  1. The Interplay between Adolescent Needs and Secondary School Structures: Fostering Developmentally Responsive Middle and High School Environments across the Transition

    Science.gov (United States)

    Ellerbrock, Cheryl R.; Kiefer, Sarah M.

    2013-01-01

    Understanding the developmental responsiveness of secondary school environments may be an important factor in supporting students as they make the transition from one school to the next. Students' needs may or may not be met depending on the nature of the fit between their basic and developmental needs and secondary school structures at the middle…

  2. A quantitative analysis of secondary RNA structure using domination based parameters on trees

    Directory of Open Access Journals (Sweden)

    Zou Yue

    2006-03-01

    Full Text Available Abstract Background It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure. Results The statistical analysis shows that the domination based parameters correctly distinguish between the trees that represent native structures and those that are not likely candidates to represent RNA. Some of the trees previously identified as candidate structures are found to be "very" RNA like, while others are not, thereby refining the space of structures likely to be found as representing secondary RNA structure. Conclusion Search algorithms are available that mine nucleotide sequence databases. However, the number of motifs identified can be quite large, making a further search for similar motif computationally difficult. Much of the work in the bioinformatics arena is toward the development of better algorithms to address the computational problem. This work, on the other hand, uses mathematical descriptors to more clearly characterize the RNA motifs and thereby reduce the corresponding search space. These

  3. How does vegetation structure influence woodpeckers and secondary cavity nesting birds in African cork oak forest?

    Science.gov (United States)

    Segura, Amalia

    2017-08-01

    The Great Spotted Woodpecker provides important information about the status of a forest in terms of structure and age. As a primary cavity creator, it provides small-medium size cavities for passerines. However, despite its interest as an ecosystem engineer, studies of this species in Africa are scarce. Here, spatially explicit predictive models were used to investigate how forest structural variables are related to both the Great Spotted Woodpecker and secondary cavity nesting birds in Maamora cork oak forest (northwest Morocco). A positive association between Great Spotted Woodpecker and both dead-tree density and large mature trees (>60 cm dbh) was found. This study area, Maamora, has an old-growth forest structure incorporating a broad range of size and condition of live and dead trees, favouring Great Spotted Woodpecker by providing high availability of foraging and excavating sites. Secondary cavity nesting birds, represented by Great Tit, African Blue Tit, and Hoopoe, were predicted by Great Spotted Woodpecker detections. The findings suggest that the conservation of the Maamora cork oak forest could be key to maintaining these hole-nesting birds. However, this forest is threatened by forestry practises and livestock overgrazing and the challenge is therefore to find sustainable management strategies that ensure conservation while allowing its exploitation.

  4. AFM observation of silk fibroin on mica substrates: morphologies reflecting the secondary structures

    Energy Technology Data Exchange (ETDEWEB)

    Yamada, Kazushi; Tsuboi, Yasuyuki; Itaya, Akira

    2003-09-01

    Bombyx mori silk fibroin was fixed on mica substrates by cast of aqueous fibroin solutions, and the microscopic morphologies of the samples were revealed by means of atomic force microscopy. By adjusting the method used to prepare the solution, we succeeded in forming quasi-2-dimensional thin films in which a network of fibroin molecules developed over the substrate. The film network consisted of fibroin in a random coil structure. The morphology of the network changed after thermal or methanol treatments, which are known to convert the secondary structure of fibroin from the random coil to the {beta}-sheet type. In both of these cases, the network morphology disappeared and characteristic island-like morphologies appeared. On the other hand, temporally evolving gelation occurred in a fibroin solution due to the formation of {beta}-sheet crystals. Such islands were also observable in a specimen prepared by the cast of the gel-containing solution. Based on these results, it was concluded that the islands consist of {beta}-sheet crystals. Of particular interest is the observation that all of the islands had a common thickness value of 1.3 nm. These morphologies are discussed in terms of the secondary structure of fibroin.

  5. Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

    Directory of Open Access Journals (Sweden)

    Tatyana Aleksandrovna Khrustaleva

    2014-01-01

    Full Text Available 3D structures of proteins with coordinated Mn2+ ions from bacteria with low, average, and high genomic GC-content have been analyzed (149 PDB files were used. Major Mn2+ binders are aspartic acid (6.82% of Asp residues, histidine (14.76% of His residues, and glutamic acid (3.51% of Glu residues. We found out that the motif of secondary structure “beta strand-major binder-random coil” is overrepresented around all the three major Mn2+ binders. That motif may be followed by either alpha helix or beta strand. Beta strands near Mn2+ binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn2+ ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. On the other hand, the percentage of Mn2+ sites with at least one amino acid in the “beta strand-major binder-random coil” motif of secondary structure (77.88% does not depend on genomic GC-content.

  6. Hierarchically Structured Recommender System for Improving NPS

    Science.gov (United States)

    Kuang, Jieyan

    2016-01-01

    Net Promoter System (NPS) is well known as an evaluation measure of the growth engine of big companies in the business area. The ultimate goal of my research is to build an action rules and meta-actions based recommender system for improving NPS scores of 34 companies (clients) dealing with similar businesses in the US and Canada. With the given…

  7. Secondary Structure Prediction of Protein using Resilient Back Propagation Learning Algorithm

    Directory of Open Access Journals (Sweden)

    Jyotshna Dongardive

    2015-12-01

    Full Text Available The paper proposes a neural network based approach to predict secondary structure of protein. It uses Multilayer Feed Forward Network (MLFN with resilient back propagation as the learning algorithm. Point Accepted Mutation (PAM is adopted as the encoding scheme and CB396 data set is used for the training and testing of the network. Overall accuracy of the network has been experimentally calculated with different window sizes for the sliding window scheme and by varying the number of units in the hidden layer. The best results were obtained with eleven as the window size and seven as the number of units in the hidden layer.

  8. Structure of the secondary xylem of Aniba Aubl. species from the Brazilian Amazon

    Directory of Open Access Journals (Sweden)

    Cláudia Viana Urbinati

    2014-09-01

    Full Text Available The aim of this study was to characterize the wood of Aniba species from the Brazilian Amazon, on the basis of specimens in the wood collection of the Herbarium of the Museu Paraense Emílio Goeldi, in the city of Belém, Brazil. The species were found to present a homogeneous structure in the secondary xylem, as defined by the location of oil cells; the presence of tyloses and crystals; and singularities of the radial and axial parenchyma.

  9. [Effects of target tree tending on community structure and diversity in subtropical natural secondary shrubs].

    Science.gov (United States)

    Zhang, Hui; Zhou, Guo Mo; Bai, Shang Bin; Wang, Yi Xiang; You, Yu Jie; Zhu, Ting Ting; Zhang, Hua Feng

    2017-05-18

    The typical natural secondary shrub community was chosen in Lin'an of Zhejiang Pro-vince to discover its possibility of restoration to arbor forest with three kinds of forest management models being taken, i.e., no care as control, closed forest management and target tree tending. Over four years growth, compared with control, closed forest management significantly increased average DBH and height by 130% and 50%, respectively, while 260% and 110% for target tree tending. In target tree tending plots, larger trees had been emerging with 4.5-8.5 cm diameter class and 4.5-8.5 m height class and formed a new storey of 4 m compared with control. The species biodiversity indexes at shrub layer were significantly increased in closed management plots, and did not decrease in target tree tending plots. Closed forest management did not change the tree species composition, following its previous succession direction. However, target tree tending increased the importance value of target species with the high potential succession direction of mixed coniferous-broadleaved forest. The results revealed that the secondary shrub community with target tree tending achieved more desired goals on DBH and height growth of dominant trees and species composition improvement compared with closed management. If the secondary shrub community could be managed when the operational conditions existed, target tree tending model should be selected to accelerate the restoration of shrub toward arbor forest.

  10. Benthic macrofaunal structure and secondary production in tropical estuaries on the Eastern Marine Ecoregion of Brazil.

    Science.gov (United States)

    Bissoli, Lorena B; Bernardino, Angelo F

    2018-01-01

    Tropical estuaries are highly productive and support diverse benthic assemblages within mangroves and tidal flats habitats. Determining differences and similarities of benthic assemblages within estuarine habitats and between regional ecosystems may provide scientific support for management of those ecosystems. Here we studied three tropical estuaries in the Eastern Marine Ecoregion of Brazil to assess the spatial variability of benthic assemblages from vegetated (mangroves) and unvegetated (tidal flats) habitats. A nested sampling design was used to determine spatial scales of variability in benthic macrofaunal density, biomass and secondary production. Habitat differences in benthic assemblage composition were evident, with mangrove forests being dominated by annelids (Oligochaeta and Capitellidae) whereas peracarid crustaceans were also abundant on tidal flats. Macrofaunal biomass, density and secondary production also differed between habitats and among estuaries. Those differences were related both to the composition of benthic assemblages and to random spatial variability, underscoring the importance of hierarchical sampling in estuarine ecological studies. Given variable levels of human impacts and predicted climate change effects on tropical estuarine assemblages in Eastern Brazil, our data support the use of benthic secondary production to address long-term changes and improved management of estuaries in Eastern Brazil.

  11. [Nurse involvement in primary care: it is the key to improve the outcomes in primary and secondary prevention?].

    Science.gov (United States)

    Scardi, Sabino; Gori, Pierpaolo; Umari, Paolo

    2010-06-01

    Difficulties in management of risk factors, lifestyle and medications adherence to achieve secondary prevention of ischemic heart disease were described. Many studies indicate that the benefit of cardiac rehabilitation therapy after acute coronary events is only partially maintained during the following year. Thereafter, new strategies of medical care are needed to improve the long-term outcomes in coronary patients. Nurse co-ordinated, multidisciplinary cardiac rehabilitative programme could help patients to improve their lifestyle, to control their risk factors and to achieve their therapeutic goals for secondary prevention of ischemic heart disease.

  12. FRAMEWORK FOR STRUCTURAL ONLINE HEALTH MONITORING OF AGING AND DEGRADATION OF SECONDARY PIPING SYSTEMS DUE TO SOME ASPECTS OF EROSION

    Energy Technology Data Exchange (ETDEWEB)

    Gribok, Andrei V.; Agarwal, Vivek

    2017-06-01

    This paper describes the current state of research related to critical aspects of erosion and selected aspects of degradation of secondary components in nuclear power plants (NPPs). The paper also proposes a framework for online health monitoring of aging and degradation of secondary components. The framework consists of an integrated multi-sensor modality system, which can be used to monitor different piping configurations under different degradation conditions. The report analyses the currently known degradation mechanisms and available predictive models. Based on this analysis, the structural health monitoring framework is proposed. The Light Water Reactor Sustainability Program began to evaluate technologies that could be used to perform online monitoring of piping and other secondary system structural components in commercial NPPs. These online monitoring systems have the potential to identify when a more detailed inspection is needed using real time measurements, rather than at a pre-determined inspection interval. This transition to condition-based, risk-informed automated maintenance will contribute to a significant reduction of operations and maintenance costs that account for the majority of nuclear power generation costs. Furthermore, of the operations and maintenance costs in U.S. plants, approximately 80% are labor costs. To address the issue of rising operating costs and economic viability, in 2017, companies that operate the national nuclear energy fleet started the Delivering the Nuclear Promise Initiative, which is a 3 year program aimed at maintaining operational focus, increasing value, and improving efficiency. There is unanimous agreement between industry experts and academic researchers that identifying and prioritizing inspection locations in secondary piping systems (for example, in raw water piping or diesel piping) would eliminate many excessive in-service inspections. The proposed structural health monitoring framework takes aim at

  13. Wafer Cakes of Improved Amino Acid Structure

    Directory of Open Access Journals (Sweden)

    Roksolana Boidunyk

    2017-11-01

    Full Text Available The article presents the results of the study of the amino acid composition of newly developed wafer cakes with adipose fillings combined with natural additives. The appropriateness of the using non-traditional raw materials (powder of willow herb, poppy oilcake, carob, as well as skimmed milk powder in order to increase the biological value of wafer cakes and improve their amino acid composition is proven.

  14. High cycle fatigue analysis of vortex suppression plate and secondary core support structures

    International Nuclear Information System (INIS)

    Xue Guohong; Li Yuan; Zhao Feiyun; Feng Shaodong; Yu Hao

    2013-01-01

    Background: Reactor internals are important equipment s in the reactor coolant system, its structure design needs high reliability in the entire lifetime, Reactor internals have occurred breakdown and the damage event due to flow induced vibrations in the domestic and foreign nuclear power plants, which make immediate influence on reactor safe operation and economic efficiency. Purpose: In this work, the dynamic response of reactor internals-vortex suppression plate and secondary core support structure (SCSS) under the loading from pump induced vibrations and flow induced vibrations are studied. Methods: Based on the finite element model of SCSS, Spectrum analysis and the harmonious analysis are performed, in order to get the response of the structure under flow induced vibrations. Then, the high fatigue of the structure is assessed according to the ASME B and PV Code. Results: The results indicate that alternate stresses of all the components satisfy the limiting value in the correlative requirements. Conclusions: The structure of SCSS could bear the vibration induced from the flow and the pump, and the method used in this article provides the reference for other reactor internals structure analysis like this. (authors)

  15. Secondary Signs May Improve the Diagnostic Accuracy of Equivocal Ultrasounds for Suspected Appendicitis in Children

    Science.gov (United States)

    Partain, Kristin N.; Patel, Adarsh; Travers, Curtis; McCracken, Courtney; Loewen, Jonathan; Braithwaite, Kiery; Heiss, Kurt F.; Raval, Mehul V.

    2016-01-01

    Introduction Ultrasound (US) is the preferred imaging modality for evaluating appendicitis. Our purpose was to determine if including secondary signs (SS) improves diagnostic accuracy in equivocal US studies. Methods Retrospective review identified 825 children presenting with concern for appendicitis and with a right lower quadrant (RLQ) US. Regression models identified which SS were associated with appendicitis. Test characteristics were demonstrated. Results 530 patients (64%) had equivocal US reports. Of 114 (22%) patients with equivocal US undergoing CT, those with SS were more likely to have appendicitis (48.6% vs 14.6%, pappendicitis (61.0% vs 33.6%, pappendicitis included fluid collection (adjusted odds ratio (OR) 13.3, 95% Confidence Interval (CI) 2.1–82.8), hyperemia (OR=2.0, 95%CI 1.5–95.5), free fluid (OR=9.8, 95%CI 3.8–25.4), and appendicolith (OR=7.9, 95%CI 1.7–37.2). Wall thickness, bowel peristalsis, and echogenic fat were not associated with appendicitis. Equivocal US that included hyperemia, a fluid collection, or an appendicolith had 96% specificity and 88% accuracy. Conclusion Use of SS in RLQ US assists in the diagnostic accuracy of appendicitis. SS may guide clinicians and reduce unnecessary CT and admissions. PMID:27039121

  16. SU-E-J-149: Secondary Emission Detection for Improved Proton Relative Stopping Power Identification

    Energy Technology Data Exchange (ETDEWEB)

    Saunders, J; Musall, B; Erickson, A [Georgia Institute of Technology, Atlanta, GA (Georgia)

    2015-06-15

    Purpose: This research investigates application of secondary prompt gamma (PG) emission spectra, resulting from nuclear reactions induced by protons, to characterize tissue composition along the particle path. The objective of utilizing the intensity of discrete high-energy peaks of PG is to improve the accuracy of relative stopping power (RSP) values available for proton therapy treatment planning on a patient specific basis and to reduce uncertainty in dose depth calculations. Methods: In this research, MCNP6 was used to simulate PG emission spectra generated from proton induced nuclear reactions in medium of varying composition of carbon, oxygen, calcium and nitrogen, the predominant elements found in human tissue. The relative peak intensities at discrete energies predicted by MCNP6 were compared to the corresponding atomic composition of the medium. Results: The results have shown a good general agreement with experimentally measured values reported by other investigators. Unexpected divergence from experimental spectra was noted in the peak intensities for some cases depending on the source of the cross-section data when using compiled proton table libraries vs. physics models built into MCNP6. While the use of proton cross-section libraries is generally recommended when available, these libraries lack data for several less abundant isotopes. This limits the range of their applicability and forces the simulations to rely on physics models for reactions with natural atomic compositions. Conclusion: Current end-of-range proton imaging provides an average RSP for the total estimated track length. The accurate identification of tissue composition along the incident particle path using PG detection and characterization allows for improved determination of the tissue RSP on the local level. While this would allow for more accurate depth calculations resulting in tighter treatment margins, precise understanding of proton beam behavior in tissue of various

  17. Needful Implements in Improving the Study and Scholastic Skills of Nigerian Secondary School Students

    Science.gov (United States)

    Adegoroye, Biodun-Smith; Ajagbe, Adesina Adunfe

    2015-01-01

    Showing concern about the consistent depreciation in expected study and scholastic behaviours among Secondary School students and the trailing failure in school test and exams and public exams, the authors gathered empirical report on the chosen variables among a randomly selected 1,200 secondary school students in JSS I, II, III, SSS I, II, III…

  18. Using music structure to improve beat tracking

    Science.gov (United States)

    Dannenberg, Roger B.

    2005-09-01

    Beats are an important feature of most music. Beats are used in music information retrieval systems for genre classification, similarity search, and segmentation. However, beats can be difficult to identify, especially in music audio. Traditional beat trackers attempt to (1) match predicted beats to observations of likely beats, and (2) maintain a fairly steady tempo. A third criterion can be added: when repetitions of musical passages occur, the beats in the first repetition should align with the beats in all other repetitions. This third criterion improves beat tracking performance significantly. Repetitions of musical passages are discovered in audio data by searching for similar sequences of chroma vectors. Beats are ``tracked'' by first locating a sequence of likely beats in the music audio using high frequency energy as an indicator of beat likelihood. This beat sequence is then extended by searching forward and backward for more matching beats, allowing slight variations in tempo, and using a relaxation algorithm to optimize the proposed beat locations with respect to the three criteria. Other high-level music features may offer further improvements in beat identification.

  19. The incidence angle influence on the structure of secondary-emission characteristics of single crystals

    International Nuclear Information System (INIS)

    Gasanov, E.R.; Aliyev, B.Z.

    2012-01-01

    Full text : The dependences of Wand MO single crystals in different atom planes have been studied in this work. It is revealed that maximums are added to each dependency and also minimums of first and second degree. This fact is explained by diffraction dynamic theory. It is established that electron diffraction oriented not perpendicularly to crystal surface is the reason of appearance of second order structure on studied secondary-emission characteristics. In the present work being the continuation and development of SEE investigations of high-melting metal single crystals begun earlier by authors, the structure dependence of SEE main characteristics of angle has been studied. This angle has been chosen because as it is mentioned before the bad repeatability in different experiments for it is observed

  20. Structure and formation of convection of secondary rainbands in a simulated typhoon Jangmi (2008)

    Science.gov (United States)

    Xiao, Jing; Tan, Zhe-Min; Chow, Kim-Chiu

    2018-04-01

    Secondary rainbands in tropical cyclone are relatively transient compared with the quasi-stationary principle rainbands. To have a better understanding on their convective structure, a cloud-resolving scale numerical simulation of the super typhoon Jangmi (2008) was performed. The results suggest that the convections in secondary rainbands have some distinctive features that may not be seen in other types of rainbands in tropical cyclone. First, they have a front-like structure and are triggered to form above the boundary layer by the convergence of the above-boundary outflow from the inner side (warmer) and the descending inflow (colder) from the outer side. These elevated convections can be further confirmed by the three-dimensional backward trajectory calculations. Second, due to the release in baroclinic energy, the lower portion of the mid-level inflow from outside may penetrate into the bottom of the convection tower and may help accelerate the boundary layer inflow in the inner side. Third, the local maximum tangential wind is concentrated in the updraft region, with a lower portion which is dipping inward. Tangential wind budget analysis also suggests that the maxima are mainly contributed by the updraft advection, and can be advected cyclonically downstream by the tangential advection.

  1. Contribution of long-range interactions to the secondary structure of an unfolded globin.

    Science.gov (United States)

    Fedyukina, Daria V; Rajagopalan, Senapathy; Sekhar, Ashok; Fulmer, Eric C; Eun, Ye-Jin; Cavagnero, Silvia

    2010-09-08

    This work explores the effect of long-range tertiary contacts on the distribution of residual secondary structure in the unfolded state of an alpha-helical protein. N-terminal fragments of increasing length, in conjunction with multidimensional nuclear magnetic resonance, were employed. A protein representative of the ubiquitous globin fold was chosen as the model system. We found that, while most of the detectable alpha-helical population in the unfolded ensemble does not depend on the presence of the C-terminal region (corresponding to the native G and H helices), specific N-to-C long-range contacts between the H and A-B-C regions enhance the helical secondary structure content of the N terminus (A-B-C regions). The simple approach introduced here, based on the evaluation of N-terminal polypeptide fragments of increasing length, is of general applicability to identify the influence of long-range interactions in unfolded proteins. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  2. Electromagnetic Fields Effects on the Secondary Structure of Lysozyme and Bioprotective Effectiveness of Trehalose

    Directory of Open Access Journals (Sweden)

    Emanuele Calabrò

    2012-01-01

    Full Text Available FTIR spectroscopy was used to investigate the effects of extremely low frequency (50 Hz electromagnetic field and of microwaves at 900 MHz on the secondary structure of a typical protein, the lysozyme, evaluating the bioprotective effectiveness of trehalose. Lysozyme in D2O solution (60 mg/ml was exposed to 50 Hz frequency electromagnetic field at 180 μT. The FTIR spectra indicated an increase of CH2 group at 1921 and 1853 cm−1 after 3 h of exposure. Such effect was not observed after the addition of trehalose (150 mg/mL at the same exposure conditions. Lysozyme dissolved in D2O at the concentration of 100 mg/mL was exposed up to 4 h to 900 MHz mobile phone microwaves at 25 mA/m. A significant increase in intensity of the amide I vibration band in the secondary structure of the protein was observed after 4 h exposure to microwaves. This effect was inhibited by the presence of trehalose at the concentration of 150 mg/mL. Fourier self-deconvolution spectral analysis of lysozyme in D2O solution after exposure to microwaves revealed an increase in intensity of the conformational components of amide I mode, particularly of β-sheet and turn that can be attributed to disorder and unfolding processes of the protein.

  3. A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction.

    Science.gov (United States)

    Edvardsson, Sverker; Gardner, Paul P; Poole, Anthony M; Hendy, Michael D; Penny, David; Moulton, Vincent

    2003-05-01

    Noncoding RNA genes produce functional RNA molecules rather than coding for proteins. One such family is the H/ACA snoRNAs. Unlike the related C/D snoRNAs these have resisted automated detection to date. We develop an algorithm to screen the yeast genome for novel H/ACA snoRNAs. To achieve this, we introduce some new methods for facilitating the search for noncoding RNAs in genomic sequences which are based on properties of predicted minimum free-energy (MFE) secondary structures. The algorithm has been implemented and can be generalized to enable screening of other eukaryote genomes. We find that use of primary sequence alone is insufficient for identifying novel H/ACA snoRNAs. Only the use of secondary structure filters reduces the number of candidates to a manageable size. From genomic context, we identify three strong H/ACA snoRNA candidates. These together with a further 47 candidates obtained by our analysis are being experimentally screened.

  4. Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding

    Directory of Open Access Journals (Sweden)

    Adami Christoph

    2003-02-01

    Full Text Available Background The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem natural that random mutations should tend to interact synergistically, such that the rate of mean fitness decline accelerates as the number of random mutations is increased. However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect has been observed. Results We studied in silico the net amount and form of epistatic interactions in RNA secondary structure folding by measuring the fraction of neutral mutants as a function of mutational distance d. We found a clear prevalence of antagonistic epistasis in RNA secondary structure folding. By relating the fraction of neutral mutants at distance d to the average neutrality at distance d, we showed that this prevalence derives from the existence of many compensatory mutations at larger mutational distances. Conclusions Our findings imply that the average direction of epistasis in simple fitness landscapes is directly related to the density with which fitness peaks are distributed in these landscapes.

  5. Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding.

    Science.gov (United States)

    Wilke, Claus O; Lenski, Richard E; Adami, Christoph

    2003-02-05

    The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem natural that random mutations should tend to interact synergistically, such that the rate of mean fitness decline accelerates as the number of random mutations is increased. However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect) has been observed. We studied in silico the net amount and form of epistatic interactions in RNA secondary structure folding by measuring the fraction of neutral mutants as a function of mutational distance d. We found a clear prevalence of antagonistic epistasis in RNA secondary structure folding. By relating the fraction of neutral mutants at distance d to the average neutrality at distance d, we showed that this prevalence derives from the existence of many compensatory mutations at larger mutational distances. Our findings imply that the average direction of epistasis in simple fitness landscapes is directly related to the density with which fitness peaks are distributed in these landscapes.

  6. Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements

    Directory of Open Access Journals (Sweden)

    Sze Sing-Hoi

    2008-07-01

    Full Text Available Abstract Background Since experimental determination of protein folding pathways remains difficult, computational techniques are often used to simulate protein folding. Most current techniques to predict protein folding pathways are computationally intensive and are suitable only for small proteins. Results By assuming that the native structure of a protein is known and representing each intermediate conformation as a collection of fully folded structures in which each of them contains a set of interacting secondary structure elements, we show that it is possible to significantly reduce the conformation space while still being able to predict the most energetically favorable folding pathway of large proteins with hundreds of residues at the mesoscopic level, including the pig muscle phosphoglycerate kinase with 416 residues. The model is detailed enough to distinguish between different folding pathways of structurally very similar proteins, including the streptococcal protein G and the peptostreptococcal protein L. The model is also able to recognize the differences between the folding pathways of protein G and its two structurally similar variants NuG1 and NuG2, which are even harder to distinguish. We show that this strategy can produce accurate predictions on many other proteins with experimentally determined intermediate folding states. Conclusion Our technique is efficient enough to predict folding pathways for both large and small proteins at the mesoscopic level. Such a strategy is often the only feasible choice for large proteins. A software program implementing this strategy (SSFold is available at http://faculty.cs.tamu.edu/shsze/ssfold.

  7. Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment

    KAUST Repository

    Hanczyc, Piotr

    2012-04-24

    We report that short, synthetic, double- as well as single-stranded DNA can be aligned in stretched humid poly(vinyl alcohol) (PVA) matrix, and the secondary structure (nucleobase orientation) can be characterized with linear dichroism (LD) spectroscopy. Oligonucleotides of lengths varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated with respect to structural properties in the gel-like polymer environment. The DNA conformation as a function of relative humidity reveals a strong dependence of helical structure of DNA on PVA hydration level, results of relevance for nanotechnical studies of DNA-based supramolecular systems. Also, the PVA gel could provide possibilities to test models for nucleic acid interactions and distribution in cell contexts, including structural stability of genetic material in the cell and PVA-packaging for gene delivery. A method by which duplex oligonucleotides, with sequences designed to provide specific binding sites, become amenable to polarized-light spectroscopy opens up new possibilities for studying structure in DNA complexes with small adduct molecules as well as proteins. © 2012 American Chemical Society.

  8. Improvement of the CFC structure to withstand high heat flux

    International Nuclear Information System (INIS)

    Pestchanyi, S.; Landman, I.

    2006-01-01

    Analysis of the peculiarities of the erosion of NB31 CFC allowed proposition of a new CFC fibre structure for considerable reduction of the erosion rate. The improvement concerns the needling and vowing fibres arrangement only and keeping the same structure of the pitch fibres - the main heat conducting component of NB31. The needling and the vowing fibres of the improved structure provide the armour stiffness, comparable to that of NB31. Numerical simulation of erosion for CFC with the improved structure has confirmed that the erosion rate is four to five times lower in comparison with that of NB31

  9. ConStruct: Improved construction of RNA consensus structures

    Directory of Open Access Journals (Sweden)

    Steger Gerhard

    2008-04-01

    Full Text Available Abstract Background Aligning homologous non-coding RNAs (ncRNAs correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions. High quality alignments, however, are a prerequisite for most consensus structure prediction approaches, homology searches, and tools for phylogeny inference. Automatically created ncRNA alignments often need manual corrections, yet this manual refinement is tedious and error-prone. Results We present an extended version of CONSTRUCT, a semi-automatic, graphical tool suitable for creating RNA alignments correct in terms of both consensus sequence and consensus structure. To this purpose CONSTRUCT combines sequence alignment, thermodynamic data and various measures of covariation. One important feature is that the user is guided during the alignment correction step by a consensus dotplot, which displays all thermodynamically optimal base pairs and the corresponding covariation. Once the initial alignment is corrected, optimal and suboptimal secondary structures as well as tertiary interaction can be predicted. We demonstrate CONSTRUCT's ability to guide the user in correcting an initial alignment, and show an example for optimal secondary consensus structure prediction on very hard to align SECIS elements. Moreover we use CONSTRUCT to predict tertiary interactions from sequences of the internal ribosome entry site of CrP-like viruses. In addition we show that alignments specifically designed for benchmarking can be easily be optimized using CONSTRUCT, although they share very little sequence identity. Conclusion CONSTRUCT's graphical interface allows for an easy alignment correction based on and guided by predicted and known structural constraints. It combines several algorithms for prediction of secondary consensus structure and even tertiary interactions. The CONSTRUCT package can be downloaded from the URL listed in the Availability and

  10. Global earthquake casualties due to secondary effects: A quantitative analysis for improving rapid loss analyses

    Science.gov (United States)

    Marano, K.D.; Wald, D.J.; Allen, T.I.

    2010-01-01

    This study presents a quantitative and geospatial description of global losses due to earthquake-induced secondary effects, including landslide, liquefaction, tsunami, and fire for events during the past 40 years. These processes are of great importance to the US Geological Survey's (USGS) Prompt Assessment of Global Earthquakes for Response (PAGER) system, which is currently being developed to deliver rapid earthquake impact and loss assessments following large/significant global earthquakes. An important question is how dominant are losses due to secondary effects (and under what conditions, and in which regions)? Thus, which of these effects should receive higher priority research efforts in order to enhance PAGER's overall assessment of earthquakes losses and alerting for the likelihood of secondary impacts? We find that while 21.5% of fatal earthquakes have deaths due to secondary (non-shaking) causes, only rarely are secondary effects the main cause of fatalities. The recent 2004 Great Sumatra-Andaman Islands earthquake is a notable exception, with extraordinary losses due to tsunami. The potential for secondary hazards varies greatly, and systematically, due to regional geologic and geomorphic conditions. Based on our findings, we have built country-specific disclaimers for PAGER that address potential for each hazard (Earle et al., Proceedings of the 14th World Conference of the Earthquake Engineering, Beijing, China, 2008). We will now focus on ways to model casualties from secondary effects based on their relative importance as well as their general predictability. ?? Springer Science+Business Media B.V. 2009.

  11. The Condition of Secondary School Physics Education in the Philippines: Recent Developments and Remaining Challenges for Substantive Improvements

    Science.gov (United States)

    Orleans, Antriman V.

    2007-01-01

    This study is aimed at assessing the state of Philippine secondary school physics education using data from a nationwide survey of 464 schools and 767 physics teachers and at identifying challenges for substantive improvements. Teacher-related indicators revealed academic qualification deficiency, low continuing professional involvements,…

  12. Catch Them Young: Developing and Improving of School Libraries and Reading Habit of Secondary School Students in Nigeria

    Science.gov (United States)

    Oriogu, Chuks Daniel

    2015-01-01

    Reading habit is a fundamental skill necessary in the life of every student. It is essential in developing a more civilized and knowledgeable society. Therefore, the study investigated reading habit of secondary school students and ways of developing and improving of school libraries in Nigeria. The study reviewed the basis of reading skills,…

  13. Developing Learning at St Mary's Secondary School, UK: Improving the Motivation and Well-Being of Students

    Science.gov (United States)

    Lambert, Clive

    2014-01-01

    This article summarises the actions taken by a Catholic secondary school in England to improve the learning, motivation and well-being of its students. It describes the theories of mindset, as proposed by Dweck (2006); aspects of self-determination, as described by Kasser and Ryan (1993); and intrinsic versus extrinsic motivation, as detailed by…

  14. The effects of two secondary science teacher education program structures on teachers' habits of mind and action

    Science.gov (United States)

    Bergman, Daniel Jay

    2007-12-01

    This study investigated the effects of the Iowa State University Secondary Science Teacher Education Program (ISU SSTEP) on the educational goals and habits of mind exhibited by its graduates. Ten teachers from ISU SSTEP participated in the study---five from the former program featuring one semester of science teaching methods, five from the current program featuring three semesters of science teaching methods (four for the graduate certification consortium). A naturalistic inquiry research approach included the following methods used with each teacher: three classroom observations, classroom artifact analysis, teacher questionnaires and semi-structured interviews, and questionnaires for students about perceived emphasis of educational goals. Evidence exists that graduates from the current ISU SSTEP format exhibited a closer match to the educational goals promoted, modeled, and advocated by the science teaching methods faculty. Graduates from the current ISU SSTEP also exhibited a closer match to the habits of mind---understanding, action, reflection, action plan for improvement---promoted and modeled by the program. This study has implications for other secondary science teacher education programs, particularly increasing the number of science teaching methods courses; teaching meaningful content of both concepts and skills through a research-based framework; modeling the appropriate teacher behaviors, strategies, habits, and goal promotion by methods instructors; and addressing issues of institutional constraints experienced by future teachers.

