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Sample records for pairwise residue contact

  1. A pairwise residue contact area-based mean force potential for discrimination of native protein structure

    Directory of Open Access Journals (Sweden)

    Pezeshk Hamid

    2010-01-01

    Full Text Available Abstract Background Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed. Results We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy sets to measure its ability to discriminate native structure from decoys. This potential has been able to distinguish native structures from the decoys in the most cases. Further, the calculated Z-scores were quite high for all protein datasets. Conclusions This knowledge-based potential of mean force can be used in protein structure prediction, fold recognition, comparative modelling and molecular recognition. The program is available at http://www.bioinf.cs.ipm.ac.ir/softwares/surfield

  2. Optimal definition of inter-residual contact in globular proteins based on pairwise interaction energy calculations, its robustness, and applications.

    Science.gov (United States)

    Fačkovec, Boris; Vondrášek, Jiří

    2012-10-25

    Although a contact is an essential measurement for the topology as well as strength of non-covalent interactions in biomolecules and their complexes, there is no general agreement in the definition of this feature. Most of the definitions work with simple geometric criteria which do not fully reflect the energy content or ability of the biomolecular building blocks to arrange their environment. We offer a reasonable solution to this problem by distinguishing between "productive" and "non-productive" contacts based on their interaction energy strength and properties. We have proposed a method which converts the protein topology into a contact map that represents interactions with statistically significant high interaction energies. We do not prove that these contacts are exclusively stabilizing, but they represent a gateway to thermodynamically important rather than geometry-based contacts. The process is based on protein fragmentation and calculation of interaction energies using the OPLS force field and relies on pairwise additivity of amino acid interactions. Our approach integrates the treatment of different types of interactions, avoiding the problems resulting from different contributions to the overall stability and the different effect of the environment. The first applications on a set of homologous proteins have shown the usefulness of this classification for a sound estimate of protein stability.

  3. Pairwise contact energy statistical potentials can help to find probability of point mutations.

    Science.gov (United States)

    Saravanan, K M; Suvaithenamudhan, S; Parthasarathy, S; Selvaraj, S

    2017-01-01

    To adopt a particular fold, a protein requires several interactions between its amino acid residues. The energetic contribution of these residue-residue interactions can be approximated by extracting statistical potentials from known high resolution structures. Several methods based on statistical potentials extracted from unrelated proteins are found to make a better prediction of probability of point mutations. We postulate that the statistical potentials extracted from known structures of similar folds with varying sequence identity can be a powerful tool to examine probability of point mutation. By keeping this in mind, we have derived pairwise residue and atomic contact energy potentials for the different functional families that adopt the (α/β) 8 TIM-Barrel fold. We carried out computational point mutations at various conserved residue positions in yeast Triose phosphate isomerase enzyme for which experimental results are already reported. We have also performed molecular dynamics simulations on a subset of point mutants to make a comparative study. The difference in pairwise residue and atomic contact energy of wildtype and various point mutations reveals probability of mutations at a particular position. Interestingly, we found that our computational prediction agrees with the experimental studies of Silverman et al. (Proc Natl Acad Sci 2001;98:3092-3097) and perform better prediction than i Mutant and Cologne University Protein Stability Analysis Tool. The present work thus suggests deriving pairwise contact energy potentials and molecular dynamics simulations of functionally important folds could help us to predict probability of point mutations which may ultimately reduce the time and cost of mutation experiments. Proteins 2016; 85:54-64. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. Perceptron learning of pairwise contact energies for proteins incorporating the amino acid environment

    Science.gov (United States)

    Heo, Muyoung; Kim, Suhkmann; Moon, Eun-Joung; Cheon, Mookyung; Chung, Kwanghoon; Chang, Iksoo

    2005-07-01

    Although a coarse-grained description of proteins is a simple and convenient way to attack the protein folding problem, the construction of a global pairwise energy function which can simultaneously recognize the native folds of many proteins has resulted in partial success. We have sought the possibility of a systematic improvement of this pairwise-contact energy function as we extended the parameter space of amino acids, incorporating local environments of amino acids, beyond a 20×20 matrix. We have studied the pairwise contact energy functions of 20×20 , 60×60 , and 180×180 matrices depending on the extent of parameter space, and compared their effect on the learnability of energy parameters in the context of a gapless threading, bearing in mind that a 20×20 pairwise contact matrix has been shown to be too simple to recognize the native folds of many proteins. In this paper, we show that the construction of a global pairwise energy function was achieved using 1006 training proteins of a homology of less than 30%, which include all representatives of different protein classes. After parametrizing the local environments of the amino acids into nine categories depending on three secondary structures and three kinds of hydrophobicity (desolvation), the 16290 pairwise contact energies (scores) of the amino acids could be determined by perceptron learning and protein threading. These could simultaneously recognize all the native folds of the 1006 training proteins. When these energy parameters were tested on the 382 test proteins of a homology of less than 90%, 370 (96.9%) proteins could recognize their native folds. We set up a simple thermodynamic framework in the conformational space of decoys to calculate the unfolded fraction and the specific heat of real proteins. The different thermodynamic stabilities of E.coli ribonuclease H (RNase H) and its mutants were well described in our calculation, agreeing with the experiment.

  5. Evaluation of residue-residue contact predictions in CASP9

    KAUST Repository

    Monastyrskyy, Bohdan; Fidelis, Krzysztof; Tramontano, Anna; Kryshtafovych, Andriy

    2011-01-01

    This work presents the results of the assessment of the intramolecular residue-residue contact predictions submitted to CASP9. The methodology for the assessment does not differ from that used in previous CASPs, with two basic evaluation measures

  6. Evaluation of residue-residue contact predictions in CASP9

    KAUST Repository

    Monastyrskyy, Bohdan

    2011-01-01

    This work presents the results of the assessment of the intramolecular residue-residue contact predictions submitted to CASP9. The methodology for the assessment does not differ from that used in previous CASPs, with two basic evaluation measures being the precision in recognizing contacts and the difference between the distribution of distances in the subset of predicted contact pairs versus all pairs of residues in the structure. The emphasis is placed on the prediction of long-range contacts (i.e., contacts between residues separated by at least 24 residues along sequence) in target proteins that cannot be easily modeled by homology. Although there is considerable activity in the field, the current analysis reports no discernable progress since CASP8.

  7. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?

    Science.gov (United States)

    Vendruscolo, M; Najmanovich, R; Domany, E

    2000-02-01

    We present a method to derive contact energy parameters from large sets of proteins. The basic requirement on which our method is based is that for each protein in the database the native contact map has lower energy than all its decoy conformations that are obtained by threading. Only when this condition is satisfied one can use the proposed energy function for fold identification. Such a set of parameters can be found (by perceptron learning) if Mp, the number of proteins in the database, is not too large. Other aspects that influence the existence of such a solution are the exact definition of contact and the value of the critical distance Rc, below which two residues are considered to be in contact. Another important novel feature of our approach is its ability to determine whether an energy function of some suitable proposed form can or cannot be parameterized in a way that satisfies our basic requirement. As a demonstration of this, we determine the region in the (Rc, Mp) plane in which the problem is solvable, i.e., we can find a set of contact parameters that stabilize simultaneously all the native conformations. We show that for large enough databases the contact approximation to the energy cannot stabilize all the native folds even against the decoys obtained by gapless threading.

  8. Evaluation of residue-residue contact prediction in CASP10

    KAUST Repository

    Monastyrskyy, Bohdan

    2013-08-31

    We present the results of the assessment of the intramolecular residue-residue contact predictions from 26 prediction groups participating in the 10th round of the CASP experiment. The most recently developed direct coupling analysis methods did not take part in the experiment likely because they require a very deep sequence alignment not available for any of the 114 CASP10 targets. The performance of contact prediction methods was evaluated with the measures used in previous CASPs (i.e., prediction accuracy and the difference between the distribution of the predicted contacts and that of all pairs of residues in the target protein), as well as new measures, such as the Matthews correlation coefficient, the area under the precision-recall curve and the ranks of the first correctly and incorrectly predicted contact. We also evaluated the ability to detect interdomain contacts and tested whether the difficulty of predicting contacts depends upon the protein length and the depth of the family sequence alignment. The analyses were carried out on the target domains for which structural homologs did not exist or were difficult to identify. The evaluation was performed for all types of contacts (short, medium, and long-range), with emphasis placed on long-range contacts, i.e. those involving residues separated by at least 24 residues along the sequence. The assessment suggests that the best CASP10 contact prediction methods perform at approximately the same level, and comparably to those participating in CASP9.

  9. Evaluation of residue-residue contact prediction in CASP10

    KAUST Repository

    Monastyrskyy, Bohdan; D'Andrea, Daniel; Fidelis, Krzysztof; Tramontano, Anna; Kryshtafovych, Andriy

    2013-01-01

    not take part in the experiment likely because they require a very deep sequence alignment not available for any of the 114 CASP10 targets. The performance of contact prediction methods was evaluated with the measures used in previous CASPs (i

  10. Identification of residue pairing in interacting β-strands from a predicted residue contact map.

    Science.gov (United States)

    Mao, Wenzhi; Wang, Tong; Zhang, Wenxuan; Gong, Haipeng

    2018-04-19

    Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a noisy contact map, due to the presence of characteristic contact patterns in β-β interactions. This information may benefit the tertiary structure prediction of mainly β proteins. In this work, we propose a novel ridge-detection-based β-β contact predictor to identify residue pairing in β strands from any predicted residue contact map. Our algorithm RDb 2 C adopts ridge detection, a well-developed technique in computer image processing, to capture consecutive residue contacts, and then utilizes a novel multi-stage random forest framework to integrate the ridge information and additional features for prediction. Starting from the predicted contact map of CCMpred, RDb 2 C remarkably outperforms all state-of-the-art methods on two conventional test sets of β proteins (BetaSheet916 and BetaSheet1452), and achieves F1-scores of ~ 62% and ~ 76% at the residue level and strand level, respectively. Taking the prediction of the more advanced RaptorX-Contact as input, RDb 2 C achieves impressively higher performance, with F1-scores reaching ~ 76% and ~ 86% at the residue level and strand level, respectively. In a test of structural modeling using the top 1 L predicted contacts as constraints, for 61 mainly β proteins, the average TM-score achieves 0.442 when using the raw RaptorX-Contact prediction, but increases to 0.506 when using the improved prediction by RDb 2 C. Our method can significantly improve the prediction of β-β contacts from any predicted residue contact maps. Prediction results of our algorithm could be directly applied to effectively facilitate the practical structure prediction of mainly β proteins. All source data and codes are available at http://166.111.152.91/Downloads.html or the GitHub address of https://github.com/wzmao/RDb2C .

  11. FreeContact: fast and free software for protein contact prediction from residue co-evolution.

    Science.gov (United States)

    Kaján, László; Hopf, Thomas A; Kalaš, Matúš; Marks, Debora S; Rost, Burkhard

    2014-03-26

    20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein three-dimensional structure. The method EVfold broke new ground using mean-field Direct Coupling Analysis (EVfold-mfDCA); the method PSICOV applied a related concept by estimating a sparse inverse covariance matrix. Both methods (EVfold-mfDCA and PSICOV) are publicly available, but both require too much CPU time for interactive applications. On top, EVfold-mfDCA depends on proprietary software. Here, we present FreeContact, a fast, open source implementation of EVfold-mfDCA and PSICOV. On a test set of 140 proteins, FreeContact was almost eight times faster than PSICOV without decreasing prediction performance. The EVfold-mfDCA implementation of FreeContact was over 220 times faster than PSICOV with negligible performance decrease. EVfold-mfDCA was unavailable for testing due to its dependency on proprietary software. FreeContact is implemented as the free C++ library "libfreecontact", complete with command line tool "freecontact", as well as Perl and Python modules. All components are available as Debian packages. FreeContact supports the BioXSD format for interoperability. FreeContact provides the opportunity to compute reliable contact predictions in any environment (desktop or cloud).

  12. Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts.

    Science.gov (United States)

    Johnson, Quentin R; Lindsay, Richard J; Nellas, Ricky B; Fernandez, Elias J; Shen, Tongye

    2015-02-24

    Understanding allosteric mechanisms is essential for the physical control of molecular switches and downstream cellular responses. However, it is difficult to decode essential allosteric motions in a high-throughput scheme. A general two-pronged approach to performing automatic data reduction of simulation trajectories is presented here. The first step involves coarse-graining and identifying the most dynamic residue-residue contacts. The second step is performing principal component analysis of these contacts and extracting the large-scale collective motions expressed via these residue-residue contacts. We demonstrated the method using a protein complex of nuclear receptors. Using atomistic modeling and simulation, we examined the protein complex and a set of 18 glycine point mutations of residues that constitute the binding pocket of the ligand effector. The important motions that are responsible for the allostery are reported. In contrast to conventional induced-fit and lock-and-key binding mechanisms, a novel "frustrated-fit" binding mechanism of RXR for allosteric control was revealed.

  13. Defining an essence of structure determining residue contacts in proteins.

    Science.gov (United States)

    Sathyapriya, R; Duarte, Jose M; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

    2009-12-01

    The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this "structural essence" has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts-such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed "cone-peeling" that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 A Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This "structural essence" opens new avenues in the

  14. Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives

    Directory of Open Access Journals (Sweden)

    Alexov Emil G

    2006-11-01

    Full Text Available Abstract Background Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the predicted 3D structures. The correlated mutations (CM method serves as the most promising approach and it has been used to predict amino acids pairs that are distant in the primary sequence but form contacts in the native 3D structure of homologous proteins. Results Here we report a new implementation of the CM method with an added set of selection rules (filters. The parameters of the algorithm were optimized against fifteen high resolution crystal structures with optimization criterion that maximized the confidentiality of the predictions. The optimization resulted in a true positive ratio (TPR of 0.08 for the CM without filters and a TPR of 0.14 for the CM with filters. The protocol was further benchmarked against 65 high resolution structures that were not included in the optimization test. The benchmarking resulted in a TPR of 0.07 for the CM without filters and to a TPR of 0.09 for the CM with filters. Conclusion Thus, the inclusion of selection rules resulted to an overall improvement of 30%. In addition, the pair-wise comparison of TPR for each protein without and with filters resulted in an average improvement of 1.7. The methodology was implemented into a web server http://www.ces.clemson.edu/compbio/recon that is freely available to the public. The purpose of this implementation is to provide the 3D structure predictors with a tool that can help with ranking alternative models by satisfying the largest number of predicted contacts, as well as it can provide a confidence score for contacts in cases where structure is known.

  15. Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications

    Czech Academy of Sciences Publication Activity Database

    Fačkovec, Boris; Vondrášek, Jiří

    2012-01-01

    Roč. 116, č. 42 (2012), s. 12651-12660 ISSN 1520-6106 R&D Projects: GA ČR GAP208/10/0725; GA MŠk(CZ) LH11020 Institutional support: RVO:61388963 Keywords : egg-white lysozyme * force-field * 3-dimensional structure * thermophilic proteins * thermal-stability * mutant Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.607, year: 2012

  16. Improving residue-residue contact prediction via low-rank and sparse decomposition of residue correlation matrix.

    Science.gov (United States)

    Zhang, Haicang; Gao, Yujuan; Deng, Minghua; Wang, Chao; Zhu, Jianwei; Li, Shuai Cheng; Zheng, Wei-Mou; Bu, Dongbo

    2016-03-25

    Strategies for correlation analysis in protein contact prediction often encounter two challenges, namely, the indirect coupling among residues, and the background correlations mainly caused by phylogenetic biases. While various studies have been conducted on how to disentangle indirect coupling, the removal of background correlations still remains unresolved. Here, we present an approach for removing background correlations via low-rank and sparse decomposition (LRS) of a residue correlation matrix. The correlation matrix can be constructed using either local inference strategies (e.g., mutual information, or MI) or global inference strategies (e.g., direct coupling analysis, or DCA). In our approach, a correlation matrix was decomposed into two components, i.e., a low-rank component representing background correlations, and a sparse component representing true correlations. Finally the residue contacts were inferred from the sparse component of correlation matrix. We trained our LRS-based method on the PSICOV dataset, and tested it on both GREMLIN and CASP11 datasets. Our experimental results suggested that LRS significantly improves the contact prediction precision. For example, when equipped with the LRS technique, the prediction precision of MI and mfDCA increased from 0.25 to 0.67 and from 0.58 to 0.70, respectively (Top L/10 predicted contacts, sequence separation: 5 AA, dataset: GREMLIN). In addition, our LRS technique also consistently outperforms the popular denoising technique APC (average product correction), on both local (MI_LRS: 0.67 vs MI_APC: 0.34) and global measures (mfDCA_LRS: 0.70 vs mfDCA_APC: 0.67). Interestingly, we found out that when equipped with our LRS technique, local inference strategies performed in a comparable manner to that of global inference strategies, implying that the application of LRS technique narrowed down the performance gap between local and global inference strategies. Overall, our LRS technique greatly facilitates

  17. Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts.

    Science.gov (United States)

    Zhu, Jianwei; Zhang, Haicang; Li, Shuai Cheng; Wang, Chao; Kong, Lupeng; Sun, Shiwei; Zheng, Wei-Mou; Bu, Dongbo

    2017-12-01

    Accurate recognition of protein fold types is a key step for template-based prediction of protein structures. The existing approaches to fold recognition mainly exploit the features derived from alignments of query protein against templates. These approaches have been shown to be successful for fold recognition at family level, but usually failed at superfamily/fold levels. To overcome this limitation, one of the key points is to explore more structurally informative features of proteins. Although residue-residue contacts carry abundant structural information, how to thoroughly exploit these information for fold recognition still remains a challenge. In this study, we present an approach (called DeepFR) to improve fold recognition at superfamily/fold levels. The basic idea of our approach is to extract fold-specific features from predicted residue-residue contacts of proteins using deep convolutional neural network (DCNN) technique. Based on these fold-specific features, we calculated similarity between query protein and templates, and then assigned query protein with fold type of the most similar template. DCNN has showed excellent performance in image feature extraction and image recognition; the rational underlying the application of DCNN for fold recognition is that contact likelihood maps are essentially analogy to images, as they both display compositional hierarchy. Experimental results on the LINDAHL dataset suggest that even using the extracted fold-specific features alone, our approach achieved success rate comparable to the state-of-the-art approaches. When further combining these features with traditional alignment-related features, the success rate of our approach increased to 92.3%, 82.5% and 78.8% at family, superfamily and fold levels, respectively, which is about 18% higher than the state-of-the-art approach at fold level, 6% higher at superfamily level and 1% higher at family level. An independent assessment on SCOP_TEST dataset showed consistent

  18. Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning.

    Science.gov (United States)

    Du, Tianchuan; Liao, Li; Wu, Cathy H; Sun, Bilin

    2016-11-01

    Protein-protein interactions play essential roles in many biological processes. Acquiring knowledge of the residue-residue contact information of two interacting proteins is not only helpful in annotating functions for proteins, but also critical for structure-based drug design. The prediction of the protein residue-residue contact matrix of the interfacial regions is challenging. In this work, we introduced deep learning techniques (specifically, stacked autoencoders) to build deep neural network models to tackled the residue-residue contact prediction problem. In tandem with interaction profile Hidden Markov Models, which was used first to extract Fisher score features from protein sequences, stacked autoencoders were deployed to extract and learn hidden abstract features. The deep learning model showed significant improvement over the traditional machine learning model, Support Vector Machines (SVM), with the overall accuracy increased by 15% from 65.40% to 80.82%. We showed that the stacked autoencoders could extract novel features, which can be utilized by deep neural networks and other classifiers to enhance learning, out of the Fisher score features. It is further shown that deep neural networks have significant advantages over SVM in making use of the newly extracted features. Copyright © 2016. Published by Elsevier Inc.

  19. Ranking multiple docking solutions based on the conservation of inter-residue contacts

    KAUST Repository

    Oliva, Romina M.; Vangone, Anna; Cavallo, Luigi

    2013-01-01

    ) conformations in the top positions is still an open problem. Herein we present CONSRANK, a simple and effective tool to rank multiple docking solutions, which relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. First

  20. Pairwise Choice Markov Chains

    OpenAIRE

    Ragain, Stephen; Ugander, Johan

    2016-01-01

    As datasets capturing human choices grow in richness and scale---particularly in online domains---there is an increasing need for choice models that escape traditional choice-theoretic axioms such as regularity, stochastic transitivity, and Luce's choice axiom. In this work we introduce the Pairwise Choice Markov Chain (PCMC) model of discrete choice, an inferentially tractable model that does not assume any of the above axioms while still satisfying the foundational axiom of uniform expansio...

  1. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

    Directory of Open Access Journals (Sweden)

    Genki Terashi

    Full Text Available Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align, which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1 agreement with the gold standard alignment, (2 alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3 consistency of the multiple alignments, and (4 classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins

  2. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

    Science.gov (United States)

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

    Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

  3. Measurement properties and usability of non-contact scanners for measuring transtibial residual limb volume.

    Science.gov (United States)

    Kofman, Rianne; Beekman, Anna M; Emmelot, Cornelis H; Geertzen, Jan H B; Dijkstra, Pieter U

    2018-06-01

    Non-contact scanners may have potential for measurement of residual limb volume. Different non-contact scanners have been introduced during the last decades. Reliability and usability (practicality and user friendliness) should be assessed before introducing these systems in clinical practice. The aim of this study was to analyze the measurement properties and usability of four non-contact scanners (TT Design, Omega Scanner, BioSculptor Bioscanner, and Rodin4D Scanner). Quasi experimental. Nine (geometric and residual limb) models were measured on two occasions, each consisting of two sessions, thus in total 4 sessions. In each session, four observers used the four systems for volume measurement. Mean for each model, repeatability coefficients for each system, variance components, and their two-way interactions of measurement conditions were calculated. User satisfaction was evaluated with the Post-Study System Usability Questionnaire. Systematic differences between the systems were found in volume measurements. Most of the variances were explained by the model (97%), while error variance was 3%. Measurement system and the interaction between system and model explained 44% of the error variance. Repeatability coefficient of the systems ranged from 0.101 (Omega Scanner) to 0.131 L (Rodin4D). Differences in Post-Study System Usability Questionnaire scores between the systems were small and not significant. The systems were reliable in determining residual limb volume. Measurement systems and the interaction between system and residual limb model explained most of the error variances. The differences in repeatability coefficient and usability between the four CAD/CAM systems were small. Clinical relevance If accurate measurements of residual limb volume are required (in case of research), modern non-contact scanners should be taken in consideration nowadays.

  4. A two-stage approach for improved prediction of residue contact maps

    Directory of Open Access Journals (Sweden)

    Pollastri Gianluca

    2006-03-01

    Full Text Available Abstract Background Protein topology representations such as residue contact maps are an important intermediate step towards ab initio prediction of protein structure. Although improvements have occurred over the last years, the problem of accurately predicting residue contact maps from primary sequences is still largely unsolved. Among the reasons for this are the unbalanced nature of the problem (with far fewer examples of contacts than non-contacts, the formidable challenge of capturing long-range interactions in the maps, the intrinsic difficulty of mapping one-dimensional input sequences into two-dimensional output maps. In order to alleviate these problems and achieve improved contact map predictions, in this paper we split the task into two stages: the prediction of a map's principal eigenvector (PE from the primary sequence; the reconstruction of the contact map from the PE and primary sequence. Predicting the PE from the primary sequence consists in mapping a vector into a vector. This task is less complex than mapping vectors directly into two-dimensional matrices since the size of the problem is drastically reduced and so is the scale length of interactions that need to be learned. Results We develop architectures composed of ensembles of two-layered bidirectional recurrent neural networks to classify the components of the PE in 2, 3 and 4 classes from protein primary sequence, predicted secondary structure, and hydrophobicity interaction scales. Our predictor, tested on a non redundant set of 2171 proteins, achieves classification performances of up to 72.6%, 16% above a base-line statistical predictor. We design a system for the prediction of contact maps from the predicted PE. Our results show that predicting maps through the PE yields sizeable gains especially for long-range contacts which are particularly critical for accurate protein 3D reconstruction. The final predictor's accuracy on a non-redundant set of 327 targets is 35

  5. [Interlaboratory Study on Evaporation Residue Test for Food Contact Products (Report 1)].

    Science.gov (United States)

    Ohno, Hiroyuki; Mutsuga, Motoh; Abe, Tomoyuki; Abe, Yutaka; Amano, Homare; Ishihara, Kinuyo; Ohsaka, Ikue; Ohno, Haruka; Ohno, Yuichiro; Ozaki, Asako; Kakihara, Yoshiteru; Kobayashi, Hisashi; Sakuragi, Hiroshi; Shibata, Hiroshi; Shirono, Katsuhiro; Sekido, Haruko; Takasaka, Noriko; Takenaka, Yu; Tajima, Yoshiyasu; Tanaka, Aoi; Tanaka, Hideyuki; Tonooka, Hiroyuki; Nakanishi, Toru; Nomura, Chie; Haneishi, Nahoko; Hayakawa, Masato; Miura, Toshihiko; Yamaguchi, Miku; Watanabe, Kazunari; Sato, Kyoko

    2018-01-01

    An interlaboratory study was performed to evaluate the equivalence between an official method and a modified method of evaporation residue test using three food-simulating solvents (water, 4% acetic acid and 20% ethanol), based on the Japanese Food Sanitation Law for food contact products. Twenty-three laboratories participated, and tested the evaporation residues of nine test solutions as blind duplicates. For evaporation, a water bath was used in the official method, and a hot plate in the modified method. In most laboratories, the test solutions were heated until just prior to evaporation to dryness, and then allowed to dry under residual heat. Statistical analysis revealed that there was no significant difference between the two methods, regardless of the heating equipment used. Accordingly, the modified method provides performance equal to the official method, and is available as an alternative method.

  6. Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

    KAUST Repository

    Oliva, Romina; Chermak, Edrisse; Cavallo, Luigi

    2015-01-01

    In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.

  7. Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

    KAUST Repository

    Oliva, Romina

    2015-07-01

    In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.

  8. Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models

    KAUST Repository

    Vangone, Anna; Cavallo, Luigi; Oliva, Romina M.

    2013-01-01

    Herein we propose the use of a consensus approach, CONSRANK, for ranking CAPRI models. CONSRANK relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. Models are ranked according to their ability to match the most

  9. CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts

    KAUST Repository

    Chermak, Edrisse; Petta, A.; Serra, L.; Vangone, A.; Scarano, V.; Cavallo, Luigi; Oliva, R.

    2014-01-01

    Summary: Herein, we present CONSRANK, a web tool for analyzing, comparing and ranking protein–protein and protein–nucleic acid docking models, based on the conservation of inter-residue contacts and its visualization in 2D and 3D interactive contact maps.

  10. CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts

    KAUST Repository

    Chermak, Edrisse

    2014-12-21

    Summary: Herein, we present CONSRANK, a web tool for analyzing, comparing and ranking protein–protein and protein–nucleic acid docking models, based on the conservation of inter-residue contacts and its visualization in 2D and 3D interactive contact maps.

  11. [Interlaboratory Study on Evaporation Residue Test for Food Contact Products (Report 2)].

    Science.gov (United States)

    Ohno, Hiroyuki; Mutsuga, Motoh; Abe, Tomoyuki; Abe, Yutaka; Amano, Homare; Ishihara, Kinuyo; Ohsaka, Ikue; Ohno, Haruka; Ohno, Yuichiro; Ozaki, Asako; Kakihara, Yoshiteru; Kobayashi, Hisashi; Sakuragi, Hiroshi; Shibata, Hiroshi; Shirono, Katsuhiro; Sekido, Haruko; Takasaka, Noriko; Takenaka, Yu; Tajima, Yoshiyasu; Tanaka, Aoi; Tanaka, Hideyuki; Nakanishi, Toru; Nomura, Chie; Haneishi, Nahoko; Hayakawa, Masato; Miura, Toshihiko; Yamaguchi, Miku; Yamada, Kyohei; Watanabe, Kazunari; Sato, Kyoko

    2018-01-01

    An interlaboratory study was performed to evaluate the equivalence between an official method and a modified method of evaporation residue test using heptane as a food-simulating solvent for oily or fatty foods, based on the Japanese Food Sanitation Law for food contact products. Twenty-three laboratories participated, and tested the evaporation residues of nine test solutions as blind duplicates. In the official method, heating for evaporation was done with a water bath. In the modified method, a hot plate was used for evaporation, and/or a vacuum concentration procedure was skipped. In most laboratories, the test solutions were heated until just prior to dryness, and then allowed to dry under residual heat. Statistical analysis revealed that there was no significant difference between the two methods. Accordingly, the modified method provides performance equal to the official method, and is available as an alternative method. Furthermore, an interlaboratory study was performed to evaluate and compare two leaching solutions (95% ethanol and isooctane) used as food-simulating solvents for oily or fatty foods in the EU. The results demonstrated that there was no significant difference between heptane and these two leaching solutions.

  12. Ranking multiple docking solutions based on the conservation of inter-residue contacts

    KAUST Repository

    Oliva, Romina M.

    2013-06-17

    Molecular docking is the method of choice for investigating the molecular basis of recognition in a large number of functional protein complexes. However, correctly scoring the obtained docking solutions (decoys) to rank native-like (NL) conformations in the top positions is still an open problem. Herein we present CONSRANK, a simple and effective tool to rank multiple docking solutions, which relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. First it calculates a conservation rate for each inter-residue contact, then it ranks decoys according to their ability to match the more frequently observed contacts. We applied CONSRANK to 102 targets from three different benchmarks, RosettaDock, DOCKGROUND, and Critical Assessment of PRedicted Interactions (CAPRI). The method performs consistently well, both in terms of NL solutions ranked in the top positions and of values of the area under the receiver operating characteristic curve. Its ideal application is to solutions coming from different docking programs and procedures, as in the case of CAPRI targets. For all the analyzed CAPRI targets where a comparison is feasible, CONSRANK outperforms the CAPRI scorers. The fraction of NL solutions in the top ten positions in the RosettaDock, DOCKGROUND, and CAPRI benchmarks is enriched on average by a factor of 3.0, 1.9, and 9.9, respectively. Interestingly, CONSRANK is also able to specifically single out the high/medium quality (HMQ) solutions from the docking decoys ensemble: it ranks 46.2 and 70.8% of the total HMQ solutions available for the RosettaDock and CAPRI targets, respectively, within the top 20 positions. © 2013 Wiley Periodicals, Inc.

  13. Analytical tools and methodologies for evaluation of residual life of contacting pressure tubes in the early generation of Indian PHWRs

    International Nuclear Information System (INIS)

    Sinha, S.K.; Madhusoodanan, K.; Rupani, B.B.; Sinha, R.K.

    2002-01-01

    In-service life of a contacting Zircaloy-2 pressure tube (PT) in the earlier generation of Indian PHWRs, is limited mainly due to the accelerated hydrogen pick-up and nucleation and growth of hydride blister(s) at the cold spot(s) formed on outside surface of pressure tube as a result of its contact with the calandria tube (CT). The activities involving development of the analytical models for simulating the degradation mechanisms leading to PT-CT contact and the methodologies for the revaluation of their safe life under such condition form the important part of our extensive programme for the life management of contacting pressure tubes. Since after the PT-CT contact, rate of hydrogen pick-up and nucleation and growth of hydride blisters govern the safe residual life of the pressure tube, two analytical models (a) hydrogen pick-up model ('HYCON') and (b) model for the nucleation and growth of hydride blister at the contact spot ('BLIST -2D') have been developed in-house to estimate the extent of degradation caused by them. Along with them, a methodology for evaluation of safe residual life has also been formulated for evaluating the safe residual life of the contacting channels. This paper gives the brief description of the models and the methodologies relevant for the contacting Zircaloy-2 pressure tubes. (author)

  14. Toward High Carrier Mobility and Low Contact Resistance:Laser Cleaning of PMMA Residues on Graphene Surfaces

    Institute of Scientific and Technical Information of China (English)

    Yuehui Jia; Xin Gong; Pei Peng; Zidong Wang; Zhongzheng Tian; Liming Ren; Yunyi Fu; Han Zhang

    2016-01-01

    Poly(methyl methacrylate)(PMMA) is widely used for graphene transfer and device fabrication.However,it inevitably leaves a thin layer of polymer residues after acetone rinsing and leads to dramatic degradation of device performance.How to eliminate contamination and restore clean surfaces of graphene is still highly demanded.In this paper,we present a reliable and position-controllable method to remove the polymer residues on graphene films by laser exposure.Under proper laser conditions,PMMA residues can be substantially reduced without introducing defects to the underlying graphene.Furthermore,by applying this laser cleaning technique to the channel and contacts of graphene fieldeffect transistors(GFETs),higher carrier mobility as well as lower contact resistance can be realized.This work opens a way for probing intrinsic properties of contaminant-free graphene and fabricating high-performance GFETs with both clean channel and intimate graphene/metal contact.