  15. Development of secondary chamber for tar cracking-improvement of wood pyrolysis performance in pre-vacuum chamber

    Science.gov (United States)

    Siahaan, S.; Homma, H.; Homma, H.

    2018-02-01

    Energy crisis and global warming, in other words, climate change are critical topics discussed in various parts of the world. Global warming primarily result from too much emission of carbon dioxide (CO2) in the atmosphere. To mitigate global warming, or climate change and improve electrification in rural areas, wood pyrolysis technology is developed in a laboratory scale, of which gases are directly applicable to the gas engine generator. Our laboratory has developed a prototype of wood pyrolysis plant with a pre-vacuum chamber. However, tar yield was around 40 wt% of feedstock. This research aims to reduce tar yield by secondary tar cracking. For the secondary tar cracking, a secondary pre-vacuum chamber is installed after primary pre-vacuum chamber. Gases generated in the primary pre-vacuum chamber are lead into the secondary chamber that is heated up to 1000 K. This paper reports performance of the secondary chamber for secondary tar cracking in homogeneous mode and heterogeneous mode with char.

  16. Does ownership structure improve credit ratings?

    Directory of Open Access Journals (Sweden)

    Aws AlHares

    2018-04-01

    Full Text Available This study seeks to examine the impact of Block Ownership structure on Credit Ratings in OECD countries. This research seeks to contribute to the extant literature by exploring the effects of Corporate Governance (CG mechanisms on corporate credit ratings. The study uses a panel data of 200 companies from Anglo American and European countries between 2010 and 2014. The ordinary least square regression is used to examine the relationships. Additionally, to alleviate the concern of potential endogeneity, we use fixed effect regression, two-stage least squares using instrumental variables. The results show there is a negative and significant relationship between block ownership and credit ratings, with a greater significance among Anglo American countries than among European countries. The rationale for this is that Anglo-American system gives preferential treatment to individual shareholders and its accounting tradition leads to a decline in risk and increase in credit ratings. The result is consistent with the multi-theoretical framework predictions derived from the agency and stewardship theories. Future research could investigate credit ratings using other credit rating agencies, selecting a larger sample that includes small, mid-size and large companies. This paper extends, as well as contributes to extant CG literature by offering new evidence on the effect of block ownership on credit ratings between two different traditions. This will be explored by employing firm-level CG mechanisms by accounting for control variables. The findings will help regulators and policymakers in OECD countries in evaluating the adequacy of current CG reforms to prevent management misconduct and scandals.

  17. R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

    Science.gov (United States)

    2011-01-01

    Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file. PMID:21205310

  18. R2R--software to speed the depiction of aesthetic consensus RNA secondary structures.

    Science.gov (United States)

    Weinberg, Zasha; Breaker, Ronald R

    2011-01-04

    With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

  19. R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Weinberg Zasha

    2011-01-01

    Full Text Available Abstract Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

  20. DOES URINARY DIVERSION IMPROVE THE QUALITY OF LIFE IN OBSTRUCTIVE UROPATHY SECONDARY TO ADVANCED PELVIC MALIGNANCY?

    Directory of Open Access Journals (Sweden)

    Shivashankarappa

    2016-02-01

    Full Text Available INTRODUCTION The incidence of patients presenting with advanced pelvic malignancy with obstructive uropathy is high in our country. Relentless progress of the malignancy will cause deterioration of renal function, aggravation of pain, infection, deterioration of Quality of Life (QOL, uremia and death. Decreased renal function is considered as a contraindication for palliative chemo and radiotherapy. However urinary diversion in these patients will lead to improvement in renal function and may help in administration of palliative therapy and thus, improve the quality of life of these patients. MATERIALS AND METHODS The present study includes the obstructive uropathy patients secondary to pelvic malignancy referred to our institution for urinary diversion between Jan 2010 to Dec 2014. Total 40 patients were included, of which, 25 patients underwent PCN, 9 patients retrograde DJ stenting, 4 patients refused the treatment, 2 patients were not fit for any intervention due to coagulopathy & comorbid conditions. Of 34 treated patients, 30 were female patients and 4 were male patients. All the patients were explained about the procedure and proper consent taken. Laboratory investigations like CBC, coagulation profile, LFT, routine urine analysis, urine C&S and serum electrolytes were carried out. Haemodialysis was done for 10 patients whose serum creatinine was >6mg% & potassium >6meq. USG guided PCN insertion was done in 8 patients, and in those who failed in this procedure, fluoroscopic C-ARM guided PCN insertion done in 17 patients. Post operatively RFT and serum electrolytes were assessed on 3, 7, 15, & 30th day. PCN catheter was changed once in 3 months. RESULTS 8 patients succeeded in USG guided PCN insertion and 17 patients who failed USG PCN insertion, was done under C–Arm guidance. 3 patients received blood transfusion. No deaths were seen during or post procedure in the hospital. Renal functions improved and normalised in most of the

  1. Secondary α-deuterium isotope effects as a probe to the relationship between structure and mechanism of pyrolysis of secondary azoalkanes

    International Nuclear Information System (INIS)

    Grizzle, P.L.

    1975-01-01

    This study was carried out to investigate the mechanism of azoalkane thermolysis and the effect of molecular structure on the potential-energy hypersurface for pyrolysis utilizing secondary α-deuterium isotope effects. Since the magnitude of the α-effect for 1,1'-diphenylazoethane is of singular importance in the interpretation of those for related compounds, it has been redetermined. To investigate the effect of molecular structure on the potential-energy hypersurface for thermolysis, α-effects have been determined for 2,2,2',2'-tetramethyl-1,1'-diphenylazoethane and (2,2-dimethyl-1-phenylpropyl)azomethane; the inability to prepare these compounds by conventional methods necessitated the development of a new method for synthesis of secondary azoalkanes. A convenient synthesis of secondary azo compounds is reported. Secondary α-deuterium isotope effects were obtained for the thermal decomposition of 1,1'-diphenylazoethane (III) and 1,1'-diphenylazoethane-1,1'-d 2 (III-d 2 ). The isotope effect is entirely consistent with a simultaneous one-step thermolysis mechanism. Secondary α-deuterium isotope effects and activation parameters were obtained in the thermolysis of 2,2,2',2'-tetramethyl-1,1'-diphenylazopropane (VIII) and (2,2-dimethyl-1-phenylpropyl)azomethane (IX). The data for VIII is considered in terms of both a one- and two-step thermolysis mechanism. The α-effect and activation energy for VIII are not obviously reconcilable with a one-step mechanism. The α-effects, activation energies, and rates of thermolysis for VIII, IX, and (1-phenylethyl)azomethane are most easily rationalized by a two-step mechanism

  2. Do quality improvement initiatives for diabetes care address social inequities? Secondary analysis of a systematic review.

    Science.gov (United States)

    Lu, Jacquie Boyang; Danko, Kristin J; Elfassy, Michael D; Welch, Vivian; Grimshaw, Jeremy M; Ivers, Noah M

    2018-02-14

    Socially disadvantaged populations carry a disproportionate burden of diabetes-related morbidity and mortality. There is an emerging interest in quality improvement (QI) strategies in the care of patients with diabetes, however, the effect of these interventions on disadvantaged groups remains unclear. This is a secondary analysis of a systematic review that seeks to examine the extent of equity considerations in diabetes QI studies, specifically quantifying the proportion of studies that target interventions toward disadvantaged populations and conduct analyses on the impact of interventions on disadvantaged groups. Studies were identified using Medline, HealthStar and the Cochrane Effective Practice and Organisation of Care database. Randomised controlled trials assessing 12 QI strategies targeting health systems, healthcare professionals and/or patients for the management of adult outpatients with diabetes were eligible. The place of residence, race/ethnicity/culture/language, occupational status, gender/sexual identity, religious affiliations, education level, socioeconomic status, social capital, plus age, disability, sexual preferences and relationships (PROGRESS-Plus) framework was used to identify trials that focused on disadvantaged patient populations, to examine the types of equity-relevant factors that are being considered and to explore temporal trends in equity-relevant diabetes QI trials. Of the 278 trials that met the inclusion criteria, 95 trials had equity-relevant considerations. These include 64 targeted trials that focused on a disadvantaged population with the aim to improve the health status of that population and 31 general trials that undertook subgroup analyses to assess the extent to which their interventions may have had differential impacts on disadvantaged subgroups. Trials predominantly focused on race/ethnicity, socioeconomic status and place of residence as potential factors for disadvantage in patients receiving diabetes care. Less

  3. 3x2 Classroom Goal Structures, Motivational Regulations, Self-Concept, and Affectivity in Secondary School.

    Science.gov (United States)

    Méndez-Giménez, Antonio; Cecchini-Estrada, José-Antonio; Fernández-Río, Javier; Prieto Saborit, José Antonio; Méndez-Alonso, David

    2017-09-20

    The main objective was to analyze relationships and predictive patterns between 3x2 classroom goal structures (CGS), and motivational regulations, dimensions of self-concept, and affectivity in the context of secondary education. A sample of 1,347 secondary school students (56.6% young men, 43.4% young women) from 10 different provinces of Spain agreed to participate (M age = 13.43, SD = 1.05). Hierarchical regression analyses indicated the self-approach CGS was the most adaptive within the spectrum of self-determination, followed by the task-approach CGS. The other-approach CGS had an ambivalent influence on motivation. Task-approach and self-approach CGS predicted academic self-concept (p approach CGS (negatively) predicted family self-concept (p approach and other-approach CGS's (p approach-oriented CGS's (p approach (positively) and self-approach (negatively) CGS (p < .001; p < .05, respectively; R 2 = .028). These results expand the 3x2 achievement goal framework to include environmental factors, and reiterate that teachers should focus on raising levels of self- and task-based goals for students in their classes.

  4. [Establishment of prescription research technology system in Chinese medicine secondary exploitation based on "component structure" theory].

    Science.gov (United States)

    Cheng, Xu-Dong; Feng, Liang; Gu, Jun-Fei; Zhang, Ming-Hua; Jia, Xiao-Bin

    2014-11-01

    Chinese medicine prescriptions are the wisdom outcomes of traditional Chinese medicine (TCM) clinical treatment determinations which based on differentiation of symptoms and signs. Chinese medicine prescriptions are also the basis of secondary exploitation of TCM. The study on prescription helps to understand the material basis of its efficacy, pharmacological mechanism, which is an important guarantee for the modernization of traditional Chinese medicine. Currently, there is not yet dissertation n the method and technology system of basic research on the prescription of Chinese medicine. This paper focuses on how to build an effective system of prescription research technology. Based on "component structure" theory, a technology system contained four-step method that "prescription analysis, the material basis screening, the material basis of analysis and optimization and verify" was proposed. The technology system analyzes the material basis of the three levels such as Chinese medicine pieces, constituents and the compounds which could respect the overall efficacy of Chinese medicine. Ideas of prescription optimization, remodeling are introduced into the system. The technology system is the combination of the existing research and associates with new techniques and methods, which used for explore the research thought suitable for material basis research and prescription remodeling. The system provides a reference for the secondary development of traditional Chinese medicine, and industrial upgrading.

  5. Aerodynamic and cephalometric analyses of velopharyngeal structure and function following re-pushback surgery for secondary correction in cleft palate.

    Science.gov (United States)

    Nakamura, Norifumi; Ogata, Yuko; Sasaguri, Masaaki; Suzuki, Akira; Kikuta, Rumiko; Ohishi, Masamichi

    2003-01-01

    The goal of this study was to clarify the efficacy of and indication for re-pushback surgery as secondary treatment for cleft palate. Fifteen patients treated by re-pushback surgery involving intravelar veloplasty (IVV) with buccal mucosal grafting on the nasal surface and followed up more than 6 months were enrolled in this study. Pre- and postoperative velopharyngeal functions were analyzed by perceptual voice analysis, blowing ratio, and nasalance scores during phonation of /i/ and /tsu/. Cephalometric analysis was used to evaluate the relationship between velopharyngeal structure and the outcome of re-pushback surgery. Control data were obtained from the longitudinal files of normal 10-year-old children in Kyushu University Dental Hospital. Eight of 15 patients obtained complete velopharyngeal closure (complete group), five patients improved remarkably (improved group), and no effective result was seen in two patients (ineffective group). Nasality disappeared or remarkably improved after the operation in 13 patients. Effective surgical results were found in 86.7% of the patients. Partial flap necrosis was seen in two patients in whom re-pushback surgery was performed using mucosal palatal flaps instead of mucoperiosteal flaps. Preoperative velar length and the length/depth ratio of the re-pushback group were significantly smaller than the controls, but there was no difference after the operation. Furthermore, the preoperative length/depth ratio of the complete group (ranged more than 100%) was significantly greater than those of the other two groups (ranged less than 100%). Re-pushback surgery by IVV with free mucous grafting on the nasal surface was effective in managing velopharyngeal incompetence secondarily, improving velopharyngeal structure and function.

  6. Secondary flow structures in a 180∘ elastic curved vessel with torsion under steady and pulsatile inflow conditions

    Science.gov (United States)

    Najjari, Mohammad Reza; Plesniak, Michael W.

    2017-11-01

    Secondary flow vortical structures were investigated in an elastic 180° curved pipe with and without torsion under steady and pulsatile flow using particle image velocimetry (PIV). The elastic thin-walled curved pipes were constructed using Sylgard 184, and inserted into a bath of refractive index matched fluid to perform PIV. A vortex identification method was employed to identify various vortical structures in the flow. The secondary flow structures in the planar compliant model with dilatation of 0.61%-3.23% under pulsatile flow rate were compared with the rigid vessel model results, and it was found that local vessel compliance has a negligible effect on secondary flow morphology. The secondary flow structures were found to be more sensitive to out of plane curvature (torsion) than to vessel compliance. Torsion distorts the symmetry of secondary flow and results in more complex vortical structures in both steady and pulsatile flows. In high Re number steady flow with torsion, a single dominant vortical structure can be detected at the middle of the 90° cross section. In pulsatile flow with torsion, the split-Dean and Lyne-type vortices with same rotation direction originating from opposite sides of the cross section tend to merge together. supported by GW Center for Biomimetics and Bioinspired Engineering.

  7. [Partially unfolded state of lysozyme with a developed secondary structure in dimethylsulfoxide].

    Science.gov (United States)

    Timchenko, A A; Kirkitadze, M D; Prokhorov, D A; Potekhin, S A; Serdiuk, I N

    1996-06-01

    The conformation of a chicken egg lysozyme molecule (dimensions, stoichiometry of its associates, and the degree of helicity) in DMSO was studied by small-angle neutron scattering, dynamic light scattering, and optical rotatory dispersion in the visible region of the spectrum. At high DMSO concentrations (70%), the protein was shown to exist as a dimer. The monomer molecules in the dimer adopt a partially unfolded conformation, with dimensions substantially greater than those in the native state and a high content of secondary structure (the degree of helicity is close to that of native lysozyme). This approach provides a unique possibility to assess the compactness of molecules in associates, which may be very useful in studying protein self-organization.

  8. Molecular and crystal structure of the antibiotic enniatin B, a secondary microbial metabolite

    International Nuclear Information System (INIS)

    Zhukhlistova, N.E.; Tishchenko, G.N.; Tolstykh, I.V.; Zenkova, V.A.

    1999-01-01

    Single crystals of the secondary microbial metabolite C 33 H 57 N 3 O 9 ·1(2/3)H 2 O with the known molecular weight were studied by the method of X-ray diffraction analysis, where a=b=15.102(3) A, c=14.548(3) A, sp. gr.R3, R=0.057. In the course of the structure determination, it was established that the substance is a natural antibiotic, namely, enniatin B. The conformation of its molecule is similar to that of the known synthetic antibiotic. The main difference between the natural and synthesized forms reduces to the different numbers of water molecules and their arrangement in the cavity of the antibiotic molecule

  9. Class Anxiety in Secondary Education: Exploring Structural Relations with Perceived Control, Engagement, Disaffection, and Performance.

    Science.gov (United States)

    González, Antonio; Faílde Garrido, José María; Rodríguez Castro, Yolanda; Carrera Rodríguez, María Victoria

    2015-09-14

    The aim of this study was to assess the relationships between class-related anxiety with perceived control, teacher-reported behavioral engagement, behavioral disaffection, and academic performance. Participants were 355 compulsory secondary students (9th and 10th grades; Mean age = 15.2 years; SD = 1.8 years). Structural equation models revealed performance was predicted by perceived control, anxiety, disaffection, and engagement. Perceived control predicted anxiety, disaffection, and engagement. Anxiety predicted disaffection and engagement, and partially mediated the effects from control on disaffection (β = -.277, p anxiety and performance was mediated by engagement and disaffection (β = -.295, p Anxiety, engagement, and disaffection mediated the effects of control on performance (β = .352, p < .003; CI = .279, .440). The implications of these results are discussed in the light of current theory and educational interventions.

  10. Modeling of a New Structure of Precision Air Conditioning System Using Secondary Condenser for Rh Regulation

    Directory of Open Access Journals (Sweden)

    Aries Subiantoro

    2012-05-01

    Full Text Available A dynamic mathematical model for a new structure of precision air conditioning (PAC has been developed. The proposed PAC uses an additional secondary condenser for relative humidity regulation compared to a basic refrigeration system. The work mechanism for this system and a vapour-compression cycle process of the system are illustrated using psychrometric chart and pressure-enthalpy diagram. A non-linear system model is derived based on the conservation of mass and energy balance principles and then linearized at steady state operating point for developing a 8th-order state space model suited for multivariable controller design. The quality of linearized model is analyzed in terms of transient response, controllability, observability, and interaction between input-output variables. The developed model is verified through simulation showing its ability for imitating the nonlinear behavior and the interaction of input-output variables.

  11. Engineered, highly reactive substrates of microbial transglutaminase enable protein labeling within various secondary structure elements.

    Science.gov (United States)

    Rachel, Natalie M; Quaglia, Daniela; Lévesque, Éric; Charette, André B; Pelletier, Joelle N

    2017-11-01

    Microbial transglutaminase (MTG) is a practical tool to enzymatically form isopeptide bonds between peptide or protein substrates. This natural approach to crosslinking the side-chains of reactive glutamine and lysine residues is solidly rooted in food and textile processing. More recently, MTG's tolerance for various primary amines in lieu of lysine have revealed its potential for site-specific protein labeling with aminated compounds, including fluorophores. Importantly, MTG can label glutamines at accessible positions in the body of a target protein, setting it apart from most labeling enzymes that react exclusively at protein termini. To expand its applicability as a labeling tool, we engineered the B1 domain of Protein G (GB1) to probe the selectivity and enhance the reactivity of MTG toward its glutamine substrate. We built a GB1 library where each variant contained a single glutamine at positions covering all secondary structure elements. The most reactive and selective variants displayed a >100-fold increase in incorporation of a recently developed aminated benzo[a]imidazo[2,1,5-cd]indolizine-type fluorophore, relative to native GB1. None of the variants were destabilized. Our results demonstrate that MTG can react readily with glutamines in α-helical, β-sheet, and unstructured loop elements and does not favor one type of secondary structure. Introducing point mutations within MTG's active site further increased reactivity toward the most reactive substrate variant, I6Q-GB1, enhancing MTG's capacity to fluorescently label an engineered, highly reactive glutamine substrate. This work demonstrates that MTG-reactive glutamines can be readily introduced into a protein domain for fluorescent labeling. © 2017 The Protein Society.

  12. Examining the dimensional structure models of secondary traumatic stress based on DSM-5 symptoms.

    Science.gov (United States)

    Mordeno, Imelu G; Go, Geraldine P; Yangson-Serondo, April

    2017-02-01

    Latent factor structure of Secondary Traumatic Stress (STS) has been examined using Diagnostic Statistic Manual-IV (DSM-IV)'s Posttraumatic Stress Disorder (PTSD) nomenclature. With the advent of Diagnostic Statistic Manual-5 (DSM-5), there is an impending need to reexamine STS using DSM-5 symptoms in light of the most updated PTSD models in the literature. The study investigated and determined the best fitted PTSD models using DSM-5 PTSD criteria symptoms. Confirmatory factor analysis (CFA) was conducted to examine model fit using the Secondary Traumatic Stress Scale in 241 registered and practicing Filipino nurses (166 females and 75 males) who worked in the Philippines and gave direct nursing services to patients. Based on multiple fit indices, the results showed the 7-factor hybrid model, comprising of intrusion, avoidance, negative affect, anhedonia, externalizing behavior, anxious arousal, and dysphoric arousal factors has excellent fit to STS. This model asserts that: (1) hyperarousal criterion needs to be divided into anxious and dysphoric arousal factors; (2) symptoms characterizing negative and positive affect need to be separated to two separate factors, and; (3) a new factor would categorize externalized, self-initiated impulse and control-deficit behaviors. Comparison of nested and non-nested models showed Hybrid model to have superior fit over other models. The specificity of the symptom structure of STS based on DSM-5 PTSD criteria suggests having more specific interventions addressing the more elaborate symptom-groupings that would alleviate the condition of nurses exposed to STS on a daily basis. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Interaction Of Calcium Phosphate Nanoparticles With Human Chorionic Gonadotropin Modifies Secondary And Tertiary Protein Structure

    Directory of Open Access Journals (Sweden)

    Al-Hakeim Hussein K

    2015-12-01

    Full Text Available Calcium phosphate nanoparticles (CaPNP have good biocompatibility and bioactivity inside human body. In this study, the interaction between CaPNP and human chorionic gonadotropin (hCG was analyzed to determine the changes in the protein structure in the presence of CaPNP and the quantity of protein adsorbed on the CaPNP surface. The results showed a significant adsorption of hCG on the CaPNP nanoparticle surface. The optimal fit was achieved using the Sips isotherm equation with a maximum adsorption capacity of 68.23 µg/mg. The thermodynamic parameters, including ∆H° and ∆G°, of the adsorption process are positive, whereas ∆S° is negative. The circular dichroism results of the adsorption of hCG on CaPNP showed the changes in its secondary structure; such changes include the decomposition of α-helix strand and the increase in β-pleated sheet and random coil percentages. Fluorescence study indicated minimal changes in the tertiary structure near the microenvironment of the aromatic amino acids such as tyrosine and phenyl alanine caused by the interaction forces between the CaPNP and hCG protein. The desorption process showed that the quantity of the hCG desorbed significantly increases as temperature increases, which indicates the weak forces between hCG and the surface.

  14. Influence of Secondary Cooling Mode on Solidification Structure and Macro-segregation Behavior for High-carbon Continuous Casting Bloom

    Science.gov (United States)

    Dou, Kun; Yang, Zhenguo; Liu, Qing; Huang, Yunhua; Dong, Hongbiao

    2017-07-01

    A cellular automaton-finite element coupling model for high-carbon continuously cast bloom of GCr15 steel is established to simulate the solidification structure and to investigate the influence of different secondary cooling modes on characteristic parameters such as equiaxed crystal ratio, grain size and secondary dendrite arm spacing, in which the effect of phase transformation and electromagnetic stirring is taken into consideration. On this basis, evolution of carbon macro-segregation for GCr15 steel bloom is researched correspondingly via industrial tests. Based on above analysis, the relationship among secondary cooling modes, characteristic parameters for solidification structure as well as carbon macro-segregation is illustrated to obtain optimum secondary cooling strategy and alleviate carbon macro-segregation degree for GCr15 steel bloom in continuous casting process. The evaluating method for element macro-segregation is applicable in various steel types.

  15. Factors that Affect Mathematics-Science (MS) Scores in the Secondary Education Institutional Exam: An Application of Structural Equation Modeling

    Science.gov (United States)

    Yavuz, Mustafa

    2009-01-01

    Discovering what determines students' success in the Secondary Education Institutional Exam is very important to parents and it is also critical for students, teachers, directors, and researchers. Research was carried out by studying the related literature and structural equation modeling techniques. A structural model was created that consisted…

  16. Structure and properties of silver sulfate complexes derived from dipyridyl methylthio ligands with secondary donor site

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Wen-Hua; Yan, Hao-Jie; Chen, Hui; Liu, Rui-Heng; Li, Ai-Min; Wang, Guo [Beijing Key Laboratory for Optical Materials and Photonic Devices, Department of Chemistry, Capital Normal University, Beijing 100048 (China); Wan, Chong-Qing, E-mail: wancq@cnu.edu.cn [Beijing Key Laboratory for Optical Materials and Photonic Devices, Department of Chemistry, Capital Normal University, Beijing 100048 (China); State Key Laboratory of Structural Chemistry in China, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002 (China)

    2017-06-15

    Dipyridyl sulphide ligands 4-(pyridin-4-ylmethylthio)pyridine (abbreviated as L1) and 3-(pyridin-4-ylmethylthio)pyridine (abbreviated as L2) have been designed and used as μ-{sub N},{sub N}-bridging linkages to construct coordination polymers with free –S–CH{sub 2}– groups as secondary donor sites. By use solvent control method, coordination polymers ([Ag{sub 3}SO{sub 4}(L1){sub 3}](Cl)·4.5H{sub 2}O){sub ∞}(1), ([Ag{sub 2}SO{sub 4}(L1){sub 2}]·6H{sub 2}O·2CH{sub 3}OH){sub ∞}(2), ([Ag{sub 2}SO{sub 4}(L2){sub 2}]·H{sub 2}O){sub ∞}(3) and ([Ag{sub 4}(SO{sub 4}){sub 2}(L2){sub 4}]·5H{sub 2}O){sub ∞}(4) with different architectures were obtained. Complexes 1, 3 and 4 feature 1D channel with different sizes and structures. Complex 1 exhibits guest exchange by THF and 1,4-dioxane, and Hg{sup 2+} sorption ability from solution due to its relative larger channel and available bonding sites of –S– exposed to the channel region. All complexes have been characterized through single-crystal and powder X-ray diffraction (PXRD), FT-IR spectra, X-ray photoelectron spectroscopy (XPS), elemental and thermogravimetric analyses. The guest exchange and Hg{sup 2+} sorption were monitored and identified, and the structure-property relationship of coordination polymers 1–4 are discussed. - Graphical abstract: Coordination polymers of silver(I) sulfate with secondary donor sites are shown guest exchange property and Hg{sup 2+} absorb ability from solution. This work provides a new method to construct functional materials with potential application. - Highlights: • New example of constructing functional coordination polymer with secondary donor methylthio group. • Guest exchange and interesting Hg(II) absorb ability from solution are investigated. • New method to construct functional materials with potential application.

  17. An Extreme-ultraviolet Wave Generating Upward Secondary Waves in a Streamer-like Solar Structure

    Science.gov (United States)

    Zheng, Ruisheng; Chen, Yao; Feng, Shiwei; Wang, Bing; Song, Hongqiang

    2018-05-01

    Extreme-ultraviolet (EUV) waves, spectacular horizontally propagating disturbances in the low solar corona, always trigger horizontal secondary waves (SWs) when they encounter the ambient coronal structure. We present the first example of upward SWs in a streamer-like structure after the passing of an EUV wave. This event occurred on 2017 June 1. The EUV wave happened during a typical solar eruption including a filament eruption, a coronal mass ejection (CME), and a C6.6 flare. The EUV wave was associated with quasi-periodic fast propagating (QFP) wave trains and a type II radio burst that represented the existence of a coronal shock. The EUV wave had a fast initial velocity of ∼1000 km s‑1, comparable to high speeds of the shock and the QFP wave trains. Intriguingly, upward SWs rose slowly (∼80 km s‑1) in the streamer-like structure after the sweeping of the EUV wave. The upward SWs seemed to originate from limb brightenings that were caused by the EUV wave. All of the results show that the EUV wave is a fast-mode magnetohydrodynamic (MHD) shock wave, likely triggered by the flare impulses. We suggest that part of the EUV wave was probably trapped in the closed magnetic fields of the streamer-like structure, and upward SWs possibly resulted from the release of slow-mode trapped waves. It is believed that the interplay of the strong compression of the coronal shock and the configuration of the streamer-like structure is crucial for the formation of upward SWs.

  18. Mobile phone text messaging to improve medication adherence in secondary prevention of cardiovascular disease.

    Science.gov (United States)

    Adler, Alma J; Martin, Nicole; Mariani, Javier; Tajer, Carlos D; Owolabi, Onikepe O; Free, Caroline; Serrano, Norma C; Casas, Juan P; Perel, Pablo

    2017-04-29

    Worldwide at least 100 million people are thought to have prevalent cardiovascular disease (CVD). This population has a five times greater chance of suffering a recurrent cardiovascular event than people without known CVD. Secondary CVD prevention is defined as action aimed to reduce the probability of recurrence of such events. Drug interventions have been shown to be cost-effective in reducing this risk and are recommended in international guidelines. However, adherence to recommended treatments remains sub-optimal. In order to influence non-adherence, there is a need to develop scalable and cost-effective behaviour-change interventions. To assess the effects of mobile phone text messaging in patients with established arterial occlusive events on adherence to treatment, fatal and non-fatal cardiovascular events, and adverse effects. We searched CENTRAL, MEDLINE, Embase, the Conference Proceedings Citation Index - Science on Web of Science on 7 November 2016, and two clinical trial registers on 12 November 2016. We contacted authors of included studies for missing information and searched reference lists of relevant papers. We applied no language or date restrictions. We included randomised trials with at least 50% of the participants with established arterial occlusive events. We included trials investigating interventions using short message service (SMS) or multimedia messaging service (MMS) with the aim to improve adherence to medication for the secondary prevention of cardiovascular events. Eligible comparators were no intervention or other modes of communication. We used standard methodological procedures expected by Cochrane. In addition, we attempted to contact all authors on how the SMS were developed. We included seven trials (reported in 13 reports) with 1310 participants randomised. Follow-up ranged from one month to 12 months. Due to heterogeneity in the methods, population and outcome measures, we were unable to conduct meta-analysis on these studies

  19. Improved tank car design development : ongoing studies on sandwich structures

    Science.gov (United States)

    2009-03-02

    The Government and industry have a common interest in : improving the safety performance of railroad tank cars carrying : hazardous materials. Research is ongoing to develop strategies : to maintain the structural integrity of railroad tank cars carr...

  20. Improving 3D structure prediction from chemical shift data

    Energy Technology Data Exchange (ETDEWEB)

    Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

    2013-09-15

    We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

  1. Experience running in and improvement of secondary circuit water chemistry of Kalinin NPP WWER-1000

    International Nuclear Information System (INIS)

    Noev, V.V.; Kukharev, N.D.; Otchenashev, G.D.; Guzeeva, G.I.; Kochetova, G.G.

    1991-01-01

    Basic characteristics of the secondary circuit water-chemical conditions at the Kalinin 1 and 2 reactors are presented. These are the WWER-1000 reactors with K-1000-1500 turbines. The analysis conducted makes it possible to conclude that all indicated values can meet the standards by introducing the hydrazine-ammonium regime in the secondary circuit with feedwater pH value equal to 9±0.2. Realization of design scheme for condensate-feeding circuit washing is necessary for acceleration of the water-chemical mode stabilization. Moreover the units should be equipped with automated chemical control instrumentation of a new generation

  2. An Improved Parametrized Representation of the Secondary He Neutral Flow in its Source Region

    Science.gov (United States)

    Wood, Brian E.

    2017-09-01

    Analysis of data from the Interstellar Boundary EXplorer (IBEX) has revealed the presence of a flow of neutral helium through the inner solar system that most likely emanates from the outer heliosheath, where a distinct population of neutral He is produced by charge exchange processes. This secondary He flow has been modeled using codes designed to study interstellar flows through the heliosphere, but a laminar flow is not a good approximation for the outer heliosheath. I present a simple parametrization for a more appropriate divergent flow, and demonstrate how the secondary He particles might provide a means to remotely measure the divergence of the ISM flow around the heliopause.

  3. Evolution of primary and secondary structures in 5S and 5.8S rRNA

    International Nuclear Information System (INIS)

    Curtiss, W.C.

    1986-01-01

    The secondary structure of Bombyx mori 5S rRNA was studied using the sing-strand specific S1 nuclease and the base pair specific cobra venom ribonuclease. The RNA was end-labeled with [ 32 P] at either the 5' or 3' end and sequenced using enzymatic digestion techniques. These enzymatic data coupled with thermodynamic structure prediction were used to generate a secondary structure for 5S rRNA. A computer algorithm has been implemented to aid in the comparison of a large set of homologous RNAs. Eukaryotic 5S rRNA sequences from thirty four diverse species were compared by (1) alignment or the sequences, (2) the positions of substitutions were located with respect to the aligned sequence and secondary structure, and (3) the R-Y model of base stacking was used to study stacking pattern relationships in the structure. Eukaryotic 5S rRNA was found to have significant sequence variation throughout much of the molecule while maintaining a relatively constant secondary structure. A detailed analysis of the sequence and structure variability in each region of the molecule is presented

  4. Improving Narrative Writing Skills of Secondary Students with Disabilities Using Strategy Instruction

    Science.gov (United States)

    Foxworth, Lauren L.; Mason, Linda H.; Hughes, Charles A.

    2017-01-01

    Writing standards and objectives outline complex skills for narrative essay writing at the secondary level. Students with disabilities often produce disorganized narratives with fewer narrative elements than their peers without disabilities. A multiple-probe design was used to examine effects of Self-Regulated Strategy Development for the Pick my…

  5. Improving Student Reflection in Experiential Learning Reports in Post-Secondary Institutions

    Science.gov (United States)

    Tiessen, Rebecca

    2018-01-01

    Work-integrated learning options--or experiential learning--(such as co-operative education, practicum placements, and community service learning/volunteer placements) offer much scope for enhancing educational opportunities for post-secondary students to learn about the workplace and to develop skills that may contribute to their future…

  6. Making Sense of Learning at Secondary School: Involving Students to Improve Teaching Practice

    Science.gov (United States)

    Kane, Ruth G.; Maw, Nicola

    2005-01-01

    Consulting students on their experiences of learning and teaching in schools, while signalled as a potentially valuable research practice fifteen years ago by Michael Fullan, is now gaining prominence in educational research within New Zealand. The "Making Sense of Learning at Secondary Schools" research began with the premise that to…

  7. Determination of Endosperm Protein Secondary Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy

    International Nuclear Information System (INIS)

    Bonwell, E.; Fisher, T.; Fritz, A.; Wetzel, D.

    2008-01-01

    One molecular aspect of mature hard wheat protein quality for breadmaking is the relative amount of endosperm protein in the a-helix form compared with that in other secondary structure forms including β-sheet. Modeling of a-helix and β-sheet absorption bands that contribute to the amide I band at 1650 cm-1 was applied to more than 1500 spectra in this study. The microscopic view of wheat endosperm is dominated by many large starch granules with protein in between. The spectrum produced from in situ microspectroscopy of this mixture is dominated by carbohydrate bands from the large starch granules that fill up the field. The high spatial resolution achievable with synchrotron infrared microspectroscopy enables revealing good in situ spectra of the protein located interstitially. Synchrotron infrared microspectroscopic mapping of 4 μm thick frozen sections of endosperm in the subaleurone region provides spectra from a large number of pixels. Pixels with protein-dominated spectra are sorted out from among adjacent pixels to minimize the starch absorption and scattering contributions. Subsequent data treatment to extract information from the amide I band requires a high signal to noise ratio. Although spectral interference of the carbohydrate band on the amide band is not a problem, the scattering produced by the large starch granules diminishes the signal to noise ratio throughout the spectrum. High density mapping was done on beamlines U2B and U10B at the National Synchrotron Light Source at Brookhaven National Laboratory, Upton, NY. Mapping with a single masked spot size of 5.5 μm diameter or confocal 5 μm x 5 μm spot size, respectively, on the two beamlines used produced spectra for new breeding lines under current consideration. Appropriate data treatment allows calculation of a numerical estimate of the a-helix population relative to other secondary protein structures from the position and shape of the amide I absorption band. Current breeding lines show a

  8. Rheological and secondary structural characterization of rice flour-zein composites for noodles slit from gluten-free sheeted dough.

    Science.gov (United States)

    Jeong, Sungmin; Kim, Hee Won; Lee, Suyong

    2017-04-15

    Rice flour-zein composites in a hydrated viscoelastic state were utilized to compensate for the role of wheat gluten in gluten-free sheeted dough. The use of zein above its glass transition temperature was able to form a viscoelastic protein network of non-wheat dough with rice flour. The mixing stability and development time of the rice dough were positively increased with increasing levels of zein. The protein secondary structural analysis by FTIR spectroscopy demonstrated that the rice doughs with high levels of zein showed significant increases in β-sheet structures whose intensity was almost doubled by the use of 10% zein. The use of zein at more than 5% (w/w) successfully produced gluten-free dough sheets that could be slit into thin and long noodle strands. In addition, the composites were effective in improving the rheological characteristics of gluten-free noodle strands by increasing their maximum force to extension, compared to wheat-based noodles. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Secondary structure of 5S RNA: NMR experiments on RNA molecules partially labeled with Nitrogen-15

    International Nuclear Information System (INIS)

    Gewirth, D.T.; Abo, S.R.; Leontis, N.B.; Moore, P.B.

    1987-01-01

    A method has been found for reassembling fragment 1 of Escherichia coli 5S RNA from mixtures containing strand III (bases 69-87) and the complex consisting of strand II (bases 89-120) and strand IV (bases 1-11). The reassembled molecule is identical with unreconstituted fragment 1. With this technique, fragment 1 molecules have been constructed 15 N-labeled either in strand III or in the strand II-strand IV complex. Spectroscopic data obtained with these partially labeled molecules show that the terminal helix of 5S RNA includes the GU and GC base pairs at positions 9 and 10 which the standard model for 5S secondary structure predicts but that these base pairs are unstable both in the fragment and in native 5S RNA. The data also assign three resonances to the helix V region of the molecule (bases 70-77 and 99-106). None of these resonances has a normal chemical shift even though two of them correspond to AU or GU base pairs in the standard model. The implications of these findings for the authors understanding of the structure of 5S RNA and its complex with ribosomal protein L25 are discussed

  10. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.

    Science.gov (United States)

    Spencer, Matt; Eickholt, Jesse; Jianlin Cheng

    2015-01-01

    Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent.

  11. Enzyme stability, thermodynamics and secondary structures of α-amylase as probed by the CD spectroscopy.

    Science.gov (United States)

    Kikani, B A; Singh, S P

    2015-11-01

    An amylase of a thermophilic bacterium, Bacillus sp. TSSC-3 (GenBank Number, EU710557) isolated from the Tulsi Shyam hot spring reservoir (Gujarat, India) was purified to the homogeneity in a single step on phenyl sepharose 6FF. The molecular weight of the enzyme was 25kD, while the temperature and pH optima for the enzyme catalysis were 80°C and 7, respectively. The purified enzyme was highly thermostable with broad pH stability and displayed remarkable resistance against surfactants, chelators, urea, guanidine HCl and various solvents as well. The stability and changes in the secondary structure of the enzyme under various extreme conditions were determined by the circular dichroism (CD) spectroscopy. The stability trends and the changes in the α-helices and β-sheets were analyzed by Mean Residual Ellipticity (MRE) and K2D3. The CD data confirmed the structural stability of the enzyme under various harsh conditions, yet it indicated reduced α-helix content and increased β-sheets upon denaturation. The thermodynamic parameters; deactivation rate constant, half-life, changes in entropy, enthalpy, activation energy and Gibb's free energy indicated that the enzyme-substrate reactions were highly stable. The overall profile of the enzyme: high thermostability, alkalitolerance, calcium independent nature, dextrose equivalent values and resistance against chemical denaturants, solvents and surfactants suggest its commercial applications. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Secondary flow vortical structures in a 180∘ elastic curved vessel with torsion under steady and pulsatile inflow conditions

    Science.gov (United States)

    Najjari, Mohammad Reza; Plesniak, Michael W.

    2018-01-01

    Secondary flow structures in a 180∘ curved pipe model of an artery are studied using particle image velocimetry. Both steady and pulsatile inflow conditions are investigated. In planar curved pipes with steady flow, multiple (two, four, six) vortices are detected. For pulsatile flow, various pairs of vortices, i.e., Dean, deformed-Dean, Lyne-type, and split-Dean, are present in the cross section of the pipe at 90∘ into the bend. The effects of nonplanar curvature (torsion) and vessel dilatation on these vortical structures are studied. Torsion distorts the symmetric secondary flows (which exist in planar curvatures) and can result in formation of more complex vortical structures. For example, the split-Dean and Lyne-type vortices with same rotation direction originating from opposite sides of the cross section tend to merge together in pulsatile flow. The vortical structures in elastic vessels with dilatation (0.61%-3.23%) are also investigated and the results are compared with rigid model results. It was found that the secondary flow structures in rigid and elastic models are similar, and hence the local compliance of the vessel does not affect the morphology of secondary flow structures.

  13. Halide salts and their structural properties in presence of secondary amine based molecule: A combined experimental and theoretical analysis

    Science.gov (United States)

    Ghosh, Pritam; Hazra, Abhijit; Ghosh, Meenakshi; Chandra Murmu, Naresh; Banerjee, Priyabrata

    2018-04-01

    Biologically relevant halide salts and its solution state structural properties are always been significant. In general, exposure of halide salts into polar solution medium results in solvation which in turn separates the cationic and anionic part of the salt. However, the conventional behaviour of salts might alter in presence of any secondary amine based compound, i.e.; moderately strong Lewis acid. In its consequence, to investigate the effect of secondary amine based compound in the salt solution, novel (E)-2-(4-bromobenzylidene)-1-(perfluorophenyl) hydrazine has been synthesized and used as secondary amine source. The secondary amine compound interestingly shows a drastic color change upon exposure to fluoride salts owing to hydrogen bonding interaction. Several experimental methods, e.g.; SCXRD, UV-Vis, FT-IR, ESI-MS and DLS together with modern DFT (i.e.; DFT-D3) have been performed to explore the structural properties of the halide salts upon exposure to secondary amine based compound. The effect of counter cation of the fluoride salt in binding with secondary amine source has also been investigated.

  14. Imaging the 3D structure of secondary osteons in human cortical bone using phase-retrieval tomography

    Energy Technology Data Exchange (ETDEWEB)

    Arhatari, B D; Peele, A G [Department of Physics, La Trobe University, Victoria 3086 (Australia); Cooper, D M L [Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon (Canada); Thomas, C D L; Clement, J G [Melbourne Dental School, University of Melbourne, Victoria 3010 (Australia)

    2011-08-21

    By applying a phase-retrieval step before carrying out standard filtered back-projection reconstructions in tomographic imaging, we were able to resolve structures with small differences in density within a densely absorbing sample. This phase-retrieval tomography is particularly suited for the three-dimensional segmentation of secondary osteons (roughly cylindrical structures) which are superimposed upon an existing cortical bone structure through the process of turnover known as remodelling. The resulting images make possible the analysis of the secondary osteon structure and the relationship between an osteon and the surrounding tissue. Our observations have revealed many different and complex 3D structures of osteons that could not be studied using previous methods. This work was carried out using a laboratory-based x-ray source, which makes obtaining these sorts of images readily accessible.

  15. Residual structure of Streptococcus mutans biofilm following complete disinfection favors secondary bacterial adhesion and biofilm re-development.

    Directory of Open Access Journals (Sweden)

    Tatsuya Ohsumi

    Full Text Available Chemical disinfection of oral biofilms often leaves biofilm structures intact. This study aimed to examine whether the residual structure promotes secondary bacterial adhesion. Streptococcus mutans biofilms generated on resin-composite disks in a rotating disc reactor were disinfected completely with 70% isopropyl alcohol, and were again cultured in the same reactor after resupplying with the same bacterial solution. Specimens were subjected to fluorescence confocal laser scanning microscopy, viable cell counts and PCR-Invader assay in order to observe and quantify secondarily adhered cells. Fluorescence microscopic analysis, particularly after longitudinal cryosectioning, demonstrated stratified patterns of viable cells on the disinfected biofilm structure. Viable cell counts of test specimens were significantly higher than those of controls, and increased according to the amount of residual structure and culture period. Linear regression analysis exhibited a high correlation between viable and total cell counts. It was concluded that disinfected biofilm structures favored secondary bacterial adhesion.

  16. Secondary structure and phylogeny of Staphylococcus and Micrococcus 5S rRNAs.

    Science.gov (United States)

    Dekio, S; Yamasaki, R; Jidoi, J; Hori, H; Osawa, S

    1984-01-01

    Nucleotide sequences of 5S rRNAs from four bacteria, Staphylococcus aureus Smith (diffuse), Staphylococcus epidermidis ATCC 14990, Micrococcus luteus ATCC 9341 and Micrococcus luteus ATCC 4698, were determined. The secondary structural models of S. aureus and S. epidermidis sequences showed characteristics of the gram-positive bacterial 5S rRNA (116-N type [H. Hori and S. Osawa, Proc. Natl. Acad. Sci. U.S.A. 76:381-385, 1979]). Those of M. luteus ATCC 9341 and M. luteus ATCC 4698 together with that of Streptomyces griseus (A. Simoncsits, Nucleic Acids Res. 8:4111-4124, 1980) showed intermediary characteristics between the gram-positive and gram-negative (120-N type [H. Hori and S. Osawa, 1979]) 5S rRNAs. This and previous studies revealed that there exist at least three major groups of eubacteria having distinct 5S rRNA and belonging to different stems in the 5S rRNA phylogenic tree. PMID:6735981

  17. Flammability of self-extinguishing kenaf/ABS nanoclays composite for aircraft secondary structure

    Science.gov (United States)

    Karunakaran, S.; Majid, D. L.; Mohd Tawil, M. L.

    2016-10-01

    This study investigates the flammability properties of kenaf fiber reinforced acrylonitrile butadiene styrene (ABS) with nanoclays composites. Natural fiber is one of the potential materials to be used with thermoplastic as a composite due to its attractive properties such as lightweight and strong. In this paper, flammability properties of this material are evaluated through Underwriters Laboratory 94 Horizontal Burning (UL94 HB), which has been conducted for both controlled and uncontrolled conditions, smoke density and limiting oxygen index tests (LOI). These flammability tests are in compliance with the Federal Aviation Regulation (FAR) requirement. The results from UL94 HB and smoke density tests show that the presence of nanoclays with effective composition of kenaf fiber reinforced ABS has enhanced the burning characteristics of the material by hindering propagation of flame spread over the surface of the material through char formation. Consequently, this decreases the burning rate and produces low amount of smoke during burning. On contrary, through LOI test, this material requires less oxygen to burn when exposed to fire, which hinders the enhancement of burning characteristics. This is due to burning mechanism exhibited by nanoclays that catalyzes barrier formation and flame propagation rate over the surface of the biocomposite material. Overall, these experimental results suggest that this biocomposite material is capable of self-extinguishing and possesses effective fire extinction. The observed novel synergism from the result obtained is promising to be implemented in secondary structures of aircraft with significant benefits such as cost-effective, lightweight and biodegradable self-extinguishing biocomposite.

  18. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinlzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

    2013-01-24

    The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

  19. Secondary metabolites of Mirabilis jalapa structurally inhibit Lactate Dehydrogenase A in silico: a potential cancer treatment

    Science.gov (United States)

    Kusumawati, R.; Nasrullah, A. H.; Pesik, R. N.; Muthmainah; Indarto, D.

    2018-03-01

    Altered energy metabolism from phosphorylated oxidation to aerobic glycolysis is one of the cancer hallmarks. Lactate dehydrogenase A (LDHA) is a major enzyme that catalyses pyruvate to lactate in such condition. The aim of this study was to explore LDHA inhibitors derived from Indonesian herbal plants. In this study, LDHA and oxamate molecular structures were obtained from protein data bank. As a standard ligand inhibitor, oxamate was molecularly re-validated using Autodock Vina 1.1.2 software and showed binding energy -4.26 ± 0.006 kcal/mol and interacted with LDHA at Gln99, Arg105, Asn137, Arg168, His192, and Thr247 residues. Molecular docking was used to visualize interaction between Indonesian phytochemicals and LDHA. Indonesian phytochemicals with the lowest binding energy and similar residues with standard ligand was Miraxanthin-III (-8.53 ± 0.006 kcal/mol), Vulgaxanthin-I (-8.46 ± 0.006 kcal/mol), Miraxanthin-II (-7.9 ± 0.2 kcal/mol) and Miraxanthin-V (-7.96 ± kcal/mol). Lower energy binding to LDHA and binding site at these residues was predicted to inhibit LDHA activity better than standard ligand. All phytochemicals were found in Mirabilis jalapa plant. Secondary metabolites in Mirabilis jalapa have LDHA inhibitor property in silico. Further in vitro study should be performed to confirm this result.

  20. Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Song Jun

    2008-06-01

    Full Text Available Abstract Background Genomes possess different levels of non-randomness, in particular, an inhomogeneity in their nucleotide composition. Inhomogeneity is manifest from the short-range where neighboring nucleotides influence the choice of base at a site, to the long-range, commonly known as isochores, where a particular base composition can span millions of nucleotides. A separate genomic issue that has yet to be thoroughly elucidated is the role that RNA secondary structure (SS plays in gene expression. Results We present novel data and approaches that show that a mid-range inhomogeneity (~30 to 1000 nt not only exists in mammalian genomes but is also significantly associated with strong RNA SS. A whole-genome bioinformatics investigation of local SS in a set of 11,315 non-redundant human pre-mRNA sequences has been carried out. Four distinct components of these molecules (5'-UTRs, exons, introns and 3'-UTRs were considered separately, since they differ in overall nucleotide composition, sequence motifs and periodicities. For each pre-mRNA component, the abundance of strong local SS ( Conclusion We demonstrate that the excess of strong local SS in pre-mRNAs is linked to the little explored phenomenon of genomic mid-range inhomogeneity (MRI. MRI is an interdependence between nucleotide choice and base composition over a distance of 20–1000 nt. Additionally, we have created a public computational resource to support further study of genomic MRI.

  1. Influence of secondary water supply systems on microbial community structure and opportunistic pathogen gene markers.

    Science.gov (United States)

    Li, Huan; Li, Shang; Tang, Wei; Yang, Yang; Zhao, Jianfu; Xia, Siqing; Zhang, Weixian; Wang, Hong

    2018-06-01

    Secondary water supply systems (SWSSs) refer to the in-building infrastructures (e.g., water storage tanks) used to supply water pressure beyond the main distribution systems. The purpose of this study was to investigate the influence of SWSSs on microbial community structure and the occurrence of opportunistic pathogens, the latter of which are an emerging public health concern. Higher numbers of bacterial 16S rRNA genes, Legionella and mycobacterial gene markers were found in public building taps served by SWSSs relative to the mains, regardless of the flushing practice (P water retention time, warm temperature and loss of disinfectant residuals promoted microbial growth and colonization of potential pathogens in SWSSs. Varied levels of microbial community shifts were found in different types of SWSSs during water transportation from the distribution main to taps, highlighting the critical role of SWSSs in shaping the drinking water microbiota. Overall, the results provided insight to factors that might aid in controlling pathogen proliferation in real-world water systems using SWSSs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Temperature Effects on Mechanical Properties of Woven Thermoplastic Composites for Secondary Aircraft Structure Applications

    Directory of Open Access Journals (Sweden)

    Wang Yue

    2017-01-01

    Full Text Available The effect of temperature on the mechanical behavior of 8-H satin woven glass fabric/polyethylene sulfide (GF/PPS was investigated in this paper. Static-tensile tests were both conducted on notched and unnotched specimens at typical temperatures (ambient, 95°C and 125°C based on the glass transition temperatures (Tg of the neat resin and composite, their strength and moduli were obtained and compared. The damage patterns of failed specimens of notched and unnotched were examined with the aid of high-definition camera and stereomicroscope. The results of stress-strain relationships showed that the slight nonlinearity of the curves were observed for these two specimens, which was associated with the plastic deformation of localized resin. The damage patterns of notched and unnotched specimens at different temperatures proved that damage and plastic deformation were two simultaneous mechanisms and it was prominent in the notched. It was the overstress accommodation mechanism that led to a relative high strength rentention for the notched and a reduction of the hole sensitivity. The results obtained in this paper indicated that GF/PPS can be used as secondary aircraft structures at elevated temperatures higher than its Tg.

  3. Three dimensional analysis of self-structuring organic thin films using time-of-flight secondary ion mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Mayerhofer, Karl E.; Heier, Jakob; Maniglio, Ylenia; Keller, Beat Andreas, E-mail: beat.keller@empa.ch

    2011-07-01

    Selective sub-micrometer structuring of phase-separating organic semiconductor materials has recently got into focus for providing the opportunity of further improvements in optoelectronic device applications. Here we present a 3D-time-of-flight secondary ion mass spectrometry (3D-TOF-SIMS) depth profiling investigation on spin-coated blends consisting of [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM) and a cationic cyanine dye (1,1'-diethyl-3,3,3',3'-tetramethylcarbocyanine iodide). TOF-SIMS provides the required lateral and depth resolution to resolve material and molecular inhomogeneities and phase separation in the blend. The data are illustrating the three-dimensional arrangement of the substances involved and confirm results of earlier studies using atomic force microscopy, UV-vis spectroscopy and x-ray photoelectron spectroscopy, and which have shown well distinguishable morphological features. The formation of this domain structure has been found to be dependent on the absolute as well as the individual film thickness, in accordance with models based on thin liquid two-layer films. Honey-comb like primary structures with micrometer dimension were found in samples containing small amounts of dye molecules in the deposition solution. In this case a thin dye deposit on PCBM was detected, which is well separated from the dye layer at the substrate. For this type of sample, we discuss an extended model of film formation based on partial depletion of dye molecules during film solidification, resulting in two individual dye layers.

  4. Molecular structure impacts on secondary organic aerosol formation from glycol ethers

    Science.gov (United States)

    Li, Lijie; Cocker, David R.

    2018-05-01

    Glycol ethers, a class of widely used solvents in consumer products, are often considered exempt as volatile organic compounds based on their vapor pressure or boiling points by regulatory agencies. However, recent studies found that glycol ethers volatilize at ambient conditions nearly as rapidly as the traditional high-volatility solvents indicating the potential of glycol ethers to form secondary organic aerosol (SOA). This is the first work on SOA formation from glycol ethers. The impact of molecular structure, specifically -OH, on SOA formation from glycol ethers and related ethers are investigated in the work. Ethers with and without -OH, with methyl group hindrance on -OH and with -OH at different location are studied in the presence of NOX and under "NOX free" conditions. Photooxidation experiments under different oxidation conditions confirm that the processing of ethers is a combination of carbonyl formation, cyclization and fragmentation. Bulk SOA chemical composition analysis and oxidation products identified in both gas and particle phase suggests that the presence and location of -OH in the carbon bond of ethers determine the occurrence of cyclization mechanism during ether oxidation. The cyclization is proposed as a critical SOA formation mechanism to prevent the formation of volatile compounds from fragmentation during the oxidation of ethers. Glycol ethers with -CH2-O-CH2CH2OH structure is found to readily form cyclization products, especially with the presence of NOx, which is more relevant to urban atmospheric conditions than without NOx. Glycol ethers are evaluated as dominating SOA precursors among all ethers studied. It is estimated that the contribution of glycol ethers to anthropogenic SOA is roughly 1% of the current organic aerosol from mobile sources. The contribution of glycol ethers to anthropogenic SOA is roughly 1% of the current organic aerosol from mobile sources and will play a more important role in future anthropogenic SOA

  5. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

    Directory of Open Access Journals (Sweden)

    Masfique Mehedi

    Full Text Available Ebolavirus (EBOV, the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen.

  6. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

    Science.gov (United States)

    Mehedi, Masfique; Hoenen, Thomas; Robertson, Shelly; Ricklefs, Stacy; Dolan, Michael A; Taylor, Travis; Falzarano, Darryl; Ebihara, Hideki; Porcella, Stephen F; Feldmann, Heinz

    2013-01-01

    Ebolavirus (EBOV), the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen.

  7. Adoption and Completeness of Documentation Using a Structured Delivery Record in Secondary Care, Subdistrict Government Hospitals of Karnataka State, India

    Directory of Open Access Journals (Sweden)

    Prem K. Mony

    2016-05-01

    Full Text Available Objective: Poor medical record documentation remains a pervasive problem in hospital delivery rooms, hampering efforts aimed at improving the quality of maternal and neonatal care in resource-limited settings. We evaluated the feasibility and completeness of labor room documentation within a quasi-experimental study aimed at improving emergency preparedness for obstetric and neonatal emergencies in 8 nonteaching, subdistrict, secondary care hospitals of Karnataka state, India. Methods: We redesigned the existing open-ended case sheet into a structured, delivery record cum job aide adhering to principles of local clinical relevance, parsimony, and computerizability. Skills and emergency drills training along with supportive supervision were introduced in 4 “intervention arm” hospitals while the new delivery records were used in eight intervention and control hospitals. Results: Introduction of the new delivery record was feasible over a “run-in” period of 4 months. About 92% (6103 of 6634 of women in intervention facilities and 80% (6205 of 7756 in control facilities had their delivery records filled in during the 1-year study period. Completeness of delivery record documentation fell into one of two subsets with one set of parameters being documented with minimal inputs (in both intervention and control sites and another set of parameters requiring more intensive training efforts (and seen more in intervention than in control sites; P < .05. Conclusion: Under the stewardship of the local government, it was possible to institute a robust, reliable, and valid medical record documentation system as part of efforts to improve intrapartum and postpartum maternal and newborn care in hospitals.

  8. [Training, the key to improving eHealth literacy of upper secondary school students].

    Science.gov (United States)

    Hernández-Rabanal, Carme; Vall, Aurora; Boter, Clara

    To explore whether training on strategies to identify and assess health-related information online has a positive impact on students' perception of their own eHealth literacy. The validated eHealth Literacy Scale (eHEALS) was administered to a sample of upper secondary school students, aged 15-18. One week later, they attended a training session on how to search and identify reliable health-related information and resources online. The eHEALS was administered again at the end of this session. Information about gender and school year was collected in both sessions. Perceived eHealth literacy was assessed by comparing the scores obtained before and after the session. Bivariate and multiple linear regressions were completed. Of the 298 students enrolled in upper secondary school (Bachillerato), 285 were included in the study. Approximately 52.28% (149) were female, and 47.72% (136) were male. The mean eHEALS score before the session was 24.19 (range: 8-40), and was 28.54 after it. The training was associated with higher perceived eHealth literacy scores (p <0,0001). Health literacy was positively associated with the usefulness and importance students give the Internet. Attendance at a training session on strategies to identify and assess health-related resources online is associated with higher levels of perceived eHealth literacy. Implementing specific training sessions on eHealth literacy in upper secondary school is a promising approach for enhancing students' eHealth literacy. Copyright © 2017 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

  9. Improvement on a science curriculum including experimental demonstration of environmental radioactivity for secondary school students

    International Nuclear Information System (INIS)

    Watanabe, Kenji; Matsubara, Shizuo; Aiba, Yoshio; Eriguchi, Hiroshi; Kiyota, Saburo; Takeyama, Tetsuji.

    1988-01-01

    A science curriculum previously prepared for teaching environmental radioactivity was modified on the basis of the results of trial instructions in secondary schools. The main subject of the revised curriculum is an understanding of the natural radioactivity through the experimental demonstration about air-borne β and γ ray emitters. The other subjects included are the radioactive decay, the biological effects of radiation, the concept of risk-benefit balance (acceptable level) and the peaceful uses of nuclear energy and radiation. The work sheets and reference data prepared as learning materials are in two levels corresponding to the ability of students for this curriculum. (author)

  10. Making Sense of Abstract Algebra: Exploring Secondary Teachers' Understandings of Inverse Functions in Relation to Its Group Structure

    Science.gov (United States)

    Wasserman, Nicholas H.

    2017-01-01

    This article draws on semi-structured, task-based interviews to explore secondary teachers' (N = 7) understandings of inverse functions in relation to abstract algebra. In particular, a concept map task is used to understand the degree to which participants, having recently taken an abstract algebra course, situated inverse functions within its…

  11. DNA secondary structure of the released strand stimulates WRN helicase action on forked duplexes without coordinate action of WRN exonuclease

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Byungchan, E-mail: bbccahn@mail.ulsan.ac.kr [Department of Life Sciences, University of Ulsan, Ulsan (Korea, Republic of); Bohr, Vilhelm A. [Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, Baltimore, MD (United States)

    2011-08-12

    Highlights: {yields} In this study, we investigated the effect of a DNA secondary structure on the two WRN activities. {yields} We found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. {yields} These results imply that WRN helicase and exonuclease activities can act independently. -- Abstract: Werner syndrome (WS) is an autosomal recessive premature aging disorder characterized by aging-related phenotypes and genomic instability. WS is caused by mutations in a gene encoding a nuclear protein, Werner syndrome protein (WRN), a member of the RecQ helicase family, that interestingly possesses both helicase and exonuclease activities. Previous studies have shown that the two activities act in concert on a single substrate. We investigated the effect of a DNA secondary structure on the two WRN activities and found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. These results imply that WRN helicase and exonuclease activities can act independently, and we propose that the uncoordinated action may be relevant to the in vivo activity of WRN.

  12. Observed Lesson Structure during the First Year of Secondary Education: Exploration of Change and Link with Academic Engagement

    Science.gov (United States)

    Maulana, Ridwan; Opdenakker, Marie-Christine; Stroet, Kim; Bosker, Roel

    2012-01-01

    This study investigates whether lesson structure (LS) matters and which components are important for academic engagement during the first grade of secondary education. Data from videoed lessons of 10 Dutch and 12 Indonesian teachers analyzed using an observation protocol show that six LS components are found, that between class and over…

  13. Observed lesson structure during the first year of secondary education : Exploration of change and link with academic engagement

    NARCIS (Netherlands)

    Maulana, Ridwan; Opdenakker, Marie-Christine; Stroet, Kim; Bosker, Roel

    This study investigates whether lesson structure (LS) matters and which components are important for academic engagement during the first grade of secondary education. Data from videoed lessons of 10 Dutch and 12 Indonesian teachers analyzed using an observation protocol show that six LS components

  14. Novel evolutionary lineages revealed in the Chaetothyriales (Fungi) based on multigene phylogenetic analyses and comparison of ITS secondary structure

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Untereiner, W. A.; Réblová, K.

    2013-01-01

    Roč. 8, č. 5 (2013), e63547 E-ISSN 1932-6203 R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 Keywords : Cyphelophora * Phialophora * secondary structure Subject RIV: EF - Botanics Impact factor: 3.534, year: 2013

  15. Variation in secondary structure of the 16S rRNA molecule in cyanobacteria with implications for phylogenetic analysis

    Czech Academy of Sciences Publication Activity Database

    Řeháková, Klára; Johansen, J. R.; Bowen, M.B.; Martin, M.P.; Sheil, C.A.

    2014-01-01

    Roč. 14, č. 2 (2014), s. 161-178 ISSN 1802-5439 Institutional support: RVO:60077344 Keywords : 16S rRNA secondary structure * cyanobacteria * phylogeny Subject RIV: EE - Microbiology, Virology Impact factor: 1.930, year: 2014

  16. Effect of Programmed Instruction on Students' Attitude towards Structure of the Atom and the Periodic Table among Kenyan Secondary Schools

    Science.gov (United States)

    Wangila, M. J.; Martin, W.; Ronald, M.

    2015-01-01

    This study examined the effect of Programmed Instruction on students' attitude towards Structure of the Atom and the Periodic Table (SAPT) among mixed (co-educational) secondary schools of Butere district, Kakamega county, Kenya. The quasi-experimental research design was adopted, using the nonrandomized Solomon four-group as a model. The sample…

  17. Rational identification of aggregation hotspots based on secondary structure and amino acid hydrophobicity.

    Science.gov (United States)

    Matsui, Daisuke; Nakano, Shogo; Dadashipour, Mohammad; Asano, Yasuhisa

    2017-08-25

    Insolubility of proteins expressed in the Escherichia coli expression system hinders the progress of both basic and applied research. Insoluble proteins contain residues that decrease their solubility (aggregation hotspots). Mutating these hotspots to optimal amino acids is expected to improve protein solubility. To date, however, the identification of these hotspots has proven difficult. In this study, using a combination of approaches involving directed evolution and primary sequence analysis, we found two rules to help inductively identify hotspots: the α-helix rule, which focuses on the hydrophobicity of amino acids in the α-helix structure, and the hydropathy contradiction rule, which focuses on the difference in hydrophobicity relative to the corresponding amino acid in the consensus protein. By properly applying these two rules, we succeeded in improving the probability that expressed proteins would be soluble. Our methods should facilitate research on various insoluble proteins that were previously difficult to study due to their low solubility.

  18. Principled Improvement in Science: Forces and proportional relations in early secondary-school teaching

    Science.gov (United States)

    Howe, Christine; Ilie, Sonia; Guardia, Paula; Hofmann, Riikka; Mercer, Neil; Riga, Fran

    2015-01-01

    In response to continuing concerns about student attainment and participation in science and mathematics, the epiSTEMe project took a novel approach to pedagogy in these two disciplines. Using principles identified as effective in the research literature (and combining these in a fashion not previously attempted), the project developed topic modules for early secondary-school teaching in the UK, arranged for their implementation in classrooms, and evaluated the results. This paper reports the development, implementation, and evaluation of one of the epiSTEMe science modules. Entitled Forces and Proportional Relations, the module covers standard curricular material in the domain of forces, while paying particular attention to the proportional nature of many key constructs. It was developed in collaboration with a small group of teachers; implemented subsequently in 16 classrooms, in all cases involving students from the first year of secondary school; and evaluated through comparison with first-year students in 13 control classrooms who were studying the topic using established methods. Evaluation addressed topic mastery and opinions about the topic and the manner in which it was taught. While further research is required before definite conclusions are warranted, results relating to topic mastery provide grounds for optimism about the epiSTEMe approach. Furthermore, student opinions about the module were positive.