  15. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  16. Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    (PROSTA) family of pairwise structure alignment methods [1, 2] that address the fragmentation issue of pockets and interfaces, and automatically align interfaces between any types of biological complexes. Our PROSTA structure alignment methods have two critical advantages comparing to existing structure alignment methods. First, our methods are completely sequence order independent, which is critical to the success of pairwise pocket and interface structure alignments. This is achieved by introducing contact groups that are not limited to backbone fragments, and by employing a maximum weighted bipartite matching solver from the beginning of the alignment process. In addition, our methods incorporate similarities of sequentially and structurally remote residues that potentially model the topology of the global structure. Comparing to existing methods that focus on local structure or whole sequence similarities, topological similarities are more reliable to find near-optimal structure alignments in the initial alignment state. As a result, a significant number of similar pockets and interfaces are newly discovered, and literatures also support that similar functions are shared between biological complexes in our cases studies. The PROSTA web-server and source codes are publicly available at "http://www.cbrc.kaust.edu.sa/prosta/".

  17. COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming.

    Science.gov (United States)

    Zhang, Huiling; Huang, Qingsheng; Bei, Zhendong; Wei, Yanjie; Floudas, Christodoulos A

    2016-03-01

    In this article, we present COMSAT, a hybrid framework for residue contact prediction of transmembrane (TM) proteins, integrating a support vector machine (SVM) method and a mixed integer linear programming (MILP) method. COMSAT consists of two modules: COMSAT_SVM which is trained mainly on position-specific scoring matrix features, and COMSAT_MILP which is an ab initio method based on optimization models. Contacts predicted by the SVM model are ranked by SVM confidence scores, and a threshold is trained to improve the reliability of the predicted contacts. For TM proteins with no contacts above the threshold, COMSAT_MILP is used. The proposed hybrid contact prediction scheme was tested on two independent TM protein sets based on the contact definition of 14 Å between Cα-Cα atoms. First, using a rigorous leave-one-protein-out cross validation on the training set of 90 TM proteins, an accuracy of 66.8%, a coverage of 12.3%, a specificity of 99.3% and a Matthews' correlation coefficient (MCC) of 0.184 were obtained for residue pairs that are at least six amino acids apart. Second, when tested on a test set of 87 TM proteins, the proposed method showed a prediction accuracy of 64.5%, a coverage of 5.3%, a specificity of 99.4% and a MCC of 0.106. COMSAT shows satisfactory results when compared with 12 other state-of-the-art predictors, and is more robust in terms of prediction accuracy as the length and complexity of TM protein increase. COMSAT is freely accessible at http://hpcc.siat.ac.cn/COMSAT/. © 2016 Wiley Periodicals, Inc.

  18. TCR-contacting residues orientation and HLA-DRβ* binding preference determine long-lasting protective immunity against malaria

    International Nuclear Information System (INIS)

    Alba, Martha P.; Suarez, Carlos F.; Varela, Yahson; Patarroyo, Manuel A.; Bermudez, Adriana; Patarroyo, Manuel E.

    2016-01-01

    Fully-protective, long-lasting, immunological (FPLLI) memory against Plasmodium falciparum malaria regarding immune protection-inducing protein structures (IMPIPS) vaccinated into monkeys previously challenged and re-challenged 60 days later with a lethal Aotus monkey-adapted P. falciparum strain was found to be associated with preferential high binding capacity to HLA-DRβ1* allelic molecules of the major histocompatibility class II (MHC-II), rather than HLA-DRβ3*, β4*, β5* alleles. Complete PPII L 3D structure, a longer distance (26.5 Å ± 1.5 Å) between residues perfectly fitting into HLA-DRβ1*PBR pockets 1 and 9, a gauche − rotamer orientation in p8 TCR-contacting polar residue and a larger volume of polar p2 residues was also found. This data, in association with previously-described p3 and p7 apolar residues having gauche + orientation to form a perfect MHC-II-peptide-TCR complex, determines the stereo-electronic and topochemical characteristics associated with FPLLI immunological memory. - Highlights: • Stereo-electronic and topochemical rules associated with FPLLI immunological memory. • Presence of very high long-lasting antibody titres against Plasmodium falciparum Spz. • Protective memory induction associated with a binding capacity to HLA-DRβ1*. • gauche − rotamer orientation in p8 polar residue is related to is related to immunological memory.

  19. TCR-contacting residues orientation and HLA-DRβ* binding preference determine long-lasting protective immunity against malaria

    Energy Technology Data Exchange (ETDEWEB)

    Alba, Martha P.; Suarez, Carlos F. [Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D. C. (Colombia); Universidad del Rosario, Bogotá D. C. (Colombia); Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá (Colombia); Varela, Yahson [Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D. C. (Colombia); Patarroyo, Manuel A.; Bermudez, Adriana [Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D. C. (Colombia); Universidad del Rosario, Bogotá D. C. (Colombia); Patarroyo, Manuel E., E-mail: mepatarr@gmail.com [Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D. C. (Colombia); Universidad Nacional de Colombia, Bogotá D. C. (Colombia)

    2016-09-02

    Fully-protective, long-lasting, immunological (FPLLI) memory against Plasmodium falciparum malaria regarding immune protection-inducing protein structures (IMPIPS) vaccinated into monkeys previously challenged and re-challenged 60 days later with a lethal Aotus monkey-adapted P. falciparum strain was found to be associated with preferential high binding capacity to HLA-DRβ1* allelic molecules of the major histocompatibility class II (MHC-II), rather than HLA-DRβ3*, β4*, β5* alleles. Complete PPII{sub L} 3D structure, a longer distance (26.5 Å ± 1.5 Å) between residues perfectly fitting into HLA-DRβ1*PBR pockets 1 and 9, a gauche{sup −} rotamer orientation in p8 TCR-contacting polar residue and a larger volume of polar p2 residues was also found. This data, in association with previously-described p3 and p7 apolar residues having gauche{sup +} orientation to form a perfect MHC-II-peptide-TCR complex, determines the stereo-electronic and topochemical characteristics associated with FPLLI immunological memory. - Highlights: • Stereo-electronic and topochemical rules associated with FPLLI immunological memory. • Presence of very high long-lasting antibody titres against Plasmodium falciparum Spz. • Protective memory induction associated with a binding capacity to HLA-DRβ1*. • gauche{sup −} rotamer orientation in p8 polar residue is related to is related to immunological memory.

  20. Pairwise harmonics for shape analysis

    KAUST Repository

    Zheng, Youyi

    2013-07-01

    This paper introduces a simple yet effective shape analysis mechanism for geometry processing. Unlike traditional shape analysis techniques which compute descriptors per surface point up to certain neighborhoods, we introduce a shape analysis framework in which the descriptors are based on pairs of surface points. Such a pairwise analysis approach leads to a new class of shape descriptors that are more global, discriminative, and can effectively capture the variations in the underlying geometry. Specifically, we introduce new shape descriptors based on the isocurves of harmonic functions whose global maximum and minimum occur at the point pair. We show that these shape descriptors can infer shape structures and consistently lead to simpler and more efficient algorithms than the state-of-the-art methods for three applications: intrinsic reflectional symmetry axis computation, matching shape extremities, and simultaneous surface segmentation and skeletonization. © 2012 IEEE.

  1. Theory of pairwise lesion interaction

    International Nuclear Information System (INIS)

    Harder, Dietrich; Virsik-Peuckert, Patricia; Bartels, Ernst

    1992-01-01

    A comparison between repair time constants measured both at the molecular and cellular levels has shown that the DNA double strand break is the molecular change of key importance in the causation of cellular effects such as chromosome aberrations and cell inactivation. Cell fusion experiments provided the evidence that it needs the pairwise interaction between two double strand breaks - or more exactly between the two ''repair sites'' arising from them in the course of enzymatic repair - to provide the faulty chromatin crosslink which leads to cytogenetic and cytolethal effects. These modern experiments have confirmed the classical assumption of pairwise lesion interaction (PLI) on which the models of Lea and Neary were based. It seems worthwhile to continue and complete the mathematical treatment of their proposed mechanism in order to show in quantitative terms that the well-known fractionation, protraction and linear energy transfer (LET) irradiation effects are consequences of or can at least be partly attributed to PLI. Arithmetic treatment of PLI - a second order reaction - has also the advantage of providing a prerequisite for further investigations into the stages of development of misrepair products such as chromatin crosslinks. It has been possible to formulate a completely arithmetic theory of PLI by consequently applying three biophysically permitted approximations - pure first order lesion repair kinetics, dose-independent repair time constants and low yield of the ionization/lesion conversion. The mathematical approach will be summarized here, including several formulae not elaborated at the time of previous publications. We will also study an application which sheds light on the chain of events involved in PLI. (author)

  2. Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein’s structural organization

    Directory of Open Access Journals (Sweden)

    Sengupta Dhriti

    2012-06-01

    Full Text Available Abstract Background The three-dimensional structure of a protein can be described as a graph where nodes represent residues and the strength of non-covalent interactions between them are edges. These protein contact networks can be separated into long and short-range interactions networks depending on the positions of amino acids in primary structure. Long-range interactions play a distinct role in determining the tertiary structure of a protein while short-range interactions could largely contribute to the secondary structure formations. In addition, physico chemical properties and the linear arrangement of amino acids of the primary structure of a protein determines its three dimensional structure. Here, we present an extensive analysis of protein contact subnetworks based on the London van der Waals interactions of amino acids at different length scales. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networks and have tried to correlate their influence in the overall topology and organization of a protein. Results The largest connected component (LCC of long (LRN-, short (SRN- and all-range (ARN networks within proteins exhibit a transition behaviour when plotted against different interaction strengths of edges among amino acid nodes. While short-range networks having chain like structures exhibit highly cooperative transition; long- and all-range networks, which are more similar to each other, have non-chain like structures and show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networks have similar transition behaviours with all residues all-range networks, but the hydrophilic and charged residues networks don’t. While the nature of transitions of LCC’s sizes is same in SRNs for thermophiles and mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnected long-range interactions in thermophiles than mesophiles, even at

  3. Analysis of core-periphery organization in protein contact networks reveals groups of structurally and functionally critical residues.

    Science.gov (United States)

    Isaac, Arnold Emerson; Sinha, Sitabhra

    2015-10-01

    The representation of proteins as networks of interacting amino acids, referred to as protein contact networks (PCN), and their subsequent analyses using graph theoretic tools, can provide novel insights into the key functional roles of specific groups of residues. We have characterized the networks corresponding to the native states of 66 proteins (belonging to different families) in terms of their core-periphery organization. The resulting hierarchical classification of the amino acid constituents of a protein arranges the residues into successive layers - having higher core order - with increasing connection density, ranging from a sparsely linked periphery to a densely intra-connected core (distinct from the earlier concept of protein core defined in terms of the three-dimensional geometry of the native state, which has least solvent accessibility). Our results show that residues in the inner cores are more conserved than those at the periphery. Underlining the functional importance of the network core, we see that the receptor sites for known ligand molecules of most proteins occur in the innermost core. Furthermore, the association of residues with structural pockets and cavities in binding or active sites increases with the core order. From mutation sensitivity analysis, we show that the probability of deleterious or intolerant mutations also increases with the core order. We also show that stabilization centre residues are in the innermost cores, suggesting that the network core is critically important in maintaining the structural stability of the protein. A publicly available Web resource for performing core-periphery analysis of any protein whose native state is known has been made available by us at http://www.imsc.res.in/ ~sitabhra/proteinKcore/index.html.

  4. Contact toxicity and residual effects of selected insecticides against the adult Paederus fuscipes (Coleoptera: Staphylinidae).

    Science.gov (United States)

    Bong, Lee-Jin; Neoh, Kok-Boon; Jaal, Zairi; Lee, Chow-Yang

    2013-12-01

    The contact toxicity of four insecticide formulations (deltamethrin, fipronil, fenitrothion, and imidacloprid) applied on three different substrates (tile, plywood, and concrete) against the adult rove beetle, Paederus fuscipes Curtis, was evaluated. The relative order of speed of killing effects was as follows: deltamethrin > imidacloprid > fipronil > fenitrothion. Although deltamethrin showed the fastest action against P. fuscipes, the recovery rate of rove beetles at 48 h posttreatment was moderate (approximately 25%) on the tile surface to high (approximately 80%) on the plywood surface. Thus, it is likely that the insects did not pick up the lethal dose especially on porous surfaces. In contrast, fipronil demonstrated delayed toxicity that might promote maximal uptake by the insects. More than 80% mortality was registered for tile and plywood surfaces up to 4 wk after exposure. High mortality (almost 100%) was recorded for imidacloprid-exposed P. fuscipes at 48 h posttreatment, but only on the tile surface. Among the four insecticides tested, fenitrothion was the least effective against P. fuscipes because low percentage to no mortality was recorded in the fenitrothion treatment.

  5. Doctoral Program Selection Using Pairwise Comparisons.

    Science.gov (United States)

    Tadisina, Suresh K.; Bhasin, Vijay

    1989-01-01

    The application of a pairwise comparison methodology (Saaty's Analytic Hierarchy Process) to the doctoral program selection process is illustrated. A hierarchy for structuring and facilitating the doctoral program selection decision is described. (Author/MLW)

  6. Statistical physics of pairwise probability models

    Directory of Open Access Journals (Sweden)

    Yasser Roudi

    2009-11-01

    Full Text Available Statistical models for describing the probability distribution over the states of biological systems are commonly used for dimensional reduction. Among these models, pairwise models are very attractive in part because they can be fit using a reasonable amount of data: knowledge of the means and correlations between pairs of elements in the system is sufficient. Not surprisingly, then, using pairwise models for studying neural data has been the focus of many studies in recent years. In this paper, we describe how tools from statistical physics can be employed for studying and using pairwise models. We build on our previous work on the subject and study the relation between different methods for fitting these models and evaluating their quality. In particular, using data from simulated cortical networks we study how the quality of various approximate methods for inferring the parameters in a pairwise model depends on the time bin chosen for binning the data. We also study the effect of the size of the time bin on the model quality itself, again using simulated data. We show that using finer time bins increases the quality of the pairwise model. We offer new ways of deriving the expressions reported in our previous work for assessing the quality of pairwise models.

  7. Metabolic network prediction through pairwise rational kernels.

    Science.gov (United States)

    Roche-Lima, Abiel; Domaratzki, Michael; Fristensky, Brian

    2014-09-26

    Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. We create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy

  8. Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models

    KAUST Repository

    Vangone, Anna

    2013-10-17

    Herein we propose the use of a consensus approach, CONSRANK, for ranking CAPRI models. CONSRANK relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. Models are ranked according to their ability to match the most frequently observed contacts. We applied CONSRANK to 19 CAPRI protein-protein targets, covering a wide range of prediction difficulty and involved in a variety of biological functions. CONSRANK results are consistently good, both in terms of native-like (NL) solutions ranked in the top positions and of values of the Area Under the receiver operating characteristic Curve (AUC). For targets having a percentage of NL solutions above 3%, an excellent performance is found, with AUC values approaching 1. For the difficult target T46, having only 3.4% NL solutions, the number of NL solutions in the top 5 and 10 ranked positions is enriched by a factor 30, and the AUC value is as high as 0.997. AUC values below 0.8 are only found for targets featuring a percentage of NL solutions within 1.1%. Remarkably, a false consensus emerges only in one case, T42, which happens to be an artificial protein, whose assembly details remain uncertain, based on controversial experimental data. We also show that CONSRANK still performs very well on a limited number of models, provided that more than 1 NL solution is included in the ensemble, thus extending its applicability to cases where few dozens of models are available.© 2013 Wiley Periodicals, Inc.

  9. Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds

    Directory of Open Access Journals (Sweden)

    Felix Simkovic

    2016-07-01

    Full Text Available For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based structure prediction. Such models can be used in structure solution by molecular replacement (MR where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions (`decoys', is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue–residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.

  10. Control of peptide nanotube diameter by chemical modifications of an aromatic residue involved in a single close contact

    Science.gov (United States)

    Tarabout, Christophe; Roux, Stéphane; Gobeaux, Frédéric; Fay, Nicolas; Pouget, Emilie; Meriadec, Cristelle; Ligeti, Melinda; Thomas, Daniel; IJsselstijn, Maarten; Besselievre, François; Buisson, David-Alexandre; Verbavatz, Jean-Marc; Petitjean, Michel; Valéry, Céline; Perrin, Lionel; Rousseau, Bernard; Artzner, Franck; Paternostre, Maité; Cintrat, Jean-Christophe

    2011-01-01

    Supramolecular self-assembly is an attractive pathway for bottom-up synthesis of novel nanomaterials. In particular, this approach allows the spontaneous formation of structures of well-defined shapes and monodisperse characteristic sizes. Because nanotechnology mainly relies on size-dependent physical phenomena, the control of monodispersity is required, but the possibility of tuning the size is also essential. For self-assembling systems, shape, size, and monodispersity are mainly settled by the chemical structure of the building block. Attempts to change the size notably by chemical modification usually end up with the loss of self-assembly. Here, we generated a library of 17 peptides forming nanotubes of monodisperse diameter ranging from 10 to 36 nm. A structural model taking into account close contacts explains how a modification of a few Å of a single aromatic residue induces a fourfold increase in nanotube diameter. The application of such a strategy is demonstrated by the formation of silica nanotubes of various diameters. PMID:21518895

  11. Preference Learning and Ranking by Pairwise Comparison

    Science.gov (United States)

    Fürnkranz, Johannes; Hüllermeier, Eyke

    This chapter provides an overview of recent work on preference learning and ranking via pairwise classification. The learning by pairwise comparison (LPC) paradigm is the natural machine learning counterpart to the relational approach to preference modeling and decision making. From a machine learning point of view, LPC is especially appealing as it decomposes a possibly complex prediction problem into a certain number of learning problems of the simplest type, namely binary classification. We explain how to approach different preference learning problems, such as label and instance ranking, within the framework of LPC. We primarily focus on methodological aspects, but also address theoretical questions as well as algorithmic and complexity issues.

  12. Statistical physics of pairwise probability models

    DEFF Research Database (Denmark)

    Roudi, Yasser; Aurell, Erik; Hertz, John

    2009-01-01

    (dansk abstrakt findes ikke) Statistical models for describing the probability distribution over the states of biological systems are commonly used for dimensional reduction. Among these models, pairwise models are very attractive in part because they can be fit using a reasonable amount of  data......: knowledge of the means and correlations between pairs of elements in the system is sufficient. Not surprisingly, then, using pairwise models for studying neural data has been the focus of many studies in recent years. In this paper, we describe how tools from statistical physics can be employed for studying...

  13. Unjamming in models with analytic pairwise potentials

    NARCIS (Netherlands)

    Kooij, S.; Lerner, E.

    Canonical models for studying the unjamming scenario in systems of soft repulsive particles assume pairwise potentials with a sharp cutoff in the interaction range. The sharp cutoff renders the potential nonanalytic but makes it possible to describe many properties of the solid in terms of the

  14. A decomposition of pairwise continuity via ideals

    Directory of Open Access Journals (Sweden)

    Mahes Wari

    2016-02-01

    Full Text Available In this paper, we introduce and study the notions of (i, j - regular - ℐ -closed sets, (i, j - Aℐ -sets, (i, j - ℐ -locally closed sets, p- Aℐ -continuous functions and p- ℐ -LC-continuous functions in ideal bitopological spaces and investigate some of their properties. Also, a new decomposition of pairwise continuity is obtained using these sets.

  15. PAIRWISE BLENDING OF HIGH LEVEL WASTE

    International Nuclear Information System (INIS)

    CERTA, P.J.

    2006-01-01

    The primary objective of this study is to demonstrate a mission scenario that uses pairwise and incidental blending of high level waste (HLW) to reduce the total mass of HLW glass. Secondary objectives include understanding how recent refinements to the tank waste inventory and solubility assumptions affect the mass of HLW glass and how logistical constraints may affect the efficacy of HLW blending

  16. Pairwise conjoint analysis of activity engagement choice

    NARCIS (Netherlands)

    Wang, Donggen; Oppewal, H.; Timmermans, H.J.P.

    2000-01-01

    Information overload is a well-known problem of conjoint choice models when respondents have to evaluate a large number of attributes and/or attribute levels. In this paper we develop an alternative conjoint modelling approach, called pairwise conjoint analysis. It differs from conventional conjoint

  17. Total effects of contact and residual exposure of bifenthrin and λ-cyhalothrin on the predatory mite Galendromus occidentalis (Acari: Phytoseiidae).

    Science.gov (United States)

    Hamby, Kelly A; Alifano, Jesse A; Zalom, Frank G

    2013-10-01

    Pyrethroid insecticides are generally regarded as acutely toxic to predatory phytoseiid mites; however, persistence of hull split spray pyrethroid residues on almond trees and their effects on phytoseiids have not been quantified over time. Hull split, the separation of the almond hull along the suture, exposes the new crop nuts to infestation by Amyelois transitella (Walker) larvae, and is the preferred timing for insecticides applied for their control. Galendromus occidentalis (Nesbitt) is the most important phytoseiid biocontrol agent for web-spinning spider mites in California (USA) almond orchards, and the impact of bifenthrin and λ-cyhalothrin pyrethroid residue on their survival, fertility, and fecundity was determined. The total effects of direct contact with esfenvalerate, permethrin, bifenthrin and λ-cyhalothrin were also evaluated for comparison. The total effects (E) of direct contact treatments of the four pyrethroids ranged from 77.8 % for esfenvalerate to 98.8 % for bifenthrin. Both bifenthrin and λ-cyhalothrin twig residue would be considered harmful (IOBC class 4) following field application at hull split timing. Bifenthrin twig residue would be considered slightly harmful (IOBC class 2) for up to 3.5 months and harmless (IOBC class 1) after 6 months. λ-cyhalothrin residue would be considered moderately harmful (IOBC class 3) for up to 3.5 months following application and harmless (IOBC class 1) after 6 months. Bifenthrin and λ-cyhalothrin twig residue on treated trees significantly reduced G. occidentalis female survival for up to 6 months post-treatment, however total effects (E) classify these residues as harmless (IOBC class 1) after 6 months. Harmful effects of direct and residual exposure following application have implications for the use of these pyrethroids in an integrated mite management program for perennial crops.

  18. Supplier Evaluation Process by Pairwise Comparisons

    Directory of Open Access Journals (Sweden)

    Arkadiusz Kawa

    2015-01-01

    Full Text Available We propose to assess suppliers by using consistency-driven pairwise comparisons for tangible and intangible criteria. The tangible criteria are simpler to compare (e.g., the price of a service is lower than that of another service with identical characteristics. Intangible criteria are more difficult to assess. The proposed model combines assessments of both types of criteria. The main contribution of this paper is the presentation of an extension framework for the selection of suppliers in a procurement process. The final weights are computed from relative pairwise comparisons. For the needs of the paper, surveys were conducted among Polish managers dealing with cooperation with suppliers in their enterprises. The Polish practice and restricted bidding are discussed, too.

  19. Selecting numerical scales for pairwise comparisons

    International Nuclear Information System (INIS)

    Elliott, Michael A.

    2010-01-01

    It is often desirable in decision analysis problems to elicit from an individual the rankings of a population of attributes according to the individual's preference and to understand the degree to which each attribute is preferred to the others. A common method for obtaining this information involves the use of pairwise comparisons, which allows an analyst to convert subjective expressions of preference between two attributes into numerical values indicating preferences across the entire population of attributes. Key to the use of pairwise comparisons is the underlying numerical scale that is used to convert subjective linguistic expressions of preference into numerical values. This scale represents the psychological manner in which individuals perceive increments of preference among abstract attributes and it has important implications about the distribution and consistency of an individual's preferences. Three popular scale types, the traditional integer scales, balanced scales and power scales are examined. Results of a study of 64 individuals responding to a hypothetical decision problem show that none of these scales can accurately capture the preferences of all individuals. A study of three individuals working on an actual engineering decision problem involving the design of a decay heat removal system for a nuclear fission reactor show that the choice of scale can affect the preferred decision. It is concluded that applications of pairwise comparisons would benefit from permitting participants to choose the scale that best models their own particular way of thinking about the relative preference of attributes.

  20. Unjamming in models with analytic pairwise potentials

    Science.gov (United States)

    Kooij, Stefan; Lerner, Edan

    2017-06-01

    Canonical models for studying the unjamming scenario in systems of soft repulsive particles assume pairwise potentials with a sharp cutoff in the interaction range. The sharp cutoff renders the potential nonanalytic but makes it possible to describe many properties of the solid in terms of the coordination number z , which has an unambiguous definition in these cases. Pairwise potentials without a sharp cutoff in the interaction range have not been studied in this context, but should in fact be considered to understand the relevance of the unjamming phenomenology in systems where such a cutoff is not present. In this work we explore two systems with such interactions: an inverse power law and an exponentially decaying pairwise potential, with the control parameters being the exponent (of the inverse power law) for the former and the number density for the latter. Both systems are shown to exhibit the characteristic features of the unjamming transition, among which are the vanishing of the shear-to-bulk modulus ratio and the emergence of an excess of low-frequency vibrational modes. We establish a relation between the pressure-to-bulk modulus ratio and the distance to unjamming in each of our model systems. This allows us to predict the dependence of other key observables on the distance to unjamming. Our results provide the means for a quantitative estimation of the proximity of generic glass-forming models to the unjamming transition in the absence of a clear-cut definition of the coordination number and highlight the general irrelevance of nonaffine contributions to the bulk modulus.

  1. Pairwise Trajectory Management (PTM): Concept Overview

    Science.gov (United States)

    Jones, Kenneth M.; Graff, Thomas J.; Chartrand, Ryan C.; Carreno, Victor; Kibler, Jennifer L.

    2017-01-01

    Pairwise Trajectory Management (PTM) is an Interval Management (IM) concept that utilizes airborne and ground-based capabilities to enable the implementation of airborne pairwise spacing capabilities in oceanic regions. The goal of PTM is to use airborne surveillance and tools to manage an "at or greater than" inter-aircraft spacing. Due to the precision of Automatic Dependent Surveillance-Broadcast (ADS-B) information and the use of airborne spacing guidance, the PTM minimum spacing distance will be less than distances a controller can support with current automation systems that support oceanic operations. Ground tools assist the controller in evaluating the traffic picture and determining appropriate PTM clearances to be issued. Avionics systems provide guidance information that allows the flight crew to conform to the PTM clearance issued by the controller. The combination of a reduced minimum distance and airborne spacing management will increase the capacity and efficiency of aircraft operations at a given altitude or volume of airspace. This paper provides an overview of the proposed application, description of a few key scenarios, high level discussion of expected air and ground equipment and procedure changes, overview of a potential flight crew human-machine interface that would support PTM operations and some initial PTM benefits results.

  2. Nonparametric predictive pairwise comparison with competing risks

    International Nuclear Information System (INIS)

    Coolen-Maturi, Tahani

    2014-01-01

    In reliability, failure data often correspond to competing risks, where several failure modes can cause a unit to fail. This paper presents nonparametric predictive inference (NPI) for pairwise comparison with competing risks data, assuming that the failure modes are independent. These failure modes could be the same or different among the two groups, and these can be both observed and unobserved failure modes. NPI is a statistical approach based on few assumptions, with inferences strongly based on data and with uncertainty quantified via lower and upper probabilities. The focus is on the lower and upper probabilities for the event that the lifetime of a future unit from one group, say Y, is greater than the lifetime of a future unit from the second group, say X. The paper also shows how the two groups can be compared based on particular failure mode(s), and the comparison of the two groups when some of the competing risks are combined is discussed

  3. Locating one pairwise interaction: Three recursive constructions

    Directory of Open Access Journals (Sweden)

    Charles J. Colbourn

    2016-09-01

    Full Text Available In a complex component-based system, choices (levels for components (factors may interact tocause faults in the system behaviour. When faults may be caused by interactions among few factorsat specific levels, covering arrays provide a combinatorial test suite for discovering the presence offaults. While well studied, covering arrays do not enable one to determine the specific levels of factorscausing the faults; locating arrays ensure that the results from test suite execution suffice to determinethe precise levels and factors causing faults, when the number of such causes is small. Constructionsfor locating arrays are at present limited to heuristic computational methods and quite specific directconstructions. In this paper three recursive constructions are developed for locating arrays to locateone pairwise interaction causing a fault.

  4. Statistical pairwise interaction model of stock market

    Science.gov (United States)

    Bury, Thomas

    2013-03-01

    Financial markets are a classical example of complex systems as they are compound by many interacting stocks. As such, we can obtain a surprisingly good description of their structure by making the rough simplification of binary daily returns. Spin glass models have been applied and gave some valuable results but at the price of restrictive assumptions on the market dynamics or they are agent-based models with rules designed in order to recover some empirical behaviors. Here we show that the pairwise model is actually a statistically consistent model with the observed first and second moments of the stocks orientation without making such restrictive assumptions. This is done with an approach only based on empirical data of price returns. Our data analysis of six major indices suggests that the actual interaction structure may be thought as an Ising model on a complex network with interaction strengths scaling as the inverse of the system size. This has potentially important implications since many properties of such a model are already known and some techniques of the spin glass theory can be straightforwardly applied. Typical behaviors, as multiple equilibria or metastable states, different characteristic time scales, spatial patterns, order-disorder, could find an explanation in this picture.

  5. Predicting community composition from pairwise interactions

    Science.gov (United States)

    Friedman, Jonathan; Higgins, Logan; Gore, Jeff

    The ability to predict the structure of complex, multispecies communities is crucial for understanding the impact of species extinction and invasion on natural communities, as well as for engineering novel, synthetic communities. Communities are often modeled using phenomenological models, such as the classical generalized Lotka-Volterra (gLV) model. While a lot of our intuition comes from such models, their predictive power has rarely been tested experimentally. To directly assess the predictive power of this approach, we constructed synthetic communities comprised of up to 8 soil bacteria. We measured the outcome of competition between all species pairs, and used these measurements to predict the composition of communities composed of more than 2 species. The pairwise competitions resulted in a diverse set of outcomes, including coexistence, exclusion, and bistability, and displayed evidence for both interference and facilitation. Most pair outcomes could be captured by the gLV framework, and the composition of multispecies communities could be predicted for communities composed solely of such pairs. Our results demonstrate the predictive ability and utility of simple phenomenology, which enables accurate predictions in the absence of mechanistic details.

  6. A scalable pairwise class interaction framework for multidimensional classification

    DEFF Research Database (Denmark)

    Arias, Jacinto; Gámez, Jose A.; Nielsen, Thomas Dyhre

    2016-01-01

    We present a general framework for multidimensional classification that cap- tures the pairwise interactions between class variables. The pairwise class inter- actions are encoded using a collection of base classifiers (Phase 1), for which the class predictions are combined in a Markov random fie...

  7. SVM-dependent pairwise HMM: an application to protein pairwise alignments.

    Science.gov (United States)

    Orlando, Gabriele; Raimondi, Daniele; Khan, Taushif; Lenaerts, Tom; Vranken, Wim F

    2017-12-15

    Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. wim.vranken@vub.be. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  8. Pseudo inputs for pairwise learning with Gaussian processes

    DEFF Research Database (Denmark)

    Nielsen, Jens Brehm; Jensen, Bjørn Sand; Larsen, Jan

    2012-01-01

    We consider learning and prediction of pairwise comparisons between instances. The problem is motivated from a perceptual view point, where pairwise comparisons serve as an effective and extensively used paradigm. A state-of-the-art method for modeling pairwise data in high dimensional domains...... is based on a classical pairwise probit likelihood imposed with a Gaussian process prior. While extremely flexible, this non-parametric method struggles with an inconvenient O(n3) scaling in terms of the n input instances which limits the method only to smaller problems. To overcome this, we derive...... to other similar approximations that have been applied in standard Gaussian process regression and classification problems such as FI(T)C and PI(T)C....

  9. 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.

  10. Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

    Science.gov (United States)

    Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

    2008-11-15

    Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions.