  19. RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules

    Directory of Open Access Journals (Sweden)

    Michaeli Shulamit

    2007-10-01

    Full Text Available Abstract Background In recent years, RNA molecules that are not translated into proteins (ncRNAs have drawn a great deal of attention, as they were shown to be involved in many cellular functions. One of the most important computational problems regarding ncRNA is to predict the secondary structure of a molecule from its sequence. In particular, we attempted to predict the secondary structure for a set of unaligned ncRNA molecules that are taken from the same family, and thus presumably have a similar structure. Results We developed the RNAspa program, which comparatively predicts the secondary structure for a set of ncRNA molecules in linear time in the number of molecules. We observed that in a list of several hundred suboptimal minimal free energy (MFE predictions, as provided by the RNAsubopt program of the Vienna package, it is likely that at least one suggested structure would be similar to the true, correct one. The suboptimal solutions of each molecule are represented as a layer of vertices in a graph. The shortest path in this graph is the basis for structural predictions for the molecule. We also show that RNA secondary structures can be compared very rapidly by a simple string Edit-Distance algorithm with a minimal loss of accuracy. We show that this approach allows us to more deeply explore the suboptimal structure space. Conclusion The algorithm was tested on three datasets which include several ncRNA families taken from the Rfam database. These datasets allowed for comparison of the algorithm with other methods. In these tests, RNAspa performed better than four other programs.

  20. Relationship between mRNA secondary structure and sequence variability in Chloroplast genes: possible life history implications.

    Science.gov (United States)

    Krishnan, Neeraja M; Seligmann, Hervé; Rao, Basuthkar J

    2008-01-28

    Synonymous sites are freer to vary because of redundancy in genetic code. Messenger RNA secondary structure restricts this freedom, as revealed by previous findings in mitochondrial genes that mutations at third codon position nucleotides in helices are more selected against than those in loops. This motivated us to explore the constraints imposed by mRNA secondary structure on evolutionary variability at all codon positions in general, in chloroplast systems. We found that the evolutionary variability and intrinsic secondary structure stability of these sequences share an inverse relationship. Simulations of most likely single nucleotide evolution in Psilotum nudum and Nephroselmis olivacea mRNAs, indicate that helix-forming propensities of mutated mRNAs are greater than those of the natural mRNAs for short sequences and vice-versa for long sequences. Moreover, helix-forming propensity estimated by the percentage of total mRNA in helices increases gradually with mRNA length, saturating beyond 1000 nucleotides. Protection levels of functionally important sites vary across plants and proteins: r-strategists minimize mutation costs in large genes; K-strategists do the opposite. Mrna length presumably predisposes shorter mRNAs to evolve under different constraints than longer mRNAs. The positive correlation between secondary structure protection and functional importance of sites suggests that some sites might be conserved due to packing-protection constraints at the nucleic acid level in addition to protein level constraints. Consequently, nucleic acid secondary structure a priori biases mutations. The converse (exposure of conserved sites) apparently occurs in a smaller number of cases, indicating a different evolutionary adaptive strategy in these plants. The differences between the protection levels of functionally important sites for r- and K-strategists reflect their respective molecular adaptive strategies. These converge with increasing domestication levels of

  1. Improving Test-Taking Performance of Secondary At-Risk Youth and Students with Disabilities

    Science.gov (United States)

    Banks, Tachelle; Eaton, India

    2014-01-01

    Preparing at-risk youth and students with mild disabilities for state and district tests is important for improving their test performance, and basic instruction in test preparation can significantly improve student test performance. The article defines noncognitive variables that adversely affect test-taker performance. The article also describes…

  2. Design of marine structures with improved safety for environment

    International Nuclear Information System (INIS)

    Klanac, Alan; Varsta, Petri

    2011-01-01

    The paper describes a method for design of marine structures with increased safety for environment, considering also the required investment costs as well as the aspects of risk distribution onto the maritime stakeholders. Practically, the paper seeks to answer what is the optimal amount that should be invested into certain safety measure for any given vessel. Due to the uneven distribution of risk, as well as the differing impact of costs emerging from safety improvements, stakeholders experience conflicting ranking of alternatives. To solve this multi-stakeholder decision-making problem, in which each stakeholder is a decision-maker, the method applies concepts of group decision-making theory, namely the Game Theory. The method fosters axiomatic definition of the optimum solution, arguing that the solution, or the final selected design, should satisfy the non-dominance, efficiency, and fairness. These three are thoroughly discussed in terms of structural design, especially the latter. Considering the coupling of environmental risk and structural design, the method also builds on the preference structure of four maritime stakeholders: yards, owners, oil receivers and the public, who either share the risks or directly influence structural design. Method is presented on a practical study of structural design of a tanker with a crashworthy side structure that is capable of reducing the risk of collision. The outcome of this study outlines a number of possibilities for successful improvement of tanker safety that can benefit, concurrently, all maritime stakeholders.

  3. Betavoltaic Battery Conversion Efficiency Improvement Based on Interlayer Structures

    International Nuclear Information System (INIS)

    Li Da-Rang; Jiang Lan; Yin Jian-Hua; Lin Nai; Tan Yuan-Yuan

    2012-01-01

    Significant differences among the doping densities of PN junctions in semiconductors cause lattice mismatch and lattice defects that increase the recombination current of betavoltaic batteries. This extensively decreases the open circuit voltage and the short current, which results in low conversion efficiency. This study proposes P + PINN + -structure based betavoltaic batteries by adding an interlayer to typical PIN structures to improve conversion efficiency. Numerical simulations are conducted for the energy deposition of beta particles along the thickness direction in semiconductors. Based on this, 63 Ni-radiation GaAs batteries with PIN and P + PINN + structures are designed and fabricated to experimentally verify the proposed design. It turns out that the conversion efficiency of the betavoltaic battery with the proposed P + PINN + structure is about 1.45 times higher than that with the traditional PIN structure. (cross-disciplinary physics and related areas of science and technology)

  4. Modelling ramp-up curves to reflect learning: improving capacity planning in secondary pharmaceutical production

    DEFF Research Database (Denmark)

    Hansen, Klaus Reinholdt Nyhuus; Grunow, Martin

    2015-01-01

    availability at market launch is ensured. Our MILP model is applied to a real industry case study using three empirically observed ramp-up curves to demonstrate its value as decision support tool. We demonstrate the superiority of our volume-dependent method over the traditional time-dependent ramp......The experience gained during production ramp-up leads to an increase of the effective production capacity over time. However, full utilisation of production capacity is not always possible during ramp-up. In such cases, the experience gained and hence the available effective capacity...... are overestimated. We develop a new method, which captures ramp-up as a function of the cumulative production volume to better reflect the experience gained while producing the new product. The use of the more accurate and computationally effective approach is demonstrated for the case of secondary pharmaceutical...

  5. Magnesium secondary alloys: Alloy design for magnesium alloys with improved tolerance limits against impurities

    Energy Technology Data Exchange (ETDEWEB)

    Blawert, C., E-mail: carsten.blawert@gkss.d [GKSS Forschungszentrum Geesthacht GmbH, Max-Planck-Str. 1, 21502 Geesthacht (Germany); Fechner, D.; Hoeche, D.; Heitmann, V.; Dietzel, W.; Kainer, K.U. [GKSS Forschungszentrum Geesthacht GmbH, Max-Planck-Str. 1, 21502 Geesthacht (Germany); Zivanovic, P.; Scharf, C.; Ditze, A.; Groebner, J.; Schmid-Fetzer, R. [TU Clausthal, Institut fuer Metallurgie, Robert-Koch-Str. 42, 38678 Clausthal-Zellerfeld (Germany)

    2010-07-15

    The development of secondary magnesium alloys requires a completely different concept compared with standard alloys which obtain their corrosion resistance by reducing the levels of impurities below certain alloy and process depending limits. The present approach suitable for Mg-Al based cast and wrought alloys uses a new concept replacing the {beta}-phase by {tau}-phase, which is able to incorporate more impurities while being electro-chemically less detrimental to the matrix. The overall experimental effort correlating composition, microstructure and corrosion resistance was reduced by using thermodynamic calculations to optimise the alloy composition. The outcome is a new, more impurity tolerant alloy class with a composition between the standard AZ and ZC systems having sufficient ductility and corrosion properties comparable to the high purity standard alloys.

  6. Improved process for the injection of water for secondary recovery of petroleum

    Energy Technology Data Exchange (ETDEWEB)

    1967-07-24

    In this process for the secondary recovery of petroleum from the formation, an aqueous displacing medium is injected through an injection well in communication with the formation. In this aqueous medium, a polymer is dissolved and the petroleum is thus displaced toward a producing well also in communication with the formation. The polymer is a liquid organic polymer, substantially linear, water-soluble, and having a resistance characteristic of at least 1.5. The polymer is dissolved in water in sufficient quantity such that the viscosity of the displacing medium is 0.5-15% of the viscosity of the crude oil to be displaced. The displacing medium is substantially free of molecular oxygen.

  7. [Secondary hypertension].

    Science.gov (United States)

    Yoshida, Yuichi; Shibata, Hirotaka

    2015-11-01

    Hypertension is a common disease and a crucial predisposing factor of cardiovascular diseases. Approximately 10% of hypertensive patients are secondary hypertension, a pathogenetic factor of which can be identified. Secondary hypertension consists of endocrine, renal, and other diseases. Primary aldosteronism, Cushing's syndrome, pheochromocytoma, hyperthyroidism, and hypothyroidism result in endocrine hypertension. Renal parenchymal hypertension and renovascular hypertension result in renal hypertension. Other diseases such as obstructive sleep apnea syndrome are also very prevalent in secondary hypertension. It is very crucial to find and treat secondary hypertension at earlier stages since most secondary hypertension is curable or can be dramatically improved by specific treatment. One should keep in mind that screening of secondary hypertension should be done at least once in a daily clinical practice.

  8. The Use of an Improved Access Structure in Dictionaries*

    African Journals Online (AJOL)

    rbr

    Page 1 ... that a frame structure and an improved use of outer texts can enhance access to the lexicographic data. Different macrostructural ordering procedures are discussed and it is suggested that the lexicographers of ..... ~-landing, maanlanding; ~less, donker(maan), sonder maan; a ~less night, donkermaan, 'n donker ...

  9. Some techniques to improve time structure of slow extracted beam

    International Nuclear Information System (INIS)

    Shoji, Y.; Sato, H.; Toyama, T.; Marutsuka, K.; Sueno, T.; Mikawa, K.; Ninomiya, S.; Yoshii, M.

    1992-01-01

    In order to improve the time structure of slow extracted beam spill for the KEK 12GeV PS, the spill control system has been upgraded by adding feed forward signal to feedback signal. Further, the wake field in the RF cavity has been cancelled by the beam bunch signal to reduce the re-bunch effect during extraction period. (author)

  10. Does a Structured Data Collection Form Improve The Accuracy of ...

    African Journals Online (AJOL)

    and multiple etiologies for similar presentation. Standardized forms may harmonize the initial assessment, improve accuracy of diagnosis and enhance outcomes. Objectives: To determine the extent to which use of a structured data collection form (SDCF) affected the diagnostic accuracy of AAP. Methodology: A before and ...

  11. an improved structural model for seismic analysis of tall frames

    African Journals Online (AJOL)

    Dr Obe

    ABSTRACT. This paper proposed and examined an improved structural model ... The equation of motion of multI-storey building shown in fig. 2 can be ... The response of the nth mode at any time t of the MDOF system demands the solution of ...

  12. Purification and the Secondary Structure of Fucoidanase from Fusarium sp. LD8

    Directory of Open Access Journals (Sweden)

    Wu Qianqian

    2011-01-01

    Full Text Available The fucoidanase from Fusarium sp. (LD8 was obtained by solid-state fermentation. The fermented solid medium was extracted by citric acid buffer, and the extracts were precipitated by acetone and purified by Sephadex G-100 successively. The results showed that the specific fucoidanase activity of purified enzyme was 22.7-fold than that of the crude enzyme. The recovery of the enzyme was 23.9%. The purified enzyme gave a single band on SDS-PAGE gel, and the molecular weight of fucoidanase was about 64 kDa. The isoelectric point of the enzyme was 4.5. The enzyme properties were also studied. The results showed that the optimum temperature and pH were 60°C and 6.0, respectively; the temperature of half inactivation was 50°C, and the most stable pH for the enzyme was 6.0. KM, and the Vmax  of the enzyme was 8.9 mg·L−1 and 2.02 mg·min−1·mL−1 by using fucoidan from Fucus vesiculosus as substrate. The compositions of the secondary structure of fucoidanase were estimated by FTIR, the second derivative spectra, and the curve-fitting analysis of the amide I bands in their spectra. The results showed that β-sheet was the dominant component (58.6% and α-helix was the least (12%; the content of β-turn and random coil were 15.39% and 14.5%, respectively.

  13. Hemin and bile pigments are the secondary structure regulators of intrinsically disordered antimicrobial peptides.

    Science.gov (United States)

    Zsila, Ferenc; Juhász, Tünde; Bősze, Szilvia; Horváti, Kata; Beke-Somfai, Tamás

    2018-02-01

    The interaction of protoporphyrin compounds of human origin with the major bee venom component melittin (26 a.a., Z +6) and its hybrid derivative (CM15, 15 a.a., Z +6) were studied by a combination of various spectroscopic methods. Throughout a two-state, concentration-dependent process, hemin and its metabolites (biliverdin, bilirubin, bilirubin ditaurate) increase the parallel β-sheet content of the natively unfolded melittin, suggesting the oligomerization of the peptide chains. In contrast, α-helix promoting effect was observed with the also disordered but more cationic CM15. According to fluorescence quenching experiments, the sole Trp residue of melittin is the key player during the binding, in the vicinity of which the first pigment molecule is accommodated presumably making indole-porphyrin π-π stacking interaction. As circular dichroism titration data suggest, cooperative association of additional ligands subsequently occurs, resulting in multimeric complexes with an apparent dissociation constant ranged from 20 to 65 μM. Spectroscopic measurements conducted with the bilirubin catabolite urobilin and stercobilin refer to the requirement of intact dipyrrinone moieties for inducing secondary structure transformations. The binding topography of porphyrin rings on a model parallel β-sheet motif was evaluated by absorption spectroscopy and computational modeling showing a slipped-cofacial binding mode responsible for the red shift and hypochromism of the Soret band. Our results may aid to recognize porphyrin-responsive binding motifs of biologically relevant, intrinsically disordered peptides and proteins, where transient conformations play a vital role in their functions. © 2017 Wiley Periodicals, Inc.

  14. 'Working with the team': an exploratory study of improved type 2 diabetes management in a new model of integrated primary/secondary care.

    Science.gov (United States)

    Hepworth, Julie; Askew, Deborah; Jackson, Claire; Russell, Anthony

    2013-01-01

    This study aimed to explore how a new model of integrated primary/secondary care for type 2 diabetes management, the Brisbane South Complex Diabetes Service (BSCDS), related to improved diabetes management in a selected group of patients. We used a qualitative research design to obtain detailed accounts from the BSCDS via semi-structured interviews with 10 patients. The interviews were fully transcribed and systematically coded using a form of thematic analysis. Participants' responses were grouped in relation to: (1) Patient-centred care; (2) Effective multiprofessional teamwork; and (3) Empowering patients. The key features of this integrated primary/secondary care model were accessibility and its delivery within a positive health care environment, clear and supportive interpersonal communication between patients and health care providers, and patients seeing themselves as being part of the team-based care. The BSCDS delivered patient-centred care and achieved patient engagement in ways that may have contributed to improved type 2 diabetes management in these participants.

  15. IMPROVEMENT OF ECONOMIC COMPETENCE OF HEADS OF SECONDARY EDUCATION FOR EFFECTIVE ACTIVITY OF GENERAL SCHOOLS

    Directory of Open Access Journals (Sweden)

    Volodymyr V. Dyvak

    2010-08-01

    Full Text Available In the article the actual problem of improvement of economic competence of professional work of directors of schools for more efficient control of activity of general schools is considered.

  16. Practices for Improving Secondary School Climate: A Systematic Review of the Research Literature.

    Science.gov (United States)

    Voight, Adam; Nation, Maury

    2016-09-01

    School climate has received increased attention in education policy and, in response, educators are seeking strategies to improve the climates of their middle and high schools. However, there has been no comprehensive synthesis of the empirical evidence for what works in school climate improvement. This article constitutes a systematic review of programs and practices with empirical support for improving school climate. It defines school climate and provides a methodology for identifying and evaluating relevant studies. The review identified 66 studies with varying strength of evidence and nine common elements that cut across reviewed programs and practices. The review concludes with a critical appraisal of what we know about school climate improvement and what we still need to know. © Society for Community Research and Action 2016.

  17. E-MSD: improving data deposition and structure quality.

    Science.gov (United States)

    Tagari, M; Tate, J; Swaminathan, G J; Newman, R; Naim, A; Vranken, W; Kapopoulou, A; Hussain, A; Fillon, J; Henrick, K; Velankar, S

    2006-01-01

    The Macromolecular Structure Database (MSD) (http://www.ebi.ac.uk/msd/) [H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res., 31, 458-462.] group is one of the three partners in the worldwide Protein DataBank (wwPDB), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data [H. Berman, K. Henrick and H. Nakamura (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.]. Since its inception, the MSD group has worked with partners around the world to improve the quality of PDB data, through a clean up programme that addresses inconsistencies and inaccuracies in the legacy archive. The improvements in data quality in the legacy archive have been achieved largely through the creation of a unified data archive, in the form of a relational database that stores all of the data in the wwPDB. The three partners are working towards improving the tools and methods for the deposition of new data by the community at large. The implementation of the MSD database, together with the parallel development of improved tools and methodologies for data harvesting, validation and archival, has lead to significant improvements in the quality of data that enters the archive. Through this and related projects in the NMR and EM realms the MSD continues to improve the quality of publicly available structural data.

  18. Comparison of primary and secondary 26S rRNA structures in two Tetrahymena species: evidence for a strong evolutionary and structural constraint in expansion segments

    DEFF Research Database (Denmark)

    Engberg, J; Nielsen, Henrik; Lenaers, G

    1990-01-01

    We have determined the nucleotide sequence of the 26S large subunit (LSU) rRNA genes for two Tetrahymena species, T. thermophila and T. pyriformis. The inferred rRNA sequences are presented in their most probable secondary structures based on compensatory mutations, energy, and conservation crite...

  19. Accurate determination of interfacial protein secondary structure by combining interfacial-sensitive amide I and amide III spectral signals.

    Science.gov (United States)

    Ye, Shuji; Li, Hongchun; Yang, Weilai; Luo, Yi

    2014-01-29

    Accurate determination of protein structures at the interface is essential to understand the nature of interfacial protein interactions, but it can only be done with a few, very limited experimental methods. Here, we demonstrate for the first time that sum frequency generation vibrational spectroscopy can unambiguously differentiate the interfacial protein secondary structures by combining surface-sensitive amide I and amide III spectral signals. This combination offers a powerful tool to directly distinguish random-coil (disordered) and α-helical structures in proteins. From a systematic study on the interactions between several antimicrobial peptides (including LKα14, mastoparan X, cecropin P1, melittin, and pardaxin) and lipid bilayers, it is found that the spectral profiles of the random-coil and α-helical structures are well separated in the amide III spectra, appearing below and above 1260 cm(-1), respectively. For the peptides with a straight backbone chain, the strength ratio for the peaks of the random-coil and α-helical structures shows a distinct linear relationship with the fraction of the disordered structure deduced from independent NMR experiments reported in the literature. It is revealed that increasing the fraction of negatively charged lipids can induce a conformational change of pardaxin from random-coil to α-helical structures. This experimental protocol can be employed for determining the interfacial protein secondary structures and dynamics in situ and in real time without extraneous labels.

  20. Structured data quality reports to improve EHR data quality.

    Science.gov (United States)

    Taggart, Jane; Liaw, Siaw-Teng; Yu, Hairong

    2015-12-01

    To examine whether a structured data quality report (SDQR) and feedback sessions with practice principals and managers improve the quality of routinely collected data in EHRs. The intervention was conducted in four general practices participating in the Fairfield neighborhood electronic Practice Based Research Network (ePBRN). Data were extracted from their clinical information systems and summarised as a SDQR to guide feedback to practice principals and managers at 0, 4, 8 and 12 months. Data quality (DQ) metrics included completeness, correctness, consistency and duplication of patient records. Information on data recording practices, data quality improvement, and utility of SDQRs was collected at the feedback sessions at the practices. The main outcome measure was change in the recording of clinical information and level of meeting Royal Australian College of General Practice (RACGP) targets. Birth date was 100% and gender 99% complete at baseline and maintained. DQ of all variables measured improved significantly (pImprovement was greatest with allergies. There was no significant change in duplicate records. SDQRs and feedback sessions support general practitioners and practice managers to focus on improving the recording of patient information. However, improved practice DQ, was not sufficient to meet RACGP targets. Randomised controlled studies are required to evaluate strategies to improve data quality and any associated improved safety and quality of care. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  1. Structural Plasticity Denoises Responses and Improves Learning Speed

    Directory of Open Access Journals (Sweden)

    Robin Spiess

    2016-09-01

    Full Text Available Despite an abundance of computational models for learning of synaptic weights, there has been relatively little research on structural plasticity, i.e. the creation and elimination of synapses. Especially, it is not clear how structural plasticity works in concert with spike-timing-dependent plasticity (STDP and what advantages their combination offers.Here we present a fairly large-scale functional model that uses leaky integrate-and-fire neurons, STDP, homeostasis, recurrent connections, and structural plasticity to learn the input encoding, the relation between inputs, and to infer missing inputs. Using this model, we compare the error and the amount of noise in the network's responses with and without structural plasticity and the influence of structural plasticity on the learning speed of the network.Using structural plasticity during learning shows good results for learning the representation of input values, i.e. structural plasticity strongly reduces the noise of the response by preventing spikes with a high error.For inferring missing inputs we see similar results, with responses having less noise if the network was trained using structural plasticity.Additionally, using structural plasticity with pruning significantly decreased the time to learn weights suitable for inference.Presumably, this is due to the clearer signal containing less spikes that misrepresent the desired value. Therefore, this work shows that structural plasticity is not only able to improve upon the performance using STDP without structural plasticity but also speeds up learning.Additionally, it addresses the practical problem of limited resources for connectivity that is not only apparent in the mammalian neocortex but also in computer hardware or neuromorphic (brain-inspired hardware by efficiently pruning synapses without losing performance.

  2. [Reduction of in-hospital mortality and improved secondary prevention after acute myocardial infarction. First results from the registry of secondary prevention after acute myocardial infarction (SAMI)].

    Science.gov (United States)

    Tebbe, U; Messer, C; Stammwitz, E; The, G S; Dietl, J; Bischoff, K-O; Schulten-Baumer, U; Tebbenjohanns, J; Gohlke, H; Bramlage, P

    2007-07-30

    In hospital mortality of acute myocardial infarction (AMI) has been reduced due to the availability of better therapeutic strategies. But there is still a gap between mortality rates in randomised trials and daily clinical practice. Thus, it was aim of the present registry to document the course and outcome of patients with AMI and to improve patient care by implementing recent guidelines. In a nationwide registry study in hospitals in Germany with a cardiology unit or an internal medicine department data on consecutive patients were recorded for six to twelve months at admission, discharge and during a follow-up of one year. From 02/2003 until 10/2004 a total of 5,353 patients with acute myocardial infarction (65.7 % male, mean age of 67.6 +/- 17.7 years; 55.1 % of them with ST elevation myocardial infarction (STEMI) were included in the registry. Of the patients with STEMI, 76.6 % underwent acute intervention, 37.1 % had thrombolysis, 69.7 % percutaneous transluminal coronary angioplasty (PTCA). 40.0 % of those with non-Stemi (NSTEMI) had an acute intervention, 6.6 % thrombolysis, 73.5 % PTCA. Recommended secondary prevention consisted of ASS (93.2 %), beta-blockers (93.0 %), CSE-inhibitors (83.5 %), ACE-inhibitors (80.9 %) and clopidogrel (74.0 %). In-hospital mortality was 10.5 % (STEMI) and 7.4 % (NSTEMI). The 9 % mortality among patients with acute myocardial infarction treated in the hospitals participating in the SAMI registry is low compared to that in similar collectives. The high number of patients who had thrombofibrinolysis and coronary interventions as well as the early initiation of drug therapy contributed to these results. Medical treatment in the prehospital phase of these patients remains still insufficient and to a substantial extent contributes to the mortality of acute myocardial infarction.

  3. WEB STRUCTURE MINING USING PAGERANK, IMPROVED PAGERANK – AN OVERVIEW

    Directory of Open Access Journals (Sweden)

    V. Lakshmi Praba

    2011-03-01

    Full Text Available Web Mining is the extraction of interesting and potentially useful patterns and information from Web. It includes Web documents, hyperlinks between documents, and usage logs of web sites. The significant task for web mining can be listed out as Information Retrieval, Information Selection / Extraction, Generalization and Analysis. Web information retrieval tools consider only the text on pages and ignore information in the links. The goal of Web structure mining is to explore structural summary about web. Web structure mining focusing on link information is an important aspect of web data. This paper presents an overview of the PageRank, Improved Page Rank and its working functionality in web structure mining.

  4. A knowledge engineering approach for improving secondary recovery in offshore reservoirs

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, Milton P.; Tovar, Felipe T.R.; Guerra, Fabio A. [Parana Institute of Technology (TECPAR), Curitiba, PR (Brazil). Artificial Intelligence Div.; Andrade, Cynthia; Baptista, Walmar [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas. Tecnologia de Materiais, Equipamentos e Corrosao

    2004-07-01

    Secondary recovery in offshore petroleum reservoirs by seawater injection is a technique traditionally applied in oil and gas industry. However, the injected water quality must be compatible with the reservoir characteristics in order to prevent corrosion, formation plugging and reservoir souring. So, the seawater must be treated before injection in the reservoirs and on-line monitoring equipment are employed to check the treatments efficacy. Nevertheless, the amount of data to analyze is quite big and involves many different experts, which make their evaluation and the establishment of correlations very difficult. For these cases, where it's crucial to detect the contaminants presence as soon as they occur to indicate corrective procedures, the application of knowledge engineering techniques and the development of expert systems are a good solution proposal. This paper presents the expert system InjeX (heuristic approach), developed for seawater injection treatment plants to maintain the water quality in offshore platforms. The description and the analysis of the problem, a proposed solution and some preliminary results are detailed and discussed along the paper. (author)

  5. Instruction in Information Structuring Improves Bayesian Judgment in Intelligence Analysts

    Directory of Open Access Journals (Sweden)

    David R. Mandel

    2015-04-01

    Full Text Available An experiment was conducted to test the effectiveness of brief instruction in information structuring (i.e., representing and integrating information for improving the coherence of probability judgments and binary choices among intelligence analysts. Forty-three analysts were presented with comparable sets of Bayesian judgment problems before and immediately after instruction. After instruction, analysts’ probability judgments were more coherent (i.e., more additive and compliant with Bayes theorem. Instruction also improved the coherence of binary choices regarding category membership: after instruction, subjects were more likely to invariably choose the category to which they assigned the higher probability of a target’s membership. The research provides a rare example of evidence-based validation of effectiveness in instruction to improve the statistical assessment skills of intelligence analysts. Such instruction could also be used to improve the assessment quality of other types of experts who are required to integrate statistical information or make probabilistic assessments.

  6. Improved hybrid optimization algorithm for 3D protein structure prediction.

    Science.gov (United States)

    Zhou, Changjun; Hou, Caixia; Wei, Xiaopeng; Zhang, Qiang

    2014-07-01

    A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins.

  7. Improvement in photoconductor film properties by changing dielectric layer structures

    International Nuclear Information System (INIS)

    Kim, S; Oh, K; Lee, Y; Jung, J; Cho, G; Jang, G; Cha, B; Nam, S; Park, J

    2011-01-01

    In recent times, digital X-ray detectors have been actively applied to the medical field; for example, digital radiography offers the potential of improved image quality and provides opportunities for advances in medical image management, computer-aided diagnosis and teleradiology. In this study, two candidate materials (HgI 2 and PbI 2 ) have been employed to study the influence of the dielectric structure on the performance of fabricated X-ray photoconducting films. Parylene C with high permittivity was deposited as a dielectric layer using a parylene deposition system (PDS 2060). The structural and morphological properties of the samples were evaluated field emission scanning electron microscopy and X-ray diffraction. Further, to investigate improvements in the electrical characteristics, a dark current in the dark room and sensitivity to X-ray exposure in the energy range of general radiography diagnosis were measured across the range of the operating voltage. The electric signals varied with the dielectric layer structure of the X-ray films. The PbI 2 film with a bottom dielectric layer showed optimized electric properties. On the other hand, in the case of HgI 2 , the film with a top dielectric layer showed superior electric characteristics. Further, although the sensitivity of the film decreased, the total electrical efficiency of the film improved as a result of the decrease in dark current. When a dielectric layer is deposited on a photoconductor, the properties of the photoconductor, such as hole-electron mobility, should be considered to improve the image quality in digital medical imaging application. In this study, we have thus demonstrated that the use of dielectric layer structures improves the performance of photoconductors.

  8. Characterizing the Secondary Protein Structure of Black Widow Dragline Silk Using Solid-State NMR & X-ray Diffraction

    Science.gov (United States)

    Jenkins, Janelle E.; Sampath, Sujatha; Butler, Emily; Kim, Jihyun; Henning, Robert W.; Holland, Gregory P.; Yarger, Jeffery L.

    2013-01-01

    This study provides a detailed secondary structural characterization of major ampullate dragline silk from Latrodectus hesperus (black widow) spiders. X-ray diffraction results show that the structure of black widow major ampullate silk fibers is comprised of stacked β-sheet nanocrystallites oriented parallel to the fiber axis and an amorphous region with oriented (anisotropic) and isotropic components. The combination of two-dimensional (2D) 13C-13C through-space and through-bond solid-state NMR experiments provide chemical shifts that are used to determine detailed information about amino acid motif secondary structure in black widow spider dragline silk. Individual amino acids are incorporated into different repetitive motifs that make up the majority of this protein-based biopolymer. From the solid-state NMR measurements, we assign distinct secondary conformations to each repetitive amino acid motif and hence to the amino acids that make up the motifs. Specifically, alanine is incorporated in β-sheet (poly(Alan) and poly(Gly-Ala)), 31-helix (poly(Gly-Gly-Xaa), and α-helix (poly(Gln-Gln-Ala-Tyr)) components. Glycine is determined to be in β-sheet (poly(Gly-Ala)) and 31-helical (poly(Gly-Gly-Xaa)) regions, while serine is present in β-sheet (poly(Gly-Ala-Ser)), 31-helix (poly(Gly-Gly-Ser)), and β-turn (poly(Gly-Pro-Ser)) structures. These various motif-specific secondary structural elements are quantitatively correlated to the primary amino acid sequence of major ampullate spidroin 1 and 2 (MaSp1 and MaSp2) and are shown to form a self-consistent model for black widow dragline silk. PMID:24024617

  9. Financing Secondary Education in Kenya: Exploring Strategic Management Approach for Improving Quality of Education

    Science.gov (United States)

    Itegi, Florence M.

    2016-01-01

    The aim of this paper is to explore the influence of strategic planning in improving the quality of education. The quality of education is directly linked to the effort expended in making arrangements or preparations of educational objectives and determining the requisite resources to facilitate the training, instruction or study that leads to the…

  10. 78 FR 37528 - Agency Information Collection Activities; Comment Request; Elementary and Secondary Improvement...

    Science.gov (United States)

    2013-06-21

    ... State educational agency (SEA) application for the School Improvement Grants (SIG) program authorized... SEA must use to award FY 2013 SIG funds to local educational agencies (LEAs). In awarding these funds... their lowest-achieving schools that are eligible to receive services provided through SIG funds in order...

  11. Moving beyond the Barriers: Supporting Meaningful Teacher Collaboration to Improve Secondary School Mathematics

    Science.gov (United States)

    Jao, Limin; McDougall, Doug

    2016-01-01

    The Collaborative Teacher Inquiry Project was a professional development initiative that sought to improve the teaching and learning of Grade 9 Applied mathematics by encouraging teachers to work collaboratively. The project brought together Grade 9 Applied mathematics teachers from 11 schools across four neighboring public school boards in the…

  12. Transabdominal amnioinfusion for improving fetal outcomes after oligohydramnios secondary to preterm prelabour rupture of membranes before 26 weeks.

    Science.gov (United States)

    Van Teeffelen, Stijn; Pajkrt, Eva; Willekes, Christine; Van Kuijk, Sander M J; Mol, Ben Willem J

    2013-08-03

    Preterm prelabour rupture of membranes (PPROM) before 26 weeks can delay lung development and can cause pulmonary hypoplasia, as a result of oligohydramnios. Restoring the amniotic fluid volume by transabdominal amnioinfusion might prevent abnormal lung development and might have a protective effect for neurological complications, fetal deformities and neonatal sepsis. To assess the effectiveness of transabdominal amnioinfusion in improving perinatal outcome in women with oligohydramnios secondary to rupture of fetal membranes before 26 weeks. We searched the Cochrane Pregnancy and Childbirth Group's Trials Register (30 April 2013). All randomised controlled trials comparing transabdominal amnioinfusion with no transabdominal amnioinfusion. Cluster- or quasi-randomised trials were not eligible for inclusion. In cases where only an abstract was available, we attempted to find the full articles. Two review authors assessed trials for inclusion. No eligible trials were identified. There are no included studies. There is currently no evidence to evaluate the use of transabdominal amnioinfusion in women with oligohydramnios secondary to rupture of fetal membranes before 26 weeks for improving perinatal outcome. Further research examining the effects of this intervention is needed. Two randomised controlled trials are ongoing but final data have not yet been published.