  11. Pairwise Constraint-Guided Sparse Learning for Feature Selection.

    Science.gov (United States)

    Liu, Mingxia; Zhang, Daoqiang

    2016-01-01

    Feature selection aims to identify the most informative features for a compact and accurate data representation. As typical supervised feature selection methods, Lasso and its variants using L1-norm-based regularization terms have received much attention in recent studies, most of which use class labels as supervised information. Besides class labels, there are other types of supervised information, e.g., pairwise constraints that specify whether a pair of data samples belong to the same class (must-link constraint) or different classes (cannot-link constraint). However, most of existing L1-norm-based sparse learning methods do not take advantage of the pairwise constraints that provide us weak and more general supervised information. For addressing that problem, we propose a pairwise constraint-guided sparse (CGS) learning method for feature selection, where the must-link and the cannot-link constraints are used as discriminative regularization terms that directly concentrate on the local discriminative structure of data. Furthermore, we develop two variants of CGS, including: 1) semi-supervised CGS that utilizes labeled data, pairwise constraints, and unlabeled data and 2) ensemble CGS that uses the ensemble of pairwise constraint sets. We conduct a series of experiments on a number of data sets from University of California-Irvine machine learning repository, a gene expression data set, two real-world neuroimaging-based classification tasks, and two large-scale attribute classification tasks. Experimental results demonstrate the efficacy of our proposed methods, compared with several established feature selection methods.

  12. Automatic Camera Calibration Using Multiple Sets of Pairwise Correspondences.

    Science.gov (United States)

    Vasconcelos, Francisco; Barreto, Joao P; Boyer, Edmond

    2018-04-01

    We propose a new method to add an uncalibrated node into a network of calibrated cameras using only pairwise point correspondences. While previous methods perform this task using triple correspondences, these are often difficult to establish when there is limited overlap between different views. In such challenging cases we must rely on pairwise correspondences and our solution becomes more advantageous. Our method includes an 11-point minimal solution for the intrinsic and extrinsic calibration of a camera from pairwise correspondences with other two calibrated cameras, and a new inlier selection framework that extends the traditional RANSAC family of algorithms to sampling across multiple datasets. Our method is validated on different application scenarios where a lack of triple correspondences might occur: addition of a new node to a camera network; calibration and motion estimation of a moving camera inside a camera network; and addition of views with limited overlap to a Structure-from-Motion model.

  13. A predictive model of music preference using pairwise comparisons

    DEFF Research Database (Denmark)

    Jensen, Bjørn Sand; Gallego, Javier Saez; Larsen, Jan

    2012-01-01

    Music recommendation is an important aspect of many streaming services and multi-media systems, however, it is typically based on so-called collaborative filtering methods. In this paper we consider the recommendation task from a personal viewpoint and examine to which degree music preference can...... be elicited and predicted using simple and robust queries such as pairwise comparisons. We propose to model - and in turn predict - the pairwise music preference using a very flexible model based on Gaussian Process priors for which we describe the required inference. We further propose a specific covariance...

  14. Structures of Preferred Human IgV Genes-Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation.

    Science.gov (United States)

    Bryson, Steve; Thomson, Christy A; Risnes, Louise F; Dasgupta, Somnath; Smith, Kenneth; Schrader, John W; Pai, Emil F

    2016-06-01

    The human Ab response to certain pathogens is oligoclonal, with preferred IgV genes being used more frequently than others. A pair of such preferred genes, IGVK3-11 and IGVH3-30, contributes to the generation of protective Abs directed against the 23F serotype of the pneumonococcal capsular polysaccharide of Streptococcus pneumoniae and against the AD-2S1 peptide of the gB membrane protein of human CMV. Structural analyses of Fab fragments of mAbs 023.102 and pn132p2C05 in complex with portions of the 23F polysaccharide revealed five germline-encoded residues in contact with the key component, l-rhamnose. In the case of the AD-2S1 peptide, the KE5 Fab fragment complex identified nine germline-encoded contact residues. Two of these germline-encoded residues, Arg91L and Trp94L, contact both the l-rhamnose and the AD-2S1 peptide. Comparison of the respective paratopes that bind to carbohydrate and protein reveals that stochastic diversity in both CDR3 loops alone almost exclusively accounts for their divergent specificity. Combined evolutionary pressure by human CMV and the 23F serotype of S. pneumoniae acted on the IGVK3-11 and IGVH3-30 genes as demonstrated by the multiple germline-encoded amino acids that contact both l-rhamnose and AD-2S1 peptide. Copyright © 2016 by The American Association of Immunologists, Inc.

  15. Dynamics of pairwise motions in the Cosmic Web

    Science.gov (United States)

    Hellwing, Wojciech A.

    2016-10-01

    We present results of analysis of the dark matter (DM) pairwise velocity statistics in different Cosmic Web environments. We use the DM velocity and density field from the Millennium 2 simulation together with the NEXUS+ algorithm to segment the simulation volume into voxels uniquely identifying one of the four possible environments: nodes, filaments, walls or cosmic voids. We show that the PDFs of the mean infall velocities v 12 as well as its spatial dependence together with the perpendicular and parallel velocity dispersions bear a significant signal of the large-scale structure environment in which DM particle pairs are embedded. The pairwise flows are notably colder and have smaller mean magnitude in wall and voids, when compared to much denser environments of filaments and nodes. We discuss on our results, indicating that they are consistent with a simple theoretical predictions for pairwise motions as induced by gravitational instability mechanism. Our results indicate that the Cosmic Web elements are coherent dynamical entities rather than just temporal geometrical associations. In addition it should be possible to observationally test various Cosmic Web finding algorithms by segmenting available peculiar velocity data and studying resulting pairwise velocity statistics.

  16. Determinants of sovereign debt yield spreads under EMU: Pairwise approach

    NARCIS (Netherlands)

    Fazlioglu, S.

    2013-01-01

    This study aims at providing an empirical analysis of long-term determinants of sovereign debt yield spreads under European EMU (Economic and Monetary Union) through pairwise approach within panel framework. Panel gravity models are increasingly used in the cross-market correlation literature while

  17. Modeling Expressed Emotions in Music using Pairwise Comparisons

    DEFF Research Database (Denmark)

    Madsen, Jens; Nielsen, Jens Brehm; Jensen, Bjørn Sand

    2012-01-01

    We introduce a two-alternative forced-choice experimental paradigm to quantify expressed emotions in music using the two wellknown arousal and valence (AV) dimensions. In order to produce AV scores from the pairwise comparisons and to visualize the locations of excerpts in the AV space, we...

  18. Dynamics of pairwise entanglement between two Tavis-Cummings atoms

    International Nuclear Information System (INIS)

    Guo Jinliang; Song Heshan

    2008-01-01

    We investigate the time evolution of pairwise entanglement between two Tavis-Cummings atoms for various entangled initial states, including pure and mixed states. We find that the phenomenon of entanglement sudden death behaviors is distinct in the evolution of entanglement for different initial states. What deserves mentioning here is that the initial portion of the excited state in the initial state is responsible for the sudden death of entanglement, and the degree of this effect also depends on the initial states

  19. Robust Subjective Visual Property Prediction from Crowdsourced Pairwise Labels.

    Science.gov (United States)

    Fu, Yanwei; Hospedales, Timothy M; Xiang, Tao; Xiong, Jiechao; Gong, Shaogang; Wang, Yizhou; Yao, Yuan

    2016-03-01

    The problem of estimating subjective visual properties from image and video has attracted increasing interest. A subjective visual property is useful either on its own (e.g. image and video interestingness) or as an intermediate representation for visual recognition (e.g. a relative attribute). Due to its ambiguous nature, annotating the value of a subjective visual property for learning a prediction model is challenging. To make the annotation more reliable, recent studies employ crowdsourcing tools to collect pairwise comparison labels. However, using crowdsourced data also introduces outliers. Existing methods rely on majority voting to prune the annotation outliers/errors. They thus require a large amount of pairwise labels to be collected. More importantly as a local outlier detection method, majority voting is ineffective in identifying outliers that can cause global ranking inconsistencies. In this paper, we propose a more principled way to identify annotation outliers by formulating the subjective visual property prediction task as a unified robust learning to rank problem, tackling both the outlier detection and learning to rank jointly. This differs from existing methods in that (1) the proposed method integrates local pairwise comparison labels together to minimise a cost that corresponds to global inconsistency of ranking order, and (2) the outlier detection and learning to rank problems are solved jointly. This not only leads to better detection of annotation outliers but also enables learning with extremely sparse annotations.

  20. Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models.

    Directory of Open Access Journals (Sweden)

    Richard R Stein

    2015-07-01

    Full Text Available Maximum entropy-based inference methods have been successfully used to infer direct interactions from biological datasets such as gene expression data or sequence ensembles. Here, we review undirected pairwise maximum-entropy probability models in two categories of data types, those with continuous and categorical random variables. As a concrete example, we present recently developed inference methods from the field of protein contact prediction and show that a basic set of assumptions leads to similar solution strategies for inferring the model parameters in both variable types. These parameters reflect interactive couplings between observables, which can be used to predict global properties of the biological system. Such methods are applicable to the important problems of protein 3-D structure prediction and association of gene-gene networks, and they enable potential applications to the analysis of gene alteration patterns and to protein design.

  1. Pairwise Trajectory Management (PTM): Concept Description and Documentation

    Science.gov (United States)

    Jones, Kenneth M.; Graff, Thomas J.; Carreno, Victor; Chartrand, Ryan C.; Kibler, Jennifer L.

    2018-01-01

    Pairwise Trajectory Management (PTM) is an Interval Management (IM) concept that utilizes airborne and ground-based capabilities to enable the implementation of airborne pairwise spacing capabilities in oceanic regions. The goal of PTM is to use airborne surveillance and tools to manage an "at or greater than" inter-aircraft spacing. Due to the accuracy of Automatic Dependent Surveillance-Broadcast (ADS-B) information and the use of airborne spacing guidance, the minimum PTM spacing distance will be less than distances a controller can support with current automation systems that support oceanic operations. Ground tools assist the controller in evaluating the traffic picture and determining appropriate PTM clearances to be issued. Avionics systems provide guidance information that allows the flight crew to conform to the PTM clearance issued by the controller. The combination of a reduced minimum distance and airborne spacing management will increase the capacity and efficiency of aircraft operations at a given altitude or volume of airspace. This document provides an overview of the proposed application, a description of several key scenarios, a high level discussion of expected air and ground equipment and procedure changes, a description of a NASA human-machine interface (HMI) prototype for the flight crew that would support PTM operations, and initial benefits analysis results. Additionally, included as appendices, are the following documents: the PTM Operational Services and Environment Definition (OSED) document and a companion "Future Considerations for the Pairwise Trajectory Management (PTM) Concept: Potential Future Updates for the PTM OSED" paper, a detailed description of the PTM algorithm and PTM Limit Mach rules, initial PTM safety requirements and safety assessment documents, a detailed description of the design, development, and initial evaluations of the proposed flight crew HMI, an overview of the methodology and results of PTM pilot training

  2. Revision of Begomovirus taxonomy based on pairwise sequence comparisons

    KAUST Repository

    Brown, Judith K.

    2015-04-18

    Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

  3. Revision of Begomovirus taxonomy based on pairwise sequence comparisons

    KAUST Repository

    Brown, Judith K.; Zerbini, F. Murilo; Navas-Castillo, Jesú s; Moriones, Enrique; Ramos-Sobrinho, Roberto; Silva, José C. F.; Fiallo-Olivé , Elvira; Briddon, Rob W.; Herná ndez-Zepeda, Cecilia; Idris, Ali; Malathi, V. G.; Martin, Darren P.; Rivera-Bustamante, Rafael; Ueda, Shigenori; Varsani, Arvind

    2015-01-01

    Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

  4. Template-based protein-protein docking exploiting pairwise interfacial residue restraints

    NARCIS (Netherlands)

    Xue, Li C; Garcia Lopes Maia Rodrigues, João; Dobbs, Drena; Honavar, Vasant; Bonvin, Alexandre M J J

    2016-01-01

    Although many advanced and sophisticatedab initioapproaches for modeling protein-protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to

  5. Measuring pair-wise molecular interactions in a complex mixture

    Science.gov (United States)

    Chakraborty, Krishnendu; Varma, Manoj M.; Venkatapathi, Murugesan

    2016-03-01

    Complex biological samples such as serum contain thousands of proteins and other molecules spanning up to 13 orders of magnitude in concentration. Present measurement techniques do not permit the analysis of all pair-wise interactions between the components of such a complex mixture to a given target molecule. In this work we explore the use of nanoparticle tags which encode the identity of the molecule to obtain the statistical distribution of pair-wise interactions using their Localized Surface Plasmon Resonance (LSPR) signals. The nanoparticle tags are chosen such that the binding between two molecules conjugated to the respective nanoparticle tags can be recognized by the coupling of their LSPR signals. This numerical simulation is done by DDA to investigate this approach using a reduced system consisting of three nanoparticles (a gold ellipsoid with aspect ratio 2.5 and short axis 16 nm, and two silver ellipsoids with aspect ratios 3 and 2 and short axes 8 nm and 10 nm respectively) and the set of all possible dimers formed between them. Incident light was circularly polarized and all possible particle and dimer orientations were considered. We observed that minimum peak separation between two spectra is 5 nm while maximum is 184nm.

  6. Extension of Pairwise Broadcast Clock Synchronization for Multicluster Sensor Networks

    Directory of Open Access Journals (Sweden)

    Bruce W. Suter

    2008-01-01

    Full Text Available Time synchronization is crucial for wireless sensor networks (WSNs in performing a number of fundamental operations such as data coordination, power management, security, and localization. The Pairwise Broadcast Synchronization (PBS protocol was recently proposed to minimize the number of timing messages required for global network synchronization, which enables the design of highly energy-efficient WSNs. However, PBS requires all nodes in the network to lie within the communication ranges of two leader nodes, a condition which might not be available in some applications. This paper proposes an extension of PBS to the more general class of sensor networks. Based on the hierarchical structure of the network, an energy-efficient pair selection algorithm is proposed to select the best pairwise synchronization sequence to reduce the overall energy consumption. It is shown that in a multicluster networking environment, PBS requires a far less number of timing messages than other well-known synchronization protocols and incurs no loss in synchronization accuracy. Moreover, the proposed scheme presents significant energy savings for densely deployed WSNs.

  7. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

    Science.gov (United States)

    Daily, Jeff

    2016-02-10

    Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar's 'striped' approach. Rognes's SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail's prefix scan implementation is generally the fastest, faster even than Farrar's 'striped' approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

  8. Calibration of Smartphone-Based Weather Measurements Using Pairwise Gossip

    Directory of Open Access Journals (Sweden)

    Jane Louie Fresco Zamora

    2015-01-01

    Full Text Available Accurate and reliable daily global weather reports are necessary for weather forecasting and climate analysis. However, the availability of these reports continues to decline due to the lack of economic support and policies in maintaining ground weather measurement systems from where these reports are obtained. Thus, to mitigate data scarcity, it is required to utilize weather information from existing sensors and built-in smartphone sensors. However, as smartphone usage often varies according to human activity, it is difficult to obtain accurate measurement data. In this paper, we present a heuristic-based pairwise gossip algorithm that will calibrate smartphone-based pressure sensors with respect to fixed weather stations as our referential ground truth. Based on actual measurements, we have verified that smartphone-based readings are unstable when observed during movement. Using our calibration algorithm on actual smartphone-based pressure readings, the updated values were significantly closer to the ground truth values.

  9. Calibration of Smartphone-Based Weather Measurements Using Pairwise Gossip.

    Science.gov (United States)

    Zamora, Jane Louie Fresco; Kashihara, Shigeru; Yamaguchi, Suguru

    2015-01-01

    Accurate and reliable daily global weather reports are necessary for weather forecasting and climate analysis. However, the availability of these reports continues to decline due to the lack of economic support and policies in maintaining ground weather measurement systems from where these reports are obtained. Thus, to mitigate data scarcity, it is required to utilize weather information from existing sensors and built-in smartphone sensors. However, as smartphone usage often varies according to human activity, it is difficult to obtain accurate measurement data. In this paper, we present a heuristic-based pairwise gossip algorithm that will calibrate smartphone-based pressure sensors with respect to fixed weather stations as our referential ground truth. Based on actual measurements, we have verified that smartphone-based readings are unstable when observed during movement. Using our calibration algorithm on actual smartphone-based pressure readings, the updated values were significantly closer to the ground truth values.

  10. Pairwise comparisons and visual perceptions of equal area polygons.

    Science.gov (United States)

    Adamic, P; Babiy, V; Janicki, R; Kakiashvili, T; Koczkodaj, W W; Tadeusiewicz, R

    2009-02-01

    The number of studies related to visual perception has been plentiful in recent years. Participants rated the areas of five randomly generated shapes of equal area, using a reference unit area that was displayed together with the shapes. Respondents were 179 university students from Canada and Poland. The average error estimated by respondents using the unit square was 25.75%. The error was substantially decreased to 5.51% when the shapes were compared to one another in pairs. This gain of 20.24% for this two-dimensional experiment was substantially better than the 11.78% gain reported in the previous one-dimensional experiments. This is the first statistically sound two-dimensional experiment demonstrating that pairwise comparisons improve accuracy.

  11. Improved scFv Anti-HIV-1 p17 Binding Affinity Guided from the Theoretical Calculation of Pairwise Decomposition Energies and Computational Alanine Scanning

    Directory of Open Access Journals (Sweden)

    Panthip Tue-ngeun

    2013-01-01

    Full Text Available Computational approaches have been used to evaluate and define important residues for protein-protein interactions, especially antigen-antibody complexes. In our previous study, pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants has indicated the key specific residues in the complementary determining regions (CDRs of scFv anti-p17. In this present investigation in order to determine whether a specific side chain group of residue in CDRs plays an important role in bioactivity, computational alanine scanning has been applied. Molecular dynamics simulations were done with several complexes of original scFv anti-p17 and scFv anti-p17mutants with HIV-1 p17 epitope variants with a production run up to 10 ns. With the combination of pairwise decomposition residue interaction and alanine scanning calculations, the point mutation has been initially selected at the position MET100 to improve the residue binding affinity. The calculated docking interaction energy between a single mutation from methionine to either arginine or glycine has shown the improved binding affinity, contributed from the electrostatic interaction with the negative favorably interaction energy, compared to the wild type. Theoretical calculations agreed well with the results from the peptide ELISA results.

  12. Optimal contact definition for reconstruction of Contact Maps

    Directory of Open Access Journals (Sweden)

    Stehr Henning

    2010-05-01

    Full Text Available Abstract Background Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure. Results We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a to what accuracy does a contact map represent its corresponding 3D structure, b what is the best contact map representation with regard to reconstructability and c what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11Å around the Cβ atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2Å RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity. Conclusions Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through

  13. Convergent cross-mapping and pairwise asymmetric inference.

    Science.gov (United States)

    McCracken, James M; Weigel, Robert S

    2014-12-01

    Convergent cross-mapping (CCM) is a technique for computing specific kinds of correlations between sets of times series. It was introduced by Sugihara et al. [Science 338, 496 (2012).] and is reported to be "a necessary condition for causation" capable of distinguishing causality from standard correlation. We show that the relationships between CCM correlations proposed by Sugihara et al. do not, in general, agree with intuitive concepts of "driving" and as such should not be considered indicative of causality. It is shown that the fact that the CCM algorithm implies causality is a function of system parameters for simple linear and nonlinear systems. For example, in a circuit containing a single resistor and inductor, both voltage and current can be identified as the driver depending on the frequency of the source voltage. It is shown that the CCM algorithm, however, can be modified to identify relationships between pairs of time series that are consistent with intuition for the considered example systems for which CCM causality analysis provided nonintuitive driver identifications. This modification of the CCM algorithm is introduced as "pairwise asymmetric inference" (PAI) and examples of its use are presented.

  14. Identifying the Academic Rising Stars via Pairwise Citation Increment Ranking

    KAUST Repository

    Zhang, Chuxu

    2017-08-02

    Predicting the fast-rising young researchers (the Academic Rising Stars) in the future provides useful guidance to the research community, e.g., offering competitive candidates to university for young faculty hiring as they are expected to have success academic careers. In this work, given a set of young researchers who have published the first first-author paper recently, we solve the problem of how to effectively predict the top k% researchers who achieve the highest citation increment in Δt years. We explore a series of factors that can drive an author to be fast-rising and design a novel pairwise citation increment ranking (PCIR) method that leverages those factors to predict the academic rising stars. Experimental results on the large ArnetMiner dataset with over 1.7 million authors demonstrate the effectiveness of PCIR. Specifically, it outperforms all given benchmark methods, with over 8% average improvement. Further analysis demonstrates that temporal features are the best indicators for rising stars prediction, while venue features are less relevant.

  15. The Role of Middlemen inEfficient and Strongly Pairwise Stable Networks

    NARCIS (Netherlands)

    Gilles, R.P.; Chakrabarti, S.; Sarangi, S.; Badasyan, N.

    2004-01-01

    We examine the strong pairwise stability concept in network formation theory under collective network benefits.Strong pairwise stability considers a pair of players to add a link through mutual consent while permitting them to unilaterally delete any subset of links under their control.We examine

  16. Language Contact.

    Science.gov (United States)

    Nelde, Peter Hans

    1995-01-01

    Examines the phenomenon of language contact and recent trends in linguistic contact research, which focuses on language use, language users, and language spheres. Also discusses the role of linguistic and cultural conflicts in language contact situations. (13 references) (MDM)

  17. ComplexContact: a web server for inter-protein contact prediction using deep learning

    KAUST Repository

    Zeng, Hong; Wang, Sheng; Zhou, Tianming; Zhao, Feifeng; Li, Xiufeng; Wu, Qing; Xu, Jinbo

    2018-01-01

    ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

  18. ComplexContact: a web server for inter-protein contact prediction using deep learning

    KAUST Repository

    Zeng, Hong

    2018-05-20

    ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

  19. ComplexContact: a web server for inter-protein contact prediction using deep learning.

    Science.gov (United States)

    Zeng, Hong; Wang, Sheng; Zhou, Tianming; Zhao, Feifeng; Li, Xiufeng; Wu, Qing; Xu, Jinbo

    2018-05-22

    ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

  20. Screening synteny blocks in pairwise genome comparisons through integer programming.

    Science.gov (United States)

    Tang, Haibao; Lyons, Eric; Pedersen, Brent; Schnable, James C; Paterson, Andrew H; Freeling, Michael

    2011-04-18

    It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events. We have formulated the synteny block screening as an optimization problem known as "Binary Integer Programming" (BIP), which is solved using existing linear programming solvers. The computer program QUOTA-ALIGN performs this task by creating a clear objective function that maximizes the compatible set of synteny blocks under given constraints on overlaps and depths (corresponding to the duplication history in respective genomes). Such a procedure is useful for any pairwise synteny alignments, but is most useful in lineages affected by multiple WGDs, like plants or fish lineages. For example, there should be a 1:2 ploidy relationship between genome A and B if genome B had an independent WGD subsequent to the divergence of the two genomes. We show through simulations and real examples using plant genomes in the rosid superorder that the quota

  1. BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis.

    Directory of Open Access Journals (Sweden)

    Allen W Bryan

    2009-03-01

    Full Text Available Amyloids and prion proteins are clinically and biologically important beta-structures, whose supersecondary structures are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Recent work has indicated the utility of pairwise probabilistic statistics in beta-structure prediction. We develop here a new strategy for beta-structure prediction, emphasizing the determination of beta-strands and pairs of beta-strands as fundamental units of beta-structure. Our program, BETASCAN, calculates likelihood scores for potential beta-strands and strand-pairs based on correlations observed in parallel beta-sheets. The program then determines the strands and pairs with the greatest local likelihood for all of the sequence's potential beta-structures. BETASCAN suggests multiple alternate folding patterns and assigns relative a priori probabilities based solely on amino acid sequence, probability tables, and pre-chosen parameters. The algorithm compares favorably with the results of previous algorithms (BETAPRO, PASTA, SALSA, TANGO, and Zyggregator in beta-structure prediction and amyloid propensity prediction. Accurate prediction is demonstrated for experimentally determined amyloid beta-structures, for a set of known beta-aggregates, and for the parallel beta-strands of beta-helices, amyloid-like globular proteins. BETASCAN is able both to detect beta-strands with higher sensitivity and to detect the edges of beta-strands in a richly beta-like sequence. For two proteins (Abeta and Het-s, there exist multiple sets of experimental data implying contradictory structures; BETASCAN is able to detect each competing structure as a potential structure variant. The ability to correlate multiple alternate beta-structures to experiment opens the possibility of computational investigation of prion strains and structural heterogeneity of amyloid

  2. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    Kolář Michal

    2012-11-01

    Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

  3. Assessment of crystalline disorder in cryo-milled samples of indomethacin using atomic pair-wise distribution functions

    DEFF Research Database (Denmark)

    Bøtker, Johan P; Karmwar, Pranav; Strachan, Clare J

    2011-01-01

    to analyse the cryo-milled samples. The high similarity between the ¿-indomethacin cryogenic ball milled samples and the crude ¿-indomethacin indicated that milled samples retained residual order of the ¿-form. The PDF analysis encompassed the capability of achieving a correlation with the physical......The aim of this study was to investigate the usefulness of the atomic pair-wise distribution function (PDF) to detect the extension of disorder/amorphousness induced into a crystalline drug using a cryo-milling technique, and to determine the optimal milling times to achieve amorphisation. The PDF...... properties determined from DSC, ss-NMR and stability experiments. Multivariate data analysis (MVDA) was used to visualize the differences in the PDF and XRPD data. The MVDA approach revealed that PDF is more efficient in assessing the introduced degree of disorder in ¿-indomethacin after cryo-milling than...

  4. Clustering biomolecular complexes by residue contacts similarity

    NARCIS (Netherlands)

    Garcia Lopes Maia Rodrigues, João; Trellet, Mikaël; Schmitz, Christophe; Kastritis, Panagiotis; Karaca, Ezgi; Melquiond, Adrien S J; Bonvin, Alexandre M J J; Garcia Lopes Maia Rodrigues, João

    Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force generation of a plethora of putative solutions. These are then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) of atomic positions.

  5. Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

    OpenAIRE

    Kelly, Brendan J.; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D.; Collman, Ronald G.; Bushman, Frederic D.; Li, Hongzhe

    2015-01-01

    Motivation: The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence–absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-...

  6. Pairwise Comparison and Distance Measure of Hesitant Fuzzy Linguistic Term Sets

    Directory of Open Access Journals (Sweden)

    Han-Chen Huang

    2014-01-01

    Full Text Available A hesitant fuzzy linguistic term set (HFLTS, allowing experts using several possible linguistic terms to assess a qualitative linguistic variable, is very useful to express people’s hesitancy in practical decision-making problems. Up to now, a little research has been done on the comparison and distance measure of HFLTSs. In this paper, we present a comparison method for HFLTSs based on pairwise comparisons of each linguistic term in the two HFLTSs. Then, a distance measure method based on the pairwise comparison matrix of HFLTSs is proposed, and we prove that this distance is equal to the distance of the average values of HFLTSs, which makes the distance measure much more simple. Finally, the pairwise comparison and distance measure methods are utilized to develop two multicriteria decision-making approaches under hesitant fuzzy linguistic environments. The results analysis shows that our methods in this paper are more reasonable.

  7. Fast and accurate estimation of the covariance between pairwise maximum likelihood distances

    Directory of Open Access Journals (Sweden)

    Manuel Gil

    2014-09-01

    Full Text Available Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989 which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

  8. Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

    Science.gov (United States)

    Gil, Manuel

    2014-01-01

    Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

  9. Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

    Science.gov (United States)

    Kelly, Brendan J; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe

    2015-08-01

    The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence-absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.

    Directory of Open Access Journals (Sweden)

    Brejnev Muhizi Muhire

    Full Text Available The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV. There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT, a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms.

  11. Document Level Assessment of Document Retrieval Systems in a Pairwise System Evaluation

    Science.gov (United States)

    Rajagopal, Prabha; Ravana, Sri Devi

    2017-01-01

    Introduction: The use of averaged topic-level scores can result in the loss of valuable data and can cause misinterpretation of the effectiveness of system performance. This study aims to use the scores of each document to evaluate document retrieval systems in a pairwise system evaluation. Method: The chosen evaluation metrics are document-level…

  12. Image ranking in video sequences using pairwise image comparisons and temporal smoothing

    CSIR Research Space (South Africa)

    Burke, Michael

    2016-12-01

    Full Text Available The ability to predict the importance of an image is highly desirable in computer vision. This work introduces an image ranking scheme suitable for use in video or image sequences. Pairwise image comparisons are used to determine image ‘interest...

  13. Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers

    NARCIS (Netherlands)

    Eisinga, R.N.; Heskes, T.M.; Pelzer, B.J.; Grotenhuis, H.F. te

    2017-01-01

    Background: The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant difference among any of the rank sums, it is typically of interest to conduct pairwise comparison tests. Current approaches to

  14. Revisiting the classification of curtoviruses based on genome-wide pairwise identity

    KAUST Repository

    Varsani, Arvind

    2014-01-25

    Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77% genome-wide pairwise identity as a species demarcation threshold and 94% genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77% genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94% identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV). © 2014 Springer-Verlag Wien.

  15. Revisiting the classification of curtoviruses based on genome-wide pairwise identity

    KAUST Repository

    Varsani, Arvind; Martin, Darren Patrick; Navas-Castillo, Jesú s; Moriones, Enrique; Herná ndez-Zepeda, Cecilia; Idris, Ali; Murilo Zerbini, F.; Brown, Judith K.

    2014-01-01

    Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77% genome-wide pairwise identity as a species demarcation threshold and 94% genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77% genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94% identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV). © 2014 Springer-Verlag Wien.

  16. A gradient approximation for calculating Debye temperatures from pairwise interatomic potentials

    International Nuclear Information System (INIS)

    Jackson, D.P.

    1975-09-01

    A simple gradient approximation is given for calculating the effective Debye temperature of a cubic crystal from central pairwise interatomic potentials. For examples of the Morse potential applied to cubic metals the results are in generally good agreement with experiment. (author)

  17. A Comparative Study of Pairwise Learning Methods Based on Kernel Ridge Regression.

    Science.gov (United States)

    Stock, Michiel; Pahikkala, Tapio; Airola, Antti; De Baets, Bernard; Waegeman, Willem

    2018-06-12

    Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction, or network inference problems. During the past decade, kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression, and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency, and spectral filtering properties. Our theoretical results provide valuable insights into assessing the advantages and limitations of existing pairwise learning methods.

  18. On the calculation of x-ray scattering signals from pairwise radial distribution functions

    DEFF Research Database (Denmark)

    Dohn, Asmus Ougaard; Biasin, Elisa; Haldrup, Kristoffer

    2015-01-01

    We derive a formulation for evaluating (time-resolved) x-ray scattering signals of solvated chemical systems, based on pairwise radial distribution functions, with the aim of this formulation to accompany molecular dynamics simulations. The derivation is described in detail to eliminate any possi...

  19. Residual stresses

    International Nuclear Information System (INIS)

    Sahotra, I.M.

    2006-01-01

    The principal effect of unloading a material strained into the plastic range is to create a permanent set (plastic deformation), which if restricted somehow, gives rise to a system of self-balancing within the same member or reaction balanced by other members of the structure., known as residual stresses. These stresses stay there as locked-in stresses, in the body or a part of it in the absence of any external loading. Residual stresses are induced during hot-rolling and welding differential cooling, cold-forming and extruding: cold straightening and spot heating, fabrication and forced fitting of components constraining the structure to a particular geometry. The areas which cool more quickly develop residual compressive stresses, while the slower cooling areas develop residual tensile stresses, and a self-balancing or reaction balanced system of residual stresses is formed. The phenomenon of residual stresses is the most challenging in its application in surface modification techniques determining endurance mechanism against fracture and fatigue failures. This paper discusses the mechanism of residual stresses, that how the residual stresses are fanned and what their behavior is under the action of external forces. Such as in the case of a circular bar under limit torque, rectangular beam under limt moment, reclaiming of shafts welds and peening etc. (author)

  20. Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

    Directory of Open Access Journals (Sweden)

    Morozov Alexandre V

    2009-08-01

    individually smaller but may have a collective effect. Together they lead to correlations which could have an important impact on the dynamics of the evolution of cross-resistance, by allowing the virus to pass through otherwise unlikely mutational states. These findings also indicate that pairwise and possibly higher-order effects should be included in the models of protein evolution, instead of assuming that all residues mutate independently of one another.