  13. Improved Cathode Structure for a Direct Methanol Fuel Cell

    Science.gov (United States)

    Valdez, Thomas; Narayanan, Sekharipuram

    2005-01-01

    An improved cathode structure on a membrane/electrode assembly has been developed for a direct methanol fuel cell, in a continuing effort to realize practical power systems containing such fuel cells. This cathode structure is intended particularly to afford better cell performance at a low airflow rate. A membrane/electrode assembly of the type for which the improved cathode structure was developed (see Figure 1) is fabricated in a process that includes brush painting and spray coating of catalyst layers onto a polymer-electrolyte membrane and onto gas-diffusion backings that also act as current collectors. The aforementioned layers are then dried and hot-pressed together. When completed, the membrane/electrode assembly contains (1) an anode containing a fine metal black of Pt/Ru alloy, (2) a membrane made of Nafion 117 or equivalent (a perfluorosulfonic acid-based hydrophilic, proton-conducting ion-exchange polymer), (3) a cathode structure (in the present case, the improved cathode structure described below), and (4) the electrically conductive gas-diffusion backing layers, which are made of Toray 060(TradeMark)(or equivalent) carbon paper containing between 5 and 6 weight percent of poly(tetrafluoroethylene). The need for an improved cathode structure arises for the following reasons: In the design and operation of a fuel-cell power system, the airflow rate is a critical parameter that determines the overall efficiency, cell voltage, and power density. It is desirable to operate at a low airflow rate in order to obtain thermal and water balance and to minimize the size and mass of the system. The performances of membrane/electrode assemblies of prior design are limited at low airflow rates. Methanol crossover increases the required airflow rate. Hence, one way to reduce the required airflow rate is to reduce the effect of methanol crossover. Improvement of the cathode structure - in particular, addition of hydrophobic particles to the cathode - has been

  14. Improvement of a separation method for the reduction of secondary waste from the water-jet abrasive suspension cutting technique

    International Nuclear Information System (INIS)

    Brandauer, M.; Gentes, S.; Heneka, A.; Krauss, C.O.; Geckeis, H.; Plaschke, M.; Schild, D.; Tobie, W.

    2017-01-01

    microscopic analysis. In addition, the microscopic analyses showed that abrasive particles are considerably larger than steel particles. Therefore, the grade of separation is related to the particle size distribution. For this reason, a measurement device was installed to measure the particle size distribution during the separation process. Based on the particle size distribution a good estimate of the separation grade could be given during the separation process. However, further optimization and additional understanding of the separation process is still needed to improve the performance of the setup. This is the main goal of the subsequent project MASK ('Magnetic Separation of granular mixtures from water-jet cutting to minimize secondary waste from the decommissioning of nuclear facilities', funded by BMBF), i.e. the improvement of the separation grade. For this purpose, a numerical simulation of the fluid flow inside the magnetic filter unit will be performed. Furthermore, experimental studies using radioactive abrasive-steel grain mixtures are envisaged, to demonstrate the applicability of the method to real radioactive contaminated secondary waste. For this purpose, a small scale separation device for the use in a radioactive controlled area will be constructed and tested. In this presentation the MASK separation device and the experimental procedures will be explained. In addition, new results obtained with the NENAWAS separation device will be presented. (authors)

  15. Improved Stochastic Subspace System Identification for Structural Health Monitoring

    Science.gov (United States)

    Chang, Chia-Ming; Loh, Chin-Hsiung

    2015-07-01

    Structural health monitoring acquires structural information through numerous sensor measurements. Vibrational measurement data render the dynamic characteristics of structures to be extracted, in particular of the modal properties such as natural frequencies, damping, and mode shapes. The stochastic subspace system identification has been recognized as a power tool which can present a structure in the modal coordinates. To obtain qualitative identified data, this tool needs to spend computational expense on a large set of measurements. In study, a stochastic system identification framework is proposed to improve the efficiency and quality of the conventional stochastic subspace system identification. This framework includes 1) measured signal processing, 2) efficient space projection, 3) system order selection, and 4) modal property derivation. The measured signal processing employs the singular spectrum analysis algorithm to lower the noise components as well as to present a data set in a reduced dimension. The subspace is subsequently derived from the data set presented in a delayed coordinate. With the proposed order selection criteria, the number of structural modes is determined, resulting in the modal properties. This system identification framework is applied to a real-world bridge for exploring the feasibility in real-time applications. The results show that this improved system identification method significantly decreases computational time, while qualitative modal parameters are still attained.

  16. Improving rutting resistance of pavement structures using geosynthetics: an overview.

    Science.gov (United States)

    Mirzapour Mounes, Sina; Karim, Mohamed Rehan; Khodaii, Ali; Almasi, Mohammad Hadi

    2014-01-01

    A pavement structure consists of several layers for the primary purpose of transmitting and distributing traffic loads to the subgrade. Rutting is one form of pavement distresses that may influence the performance of road pavements. Geosynthetics is one type of synthetic materials utilized for improving the performance of pavements against rutting. Various studies have been conducted on using different geosynthetic materials in pavement structures by different researchers. One of the practices is a reinforcing material in asphalt pavements. This paper intends to present and discuss the discoveries from some of the studies on utilizing geosynthetics in flexible pavements as reinforcement against permanent deformation (rutting).

  17. Improving Rutting Resistance of Pavement Structures Using Geosynthetics: An Overview

    Directory of Open Access Journals (Sweden)

    Sina Mirzapour Mounes

    2014-01-01

    Full Text Available A pavement structure consists of several layers for the primary purpose of transmitting and distributing traffic loads to the subgrade. Rutting is one form of pavement distresses that may influence the performance of road pavements. Geosynthetics is one type of synthetic materials utilized for improving the performance of pavements against rutting. Various studies have been conducted on using different geosynthetic materials in pavement structures by different researchers. One of the practices is a reinforcing material in asphalt pavements. This paper intends to present and discuss the discoveries from some of the studies on utilizing geosynthetics in flexible pavements as reinforcement against permanent deformation (rutting.

  18. The Inclusion of Chitosan in Poly-ε-caprolactone Nanoparticles: Impact on the Delivery System Characteristics and on the Adsorbed Ovalbumin Secondary Structure.

    Science.gov (United States)

    Jesus, Sandra; Fragal, Elizangela H; Rubira, Adley F; Muniz, Edvani C; Valente, Artur J M; Borges, Olga

    2018-01-01

    This report extensively explores the benefits of including chitosan into poly-ε-caprolactone (PCL) nanoparticles (NPs) to obtain an improved protein/antigen delivery system. Blend NPs (PCL/chitosan NPs) showed improved protein adsorption efficacy (84%) in low shear stress and aqueous environment, suggesting that a synergistic effect between PCL hydrophobic nature and the positive charges of chitosan present at the particle surface was responsible for protein interaction. Additionally, thermal analysis suggested the blend NPs were more stable than the isolated polymers and cytotoxicity assays in a primary cell culture revealed chitosan inclusion in PCL NPs reduced the toxicity of the delivery system. A quantitative 6-month stability study showed that the inclusion of chitosan in PCL NPs did not induce a change in adsorbed ovalbumin (OVA) secondary structure characterized by the increase in the unordered conformation (random coil), as it was observed for OVA adsorbed to chitosan NPs. Additionally, the slight conformational changes occurred, are not expected to compromise ovalbumin secondary structure and activity, during a 6-month storage even at high temperatures (45°C). In simulated biological fluids, PCL/chitosan NPs showed an advantageous release profile for oral delivery. Overall, the combination of PCL and chitosan characteristics provide PCL/chitosan NPs valuable features particularly important to the development of vaccines for developing countries, where it is difficult to ensure cold chain transportation and non-parenteral formulations would be preferred.

  19. Time-of-flight secondary ion mass spectrometry with energetic cluster ion impact ionization for highly sensitive chemical structure characterization

    Energy Technology Data Exchange (ETDEWEB)

    Hirata, K., E-mail: k.hirata@aist.go.jp [National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565 (Japan); Saitoh, Y.; Chiba, A.; Yamada, K.; Narumi, K. [Takasaki Advanced Radiation Research Institute (TARRI), Japan Atomic Energy Agency (JAEA), Takasaki, Gumma 370-1292 (Japan)

    2013-11-01

    Energetic cluster ions with energies of the order of sub MeV or greater were applied to time-of-flight (TOF) secondary ion (SI) mass spectrometry. This gave various advantages including enhancement of SIs required for chemical structure characterization and prevention of charging effects in SI mass spectra for organic targets. We report some characteristic features of TOF SI mass spectrometry using energetic cluster ion impact ionization and discuss two future applications of it.

  20. Application of secondary and residual stresses to the assessment of the structural integrity of nuclear power-generating plant

    International Nuclear Information System (INIS)

    Banahan, B.D.

    2008-01-01

    the perceived structural integrity. Finally, the future requirements for the residual stresses to be incorporated into structural integrity assessments of ferritic steel nuclear power plant components and structures will be discussed. This will be by reference to various weldment geometries and heat treatment cycles including repair welds and fillet attachment welds. In particular, there is a need for improved measurement techniques and analytical/computer models to provide more realistic three-dimensional stress distributions for a range of weldment geometries. In addition, there is a need to revisit the criteria adopted to establish the initiation fracture toughness of ductile ferritic steels with respect to the attendant redistribution of residual stresses

  1. Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

    Directory of Open Access Journals (Sweden)

    Uzilov Andrew V

    2006-03-01

    Full Text Available Abstract Background Non-coding RNAs (ncRNAs have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical screens. To advance biological knowledge, computational methods that can accurately detect ncRNAs in sequenced genomes are therefore desirable. The increasing number of genomic sequences provides a rich dataset for computational comparative sequence analysis and detection of novel ncRNAs. Results Here, Dynalign, a program for predicting secondary structures common to two RNA sequences on the basis of minimizing folding free energy change, is utilized as a computational ncRNA detection tool. The Dynalign-computed optimal total free energy change, which scores the structural alignment and the free energy change of folding into a common structure for two RNA sequences, is shown to be an effective measure for distinguishing ncRNA from randomized sequences. To make the classification as a ncRNA, the total free energy change of an input sequence pair can either be compared with the total free energy changes of a set of control sequence pairs, or be used in combination with sequence length and nucleotide frequencies as input to a classification support vector machine. The latter method is much faster, but slightly less sensitive at a given specificity. Additionally, the classification support vector machine method is shown to be sensitive and specific on genomic ncRNA screens of two different Escherichia coli and Salmonella typhi genome alignments, in which many ncRNAs are known. The Dynalign computational experiments are also compared with two other ncRNA detection programs, RNAz and QRNA. Conclusion The Dynalign-based support vector machine method is more sensitive for known ncRNAs in the test genomic screens than RNAz and QRNA. Additionally, both Dynalign-based methods are more sensitive than RNAz and QRNA at low sequence pair identities. Dynalign can be used as a

  2. CONFOLD2: improved contact-driven ab initio protein structure modeling.

    Science.gov (United States)

    Adhikari, Badri; Cheng, Jianlin

    2018-01-25

    Contact-guided protein structure prediction methods are becoming more and more successful because of the latest advances in residue-residue contact prediction. To support contact-driven structure prediction, effective tools that can quickly build tertiary structural models of good quality from predicted contacts need to be developed. We develop an improved contact-driven protein modelling method, CONFOLD2, and study how it may be effectively used for ab initio protein structure prediction with predicted contacts as input. It builds models using various subsets of input contacts to explore the fold space under the guidance of a soft square energy function, and then clusters the models to obtain the top five models. CONFOLD2 obtains an average reconstruction accuracy of 0.57 TM-score for the 150 proteins in the PSICOV contact prediction dataset. When benchmarked on the CASP11 contacts predicted using CONSIP2 and CASP12 contacts predicted using Raptor-X, CONFOLD2 achieves a mean TM-score of 0.41 on both datasets. CONFOLD2 allows to quickly generate top five structural models for a protein sequence when its secondary structures and contacts predictions at hand. The source code of CONFOLD2 is publicly available at https://github.com/multicom-toolbox/CONFOLD2/ .

  3. Status of Credentialing Structures Related to Secondary Transition: A State-Level Policy Analysis

    Science.gov (United States)

    Simonsen, Monica L.; Novak, Jeanne A.; Mazzotti, Valerie L.

    2018-01-01

    To understand the current status of transition-related credentialing systems in driving personnel preparation, it is necessary to identify which state education and rehabilitation services agencies are currently providing certification and licensure in the area of secondary transition. The purpose of this study was to examine the current state of…

  4. Does Family Structure Matter? Comparing the Life Goals and Aspirations of Learners in Secondary Schools

    Science.gov (United States)

    Davids, Eugene Lee; Roman, Nicolette Vanessa

    2013-01-01

    The aim of this study was to compare the goals and aspirations of learners from single- and two-parent families. The study used a quantitative methodology with a cross-sectional comparative group design. The sample consisted of 853 Grade 11 learners from secondary schools in the Northern, Southern and Metro Central education districts in the…

  5. Plant secondary metabolite-induced shifts in bacterial community structure and degradative ability in contaminated soil

    Czech Academy of Sciences Publication Activity Database

    Uhlík, O.; Musilová, L.; Rídl, Jakub; Hroudová, Miluše; Vlček, Čestmír; Koubek, J.; Holečková, M.; Mackova, M.; Macek, T.

    2013-01-01

    Roč. 97, č. 20 (2013), s. 9245-9256 ISSN 0175-7598 Grant - others:EK(XE) 265946; GA MŠk(CZ) ME10041 Institutional support: RVO:68378050 Keywords : plant secondary metabolites (PSM) * bacterial community * metabolic activity * bioremediation * pyrosequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.811, year: 2013

  6. Improving the representation of secondary organic aerosol (SOA in the MOZART-4 global chemical transport model

    Directory of Open Access Journals (Sweden)

    A. Mahmud

    2013-07-01

    Full Text Available The secondary organic aerosol (SOA module in the Model for Ozone and Related Chemical Tracers, version 4 (MOZART-4 was updated by replacing existing two-product (2p parameters with those obtained from two-product volatility basis set (2p-VBS fits (MZ4-C1, and by treating SOA formation from the following additional volatile organic compounds (VOCs: isoprene, propene and lumped alkenes (MZ4-C2. Strong seasonal and spatial variations in global SOA distributions were demonstrated, with significant differences in the predicted concentrations between the base case and updated model simulations. Updates to the model resulted in significant increases in annual average SOA mass concentrations, particularly for the MZ4-C2 simulation in which the additional SOA precursor VOCs were treated. Annual average SOA concentrations predicted by the MZ4-C2 simulation were 1.00 ± 1.04 μg m−3 in South America, 1.57 ± 1.88 μg m−3 in Indonesia, 0.37 ± 0.27 μg m−3 in the USA, and 0.47 ± 0.29 μg m−3 in Europe with corresponding increases of 178, 406, 311 and 292% over the base-case simulation, respectively, primarily due to inclusion of isoprene. The increases in predicted SOA mass concentrations resulted in corresponding increases in SOA contributions to annual average total aerosol optical depth (AOD by ~ 1–6%. Estimated global SOA production was 5.8, 6.6 and 19.1 Tg yr−1 with corresponding burdens of 0.22, 0.24 and 0.59 Tg for the base-case, MZ4-C1 and MZ4-C2 simulations, respectively. The predicted SOA budgets fell well within reported ranges for comparable modeling studies, 6.7 to 96 Tg yr−1, but were lower than recently reported observationally constrained values, 50 to 380 Tg yr−1. For MZ4-C2, simulated SOA concentrations at the surface also were in reasonable agreement with comparable modeling studies and observations. Total organic aerosol (OA mass concentrations at the surface, however, were slightly over-predicted in Europe, Amazonian

  7. The secondary structure of large-subunit rRNA divergent domains, a marker for protist evolution

    DEFF Research Database (Denmark)

    Lenaers, G; Nielsen, Henrik; Engberg, J

    1988-01-01

    The secondary structure of the large-subunit ribosomal RNA (24-26S rRNA) has been studied with emphasis on comparative analysis of the folding patterns of the divergent domains in the available protist sequences, that is Prorocentrum micans (dinoflagellate), Saccharomyces carlsbergensis (yeast......), Tetrahymena thermophila (ciliate), Physarum polycephalum and Dictyostelium discoideum (slime moulds), Crithidia fasciculata and Giardia lamblia (parasitic flagellates). The folding for the D3, D7a and D10 divergent domains has been refined and a consensus model for the protist 24-26S rRNA structure...

  8. Structured reporting platform improves CAD-RADS assessment.

    Science.gov (United States)

    Szilveszter, Bálint; Kolossváry, Márton; Karády, Júlia; Jermendy, Ádám L; Károlyi, Mihály; Panajotu, Alexisz; Bagyura, Zsolt; Vecsey-Nagy, Milán; Cury, Ricardo C; Leipsic, Jonathon A; Merkely, Béla; Maurovich-Horvat, Pál

    2017-11-01

    Structured reporting in cardiac imaging is strongly encouraged to improve quality through consistency. The Coronary Artery Disease - Reporting and Data System (CAD-RADS) was recently introduced to facilitate interdisciplinary communication of coronary CT angiography (CTA) results. We aimed to assess the agreement between manual and automated CAD-RADS classification using a structured reporting platform. Five readers prospectively interpreted 500 coronary CT angiographies using a structured reporting platform that automatically calculates the CAD-RADS score based on stenosis and plaque parameters manually entered by the reader. In addition, all readers manually assessed CAD-RADS blinded to the automatically derived results, which was used as the reference standard. We evaluated factors influencing reader performance including CAD-RADS training, clinical load, time of the day and level of expertise. Total agreement between manual and automated classification was 80.2%. Agreement in stenosis categories was 86.7%, whereas the agreement in modifiers was 95.8% for "N", 96.8% for "S", 95.6% for "V" and 99.4% for "G". Agreement for V improved after CAD-RADS training (p = 0.047). Time of the day and clinical load did not influence reader performance (p > 0.05 both). Less experienced readers had a higher total agreement as compared to more experienced readers (87.0% vs 78.0%, respectively; p = 0.011). Even though automated CAD-RADS classification uses data filled in by the readers, it outperforms manual classification by preventing human errors. Structured reporting platforms with automated calculation of the CAD-RADS score might improve data quality and support standardization of clinical decision making. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Techniques for improving material fidelity and contrast consistency in secondary electron mode helium ion microscope (HIM) imaging

    Science.gov (United States)

    Thompson, William; Stern, Lewis; Ferranti, Dave; Huynh, Chuong; Scipioni, Larry; Notte, John; Sanford, Colin

    2010-06-01

    Recent helium ion microscope (HIM) imaging studies have shown the strong sensitivity of HIM induced secondary electron (SE) yields [1] to the sample physical and chemical properties and to its surface topography. This SE yield sensitivity is due to the low recoil energy of the HIM initiated electrons and their resulting short mean free path. Additionally, a material's SE escape probability is modulated by changes in the material's work function and surface potential. Due to the escape electrons' roughly 2eV mean energy and their nanometer range mean free path, HIM SE mode image contrast has significant material and surface sensitivity. The latest generation of HIM has a 0.35 nanometer resolution specification and is equipped with a plasma cleaning process to mitigate the effects of hydrocarbon contamination. However, for surfaces that may have native oxide chemistries influencing the secondary electron yield, a new process of low energy, shallow angle argon sputtering, was evaluated. The intent of this work was to study the effect of removing pre-existing native oxides and any in-situ deposited surface contaminants. We will introduce the sputter yield predictions of two established computer models and the sputter yield and sample modification forecasts of the molecular dynamics program, Kalypso. We will review the experimental technique applied to copper samples and show the copper grain contrast improvement that resulted when argon cleaned samples were imaged in HIM SE mode.

  10. Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

    Science.gov (United States)

    Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y F; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie; Martin, Darren Patrick

    2014-02-01

    Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.

  11. Quantitation of base substitutions in eukaryotic 5S rRNA: selection for the maintenance of RNA secondary structure.

    Science.gov (United States)

    Curtiss, W C; Vournakis, J N

    1984-01-01

    Eukaryotic 5S rRNA sequences from 34 diverse species were compared by the following method: (1) The sequences were aligned; (2) the positions of substitutions were located by comparison of all possible pairs of sequences; (3) the substitution sites were mapped to an assumed general base pairing model; and (4) the R-Y model of base stacking was used to study stacking pattern relationships in the structure. An analysis of the sequence and structure variability in each region of the molecule is presented. It was found that the degree of base substitution varies over a wide range, from absolute conservation to occurrence of over 90% of the possible observable substitutions. The substitutions are located primarily in stem regions of the 5S rRNA secondary structure. More than 88% of the substitutions in helical regions maintain base pairing. The disruptive substitutions are primarily located at the edges of helical regions, resulting in shortening of the helical regions and lengthening of the adjacent nonpaired regions. Base stacking patterns determined by the R-Y model are mapped onto the general secondary structure. Intrastrand and interstrand stacking could stabilize alternative coaxial structures and limit the conformational flexibility of nonpaired regions. Two short contiguous regions are 100% conserved in all species. This may reflect evolutionary constraints imposed at the DNA level by the requirement for binding of a 5S gene transcription initiation factor during gene expression.

  12. Framework for Structural Online Health Monitoring of Aging and Degradation of Secondary Systems due to some Aspects of Erosion

    Energy Technology Data Exchange (ETDEWEB)

    Gribok, Andrei [Idaho National Lab. (INL), Idaho Falls, ID (United States); Patnaik, Sobhan [Idaho National Lab. (INL), Idaho Falls, ID (United States); Williams, Christian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Pattanaik, Marut [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kanakala, Raghunath [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2016-09-01

    This report describes the current state of research related to critical aspects of erosion and selected aspects of degradation of secondary components in nuclear power plants. The report also proposes a framework for online health monitoring of aging and degradation of secondary components. The framework consists of an integrated multi-sensor modality system which can be used to monitor different piping configurations under different degradation conditions. The report analyses the currently known degradation mechanisms and available predictive models. Based on this analysis, the structural health monitoring framework is proposed. The Light Water Reactor Sustainability Program began to evaluate technologies that could be used to perform online monitoring of piping and other secondary system structural components in commercial NPPs. These online monitoring systems have the potential to identify when a more detailed inspection is needed using real-time measurements, rather than at a pre-determined inspection interval. This transition to condition-based, risk informed automated maintenance will contribute to a significant reduction of operations and maintenance costs that account for the majority of nuclear power generation costs. There is unanimous agreement between industry experts and academic researchers that identifying and prioritizing inspection locations in secondary piping systems (for example, in raw water piping or diesel piping) would eliminate many excessive in-service inspections. The proposed structural health monitoring framework takes aim at answering this challenge by combining long-range guided wave technologies with other monitoring techniques, which can significantly increase the inspection length and pinpoint the locations that degraded the most. More widely, the report suggests research efforts aimed at developing, validating, and deploying online corrosion monitoring techniques for complex geometries, which are pervasive in NPPs.

  13. Framework for Structural Online Health Monitoring of Aging and Degradation of Secondary Systems due to some Aspects of Erosion

    International Nuclear Information System (INIS)

    Gribok, Andrei; Patnaik, Sobhan; Williams, Christian; Pattanaik, Marut; Kanakala, Raghunath

    2016-01-01

    This report describes the current state of research related to critical aspects of erosion and selected aspects of degradation of secondary components in nuclear power plants. The report also proposes a framework for online health monitoring of aging and degradation of secondary components. The framework consists of an integrated multi-sensor modality system which can be used to monitor different piping configurations under different degradation conditions. The report analyses the currently known degradation mechanisms and available predictive models. Based on this analysis, the structural health monitoring framework is proposed. The Light Water Reactor Sustainability Program began to evaluate technologies that could be used to perform online monitoring of piping and other secondary system structural components in commercial NPPs. These online monitoring systems have the potential to identify when a more detailed inspection is needed using real-time measurements, rather than at a pre-determined inspection interval. This transition to condition-based, risk informed automated maintenance will contribute to a significant reduction of operations and maintenance costs that account for the majority of nuclear power generation costs. There is unanimous agreement between industry experts and academic researchers that identifying and prioritizing inspection locations in secondary piping systems (for example, in raw water piping or diesel piping) would eliminate many excessive in-service inspections. The proposed structural health monitoring framework takes aim at answering this challenge by combining long-range guided wave technologies with other monitoring techniques, which can significantly increase the inspection length and pinpoint the locations that degraded the most. More widely, the report suggests research efforts aimed at developing, validating, and deploying online corrosion monitoring techniques for complex geometries, which are pervasive in NPPs.

  14. Predictors of improvement in sexual function of women with urinary incontinence after treatment with pelvic floor exercises: a secondary analysis.

    Science.gov (United States)

    Sacomori, Cinara; Cardoso, Fernando Luiz

    2015-03-01

    Women with urinary incontinence (UI) frequently present with complaints of sexual problems. To evaluate the predictors of sexual function improvement after participating in three physical therapy sessions and performing home-based pelvic floor muscle exercises (PFME) for the treatment of female UI. This is a secondary analysis of a randomized trial with a 3-month follow-up in which the sexual function of 54 women with UI was evaluated. These women joined three supervised physiotherapy sessions that included PFME and health education during 1 month, with a 15-day interval between each session, and kept practicing home-based PFME for a further 2 months. Sexual function was assessed using the Female Sexual Quotient, the pelvic floor muscle strength was measured using the modified Oxford scale, and UI was assessed using the International Consultation on Incontinence Questionnaire. The mean of sexual quotient score improved after treatment (P = 0.001). With respect to specific domains of sexual function, improvement was observed only in the questions about sexual desire, arousal/excitement, and orgasm. Before treatment, 18 women (33.3%) were classified as having sexual dysfunction, and after treatment, eight remained with sexual dysfunction and two other joined this category (total of 18.5%). Those women who had sexual dysfunction at baseline experienced a higher level of improvement of the sexual quotient compared with those without sexual dysfunction (P = 0.001, 95% CI = 9.1-31.9). A multivariate linear regression with backward elimination revealed the following predictors of improvement of the sexual quotient: higher parity, higher adherence to PFME, improvement in the strength of PFM, and a decrease in the frequency of urine leakage (R(2)  = 0.497). PFME was more beneficial with regard to sexual function in those women who presented with sexual dysfunction at baseline. © 2015 International Society for Sexual Medicine.

  15. Improvement of Corrosion Inhibitors of Primary and Secondary Closed Cooling Water System

    International Nuclear Information System (INIS)

    Choi, Byung Seon; Kim, K. M.; Kim, K. H.

    2010-08-01

    In nuclear power plants, the Closed Cooling Water (CCW) system provide cooling to both safety-related and non-safety-related heat exchange equipment. Various chemicals are used to mitigate corrosion, fouling, and microbiological growth in the CCW systems. In nuclear plants, these inhibitors have included chromates, nitrites, molybdates, hydrazine, and silicate. In the case of the CCW of some domestic nuclear power plants, there is during the overhaul period, a saturation of ion exchange resin caused by an inhibitor which has high conductivity for an increase in radiation exposure and radioactive waste. The objective of this study is to evaluate the corrosion behavior of structural materials with various corrosion inhibitors. In the present study, more than 50 ppm hydrazine concentration is needed to reduce the corrosion rate of carbon steel to satisfy the CCW operational guidelines. However, if hydrazine is continuously injected into the CCW system, the critical concentration of hydrazine will be lower. Hydrazine might be an alternative corrosion inhibitor for nitrite in the CCW system of nuclear power plant

  16. Never Too Late: Approaches to Reading Instruction for Secondary Students with Disabilities. Research to Practice Brief: Improving Secondary Education and Transition Services through Research.

    Science.gov (United States)

    Clapper, Ann T.; Bremer, Christine D.; Kachgal, Mera M.

    This research brief discusses two reading instruction models for teaching secondary school students with disabilities. The first, Collaborative Strategic Reading (CSR), is designed specifically for students with learning disabilities and students who are at risk of reading failure. This strategy adapts reciprocal reading and incorporates…

  17. Effectiveness of Oral Proficiency in English for Secondary Schools (OPS-English) Programme in Improving English Language Vocabulary among Secondary School Students

    Science.gov (United States)

    Singh, Manesha Kaur Rajendra; Singh, Manjet Kaur Mehar; Eng, Lin Siew

    2015-01-01

    Speaking is an important skill that needs to be mastered as it is the best way to communicate with other people in order to deliver opinions and express ideas, but the fact is that secondary school students' ability in speaking English is low in Malaysia. It is caused by several factors such as lack of vocabulary, poor pronunciation, weak grammar…

  18. Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

    Directory of Open Access Journals (Sweden)

    Leitner Dietmar

    2005-04-01

    Full Text Available Abstract Background A reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods. We have analyzed the Protein Data Bank and show that the combined use of sequential and structural information has a predictive value for the assessment of the cis versus trans peptide bond conformation of Xaa-Pro within proteins. For the analysis of the data sets different statistical methods such as the calculation of the Chou-Fasman parameters and occurrence matrices were used. Furthermore we analyzed the relationship between the relative solvent accessibility and the relative occurrence of prolines in the cis and in the trans conformation. Results One of the main results of the statistical investigations is the ranking of the secondary structure and sequence information with respect to the prediction of the Xaa-Pro peptide bond conformation. We observed a significant impact of secondary structure information on the occurrence of the Xaa-Pro peptide bond conformation, while the sequence information of amino acids neighboring proline is of little predictive value for the conformation of this bond. Conclusion In this work, we present an extensive analysis of the occurrence of the cis and trans proline conformation in proteins. Based on the data set, we derived patterns and rules for a possible prediction of the proline conformation. Upon adoption of the Chou-Fasman parameters, we are able to derive statistically relevant correlations between the secondary structure of amino acid fragments and the Xaa-Pro peptide bond conformation.

  19. Improved Method for In Vitro Secondary Amastigogenesis of Trypanosoma cruzi: Morphometrical and Molecular Analysis of Intermediate Developmental Forms

    Directory of Open Access Journals (Sweden)

    L. A. Hernández-Osorio

    2010-01-01

    Full Text Available Trypanosoma cruzi undergoes a biphasic life cycle that consists of four alternate developmental stages. In vitro conditions to obtain a synchronic transformation and efficient rates of pure intermediate forms (IFs, which are indispensable for further biochemical, biological, and molecular studies, have not been reported. In the present study, we established an improved method to obtain IFs from secondary amastigogenesis. During the transformation kinetics, we observed progressive decreases in the size of the parasite body, undulating membrane and flagellum that were concomitant with nucleus remodeling and kinetoplast displacement. In addition, a gradual reduction in parasite movement and acquisition of the amastigote-specific Ssp4 antigen were observed. Therefore, our results showed that the in vitro conditions used obtained large quantities of highly synchronous and pure IFs that were clearly distinguished by morphometrical and molecular analyses. Obtaining these IFs represents the first step towards an understanding of the molecular mechanisms involved in amastigogenesis.

  20. Glucose administration after traumatic brain injury improves cerebral metabolism and reduces secondary neuronal injury.

    Science.gov (United States)

    Moro, Nobuhiro; Ghavim, Sima; Harris, Neil G; Hovda, David A; Sutton, Richard L

    2013-10-16

    Clinical studies have indicated an association between acute hyperglycemia and poor outcomes in patients with traumatic brain injury (TBI), although optimal blood glucose levels needed to maximize outcomes for these patients' remain under investigation. Previous results from experimental animal models suggest that post-TBI hyperglycemia may be harmful, neutral, or beneficial. The current studies determined the effects of single or multiple episodes of acute hyperglycemia on cerebral glucose metabolism and neuronal injury in a rodent model of unilateral controlled cortical impact (CCI) injury. In Experiment 1, a single episode of hyperglycemia (50% glucose at 2 g/kg, i.p.) initiated immediately after CCI was found to significantly attenuate a TBI-induced depression of glucose metabolism in cerebral cortex (4 of 6 regions) and subcortical regions (2 of 7) as well as to significantly reduce the number of dead/dying neurons in cortex and hippocampus at 24 h post-CCI. Experiment 2 examined effects of more prolonged and intermittent hyperglycemia induced by glucose administrations (2 g/kg, i.p.) at 0, 1, 3 and 6h post-CCI. The latter study also found significantly improved cerebral metabolism (in 3 of 6 cortical and 3 of 7 subcortical regions) and significant neuroprotection in cortex and hippocampus 1 day after CCI and glucose administration. These results indicate that acute episodes of post-TBI hyperglycemia can be beneficial and are consistent with other recent studies showing benefits of providing exogenous energy substrates during periods of increased cerebral metabolic demand. © 2013 Elsevier B.V. All rights reserved.

  1. A new online secondary path modeling method for adaptive active structure vibration control

    International Nuclear Information System (INIS)

    Pu, Yuxue; Zhang, Fang; Jiang, Jinhui

    2014-01-01

    This paper proposes a new variable step size FXLMS algorithm with an auxiliary noise power scheduling strategy for online secondary path modeling. The step size for the secondary path modeling filter and the gain of auxiliary noise are varied in accordance with the parameters available directly. The proposed method has a low computational complexity. Computer simulations show that an active vibration control system with the proposed method gives much better vibration attenuation and modeling accuracy at a faster convergence rate than existing methods. National Instruments’ CompactRIO is used as an embedded processor to control simply supported beam vibration. Experimental results indicate that the vibration of the beam has been effectively attenuated. (papers)

  2. Improvements of knowledge and perception towards HIV/AIDS among secondary school students after two hours talk.

    Science.gov (United States)

    Jahanfar, S; Lim, A W; Loh, M A; Yeoh, A G; Charles, A

    2008-10-01

    Malaysia is confronted with an increasing incidence of HIV and AIDS among adolescents and young adults. The effectiveness of various programs offered to school going teenagers is unknown. The objective of this study is to measure the effectiveness of two hours talk on sex education offered by a non governmental organization (NGO) in improving youngsters' knowledge and perception towards HIV and AIDS. A cross sectional study was conducted among the adolescent students from a secondary school in Ipoh, Perak, a province of Malaysia. A total of 182 students participated in the study. A standard questionnaire consisting of demographic data, knowledge and perception towards HIV/ADIS were distributed before (pre-test) and after the intervention (post-test). Performance of participants was compared to establish the effectiveness of the intervention. Our findings suggests that there was a significant increase in participants' knowledge and perception after the intervention (p = 0.000). Knowledge improvement was found in both genders however, improvement in perception was higher among female students. Interestingly, 80% of participants disagree that sexual education will encourage sex among youngsters. NGOs are playing a supplementary role in providing sex education programs in schools. This program although of short duration but it is effective in enhancing adolescence awareness about HIV/AIDS.

  3. Structure and reactivity of boron-ate complexes derived from primary and secondary boronic esters.

    Science.gov (United States)

    Feeney, Kathryn; Berionni, Guillaume; Mayr, Herbert; Aggarwal, Varinder K

    2015-06-05

    Boron-ate complexes derived from primary and secondary boronic esters and aryllithiums have been isolated, and the kinetics of their reactions with carbenium ions studied. The second-order rate constants have been used to derive nucleophilicity parameters for the boron-ate complexes, revealing that nucleophilicity increased with (i) electron-donating aromatics on boron, (ii) neopentyl glycol over pinacol boronic esters, and (iii) 12-crown-4 ether.

  4. Secondary Plant Products Causing Photosensitization in Grazing Herbivores: Their Structure, Activity and Regulation

    Directory of Open Access Journals (Sweden)

    Jane C. Quinn

    2014-01-01

    Full Text Available Photosensitivity in animals is defined as a severe dermatitis that results from a heightened reactivity of skin cells and associated dermal tissues upon their exposure to sunlight, following ingestion or contact with UV reactive secondary plant products. Photosensitivity occurs in animal cells as a reaction that is mediated by a light absorbing molecule, specifically in this case a plant-produced metabolite that is heterocyclic or polyphenolic. In sensitive animals, this reaction is most severe in non-pigmented skin which has the least protection from UV or visible light exposure. Photosensitization in a biological system such as the epidermis is an oxidative or other chemical change in a molecule in response to light-induced excitation of endogenous or exogenously-delivered molecules within the tissue. Photo-oxidation can also occur in the plant itself, resulting in the generation of reactive oxygen species, free radical damage and eventual DNA degradation. Similar cellular changes occur in affected herbivores and are associated with an accumulation of photodynamic molecules in the affected dermal tissues or circulatory system of the herbivore. Recent advances in our ability to identify and detect secondary products at trace levels in the plant and surrounding environment, or in organisms that ingest plants, have provided additional evidence for the role of secondary metabolites in photosensitization of grazing herbivores. This review outlines the role of unique secondary products produced by higher plants in the animal photosensitization process, describes their chemistry and localization in the plant as well as impacts of the environment upon their production, discusses their direct and indirect effects on associated animal systems and presents several examples of well-characterized plant photosensitization in animal systems.

  5. Application of nonlinear rheology to assess the effect of secondary nanofiller on network structure of hybrid polymer nanocomposites

    Science.gov (United States)

    Kamkar, Milad; Aliabadian, Ehsan; Shayesteh Zeraati, Ali; Sundararaj, Uttandaraman

    2018-02-01

    Carbon nanotube (CNT)/polymer nanocomposites exhibit excellent electrical properties by forming a percolated network. Adding a secondary filler can significantly affect the CNTs' network, resulting in changing the electrical properties. In this work, we investigated the effect of adding manganese dioxide nanowires (MnO2NWs) as a secondary nanofiller on the CNTs' network structure inside a poly(vinylidene fluoride) (PVDF) matrix. Incorporating MnO2NWs to PVDF/CNT samples produced a better state of dispersion of CNTs, as corroborated by light microscopy and transmission electron microscopy. The steady shear and oscillatory shear flows were employed to obtain a better insight into the nanofiller structure and viscoelastic behavior of the nanocomposites. The transient response under steady shear flow revealed that the stress overshoot of hybrid nanocomposites (two-fillers), PVDF/CNT/MnO2NWs, increased dramatically in comparison to binary nanocomposites (single-filler), PVDF/CNT and PVDF/MnO2NWs. This can be attributed to microstructural changes. Large amplitude oscillatory shear characterization was also performed to further investigate the effect of the secondary nanofiller on the nonlinear viscoelastic behavior of the samples. The nonlinear rheological observations were explained using quantitative nonlinear parameters [strain-stiffening ratio (S) and shear-thickening ratio (T)] and Lissajous-Bowditch plots. Results indicated that a more rigid nanofiller network was formed for the hybrid nanocomposites due to the better dispersion state of CNTs and this led to a more nonlinear viscoelastic behavior.

  6. Improving the Dynamic Characteristics of Body-in-White Structure Using Structural Optimization

    Directory of Open Access Journals (Sweden)

    Aizzat S. Yahaya Rashid

    2014-01-01

    Full Text Available The dynamic behavior of a body-in-white (BIW structure has significant influence on the noise, vibration, and harshness (NVH and crashworthiness of a car. Therefore, by improving the dynamic characteristics of BIW, problems and failures associated with resonance and fatigue can be prevented. The design objectives attempt to improve the existing torsion and bending modes by using structural optimization subjected to dynamic load without compromising other factors such as mass and stiffness of the structure. The natural frequency of the design was modified by identifying and reinforcing the structure at critical locations. These crucial points are first identified by topology optimization using mass and natural frequencies as the design variables. The individual components obtained from the analysis go through a size optimization step to find their target thickness of the structure. The thickness of affected regions of the components will be modified according to the analysis. The results of both optimization steps suggest several design modifications to achieve the target vibration specifications without compromising the stiffness of the structure. A method of combining both optimization approaches is proposed to improve the design modification process.

  7. Improving Intervention Decisions to Prevent Genocide: Less Muddle, More Structure

    Directory of Open Access Journals (Sweden)

    Robin Gregory

    2018-03-01

    Full Text Available Decisions to intervene in a foreign country to prevent genocide and mass atrocities are among the most challenging and controversial choices facing national leaders. Drawing on techniques from decision analysis, psychology, and negotiation analysis, we propose a structured approach to these difficult choices that can provide policy makers with additional insight, consistency, efficiency, and defensibility. We propose the use of a values-based framework to clarify the key elements of these complex choices and to provide a consistent structure for comparison of the likely benefits, risks, and tradeoffs associated with alternative intervention strategies. Results from a workshop involving Ambassadors and experienced policy makers provide a first test of this new method for clarifying intervention choices. A decision-aiding framework is shown to improve the clarity and relevance of intervention deliberations, laying the groundwork for a more comprehensive and clearer understanding of the threats and opportunities associated with various intervention options.

  8. On the secondary charging effects and structure of mesospheric dust particles impacting on rocket probes

    Directory of Open Access Journals (Sweden)

    O. Havnes

    2007-03-01

    Full Text Available The dust probe DUSTY, first launched during the summer of 1994 (flights ECT–02 and ECT–07 from Andøya Rocket Range, northern Norway, was the first probe to unambiguously detect heavy charged mesospheric aerosols, from hereon referred to as dust. In ECT–02 the probe detected negatively charged dust particles in the height interval of 83 to 88.5 km. In this flight, the lower grid in the detector (Grid 2 measures both positive and negative currents in various regions, and we find that the relationship between the current measurements of Grid 2 and the bottom plate can only be explained by influence from secondary charge production on Grid 2. In ECT–07, which had a large coning, positive currents reaching the top grid of the probe were interpreted as due to the impact of positively charged dust particles. We have now reanalyzed the data from ECT–07 and arrived at the conclusion that the measured positive currents to this grid must have been mainly due to secondary charging effects from the impacting dust particles. The grid consists of a set of parallel wires crossed with an identical set of wires on top of it, and we find that if the observed currents were created from the direct impact of charged dust particles, then they should be very weakly modulated at four times the rocket spin rate ωR. Observations show, however, that the observed currents are strongly modulated at 2ωR. We cannot reproduce the observed large modulations of the impact currents in the dust layer if the currents are due only to the transfer of the charges on the impacted dust particles. Based on the results of recent ice cluster impact secondary charging experiments by Tomsic (2003, which found that a small fraction of the ice clusters, when impacting with nearly grazing incidence, carried away one negative charge −1e, we have arrived at the conclusion that similar, but significantly more effective, charging effects must be predominantly responsible for the

  9. On the secondary charging effects and structure of mesospheric dust particles impacting on rocket probes

    Directory of Open Access Journals (Sweden)

    O. Havnes

    2007-03-01

    Full Text Available The dust probe DUSTY, first launched during the summer of 1994 (flights ECT–02 and ECT–07 from Andøya Rocket Range, northern Norway, was the first probe to unambiguously detect heavy charged mesospheric aerosols, from hereon referred to as dust. In ECT–02 the probe detected negatively charged dust particles in the height interval of 83 to 88.5 km. In this flight, the lower grid in the detector (Grid 2 measures both positive and negative currents in various regions, and we find that the relationship between the current measurements of Grid 2 and the bottom plate can only be explained by influence from secondary charge production on Grid 2. In ECT–07, which had a large coning, positive currents reaching the top grid of the probe were interpreted as due to the impact of positively charged dust particles. We have now reanalyzed the data from ECT–07 and arrived at the conclusion that the measured positive currents to this grid must have been mainly due to secondary charging effects from the impacting dust particles. The grid consists of a set of parallel wires crossed with an identical set of wires on top of it, and we find that if the observed currents were created from the direct impact of charged dust particles, then they should be very weakly modulated at four times the rocket spin rate ωR. Observations show, however, that the observed currents are strongly modulated at 2ωR. We cannot reproduce the observed large modulations of the impact currents in the dust layer if the currents are due only to the transfer of the charges on the impacted dust particles. Based on the results of recent ice cluster impact secondary charging experiments by Tomsic (2003, which found that a small fraction of the ice clusters, when impacting with nearly grazing incidence, carried away one negative charge −1e, we have arrived at the conclusion that similar, but significantly more effective, charging effects must

  10. Gasket structure improvement for the spent fuel pool cooler

    International Nuclear Information System (INIS)

    Li Yun; He Shaohua; Qi Hongchang; Wang Cong; Wang Chenglin; Zhong Boling

    2014-01-01

    The two spent fuel pool coolers for the 320 MW unit in CNNC Nuclear Power Operation Management Co., Ltd. have operated for more than 20 years. In accordance with the preventive maintenance programs, they must be overhauled. It is decided to improve the original gasket structure of the component and adopt the method of a short-length U-tubes pulling after analysis and study. There are no leakages and other abnormal situations after the equipment being put into operation. The unit is kept safe and stable. At the same time, thought and method for the maintenance of other similar equipment are provided. (authors)

  11. Topology Optimization of Vehicle Body Structure for Improved Ride & Handling

    OpenAIRE

    Lövgren, Sebastian; Norberg, Emil

    2011-01-01

    Ride and handling are important areas for safety and improved vehicle control during driving. To meet the demands on ride and handling a number of measures can be taken. This master thesis work has focused on the early design phase. At the early phases of design, the level of details is low and the design freedom is big. By introducing a tool to support the early vehicle body design, the potential of finding more efficient structures increases. In this study, topology optimization of a vehicl...

  12. Structural improvement of strengthened deck panels with externally bonded plates

    International Nuclear Information System (INIS)

    Sim, Jongsung; Oh, Hongseob

    2005-01-01

    Concrete bridge decks require eventual replacement and rehabilitation due to decreasing load-carrying capacity. This paper compares different strengthening design procedures that improve the usability and structural performance of bridge decks. The failure characteristics of bridge decks strengthened with various materials such as carbon fiber sheet, glass fiber sheet, steel plate, and grid CFRP and GFRP are analyzed, and the theoretical load-carrying capacities are evaluated using traditional beam and yield line theory, and punching shear analysis. The strengthening materials increase the punching shear strength of the deck and change the failure mode of the strengthened panel

  13. A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.

    Science.gov (United States)

    Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

    2013-07-01

    The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for large-scale applications as it could presumably be used to design sequences with better transcription rates and/or structural plasticity. In this article, we introduce IncaRNAtion, a novel algorithm to design RNA sequences folding into target secondary structures with a predefined nucleotide distribution. IncaRNAtion uses a global sampling approach and weighted sampling techniques. We show that our approach is fast (i.e. running time comparable or better than local search methods), seedless (we remove the bias of the seed in local search heuristics) and successfully generates high-quality sequences (i.e. thermodynamically stable) for any GC-content. To complete this study, we develop a hybrid method combining our global sampling approach with local search strategies. Remarkably, our glocal methodology overcomes both local and global approaches for sampling sequences with a specific GC-content and target structure. IncaRNAtion is available at csb.cs.mcgill.ca/incarnation/. Supplementary data are available at Bioinformatics online.

  14. The secondary structure and the thermal unfolding parameters of the S-layer protein from Lactobacillus salivarius.

    Science.gov (United States)

    Lighezan, Liliana; Georgieva, Ralitsa; Neagu, Adrian

    2016-09-01

    Surface layer (S-layer) proteins have been identified in the cell envelope of many organisms, such as bacteria and archaea. They self-assemble, forming monomolecular crystalline arrays. Isolated S-layer proteins are able to recrystallize into regular lattices, which proved useful in biotechnology. Here we investigate the structure and thermal unfolding of the S-layer protein isolated from Lactobacillus salivarius 16 strain of human origin. Using circular dichroism (CD) spectroscopy, and the software CDSSTR from DICHROWEB, CONTINLL from CDPro, as well as CDNN, we assess the fractions of the protein's secondary structural elements at temperatures ranging between 10 and 90 °C, and predict the tertiary class of the protein. To study the thermal unfolding of the protein, we analyze the temperature dependence of the CD signal in the far- and near-UV domains. Fitting the experimental data by two- and three-state models of thermal unfolding, we infer the midpoint temperatures, the temperature dependence of the changes in Gibbs free energy, enthalpy, and entropy of the unfolding transitions in standard conditions, and the temperature dependence of the equilibrium constant. We also estimate the changes in heat capacity at constant pressure in standard conditions. The results indicate that the thermal unfolding of the S-layer protein from L. salivarius is highly cooperative, since changes in the secondary and tertiary structures occur simultaneously. The thermodynamic analysis predicts a "cold" transition, at about -3 °C, of both the secondary and tertiary structures. Our findings may be important for the use of S-layer proteins in biotechnology and in biomedical applications.

  15. Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex.

    Science.gov (United States)

    Jenkins, Adam M; Waterhouse, Robert M; Muskavitch, Marc A T

    2015-04-23

    Long non-coding RNAs (lncRNAs) have been defined as mRNA-like transcripts longer than 200 nucleotides that lack significant protein-coding potential, and many of them constitute scaffolds for ribonucleoprotein complexes with critical roles in epigenetic regulation. Various lncRNAs have been implicated in the modulation of chromatin structure, transcriptional and post-transcriptional gene regulation, and regulation of genomic stability in mammals, Caenorhabditis elegans, and Drosophila melanogaster. The purpose of this study is to identify the lncRNA landscape in the malaria vector An. gambiae and assess the evolutionary conservation of lncRNAs and their secondary structures across the Anopheles genus. Using deep RNA sequencing of multiple Anopheles gambiae life stages, we have identified 2,949 lncRNAs and more than 300 previously unannotated putative protein-coding genes. The lncRNAs exhibit differential expression profiles across life stages and adult genders. We find that across the genus Anopheles, lncRNAs display much lower sequence conservation than protein-coding genes. Additionally, we find that lncRNA secondary structure is highly conserved within the Gambiae complex, but diverges rapidly across the rest of the genus Anopheles. This study offers one of the first lncRNA secondary structure analyses in vector insects. Our description of lncRNAs in An. gambiae offers the most comprehensive genome-wide insights to date into lncRNAs in this vector mosquito, and defines a set of potential targets for the development of vector-based interventions that may further curb the human malaria burden in disease-endemic countries.

  16. A cell-compatible PEO–PPO–PEO (Pluronic®)-based hydrogel stabilized through secondary structures

    International Nuclear Information System (INIS)

    Peng, Sydney; Lin, Ji-Yu; Cheng, Ming-Huei; Wu, Chih-Wei; Chu, I-Ming

    2016-01-01

    Pluronic F-127 (PF127) is a thermosensitive polymer that has been widely recognized as a potential candidate for various bio-applications. However, in hydrogel form, its rapid disintegration and inhospitality toward cells have significantly limited its usage. As a means to increase the integrity and cell compatibility of a PF127 hydrogel, we propose the introduction of stabilizing secondary structures to the gel network by the addition of secondary structure-forming oligo-alanine and oligo-phenylalanine. Results indicate that increasing the oligo(peptides) attached to PF127 led to a significant decrease in the gelation concentration and temperature. A selected oligo(peptide)-modified PF127 was capable of forming a stable hydrogel network at 5% and suffered only 20% weight loss after 7 days of incubation in media. Scanning electron microscopy (SEM) revealed comparably more interconnected morphology in modified hydrogels which may be attributed to the presence of secondary structures, as verified by circular dichroism (CD) and Fourier-transformed infrared (FT-IR) spectroscopy. Nuclear magnetic resonance (NMR) provided insights into the extensive interactions at the micelle core, which is the key to altered gelation behavior. Furthermore, modified hydrogels maintained structural integrity within culturing media and supported the proliferation of encapsulated chondrocytes. In addition, in vivo residence time was extended to well beyond 2 weeks after oligo(peptide) modification, thereby broadening the application scope of the PF127 hydrogel to encompass long-term drug delivery and cell culturing. - Highlights: • Modification of Pluronic-F127 with oligo(peptides) decreased gelation concentration and prolonged residence time in vitro and in vivo. • Oligo(peptide)-modified Pluronic-F127 exhibited critical gelation concentration as low as 5%. • Cells encapsulated within 5% oligo(peptide)-modified hydrogel proliferated within a period of 7 days. • Oligo

  17. A cell-compatible PEO–PPO–PEO (Pluronic®)-based hydrogel stabilized through secondary structures

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Sydney; Lin, Ji-Yu [Deparment of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Cheng, Ming-Huei [Division of Microsurgery Reconstructive Microsurgery, Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan (China); Center for Tissue Engineering, Chang Gung Memorial Hospital, Taoyuan, Taiwan (China); Wu, Chih-Wei, E-mail: drwu.jerry@gmail.com [Division of Microsurgery Reconstructive Microsurgery, Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan (China); Center for Tissue Engineering, Chang Gung Memorial Hospital, Taoyuan, Taiwan (China); Chu, I-Ming, E-mail: chuiming456@gmail.com [Deparment of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan (China)

    2016-12-01

    Pluronic F-127 (PF127) is a thermosensitive polymer that has been widely recognized as a potential candidate for various bio-applications. However, in hydrogel form, its rapid disintegration and inhospitality toward cells have significantly limited its usage. As a means to increase the integrity and cell compatibility of a PF127 hydrogel, we propose the introduction of stabilizing secondary structures to the gel network by the addition of secondary structure-forming oligo-alanine and oligo-phenylalanine. Results indicate that increasing the oligo(peptides) attached to PF127 led to a significant decrease in the gelation concentration and temperature. A selected oligo(peptide)-modified PF127 was capable of forming a stable hydrogel network at 5% and suffered only 20% weight loss after 7 days of incubation in media. Scanning electron microscopy (SEM) revealed comparably more interconnected morphology in modified hydrogels which may be attributed to the presence of secondary structures, as verified by circular dichroism (CD) and Fourier-transformed infrared (FT-IR) spectroscopy. Nuclear magnetic resonance (NMR) provided insights into the extensive interactions at the micelle core, which is the key to altered gelation behavior. Furthermore, modified hydrogels maintained structural integrity within culturing media and supported the proliferation of encapsulated chondrocytes. In addition, in vivo residence time was extended to well beyond 2 weeks after oligo(peptide) modification, thereby broadening the application scope of the PF127 hydrogel to encompass long-term drug delivery and cell culturing. - Highlights: • Modification of Pluronic-F127 with oligo(peptides) decreased gelation concentration and prolonged residence time in vitro and in vivo. • Oligo(peptide)-modified Pluronic-F127 exhibited critical gelation concentration as low as 5%. • Cells encapsulated within 5% oligo(peptide)-modified hydrogel proliferated within a period of 7 days. • Oligo

  18. Fourier transform infrared spectroscopic studies of the secondary structure and thermal denaturation of CaATPase from rabbit skeletal muscle

    Science.gov (United States)

    Jaworsky, Mark; Brauner, Joseph W.; Mendelsohn, Richard

    Fourier transform i.r. spectroscopy has been used to monitor structural alterations induced by thermal denaturation of the intrinsic membrane protein CaATPase in aqueous media. The protein has been isolated, purified and studied in five forms: (i) In its native lipid environment after isolation from rabbit sarcoplasmic reticulum, both in H 2O and D 2O suspensions. (ii) After both mild and extensive tryptic digestion has cleaved those residues external to the membrane bilayer. (iii) Reconstituted in vesicle form with bovine brain sphingomyelin. Fourier deconvolution techniques have been used to enhance the resolution of the intrinsically overlapped Amide I and Amide II spectral regions. Large spectral alterations apparent in the deconvoluted spectra occur in these regions upon thermal denaturation of the protein which are consistent with the formation of a large proportion of β-antiparallel sheet form. The alteration parallels the loss in ATPase activity. A mild tryptic digestion increases slightly the proportion of α-helix and/or random coil secondary structure. A thermal transition to a form containing a high proportion of β structure is still evident. Extensive tryptic digestion nearly abolishes the alpha helical plus random coil secondary structure, while producing a high proportion of β form which is resistant to further thermally induced structural alterations. Studies of CaATPase reconstituted into vesicles with bovine brain sphingomyelin reveal a higher proportion of β structure than the native enzyme, with further introduction of β structure on thermal denaturation. Both the utility of deconvolution techniques and the necessity for caution in their application are apparent from the current experiments.

  19. Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum

    Science.gov (United States)

    Pei, Haisheng; Chen, Zhou; Tan, Xiaoyan; Hu, Jing; Yang, Bin; Sun, Junshe

    2017-01-01

    Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS) sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1–3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP) site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality control in the

  20. Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum.

    Directory of Open Access Journals (Sweden)

    Xiuqing Zhang

    Full Text Available Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1-3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality

  1. Residual stress improving method for reactor structural component and residual stress improving device therefor

    Energy Technology Data Exchange (ETDEWEB)

    Enomoto, Kunio; Otaka, Masahiro; Kurosawa, Koichi; Saito, Hideyo; Tsujimura, Hiroshi; Tamai, Yasukata; Urashiro, Keiichi; Mochizuki, Masato

    1996-09-03

    The present invention is applied to a BWR type reactor, in which a high speed jetting flow incorporating cavities is collided against the surface of reactor structural components to form residual compression stresses on the surface layer of the reactor structural components thereby improving the stresses on the surface. Namely, a water jetting means is inserted into the reactor container filled with reactor water. Purified water is pressurized by a pump and introduced to the water jetting means. The purified water jetted from the water jetting means and entraining cavities is abutted against the surface of the reactor structural components. With such procedures, since the purified water is introduced to the water jetting means by the pump, the pump is free from contamination of radioactive materials. As a result, maintenance and inspection for the pump can be facilitated. Further, since the purified water injection flow entraining cavities is abutted against the surface of the reactor structural components being in contact with reactor water, residual compression stresses are exerted on the surface of the reactor structural components. As a result, occurrence of stress corrosion crackings of reactor structural components is suppressed. (I.S.)

  2. Residual stress improving method for reactor structural component and residual stress improving device therefor

    International Nuclear Information System (INIS)

    Enomoto, Kunio; Otaka, Masahiro; Kurosawa, Koichi; Saito, Hideyo; Tsujimura, Hiroshi; Tamai, Yasukata; Urashiro, Keiichi; Mochizuki, Masato.

    1996-01-01

    The present invention is applied to a BWR type reactor, in which a high speed jetting flow incorporating cavities is collided against the surface of reactor structural components to form residual compression stresses on the surface layer of the reactor structural components thereby improving the stresses on the surface. Namely, a water jetting means is inserted into the reactor container filled with reactor water. Purified water is pressurized by a pump and introduced to the water jetting means. The purified water jetted from the water jetting means and entraining cavities is abutted against the surface of the reactor structural components. With such procedures, since the purified water is introduced to the water jetting means by the pump, the pump is free from contamination of radioactive materials. As a result, maintenance and inspection for the pump can be facilitated. Further, since the purified water injection flow entraining cavities is abutted against the surface of the reactor structural components being in contact with reactor water, residual compression stresses are exerted on the surface of the reactor structural components. As a result, occurrence of stress corrosion crackings of reactor structural components is suppressed. (I.S.)

  3. Thermal Inactivation Kinetics and Secondary Structure Change of a Low Molecular Weight Halostable Exoglucanase from a Marine Aspergillus niger at High Salinities.

    Science.gov (United States)

    Xue, Dong-Sheng; Liang, Long-Yuan; Lin, Dong-Qiang; Yao, Shan-Jing

    2017-11-01

    Two kinds of exoglucanase were purified from a marine Aspergillus niger. Catalytic ability of halophilic exoglucanase with a lower molecular weight and secondary structure change was analyzed at different salinities. Activity of the low molecular weight exoglucanase in 10% NaCl solution (w/v) was 1.69-fold higher of that in NaCl-free solution. Half-life time in 10% NaCl solution (w/v) was over 1.27-fold longer of that in NaCl-free solution. Free energy change of the low molecular weight exoglucanase denaturation, △G, in 10% NaCl solution (w/v) was 0.54 kJ/mol more than that in NaCl-free solution. Melt point in 10% NaCl solution (w/v), 52.01 °C, was 4.21 °C higher than that in NaCl-free solution, 47.80 °C. K m value, 0.179 mg/ml in 10% NaCl solution (w/v) was less 0.044 mg/ml than that, 0.224 mg/ml, in NaCl-free solution. High salinity made content of α-helix increased. Secondary structure change caused by high salinities improved exoglucanase thermostability and catalysis activity. The halophilic exoglucanase from a marine A. niger was valuable for hydrolyzing cellulose at high salinities.

  4. Application of Nano-Structured Coatings for Mitigation of Flow-Accelerated Corrosion in Secondary Pipe Systems of Nuclear Power Plants

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seung Hyun; Kim, Jong Jin; Yoo, Seung Chang; Huh, Jae Hoon; Kim, Ji Hyun [Ulsan National Institute of Science and Technology, Ulsan (Korea, Republic of)

    2014-05-15

    Flow-accelerated corrosion (FAC) is a complex corrosion process combined with mechanical reaction with fluid. There were lots of research to mitigate FAC such as controlling temperature or water chemistry but in this research, we adopt active coating techniques especially nano-particle reinforced coatings. One of the general characteristics of FAC and its mitigation is that surface friction due to surface morphology makes a significant effect on FAC. Therefore to form a uniform coating layers, nano-particles including TiO2, SiC, Fe-Cr-W and Graphene were utilized. Those materials are known as greatly improve the corrosion resistance of substrates such as carbon steels but their effects on mitigation of FAC are not revealed clearly. Therefore in this research, the FAC resistive performance of nano-structured coatings were tested by electrochemical impedance spectroscopy (EIS) in room temperature 15 wt% sulfuric acid. As the flow-accelerated corrosion inhibitors in secondary piping system of nuclear power plants, various kinds of nano-structured coatings were prepared and tested in room-temperature electrochemical cells. SHS7740 with two types of Densifiers, electroless nickel plating with TiO2 are prepared. Electropolarization curves shows the outstanding corrosion mitigation performance of SHS7740 but EIS results shows the promising potential of Ni-P and Ni-P-TiO2 electroless nickel plating. For future work, high-temperature electrochemical analysis system will be constructed and in secondary water chemistry will be simulated.

  5. Experimental tests on ratchet of structural elements diagrams for primary tension and secondary twist

    International Nuclear Information System (INIS)

    Lebey, J.; Roche, R.L.; Cousseran, P.

    1980-05-01

    Design by analysis of pressure vessels is not complete without an appraisal of failure by progressive distortion or stress ratchet. Ratchet tests under constant axial stress associated with cyclic torsion deformation have been carried out on 304 L and 316 L thin tubular specimens, at room temperature. Results are given in the form of iso-deformation curves ranging from 0.1% to 2.5%, in the field definite by the primary and secondary stress intensities (Bree's diagram type). The use of an effective primary stress is proposed, as a practical way, to assess the elongation due to the ratchet effect

  6. Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database.

    Science.gov (United States)

    Billoud, B; Kontic, M; Viari, A

    1996-01-01

    At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usually dedicated to particular structures and are written using general purpose programming languages through a complex and time consuming process where the biological problem of defining the structure and the computer engineering problem of looking for it are intimately intertwined. In this paper, we describe a general representation of structures, suitable for database scanning, together with a programming language, Palingol, designed to manipulate it. Palingol has specific data types, corresponding to structural elements-basically helices-that can be arranged in any way to form a complex structure. As a consequence of the declarative approach used in Palingol, the user should only focus on 'what to search for' while the language engine takes care of 'how to look for it'. Therefore, it becomes simpler to write a scanning program and the structural constraints that define the required structure are more clearly identified. PMID:8628670

  7. The Prime Numbers Hidden Symmetric Structure and its Relation to the Twin Prime Infinitude and an Improved Prime Number Theorem

    CERN Document Server

    Mikoss, I

    2006-01-01

    Due to the sieving process represented by a Secondary Sieving Map; during the generation of the prime numbers, geometric structures with definite symmetries are formed which become evident through their geometrical representations. The study of these structures allows the development of a constructive prime generating formula. This defines a mean prime density yielding a second order recursive and discrete prime producing formula and a second order differential equation whose solutions produce an improved Prime Number Theorem. Applying these results to twin prime pairs is possible to generate a Twin Prime Number Theorem and important conclusions about the infinitude of the twin primes.

  8. Low pressure-induced secondary structure transitions of regenerated silk fibroin in its wet film studied by time-resolved infrared spectroscopy.

    Science.gov (United States)

    He, Zhipeng; Liu, Zhao; Zhou, Xiaofeng; Huang, He

    2018-06-01

    The secondary structure transitions of regenerated silk fibroin (RSF) under different external perturbations have been studied extensively, except for pressure. In this work, time-resolved infrared spectroscopy with the attenuated total reflectance (ATR) accessory was employed to follow the secondary structure transitions of RSF in its wet film under low pressure. It has been found that pressure alone is favorable only to the formation of β-sheet structure. Under constant pressure there is an optimum amount of D 2 O in the wet film (D 2 O : film = 2:1) so as to provide the optimal condition for the reorganization of the secondary structure and to have the largest formation of β-sheet structure. Under constant amount of D 2 O and constant pressure, the secondary structure transitions of RSF in its wet film can be divided into three stages along with time. In the first stage, random coil, α-helix, and β-turn were quickly transformed into β-sheet. In the second stage, random coil and β-turn were relatively slowly transformed into β-sheet and α-helix, and the content of α-helix was recovered to the value prior to the application of pressure. In the third and final stage, no measurable changes can be found for each secondary structure. This study may be helpful to understand the secondary structure changes of silk fibroin in silkworm's glands under hydrostatic pressure. © 2018 Wiley Periodicals, Inc.

  9. Surry Power Station secondary water chemistry improvement since steam generator replacement and the unit two feedwater pipe rupture

    International Nuclear Information System (INIS)

    Swindell, E.T.

    1988-01-01

    Surry Power Station has two Westinghouse-designed three-loop PWRs of 811 MWe design rating. The start of commercial operation was in July, 1972 in No.1 plant, and May, 1973 in No.2 plant. Both plants began the operation using controlled phosphate chemistry for the steam generators. In 1975, both plants were converted to all volatile treatment on the secondary side due to the tube wall thinning corrosion in the steam generators, which was associated with the phosphate sludge that was building up on the tube sheets and created acidic condition. Thereafter, condenser and air leakage and steam generator denting occurred, and after the operation of 8 years 2 month of No.1 plant and 5 years 9 months of No.2 plant, the steam generators were replaced. A major plant improvement program was designed and implemented from 1979 to 1980. The improvement in new steam generators, the modification for preventing corrosion, the addition of a steam generator blowdown recovery system, the reconstruction of condensers, the installation of full flow, deep bed condensate polishers, the addition of Dionex 8,000 on-line ion chromatograph, a long term maintenance agreement with Westinghouse and so on are reported. (Kako, I.)