  1. Plastic deformation and contact area of an elastic-plastic contact of ellipsoid bodies after unloading

    NARCIS (Netherlands)

    Jamari, Jamari; Schipper, Dirk J.

    2007-01-01

    This paper presents theoretical and experimental results of the residual or plastic deformation and the plastic contact area of an elastic–plastic contact of ellipsoid bodies after unloading. There are three regime responses of the deformation and contact area: elastic, elastic–plastic and fully

  2. Residual stresses

    International Nuclear Information System (INIS)

    Macherauch, E.

    1978-01-01

    Residual stresses are stresses which exist in a material without the influence of external powers and moments. They come into existence when the volume of a material constantly changes its form as a consequence of mechanical, thermal, and/or chemical processes and is hindered by neighbouring volumes. Bodies with residual stress are in mechanical balance. These residual stresses can be manifested by means of all mechanical interventions disturbing this balance. Acoustical, optical, radiological, and magnetical methods involving material changes caused by residual stress can also serve for determining residual stress. Residual stresses have an ambivalent character. In technical practice, they are feared and liked at the same time. They cause trouble because they can be the cause for unexpected behaviour of construction elements. They are feared since they can cause failure, in the worst case with catastrophical consequences. They are appreciated, on the other hand, because, in many cases, they can contribute to improvements of the material behaviour under certain circumstances. But they are especially liked for their giving convenient and (this is most important) mostly uncontrollable explanations. For only in very few cases we have enough knowledge and possibilities for the objective evaluation of residual stresses. (orig.) [de

  3. LANL Contacts

    Science.gov (United States)

    : (505) 665-3664 ethics@lanl.gov Journalist queries Communications Office (505) 667-7000 Media contacts programs and employee resources. General Employee directory Emergency communication Communications Office (505) 667-7000 Ethics & Audits Internal Audit: (505) 665-3104 Ethics Office: (505) 667-7506 Fax

  4. Classification between normal and tumor tissues based on the pair-wise gene expression ratio

    International Nuclear Information System (INIS)

    Yap, YeeLeng; Zhang, XueWu; Ling, MT; Wang, XiangHong; Wong, YC; Danchin, Antoine

    2004-01-01

    Precise classification of cancer types is critically important for early cancer diagnosis and treatment. Numerous efforts have been made to use gene expression profiles to improve precision of tumor classification. However, reliable cancer-related signals are generally lacking. Using recent datasets on colon and prostate cancer, a data transformation procedure from single gene expression to pair-wise gene expression ratio is proposed. Making use of the internal consistency of each expression profiling dataset this transformation improves the signal to noise ratio of the dataset and uncovers new relevant cancer-related signals (features). The efficiency in using the transformed dataset to perform normal/tumor classification was investigated using feature partitioning with informative features (gene annotation) as discriminating axes (single gene expression or pair-wise gene expression ratio). Classification results were compared to the original datasets for up to 10-feature model classifiers. 82 and 262 genes that have high correlation to tissue phenotype were selected from the colon and prostate datasets respectively. Remarkably, data transformation of the highly noisy expression data successfully led to lower the coefficient of variation (CV) for the within-class samples as well as improved the correlation with tissue phenotypes. The transformed dataset exhibited lower CV when compared to that of single gene expression. In the colon cancer set, the minimum CV decreased from 45.3% to 16.5%. In prostate cancer, comparable CV was achieved with and without transformation. This improvement in CV, coupled with the improved correlation between the pair-wise gene expression ratio and tissue phenotypes, yielded higher classification efficiency, especially with the colon dataset – from 87.1% to 93.5%. Over 90% of the top ten discriminating axes in both datasets showed significant improvement after data transformation. The high classification efficiency achieved suggested

  5. Ink-Jet Printer Forms Solar-Cell Contacts

    Science.gov (United States)

    Alexander, Paul, Jr.; Vest, R. W.; Binford, Don A.; Tweedell, Eric P.

    1988-01-01

    Contacts formed in controllable patterns with metal-based inks. System forms upper metal contact patterns on silicon photovoltaic cells. Uses metallo-organic ink, decomposes when heated, leaving behind metallic, electrically conductive residue in printed area.

  6. Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures.

    Science.gov (United States)

    Filippi, Sarah; Holmes, Chris C; Nieto-Barajas, Luis E

    2016-11-16

    In this article we propose novel Bayesian nonparametric methods using Dirichlet Process Mixture (DPM) models for detecting pairwise dependence between random variables while accounting for uncertainty in the form of the underlying distributions. A key criteria is that the procedures should scale to large data sets. In this regard we find that the formal calculation of the Bayes factor for a dependent-vs.-independent DPM joint probability measure is not feasible computationally. To address this we present Bayesian diagnostic measures for characterising evidence against a "null model" of pairwise independence. In simulation studies, as well as for a real data analysis, we show that our approach provides a useful tool for the exploratory nonparametric Bayesian analysis of large multivariate data sets.

  7. Pairwise correlations via quantum discord and its geometric measure in a four-qubit spin chain

    Directory of Open Access Journals (Sweden)

    Abdel-Baset A. Mohamed

    2013-04-01

    Full Text Available The dynamic of pairwise correlations, including quantum entanglement (QE and discord (QD with geometric measure of quantum discord (GMQD, are shown in the four-qubit Heisenberg XX spin chain. The results show that the effect of the entanglement degree of the initial state on the pairwise correlations is stronger for alternate qubits than it is for nearest-neighbor qubits. This parameter results in sudden death for QE, but it cannot do so for QD and GMQD. With different values for this entanglement parameter of the initial state, QD and GMQD differ and are sensitive for any change in this parameter. It is found that GMQD is more robust than both QD and QE to describe correlations with nonzero values, which offers a valuable resource for quantum computation.

  8. A Relative-Localization Algorithm Using Incomplete Pairwise Distance Measurements for Underwater Applications

    Directory of Open Access Journals (Sweden)

    Kae Y. Foo

    2010-01-01

    Full Text Available The task of localizing underwater assets involves the relative localization of each unit using only pairwise distance measurements, usually obtained from time-of-arrival or time-delay-of-arrival measurements. In the fluctuating underwater environment, a complete set of pair-wise distance measurements can often be difficult to acquire, thus hindering a straightforward closed-form solution in deriving the assets' relative coordinates. An iterative multidimensional scaling approach is presented based upon a weighted-majorization algorithm that tolerates missing or inaccurate distance measurements. Substantial modifications are proposed to optimize the algorithm, while the effects of refractive propagation paths are considered. A parametric study of the algorithm based upon simulation results is shown. An acoustic field-trial was then carried out, presenting field measurements to highlight the practical implementation of this algorithm.

  9. A pragmatic pairwise group-decision method for selection of sites for nuclear power plants

    International Nuclear Information System (INIS)

    Kutbi, I.I.

    1987-01-01

    A pragmatic pairwise group-decision approach is applied to compare two regions in order to select the more suitable one for construction of nulcear power plants in the Kingdom of Saudi Arabia. The selection methodology is based on pairwise comparison by forced choice. The method facilitates rating of the regions or sites using simple calculations. Two regions, one close to Dhahran on the Arabian Gulf and another close to Jeddah on the Red Sea, are evaluated. No specific site in either region is considered at this stage. The comparison is based on a set of selection criteria which include (i) topography, (ii) geology, (iii) seismology, (iv) meteorology, (v) oceanography, (vi) hydrology and (vii) proximetry to oil and gas fields. The comparison shows that the Jeddah region is more suitable than the Dhahran region. (orig.)

  10. Geometric measure of pairwise quantum discord for superpositions of multipartite generalized coherent states

    International Nuclear Information System (INIS)

    Daoud, M.; Ahl Laamara, R.

    2012-01-01

    We give the explicit expressions of the pairwise quantum correlations present in superpositions of multipartite coherent states. A special attention is devoted to the evaluation of the geometric quantum discord. The dynamics of quantum correlations under a dephasing channel is analyzed. A comparison of geometric measure of quantum discord with that of concurrence shows that quantum discord in multipartite coherent states is more resilient to dissipative environments than is quantum entanglement. To illustrate our results, we consider some special superpositions of Weyl–Heisenberg, SU(2) and SU(1,1) coherent states which interpolate between Werner and Greenberger–Horne–Zeilinger states. -- Highlights: ► Pairwise quantum correlations multipartite coherent states. ► Explicit expression of geometric quantum discord. ► Entanglement sudden death and quantum discord robustness. ► Generalized coherent states interpolating between Werner and Greenberger–Horne–Zeilinger states

  11. Geometric measure of pairwise quantum discord for superpositions of multipartite generalized coherent states

    Energy Technology Data Exchange (ETDEWEB)

    Daoud, M., E-mail: m_daoud@hotmail.com [Department of Physics, Faculty of Sciences, University Ibnou Zohr, Agadir (Morocco); Ahl Laamara, R., E-mail: ahllaamara@gmail.com [LPHE-Modeling and Simulation, Faculty of Sciences, University Mohammed V, Rabat (Morocco); Centre of Physics and Mathematics, CPM, CNESTEN, Rabat (Morocco)

    2012-07-16

    We give the explicit expressions of the pairwise quantum correlations present in superpositions of multipartite coherent states. A special attention is devoted to the evaluation of the geometric quantum discord. The dynamics of quantum correlations under a dephasing channel is analyzed. A comparison of geometric measure of quantum discord with that of concurrence shows that quantum discord in multipartite coherent states is more resilient to dissipative environments than is quantum entanglement. To illustrate our results, we consider some special superpositions of Weyl–Heisenberg, SU(2) and SU(1,1) coherent states which interpolate between Werner and Greenberger–Horne–Zeilinger states. -- Highlights: ► Pairwise quantum correlations multipartite coherent states. ► Explicit expression of geometric quantum discord. ► Entanglement sudden death and quantum discord robustness. ► Generalized coherent states interpolating between Werner and Greenberger–Horne–Zeilinger states.

  12. PTM Along Track Algorithm to Maintain Spacing During Same Direction Pair-Wise Trajectory Management Operations

    Science.gov (United States)

    Carreno, Victor A.

    2015-01-01

    Pair-wise Trajectory Management (PTM) is a cockpit based delegated responsibility separation standard. When an air traffic service provider gives a PTM clearance to an aircraft and the flight crew accepts the clearance, the flight crew will maintain spacing and separation from a designated aircraft. A PTM along track algorithm will receive state information from the designated aircraft and from the own ship to produce speed guidance for the flight crew to maintain spacing and separation

  13. Criteria for the singularity of a pairwise l1-distance matrix and their generalizations

    International Nuclear Information System (INIS)

    D'yakonov, Alexander G

    2012-01-01

    We study the singularity problem for the pairwise distance matrix of a system of points, as well as generalizations of this problem that are connected with applications to interpolation theory and with an algebraic approach to recognition problems. We obtain necessary and sufficient conditions on a system under which the dimension of the range space of polynomials of bounded degree over the columns of the distance matrix is less than the number of points in the system.

  14. Criteria for the singularity of a pairwise l{sub 1}-distance matrix and their generalizations

    Energy Technology Data Exchange (ETDEWEB)

    D' yakonov, Alexander G [M. V. Lomonosov Moscow State University, Faculty of Computational Mathematics and Cybernetics, Moscow (Russian Federation)

    2012-06-30

    We study the singularity problem for the pairwise distance matrix of a system of points, as well as generalizations of this problem that are connected with applications to interpolation theory and with an algebraic approach to recognition problems. We obtain necessary and sufficient conditions on a system under which the dimension of the range space of polynomials of bounded degree over the columns of the distance matrix is less than the number of points in the system.

  15. Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.

    Science.gov (United States)

    Ruan, Peiying; Hayashida, Morihiro; Akutsu, Tatsuya; Vert, Jean-Philippe

    2018-02-19

    Since many proteins become functional only after they interact with their partner proteins and form protein complexes, it is essential to identify the sets of proteins that form complexes. Therefore, several computational methods have been proposed to predict complexes from the topology and structure of experimental protein-protein interaction (PPI) network. These methods work well to predict complexes involving at least three proteins, but generally fail at identifying complexes involving only two different proteins, called heterodimeric complexes or heterodimers. There is however an urgent need for efficient methods to predict heterodimers, since the majority of known protein complexes are precisely heterodimers. In this paper, we use three promising kernel functions, Min kernel and two pairwise kernels, which are Metric Learning Pairwise Kernel (MLPK) and Tensor Product Pairwise Kernel (TPPK). We also consider the normalization forms of Min kernel. Then, we combine Min kernel or its normalization form and one of the pairwise kernels by plugging. We applied kernels based on PPI, domain, phylogenetic profile, and subcellular localization properties to predicting heterodimers. Then, we evaluate our method by employing C-Support Vector Classification (C-SVC), carrying out 10-fold cross-validation, and calculating the average F-measures. The results suggest that the combination of normalized-Min-kernel and MLPK leads to the best F-measure and improved the performance of our previous work, which had been the best existing method so far. We propose new methods to predict heterodimers, using a machine learning-based approach. We train a support vector machine (SVM) to discriminate interacting vs non-interacting protein pairs, based on informations extracted from PPI, domain, phylogenetic profiles and subcellular localization. We evaluate in detail new kernel functions to encode these data, and report prediction performance that outperforms the state-of-the-art.

  16. Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

    OpenAIRE

    Liu, Jian-Bin; Wang, Fan; Lang, Xia; Zha, Xi; Sun, Xiao-Ping; Yue, Yao-Jing; Feng, Rui-Lin; Yang, Bo-Hui; Guo, Jian

    2013-01-01

    This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism i...

  17. Simultaneous-Fault Diagnosis of Gas Turbine Generator Systems Using a Pairwise-Coupled Probabilistic Classifier

    Directory of Open Access Journals (Sweden)

    Zhixin Yang

    2013-01-01

    Full Text Available A reliable fault diagnostic system for gas turbine generator system (GTGS, which is complicated and inherent with many types of component faults, is essential to avoid the interruption of electricity supply. However, the GTGS diagnosis faces challenges in terms of the existence of simultaneous-fault diagnosis and high cost in acquiring the exponentially increased simultaneous-fault vibration signals for constructing the diagnostic system. This research proposes a new diagnostic framework combining feature extraction, pairwise-coupled probabilistic classifier, and decision threshold optimization. The feature extraction module adopts wavelet packet transform and time-domain statistical features to extract vibration signal features. Kernel principal component analysis is then applied to further reduce the redundant features. The features of single faults in a simultaneous-fault pattern are extracted and then detected using a probabilistic classifier, namely, pairwise-coupled relevance vector machine, which is trained with single-fault patterns only. Therefore, the training dataset of simultaneous-fault patterns is unnecessary. To optimize the decision threshold, this research proposes to use grid search method which can ensure a global solution as compared with traditional computational intelligence techniques. Experimental results show that the proposed framework performs well for both single-fault and simultaneous-fault diagnosis and is superior to the frameworks without feature extraction and pairwise coupling.

  18. Solid residues

    International Nuclear Information System (INIS)

    Mulder, E.; Duin, P.J. van; Grootenboer, G.J.

    1995-01-01

    A summary is presented of the many investigations that have been done on solid residues of atmospheric fluid bed combustion (AFBC). These residues are bed ash, cyclone ash and bag filter ash. Physical and chemical properties are discussed and then the various uses of residues (in fillers, bricks, gravel, and for recovery of aluminium) are summarised. Toxicological properties of fly ash and stack ash are discussed as are risks of pneumoconiosis for workers handling fly ash, and contamination of water by ashes. On the basis of present information it is concluded that risks to public health from exposure to emissions of coal fly ash from AFBC appear small or negligible as are health risk to workers in the coal fly ash processing industry. 35 refs., 5 figs., 12 tabs

  19. Prioritized Contact Transport Stream

    Science.gov (United States)

    Hunt, Walter Lee, Jr. (Inventor)

    2015-01-01

    A detection process, contact recognition process, classification process, and identification process are applied to raw sensor data to produce an identified contact record set containing one or more identified contact records. A prioritization process is applied to the identified contact record set to assign a contact priority to each contact record in the identified contact record set. Data are removed from the contact records in the identified contact record set based on the contact priorities assigned to those contact records. A first contact stream is produced from the resulting contact records. The first contact stream is streamed in a contact transport stream. The contact transport stream may include and stream additional contact streams. The contact transport stream may be varied dynamically over time based on parameters such as available bandwidth, contact priority, presence/absence of contacts, system state, and configuration parameters.

  20. The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks

    Directory of Open Access Journals (Sweden)

    Wingender Edgar

    2008-05-01

    Full Text Available Abstract Background Currently, there is a gap between purely theoretical studies of the topology of large bioregulatory networks and the practical traditions and interests of experimentalists. While the theoretical approaches emphasize the global characterization of regulatory systems, the practical approaches focus on the role of distinct molecules and genes in regulation. To bridge the gap between these opposite approaches, one needs to combine 'general' with 'particular' properties and translate abstract topological features of large systems into testable functional characteristics of individual components. Here, we propose a new topological parameter – the pairwise disconnectivity index of a network's element – that is capable of such bridging. Results The pairwise disconnectivity index quantifies how crucial an individual element is for sustaining the communication ability between connected pairs of vertices in a network that is displayed as a directed graph. Such an element might be a vertex (i.e., molecules, genes, an edge (i.e., reactions, interactions, as well as a group of vertices and/or edges. The index can be viewed as a measure of topological redundancy of regulatory paths which connect different parts of a given network and as a measure of sensitivity (robustness of this network to the presence (absence of each individual element. Accordingly, we introduce the notion of a path-degree of a vertex in terms of its corresponding incoming, outgoing and mediated paths, respectively. The pairwise disconnectivity index has been applied to the analysis of several regulatory networks from various organisms. The importance of an individual vertex or edge for the coherence of the network is determined by the particular position of the given element in the whole network. Conclusion Our approach enables to evaluate the effect of removing each element (i.e., vertex, edge, or their combinations from a network. The greatest potential value of

  1. Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models.

    Science.gov (United States)

    Rostami, Vahid; Porta Mana, PierGianLuca; Grün, Sonja; Helias, Moritz

    2017-10-01

    Pairwise maximum-entropy models have been used in neuroscience to predict the activity of neuronal populations, given only the time-averaged correlations of the neuron activities. This paper provides evidence that the pairwise model, applied to experimental recordings, would produce a bimodal distribution for the population-averaged activity, and for some population sizes the second mode would peak at high activities, that experimentally would be equivalent to 90% of the neuron population active within time-windows of few milliseconds. Several problems are connected with this bimodality: 1. The presence of the high-activity mode is unrealistic in view of observed neuronal activity and on neurobiological grounds. 2. Boltzmann learning becomes non-ergodic, hence the pairwise maximum-entropy distribution cannot be found: in fact, Boltzmann learning would produce an incorrect distribution; similarly, common variants of mean-field approximations also produce an incorrect distribution. 3. The Glauber dynamics associated with the model is unrealistically bistable and cannot be used to generate realistic surrogate data. This bimodality problem is first demonstrated for an experimental dataset from 159 neurons in the motor cortex of macaque monkey. Evidence is then provided that this problem affects typical neural recordings of population sizes of a couple of hundreds or more neurons. The cause of the bimodality problem is identified as the inability of standard maximum-entropy distributions with a uniform reference measure to model neuronal inhibition. To eliminate this problem a modified maximum-entropy model is presented, which reflects a basic effect of inhibition in the form of a simple but non-uniform reference measure. This model does not lead to unrealistic bimodalities, can be found with Boltzmann learning, and has an associated Glauber dynamics which incorporates a minimal asymmetric inhibition.

  2. Effect of pairwise additivity on finite-temperature behavior of classical ideal gas

    Science.gov (United States)

    Shekaari, Ashkan; Jafari, Mahmoud

    2018-05-01

    Finite-temperature molecular dynamics simulations have been applied to inquire into the effect of pairwise additivity on the behavior of classical ideal gas within the temperature range of T = 250-4000 K via applying a variety of pair potentials and then examining the temperature dependence of a number of thermodynamical properties. Examining the compressibility factor reveals the most deviation from ideal-gas behavior for the Lennard-Jones system mainly due to the presence of both the attractive and repulsive terms. The systems with either attractive or repulsive intermolecular potentials are found to present no resemblance to real gases, but the most similarity to the ideal one as temperature rises.

  3. Structural profiles of human miRNA families from pairwise clustering

    DEFF Research Database (Denmark)

    Kaczkowski, Bogumil; Þórarinsson, Elfar; Reiche, Kristin

    2009-01-01

    secondary structure already predicted, little is known about the patterns of structural conservation among pre-miRNAs. We address this issue by clustering the human pre-miRNA sequences based on pairwise, sequence and secondary structure alignment using FOLDALIGN, followed by global multiple alignment...... of obtained clusters by WAR. As a result, the common secondary structure was successfully determined for four FOLDALIGN clusters: the RF00027 structural family of the Rfam database and three clusters with previously undescribed consensus structures. Availability: http://genome.ku.dk/resources/mirclust...

  4. The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Lyngsø, Rune B.; Gorodkin, Jan

    2005-01-01

    FOLDALIGN is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of FOLDALIGN. The server can be used to scan two sequences for a common structural RNA...... motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. the web server can be accessed at http://foldalign.kvl.dk...

  5. Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time

    DEFF Research Database (Denmark)

    Tsirogiannis, Constantinos; Sandel, Brody Steven

    2014-01-01

    The phylogenetic Mean Pairwise Distance (MPD) is one of the most popular measures for computing the phylogenetic distance between a given group of species. More specifically, for a phylogenetic tree and for a set of species R represented by a subset of the leaf nodes of , the MPD of R is equal...... to the average cost of all possible simple paths in that connect pairs of nodes in R. Among other phylogenetic measures, the MPD is used as a tool for deciding if the species of a given group R are closely related. To do this, it is important to compute not only the value of the MPD for this group but also...

  6. Benefits of Using Pairwise Trajectory Management in the Central East Pacific

    Science.gov (United States)

    Chartrand, Ryan; Ballard, Kathryn

    2017-01-01

    Pairwise Trajectory Management (PTM) is a concept that utilizes airborne and ground-based capabilities to enable airborne spacing operations in procedural airspace. This concept makes use of updated ground automation, Automatic Dependent Surveillance-Broadcast (ADS-B) and on board avionics generating real time guidance. An experiment was conducted to examine the potential benefits of implementing PTM in the Central East Pacific oceanic region. An explanation of the experiment and some of the results are included in this paper. The PTM concept allowed for an increase in the average time an aircraft is able to spend at its desired flight level and a reduction in fuel burn.

  7. Atomic pairwise distribution function analysis of the amorphous phase prepared by different manufacturing routes

    DEFF Research Database (Denmark)

    Boetker, Johan P.; Koradia, Vishal; Rades, Thomas

    2012-01-01

    was subjected to quench cooling thereby creating an amorphous form of the drug from both starting materials. The milled and quench cooled samples were, together with the crystalline starting materials, analyzed with X-ray powder diffraction (XRPD), Raman spectroscopy and atomic pair-wise distribution function...... (PDF) analysis of the XRPD pattern. When compared to XRPD and Raman spectroscopy, the PDF analysis was superior in displaying the difference between the amorphous samples prepared by milling and quench cooling approaches of the two starting materials....

  8. Residual basins

    International Nuclear Information System (INIS)

    D'Elboux, C.V.; Paiva, I.B.

    1980-01-01

    Exploration for uranium carried out over a major portion of the Rio Grande do Sul Shield has revealed a number of small residual basins developed along glacially eroded channels of pre-Permian age. Mineralization of uranium occurs in two distinct sedimentary units. The lower unit consists of rhythmites overlain by a sequence of black shales, siltstones and coal seams, while the upper one is dominated by sandstones of probable fluvial origin. (Author) [pt

  9. Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r-1 summation

    International Nuclear Information System (INIS)

    Wolf, D.; Keblinski, P.; Phillpot, S.R.; Eggebrecht, J.

    1999-01-01

    Based on a recent result showing that the net Coulomb potential in condensed ionic systems is rather short ranged, an exact and physically transparent method permitting the evaluation of the Coulomb potential by direct summation over the r -1 Coulomb pair potential is presented. The key observation is that the problems encountered in determining the Coulomb energy by pairwise, spherically truncated r -1 summation are a direct consequence of the fact that the system summed over is practically never neutral. A simple method is developed that achieves charge neutralization wherever the r -1 pair potential is truncated. This enables the extraction of the Coulomb energy, forces, and stresses from a spherically truncated, usually charged environment in a manner that is independent of the grouping of the pair terms. The close connection of our approach with the Ewald method is demonstrated and exploited, providing an efficient method for the simulation of even highly disordered ionic systems by direct, pairwise r -1 summation with spherical truncation at rather short range, i.e., a method which fully exploits the short-ranged nature of the interactions in ionic systems. The method is validated by simulations of crystals, liquids, and interfacial systems, such as free surfaces and grain boundaries. copyright 1999 American Institute of Physics

  10. GapMis: a tool for pairwise sequence alignment with a single gap.

    Science.gov (United States)

    Flouri, Tomás; Frousios, Kimon; Iliopoulos, Costas S; Park, Kunsoo; Pissis, Solon P; Tischler, German

    2013-08-01

    Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference sequence. After the fast alignment between a factor of the reference sequence and a high-quality fragment of a short read by a short-read alignment programme, an important problem is to find the alignment between a relatively short succeeding factor of the reference sequence and the remaining low-quality part of the read allowing a number of mismatches and the insertion of a single gap in the alignment. We present GapMis, a tool for pairwise sequence alignment with a single gap. It is based on a simple algorithm, which computes a different version of the traditional dynamic programming matrix. The presented experimental results demonstrate that GapMis is more suitable and efficient than most popular tools for this task.

  11. Pairwise registration of TLS point clouds using covariance descriptors and a non-cooperative game

    Science.gov (United States)

    Zai, Dawei; Li, Jonathan; Guo, Yulan; Cheng, Ming; Huang, Pengdi; Cao, Xiaofei; Wang, Cheng

    2017-12-01

    It is challenging to automatically register TLS point clouds with noise, outliers and varying overlap. In this paper, we propose a new method for pairwise registration of TLS point clouds. We first generate covariance matrix descriptors with an adaptive neighborhood size from point clouds to find candidate correspondences, we then construct a non-cooperative game to isolate mutual compatible correspondences, which are considered as true positives. The method was tested on three models acquired by two different TLS systems. Experimental results demonstrate that our proposed adaptive covariance (ACOV) descriptor is invariant to rigid transformation and robust to noise and varying resolutions. The average registration errors achieved on three models are 0.46 cm, 0.32 cm and 1.73 cm, respectively. The computational times cost on these models are about 288 s, 184 s and 903 s, respectively. Besides, our registration framework using ACOV descriptors and a game theoretic method is superior to the state-of-the-art methods in terms of both registration error and computational time. The experiment on a large outdoor scene further demonstrates the feasibility and effectiveness of our proposed pairwise registration framework.

  12. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

    International Nuclear Information System (INIS)

    Hardy, David J.; Schulten, Klaus; Wolff, Matthew A.; Skeel, Robert D.; Xia, Jianlin

    2016-01-01

    The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle–mesh Ewald method falls short.

  13. A water market simulator considering pair-wise trades between agents

    Science.gov (United States)

    Huskova, I.; Erfani, T.; Harou, J. J.

    2012-04-01

    In many basins in England no further water abstraction licences are available. Trading water between water rights holders has been recognized as a potentially effective and economically efficient strategy to mitigate increasing scarcity. A screening tool that could assess the potential for trade through realistic simulation of individual water rights holders would help assess the solution's potential contribution to local water management. We propose an optimisation-driven water market simulator that predicts pair-wise trade in a catchment and represents its interaction with natural hydrology and engineered infrastructure. A model is used to emulate licence-holders' willingness to engage in short-term trade transactions. In their simplest form agents are represented using an economic benefit function. The working hypothesis is that trading behaviour can be partially predicted based on differences in marginal values of water over space and time and estimates of transaction costs on pair-wise trades. We discuss the further possibility of embedding rules, norms and preferences of the different water user sectors to more realistically represent the behaviours, motives and constraints of individual licence holders. The potential benefits and limitations of such a social simulation (agent-based) approach is contrasted with our simulator where agents are driven by economic optimization. A case study based on the Dove River Basin (UK) demonstrates model inputs and outputs. The ability of the model to suggest impacts of water rights policy reforms on trading is discussed.

  14. Extraction of tacit knowledge from large ADME data sets via pairwise analysis.

    Science.gov (United States)

    Keefer, Christopher E; Chang, George; Kauffman, Gregory W

    2011-06-15

    Pharmaceutical companies routinely collect data across multiple projects for common ADME endpoints. Although at the time of collection the data is intended for use in decision making within a specific project, knowledge can be gained by data mining the entire cross-project data set for patterns of structure-activity relationships (SAR) that may be applied to any project. One such data mining method is pairwise analysis. This method has the advantage of being able to identify small structural changes that lead to significant changes in activity. In this paper, we describe the process for full pairwise analysis of our high-throughput ADME assays routinely used for compound discovery efforts at Pfizer (microsomal clearance, passive membrane permeability, P-gp efflux, and lipophilicity). We also describe multiple strategies for the application of these transforms in a prospective manner during compound design. Finally, a detailed analysis of the activity patterns in pairs of compounds that share the same molecular transformation reveals multiple types of transforms from an SAR perspective. These include bioisosteres, additives, multiplicatives, and a type we call switches as they act to either turn on or turn off an activity. Copyright © 2011 Elsevier Ltd. All rights reserved.

  15. Hierarchical ordering with partial pairwise hierarchical relationships on the macaque brain data sets.

    Directory of Open Access Journals (Sweden)

    Woosang Lim

    Full Text Available Hierarchical organizations of information processing in the brain networks have been known to exist and widely studied. To find proper hierarchical structures in the macaque brain, the traditional methods need the entire pairwise hierarchical relationships between cortical areas. In this paper, we present a new method that discovers hierarchical structures of macaque brain networks by using partial information of pairwise hierarchical relationships. Our method uses a graph-based manifold learning to exploit inherent relationship, and computes pseudo distances of hierarchical levels for every pair of cortical areas. Then, we compute hierarchy levels of all cortical areas by minimizing the sum of squared hierarchical distance errors with the hierarchical information of few cortical areas. We evaluate our method on the macaque brain data sets whose true hierarchical levels are known as the FV91 model. The experimental results show that hierarchy levels computed by our method are similar to the FV91 model, and its errors are much smaller than the errors of hierarchical clustering approaches.

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

    Science.gov (United States)

    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.

  17. Contact Lens Care

    Science.gov (United States)

    ... Consumers Consumer Information by Audience For Women Contact Lens Care Share Tweet Linkedin Pin it More sharing ... www.fda.gov/medwatch Learn More about Contact Lens Care Other Tips on Contact Lenses Decorative Contact ...

  18. A general transformation to canonical form for potentials in pairwise interatomic interactions.

    Science.gov (United States)

    Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

    2015-06-14

    A generalized formulation of explicit force-based transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a chosen canonical potential illustrating application of such transformations. Specifically, accurately determined potentials of the diatomic molecules H2, H2(+), HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl2 are investigated throughout their bound potentials. Advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has significance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

  19. Market Competitiveness Evaluation of Mechanical Equipment with a Pairwise Comparisons Hierarchical Model.

    Science.gov (United States)

    Hou, Fujun

    2016-01-01

    This paper provides a description of how market competitiveness evaluations concerning mechanical equipment can be made in the context of multi-criteria decision environments. It is assumed that, when we are evaluating the market competitiveness, there are limited number of candidates with some required qualifications, and the alternatives will be pairwise compared on a ratio scale. The qualifications are depicted as criteria in hierarchical structure. A hierarchical decision model called PCbHDM was used in this study based on an analysis of its desirable traits. Illustration and comparison shows that the PCbHDM provides a convenient and effective tool for evaluating the market competitiveness of mechanical equipment. The researchers and practitioners might use findings of this paper in application of PCbHDM.

  20. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Torarinsson, Elfar; Gorodkin, Jan

    2007-01-01

    and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool...... the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained....... Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned...

  1. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Lyngsø, Rune B.; Stormo, Gary D.