  10. Improvement of Structural Life Management System(SLMS) for N.P.P. Structures

    International Nuclear Information System (INIS)

    Cho, Myung Sug; Noh, Jae Myung; Lee, Jong Suk; Kim, Do Gyeum

    2009-01-01

    The first investigation on the degradation mechanism and establishment of systematic inspection procedure for nuclear power plant (NPP) structures in Korea were conducted through a research project performed from 1993 to 19961). Accordingly, the Structural Life Management System (SLMS) was developed in 1998. Currently, SLMS is still operating for the lifetime management of NPP structures. However, the function of currently operating SLMS is focusing essentially on the management of degradation data detected during periodical inspections. Such limited function is today stressing the necessity to supplement its functions by improving the inefficiency of D/B due to the huge volume of data as well as by reflecting additional requirements. Accordingly, this research intends to develop a system improving the former SLMS so as to accommodate to the various demands of the users like integrated D/B system exploiting web-server, integrity assessment and durability management

  11. A call for parental monitoring to improve condom use among secondary school students in Dar es Salaam, Tanzania

    Directory of Open Access Journals (Sweden)

    Mlunde Linda B

    2012-12-01

    Full Text Available Abstract Background The number of people newly infected with human immunodeficiency virus (HIV has been decreasing in sub-Saharan Africa, but prevalence of the infection remains unacceptably high among young people. Despite the alarming pervasiveness of the virus, young people in this region continue to engage in risky sexual behaviors including unprotected sexual intercourse. In developed countries, parents can play important roles in protecting young people from such behaviors, but evidence regarding the impact of parental involvement is still limited in sub-Saharan Africa. Therefore, we conducted this study to examine the magnitude of risky sexual behaviors and the association of parental monitoring and parental communication with condom use at last sexual intercourse among secondary school students in Dar es Salaam, Tanzania. Methods We conducted this cross-sectional study among 2,217 male and female students aged 15 to 24 years from 12 secondary schools in Dar es Salaam. From October to November 2011, we collected data using a self-administered questionnaire. Multiple logistic regression analyses were conducted to examine the association of parental monitoring and parental communication with condom use at last sexual intercourse, adjusting for potential confounders. Results A total of 665 (30.3% secondary school students reported being sexually active within the year prior to data collection. Among them, 41.7% had multiple sexual partners, 10.5% had concurrent sexual partners, and 41.1% did not use a condom at last sexual intercourse. A higher level of parental monitoring was associated with increased likelihood of condom use at last sexual intercourse among male students (AOR: 1.56, 95% CI: 1.05-2.32; p = 0.03 but not among female students (AOR: 1.54, 95% CI: 0.71-3.37; p = 0.28. The association between parental communication and condom use at last sexual intercourse among both male and female students was not statistically

  12. Improving Communication of Diagnostic Radiology Findings through Structured Reporting

    Science.gov (United States)

    Panicek, David M.; Berk, Alexandra R.; Li, Yuelin; Hricak, Hedvig

    2011-01-01

    Purpose: To compare the content, clarity, and clinical usefulness of conventional (ie, free-form) and structured radiology reports of body computed tomographic (CT) scans, as evaluated by referring physicians, attending radiologists, and radiology fellows at a tertiary care cancer center. Materials and Methods: The institutional review board approved the study as a quality improvement initiative; no written consent was required. Three radiologists, three radiology fellows, three surgeons, and two medical oncologists evaluated 330 randomly selected conventional and structured radiology reports of body CT scans. For nonradiologists, reports were randomly selected from patients with diagnoses relevant to the physician’s area of specialization. Each physician read 15 reports in each format and rated both the content and clarity of each report from 1 (very dissatisfied or very confusing) to 10 (very satisfied or very clear). By using a previously published radiology report grading scale, physicians graded each report’s effectiveness in advancing the patient’s position on the clinical spectrum. Mixed-effects models were used to test differences between report types. Results: Mean content satisfaction ratings were 7.61 (95% confidence interval [CI]: 7.12, 8.16) for conventional reports and 8.33 (95% CI: 7.82, 8.86) for structured reports, and the difference was significant (P radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.11101913/-/DC1 PMID:21518775

  13. mRNA secondary structure at start AUG codon is a key limiting factor for human protein expression in Escherichia coli

    International Nuclear Information System (INIS)

    Zhang Weici; Xiao Weihua; Wei Haiming; Zhang Jian; Tian Zhigang

    2006-01-01

    Codon usage and thermodynamic optimization of the 5'-end of mRNA have been applied to improve the efficiency of human protein production in Escherichia coli. However, high level expression of human protein in E. coli is still a challenge that virtually depends upon each individual target genes. Using human interleukin 10 (huIL-10) and interferon α (huIFN-α) coding sequences, we systematically analyzed the influence of several major factors on expression of human protein in E. coli. The results from huIL-10 and reinforced by huIFN-α showed that exposing AUG initiator codon from base-paired structure within mRNA itself significantly improved the translation of target protein, which resulted in a 10-fold higher protein expression than the wild-type genes. It was also noted that translation process was not affected by the retained short-range stem-loop structure at Shine-Dalgarno (SD) sequences. On the other hand, codon-optimized constructs of huIL-10 showed unimproved levels of protein expression, on the contrary, led to a remarkable RNA degradation. Our study demonstrates that exposure of AUG initiator codon from long-range intra-strand secondary structure at 5'-end of mRNA may be used as a general strategy for human protein production in E. coli

  14. On the secondary charging effects and structure of mesospheric dust particles impacting on rocket probes

    Energy Technology Data Exchange (ETDEWEB)

    Havnes, O.; Naesheim, L.I. [Inst. of Physics, Univ. of Tromso (Norway)

    2007-07-01

    The dust probe DUSTY, first launched during the summer of 1994 (flights ECT-02 and ECT-07) from Andoeya Rocket Range, northern Norway, was the first probe to unambiguously detect heavy charged mesospheric aerosols, from hereon referred to as dust. In ECT-02 the probe detected negatively charged dust particles in the height interval of 83 to 88.5 km. In this flight, the lower grid in the detector (Grid 2) measures both positive and negative currents in various regions, and we find that the relationship between the current measurements of Grid 2 and the bottom plate can only be explained by influence from secondary charge production on Grid 2. In ECT-07, which had a large coning, positive currents reaching the top grid of the probe were interpreted as due to the impact of positively charged dust particles. We have now reanalyzed the data from ECT-07 and arrived at the conclusion that the measured positive currents to this grid must have been mainly due to secondary charging effects from the impacting dust particles. The grid consists of a set of parallel wires crossed with an identical set of wires on top of it, and we find that if the observed currents were created from the direct impact of charged dust particles, then they should be very weakly modulated at four times the rocket spin rate {omega}{sub R}. Observations show, however, that the observed currents are strongly modulated at 2{omega}{sub R}. We cannot reproduce the observed large modulations of the impact currents in the dust layer if the currents are due only to the transfer of the charges on the impacted dust particles. Based on the results of recent ice cluster impact secondary charging experiments by Tomsic (2003), which found that a small fraction of the ice clusters, when impacting with nearly grazing incidence, carried away one negative charge - 1e, we have arrived at the conclusion that similar, but significantly more effective, charging effects must be predominantly responsible for the positive

  15. Primary and secondary structural determinants in the receptor binding sequence β-(38-57) from human luteinizing hormone

    International Nuclear Information System (INIS)

    Keutmann, H.T.; Charlesworth, M.C.; Kitzmann, K.; Mason, K.A.; Johnson, L.; Ryan, R.J.

    1988-01-01

    The intercysteine loop sequence 38-57 in the β subunit has been shown to be a determinant for expression of biological activity in human lutropin (hLH) and choriogonadotropin (hCG). Together with other sequences, the 38-57 region may contribute to a multicomponent receptor binding domain in hLH/hCG. Because the structural features influencing activity in this important region are not easy to evaluate in the full-length subunit, the authors have used analogues of hLHβ-(38-57) prepared by solid-phase synthesis. The peptides were tested for inhibition of 125 I-labeled hCG binding to rat ovarian membrane receptors. Secondary structure was analyzed by circular dichroism (CD) and by reactivity with antibodies to the native 38-57 peptide. An analogue lacking the 38-57 disulfide linkage retained 20% receptor binding and full immunoreactivity. Far-ultraviolet CD profiles were essentially identical with those of the disulfide-intact peptide; a transition from 10% to 30% α-helix in 90% trifluoroethanol was characteristic of both. The peptide thus appears not to require the disulfide bridge to retain a looped conformation with amphipathic secondary structure. An essential positive charge at position 43 was shown by complete loss of activity upon substitution of Asp or Ala for the Arg found in all known species of LH. These results indicate that the 38-57 sequence is a relatively rigid and structurally autonomous region, not merely a series of residues constrained passively into a loop by a disulfide linkage. It includes segments of ordered structure, probably including both amphipathic helical and turn sequences. Evidence from studies of other hormones suggests that this region may be important to binding and specificity in the glycoprotein hormones as a group

  16. Carbon Policy and Technical Change: Market Structure, Increasing Returns, and Secondary Benefits. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Peretto, P.; Smith, V. K.

    2001-11-19

    An economic evaluation of the impact of policies intended to control emissions of CO{sub 2} and other ''greenhouse gases'' (GHGS) depends on the net costs of these controls and their distribution throughout the production sectors of developed and developing economics. The answers derived from appraisals of these net costs, in turn, stem from what is assumed about the timing of the controls, the pace of technological change, and any short-term secondary benefits from their control. There have only been a few serious attempts to estimate the economic benefits from the policies associated with such long run outcomes. All of the approaches to date have made fairly strong assumptions or relied on contingent valuation estimates of hypothetical situations.

  17. CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

    International Nuclear Information System (INIS)

    Swain, Monalisa; Atreya, Hanudatta S.

    2009-01-01

    Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1 H α and 13 C' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment

  18. Ventilation Structure Improvement of Induction Motor Using Multiphysics Simulations

    Directory of Open Access Journals (Sweden)

    Tao Huang

    2012-09-01

    Full Text Available Temperature rise analysis has significant impact in the design of air-cooled asynchronous induction motor. However, the affection cannot be accurately evaluated by using traditional empirical curves method due to the complexity of the inductor architecture. Considering Joules losses in stator windings and the induced eddy current in squirrel cages, and heat dissipation by air convection and solid conduction, in this paper a 3-D coupled-field finite-element method (FEM is investigated to demonstrate the temperature distribution. The Joules losses calculated by 3-D eddy- current field analysis are used as the input for the thermal field analysis, which is deeply dependent on accurate air fluid field analysis. A novel multi-component fluid model is employed to deal with the influence of rotor rotation upon the air convection. The simulation results show the fatal influence of the ventilation structure and the effectiveness of the proposed cooling improvement way.

  19. Improved Study of the Antiprotonic Helium Hyperfine Structure

    CERN Document Server

    Pask, T.; Dax, A.; Hayano, R.S.; Hori, M.; Horvath, D.; Juhasz, B.; Malbrunot, C.; Marton, J.; Ono, N.; Suzuki, K.; Zmeskal, J.; Widmann, E.

    2008-01-01

    We report the initial results from a systematic study of the hyperfine (HF) structure of antiprotonic helium (n,l) = (37,~35) carried out at the Antiproton Decelerator (AD) at CERN. We performed a laser-microwave-laser resonance spectroscopy using a continuous wave (cw) pulse-amplified laser system and microwave cavity to measure the HF transition frequencies. Improvements in the spectral linewidth and stability of our laser system have increased the precision of these measurements by a factor of five and reduced the line width by a factor of three compared to our previous results. A comparison of the experimentally measured transition frequencies with three body QED calculations can be used to determine the antiproton spin magnetic moment, leading towards a test of CPT invariance.

  20. Management strategies to improve the academic performance of previously disadvantaged secondary schools in the grade 12 examination.

    OpenAIRE

    2004-01-01

    The importance of secondary school education in moulding learners into responsible citizens of tomorrow cannot be ignored or undermined. Secondary school education is the stepping stone for unlimited opportunities for learners to explore the career choices that they have to pursue further in their lives. Every year the performance of secondary schools in the matric examination come under spotlight as soon as the results are published. Many schools in the previously disadvantaged communities p...

  1. Nano-structured carbon materials for improved biosensing applications

    Energy Technology Data Exchange (ETDEWEB)

    Razumiene, J., E-mail: julija.razumiene@bchi.vu.lt [Institute of Biochemistry, Vilnius University, Mokslininku 12, Vilnius 08662 (Lithuania); Sakinyte, I. [Institute of Biochemistry, Vilnius University, Mokslininku 12, Vilnius 08662 (Lithuania); Barkauskas, J. [Faculty of Chemistry, Vilnius University, Naugarduko 24, Vilnius 03225 (Lithuania); Baronas, R. [Faculty of Mathematics and Informatics, Vilnius University, Naugarduko 24, Vilnius 03225 (Lithuania)

    2015-04-15

    Graphical abstract: - Highlights: • Novel protocols of graphite oxidation were used for successful synthesis of GOPs. • Newly synthesized GOPs were applicable for electrode design in reagentless bioelectrocatalytic systems operating on direct electron transfer. • We show that bioelectrocatalytic processes strongly depend on functionalities, morphology and structural features of GOPs. - Abstract: A set of oxidized graphite samples have been newly synthesized using different protocols. Atomic force microscopy, Raman spectroscopy, thermal gravimetric analysis and Brunauer–Emmett–Teller analysis revealed the changes in structure and functionalities of obtained graphite oxidation products (GOPs) compared to pristine graphite. The substances have been tested as electrode materials applicable for bioelectrocatalytic systems using pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH). The application of GOPs allowed achieving the direct electron transfer (DET) from active site of PQQ-GDH to the electrode surface. Needless of additional electron transfer (ET) mediating compounds highly improved features of the biosensors. The efficiency of the biosensors has been evaluated for all types of biosensors varied from 32 μA/cm{sup 2} to 64 μA/cm{sup 2} using as electrode materials GOP1 and thermally reduced graphite oxide (TRGO), respectively. TRGO containing function groups (according TGA, ∼6% of the weight loss) and smallest particles (average diameter was ∼11 nm and the average height was ∼0.5 nm) exhibited the higher efficiency for ET acceleration in the biosensor acting on principle of DET.

  2. Influence of Philosamia ricini silk fibroin components on morphology, secondary structure and thermal properties of chitosan biopolymer film.

    Science.gov (United States)

    Prasong, S; Nuanchai, K; Wilaiwan, S

    2009-09-15

    This study aimed to prepare Eri (Philosamia ricini) Silk Fibroin (SF)/chitosan (CS) blend films by a solvent evaporation method and to compare the blend films with both native SF and CS films. Influence of SF ratios on the morphology, secondary structure and thermal decomposition of the CS blend films were investigated. The native SF and CS films were uniform and homogeneous without phase separation. For the blend films, the uniform can be found less than 60% of SF composition. All of SF/CS blend films showed both SF and CS characteristics. FT-IR results showed that the blend films composed of both random coil and beta-sheet with predominant of beta-sheet form. Interaction of intermolecular between SF and CS have occurred which were measured by thermogravimetric thermograms. Increasing of SF contents was leading to the increase of beta-sheet structures which were enhanced the thermal stability of the CS blend films.

  3. Single-fluorophore monitoring of DNA hybridization for investigating the effect of secondary structure on the nucleation step.

    Science.gov (United States)

    Jo, Joon-Jung; Kim, Min-Ji; Son, Jung-Tae; Kim, Jandi; Shin, Jong-Shik

    2009-07-17

    Nucleic acid hybridization is one of the essential biological processes involved in storage and transmission of genetic information. Here we quantitatively determined the effect of secondary structure on the hybridization activation energy using structurally defined oligonucleotides. It turned out that activation energy is linearly proportional to the length of a single-stranded region flanking a nucleation site, generating a 0.18 kcal/mol energy barrier per nucleotide. Based on this result, we propose that the presence of single-stranded segments available for non-productive base pairing with a nucleation counterpart extends the searching process for nucleation sites to find a perfect match. This result may provide insights into rational selection of a target mRNA site for siRNA and antisense gene silencing.

  4. Life prediction of simple structures subject to cyclic primary and secondary loading resulting in creep and platicity

    International Nuclear Information System (INIS)

    Otter, N.R.; Jones, R.T.

    1979-01-01

    High temperature reactors are subject to cyclic mechanical and thermal loadings resulting from start up and shut down operations. The design must therefore guard against structural failure resulting from excessive deformation and creep-fatigue damage. Before any simplified inelastic analysis techniques can be applied, their validity needs to be examined under situations representative of the reactor. For this to be carried out it is necessary to determine the behaviour of components, initially geometrically simple, subject to loadings, cyclic primary and secondary in nature, which result in creep and plasticity. Beam-like structures have been investigated on a finite element basis with the aim of determining how cyclic plasticity, creep enhancement and plastic ratchetting vary in relationship with modified shakedown criteria, magnitude of loading and hold time. (orig.)

  5. Dopamine agonist suppression of rapid-eye-movement sleep is secondary to sleep suppression mediated via limbic structures

    International Nuclear Information System (INIS)

    Miletich, R.S.

    1985-01-01

    The effects of pergolide, a direct dopamine receptor agonist, on sleep and wakefulness, motor behavior and 3 H-spiperone specific binding in limbic structures and striatum in rats was studied. The results show that pergolide induced a biphasic dose effect, with high doses increasing wakefulness and suppressing sleep while low dose decreased wakefulness, but increased sleep. It was shown that pergolide-induced sleep suppression was blocked by α-glupenthixol and pimozide, two dopamine receptor antagonists. It was further shown that pergolide merely delayed the rebound resulting from rapid-eye-movement (REM) sleep deprivation, that dopamine receptors stimulation had no direct effect on the period, phase or amplitude of the circadian rhythm of REM sleep propensity and that there was no alteration in the coupling of REM sleep episodes with S 2 episodes. Rapid-eye-movement sleep deprivation resulted in increased sensitivity to the pergolide-induced wakefulness stimulation and sleep suppression and pergolide-induced motor behaviors of locomotion and head bobbing. 3 H-spiperone specific binding to dopamine receptors was shown to be altered by REM sleep deprivation in the subcortical limbic structures. It is concluded that the REM sleep suppressing action of dopamine receptor stimulation is secondary to sleep suppression per se and not secondary to a unique effect on the REM sleep. Further, it is suggested that the wakefulness stimulating action of dopamine receptor agonists is mediated by activation of the dopamine receptors in the terminal areas of the mesolimbocortical dopamine projection system

  6. Community structure, life histories and secondary production of stoneflies in two small mountain streams with different degree of forest cover

    Directory of Open Access Journals (Sweden)

    Pavel Beracko

    2015-10-01

    Full Text Available Our study examines community structure and nymphal biology (life cycles and secondary production of stoneflies in two adjacent mountain streams with different degree of forest cover in the Prosiečanka River Basin (Chočské Vrchy Mts., West Carpathians. One of the streams has non-forested catchment, converted to meadows and pastures, while the other one has catchment with 60% covered by spruce forest. Differences in forest cover and in thermal regime of the streams were reflected by the difference of stonefly communities at their structural and functional level. Species Nemoura cinerea and Leuctra aurita created stonefly assemblage in non-forested stream, whereas Nemoura cinerea also occurred in naturally forested stream together with species Leuctra armata, Leuctra nigra, Leuctra prima, Siphonoperla neglecta and Arcynopteryx dichroa. All examined species had maximally annual life cycle and in eudominant species Nemoura cinerea one month shift was found in nymphal hatching and adult emergence between streams. Total secondary production of stoneflies in undisturbed stream (126.46 mg DW m-2 y-1 was more than two times higher than the production in non-forested stream (47.39 mg DW m-2 y-1. 

  7. Improvement of Ride Quality of Railway Vehicle by Semiactive Secondary Suspension System on Roller Rig Using Magnetorheological Damper

    Directory of Open Access Journals (Sweden)

    Yu-Jeong Shin

    2014-07-01

    Full Text Available Ride quality became a very important factor in the performance of railway vehicles according to the expansion of high-speed railways and speedup of velocity of railway vehicles. In this study, the results of applying the MR (magnetorheological lateral damper on the secondary suspension to reduce the vibration of the car body, directly relating to the ride quality of railway vehicles, were mentioned. In order to verify the control performance of MR dampers, a 1/5 scaled railway vehicle model was constructed, and numerical simulation and experimental tests were conducted. The MR damper for the experimental tests was produced and was attached between the car body and bogie of a full scaled vehicle, and a vibration controlling test was performed to improve ride quality on a roller rig. The skyhook control algorithm was used as the controlling technique, and regarding the test results, the RMS (root mean square value was found by compensating the frequency of the lateral vibration based on the UIC 513 R Standard about the ride quality of railway vehicles. As a result of the test, it could be confirmed that vibration was reduced by approximately 24% when attaching the MR damper between the bogie and the car body compared to when applying a passive damper.

  8. Stacking faults in Zr(Fe, Cr)2 Laves structured secondary phase particle in Zircaloy-4 alloy.

    Science.gov (United States)

    Liu, Chengze; Li, Geping; Yuan, Fusen; Han, Fuzhou; Zhang, Yingdong; Gu, Hengfei

    2018-02-01

    Stacking faults (SFs) in secondary phase particles (SPPs), which generally crystallize in the Laves phase in Zircaloy-4 (Zr-4) alloy, have been frequently observed by researchers. However, few investigations on the nano-scale structure of SFs have been carried out. In the present study, an SF containing C14 structured SPP, which located at grain boundaries (GBs) in the α-Zr matrix, was chosen to be investigated, for its particular substructure as well as location, aiming to reveal the nature of the SFs in the SPPs in Zr-4 alloy. It was indicated that the SFs in the C14 structured SPP actually existed in the local C36 structured Laves phase, for their similarities in crystallography. The C14 → C36 phase transformation, which was driven by synchroshearing among the (0001) basal planes, was the formation mechanism of the SFs in the SPPs. By analyzing the strained regions near the SPP, a model for understanding the driving force of the synchroshear was proposed: the interaction between SPP and GB resulted in the Zener pinning effect, leading to the shearing parallel to the (0001) basal planes of the C14 structured SPP, and the synchroshear was therefore activated.

  9. Comprehensive secondary structure elucidation of four genera of the family Pospiviroidae.

    Directory of Open Access Journals (Sweden)

    Tamara Giguère

    Full Text Available Viroids are small, circular, single stranded RNA molecules that infect plants. Since they are non-coding, their structures play a critical role in their life cycles. To date, little effort has been spend on elucidating viroid structures in solution due to both the experimental difficulties and the time-consuming nature of the methodologies implicated. Recently, the technique of high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE was adapted for the probing of the members of family Avsunviroidae, all of whom replicate in the chloroplast and demonstrate ribozyme activity. In the present work, twelve viroid species belonging to four different genera of the family Pospiviroidae, whose members are characterized by the presence of a central conserved region (CCR and who replicate in nucleus of the host, were probed. Given that the structures of five distinct viroid species from the family Pospiviroidae have been previously reported, an overview of the different structural characteristics for all genera and the beginning of a manual classification of the different viroids based on their structural features are presented here.

  10. Secondary structure of prokaryotic 5S ribosomal ribonucleic acids: a study with ribonucleases

    DEFF Research Database (Denmark)

    Douthwaite, S; Garrett, R A

    1981-01-01

    The structures of 5S ribosomal RNAs from Escherichia coli and Bacillus stearothermophilus were examined by using ribonucleases A, T1, and T2 and a double helix specific cobra venom ribonuclease. By using both 5' and 3'-32P-end labeling methods and selecting for digested but intact 5S RNA molecules...... evidence for three of the helical regions of the Fox and Woese model of 5S RNA [Fox, G. E., & Woese, C. (1975) Nature (London) 256, 505] and support other important structural features which include a nucleotide looped out from a helical region which has been proposed as a recognition site for protein L18....

  11. Differentiation to improve the articulation between levels : In the teaching of English in primary and secondary education in the Netherlands

    NARCIS (Netherlands)

    A.P. de Kraay

    2016-01-01

    In 1986, English became a compulsory subject in primary education in The Netherlands1. While secondary schools have, by law, been required to offer English since 1863 (Wilhelm, 2005) the articulation between Dutch primary and secondary education levels of English language teaching has always been

  12. Evidence-Based Strategies for Improving the Reading Comprehension of Secondary Students: Implications for Students with Learning Disabilities

    Science.gov (United States)

    Watson, Silvana M. R.; Gable, Robert A.; Gear, Sabra B.; Hughes, Kimberly C.

    2012-01-01

    Reading comprehension is a complex skill that places significant demands on students, beginning with elementary school and continuing through the secondary grades. In this article, we provide an overview of possible factors associated with problems in reading comprehension among secondary students with learning disabilities. Discussion underscores…

  13. Dynamic changes in the secondary structure of ECE-1 and XCE account for their different substrate specificities

    Directory of Open Access Journals (Sweden)

    Ul-Haq Zaheer

    2012-11-01

    Full Text Available Abstract Background X-converting enzyme (XCE involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it’s well characterized homologue endothelin-converting enzyme-1 (ECE-1 showed broad substrate specificity and acts as endopeptidase as well as dipeptidase. To explore the structural differences between XCE and ECE-1, homology model of XCE was built using the complex structure of ECE-1 with phosphoramidon (pdb-id: 3DWB as template. Phosphoramidon was docked into the binding site of XCE whereas phosphate oxygen of the inhibitor was used as water molecule to design the apo forms of both enzymes. Molecular dynamics simulation of both enzymes was performed to analyze the dynamic nature of their active site residues in the absence and presence of the inhibitor. Results Homology model of XCE explained the role of non-conserved residues of its S2’ subsite. Molecular dynamics (MD simulations identified the flexible transitions of F149/I150, N566/N571, W714/W719, and R145/R723 residues of ECE-1/XCE for the strong binding of the inhibitor. Secondary structure calculations using DSSP method reveals the folding of R145/R723 residue of ECE-1/XCE into β-sheet structure while unfolding of the S2’ subsite residues in aECE-1 and sustained compact folding of that of aXCE. The results evaluated are in good agreement with available experimental data, thus providing detailed molecular models which can explain the structural and specificities differences between both zinc peptidases. Conclusions Secondary structure changes of both enzymes during the simulation time revealed the importance of β-sheet structure of R145/R723 for its binding with the terminal carboxylate group of the inhibitor. Unfolding of the α-helix comprising the S2’ subsite residues in aECE-1 correlate well with its endopeptidase activity while their compact folding in aXCE may

  14. Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment

    KAUST Repository

    Hanczyc, Piotr; Å kerman, Bjö rn; Nordé n, Bengt

    2012-01-01

    ) spectroscopy. Oligonucleotides of lengths varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated with respect to structural properties in the gel-like polymer environment. The DNA conformation as a function of relative humidity reveals a strong

  15. Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes

    DEFF Research Database (Denmark)

    Weile, Christian; Gardner, Paul P; Hedegaard, Mads M

    2007-01-01

    neuroblastoma cell line SK-N-AS. Using this strategy, we identify thousands of human candidate RNA genes. To further verify the expression of these genes, we focused on candidate genes that had a stable hairpin structures or a high level of covariance. Using northern blotting, we verify the expression of 2 out...

  16. GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops

    DEFF Research Database (Denmark)

    Swenson, M Shel; Anderson, Joshua; Ash, Andrew

    2012-01-01

    achieved significant improvements in runtime, but their implementations were not portable from niche high-performance computers or easily accessible to most RNA researchers. With the increasing prevalence of multi-core desktop machines, a new parallel prediction program is needed to take full advantage...

  17. Improvement in Mechanical Properties through Structural Hierarchies in Bio-Inspired Materials

    Science.gov (United States)

    2011-02-01

    made almost completely of brittle silica. Hierarchical arrangements in protein structures from amino acids up to secondary structures, have been...138(1):101 137, 2006. [37] S. Mann, D. D. Archibald, J. M. Didymus. T. Douglas, B. R. Heywood, F. C. Meldrum , and N. J. Reeves. Crystallization at

  18. Secondary production in shallow marine environments

    International Nuclear Information System (INIS)

    Pomeroy, L.R.

    1976-01-01

    Recommendations are discussed with regard to population ecology, microbial food webs, marine ecosystems, improved instrumentation, and effects of land and sea on shallow marine systems. The control of secondary production is discussed with regard to present status of knowledge; research needs for studies on dominant secondary producers, food webs that lead to commercial species, and significant features of the trophic structure of shallow water marine communities. Secondary production at the land-water interface is discussed with regard to present status of knowledge; importance of macrophytes to secondary production; export to secondary consumers; utilization of macrophyte primary production; and correlations between secondary production and river discharge. The role of microorganisms in secondary production is also discussed

  19. New Comparative Analysis Based on the Secondary Structure of SSU-rRNA Gene Reveals the Evolutionary Trend and the Family-Genus Characters of Mobilida (Ciliophora, Peritrichia).

    Science.gov (United States)

    Zhang, Yong; Zhao, Yuan-Jun; Wang, Qin; Tang, Fa-Hui

    2015-08-01

    In order to reveal the structural evolutionary trend of Mobilida ciliates, twenty-six SSU-rRNA sequences of mobilid species, including seven ones newly sequenced in the present work, were used for comparative phylogenic analysis based on the RNA secondary structure. The research results indicate that all the secondary structures except domains Helix 10, Helix 12, and Helix 37 could be regarded as the criterions in classification between the family Trichodinidae and Urceolariida, and four regions including Helix E10-1, Helix 29, Helix 43, and Helix 45-Helix 46 could be as criterions in classification between the genus Trichodinella and Trichodina in family Trichodinidae. After the analysis of common structural feature within the Mobilida, it was found that the secondary structure of V6 could prove the family Urceolariidae primitive status. This research has further suggested that the genus Trichodina could be divergent earlier than Trichodinella in the family Trichodinidae. In addition, the relationship between the secondary structure and topology of phylogenic tree that the branching order of most clades corresponds with the secondary structure of species within each clade of phylogenetic tree was first uncovered and discussed in the present study.

  20. Study on the Effect of Secondary Banded Structure on the Fatigue Property of Non-Quenched and Tempered Micro Alloyed Steel

    Science.gov (United States)

    Yajie, Cheng; Qingliang, Liao; Yue, Zhang

    Due to composition segregation and cooling speed, streamline or banded structure were often obtained in the thermal forming parts along the direction of parts forming. Generally speaking, banded structure doesn't decrease the longitudinal mechanical properties, so the secondary banded structure can't get enough attention. The effect of secondary banded structure on the fatigue properties of micro alloyed DG20Mn and 35CrMo steel was investigated using the axial tensile fatigue test of stress ratio of 0.1. The result shows that secondary banded structure was obtained in the center of the steel parts, because of the composition segregation and the lower cooling rate in center part of steel. Secondary banded structure has no significant effect on axial tensile properties of both DG20Mn and 35CrMo, but decreases the axial tensile fatigue performance of DG20Mn steel. This study suggests that under the high cyclic tensile stress, multi-source damage cracks in steel initiated by large strain of pearlite of secondary banded structure, which is larger than damage strain, is the major factor of the decrease of fatigue life of steel.

  1. Zoledronic acid improves bone mineral density, reduces bone turnover and improves skeletal architecture over 2 years of treatment in children with secondary osteoporosis

    DEFF Research Database (Denmark)

    Simm, Peter J; Johannesen, Jesper; Briody, Julie

    2011-01-01

    There are limited data on the use of bisphosphonate therapy for secondary osteoporoses in childhood, and no previous reports of the use of zoledronic acid in this group. We report 20 children with a variety of underlying primary diagnoses with associated secondary osteoporosis, who were treated w...

  2. Secondary structure of the rRNA ITS2 region reveals key evolutionary patterns in acroporid corals.

    Science.gov (United States)

    Coleman, Annette W; van Oppen, Madeleine J H

    2008-10-01

    This study investigates the ribosomal RNA transcript secondary structure in corals as confirmed by compensatory base changes in Isopora/Acropora species. These species are unique versus all other corals in the absence of a eukaryote-wide conserved structural component, the helix III in internal transcriber spacer (ITS) 2, and their variability in the 5.8S-LSU helix basal to ITS2, a helix with pairings identical among all other scleractinian corals. Furthermore, Isopora/Acropora individuals display at least two, and as many as three, ITS sequence isotypes in their genome which appear to be capable of function. From consideration of the conserved elements in ITS2 and flanking regions, it appears that there are three major groups within the IsoporaAcropora lineage: the Isopora + Acropora "longi" group, the large group including Caribbean Acropora + the Acropora "carib" types plus the bulk of the Indo-Pacific Acropora species, and the remaining enigmatic "pseudo" group found in the Pacific. Interbreeding is possible among Caribbean A. palmata and A. cervicornis and among some species of Indo-Pacific Acropora. Recombinant ITS sequences are obvious among these latter, such that morphology (as represented by species name) does not correlate with common ITS sequence. The combination of characters revealed by RNA secondary structure analyses suggests a recent past/current history of interbreeding among the Indo-Pacific Acropora species and a shared ancestry of some of these with the Caribbean Acropora. The unusual absence of helix III of ITS2 of Isopora/Acropora species may have some causative role in the equally unusual instability in the 5.8S-LSU helix basal to ITS2 of this species complex.