    2005-01-01

    detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on FILDALIGN and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include...... the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy....... The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. Availability...

  2. Linear VSS and Distributed Commitments Based on Secret Sharing and Pairwise Checks

    DEFF Research Database (Denmark)

    Fehr, Serge; Maurer, Ueli M.

    2002-01-01

    . VSS and DC are main building blocks for unconditional secure multi-party computation protocols. This general approach covers all known linear VSS and DC schemes. The main theorem states that the security of a scheme is equivalent to a pure linear-algebra condition on the linear mappings (e.......g. described as matrices and vectors) describing the scheme. The security of all known schemes follows as corollaries whose proofs are pure linear-algebra arguments, in contrast to some hybrid arguments used in the literature. Our approach is demonstrated for the CDM DC scheme, which we generalize to be secure......We present a general treatment of all non-cryptographic (i.e., information-theoretically secure) linear veriable-secret-sharing (VSS) and distributed-commitment (DC) schemes, based on an underlying secret sharing scheme, pairwise checks between players, complaints, and accusations of the dealer...

  3. The pairwise phase consistency in cortical network and its relationship with neuronal activation

    Directory of Open Access Journals (Sweden)

    Wang Daming

    2017-01-01

    Full Text Available Gamma-band neuronal oscillation and synchronization with the range of 30-90 Hz are ubiquitous phenomenon across numerous brain areas and various species, and correlated with plenty of cognitive functions. The phase of the oscillation, as one aspect of CTC (Communication through Coherence hypothesis, underlies various functions for feature coding, memory processing and behaviour performing. The PPC (Pairwise Phase Consistency, an improved coherence measure, statistically quantifies the strength of phase synchronization. In order to evaluate the PPC and its relationships with input stimulus, neuronal activation and firing rate, a simplified spiking neuronal network is constructed to simulate orientation columns in primary visual cortex. If the input orientation stimulus is preferred for a certain orientation column, neurons within this corresponding column will obtain higher firing rate and stronger neuronal activation, which consequently engender higher PPC values, with higher PPC corresponding to higher firing rate. In addition, we investigate the PPC in time resolved analysis with a sliding window.

  4. Video-based depression detection using local Curvelet binary patterns in pairwise orthogonal planes.

    Science.gov (United States)

    Pampouchidou, Anastasia; Marias, Kostas; Tsiknakis, Manolis; Simos, Panagiotis; Fan Yang; Lemaitre, Guillaume; Meriaudeau, Fabrice

    2016-08-01

    Depression is an increasingly prevalent mood disorder. This is the reason why the field of computer-based depression assessment has been gaining the attention of the research community during the past couple of years. The present work proposes two algorithms for depression detection, one Frame-based and the second Video-based, both employing Curvelet transform and Local Binary Patterns. The main advantage of these methods is that they have significantly lower computational requirements, as the extracted features are of very low dimensionality. This is achieved by modifying the previously proposed algorithm which considers Three-Orthogonal-Planes, to only Pairwise-Orthogonal-Planes. Performance of the algorithms was tested on the benchmark dataset provided by the Audio/Visual Emotion Challenge 2014, with the person-specific system achieving 97.6% classification accuracy, and the person-independed one yielding promising preliminary results of 74.5% accuracy. The paper concludes with open issues, proposed solutions, and future plans.

  5. Estimators of the Relations of Equivalence, Tolerance and Preference Based on Pairwise Comparisons with Random Errors

    Directory of Open Access Journals (Sweden)

    Leszek Klukowski

    2012-01-01

    Full Text Available This paper presents a review of results of the author in the area of estimation of the relations of equivalence, tolerance and preference within a finite set based on multiple, independent (in a stochastic way pairwise comparisons with random errors, in binary and multivalent forms. These estimators require weaker assumptions than those used in the literature on the subject. Estimates of the relations are obtained based on solutions to problems from discrete optimization. They allow application of both types of comparisons - binary and multivalent (this fact relates to the tolerance and preference relations. The estimates can be verified in a statistical way; in particular, it is possible to verify the type of the relation. The estimates have been applied by the author to problems regarding forecasting, financial engineering and bio-cybernetics. (original abstract

  6. Memory-efficient dynamic programming backtrace and pairwise local sequence alignment.

    Science.gov (United States)

    Newberg, Lee A

    2008-08-15

    A backtrace through a dynamic programming algorithm's intermediate results in search of an optimal path, or to sample paths according to an implied probability distribution, or as the second stage of a forward-backward algorithm, is a task of fundamental importance in computational biology. When there is insufficient space to store all intermediate results in high-speed memory (e.g. cache) existing approaches store selected stages of the computation, and recompute missing values from these checkpoints on an as-needed basis. Here we present an optimal checkpointing strategy, and demonstrate its utility with pairwise local sequence alignment of sequences of length 10,000. Sample C++-code for optimal backtrace is available in the Supplementary Materials. Supplementary data is available at Bioinformatics online.

  7. Solution to urn models of pairwise interaction with application to social, physical, and biological sciences

    Science.gov (United States)

    Pickering, William; Lim, Chjan

    2017-07-01

    We investigate a family of urn models that correspond to one-dimensional random walks with quadratic transition probabilities that have highly diverse applications. Well-known instances of these two-urn models are the Ehrenfest model of molecular diffusion, the voter model of social influence, and the Moran model of population genetics. We also provide a generating function method for diagonalizing the corresponding transition matrix that is valid if and only if the underlying mean density satisfies a linear differential equation and express the eigenvector components as terms of ordinary hypergeometric functions. The nature of the models lead to a natural extension to interaction between agents in a general network topology. We analyze the dynamics on uncorrelated heterogeneous degree sequence networks and relate the convergence times to the moments of the degree sequences for various pairwise interaction mechanisms.

  8. PairWise Neighbours database: overlaps and spacers among prokaryote genomes

    Directory of Open Access Journals (Sweden)

    Garcia-Vallvé Santiago

    2009-06-01

    Full Text Available Abstract Background Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD sequence, which is responsible of an efficient translation. Description PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.

  9. Improving pairwise comparison of protein sequences with domain co-occurrence

    Science.gov (United States)

    Gascuel, Olivier

    2018-01-01

    Comparing and aligning protein sequences is an essential task in bioinformatics. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss several hits, especially for species that are phylogenetically distant from reference organisms. A solution to this problem is then to integrate additional contextual information to the procedure. Here, we propose to use domain co-occurrence to increase the sensitivity of pairwise sequence comparisons. Domain co-occurrence is a strong feature of proteins, since most protein domains tend to appear with a limited number of other domains on the same protein. We propose a method to take this information into account in a typical BLAST analysis and to construct new domain families on the basis of these results. We used Plasmodium falciparum as a case study to evaluate our method. The experimental findings showed an increase of 14% of the number of significant BLAST hits and an increase of 25% of the proteome area that can be covered with a domain. Our method identified 2240 new domains for which, in most cases, no model of the Pfam database could be linked. Moreover, our study of the quality of the new domains in terms of alignment and physicochemical properties show that they are close to that of standard Pfam domains. Source code of the proposed approach and supplementary data are available at: https://gite.lirmm.fr/menichelli/pairwise-comparison-with-cooccurrence PMID:29293498

  10. Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

    Directory of Open Access Journals (Sweden)

    Jian-Bin Liu

    2013-03-01

    Full Text Available This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO and the International Society for Animal Genetics (ISAG. In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright’s F-statistics of subpopulation within total (FST was 0.1184; the genetic differentiation coefficient (GST was 0.0940; and the average gene flow (Nm was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001, suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding.

  11. Residual nilpotence and residual solubility of groups

    International Nuclear Information System (INIS)

    Mikhailov, R V

    2005-01-01

    The properties of the residual nilpotence and the residual solubility of groups are studied. The main objects under investigation are the class of residually nilpotent groups such that each central extension of these groups is also residually nilpotent and the class of residually soluble groups such that each Abelian extension of these groups is residually soluble. Various examples of groups not belonging to these classes are constructed by homological methods and methods of the theory of modules over group rings. Several applications of the theory under consideration are presented and problems concerning the residual nilpotence of one-relator groups are considered.

  12. Occupational contact urticaria and protein contact dermatitis.

    Science.gov (United States)

    Doutre, Marie-Sylvie

    2005-01-01

    Irritant dermatitis and eczema are the most prevalent occupational skin diseases. Less common are immediate contact reactions such as contact urticaria and protein contact dermatitis. Occupational contact urticaria can be subdivided into two categories, immunological and non immunological. However, some agents can induce these two types of reactions. Contact urticaria to natural rubber latex is particularly frequent among health care personnel, but contact urticaria to a wide variety of other substances occurs in many other occupations. Among those at risk are cooks, bakers, butchers, restaurant personnel, veterinarians, hairdressers, florists, gardeners, and forestry workers. Protein contact dermatitis in some of these occupations is caused principally by proteins of animal or plant origin, especially among individuals with a history of atopic dermatitis. Diagnosis requires careful interrogation, clinical examination and skin tests (open tests and prick tests with immediate lecture) to identify a particular contact allergen.

  13. Contact Estimation in Robot Interaction

    Directory of Open Access Journals (Sweden)

    Filippo D'Ippolito

    2014-07-01

    Full Text Available In the paper, safety issues are examined in a scenario in which a robot manipulator and a human perform the same task in the same workspace. During the task execution, the human should be able to physically interact with the robot, and in this case an estimation algorithm for both interaction forces and a contact point is proposed in order to guarantee safety conditions. The method, starting from residual joint torque estimation, allows both direct and adaptive computation of the contact point and force, based on a principle of equivalence of the contact forces. At the same time, all the unintended contacts must be avoided, and a suitable post-collision strategy is considered to move the robot away from the collision area or else to reduce impact effects. Proper experimental tests have demonstrated the applicability in practice of both the post-impact strategy and the estimation algorithms; furthermore, experiments demonstrate the different behaviour resulting from the adaptation of the contact point as opposed to direct calculation.

  14. Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

    KAUST Repository

    Cui, Xuefeng; Naveed, Hammad; Gao, Xin

    2015-01-01

    that are not limited to backbone fragments, and by employing a maximum weighted bipartite matching solver from the beginning of the alignment process. In addition, our methods incorporate similarities of sequentially and structurally remote residues that potentially

  15. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... One Use Facts About Colored Contacts and Halloween Safety Colored Contact Lens Facts Over-the-Counter Costume ... Costume Contact Lenses Can Ruin Vision Eye Makeup Safety In fact, it is illegal to sell colored ...

  16. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... One Use Facts About Colored Contacts and Halloween Safety Colored Contact Lens Facts Over-the-Counter Costume ... use of colored contact lenses , from the U.S. Food and Drug Administration (FDA). Are the colored lenses ...

  17. Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS

    Directory of Open Access Journals (Sweden)

    Kim Nora

    2012-07-01

    Full Text Available Abstract Background It is increasingly clear that common human diseases have a complex genetic architecture characterized by both additive and nonadditive genetic effects. The goal of the present study was to determine whether patterns of both additive and nonadditive genetic associations aggregate in specific functional groups as defined by the Gene Ontology (GO. Results We first estimated all pairwise additive and nonadditive genetic effects using the multifactor dimensionality reduction (MDR method that makes few assumptions about the underlying genetic model. Statistical significance was evaluated using permutation testing in two genome-wide association studies of ALS. The detection data consisted of 276 subjects with ALS and 271 healthy controls while the replication data consisted of 221 subjects with ALS and 211 healthy controls. Both studies included genotypes from approximately 550,000 single-nucleotide polymorphisms (SNPs. Each SNP was mapped to a gene if it was within 500 kb of the start or end. Each SNP was assigned a p-value based on its strongest joint effect with the other SNPs. We then used the Exploratory Visual Analysis (EVA method and software to assign a p-value to each gene based on the overabundance of significant SNPs at the α = 0.05 level in the gene. We also used EVA to assign p-values to each GO group based on the overabundance of significant genes at the α = 0.05 level. A GO category was determined to replicate if that category was significant at the α = 0.05 level in both studies. We found two GO categories that replicated in both studies. The first, ‘Regulation of Cellular Component Organization and Biogenesis’, a GO Biological Process, had p-values of 0.010 and 0.014 in the detection and replication studies, respectively. The second, ‘Actin Cytoskeleton’, a GO Cellular Component, had p-values of 0.040 and 0.046 in the detection and replication studies, respectively. Conclusions Pathway

  18. Classification of forest-based ecotourism areas in Pocahontas County of West Virginia using GIS and pairwise comparison method

    Science.gov (United States)

    Ishwar Dhami; Jinyang. Deng

    2012-01-01

    Many previous studies have examined ecotourism primarily from the perspective of tourists while largely ignoring ecotourism destinations. This study used geographical information system (GIS) and pairwise comparison to identify forest-based ecotourism areas in Pocahontas County, West Virginia. The study adopted the criteria and scores developed by Boyd and Butler (1994...

  19. Pair-Wise Trajectory Management-Oceanic (PTM-O) . [Concept of Operations—Version 3.9

    Science.gov (United States)

    Jones, Kenneth M.

    2014-01-01

    This document describes the Pair-wise Trajectory Management-Oceanic (PTM-O) Concept of Operations (ConOps). Pair-wise Trajectory Management (PTM) is a concept that includes airborne and ground-based capabilities designed to enable and to benefit from, airborne pair-wise distance-monitoring capability. PTM includes the capabilities needed for the controller to issue a PTM clearance that resolves a conflict for a specific pair of aircraft. PTM avionics include the capabilities needed for the flight crew to manage their trajectory relative to specific designated aircraft. Pair-wise Trajectory Management PTM-Oceanic (PTM-O) is a regional specific application of the PTM concept. PTM is sponsored by the National Aeronautics and Space Administration (NASA) Concept and Technology Development Project (part of NASA's Airspace Systems Program). The goal of PTM is to use enhanced and distributed communications and surveillance along with airborne tools to permit reduced separation standards for given aircraft pairs, thereby increasing the capacity and efficiency of aircraft operations at a given altitude or volume of airspace.

  20. The structure of pairwise correlation in mouse primary visual cortex reveals functional organization in the absence of an orientation map.

    Science.gov (United States)

    Denman, Daniel J; Contreras, Diego

    2014-10-01

    Neural responses to sensory stimuli are not independent. Pairwise correlation can reduce coding efficiency, occur independent of stimulus representation, or serve as an additional channel of information, depending on the timescale of correlation and the method of decoding. Any role for correlation depends on its magnitude and structure. In sensory areas with maps, like the orientation map in primary visual cortex (V1), correlation is strongly related to the underlying functional architecture, but it is unclear whether this correlation structure is an essential feature of the system or arises from the arrangement of cells in the map. We assessed the relationship between functional architecture and pairwise correlation by measuring both synchrony and correlated spike count variability in mouse V1, which lacks an orientation map. We observed significant pairwise synchrony, which was organized by distance and relative orientation preference between cells. We also observed nonzero correlated variability in both the anesthetized (0.16) and awake states (0.18). Our results indicate that the structure of pairwise correlation is maintained in the absence of an underlying anatomical organization and may be an organizing principle of the mammalian visual system preserved by nonrandom connectivity within local networks. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. Theory of pairwise coupling embedded in more general local dispersion relations

    International Nuclear Information System (INIS)

    Fuchs, V.; Bers, A.; Harten, L.

    1985-01-01

    Earlier work on the mode conversion theory by Fuchs, Ko, and Bers is detailed and expanded upon, and its relation to energy conservation is discussed. Given a local dispersion relation, D(ω; k, z) = 0, describing stable waves excited at an externally imposed frequency ω, a pairwise mode-coupling event embedded therein is extracted by expanding D(k, z) around a contour k = k/sub c/(z) given by partialD/partialk = 0. The branch points of D(k, z) = 0 are the turning points of a second-order differential-equation representation. In obtaining the fraction of mode-converted energy, the connection formula and conservation of energy must be used together. Also, proper attention must be given to distinguish cases for which the coupling disappears or persists upon confluence of the branches, a property which is shown to depend on the forward (v/sub g/v/sub ph/>0) or backward (v/sub g/v/sub ph/<0) nature of the waves. Examples occurring in ion-cyclotron and lower-hybrid heating are presented, illustrating the use of the theory

  2. ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.

    Science.gov (United States)

    Otto, Thomas Dan; Catanho, Marcos; Tristão, Cristian; Bezerra, Márcia; Fernandes, Renan Mathias; Elias, Guilherme Steinberger; Scaglia, Alexandre Capeletto; Bovermann, Bill; Berstis, Viktors; Lifschitz, Sergio; de Miranda, Antonio Basílio; Degrave, Wim

    2010-03-01

    Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith-Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach. The database can be accessed through http://proteinworlddb.org

  3. pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling.

    Science.gov (United States)

    Gil, Víctor A; Guallar, Víctor

    2013-09-15

    We introduce pyRMSD, an open source standalone Python package that aims at offering an integrative and efficient way of performing Root Mean Square Deviation (RMSD)-related calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices, implementing up to three well-known superposition algorithms. pyRMSD provides its own symmetric distance matrix class that, besides the fact that it can be used as a regular matrix, helps to save memory and increases memory access speed. This last feature can dramatically improve the overall performance of any Python algorithm using it. In addition, its extensibility, testing suites and documentation make it a good choice to those in need of a workbench for developing or testing new algorithms. The source code (under MIT license), installer, test suites and benchmarks can be found at https://pele.bsc.es/ under the tools section. victor.guallar@bsc.es Supplementary data are available at Bioinformatics online.

  4. Optimal Inconsistency Repairing of Pairwise Comparison Matrices Using Integrated Linear Programming and Eigenvector Methods

    Directory of Open Access Journals (Sweden)

    Haiqing Zhang

    2014-01-01

    Full Text Available Satisfying consistency requirements of pairwise comparison matrix (PCM is a critical step in decision making methodologies. An algorithm has been proposed to find a new modified consistent PCM in which it can replace the original inconsistent PCM in analytic hierarchy process (AHP or in fuzzy AHP. This paper defines the modified consistent PCM by the original inconsistent PCM and an adjustable consistent PCM combined. The algorithm adopts a segment tree to gradually approach the greatest lower bound of the distance with the original PCM to obtain the middle value of an adjustable PCM. It also proposes a theorem to obtain the lower value and the upper value of an adjustable PCM based on two constraints. The experiments for crisp elements show that the proposed approach can preserve more of the original information than previous works of the same consistent value. The convergence rate of our algorithm is significantly faster than previous works with respect to different parameters. The experiments for fuzzy elements show that our method could obtain suitable modified fuzzy PCMs.

  5. High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

    Directory of Open Access Journals (Sweden)

    Khaled Benkrid

    2012-01-01

    Full Text Available This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs, Graphics Processor Units (GPUs, and IBM’s Cell Broadband Engine (Cell BE, in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion and perform better than all other platforms on performance per dollar criterion, although by a much smaller margin. Cell BE and GPU come second and third, respectively, on both performance per watt and performance per dollar criteria. In general, in order to outperform other technologies on performance per dollar criterion (using currently available hardware and development tools, FPGAs need to achieve at least two orders of magnitude speed-up compared to general-purpose processors and one order of magnitude speed-up compared to domain-specific technologies such as GPUs.

  6. Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis.

    Science.gov (United States)

    Tamura, Tomonori; Osawa, Motoki; Ochiai, Eriko; Suzuki, Takanori; Nakamura, Takashi

    2015-09-01

    The AmpFLSTR Identifiler Kit, comprising 15 autosomal short tandem repeat (STR) loci, is commonly employed in forensic practice for calculating match probabilities and parentage testing. The conventional system exhibits insufficient estimation for kinship analysis such as sibship testing because of shortness of examined loci. This study evaluated the power of the PowerPlex Fusion System, GlobalFiler Kit, and PowerPlex 21 System, which comprise more than 20 autosomal STR loci, to estimate pairwise blood relatedness (i.e., parent-child, full siblings, second-degree relatives, and first cousins). The genotypes of all 24 STR loci in 10,000 putative pedigrees were constructed by simulation. The likelihood ratio for each locus was calculated from joint probabilities for relatives and non-relatives. The combined likelihood ratio was calculated according to the product rule. The addition of STR loci improved separation between relatives and non-relatives. However, these systems were less effectively extended to the inference for first cousins. In conclusion, these advanced systems will be useful in forensic personal identification, especially in the evaluation of full siblings and second-degree relatives. Moreover, the additional loci may give rise to two major issues of more frequent mutational events and several pairs of linked loci on the same chromosome. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  7. DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors

    Directory of Open Access Journals (Sweden)

    Kaufmann Michael

    2004-09-01

    Full Text Available Abstract Background Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Results Herein, a parallel version of the multi-alignment program DIALIGN is introduced. We propose two ways of dividing the program into independent sub-routines that can be run on different processors: (a pair-wise sequence alignments that are used as a first step to multiple alignment account for most of the CPU time in DIALIGN. Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments. (b For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced anchored alignment procedure. For our test sequences, this combined approach reduces the program running time of DIALIGN by up to 97%. Conclusions By distributing sub-routines to multiple processors, the running time of DIALIGN can be crucially improved. With these improvements, it is possible to apply the program in large-scale genomics and proteomics projects that were previously beyond its scope.

  8. The Dynamics of Multiple Pair-Wise Collisions in a Chain for Designing Optimal Shock Amplifiers

    Directory of Open Access Journals (Sweden)

    Bryan Rodgers

    2009-01-01

    Full Text Available The major focus of this work is to examine the dynamics of velocity amplification through pair-wise collisions between multiple masses in a chain, in order to develop useful machines. For instance low-cost machines based on this principle could be used for detailed, very-high acceleration shock-testing of MEMS devices. A theoretical basis for determining the number and mass of intermediate stages in such a velocity amplifier, based on simple rigid body mechanics, is proposed. The influence of mass ratios and the coefficient of restitution on the optimisation of the system is identified and investigated. In particular, two cases are examined: in the first, the velocity of the final mass in the chain (that would have the object under test mounted on it is maximised by defining the ratio of adjacent masses according to a power law relationship; in the second, the energy transfer efficiency of the system is maximised by choosing the mass ratios such that all masses except the final mass come to rest following impact. Comparisons are drawn between both cases and the results are used in proposing design guidelines for optimal shock amplifiers. It is shown that for most practical systems, a shock amplifier with mass ratios based on a power law relationship is optimal and can easily yield velocity amplifications of a factor 5–8 times. A prototype shock testing machine that was made using above principles is briefly introduced.

  9. Visualization of pairwise and multilocus linkage disequilibrium structure using latent forests.

    Directory of Open Access Journals (Sweden)

    Raphaël Mourad

    Full Text Available Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data.

  10. Benefits of Using Pairwise Trajectory Management in the Central East Pacific

    Science.gov (United States)

    Chartrand, Ryan; Ballard, Kathryn

    2016-01-01

    Pairwise Trajectory Management (PTM) is a concept that utilizes airborne and ground-based capabilities to enable airborne spacing operations in oceanic regions. The goal of PTM is to use enhanced surveillance, along with airborne tools, to manage the spacing between aircraft. Due to the enhanced airborne surveillance of Automatic Dependent Surveillance-Broadcast (ADS-B) information and reduced communication, the PTM minimum spacing distance will be less than distances currently required of an air traffic controller. Reduced minimum distance will increase the capacity of aircraft operations at a given altitude or volume of airspace, thereby increasing time on desired trajectory and overall flight efficiency. PTM is designed to allow a flight crew to resolve a specific traffic conflict (or conflicts), identified by the air traffic controller, while maintaining the flight crew's desired altitude. The air traffic controller issues a PTM clearance to a flight crew authorized to conduct PTM operations in order to resolve a conflict for the pair (or pairs) of aircraft (i.e., the PTM aircraft and a designated target aircraft). This clearance requires the flight crew of the PTM aircraft to use their ADS-B-enabled onboard equipment to manage their spacing relative to the designated target aircraft to ensure spacing distances that are no closer than the PTM minimum distance. When the air traffic controller determines that PTM is no longer required, the controller issues a clearance to cancel the PTM operation.

  11. constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints.

    Science.gov (United States)

    Matsen, Frederick A

    2010-06-01

    This article introduces constNJ (constrained neighbor-joining), an algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune-regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees that must fit into a recombination, hybridization, or similar network. Rather than first finding a set of trees that are optimal according to a phylogenetic criterion (e.g., likelihood or parsimony) and then attempting to fit them into a network, constNJ estimates the trees while enforcing specified rSPR distance constraints. The primary input for constNJ is a collection of distance matrices derived from sequence blocks which are assumed to have evolved in a tree-like manner, such as blocks of an alignment which do not contain any recombination breakpoints. The other input is a set of rSPR constraint inequalities for any set of pairs of trees. constNJ is consistent and a strict generalization of the neighbor-joining algorithm; it uses the new notion of maximum agreement partitions (MAPs) to assure that the resulting trees satisfy the given rSPR distance constraints.

  12. Prediction of microsleeps using pairwise joint entropy and mutual information between EEG channels.

    Science.gov (United States)

    Baseer, Abdul; Weddell, Stephen J; Jones, Richard D

    2017-07-01

    Microsleeps are involuntary and brief instances of complete loss of responsiveness, typically of 0.5-15 s duration. They adversely affect performance in extended attention-driven jobs and can be fatal. Our aim was to predict microsleeps from 16 channel EEG signals. Two information theoretic concepts - pairwise joint entropy and mutual information - were independently used to continuously extract features from EEG signals. k-nearest neighbor (kNN) with k = 3 was used to calculate both joint entropy and mutual information. Highly correlated features were discarded and the rest were ranked using Fisher score followed by an average of 3-fold cross-validation area under the curve of the receiver operating characteristic (AUC ROC ). Leave-one-out method (LOOM) was performed to test the performance of microsleep prediction system on independent data. The best prediction for 0.25 s ahead was AUCROC, sensitivity, precision, geometric mean (GM), and φ of 0.93, 0.68, 0.33, 0.75, and 0.38 respectively with joint entropy using single linear discriminant analysis (LDA) classifier.

  13. Contact Dermatitis in Pediatrics.

    Science.gov (United States)

    Pelletier, Janice L; Perez, Caroline; Jacob, Sharon E

    2016-08-01

    Contact dermatitis is an umbrella term that describes the skin's reaction to contacted noxious or allergenic substances. The two main categories of contact dermatitis are irritant type and allergic type. This review discusses the signs, symptoms, causes, and complications of contact dermatitis. It addresses the testing, treatment, and prevention of contact dermatitis. Proper management of contact dermatitis includes avoidance measures for susceptible children. Implementation of a nickel directive (regulating the use of nickel in jewelry and other products that come into contact with the skin) could further reduce exposure to the most common allergens in the pediatric population. [Pediatr Ann. 2016;45(8):e287-e292.]. Copyright 2016, SLACK Incorporated.

  14. Applications of contact predictions to structural biology

    Directory of Open Access Journals (Sweden)

    Felix Simkovic

    2017-05-01

    Full Text Available Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallography, cryo-EM or NMR. Integrative structural bioinformatics packages such as Rosetta can already exploit contact predictions in a variety of ways. The contribution of contact predictions begins at construct design, where structural domains may need to be expressed separately and contact predictions can help to predict domain limits. Structure solution by molecular replacement (MR benefits from contact predictions in diverse ways: in difficult cases, more accurate search models can be constructed using ab initio modelling when predictions are available, while intermolecular contact predictions can allow the construction of larger, oligomeric search models. Furthermore, MR using supersecondary motifs or large-scale screens against the PDB can exploit information, such as the parallel or antiparallel nature of any β-strand pairing in the target, that can be inferred from contact predictions. Contact information will be particularly valuable in the determination of lower resolution structures by helping to assign sequence register. In large complexes, contact information may allow the identity of a protein responsible for a certain region of density to be determined and then assist in the orientation of an available model within that density. In NMR, predicted contacts can provide long-range information to extend the upper size limit of the technique in a manner analogous but complementary to experimental

  15. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.

    Directory of Open Access Journals (Sweden)

    Jakob H Havgaard

    2007-10-01

    Full Text Available It has become clear that noncoding RNAs (ncRNA play important roles in cells, and emerging studies indicate that there might be a large number of unknown ncRNAs in mammalian genomes. There exist computational methods that can be used to search for ncRNAs by comparing sequences from different genomes. One main problem with these methods is their computational complexity, and heuristics are therefore employed. Two heuristics are currently very popular: pre-folding and pre-aligning. However, these heuristics are not ideal, as pre-aligning is dependent on sequence similarity that may not be present and pre-folding ignores the comparative information. Here, pruning of the dynamical programming matrix is presented as an alternative novel heuristic constraint. All subalignments that do not exceed a length-dependent minimum score are discarded as the matrix is filled out, thus giving the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained. Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool for searching for new ncRNAs. The software package is available for download at http://foldalign.ku.dk.

  16. Pharmacological treatments in asthma-affected horses: A pair-wise and network meta-analysis.

    Science.gov (United States)

    Calzetta, L; Roncada, P; di Cave, D; Bonizzi, L; Urbani, A; Pistocchini, E; Rogliani, P; Matera, M G

    2017-11-01

    Equine asthma is a disease characterised by reversible airflow obstruction, bronchial hyper-responsiveness and airway inflammation following exposure of susceptible horses to specific airborne agents. Although clinical remission can be achieved in a low-airborne dust environment, repeated exacerbations may lead to irreversible airway remodelling. The available data on the pharmacotherapy of equine asthma result from several small studies, and no head-to-head clinical trials have been conducted among the available medications. To assess the impact of the pharmacological interventions in equine asthma and compare the effect of different classes of drugs on lung function. Pair-wise and network meta-analysis. Literature searches for clinical trials on the pharmacotherapy of equine asthma were performed. The risk of publication bias was assessed by funnel plots and Egger's test. Changes in maximum transpulmonary or pleural pressure, pulmonary resistance and dynamic lung compliance vs. control were analysed via random-effects models and Bayesian networks. The results obtained from 319 equine asthma-affected horses were extracted from 32 studies. Bronchodilators, corticosteroids and chromones improved maximum transpulmonary or pleural pressure (range: -8.0 to -21.4 cmH 2 O; Ptherapies. Long-term treatments were more effective than short-term treatments. Weak publication bias was detected. This study demonstrates that long-term treatments with inhaled corticosteroids and long-acting β 2 -AR agonists may represent the first choice for treating equine asthma. Further high quality clinical trials are needed to clarify whether inhaled bronchodilators should be preferred to inhaled corticosteroids or vice versa, and to investigate the potential superiority of combination therapy in equine asthma. © 2017 EVJ Ltd.

  17. Further investigations of the W-test for pairwise epistasis testing [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Richard Howey

    2017-07-01

    Full Text Available Background: In a recent paper, a novel W-test for pairwise epistasis testing was proposed that appeared, in computer simulations, to have higher power than competing alternatives. Application to genome-wide bipolar data detected significant epistasis between SNPs in genes of relevant biological function. Network analysis indicated that the implicated genes formed two separate interaction networks, each containing genes highly related to autism and neurodegenerative disorders. Methods: Here we investigate further the properties and performance of the W-test via theoretical evaluation, computer simulations and application to real data. Results: We demonstrate that, for common variants, the W-test is closely related to several existing tests of association allowing for interaction, including logistic regression on 8 degrees of freedom, although logistic regression can show inflated type I error for low minor allele frequencies,  whereas the W-test shows good/conservative type I error control. Although in some situations the W-test can show higher power, logistic regression is not limited to tests on 8 degrees of freedom but can instead be taylored to impose greater structure on the assumed alternative hypothesis, offering a power advantage when the imposed structure matches the true structure. Conclusions: The W-test is a potentially useful method for testing for association - without necessarily implying interaction - between genetic variants disease, particularly when one or more of the genetic variants are rare. For common variants, the advantages of the W-test are less clear, and, indeed, there are situations where existing methods perform better. In our investigations, we further uncover a number of problems with the practical implementation and application of the W-test (to bipolar disorder previously described, apparently due to inadequate use of standard data quality-control procedures. This observation leads us to urge caution in

  18. Heisenberg coupling constant predicted for molecular magnets with pairwise spin-contamination correction

    Energy Technology Data Exchange (ETDEWEB)

    Masunov, Artëm E., E-mail: amasunov@ucf.edu [NanoScience Technology Center, Department of Chemistry, and Department of Physics, University of Central Florida, Orlando, FL 32826 (United States); Photochemistry Center RAS, ul. Novatorov 7a, Moscow 119421 (Russian Federation); Gangopadhyay, Shruba [Department of Physics, University of California, Davis, CA 95616 (United States); IBM Almaden Research Center, 650 Harry Road, San Jose, CA 95120 (United States)

    2015-12-15

    New method to eliminate the spin-contamination in broken symmetry density functional theory (BS DFT) calculations is introduced. Unlike conventional spin-purification correction, this method is based on canonical Natural Orbitals (NO) for each high/low spin coupled electron pair. We derive an expression to extract the energy of the pure singlet state given in terms of energy of BS DFT solution, the occupation number of the bonding NO, and the energy of the higher spin state built on these bonding and antibonding NOs (not self-consistent Kohn–Sham orbitals of the high spin state). Compared to the other spin-contamination correction schemes, spin-correction is applied to each correlated electron pair individually. We investigate two binuclear Mn(IV) molecular magnets using this pairwise correction. While one of the molecules is described by magnetic orbitals strongly localized on the metal centers, and spin gap is accurately predicted by Noodleman and Yamaguchi schemes, for the other one the gap is predicted poorly by these schemes due to strong delocalization of the magnetic orbitals onto the ligands. We show our new correction to yield more accurate results in both cases. - Highlights: • Magnetic orbitails obtained for high and low spin states are not related. • Spin-purification correction becomes inaccurate for delocalized magnetic orbitals. • We use the natural orbitals of the broken symmetry state to build high spin state. • This new correction is made separately for each electron pair. • Our spin-purification correction is more accurate for delocalised magnetic orbitals.

  19. A discrete model of Ostwald ripening based on multiple pairwise interactions

    Science.gov (United States)

    Di Nunzio, Paolo Emilio

    2018-06-01

    A discrete multi-particle model of Ostwald ripening based on direct pairwise interactions is developed for particles with incoherent interfaces as an alternative to the classical LSW mean field theory. The rate of matter exchange depends on the average surface-to-surface interparticle distance, a characteristic feature of the system which naturally incorporates the effect of volume fraction of second phase. The multi-particle diffusion is described through the definition of an interaction volume containing all the particles involved in the exchange of solute. At small volume fractions this is proportional to the size of the central particle, at higher volume fractions it gradually reduces as a consequence of diffusion screening described on a geometrical basis. The topological noise present in real systems is also included. For volume fractions below about 0.1 the model predicts broad and right-skewed stationary size distributions resembling a lognormal function. Above this value, a transition to sharper, more symmetrical but still right-skewed shapes occurs. An excellent agreement with experiments is obtained for 3D particle size distributions of solid-solid and solid-liquid systems with volume fraction 0.07, 0.30, 0.52 and 0.74. The kinetic constant of the model depends on the cube root of volume fraction up to about 0.1, then increases rapidly with an upward concavity. It is in good agreement with the available literature data on solid-liquid mixtures in the volume fraction range from 0.20 to about 0.75.

  20. Pairwise additivity in the nuclear magnetic resonance interactions of atomic xenon.

    Science.gov (United States)

    Hanni, Matti; Lantto, Perttu; Vaara, Juha

    2009-04-14

    Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xe(n) (n = 2-12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe(2) at different internuclear distances were obtained at the nonrelativistic Hartree-Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xe(n) (n = 2-12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe(2) can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xe(n) clusters. Particularly, the chemical shift in Xe(n) is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.

  1. Contact mechanics: contact area and interfacial separation from small contact to full contact

    International Nuclear Information System (INIS)

    Yang, C; Persson, B N J

    2008-01-01

    We present a molecular dynamics study of the contact between a rigid solid with a randomly rough surface and an elastic block with a flat surface. The numerical calculations mainly focus on the contact area and the interfacial separation from small contact (low load) to full contact (high load). For a small load the contact area varies linearly with the load and the interfacial separation depends logarithmically on the load. For a high load the contact area approaches the nominal contact area (i.e. complete contact), and the interfacial separation approaches zero. The numerical results have been compared with analytical theory and experimental results. They are in good agreement with each other. The present findings may be very important for soft solids, e.g. rubber, or for very smooth surfaces, where complete contact can be reached at moderately high loads without plastic deformation of the solids

  2. Pair-Wise and Many-Body Dispersive Interactions Coupled to an Optimally Tuned Range-Separated Hybrid Functional.

    Science.gov (United States)

    Agrawal, Piyush; Tkatchenko, Alexandre; Kronik, Leeor

    2013-08-13

    We propose a nonempirical, pair-wise or many-body dispersion-corrected, optimally tuned range-separated hybrid functional. This functional retains the advantages of the optimal-tuning approach in the prediction of the electronic structure. At the same time, it gains accuracy in the prediction of binding energies for dispersively bound systems, as demonstrated on the S22 and S66 benchmark sets of weakly bound dimers.

  3. Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

    Science.gov (United States)

    Lindsay, Richard J.; Siess, Jan; Lohry, David P.; McGee, Trevor S.; Ritchie, Jordan S.; Johnson, Quentin R.; Shen, Tongye

    2018-01-01

    We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

  4. Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

    Energy Technology Data Exchange (ETDEWEB)

    Bernardis, F. De; Vavagiakis, E.M.; Niemack, M.D.; Gallardo, P.A. [Department of Physics, Cornell University, Ithaca, NY 14853 (United States); Aiola, S. [Department of Physics and Astronomy, University of Pittsburgh, and Pittsburgh Particle Physics, Astrophysics, and Cosmology Center, 3941 O' Hara Street, Pittsburgh, PA 15260 (United States); Battaglia, N. [Department of Astrophysical Sciences, Peyton Hall, Princeton University, Princeton, NJ 08544 (United States); Beall, J.; Becker, D.T.; Cho, H.; Fox, A. [National Institute of Standards and Technology, Boulder, CO 80305 (United States); Bond, J.R. [CITA, University of Toronto, 60 St. George St., Toronto, ON M5S 3H8 (Canada); Calabrese, E.; Dunkley, J. [Sub-Department of Astrophysics, University of Oxford, Keble Road, Oxford, OX1 3RH (United Kingdom); Coughlin, K.; Datta, R. [Department of Physics, University of Michigan Ann Arbor, MI 48109 (United States); Devlin, M. [Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104 (United States); Dunner, R. [Instituto de Astrofísica and Centro de Astro-Ingeniería, Facultad de Física, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, 7820436 Macul, Santiago (Chile); Ferraro, S. [Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720 (United States); Halpern, M. [University of British Columbia, Department of Physics and Astronomy, 6224 Agricultural Road, Vancouver BC V6T 1Z1 (Canada); Hand, N., E-mail: fdeberna@gmail.com [Astronomy Department, University of California, Berkeley, CA 94720 (United States); and others

    2017-03-01

    We present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariance matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.

  5. Probing dark energy models with extreme pairwise velocities of galaxy clusters from the DEUS-FUR simulations

    Science.gov (United States)

    Bouillot, Vincent R.; Alimi, Jean-Michel; Corasaniti, Pier-Stefano; Rasera, Yann

    2015-06-01

    Observations of colliding galaxy clusters with high relative velocity probe the tail of the halo pairwise velocity distribution with the potential of providing a powerful test of cosmology. As an example it has been argued that the discovery of the Bullet Cluster challenges standard Λ cold dark matter (ΛCDM) model predictions. Halo catalogues from N-body simulations have been used to estimate the probability of Bullet-like clusters. However, due to simulation volume effects previous studies had to rely on a Gaussian extrapolation of the pairwise velocity distribution to high velocities. Here, we perform a detail analysis using the halo catalogues from the Dark Energy Universe Simulation Full Universe Runs (DEUS-FUR), which enables us to resolve the high-velocity tail of the distribution and study its dependence on the halo mass definition, redshift and cosmology. Building upon these results, we estimate the probability of Bullet-like systems in the framework of Extreme Value Statistics. We show that the tail of extreme pairwise velocities significantly deviates from that of a Gaussian, moreover it carries an imprint of the underlying cosmology. We find the Bullet Cluster probability to be two orders of magnitude larger than previous estimates, thus easing the tension with the ΛCDM model. Finally, the comparison of the inferred probabilities for the different DEUS-FUR cosmologies suggests that observations of extreme interacting clusters can provide constraints on dark energy models complementary to standard cosmological tests.

  6. CHARACTERIZING RESIDUE TRANSFER EFFICIENCIES USING A FLUORESCENT IMAGING TECHNIQUE

    Science.gov (United States)

    To reduce the uncertainty associated with current estimates of children's exposure to pesticides by dermal contact and indirect ingestion, residue transfer data are required. Prior to conducting exhaustive studies, a screening study to identify the important parameters for chara...

  7. Thermal Adsorption Processing Of Hydrocarbon Residues

    Directory of Open Access Journals (Sweden)

    Sudad H. Al.

    2017-04-01

    Full Text Available The raw materials of secondary catalytic processes must be pre-refined. Among these refining processes are the deasphalting and demetallization including their thermo adsorption or thermo-contact adsorption variety. In oil processing four main processes of thermo-adsorption refining of hydrocarbon residues are used ART Asphalt Residual Treating - residues deasphaltizing 3D Discriminatory Destructive Distillation developed in the US ACT Adsorption-Contact Treatment and ETCC Express Thermo-Contact Cracking developed in Russia. ART and ACT are processes with absorbers of lift type reactor while 3D and ETCC processes are with an adsorbing reactor having ultra-short contact time of the raw material with the adsorbent. In all these processes refining of hydrocarbon residues is achieved by partial Thermo-destructive transformations of hydrocarbons and hetero-atomic compounds with simultaneous adsorption of the formed on the surface of the adsorbents resins asphaltene and carboids as well as metal- sulphur - and nitro-organic compounds. Demetallized and deasphalted light and heavy gas oils or their mixtures are a quality raw material for secondary deepening refining processes catalytic and hydrogenation cracking etc. since they are characterized by low coking ability and low content of organometallic compounds that lead to irreversible deactivation of the catalysts of these deepening processes.

  8. High-throughput detection of prostate cancer in histological sections using probabilistic pairwise Markov models.

    Science.gov (United States)

    Monaco, James P; Tomaszewski, John E; Feldman, Michael D; Hagemann, Ian; Moradi, Mehdi; Mousavi, Parvin; Boag, Alexander; Davidson, Chris; Abolmaesumi, Purang; Madabhushi, Anant

    2010-08-01

    In this paper we present a high-throughput system for detecting regions of carcinoma of the prostate (CaP) in HSs from radical prostatectomies (RPs) using probabilistic pairwise Markov models (PPMMs), a novel type of Markov random field (MRF). At diagnostic resolution a digitized HS can contain 80Kx70K pixels - far too many for current automated Gleason grading algorithms to process. However, grading can be separated into two distinct steps: (1) detecting cancerous regions and (2) then grading these regions. The detection step does not require diagnostic resolution and can be performed much more quickly. Thus, we introduce a CaP detection system capable of analyzing an entire digitized whole-mount HS (2x1.75cm(2)) in under three minutes (on a desktop computer) while achieving a CaP detection sensitivity and specificity of 0.87 and 0.90, respectively. We obtain this high-throughput by tailoring the system to analyze the HSs at low resolution (8microm per pixel). This motivates the following algorithm: (Step 1) glands are segmented, (Step 2) the segmented glands are classified as malignant or benign, and (Step 3) the malignant glands are consolidated into continuous regions. The classification of individual glands leverages two features: gland size and the tendency for proximate glands to share the same class. The latter feature describes a spatial dependency which we model using a Markov prior. Typically, Markov priors are expressed as the product of potential functions. Unfortunately, potential functions are mathematical abstractions, and constructing priors through their selection becomes an ad hoc procedure, resulting in simplistic models such as the Potts. Addressing this problem, we introduce PPMMs which formulate priors in terms of probability density functions, allowing the creation of more sophisticated models. To demonstrate the efficacy of our CaP detection system and assess the advantages of using a PPMM prior instead of the Potts, we alternately

  9. Pairwise protein expression classifier for candidate biomarker discovery for early detection of human disease prognosis

    Directory of Open Access Journals (Sweden)

    Kaur Parminder

    2012-08-01

    spectrometry data from “bottom up” proteomics methods, functionally related proteins/peptide pairs exhibiting co-ordinated changes expression profile are discovered, which represent a signature for patients progressing to various disease conditions. The method has been tested against clinical data from patients progressing to idiopthatic pneumonia syndrome (IPS following a bone marrow transplant. The data indicates that patients with improper regulation in the concentration of specific acute phase response proteins at the time of bone marrow transplant are highly likely to develop IPS within few weeks. The results lead to a specific set of protein pairs that can be efficiently verified by investigating the pairwise abundance change in independent cohorts using ELISA or targeted mass spectrometry techniques. This generalized classifier can be extended to other clinical problems in a variety of contexts.

  10. Process to recycle shredder residue

    Science.gov (United States)

    Jody, Bassam J.; Daniels, Edward J.; Bonsignore, Patrick V.

    2001-01-01

    A system and process for recycling shredder residue, in which separating any polyurethane foam materials are first separated. Then separate a fines fraction of less than about 1/4 inch leaving a plastics-rich fraction. Thereafter, the plastics rich fraction is sequentially contacted with a series of solvents beginning with one or more of hexane or an alcohol to remove automotive fluids; acetone to remove ABS; one or more of EDC, THF or a ketone having a boiling point of not greater than about 125.degree. C. to remove PVC; and one or more of xylene or toluene to remove polypropylene and polyethylene. The solvents are recovered and recycled.

  11. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... Cleveland. "This is far from the truth." Real People, Real Problems with Colored Contact Lenses Julian: Teenager ... about the members of the eye-care team . Consumer warning about the improper use of colored contact ...

  12. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... One Use Facts About Colored Contacts and Halloween Safety Colored Contact Lens Facts Over-the-Counter Costume ... new application of artificial intelligence shows whether a patient’s eyes point to high blood pressure or risk ...

  13. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... Costume Contacts May Contain Chemicals Harmful to Eyes Four Ways Over-the-Counter Costume Contact Lenses Can ... was in severe pain and on medication for four weeks, and couldn't see well enough to ...

  14. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... sell contacts without a prescription are breaking the law, and may be fined $11,000 per violation. " ... wear any kind of contact lens. In Butler's case, the lenses caused an infection and left her ...

  15. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... Hazard: The Hidden Dangers of Buying Decorative Contact Lenses Without a Prescription Leer en Español: Peligros asociados ... truth." Real People, Real Problems with Colored Contact Lenses Julian: Teenager Blinded In One Eye By Non- ...

  16. Colored Contact Lens Dangers

    Science.gov (United States)

    ... Hazard: The Hidden Dangers of Buying Decorative Contact Lenses Without a Prescription Leer en Español: Peligros asociados ... truth." Real People, Real Problems with Colored Contact Lenses Julian: Teenager Blinded In One Eye By Non- ...

  17. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... Cleveland. "This is far from the truth." Real People, Real Problems with Colored Contact Lenses Julian: Teenager ... the lenses. Never share contact lenses with another person. Get follow up exams with your eye care ...

  18. Contact Angle Goniometer

    Data.gov (United States)

    Federal Laboratory Consortium — Description:The FTA32 goniometer provides video-based contact angle and surface tension measurement. Contact angles are measured by fitting a mathematical expression...

  19. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... like a suction cup." Halloween is a popular time for people to use colored contact lenses to ... wear costume contact lenses for Halloween or any time of year, follow these guidelines: Get an eye ...

  20. Colored Contact Lens Dangers

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    Full Text Available ... glow-in-the-dark lizard lenses, costume contacts can certainly add a spooky, eye-popping touch. But ... consideration as a standard contact lens because they can be purchased over-the-counter or on the ...

  1. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... contact lenses , from the U.S. Food and Drug Administration (FDA). Are the colored lenses you are considering ... Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About the Academy Jobs at ...

  2. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... not require the same level of care or consideration as a standard contact lens because they can ... sell contacts without a prescription are breaking the law, and may be fined $11,000 per violation. " ...

  3. Dermatitis, contact (image)

    Science.gov (United States)

    This picture shows a skin inflammation (dermatitis) caused by contact with a material that causes an allergic reaction in this person. Contact dermatitis is a relatively common condition, and can be caused ...

  4. Contact materials for nanoelectronics

    KAUST Repository

    Alshareef, Husam N.; Quevedo-Ló pez, Manuel Angel Quevedo; Majhi, Prashant

    2011-01-01

    In this article, we review current research activities in contact material development for electronic and nanoelectronic devices. A fundamental issue in contact materials research is to understand and control interfacial reactions and phenomena

  5. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... the United States. All contact lenses are medical devices that require a prescription and proper fitting by an eye-care professional. Retailers that sell contacts without a ...

  6. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... prescription. Follow the contact lens care directions for cleaning, disinfecting, and wearing the lenses. Never share contact ... with Industry Medical Disclaimer Privacy Policy Terms of Service For Advertisers For Media Ophthalmology Job Center © American ...

  7. Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study.

    Science.gov (United States)

    Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias; Salanti, Georgia

    2018-02-28

    To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) ("living" network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analyses were performed for each selected comparison. Monitoring boundaries of statistical significance were constructed and the evidence against the null hypothesis was considered to be strong when the monitoring boundaries were crossed. A significance level was defined as α=5%, power of 90% (β=10%), and an anticipated treatment effect to detect equal to the final estimate from the network meta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided

  8. Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study

    Science.gov (United States)

    Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias

    2018-01-01

    Abstract Objective To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) (“living” network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Design Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Data sources Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Eligibility criteria for study selection Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. Results 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided strong evidence against the null hypothesis (P=0.002). The median time to strong evidence against the null hypothesis was 19 years with living network meta-analysis and 23 years with living pairwise meta-analysis (hazard ratio 2.78, 95% confidence interval 1.00 to 7.72, P=0.05). Studies directly comparing

  9. Improving contact prediction along three dimensions.

    Directory of Open Access Journals (Sweden)

    Christoph Feinauer

    2014-10-01

    Full Text Available Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their members. The typical pipeline to address this task, which we in this paper refer to as the three dimensions of contact prediction, is to (i filter and align the raw sequence data representing the evolutionarily related proteins; (ii choose a predictive model to describe a sequence alignment; (iii infer the model parameters and interpret them in terms of structural properties, such as an accurate contact map. We show here that all three dimensions are important for overall prediction success. In particular, we show that it is possible to improve significantly along the second dimension by going beyond the pair-wise Potts models from statistical physics, which have hitherto been the focus of the field. These (simple extensions are motivated by multiple sequence alignments often containing long stretches of gaps which, as a data feature, would be rather untypical for independent samples drawn from a Potts model. Using a large test set of proteins we show that the combined improvements along the three dimensions are as large as any reported to date.

  10. Contact Lens Risks

    Science.gov (United States)

    ... There is a risk of eye infection from bacteria in swimming pool water, hot tubs, lakes and the ocean Replace your contact lens storage case every 3 months or as directed by your eye care professional. Other Risks of Contact Lenses Other risks of contact lenses include pink eye ( ...

  11. Hydrogenation of passivated contacts

    Energy Technology Data Exchange (ETDEWEB)

    Nemeth, William; Yuan, Hao-Chih; LaSalvia, Vincenzo; Stradins, Pauls; Page, Matthew R.

    2018-03-06

    Methods of hydrogenation of passivated contacts using materials having hydrogen impurities are provided. An example method includes applying, to a passivated contact, a layer of a material, the material containing hydrogen impurities. The method further includes subsequently annealing the material and subsequently removing the material from the passivated contact.

  12. Mixed Lubricated Line Contacts

    NARCIS (Netherlands)

    Faraon, I.C.

    2005-01-01

    The present work deals with friction in mixed lubricated line contacts. Components in systems are becoming smaller and due to, for instance power transmitted, partial contact may occur. In industrial applications, friction between the moving contacting surfaces cannot be avoided, therefore it is

  13. New Cosmetic Contact Allergens

    Directory of Open Access Journals (Sweden)

    An Goossens

    2015-02-01

    Full Text Available Allergic and photo-allergic contact dermatitis, and immunologic contact urticaria are potential immune-mediated adverse effects from cosmetics. Fragrance components and preservatives are certainly the most frequently observed allergens; however, all ingredients must be considered when investigating for contact allergy.

  14. Lifetime limitations of ohmic, contacting RF MEMS switches with Au, Pt and Ir contact materials due to accumulation of ‘friction polymer’ on the contacts

    International Nuclear Information System (INIS)

    Czaplewski, David A; Nordquist, Christopher D; Dyck, Christopher W; Patrizi, Gary A; Kraus, Garth M; Cowan, William D

    2012-01-01

    We present lifetime limitations and failure analysis of many packaged RF MEMS ohmic contacting switches with Au–Au, Au–Ir, and Au–Pt contact materials operating with 100 µN of contact force per contact in hermetically sealed glass wall packages. All metals were tested using the same switch design in a controlled environment to provide a comparison between the performance of the different materials and their corresponding failure mechanisms. The switch lifetimes of the different contact materials varied from several hundred cycles to 200 million cycles with different mechanisms causing failures for different contact materials. Switches with Au–Au contacts failed due to adhesion when thoroughly cleaned while switches with dissimilar metal contacts (Au–Ir and Au–Pt) operated without adhesion failures but failed due to carbon accumulation on the contacts even in a clean, packaged environment as a result of the catalytic behavior of the contact materials. Switch lifetimes correlated inversely with catalytic behavior of the contact metals. The data suggests the path to increase switch lifetime is to use favorable catalytic materials as contacts, design switches with higher contact forces to break through any residual contamination, and use cleaner, probably smaller, packages. (paper)

  15. CONTACT RESISTANCE MODELING

    Directory of Open Access Journals (Sweden)

    S. V. LOSKUTOV

    2018-05-01

    Full Text Available Purpose. To determine the contribution of the real contact spots distribution in the total conductivity of the conductors contact. Methodology. The electrical contact resistance research was carried out on models. The experimental part of this work was done on paper with a graphite layer with membranes (the first type and conductive liquids with discrete partitions (the second type. Findings. It is shown that the contact electrical resistance is mainly determined by the real area of metal contact. The experimental dependence of the electrical resistance of the second type model on the distance between the electrodes and the potential distribution along the sample surface for the first type model were obtained. The theoretical model based on the principle of electric field superposition was considered. The dependences obtained experimentally and calculated by using the theoretical model are in good agreement. Originality. The regularity of the electrical contact resistance formation on a large number of membranes was researched for the first time. A new model of discrete electrical contact based on the liquid as the conducting environment with nuclear membrane partitions was developed. The conclusions of the additivity of contact and bulk electrical resistance were done. Practical value. Based on these researches, a new experimental method of kinetic macroidentation that as a parameter of the metal surface layer deformation uses the real contact area was developed. This method allows to determine the value of average contact stresses, yield point, change of the stress on the depth of deformation depending on the surface treatment.

  16. A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

    OpenAIRE

    Maréchal Eric; Ortet Philippe; Roy Sylvaine; Bastien Olivier

    2005-01-01

    Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic recon...

  17. Bispectral pairwise interacting source analysis for identifying systems of cross-frequency interacting brain sources from electroencephalographic or magnetoencephalographic signals

    Science.gov (United States)

    Chella, Federico; Pizzella, Vittorio; Zappasodi, Filippo; Nolte, Guido; Marzetti, Laura

    2016-05-01

    Brain cognitive functions arise through the coordinated activity of several brain regions, which actually form complex dynamical systems operating at multiple frequencies. These systems often consist of interacting subsystems, whose characterization is of importance for a complete understanding of the brain interaction processes. To address this issue, we present a technique, namely the bispectral pairwise interacting source analysis (biPISA), for analyzing systems of cross-frequency interacting brain sources when multichannel electroencephalographic (EEG) or magnetoencephalographic (MEG) data are available. Specifically, the biPISA makes it possible to identify one or many subsystems of cross-frequency interacting sources by decomposing the antisymmetric components of the cross-bispectra between EEG or MEG signals, based on the assumption that interactions are pairwise. Thanks to the properties of the antisymmetric components of the cross-bispectra, biPISA is also robust to spurious interactions arising from mixing artifacts, i.e., volume conduction or field spread, which always affect EEG or MEG functional connectivity estimates. This method is an extension of the pairwise interacting source analysis (PISA), which was originally introduced for investigating interactions at the same frequency, to the study of cross-frequency interactions. The effectiveness of this approach is demonstrated in simulations for up to three interacting source pairs and for real MEG recordings of spontaneous brain activity. Simulations show that the performances of biPISA in estimating the phase difference between the interacting sources are affected by the increasing level of noise rather than by the number of the interacting subsystems. The analysis of real MEG data reveals an interaction between two pairs of sources of central mu and beta rhythms, localizing in the proximity of the left and right central sulci.

  18. An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

    Directory of Open Access Journals (Sweden)

    Taneda Akito

    2008-12-01

    Full Text Available Abstract Background Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA discovery. Results We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared S. cerevisiae genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%. By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences. Conclusion The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.

  19. Contact and symplectic topology

    CERN Document Server

    Colin, Vincent; Stipsicz, András

    2014-01-01

    Symplectic and contact geometry naturally emerged from the mathematical description of classical physics. The discovery of new rigidity phenomena and properties satisfied by these geometric structures launched a new research field worldwide. The intense activity of many European research groups in this field is reflected by the ESF Research Networking Programme "Contact And Symplectic Topology" (CAST). The lectures of the Summer School in Nantes (June 2011) and of the CAST Summer School in Budapest (July 2012) provide a nice panorama of many aspects of the present status of contact and symplectic topology. The notes of the minicourses offer a gentle introduction to topics which have developed in an amazing speed in the recent past. These topics include 3-dimensional and higher dimensional contact topology, Fukaya categories, asymptotically holomorphic methods in contact topology, bordered Floer homology, embedded contact homology, and flexibility results for Stein manifolds.

  20. Introduction to contact mechanics

    CERN Document Server

    Fischer-Cripps, Anthony C

    2000-01-01

    Contact mechanics deals with the elastic or plastic contact between two solid objects, and is thus intimately connected with such topics as fracture, hardness, and elasticity.This text, intended for advanced undergraduates, begins with an introduction to the mechanical properties of materials, general fracture mechanics, and fractures in brittle solids.This is followed by a detailed discussion of stresses and the nature of elastic and elastic-plastic contact.

  1. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... also available in Spanish . Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About the Academy Jobs at the Academy Financial ...

  2. Allergic Contact Dermatitis

    Directory of Open Access Journals (Sweden)

    Meltem Önder

    2009-03-01

    Full Text Available Allergic contact dermatitis is the delayed type hypersensitivity reaction to exogenous agents. Allergic contact dermatitis may clinically present acutely after allergen exposure and initial sensitization in a previously sensitized individual. Acute phase is characterized by erythematous, scaly plaques. In severe cases vesiculation and bullae in exposed areas are very characteristic. Repeated or continuous exposure of sensitized individual with allergen result in chronic dermatitis. Lichenification, erythematous plaques, hyperkeratosis and fissuring may develop in chronic patients. Allergic contact dermatitis is very common dermatologic problem in dermatology daily practice. A diagnosis of contact dermatitis requires the careful consideration of patient history, physical examination and patch testing. The knowledge of the clinical features of the skin reactions to various contactans is important to make a correct diagnosis of contact dermatitis. It can be seen in every age, in children textile product, accessories and touch products are common allergens, while in adults allergic contact dermatitis may be related with topical medicaments. The contact pattern of contact dermatitis depends on fashion and local traditions as well. The localization of allergic reaction should be evaluated and patients’ occupation and hobbies should be asked. The purpose of this review is to introduce to our collaques up dated allergic contact dermatitis literatures both in Turkey and in the World.

  3. Colors and contact dermatitis.

    Science.gov (United States)

    Bonamonte, Domenico; Foti, Caterina; Romita, Paolo; Vestita, Michelangelo; Angelini, Gianni

    2014-01-01

    The diagnosis of skin diseases relies on several clinical signs, among which color is of paramount importance. In this review, we consider certain clinical presentations of both eczematous and noneczematous contact dermatitis in which color plays a peculiar role orientating toward the right diagnosis. The conditions that will be discussed include specific clinical-morphologic subtypes of eczematous contact dermatitis, primary melanocytic, and nonmelanocytic contact hyperchromia, black dermographism, contact chemical leukoderma, and others. Based on the physical, chemical, and biologic factors underlying a healthy skin color, the various skin shades drawing a disease picture are thoroughly debated, stressing their etiopathogenic origins and histopathologic aspects.

  4. Multilevel summation methods for efficient evaluation of long-range pairwise interactions in atomistic and coarse-grained molecular simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Bond, Stephen D.

    2014-01-01

    The availability of efficient algorithms for long-range pairwise interactions is central to the success of numerous applications, ranging in scale from atomic-level modeling of materials to astrophysics. This report focuses on the implementation and analysis of the multilevel summation method for approximating long-range pairwise interactions. The computational cost of the multilevel summation method is proportional to the number of particles, N, which is an improvement over FFTbased methods whos cost is asymptotically proportional to N logN. In addition to approximating electrostatic forces, the multilevel summation method can be use to efficiently approximate convolutions with long-range kernels. As an application, we apply the multilevel summation method to a discretized integral equation formulation of the regularized generalized Poisson equation. Numerical results are presented using an implementation of the multilevel summation method in the LAMMPS software package. Preliminary results show that the computational cost of the method scales as expected, but there is still a need for further optimization.

  5. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... eye-care professional. Retailers that sell contacts without a prescription are breaking the law, and may be fined $11,000 per violation. "Many of the lenses found online or in beauty salons, novelty shops or in pop-up ... contact lenses from a retailer that does not ask for a prescription. ...

  6. Electric contact arcing

    International Nuclear Information System (INIS)

    Cuthrell, R.E.

    1976-01-01

    Electrical contacts must function properly in many types of components used in nuclear weapon systems. Design, application, and testing of these components require detailed knowledge of chemical and physical phenomena associated with stockpile storage, stockpile testing, and operation. In the past, investigation of these phenomena has led to significant discoveries on the effects of surface contaminants, friction and wear, and the mechanics of closure on contact performance. A recent investigation of contact arcing phenomena which revealed that, preceding contact closure, arcs may occur at voltages lower than had been previously known is described. This discovery is important, since arcing may damage contacts, and repetitive testing of contacts performed as part of a quality assurance program might produce cumulative damage that would yield misleading life-test data and could prevent proper operation of the contacts at some time in the future. This damage can be avoided by determining the conditions under which arcing occurs, and ensuring that these conditions are avoided in contact testing

  7. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... Get follow up exams with your eye care provider. If you notice redness, swelling, excessive discharge, pain or discomfort from wearing contact lenses, remove the lenses and seek immediate medical attention from an ophthalmologist. Related resources: Learn how to properly care for contact lenses . ...

  8. Sciences & Nature: Contact

    African Journals Online (AJOL)

    Principal Contact. Ehouan Etienne Ehile Professor University of Abobo-Adjamé 02 BP 801 Abidjan 02. Phone: (+225) 2030 4201. Fax: (+225) 2030 4203. Email: eh_ehile@yahoo.fr. Support Contact. Irie Zoro Bi Email: banhiakalou@yahoo.fr. ISSN: 1812-0741. AJOL African Journals Online. HOW TO USE AJOL.

  9. Contact Us | DOepatents

    Science.gov (United States)

    advance. Your help is appreciated. Contact us by email Email doepatentscomments@osti.gov NOTE: Email us by phone Phone Phone (865) 241-5275 Contact us in writing Mail U.S. Department of Energy Office of non-federal websites. Their policies may differ from this site. Javascript Not Enabled Email Link

  10. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... eye-care team . Consumer warning about the improper use of colored contact lenses , from the U.S. Food and Drug Administration (FDA). Are the colored lenses you are considering buying approved by the FDA? Check the FDA's database of approved contact lenses . Related Stories Prevent Infection ...

  11. Contact dermatitis. A review

    DEFF Research Database (Denmark)

    Andersen, Klaus Ejner; Benezra, C; Burrows, D

    1987-01-01

    In recent years, there has been a dramatic rise in our understanding of contact dermatitis. This paper is a review of our knowledge of the mechanisms involved in contact dermatitis and related phenomena, the investigation of these events and the emergence of significant new allergens during...