  3. Novel sequence variations in LAMA2 and SGCG genes modulating cis-acting regulatory elements and RNA secondary structure

    Directory of Open Access Journals (Sweden)

    Olfa Siala

    2010-01-01

    Full Text Available In this study, we detected new sequence variations in LAMA2 and SGCG genes in 5 ethnic populations, and analysed their effect on enhancer composition and mRNA structure. PCR amplification and DNA sequencing were performed and followed by bioinformatics analyses using ESEfinder as well as MFOLD software. We found 3 novel sequence variations in the LAMA2 (c.3174+22_23insAT and c.6085 +12delA and SGCG (c.*102A/C genes. These variations were present in 210 tested healthy controls from Tunisian, Moroccan, Algerian, Lebanese and French populations suggesting that they represent novel polymorphisms within LAMA2 and SGCG genes sequences. ESEfinder showed that the c.*102A/C substitution created a new exon splicing enhancer in the 3'UTR of SGCG genes, whereas the c.6085 +12delA deletion was situated in the base pairing region between LAMA2 mRNA and the U1snRNA spliceosomal components. The RNA structure analyses showed that both variations modulated RNA secondary structure. Our results are suggestive of correlations between mRNA folding and the recruitment of spliceosomal components mediating splicing, including SR proteins. The contribution of common sequence variations to mRNA structural and functional diversity will contribute to a better study of gene expression.

  4. Membrane interaction and secondary structure of de novo designed arginine-and tryptophan peptides with dual function

    KAUST Repository

    Rydberg, Hanna A.

    2012-10-01

    Cell-penetrating peptides and antimicrobial peptides are two classes of positively charged membrane active peptides with several properties in common. The challenge is to combine knowledge about the membrane interaction mechanisms and structural properties of the two classes to design peptides with membrane-specific actions, useful either as transporters of cargo or as antibacterial substances. Membrane active peptides are commonly rich in arginine and tryptophan. We have previously designed a series of arg/trp peptides and investigated how the position and number of tryptophans affect cellular uptake. Here we explore the antimicrobial properties and the interaction with lipid model membranes of these peptides, using minimal inhibitory concentrations assay (MIC), circular dichroism (CD) and linear dichroism (LD). The results show that the arg/trp peptides inhibit the growth of the two gram positive strains Staphylococcus aureus and Staphylococcus pyogenes, with some individual variations depending on the position of the tryptophans. No inhibition of the gram negative strains Proteus mirabilis or Pseudomonas aeruginosa was noticed. CD indicated that when bound to lipid vesicles one of the peptides forms an α-helical like structure, whereas the other five exhibited rather random coiled structures. LD indicated that all six peptides were somehow aligned parallel with the membrane surface. Our results do not reveal any obvious connection between membrane interaction and antimicrobial effect for the studied peptides. By contrast cell-penetrating properties can be coupled to both the secondary structure and the degree of order of the peptides. © 2012 Elsevier Inc.

  5. An RNA secondary structure bias for non-homologous reverse transcriptase-mediated deletions in vivo

    DEFF Research Database (Denmark)

    Duch, Mogens; Carrasco, Maria L; Jespersen, Thomas

    2004-01-01

    Murine leukemia viruses harboring an internal ribosome entry site (IRES)-directed translational cassette are able to replicate, but undergo loss of heterologous sequences upon continued passage. While complete loss of heterologous sequences is favored when these are flanked by a direct repeat......, deletion mutants with junction sites within the heterologous cassette may also be retrieved, in particular from vectors without flanking repeats. Such deletion mutants were here used to investigate determinants of reverse transcriptase-mediated non-homologous recombination. Based upon previous structural...... result from template switching during first-strand cDNA synthesis and that the choice of acceptor sites for non-homologous recombination are guided by non-paired regions. Our results may have implications for recombination events taking place within structured regions of retroviral RNA genomes...

  6. RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs

    DEFF Research Database (Denmark)

    Radhakrishnan, Sabarinathan; Tafer, Hakim; Seemann, Ernst Stefan

    2013-01-01

    into structural effects of SNPs. The global measures employed so far suffer from limited accuracy of folding programs on large RNAs and are computationally too demanding for genome-wide applications. Here, we present a strategy that focuses on the local regions of maximal structural change between mutant and wild......-type. These local regions are approximated in a "screening mode" that is intended for genome-wide applications. Furthermore, localized regions are identified as those with maximal discrepancy. The mutation effects are quantified in terms of empirical P values. To this end, the RNAsnp software uses extensive...... precomputed tables of the distribution of SNP effects as function of length and GC content. RNAsnp thus achieves both a noise reduction and speed-up of several orders of magnitude over shuffling-based approaches. On a data set comprising 501 SNPs associated with human-inherited diseases, we predict 54 to have...

  7. 3D CAFE modeling of grain structures: application to primary dendritic and secondary eutectic solidification

    International Nuclear Information System (INIS)

    Carozzani, T; Digonnet, H; Gandin, Ch-A

    2012-01-01

    A three-dimensional model is presented for the prediction of grain structures formed in casting. It is based on direct tracking of grain boundaries using a cellular automaton (CA) method. The model is fully coupled with a solution of the heat flow computed with a finite element (FE) method. Several unique capabilities are implemented including (i) the possibility to track the development of several types of grain structures, e.g. dendritic and eutectic grains, (ii) a coupling scheme that permits iterations between the FE method and the CA method, and (iii) tabulated enthalpy curves for the solid and liquid phases that offer the possibility to work with multicomponent alloys. The present CAFE model is also fully parallelized and runs on a cluster of computers. Demonstration is provided by direct comparison between simulated and recorded cooling curves for a directionally solidified aluminum–7 wt% silicon alloy

  8. Secondary structure of cell-penetrating peptides during interaction with fungal cells.

    Science.gov (United States)

    Gong, Zifan; Ikonomova, Svetlana P; Karlsson, Amy J

    2018-03-01

    Cell-penetrating peptides (CPPs) are peptides that cross cell membranes, either alone or while carrying molecular cargo. Although their interactions with mammalian cells have been widely studied, much less is known about their interactions with fungal cells, particularly at the biophysical level. We analyzed the interactions of seven CPPs (penetratin, Pep-1, MPG, pVEC, TP-10, MAP, and cecropin B) with the fungal pathogen Candida albicans using experiments and molecular simulations. Circular dichroism (CD) of the peptides revealed a structural transition from a random coil or weak helix to an α-helix occurs for all peptides when the solvent is changed from aqueous to hydrophobic. However, CD performed in the presence of C. albicans cells showed that proximity to the cell membrane is not necessarily sufficient to induce this structural transition, as penetratin, Pep-1, and MPG did not display a structural shift in the presence of cells. Monte Carlo simulations were performed to further probe the molecular-level interaction with the cell membrane, and these simulations suggested that pVEC, TP-10, MAP, and cecropin B strongly penetrate into the hydrophobic domain of the membrane lipid bilayer, inducing a transition to an α-helical conformation. In contrast, penetratin, Pep-1 and MPG remained in the hydrophilic region without a shift in conformation. The experimental data and MC simulations combine to explain how peptide structure affects their interaction with cells and their mechanism of translocation into cells (direct translocation vs. endocytosis). Our work also highlights the utility of combining biophysical experiments, biological experiments, and molecular modeling to understand biological phenomena. © 2017 The Protein Society.

  9. Primary and secondary structural analyses of glutathione S-transferase pi from human placenta.

    Science.gov (United States)

    Ahmad, H; Wilson, D E; Fritz, R R; Singh, S V; Medh, R D; Nagle, G T; Awasthi, Y C; Kurosky, A

    1990-05-01

    The primary structure of glutathione S-transferase (GST) pi from a single human placenta was determined. The structure was established by chemical characterization of tryptic and cyanogen bromide peptides as well as automated sequence analysis of the intact enzyme. The structural analysis indicated that the protein is comprised of 209 amino acid residues and gave no evidence of post-translational modifications. The amino acid sequence differed from that of the deduced amino acid sequence determined by nucleotide sequence analysis of a cDNA clone (Kano, T., Sakai, M., and Muramatsu, M., 1987, Cancer Res. 47, 5626-5630) at position 104 which contained both valine and isoleucine whereas the deduced sequence from nucleotide sequence analysis identified only isoleucine at this position. These results demonstrated that in the one individual placenta studied at least two GST pi genes are coexpressed, probably as a result of allelomorphism. Computer assisted consensus sequence evaluation identified a hydrophobic region in GST pi (residues 155-181) that was predicted to be either a buried transmembrane helical region or a signal sequence region. The significance of this hydrophobic region was interpreted in relation to the mode of action of the enzyme especially in regard to the potential involvement of a histidine in the active site mechanism. A comparison of the chemical similarity of five known human GST complete enzyme structures, one of pi, one of mu, two of alpha, and one microsomal, gave evidence that all five enzymes have evolved by a divergent evolutionary process after gene duplication, with the microsomal enzyme representing the most divergent form.

  10. Principals Management Support Practices to Promote Teachers' Instructional Improvement for Sustainable Development in Secondary Education in Anambra State, Nigeria

    Science.gov (United States)

    Victor, Akinfolarin Akinwale; Emetarom, Uche Grace

    2017-01-01

    This study ascertained the principals management support practices to promote teachers instructional improvement for sustainable development in secondary education in Anambra State. Two specific purposes were formulated and two research questions guided the study. The study adopted a descriptive survey design. The study was conducted in the six…

  11. An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

    Directory of Open Access Journals (Sweden)

    Shenkar Noa

    2009-08-01

    Full Text Available Abstract Background Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea. Results Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1 Phlebobranchia + Thaliacea + Aplousobranchia, 2 Appendicularia, and 3 Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models

  12. The most important structures utilizing primary and secondary hydroenergetic potential for electric energy production

    International Nuclear Information System (INIS)

    Zacharovsky, M.

    1997-01-01

    In this paper the construction, technological parameters and operation of Gabcikovo (primary hydro energy power) and Cierny Vah (secondary hydro energy power) are described. Construction of the hydroelectric power plant (HPP) Gabcikovo started in 1978 as a part of a system of hydro power projects Gabcikovo-Nagymaros. Basic technical data are: installed capacity 8 x 90 MW, production in an average aqueous year 2.650 GWh, number of hydroelectric generating sets (HGS) 8, turbine flow 8 x 413-636 m 3 /s, head 12.9-24 m.The Gabcikovo plant produced 9.163 GWh of electricity from the beginning of its operation till the end of 1966. The construction of the pumped storage plant (PSP) Cierny Vah started in 1976 and it was put into operation at the end of 1980. The main goal of the PSP Cierny Vah is to meet the control functions of an electrification system of the Slovak Republic, a substitute function in the cases of unexpected power outages and a planned electricity production from re-pumping. Technological parts are: six re-pumping vertical HGS in a three machine arrangement - a motor-generator, a turbine, a pump - are located in three double-blocks. Basic technical data: installed capacity 6 x 122.4 MW + 0.768 MW, yearly production 1,281 GWh, number of HGS 6, number of domestic hydroelectric generating sets 1, turbine flow 3 x 30 m / s, pump flow 6 x 22 m 3 /s, upper reservoir volume 3.7 mil. m 3 , max. head 434 m, peak time 5.71 hour, pumping time 7.78 hour, re-pumping cycle efficiency 74.36%. From putting the PSP into operation till the end of 1996, the HGS in operation 145,269 hours in total, including 53,332 hours in a turbine mode of operation, 70,293 hours in a pumping mode operation and 21,644 hours in a compensation mode operation. Whereas they supplied 5,346 GWh in the mains and the consumed 6,933 GWh of electricity for pumping. Hydroenergetic potential is a primary source of energy which is recyclable, i.e. unexhaustible and also ecologically the most tolerable

  13. The most important structures utilizing primary and secondary hydroenergetic potential for electric energy production

    Energy Technology Data Exchange (ETDEWEB)

    Zacharovsky, M [Slovenske elektrarne, a.s., Vodne elektrarne Trencin (Slovakia)

    1997-12-01

    In this paper the construction, technological parameters and operation of Gabcikovo (primary hydro energy power) and Cierny Vah (secondary hydro energy power) are described. Construction of the hydroelectric power plant (HPP) Gabcikovo started in 1978 as a part of a system of hydro power projects Gabcikovo-Nagymaros. Basic technical data are: installed capacity 8 x 90 MW, production in an average aqueous year 2.650 GWh, number of hydroelectric generating sets (HGS) 8, turbine flow 8 x 413-636 m{sup 3}/s, head 12.9-24 m.The Gabcikovo plant produced 9.163 GWh of electricity from the beginning of its operation till the end of 1966. The construction of the pumped storage plant (PSP) Cierny Vah started in 1976 and it was put into operation at the end of 1980. The main goal of the PSP Cierny Vah is to meet the control functions of an electrification system of the Slovak Republic, a substitute function in the cases of unexpected power outages and a planned electricity production from re-pumping. Technological parts are: six re-pumping vertical HGS in a three machine arrangement - a motor-generator, a turbine, a pump - are located in three double-blocks. Basic technical data: installed capacity 6 x 122.4 MW + 0.768 MW, yearly production 1,281 GWh, number of HGS 6, number of domestic hydroelectric generating sets 1, turbine flow 3 x 30 m{sup /}s, pump flow 6 x 22 m{sup 3}/s, upper reservoir volume 3.7 mil. m{sup 3}, max. head 434 m, peak time 5.71 hour, pumping time 7.78 hour, re-pumping cycle efficiency 74.36%. From putting the PSP into operation till the end of 1996, the HGS in operation 145,269 hours in total, including 53,332 hours in a turbine mode of operation, 70,293 hours in a pumping mode operation and 21,644 hours in a compensation mode operation. Whereas they supplied 5,346 GWh in the mains and the consumed 6,933 GWh of electricity for pumping. Hydroenergetic potential is a primary source of energy which is recyclable, i.e. unexhaustible and also ecologically the

  14. Implications of secondary structure prediction and amino acid sequence comparison of class I and class II phosphoribosyl diphosphate synthases on catalysis, regulation, and quaternary structure

    DEFF Research Database (Denmark)

    Krath, B N; Hove-Jensen, B

    2001-01-01

    Spinach 5-phospho-D-ribosyl alpha-1-diphosphate (PRPP) synthase isozyme 4 was synthesized in Escherichia coli and purified to near homogeneity. The activity of the enzyme is independent of P(i); it is inhibited by ADP in a competitive manner, indicating a lack of an allosteric site; and it accepts...... is consistent with a homotrimer. Secondary structure prediction shows that spinach PRPP synthase isozyme 4 has a general folding similar to that of Bacillus subtilis class I PRPP synthase, for which the three-dimensional structure has been solved, as the position and extent of helices and beta-sheets of the two...... in the spinach enzyme. In contrast, residues of the active site of B. subtilis PRPP synthase show extensive conservation in spinach PRPP synthase isozyme 4....

  15. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

    Directory of Open Access Journals (Sweden)

    Lucie Musilova

    2016-07-01

    Full Text Available Secondary plant metabolites (SPMEs play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs and polyaromatic hydrocarbons (PAHs. Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the “secondary compound hypothesis” and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.

  16. Feasibility Study on Nano-structured Coatings to Mitigate Flow-accelerated Corrosion in Secondary System of Nuclear Power Plants

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seunghyun; Kim, Jeong Won; Kim, Ji Hyun [Ulsan National Institute of Science and Technology, Banyeon-ri, Eonyang-eup, Ulju-gun, Ulsan (Korea, Republic of)

    2015-05-15

    There have been many efforts to mitigate FAC through the adoption of the advanced and modified water chemistries such as optimized dissolved oxygen (DO) concentration and temperature. However, these mitigation techniques pose certain challenges relating to the compatibility of new water chemistries with the steam generator, the thermal efficiency of the secondary side, etc. In this context, nano-particle reinforced electroless nickel plating (NP ENP) could help solve the FAC issues in secondary pipe systems. This does not require modification of water chemistry or structural materials, and hence, its application is reasonable and time-saving compared to previous FAC mitigation techniques. The main parameters of FAC are known as electrochemical reaction at the interface, dissolution of magnetite and ferrous ions due to concentration gradient between carbon steels and water and wear due to a fast-flowing fluid. High-temperature corrosion characteristics of the both coatings have potential as FAC barrier for carbon steel. Feasibility study will be carried out with FAC simulation experiments.

  17. Secondary School Students' LLL Competencies, and Their Relation with Classroom Structure and Achievement.

    Science.gov (United States)

    Klug, Julia; Lüftenegger, Marko; Bergsmann, Evelyn; Spiel, Christiane; Schober, Barbara

    2016-01-01

    There is a strong urge to foster lifelong learning (LLL) competencies with its key components - motivation and self-regulated learning - from early on in the education system. School in general is presently not considered to be successful in systematically imparting motivation and self-regulated learning strategies. There is strong evidence that decisive motivational determinants decrease the longer students stay in school. At present, the central sources of information about the situation in Austria are international monitoring studies, which only examine selected aspects of specific target groups, and their interpretability concerning mean values is constricted due to cultural differences. Thus, it is important to conduct additional and more differentiated national surveys of the actual state. This is why this study aimed at answering the following questions: (1) how well are Austrian students equipped for the future, in terms of their lifelong learning competencies, (2) can perceived classroom structure predict students' LLL, and (3) is there a correlation of students' LLL with their achievement in the school subjects math and German language. 5366 students (52.1% female) from 36 Austrian schools took part in the online-questionnaire (mean age 15.35 years, SD = 2.45), which measured their perceived LLL competencies in the subjects math and German language, their perceived classroom structure and their achievement. Results showed that the great majority of Austrian students - independent from domain and sex - know and are able to apply cognitive as well as metacognitive learning strategies. With regard to motivation the picture is less satisfactory: whilst students' self-efficacy is not the problem, there is a lack of interest in the school subjects and they often report to follow performance approach goals. Classroom structure positively predicted students' goals, interest, self-efficacy and learning strategies. Self-efficacy, performance approach goals, meta

  18. Secondary school students' LLL competencies, and their relation with classroom structure and achievement

    Directory of Open Access Journals (Sweden)

    Julia eKlug

    2016-05-01

    Full Text Available There is a strong urge to foster lifelong learning (LLL competencies with its key components - motivation and self-regulated learning - from early on in the education system. School in general is presently not considered to be successful in systematically imparting motivation and self-regulated learning strategies. There is strong evidence that decisive motivational determinants decrease the longer students stay in school. At present, the central sources of information about the situation in Austria are international monitoring studies, which only examine selected aspects of specific target groups, and their interpretability concerning mean values is constricted due to cultural differences. Thus, it is important to conduct additional and more differentiated national surveys of the actual state. This is why this study aimed at answering the following questions: (1 how well are Austrian students equipped for the future, in terms of their lifelong learning competencies, (2 can perceived classroom structure predict students’ LLL, and (3 is there a correlation of students’ LLL with their achievement in the school subjects math and German language. 5366 students (52.1% female from Thirty-six Austrian schools took part in the online-questionnaire (mean age 15.35 years, SD=2.45, which measured their perceived LLL competencies in the subjects math and German language, their perceived classroom structure and their achievement. Results showed that the great majority of Austrian students – independent from domain and sex - know and are able to apply cognitive as well as metacognitive learning strategies. With regard to motivation the picture is less satisfactory: whilst students’ self-efficacy is not the problem, there is a lack of interest in the school subjects and they often report to follow performance approach goals. Classroom structure positively predicted students’ goals, interest, self-efficacy and learning strategies. Self

  19. Secondary School Students’ LLL Competencies, and Their Relation with Classroom Structure and Achievement

    Science.gov (United States)

    Klug, Julia; Lüftenegger, Marko; Bergsmann, Evelyn; Spiel, Christiane; Schober, Barbara

    2016-01-01

    There is a strong urge to foster lifelong learning (LLL) competencies with its key components – motivation and self-regulated learning – from early on in the education system. School in general is presently not considered to be successful in systematically imparting motivation and self-regulated learning strategies. There is strong evidence that decisive motivational determinants decrease the longer students stay in school. At present, the central sources of information about the situation in Austria are international monitoring studies, which only examine selected aspects of specific target groups, and their interpretability concerning mean values is constricted due to cultural differences. Thus, it is important to conduct additional and more differentiated national surveys of the actual state. This is why this study aimed at answering the following questions: (1) how well are Austrian students equipped for the future, in terms of their lifelong learning competencies, (2) can perceived classroom structure predict students’ LLL, and (3) is there a correlation of students’ LLL with their achievement in the school subjects math and German language. 5366 students (52.1% female) from 36 Austrian schools took part in the online-questionnaire (mean age 15.35 years, SD = 2.45), which measured their perceived LLL competencies in the subjects math and German language, their perceived classroom structure and their achievement. Results showed that the great majority of Austrian students – independent from domain and sex – know and are able to apply cognitive as well as metacognitive learning strategies. With regard to motivation the picture is less satisfactory: whilst students’ self-efficacy is not the problem, there is a lack of interest in the school subjects and they often report to follow performance approach goals. Classroom structure positively predicted students’ goals, interest, self-efficacy and learning strategies. Self-efficacy, performance

  20. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins

    DEFF Research Database (Denmark)

    Kushon, S A; Jordan, J P; Seifert, J L

    2001-01-01

    The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA...... structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic...

  1. CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking.

    Directory of Open Access Journals (Sweden)

    Lei Hua

    Full Text Available RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/.

  2. Figures of merit for detectors in digital radiography. II. Finite number of secondaries and structured backgrounds

    International Nuclear Information System (INIS)

    Pineda, Angel R.; Barrett, Harrison H.

    2004-01-01

    The current paradigm for evaluating detectors in digital radiography relies on Fourier methods. Fourier methods rely on a shift-invariant and statistically stationary description of the imaging system. The theoretical justification for the use of Fourier methods is based on a uniform background fluence and an infinite detector. In practice, the background fluence is not uniform and detector size is finite. We study the effect of stochastic blurring and structured backgrounds on the correlation between Fourier-based figures of merit and Hotelling detectability. A stochastic model of the blurring leads to behavior similar to what is observed by adding electronic noise to the deterministic blurring model. Background structure does away with the shift invariance. Anatomical variation makes the covariance matrix of the data less amenable to Fourier methods by introducing long-range correlations. It is desirable to have figures of merit that can account for all the sources of variation, some of which are not stationary. For such cases, we show that the commonly used figures of merit based on the discrete Fourier transform can provide an inaccurate estimate of Hotelling detectability

  3. Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing.

    Science.gov (United States)

    Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

    2017-10-03

    Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure.

  4. Isolation and structural elucidation of secondary metabolites of plants of the families asteraceae and urticaceae

    International Nuclear Information System (INIS)

    Villagra Quesada, E.

    2002-01-01

    A phytochemistry study of plant's species of the Asteraceae and Urticaceae family is proposed in order to isolate and to elucidate the structure of active principles; due to the fact that several studies have found that some of these families have compounds with anti-inflammatory activity, mainly lactonas sesquiterpenicas . The phytochemistry study was carried out through the application of chromatography techniques, for the separation and purification of the compounds. Includes chromatography of column, fine and liquid layer of high resolution. On the other hand, spectroscopic techniques were used for the elucidation, mainly of nuclear magnetic resonance (RMN) as much of one as of two dimensions. In this way, it was possible to isolate 14 compounds in Decachaeta thieleana and 10 in Phenax mexicanus, from which 6 correspond compounds of innovative structure. The comparison of the results obtained in Decachaeta thieleana (with previous studies) evidences that specimens, orphologically identical (the same species, but different locations), possess totally different compounds. This suggests that the studied specimens do not correspond to the same species. However, the determination of such a cause not only evade the objectives of this work but also the area of study of Chemistry [es

  5. Improving COIL Efficiency By Iodine Pre-Dissociation Via Corona Discharge In The Transonic Section Of The Secondary Flow

    National Research Council Canada - National Science Library

    Rosenwaks, Zamik; Barmashenko, Boris

    2006-01-01

    ...: We intend to carry out a comprehensive experimental study of I2 pre-dissociation, based on applying corona discharge in the transonic section of the secondary flow in the COIL supersonic nozzle...

  6. The Office Guidelines Applied to Practice program improves secondary prevention of heart disease in Federally Qualified Healthcare Centers

    Directory of Open Access Journals (Sweden)

    Adesuwa Olomu

    2016-12-01

    Office-GAP resulted in increased use of guideline-based medications for secondary CVD prevention in underserved populations. The Office-GAP program could serve as a model for implementing guideline-based care for other chronic diseases.

  7. Marrying Step Feed with Secondary Clarifier Improvements to Significantly Increase Peak Wet Weather Treatment Capacity: An Integrated Methodology.

    Science.gov (United States)

    Daigger, Glen T; Siczka, John S; Smith, Thomas F; Frank, David A; McCorquodale, J A

    2017-08-01

      The need to increase the peak wet weather secondary treatment capacity of the City of Akron, Ohio, Water Reclamation Facility (WRF) provided the opportunity to test an integrated methodology for maximizing the peak wet weather secondary treatment capacity of activated sludge systems. An initial investigation, consisting of process modeling of the secondary treatment system and computational fluid dynamics (CFD) analysis of the existing relatively shallow secondary clarifiers (3.3 and 3.7 m sidewater depth in 30.5 m diameter units), indicated that a significant increase in capacity from 416 000 to 684 000 m3/d or more was possible by adding step feed capabilities to the existing bioreactors and upgrading the existing secondary clarifiers. One of the six treatment units at the WRF was modified, and an extensive 2-year testing program was conducted to determine the total peak wet weather secondary treatment capacity achievable. The results demonstrated that a peak wet weather secondary treatment capacity approaching 974 000 m3/d is possible as long as secondary clarifier solids and hydraulic loadings could be separately controlled using the step feed capability provided. Excellent sludge settling characteristics are routinely experienced at the City of Akron WRF, raising concerns that the identified peak wet weather secondary treatment capacity could not be maintained should sludge settling characteristics deteriorate for some reason. Computational fluid dynamics analysis indicated that the impact of the deterioration of sludge settling characteristics could be mitigated and the identified peak wet weather secondary treatment capacity maintained by further use of the step feed capability provided to further reduce secondary clarifier solids loading rates at the identified high surface overflow rates. The results also demonstrated that effluent limits not only for total suspended solids (TSS) and five-day carbonaceous biochemical oxygen demand (cBOD5) could be

  8. Participatory design facilitates Person Centred Nursing in service improvement with older people: a secondary directed content analysis.

    Science.gov (United States)

    Wolstenholme, Daniel; Ross, Helen; Cobb, Mark; Bowen, Simon

    2017-05-01

    To explore, using the example of a project working with older people in an outpatient setting in a large UK NHS Teaching hospital, how the constructs of Person Centred Nursing are reflected in interviews from participants in a Co-design led service improvement project. Person Centred Care and Person Centred Nursing are recognised terms in healthcare. Co-design (sometimes called participatory design) is an approach that seeks to involve all stakeholders in a creative process to deliver the best result, be this a product, technology or in this case a service. Co-design practice shares some of the underpinning philosophy of Person Centred Nursing and potentially has methods to aid in Person Centred Nursing implementation. The research design was a qualitative secondary Directed analysis. Seven interview transcripts from nurses and older people who had participated in a Co-design led improvement project in a large teaching hospital were transcribed and analysed. Two researchers analysed the transcripts for codes derived from McCormack & McCance's Person Centred Nursing Framework. The four most expressed codes were as follows: from the pre-requisites: knowing self; from care processes, engagement, working with patient's beliefs and values and shared Decision-making; and from Expected outcomes, involvement in care. This study describes the Co-design theory and practice that the participants responded to in the interviews and look at how the co-design activity facilitated elements of the Person Centred Nursing framework. This study adds to the rich literature about using emancipatory and transformational approaches to Person Centred Nursing development, and is the first study exploring explicitly the potential contribution of Co-design to this area. Methods from Co-design allow older people to contribute as equals in a practice development project, co-design methods can facilitate nursing staff to engage meaningfully with older participants and develop a shared

  9. Formation of secondary phases during deep geological final disposal of research reactor fuel elements. Structure and phase analysis

    International Nuclear Information System (INIS)

    Neumann, Andreas

    2012-01-01

    For the assessment of a confident und sustainable final disposal of high level radioactive waste - fuel elements of german research reactors also account for such waste - in suitable, deep geological facilities, processes of the alteration of the disposed of waste and therefore the formation of the corrosion products, i. e. secondary phases must be well understood considering an accident scenario of a potential water inflow. In order to obtain secondary phases non-irradiated research reactor fuel elements (FR-BE) consisting of UAl x -Al were subjected to magnesium chloride rich brine (brine 2, salt repository) and to clay pore solution, respectively and furthermore of the type U 3 Si 2 -Al were solely subjected to magnesium chloride rich brine. Considering environmental aspects of final repositories the test conditions of the corrosion experiments were adjusted in a way that the temperature was kept constant at 90 C and a reducing anaerobic environment was ensured. As major objective of this research secondary phases, obtained from the autoclave experiments after appropriate processing and grain size separation have been identified and quantified. Powder X-ray diffraction (PXRD) and the application of Rietveld refinement methods allowed the identification of the corrosion products and a quantitative assessment of crystalline and amorphous contents. Scanning and transmission electron microscopy were additionally applied as a complementary method for the characterisation of the secondary phases. The qualitative phase analysis of the preprocessed secondary phases of the systems UAl x -Al and U 3 Si 2 -Al in brine 2 shows many similarities. Lesukite - an aluminium chloro hydrate - was observed for the first time considering the given experimental conditions. Further on different layered structures of the LDH type, iron oxyhydroxide and possibly iron chlorides, uncorroded residues of nuclear fuel and elementary iron were identified as well. Depending on preceding

  10. Dopamine agonist suppression of rapid-eye-movement sleep is secondary to sleep suppression mediated via limbic structures

    Energy Technology Data Exchange (ETDEWEB)

    Miletich, R.S.

    1985-01-01

    The effects of pergolide, a direct dopamine receptor agonist, on sleep and wakefulness, motor behavior and /sup 3/H-spiperone specific binding in limbic structures and striatum in rats was studied. The results show that pergolide induced a biphasic dose effect, with high doses increasing wakefulness and suppressing sleep while low dose decreased wakefulness, but increased sleep. It was shown that pergolide-induced sleep suppression was blocked by ..cap alpha..-glupenthixol and pimozide, two dopamine receptor antagonists. It was further shown that pergolide merely delayed the rebound resulting from rapid-eye-movement (REM) sleep deprivation, that dopamine receptors stimulation had no direct effect on the period, phase or amplitude of the circadian rhythm of REM sleep propensity and that there was no alteration in the coupling of REM sleep episodes with S/sub 2/ episodes. Rapid-eye-movement sleep deprivation resulted in increased sensitivity to the pergolide-induced wakefulness stimulation and sleep suppression and pergolide-induced motor behaviors of locomotion and head bobbing. /sup 3/H-spiperone specific binding to dopamine receptors was shown to be altered by REM sleep deprivation in the subcortical limbic structures. It is concluded that the REM sleep suppressing action of dopamine receptor stimulation is secondary to sleep suppression per se and not secondary to a unique effect on the REM sleep. Further, it is suggested that the wakefulness stimulating action of dopamine receptor agonists is mediated by activation of the dopamine receptors in the terminal areas of the mesolimbocortical dopamine projection system.

  11. Variability in secondary structure of 18S ribosomal RNA as topological marker for identification of Paramecium species.

    Science.gov (United States)

    Shakoori, Farah R; Tasneem, Fareeda; Al-Ghanim, K; Mahboob, S; Al-Misned, F; Jahan, Nusrat; Shakoori, Abdul Rauf

    2014-12-01

    Besides cytological and molecular applications, Paramecium is being used in water quality assessment and for determination of saprobic levels. An unambiguous identification of these unicellular eukaryotes is not only essential, but its ecological diversity must also be explored in the local environment. 18SrRNA genes of all the strains of Paramecium species isolated from waste water were amplified, cloned and sequenced. Phylogenetic comparison of the nucleotide sequences of these strains with 23 closely related Paramecium species from GenBank Database enabled identification of Paramecium multimicronucleatum and Paramecium jenningsi. Some isolates did not show significant close association with other Paramecium species, and because of their unique position in the phylogenetic tree, they were considered new to the field. In the present report, these isolates are being designated as Paramecium caudatum pakistanicus. In this article, secondary structure of 18SrRNA has also been analyzed as an additional and perhaps more reliable topological marker for species discrimination and for determining possible phylogenetic relationship between the ciliate species. On the basis of comparison of secondary structure of 18SrRNA of various isolated Paramacium strains, and among Paramecium caudatum pakistanicus, Tetrahymena thermophila, Drosophila melanogaster, and Homo sapiens, it can be deduced that variable regions are more helpful in differentiating the species at interspecific level rather than at intraspecific level. It was concluded that V3 was the least variable region in all the organisms, V2 and V7 were the longest expansion segments of D. melanogaster and there was continu