  12. Contact Hamiltonian mechanics

    Energy Technology Data Exchange (ETDEWEB)

    Bravetti, Alessandro, E-mail: alessandro.bravetti@iimas.unam.mx [Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, A. P. 70543, México, DF 04510 (Mexico); Cruz, Hans, E-mail: hans@ciencias.unam.mx [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, A. P. 70543, México, DF 04510 (Mexico); Tapias, Diego, E-mail: diego.tapias@nucleares.unam.mx [Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P. 70543, México, DF 04510 (Mexico)

    2017-01-15

    In this work we introduce contact Hamiltonian mechanics, an extension of symplectic Hamiltonian mechanics, and show that it is a natural candidate for a geometric description of non-dissipative and dissipative systems. For this purpose we review in detail the major features of standard symplectic Hamiltonian dynamics and show that all of them can be generalized to the contact case.

  13. Contact Quality in Participation

    DEFF Research Database (Denmark)

    Simonsen, Jesper; Jensen, Olav Storm

    2016-01-01

    We investigate the concept of participation from the perspective of quality of the contact in the communicative interactions between participants. We argue for the need for an academic-personal competence that qualifies the human contact central in all Participatory Design (PD) activities as a way...

  14. Nigerian Food Journal: Contact

    African Journals Online (AJOL)

    Nigerian Food Journal. ... Nigerian Food Journal: Contact. Journal Home > About the Journal > Nigerian Food Journal: Contact. Log in or Register to get access to full text downloads. ... Mailing Address. Department of Food Science and Technology University of Agriculture, Makurdi, Nigeria ...

  15. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... like a suction cup." Halloween is a popular time for people to use colored contact lenses to enhance their costumes. From ... MD, professor of ophthalmology at Case Western Reserve University in Cleveland. "This is far ... Use Facts About Colored Contacts and Halloween Safety Colored ...

  16. Dry cleaning of fluorocarbon residues by low-power electron cyclotron resonance hydrogen plasma

    CERN Document Server

    Lim, S H; Yuh, H K; Yoon Eui Joon; Lee, S I

    1988-01-01

    A low-power ( 50 W) electron cyclotron resonance hydrogen plasma cleaning process was demonstrated for the removal of fluorocarbon residue layers formed by reactive ion etching of silicon dioxide. The absence of residue layers was confirmed by in-situ reflection high energy electron diffraction and cross-sectional high resolution transmission electron microscopy. The ECR hydrogen plasma cleaning was applied to contact cleaning of a contact string structure, resulting in comparable contact resistance arising during by a conventional contact cleaning procedure. Ion-assisted chemical reaction involving reactive atomic hydrogen species generated in the plasma is attributed for the removal of fluorocarbon residue layers.

  17. Contact materials for nanoelectronics

    KAUST Repository

    Alshareef, Husam N.

    2011-02-01

    In this article, we review current research activities in contact material development for electronic and nanoelectronic devices. A fundamental issue in contact materials research is to understand and control interfacial reactions and phenomena that modify the expected device performance. These reactions have become more challenging and more difficult to control as new materials have been introduced and as device sizes have entered the deep nanoscale. To provide an overview of this field of inquiry, this issue of MRS Bulletin includes articles on gate and contact materials for Si-based devices, junction contact materials for Si-based devices, and contact materials for alternate channel substrates (Ge and III-V), nanodevices. © 2011 Materials Research Society.

  18. Noneczematous Contact Dermatitis

    Science.gov (United States)

    Foti, Caterina; Vestita, Michelangelo; Angelini, Gianni

    2013-01-01

    Irritant or allergic contact dermatitis usually presents as an eczematous process, clinically characterized by erythematoedematovesicous lesions with intense itching in the acute phase. Such manifestations become erythematous-scaly as the condition progresses to the subacute phase and papular-hyperkeratotic in the chronic phase. Not infrequently, however, contact dermatitis presents with noneczematous features. The reasons underlying this clinical polymorphism lie in the different noxae and contact modalities, as well as in the individual susceptibility and the various targeted cutaneous structures. The most represented forms of non-eczematous contact dermatitis include the erythema multiforme-like, the purpuric, the lichenoid, and the pigmented kinds. These clinical entities must obviously be discerned from the corresponding “pure” dermatitis, which are not associated with contact with exogenous agents. PMID:24109520

  19. Analysis of deep learning methods for blind protein contact prediction in CASP12.

    Science.gov (United States)

    Wang, Sheng; Sun, Siqi; Xu, Jinbo

    2018-03-01

    Here we present the results of protein contact prediction achieved in CASP12 by our RaptorX-Contact server, which is an early implementation of our deep learning method for contact prediction. On a set of 38 free-modeling target domains with a median family size of around 58 effective sequences, our server obtained an average top L/5 long- and medium-range contact accuracy of 47% and 44%, respectively (L = length). A complete implementation has an average accuracy of 59% and 57%, respectively. Our deep learning method formulates contact prediction as a pixel-level image labeling problem and simultaneously predicts all residue pairs of a protein using a combination of two deep residual neural networks, taking as input the residue conservation information, predicted secondary structure and solvent accessibility, contact potential, and coevolution information. Our approach differs from existing methods mainly in (1) formulating contact prediction as a pixel-level image labeling problem instead of an image-level classification problem; (2) simultaneously predicting all contacts of an individual protein to make effective use of contact occurrence patterns; and (3) integrating both one-dimensional and two-dimensional deep convolutional neural networks to effectively learn complex sequence-structure relationship including high-order residue correlation. This paper discusses the RaptorX-Contact pipeline, both contact prediction and contact-based folding results, and finally the strength and weakness of our method. © 2017 Wiley Periodicals, Inc.

  20. Neutron diffraction measurements of residual stress in a powder metallurgy component

    International Nuclear Information System (INIS)

    Schneider, L.C.R.; Hainsworth, S.V.; Cocks, A.C.F.; Fitzpatrick, M.E.

    2005-01-01

    Residual stresses in a typical industrial green component were determined using neutron diffraction. The measured residual stresses were found to correlate with cross-sectional variations. Residual stress at the edge of the compact in contact with the die wall during compaction reached up to +80 MPa (tension) and -100 MPa (compression)

  1. Residual gas analysis

    International Nuclear Information System (INIS)

    Berecz, I.

    1982-01-01

    Determination of the residual gas composition in vacuum systems by a special mass spectrometric method was presented. The quadrupole mass spectrometer (QMS) and its application in thin film technology was discussed. Results, partial pressure versus time curves as well as the line spectra of the residual gases in case of the vaporization of a Ti-Pd-Au alloy were demonstrated together with the possible construction schemes of QMS residual gas analysers. (Sz.J.)

  2. Contacts to semiconductors

    International Nuclear Information System (INIS)

    Tove, P.A.

    1975-08-01

    Contacts to semiconductors play an important role in most semiconductor devices. These devices range from microelectronics to power components, from high-sensitivity light or radiation detectors to light-emitting of microwave-generating components. Silicon is the dominating material but compound semiconductors are increasing in importance. The following survey is an attempt to classify contact properties and the physical mechanisms involved, as well as fabrication methods and methods of investigation. The main interest is in metal-semiconductor type contacts where a few basic concepts are dealt with in some detail. (Auth.)

  3. Analysis of pairwise correlations in multi-parametric PET/MR data for biological tumor characterization and treatment individualization strategies

    Energy Technology Data Exchange (ETDEWEB)

    Leibfarth, Sara; Moennich, David; Thorwarth, Daniela [University Hospital Tuebingen, Section for Biomedical Physics, Department of Radiation Oncology, Tuebingen (Germany); Simoncic, Urban [University Hospital Tuebingen, Section for Biomedical Physics, Department of Radiation Oncology, Tuebingen (Germany); University of Ljubljana, Faculty of Mathematics and Physics, Ljubljana (Slovenia); Jozef Stefan Institute, Ljubljana (Slovenia); Welz, Stefan; Zips, Daniel [University Hospital Tuebingen, Department of Radiation Oncology, Tuebingen (Germany); Schmidt, Holger; Schwenzer, Nina [University Hospital Tuebingen, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany)

    2016-07-15

    The aim of this pilot study was to explore simultaneous functional PET/MR for biological characterization of tumors and potential future treatment adaptations. To investigate the extent of complementarity between different PET/MR-based functional datasets, a pairwise correlation analysis was performed. Functional datasets of N=15 head and neck (HN) cancer patients were evaluated. For patients of group A (N=7), combined PET/MR datasets including FDG-PET and ADC maps were available. Patients of group B (N=8) had FMISO-PET, DCE-MRI and ADC maps from combined PET/MRI, an additional dynamic FMISO-PET/CT acquired directly after FMISO tracer injection as well as an FDG-PET/CT acquired a few days earlier. From DCE-MR, parameter maps K{sup trans}, v{sub e} and v{sub p} were obtained with the extended Tofts model. Moreover, parameter maps of mean DCE enhancement, ΔS{sub DCE}, and mean FMISO signal 0-4 min p.i., anti A{sub FMISO}, were derived. Pairwise correlations were quantified using the Spearman correlation coefficient (r) on both a voxel and a regional level within the gross tumor volume. Between some pairs of functional imaging modalities moderate correlations were observed with respect to the median over all patient datasets, whereas distinct correlations were only present on an individual basis. Highest inter-modality median correlations on the voxel level were obtained for FDG/FMISO (r = 0.56), FDG/ anti A{sub FMISO} (r = 0.55), anti A{sub FMISO}/ΔS{sub DCE} (r = 0.46), and FDG/ADC (r = -0.39). Correlations on the regional level showed comparable results. The results of this study suggest that the examined functional datasets provide complementary information. However, only pairwise correlations were examined, and correlations could still exist between combinations of three or more datasets. These results might contribute to the future design of individually adapted treatment approaches based on multiparametric functional imaging.

  4. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... not been properly fitted by an eye care professional, the lenses stuck to my eye like a ... prescription and proper fitting by an eye-care professional. Retailers that sell contacts without a prescription are ...

  5. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... about the members of the eye-care team . Consumer warning about the improper use of colored contact ... About the Academy Jobs at the Academy Financial Relationships with Industry Medical Disclaimer Privacy Policy Terms of ...

  6. Contact Line Dynamics

    Science.gov (United States)

    Kreiss, Gunilla; Holmgren, Hanna; Kronbichler, Martin; Ge, Anthony; Brant, Luca

    2017-11-01

    The conventional no-slip boundary condition leads to a non-integrable stress singularity at a moving contact line. This makes numerical simulations of two-phase flow challenging, especially when capillarity of the contact point is essential for the dynamics of the flow. We will describe a modeling methodology, which is suitable for numerical simulations, and present results from numerical computations. The methodology is based on combining a relation between the apparent contact angle and the contact line velocity, with the similarity solution for Stokes flow at a planar interface. The relation between angle and velocity can be determined by theoretical arguments, or from simulations using a more detailed model. In our approach we have used results from phase field simulations in a small domain, but using a molecular dynamics model should also be possible. In both cases more physics is included and the stress singularity is removed.

  7. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... use of colored contact lenses , from the U.S. Food and Drug Administration (FDA). Are the colored lenses ... away without suffering an eye injury. However, the natural protective mechanisms of the eye – such as the ...

  8. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... about the members of the eye-care team . Consumer warning about the improper use of colored contact ... a laser pointer several times, according to a report published this month in the New England Journal ...

  9. SAM Technical Contacts

    Science.gov (United States)

    These technical contacts are available to help with questions regarding method deviations, modifications, sample problems or interferences, quality control requirements, the use of alternative methods, or the need to address analytes or sample types.

  10. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... colored contact lenses , from the U.S. Food and Drug Administration (FDA). Are the colored lenses you are ... this month in the New England Journal of Medicine. Unfortunately, this kind of injury is all too ...

  11. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... a souvenir shop, but 10 hours after she first put in a pair of colored contact lenses, ... APR 24, 2018 By Kate Rauch In a first, scientists in China have created artificial photoreceptors to ...

  12. GAS-FOVEAL CONTACT

    DEFF Research Database (Denmark)

    Alberti, Mark; la Cour, Morten

    2018-01-01

    PURPOSE: To compare gas-foveal contact in face-down positioning (FDP) and nonsupine positioning (NSP), to analyze causes of gas-foveal separation and to determine how gas-foveal contact affects clinical outcome after idiopathic macular hole repair. METHODS: Single center, randomized controlled...... study. Participants with an idiopathic macular hole were allocated to either FDP or NSP. Primary outcome was gas-foveal contact, calculated by analyzing positioning in relation to intraocular gas fill. Positioning was measured with an electronic device recording positioning for 72 hours postoperatively....... RESULTS: Positioning data were available for 33/35 in the FDP group and 35/37 in the NSP group, thus results are based on 68 analyzed participants. Median gas-foveal contact was 99.82% (range 73.6-100.0) in the FDP group and 99.57% (range 85.3-100.0) in the NSP group (P = 0.22). In a statistical model...

  13. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... Sep. 26, 2013 It started as an impulsive buy from a souvenir shop, but 10 hours after ... are being sold illegally," Dr. Steinemann said. Never buy colored contact lenses from a retailer that does ...

  14. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... use of colored contact lenses , from the U.S. Food and Drug Administration (FDA). Are the colored lenses ... 2018 By Dan T. Gudgel Do you know what the difference is between ophthalmologists and optometrists? A ...

  15. Colored Contact Lens Dangers

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    Full Text Available ... Halloween or any time of year, follow these guidelines: Get an eye exam from a licensed eye ... available in Spanish . Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About the ...

  16. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... contacto de color Sep. 26, 2013 It started as an impulsive buy from a souvenir shop, but ... require the same level of care or consideration as a standard contact lens because they can be ...

  17. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... seek immediate medical attention from an ophthalmologist. Related resources: Learn how to properly care for contact lenses . ... have given blind patients some functional vision, using human embryonic stem cells. Two blind patients regained enough ...

  18. Colored Contact Lens Dangers

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    Full Text Available ... that decorative lenses do not require the same level of care or consideration as a standard contact ... By Kate Rauch In a small but intriguing study, scientists in England have given blind patients some ...

  19. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... MD, professor of ophthalmology at Case Western Reserve University in Cleveland. "This is far from the truth." Real People, Real Problems with Colored Contact Lenses Julian: Teenager Blinded In ...

  20. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... also available in Spanish . Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About the Academy Jobs at the Academy Financial Relationships with Industry Medical Disclaimer Privacy Policy Terms ...

  1. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... lentes de contacto de color Sep. 26, 2013 It started as an impulsive buy from a souvenir ... Can Ruin Vision Eye Makeup Safety In fact, it is illegal to sell colored contact lenses without ...

  2. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... With Proper Contact Lens Care Apr 23, 2018 Solar Eclipse Inflicts Damage in the Shape of the ... edging closer, thanks to a wave of new technologies aiming to fix failing eye parts with human- ...

  3. Colored Contact Lens Dangers

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    Full Text Available ... videos on your website Promotional materials for eye health observances EyeSmart resources are also available in Spanish . Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About the Academy Jobs at ...

  4. Colored Contact Lens Dangers

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    Full Text Available ... valid prescription that includes the brand name, lens measurements, and expiration date. Purchase the colored contact lenses ... with human-made versions. U.S. News Highlights the Value of Ophthalmologists APR 20, 2018 By Dan T. ...

  5. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... sell contacts without a prescription are breaking the law, and may be fined $11,000 per violation. " ... Us About the Academy Jobs at the Academy Financial Relationships with Industry Medical Disclaimer Privacy Policy Terms ...

  6. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... sell contacts without a prescription are breaking the law, and may be fined $11,000 per violation. " ... 13, 2017 Histoplasmosis Diagnosis Sep 01, 2017 How common is retinal detachment for people with high myopia? ...

  7. Colored Contact Lens Dangers

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    Full Text Available ... Ophthalmology/Strabismus Ocular Pathology/Oncology Oculoplastics/Orbit Refractive Management/Intervention Retina/Vitreous Uveitis Focus ... Eye Health A-Z Symptoms Glasses & Contacts Tips & ...

  8. Colored Contact Lens Dangers

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    Full Text Available ... use of colored contact lenses , from the U.S. Food and Drug Administration (FDA). Are the colored lenses you are considering buying approved by the ... Service For Advertisers For Media Ophthalmology Job Center © American ...

  9. Colored Contact Lens Dangers

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    Full Text Available ... be purchased over-the-counter or on the Internet," says Thomas Steinemann, MD, professor of ophthalmology at ... also available in Spanish . Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About ...

  10. Ergonomics SA: Contact

    African Journals Online (AJOL)

    Principal Contact. Mrs June McDougall. Rhodes University. Department of Human Kinetics and Ergonomics. P.O. Box 94. Rhodes University. Grahamstown. 6140. Phone: +27 46 6038471. Email: j.mcdougall@ru.ac.za ...

  11. Colored Contact Lens Dangers

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    Full Text Available ... contact lenses , from the U.S. Food and Drug Administration (FDA). Are the colored lenses you are considering buying approved by ... 23, 2018 Solar Eclipse Inflicts Damage in the Shape of ...

  12. Colored Contact Lens Dangers

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    Full Text Available ... had not been properly fitted by an eye care professional, the lenses stuck to my eye like ... lenses do not require the same level of care or consideration as a standard contact lens because ...

  13. Colored Contact Lens Dangers

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    Full Text Available ... colored contact lenses to enhance their costumes. From blood-drenched vampire eyes to glow-in-the-dark ... properly fitted may scratch the eye or cause blood vessels to grow into the cornea. Even if ...

  14. Colored Contact Lens Dangers

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    Full Text Available ... to the journals may be interrupted during this time. We are working to resolve the issue quickly ... like a suction cup." Halloween is a popular time for people to use colored contact lenses to ...

  15. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... the United States. All contact lenses are medical devices that require a prescription and proper fitting by ... Care Apr 23, 2018 How long does it take the eye to go back to its original ...

  16. Tomato contact dermatitis

    DEFF Research Database (Denmark)

    Paulsen, Evy; Christensen, Lars P; Andersen, Klaus Ejner

    2012-01-01

    The tomato plant (Solanum lycopersicum) is an important crop worldwide. Whereas immediate-type reactions to tomato fruits are well known, contact dermatitis caused by tomatoes or tomato plants is rarely reported. The aims of this study were to present new data on contact sensitization to tomato...... plants and review the literature on contact dermatitis caused by both plants and fruits. An ether extract of tomato plants made as the original oleoresin plant extracts, was used in aimed patch testing, and between 2005 and 2011. 8 of 93 patients (9%) tested positive to the oleoresin extracts....... This prevalence is in accordance with the older literature that reports tomato plants as occasional sensitizers. The same applies to tomato fruits, which, in addition, may cause protein contact dermatitis. The allergens of the plant are unknown, but both heat-stable and heat-labile constituents seem...

  17. Fragrance allergic contact dermatitis.

    Science.gov (United States)

    Cheng, Judy; Zug, Kathryn A

    2014-01-01

    Fragrances are a common cause of allergic contact dermatitis in Europe and in North America. They can affect individuals at any age and elicit a spectrum of reactions from contact urticaria to systemic contact dermatitis. Growing recognition of the widespread use of fragrances in modern society has fueled attempts to prevent sensitization through improved allergen identification, labeling, and consumer education. This review provides an overview and update on fragrance allergy. Part 1 discusses the epidemiology and evaluation of suspected fragrance allergy. Part 2 reviews screening methods, emerging fragrance allergens, and management of patients with fragrance contact allergy. This review concludes by examining recent legislation on fragrances and suggesting potential additions to screening series to help prevent and detect fragrance allergy.

  18. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About the Academy Jobs at the Academy Financial Relationships with Industry Medical Disclaimer Privacy Policy Terms of Service For Advertisers For Media Ophthalmology ...

  19. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... be purchased over-the-counter or on the Internet," says Thomas Steinemann, MD, professor of ophthalmology at ... about the members of the eye-care team . Consumer warning about the improper use of colored contact ...

  20. Colored Contact Lens Dangers

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    Full Text Available ... Peligros asociados con los lentes de contacto de color Sep. 26, 2013 It started as an impulsive ... Halloween is a popular time for people to use colored contact lenses to enhance their costumes. From ...

  1. Colored Contact Lens Dangers

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    Full Text Available ... The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About the Academy Jobs at the Academy Financial Relationships with Industry Medical Disclaimer Privacy Policy Terms of ...

  2. Colored Contact Lens Dangers

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    Full Text Available ... not require the same level of care or consideration as a standard contact lens because they can ... Us About the Academy Jobs at the Academy Financial Relationships with Industry Medical Disclaimer Privacy Policy Terms ...

  3. Colored Contact Lens Dangers

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    Full Text Available ... be purchased over-the-counter or on the Internet," says Thomas Steinemann, MD, professor of ophthalmology at ... ask for a prescription. There is no such thing as a "one size fits all" contact lens. ...

  4. Colored Contact Lens Dangers

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    Full Text Available ... also available in Spanish . Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About the Academy Jobs at the Academy Financial Relationships with Industry Medical ...

  5. Colored Contact Lens Dangers

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    Full Text Available ... Ophthalmology/Strabismus Ocular Pathology/Oncology Oculoplastics/Orbit Refractive Management/Intervention Retina/Vitreous Uveitis Focus ... Halloween Hazard: The Hidden Dangers of Buying Decorative Contact Lenses Without ...

  6. Amino acid empirical contact energy definitions for fold recognition in the space of contact maps

    Directory of Open Access Journals (Sweden)

    Fogolari Federico

    2003-02-01

    Full Text Available Abstract Background Contradicting evidence has been presented in the literature concerning the effectiveness of empirical contact energies for fold recognition. Empirical contact energies are calculated on the basis of information available from selected protein structures, with respect to a defined reference state, according to the quasi-chemical approximation. Protein-solvent interactions are estimated from residue solvent accessibility. Results In the approach presented here, contact energies are derived from the potential of mean force theory, several definitions of contact are examined and their performance in fold recognition is evaluated on sets of decoy structures. The best definition of contact is tested, on a more realistic scenario, on all predictions including sidechains accepted in the CASP4 experiment. In 30 out of 35 cases the native structure is correctly recognized and best predictions are usually found among the 10 lowest energy predictions. Conclusion The definition of contact based on van der Waals radii of alpha carbon and side chain heavy atoms is seen to perform better than other definitions involving only alpha carbons, only beta carbons, all heavy atoms or only backbone atoms. An important prerequisite for the applicability of the approach is that the protein structure under study should not exhibit anomalous solvent accessibility, compared to soluble proteins whose structure is deposited in the Protein Data Bank. The combined evaluation of a solvent accessibility parameter and contact energy allows for an effective gross screening of predictive models.

  7. Socio-economic scenario development for the assessment of climate change impacts on agricultural land use: a pairwise comparison approach

    DEFF Research Database (Denmark)

    Abildtrup, Jens; Audsley, E.; Fekete-Farkas, M.

    2006-01-01

    Assessment of the vulnerability of agriculture to climate change is strongly dependent on concurrent changes in socio-economic development pathways. This paper presents an integrated approach to the construction of socio-economic scenarios required for the analysis of climate change impacts...... on European agricultural land use. The scenarios are interpreted from the storylines described in the intergovernmental panel on climate change (IPCC) special report on emission scenarios (SRES), which ensures internal consistency between the evolution of socio-economics and climate change. A stepwise...... downscaling procedure based on expert-judgement and pairwise comparison is presented to obtain quantitative socio-economic parameters, e.g. prices and productivity estimates that are input to the ACCELERATES integrated land use model. In the first step, the global driving forces are identified and quantified...

  8. Dynamical pairwise entanglement and two-point correlations in the three-ligand spin-star structure

    Science.gov (United States)

    Motamedifar, M.

    2017-10-01

    We consider the three-ligand spin-star structure through homogeneous Heisenberg interactions (XXX-3LSSS) in the framework of dynamical pairwise entanglement. It is shown that the time evolution of the central qubit ;one-particle; state (COPS) brings about the generation of quantum W states at periodical time instants. On the contrary, W states cannot be generated from the time evolution of a ligand ;one-particle; state (LOPS). We also investigate the dynamical behavior of two-point quantum correlations as well as the expectation values of the different spin-components for each element in the XXX-3LSSS. It is found that when a W state is generated, the same value of the concurrence between any two arbitrary qubits arises from the xx and yy two-point quantum correlations. On the opposite, zz quantum correlation between any two qubits vanishes at these time instants.

  9. Pairwise NMR experiments for the determination of protein backbone dihedral angle Φ based on cross-correlated spin relaxation

    International Nuclear Information System (INIS)

    Takahashi, Hideo; Shimada, Ichio

    2007-01-01

    Novel cross-correlated spin relaxation (CCR) experiments are described, which measure pairwise CCR rates for obtaining peptide dihedral angles Φ. The experiments utilize intra-HNCA type coherence transfer to refocus 2-bond J NCα coupling evolution and generate the N (i)-C α (i) or C'(i-1)-C α (i) multiple quantum coherences which are required for measuring the desired CCR rates. The contribution from other coherences is also discussed and an appropriate setting of the evolution delays is presented. These CCR experiments were applied to 15 N- and 13 C-labeled human ubiquitin. The relevant CCR rates showed a high degree of correlation with the Φ angles observed in the X-ray structure. By utilizing these CCR experiments in combination with those previously established for obtaining dihedral angle Ψ, we can determine high resolution structures of peptides that bind weakly to large target molecules

  10. Plant lock and ant key: pairwise coevolution of an exclusion filter in an ant-plant mutualism.

    Science.gov (United States)

    Brouat, C; Garcia, N; Andary, C; McKey, D

    2001-10-22

    Although observations suggest pairwise coevolution in specific ant-plant symbioses, coevolutionary processes have rarely been demonstrated. We report on, what is to the authors' knowledge, the strongest evidence yet for reciprocal adaptation of morphological characters in a species-specific ant-plant mutualism. The plant character is the prostoma, which is a small unlignified organ at the apex of the domatia in which symbiotic ants excavate an entrance hole. Each myrmecophyte in the genus Leonardoxa has evolved a prostoma with a different shape. By performing precise measurements on the prostomata of three related myrmecophytes, on their specific associated ants and on the entrance holes excavated by symbiotic ants at the prostomata, we showed that correspondence of the plant and ant traits forms a morphological and behavioural filter. We have strong evidence for coevolution between the dimensions and shape of the symbiotic ants and the prostoma in one of the three ant-Leonardoxa associations.

  11. Galaxy and Mass Assembly (GAMA): small-scale anisotropic galaxy clustering and the pairwise velocity dispersion of galaxies

    Science.gov (United States)

    Loveday, J.; Christodoulou, L.; Norberg, P.; Peacock, J. A.; Baldry, I. K.; Bland-Hawthorn, J.; Brown, M. J. I.; Colless, M.; Driver, S. P.; Holwerda, B. W.; Hopkins, A. M.; Kafle, P. R.; Liske, J.; Lopez-Sanchez, A. R.; Taylor, E. N.

    2018-03-01

    The galaxy pairwise velocity dispersion (PVD) can provide important tests of non-standard gravity and galaxy formation models. We describe measurements of the PVD of galaxies in the Galaxy and Mass Assembly (GAMA) survey as a function of projected separation and galaxy luminosity. Due to the faint magnitude limit (r PVD to smaller scales (r⊥ = 0.01 h - 1 Mpc) than previous work. The measured PVD at projected separations r⊥ ≲ 1 h - 1 Mpc increases near monotonically with increasing luminosity from σ12 ≈ 200 km s - 1 at Mr = -17 mag to σ12 ≈ 600 km s - 1 at Mr ≈ -22 mag. Analysis of the Gonzalez-Perez et al. (2014) GALFORM semi-analytic model yields no such trend of PVD with luminosity: the model overpredicts the PVD for faint galaxies. This is most likely a result of the model placing too many low-luminosity galaxies in massive haloes.

  12. Lettuce contact allergy.

    Science.gov (United States)

    Paulsen, Evy; Andersen, Klaus E

    2016-02-01

    Lettuce (Lactuca sativa L.) and its varieties are important vegetable crops worldwide. They are also well-known, rarely reported, causes of contact allergy. As lettuce allergens and extracts are not commercially available, the allergy may be underdiagnosed. The aims of this article are to present new data on lettuce contact allergy and review the literature. Lettuce is weakly allergenic, and occupational cases are mainly reported. Using aimed patch testing in Compositae-allergic patients, two recent Danish studies showed prevalence rates of positive lettuce reactions of 11% and 22%. The majority of cases are non-occupational, and may partly be caused by cross-reactivity. The sesquiterpene lactone mix seems to be a poor screening agent for lettuce contact allergy, as the prevalence of positive reactions is significantly higher in non-occupationally sensitized patients. Because of the easy degradability of lettuce allergens, it is recommended to patch test with freshly cut lettuce stem and supplement this with Compositae mix. As contact urticaria and protein contact dermatitis may present as dermatitis, it is important to perform prick-to-prick tests, and possibly scratch patch tests as well. Any person who is occupationally exposed to lettuce for longer periods, especially atopics, amateur gardeners, and persons keeping lettuce-eating pets, is potentially at risk of developing lettuce contact allergy. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  13. AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins.

    Directory of Open Access Journals (Sweden)

    Hon Cheng Muh

    Full Text Available Allergy is a major health problem in industrialized countries. The number of transgenic food crops is growing rapidly creating the need for allergenicity assessment before they are introduced into human food chain. While existing bioinformatic methods have achieved good accuracies for highly conserved sequences, the discrimination of allergens and non-allergens from allergen-like non-allergen sequences remains difficult. We describe AllerHunter, a web-based computational system for the assessment of potential allergenicity and allergic cross-reactivity in proteins. It combines an iterative pairwise sequence similarity encoding scheme with SVM as the discriminating engine. The pairwise vectorization framework allows the system to model essential features in allergens that are involved in cross-reactivity, but not limited to distinct sets of physicochemical properties. The system was rigorously trained and tested using 1,356 known allergen and 13,449 putative non-allergen sequences. Extensive testing was performed for validation of the prediction models. The system is effective for distinguishing allergens and non-allergens from allergen-like non-allergen sequences. Testing results showed that AllerHunter, with a sensitivity of 83.4% and specificity of 96.4% (accuracy = 95.3%, area under the receiver operating characteristic curve AROC = 0.928+/-0.004 and Matthew's correlation coefficient MCC = 0.738, performs significantly better than a number of existing methods using an independent dataset of 1443 protein sequences. AllerHunter is available at (http://tiger.dbs.nus.edu.sg/AllerHunter.

  14. Surface feeding and aggressive behaviour of diploid and triploid brown trout Salmo trutta during allopatric pair-wise matchings.

    Science.gov (United States)

    Preston, A C; Taylor, J F; Adams, C E; Migaud, H

    2014-09-01

    Diploid and triploid brown trout Salmo trutta were acclimated for 6 weeks on two feeding regimes (floating and sinking). Thereafter, aggression and surface feeding response were compared between pairs of all diploid, all triploid and diploid and triploid S. trutta in an experimental stream. In each pair-wise matching, fish of similar size were placed in allopatry and rank was determined by the total number of aggressive interactions recorded. Dominant individuals initiated more aggression than subordinates, spent more time defending a territory and positioned themselves closer to the surface food source (Gammarus pulex), whereas subordinates occupied the peripheries. In cross ploidy trials, diploid S. trutta were more aggressive than triploid, and dominated their sibling when placed in pair-wise matchings. Surface feeding, however, did not differ statistically between ploidy irrespective of feeding regime. Triploids adopted a sneak feeding strategy while diploids expended more time defending a territory. In addition, we also tested whether triploids exhibit a similar social dominance to diploids when placed in allopatry. Although aggression was lower in triploid pairs than in the diploid and triploid pairs, a dominance hierarchy was also observed between individuals of the same ploidy. Dominant triploid fish were more aggressive and consumed more feed items than subordinate individuals. Subordinate fish displayed a darker colour index than dominant fish suggesting increased stress levels. Dominant triploid fish, however, appeared to be more tolerant of subordinate individuals and did not display the same degree of invasive aggression as seen in the diploid and diploid or diploid and triploid matchings. These novel findings suggest that sterile triploid S. trutta feed similarly but are less aggressive than diploid trout. Future studies should determine the habitat choice of triploid S. trutta after release and the interaction between wild fish and triploids during

  15. Synchronization of pairwise-coupled, identical, relaxation oscillators based on metal-insulator phase transition devices: A model study

    Science.gov (United States)

    Parihar, Abhinav; Shukla, Nikhil; Datta, Suman; Raychowdhury, Arijit

    2015-02-01

    Computing with networks of synchronous oscillators has attracted wide-spread attention as novel materials and device topologies have enabled realization of compact, scalable and low-power coupled oscillatory systems. Of particular interest are compact and low-power relaxation oscillators that have been recently demonstrated using MIT (metal-insulator-transition) devices using properties of correlated oxides. Further the computational capability of pairwise coupled relaxation oscillators has also been shown to outperform traditional Boolean digital logic circuits. This paper presents an analysis of the dynamics and synchronization of a system of two such identical coupled relaxation oscillators implemented with MIT devices. We focus on two implementations of the oscillator: (a) a D-D configuration where complementary MIT devices (D) are connected in series to provide oscillations and (b) a D-R configuration where it is composed of a resistor (R) in series with a voltage-triggered state changing MIT device (D). The MIT device acts like a hysteresis resistor with different resistances in the two different states. The synchronization dynamics of such a system has been analyzed with purely charge based coupling using a resistive (RC) and a capacitive (CC) element in parallel. It is shown that in a D-D configuration symmetric, identical and capacitively coupled relaxation oscillator system synchronizes to an anti-phase locking state, whereas when coupled resistively the system locks in phase. Further, we demonstrate that for certain range of values of RC and CC, a bistable system is possible which can have potential applications in associative computing. In D-R configuration, we demonstrate the existence of rich dynamics including non-monotonic flows and complex phase relationship governed by the ratios of the coupling impedance. Finally, the developed theoretical formulations have been shown to explain experimentally measured waveforms of such pairwise coupled

  16. Patients with multiple contact allergies

    DEFF Research Database (Denmark)

    Carlsen, Berit Christina; Andersen, Klaus Ejner; Menné, Torkil

    2008-01-01

    Patients with multiple contact allergies, also referred to as polysensitized, are more frequent than predicted from prevalence of single sensitivities. The understanding of why some people develop multiple contact allergies, and characterization of patients with multiple contact allergies...... of developing multiple contact allergies. Evidence of allergen clusters among polysensitized individuals is also reviewed. The literature supports the idea that patients with multiple contact allergies constitute a special entity within the field of contact allergy. There is no generally accepted definition...... of patients with multiple contact allergies. We suggest that contact allergy to 3 or more allergens are defined as multiple contact allergies....

  17. Smoothed particle hydrodynamics study of the roughness effect on contact angle and droplet flow.

    Science.gov (United States)

    Shigorina, Elena; Kordilla, Jannes; Tartakovsky, Alexandre M

    2017-09-01

    We employ a pairwise force smoothed particle hydrodynamics (PF-SPH) model to simulate sessile and transient droplets on rough hydrophobic and hydrophilic surfaces. PF-SPH allows modeling of free-surface flows without discretizing the air phase, which is achieved by imposing the surface tension and dynamic contact angles with pairwise interaction forces. We use the PF-SPH model to study the effect of surface roughness and microscopic contact angle on the effective contact angle and droplet dynamics. In the first part of this work, we investigate static contact angles of sessile droplets on different types of rough surfaces. We find that the effective static contact angles of Cassie and Wenzel droplets on a rough surface are greater than the corresponding microscale static contact angles. As a result, microscale hydrophobic rough surfaces also show effective hydrophobic behavior. On the other hand, microscale hydrophilic surfaces may be macroscopically hydrophilic or hydrophobic, depending on the type of roughness. We study the dependence of the transition between Cassie and Wenzel states on roughness and droplet size, which can be linked to the critical pressure for the given fluid-substrate combination. We observe good agreement between simulations and theoretical predictions. Finally, we study the impact of the roughness orientation (i.e., an anisotropic roughness) and surface inclination on droplet flow velocities. Simulations show that droplet flow velocities are lower if the surface roughness is oriented perpendicular to the flow direction. If the predominant elements of surface roughness are in alignment with the flow direction, the flow velocities increase compared to smooth surfaces, which can be attributed to the decrease in fluid-solid contact area similar to the lotus effect. We demonstrate that classical linear scaling relationships between Bond and capillary numbers for droplet flow on flat surfaces also hold for flow on rough surfaces.

  18. Handling of Solid Residues

    International Nuclear Information System (INIS)

    Medina Bermudez, Clara Ines

    1999-01-01

    The topic of solid residues is specifically of great interest and concern for the authorities, institutions and community that identify in them a true threat against the human health and the atmosphere in the related with the aesthetic deterioration of the urban centers and of the natural landscape; in the proliferation of vectorial transmitters of illnesses and the effect on the biodiversity. Inside the wide spectrum of topics that they keep relationship with the environmental protection, the inadequate handling of solid residues and residues dangerous squatter an important line in the definition of political and practical environmentally sustainable. The industrial development and the population's growth have originated a continuous increase in the production of solid residues; of equal it forms, their composition day after day is more heterogeneous. The base for the good handling includes the appropriate intervention of the different stages of an integral administration of residues, which include the separation in the source, the gathering, the handling, the use, treatment, final disposition and the institutional organization of the administration. The topic of the dangerous residues generates more expectation. These residues understand from those of pathogen type that are generated in the establishments of health that of hospital attention, until those of combustible, inflammable type, explosive, radio-active, volatile, corrosive, reagent or toxic, associated to numerous industrial processes, common in our countries in development

  19. Rough Surface Contact

    Directory of Open Access Journals (Sweden)

    T Nguyen

    2017-06-01

    Full Text Available This paper studies the contact of general rough curved surfaces having nearly identical geometries, assuming the contact at each differential area obeys the model proposed by Greenwood and Williamson. In order to account for the most general gross geometry, principles of differential geometry of surface are applied. This method while requires more rigorous mathematical manipulations, the fact that it preserves the original surface geometries thus makes the modeling procedure much more intuitive. For subsequent use, differential geometry of axis-symmetric surface is considered instead of general surface (although this “general case” can be done as well in Chapter 3.1. The final formulas for contact area, load, and frictional torque are derived in Chapter 3.2.

  20. Acrylate Systemic Contact Dermatitis.

    Science.gov (United States)

    Sauder, Maxwell B; Pratt, Melanie D

    2015-01-01

    Acrylates, the 2012 American Contact Dermatitis Society allergen of the year, are found in a range of products including the absorbent materials within feminine hygiene pads. When fully polymerized, acrylates are nonimmunogenic; however, if not completely cured, the monomers can be potent allergens.A 28-year-old woman is presented, who had her teeth varnished with Isodan (Septodont, Saint-Maur-des-Fossés, France) containing HEMA (2-hydroxyethyl methacrylate) with no initial reaction. Approximately 1 month later, the patient developed a genital dermatitis secondary to her feminine hygiene pads. The initial reaction resolved, but 5 months later, the patient developed a systemic contact dermatitis after receiving a second varnishing.The patient was dramatically patch test positive to many acrylates. This case demonstrates a reaction to likely unpolymerized acrylates within a feminine hygiene pad, as well as broad cross-reactivity or cosensitivity to acrylates, and possibly a systemic contact dermatitis with systemic re-exposure to unpolymerized acrylates.

  1. Shoe allergic contact dermatitis.

    Science.gov (United States)

    Matthys, Erin; Zahir, Amir; Ehrlich, Alison

    2014-01-01

    Foot dermatitis is a widespread condition, affecting men and women of all ages. Because of the location, this condition may present as a debilitating problem to those who have it. Allergic contact dermatitis involving the feet is frequently due to shoes or socks. The allergens that cause shoe dermatitis can be found in any constituent of footwear, including rubber, adhesives, leather, dyes, metals, and medicaments. The goal of treatment is to identify and minimize contact with the offending allergen(s). The lack of product information released from shoe manufacturers and the continually changing trends in footwear present a challenge in treating this condition. The aim of this study is to review the current literature on allergic contact shoe dermatitis; clinical presentation, allergens, patch testing, and management will be discussed. PubMed and MEDLINE databases were used for the search, with a focus on literature updates from the last 15 years.

  2. ALLERGIC CONTACT DERMATITIS

    Directory of Open Access Journals (Sweden)

    Trisna Yuliharti Tersinanda

    2013-07-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE Allergic contact dermatitis is an immunologic reaction that tends to involve the surrounding skin and may even spread beyond affected sites. This skin disease is one of the more frequent, and costly dermatologic problems. Recent data from United Kingdom and United States suggest that the percentage of occupational contact dermatitis due to allergy may be much higher, thus raising the economic impact of occupational allergic contact dermatitis. There is not enough data about the epidemiology of allergic contact dermatitis in Indonesia, however based on research that include beautician in Denpasar, about 27,6 percent had side effect of cosmetics, which is 25,4 percent of it manifested as allergic contact dermatitis. Diagnosis of allergic contact dermatitis is based on anamnesis, physical examination, patch test, and this disease should be distinguished from other eczematous skin disease. The management is prevention of allergen exposure, symptomatic treatment, and physicochemical barrier /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin-top:0in; mso-para-margin-right:0in; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0in; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}

  3. Numerical simulations of rough contacts between viscoelastic materials

    Science.gov (United States)

    Spinu, S.; Cerlinca, D.

    2017-08-01

    The durability of the mechanical contact is often plagued by surface-related phenomena like rolling contact fatigue, wear or crack propagation, which are linked to the important gradients of stress arising in the contacting bodies due to interaction at the asperity level. The semi-analytical computational approach adopted in this paper is based on a previously reported algorithm capable of simulating the contact between bodies with arbitrary limiting surfaces and viscoelastic behaviour, which is enhanced and adapted for the contact of real surfaces with microtopography. As steep slopes at the asperity level inevitably lead to localized plastic deformation at the tip of the asperities that are first brought into contact, the viscoelastic behaviour is amended by limiting the maximum value of the pressure on the contact area to that of the material hardness, according to the Tabor equation. In this manner, plasticity is considered in a simplified manner that assures the knowledge of the contact area and of the pressure distribution without estimation of the residual state. The main advantage of this approach is the preservation of the algorithmic complexity, allowing the simulation of very fine meshes capable of capturing particular features of the investigated contacting surface. The newly advanced model is expected to predict the contact specifics of rough surfaces as resulting from various manufacturing processes, thus assisting the design of durable machine elements using elastomers or rubbers.

  4. A noise-resistant ADSA-PH algorithm for superhydrophobic surface’s static contact angle evaluation

    OpenAIRE

    Z. N. Xu

    2017-01-01

    The blur around the contact points significantly decreases the evaluated static contact angle for superhydrophobic surface which is clearly presented in the paper. To improve the accuracy in the evaluated static contact angle for superhydrophobic surface, an accurate static contact angle algorithm, namely ADSA-PH (axisymmetric drop shape analysis-profile and height), is proposed. It discards the extracted drop edge points close to the contact points and makes use of the residual points and th...

  5. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... Spanish . Follow The Academy Professionals: Education Guidelines News Multimedia Public & Patients: Contact Us About the Academy Jobs at the Academy Financial Relationships with Industry Medical Disclaimer Privacy Policy Terms of Service For Advertisers For Media Ophthalmology Job Center © American ...

  6. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... Tips & Prevention News Ask an Ophthalmologist Patient Stories Español Eye Health / News Halloween Hazard: The Hidden Dangers ... Decorative Contact Lenses Without a Prescription Leer en Español: Peligros asociados con los lentes de contacto de ...

  7. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... prescription. There is no such thing as a "one size fits all" contact lens. Lenses that are not properly fitted may scratch the eye or cause blood vessels to grow into the cornea. Even if you have perfect vision, you need to get an eye exam and a prescription ...

  8. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... MD, professor of ophthalmology at Case Western Reserve University in Cleveland. "This is far from the truth." ... use of colored contact lenses , from the U.S. Food and Drug Administration (FDA). Are the colored lenses you are considering buying approved by the ... Service For Advertisers For Media Ophthalmology Job Center © American ...

  9. Fermilab | Contact Fermilab

    Science.gov (United States)

    Education Safety Sustainability and Environment Contact Related Links DOE FRA UChicago URA Newsroom -840-3000 Fax: 630-840-4343 Shipping address Fermilab Receiving Wilson Street and Kirk Road Batavia IL 60510-5011 Phone: 630-840-3000 Visiting address Fermilab entrance Kirk Road and Pine Street Batavia IL

  10. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... Español Eye Health / News Halloween Hazard: The Hidden Dangers of Buying Decorative Contact Lenses Without a Prescription ... be purchased over-the-counter or on the Internet," says Thomas Steinemann, MD, professor of ophthalmology at ...

  11. Lettuce contact allergy

    DEFF Research Database (Denmark)

    Paulsen, Evy; Andersen, Klaus E

    2016-01-01

    Lettuce (Lactuca sativa L.) and its varieties are important vegetable crops worldwide. They are also well-known, rarely reported, causes of contact allergy. As lettuce allergens and extracts are not commercially available, the allergy may be underdiagnosed. The aims of this article are to present...... person who is occupationally exposed to lettuce for longer periods, especially atopics, amateur gardeners, and persons keeping lettuce-eating pets, is potentially at risk of developing lettuce contact allergy.......Lettuce (Lactuca sativa L.) and its varieties are important vegetable crops worldwide. They are also well-known, rarely reported, causes of contact allergy. As lettuce allergens and extracts are not commercially available, the allergy may be underdiagnosed. The aims of this article are to present...... new data on lettuce contact allergy and review the literature. Lettuce is weakly allergenic, and occupational cases are mainly reported. Using aimed patch testing in Compositae-allergic patients, two recent Danish studies showed prevalence rates of positive lettuce reactions of 11% and 22...

  12. Contact allergy to spices

    NARCIS (Netherlands)

    W. Van den Akker Th. (W.); I.D. Roesyanto-Mahadi (I.); A.W. van Toorenenbergen (Albert); Th. van Joost (Theo)

    1990-01-01

    textabstractA group of 103 patients suspected of contact allergy was tested with the European standard series, wood tars and spices; paprika, cinnamon, laurel, celery seed, nutmeg, curry, black pepper, cloves, while pepper, coriander, cacao and garlic. 32 patients (Group I) were selected on the

  13. Fermilab Education Office - Contacts

    Science.gov (United States)

    Search The Office of Education and Public Outreach: Contacts All telephone numbers require area code Presentations for Presenters 840-3094 Office of Education and Public Outreach Spencer Pasero spasero@fnal.gov Education Office 840-3076 Fermilab Friends for Science Education General Questions Susan Dahl sdahl@fnal.gov

  14. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... A medical degree and many more years of training, for starters. A recent article from U.S. News and World Report explains what ophthalmologists are and how they can help you look after ... Contact Us About the Academy Jobs at the Academy Financial Relationships with Industry Medical ...

  15. Mathematics Connection: Contact

    African Journals Online (AJOL)

    Principal Contact. Dr. Kofi Mereku Executive Editor Department of Mathematics Education, UCE Mathematical Association of Ghana, C/o Department of Mathematics Education University College of Education of Winneba P. O. Box 25, Winneba, Ghana Phone: +233244961318. Email: dkmereku@uew.edu.gh ...

  16. Contact activation: a revision.

    Science.gov (United States)

    Schmaier, A H

    1997-07-01

    In conclusion, a revised view of the contact system has been presented. This system has little to do with the initiation of hemostasis. Like lupus anticoagulants, deficiencies of contact proteins give prolonged APTTs but may be risk factors for thrombosis. BK from kininogens is a potent modulator of vascular biology inducing vasodilation, tissue plasminogen activator release, and prostacyclin liberation. Kininogens, themselves, are selective inhibitors of alpha-thrombin-induced platelet activation preventing alpha-thrombin from cleaving the cloned thrombin receptor after arginine41. Kininogens' alpha-thrombin inhibitory activity exists in intact kininogens, BK, and all of BK's breakdown products. HK also is the pivotal protein for contact protein assembly on endothelium. It is the receptor for prekallikrein which when bound to HK becomes activated to kallikrein by an endothelial cell enzyme system independent of activated forms of plasma factor XII. Prekallikrein activation on endothelial cells results in kinetically favorable single chain urokinase and plasminogen activation. Thus the "physiologic, negatively charged surface" for contact system activation is really the assembly of these proteins on cell membranes and activation by membrane-associated enzymes.

  17. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... wear any kind of contact lens. In Butler's case, the lenses caused an infection and left her with a corneal ... A recent article from U.S. News and World Report explains what ophthalmologists are and how they can ...

  18. Language Contact and Bilingualism

    NARCIS (Netherlands)

    Appel, René; Muysken, Pieter

    2006-01-01

    What happens - sociologically, linguistically, educationally, politically - when more than one language is in regular use in a community? How do speakers handle these languages simultaneously, and what influence does this language contact have on the languages involved? Although most people in the

  19. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... Health / News Halloween Hazard: The Hidden Dangers of Buying Decorative Contact Lenses Without a Prescription Leer en Español: Peligros asociados con los lentes de contacto de color Sep. 26, 2013 It started as an impulsive buy from a souvenir shop, but 10 hours ...

  20. Pizza makers' contact dermatitis.

    Science.gov (United States)

    Lembo, Serena; Lembo, Claudio; Patruno, Cataldo; Balato, Anna; Balato, Nicola; Ayala, Fabio

    2014-01-01

    Contact eczema to foods, spices, and food additives can occur in occupational and nonoccupational settings in those who grow, handle, prepare, or cook food. Pizza is one of the most eaten foods in every continent, and pizza making is a common work in many countries. We aimed to evaluate the occurrence and the causes of contact dermatitis in pizza makers in Naples. We performed an observational study in 45 pizza makers: all the enrolled subjects had to answer a questionnaire designed to detect personal history of respiratory or cutaneous allergy, atopy; work characteristics and timing were also investigated. Every subject attended the dermatology clinic for a complete skin examination, and when needed, patients were patch tested using the Italian baseline series of haptens integrated with an arbitrary pizza makers series. Our results reported that 13.3% of the enrolled pizza makers (6/45) presented hand eczema, and that 8.9% (4/45) were affected by occupational allergic contact dermatitis. Diallyl disulfide and ammonium persulfate were the responsible substances. Performing patch tests in pizza makers and food handlers affected by hand contact dermatitis is useful. We propose a specific series of haptens for this wide working category.

  1. Contact: Releasing the news

    Science.gov (United States)

    Pinotti, Roberto

    The problem of mass behavior after man's future contacts with other intelligences in the universe is not only a challenge for social scientists and political leaders all over the world, but also a cultural time bomb as well. In fact, since the impact of CETI (Contact with Extraterrestrial Intelligence) on human civilization, with its different cultures, might cause a serious socio-anthropological shock, a common and predetermined worldwide strategy is necessary in releasing the news after the contact, in order to keep possible manifestations of fear, panic and hysteria under control. An analysis of past studies in this field and of parallel historical situations as analogs suggests a definite "authority crisis" in the public as a direct consequence of an unexpected release of the news, involving a devastating "chain reaction" process (from both the psychological and sociological viewpoints) of anomie and maybe the collapse of today's society. The only way to prevent all this is to prepare the world's public opinion concerning contact before releasing the news, and to develop a long-term strategy through the combined efforts of scientists, political leaders, intelligence agencies and the mass media, in order to create the cultural conditions in which a confrontation with ETI won't affect mankind in a traumatic way. Definite roles and tasks in this multi-level model are suggested.

  2. Rigid Bodies in Contact

    DEFF Research Database (Denmark)

    Niebe, Sarah Maria

    . A contact point determination method, based on boolean surface maps, is developed to handle collisions between tetrahedral meshes. The novel nonsmooth nonlinear conjugate gradient (NNCG) method is presented. The NNCG method is comparable in terms of accuracy to the state-of-the-art method, projected Gauss...

  3. Colored Contact Lens Dangers

    Medline Plus

    Full Text Available ... can be purchased over-the-counter or on the Internet," says Thomas Steinemann, MD, professor of ophthalmology at ... ask for a prescription. There is no such thing as a "one size fits all" contact lens. Lenses that are not properly fitted may scratch the eye or cause blood vessels to grow into ...

  4. Contact allergy to cosmetics

    DEFF Research Database (Denmark)

    Held, E; Johansen, J D; Agner, T

    1999-01-01

    In a 2-year period, 1527 patients with contact dermatitis were investigated in the patch-test clinic. In 531 patients, allergy to cosmetics was suspected from the history and they were tested with their own cosmetic products. 40 (7.5%) (of the 531 patients) had 1 or more positive reactions, 82 (15...

  5. Ghana Mining Journal: Contact

    African Journals Online (AJOL)

    Principal Contact. Professor Daniel Mireku-Gyimah Editor-in-Chief University of Mines & Technology Ghana Mining Journal University of Mines & Technology P. O. BOX 237 Tarkwa Ghana Phone: +233 362 20280/20324. Fax: +233 362 20306. Email: dm.gyimah@umat.edu.gh ...

  6. Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level

    International Nuclear Information System (INIS)

    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal; Thomsen, Bo; Larsen, Knud; Hedegaard, Jakob; Bendixen, Christian; Madsen, Lone Bruhn

    2013-01-01

    Highlights: •Transcriptome sequencing yielded 223 mill porcine RNA-seq reads, and 59,000 transcribed locations. •Establishment of unique transcription profiles for ten porcine tissues including four brain tissues. •Comparison of transcription profiles at gene, isoform, promoter and transcription start site level. •Highlights a high level of regulation of neuro-related genes at both gene, isoform, and TSS level. •Our results emphasize the pig as a valuable animal model with respect to human biological issues. -- Abstract: The transcriptome is the absolute set of transcripts in a tissue or cell at the time of sampling. In this study RNA-Seq is employed to enable the differential analysis of the transcriptome profile for ten porcine tissues in order to evaluate differences between the tissues at the gene and isoform expression level, together with an analysis of variation in transcription start sites, promoter usage, and splicing. Totally, 223 million RNA fragments were sequenced leading to the identification of 59,930 transcribed gene locations and 290,936 transcript variants using Cufflinks with similarity to approximately 13,899 annotated human genes. Pairwise analysis of tissues for differential expression at the gene level showed that the smallest differences were between tissues originating from the porcine brain. Interestingly, the relative level of differential expression at the isoform level did generally not vary between tissue contrasts. Furthermore, analysis of differential promoter usage between tissues, revealed a proportionally higher variation between cerebellum (CBE) versus frontal cortex and cerebellum versus hypothalamus (HYP) than in the remaining comparisons. In addition, the comparison of differential transcription start sites showed that the number of these sites is generally increased in comparisons including hypothalamus in contrast to other pairwise assessments. A comprehensive analysis of one of the tissue contrasts, i

  7. Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores.

    Science.gov (United States)

    Bastien, Olivier; Maréchal, Eric

    2008-08-07

    Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2) following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory) is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure). Homologous sequences were considered as systems 1) having a high redundancy of information reflected by the magnitude of their alignment scores, 2) which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a constant rate, corresponding to the

  8. Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores

    Directory of Open Access Journals (Sweden)

    Maréchal Eric

    2008-08-01

    Full Text Available Abstract Background Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2 following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. Results We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure. Homologous sequences were considered as systems 1 having a high redundancy of information reflected by the magnitude of their alignment scores, 2 which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a

  9. Characterization of Hospital Residuals

    International Nuclear Information System (INIS)

    Blanco Meza, A.; Bonilla Jimenez, S.

    1997-01-01

    The main objective of this investigation is the characterization of the solid residuals. A description of the handling of the liquid and gassy waste generated in hospitals is also given, identifying the source where they originate. To achieve the proposed objective the work was divided in three stages: The first one was the planning and the coordination with each hospital center, in this way, to determine the schedule of gathering of the waste can be possible. In the second stage a fieldwork was made; it consisted in gathering the quantitative and qualitative information of the general state of the handling of residuals. In the third and last stage, the information previously obtained was organized to express the results as the production rate per day by bed, generation of solid residuals for sampled services, type of solid residuals and density of the same ones. With the obtained results, approaches are settled down to either determine design parameters for final disposition whether for incineration, trituration, sanitary filler or recycling of some materials, and storage politics of the solid residuals that allow to determine the gathering frequency. The study concludes that it is necessary to improve the conditions of the residuals handling in some aspects, to provide the cleaning personnel of the equipment for gathering disposition and of security, minimum to carry out this work efficiently, and to maintain a control of all the dangerous waste, like sharp or polluted materials. In this way, an appreciable reduction is guaranteed in the impact on the atmosphere. (Author) [es

  10. Molecular dynamics study of contact mechanics: contact area and interfacial separation from small to full contact

    OpenAIRE

    Yang, C.; Persson, B. N. J.

    2007-01-01

    We report a molecular dynamics study of the contact between a rigid solid with a randomly rough surface and an elastic block with a flat surface. We study the contact area and the interfacial separation from small contact (low load) to full contact (high load). For small load the contact area varies linearly with the load and the interfacial separation depends logarithmically on the load. For high load the contact area approaches to the nominal contact area (i.e., complete contact), and the i...

  11. Focusing on Contact Lens Safety

    Science.gov (United States)

    ... their practices. Decorative contacts (also called “costume,” colored,” “fashion,” or “plano” contacts). The FDA has often warned ... Lenses Decorative Contact Lenses Hydrogen Peroxide Solution Related Consumer Updates 'Colored' and Decorative Contact Lenses: A Prescription ...

  12. Electrical contacts principles and applications

    CERN Document Server

    Slade, Paul G

    2013-01-01

    Covering the theory, application, and testing of contact materials, Electrical Contacts: Principles and Applications, Second Edition introduces a thorough discussion on making electric contact and contact interface conduction; presents a general outline of, and measurement techniques for, important corrosion mechanisms; considers the results of contact wear when plug-in connections are made and broken; investigates the effect of thin noble metal plating on electronic connections; and relates crucial considerations for making high- and low-power contact joints. It examines contact use in switch

  13. [News on occupational contact dermatitis].

    Science.gov (United States)

    Crépy, Marie-Noëlle; Bensefa-Colas, Lynda

    2014-03-01

    Contact dermatitis--irritant contact dermatitis, allergic contact dermatitis and protein contact dermatitis--are the most common occupational skin diseases, most often localized to the hands. Contact urticaria is rarer The main occupational irritants are wet work, detergents and disinfectants, cutting oils, and solvents. The main occupational allergens are rubber additives, metals (chromium, nickel, cobalt), plastics (epoxy resins, acrylic), biocides and plants. Diagnosis is based on clinical examination, medical history and allergy testing. For a number of irritating or sensitizing agents, irritant or allergic dermatitis can be notified as occupational diseases. The two main prevention measures are reducing skin contact with irritants and complete avoidance of skin contact with offending allergens.

  14. The use of a modified pairwise comparison method in evaluating critical success factors for community-based rural homestay programmes

    Science.gov (United States)

    Daud, Shahidah Md; Ramli, Razamin; Kasim, Maznah Mat; Kayat, Kalsom; Razak, Rafidah Abd

    2014-12-01

    Tourism industry has become the highlighted sector which has amazingly increased the national income level. Despite the tourism industry being one of the highest income generating sectors, Homestay Programme as a Community-Based Tourism (CBT) product in Malaysia does not absorbed much of the incoming wealth. Homestay Programme refers to a programme in a community where a tourist stays together with a host family and experiences the everyday way of life of the family in both direct and indirect manner. There are over 100 Homestay Programme currently being registered with the Ministry of Culture and Tourism Malaysia which mostly are located in rural areas, but only a few excel and enjoying the fruit of the booming industry. Hence, this article seeks to identify the critical success factors for a Community-Based Rural Homestay Programme in Malaysia. A modified pairwise method is utilized to further evaluate the identified success factors in a more meaningful way. The findings will help Homestay Programme function as a community development tool that manages tourism resources. Thus, help the community in improving local economy and creating job opportunities.

  15. Prediction of Antimicrobial Peptides Based on Sequence Alignment and Support Vector Machine-Pairwise Algorithm Utilizing LZ-Complexity

    Directory of Open Access Journals (Sweden)

    Xin Yi Ng

    2015-01-01

    Full Text Available This study concerns an attempt to establish a new method for predicting antimicrobial peptides (AMPs which are important to the immune system. Recently, researchers are interested in designing alternative drugs based on AMPs because they have found that a large number of bacterial strains have become resistant to available antibiotics. However, researchers have encountered obstacles in the AMPs designing process as experiments to extract AMPs from protein sequences are costly and require a long set-up time. Therefore, a computational tool for AMPs prediction is needed to resolve this problem. In this study, an integrated algorithm is newly introduced to predict AMPs by integrating sequence alignment and support vector machine- (SVM- LZ complexity pairwise algorithm. It was observed that, when all sequences in the training set are used, the sensitivity of the proposed algorithm is 95.28% in jackknife test and 87.59% in independent test, while the sensitivity obtained for jackknife test and independent test is 88.74% and 78.70%, respectively, when only the sequences that has less than 70% similarity are used. Applying the proposed algorithm may allow researchers to effectively predict AMPs from unknown protein peptide sequences with higher sensitivity.

  16. Evaluation of criteria for sustainability of community-based rural homestay programs via a modified pairwise comparison method

    Science.gov (United States)

    Ramli, Rohaini; Kasim, Maznah Mat; Ramli, Razamin; Kayat, Kalsom; Razak, Rafidah Abd

    2014-12-01

    Ministry of Tourism and Culture Malaysia has long introduced homestay programs across the country to enhance the quality of life of people, especially those living in rural areas. This type of program is classified as a community-based tourism (CBT) as it is expected to economically improve livelihood through cultural and community associated activities. It is the aspiration of the ministry to see that the income imbalance between people in the rural and urban areas is reduced, thus would contribute towards creating more developed states of Malaysia. Since 1970s, there are 154 homestay programs registered with the ministry. However, the performance and sustainability of the programs are still not satisfying. There are only a number of homestay programs that perform well and able to sustain. Thus, the aim of this paper is to identify relevant criteria contributing to the sustainability of a homestay program. The criteria are evaluated for their levels of importance via the use of a modified pairwise method and analyzed for other potentials. The findings will help the homestay operators to focus on the necessary criteria and thus, effectively perform as the CBT business initiative.

  17. Randomized Approaches for Nearest Neighbor Search in Metric Space When Computing the Pairwise Distance Is Extremely Expensive

    Science.gov (United States)

    Wang, Lusheng; Yang, Yong; Lin, Guohui

    Finding the closest object for a query in a database is a classical problem in computer science. For some modern biological applications, computing the similarity between two objects might be very time consuming. For example, it takes a long time to compute the edit distance between two whole chromosomes and the alignment cost of two 3D protein structures. In this paper, we study the nearest neighbor search problem in metric space, where the pair-wise distance between two objects in the database is known and we want to minimize the number of distances computed on-line between the query and objects in the database in order to find the closest object. We have designed two randomized approaches for indexing metric space databases, where objects are purely described by their distances with each other. Analysis and experiments show that our approaches only need to compute O(logn) objects in order to find the closest object, where n is the total number of objects in the database.

  18. Measurement of residual stresses by the moire method

    Science.gov (United States)

    Sciammarella, C. A.; Albertazzi, A., Jr.

    Three different applications of the moire method to the determination of residual stresses and strains are presented. The three applications take advantage of the property of ratings to record the changes of the surface they are printed on. One of the applications deals with thermal residual stresses, another with contact residual stress and the third one is a generalization of the blind hole technique. This last application is based on a computer assisted moire technique and on the generalization of the quasi-heterodyne techniques of fringe pattern analysis.

  19. Refining intra-protein contact prediction by graph analysis

    Directory of Open Access Journals (Sweden)

    Eyal Eran

    2007-05-01

    Full Text Available Abstract Background Accurate prediction of intra-protein residue contacts from sequence information will allow the prediction of protein structures. Basic predictions of such specific contacts can be further refined by jointly analyzing predicted contacts, and by adding information on the relative positions of contacts in the protein primary sequence. Results We introduce a method for graph analysis refinement of intra-protein contacts, termed GARP. Our previously presented intra-contact prediction method by means of pair-to-pair substitution matrix (P2PConPred was used to test the GARP method. In our approach, the top contact predictions obtained by a basic prediction method were used as edges to create a weighted graph. The edges were scored by a mutual clustering coefficient that identifies highly connected graph regions, and by the density of edges between the sequence regions of the edge nodes. A test set of 57 proteins with known structures was used to determine contacts. GARP improves the accuracy of the P2PConPred basic prediction method in whole proteins from 12% to 18%. Conclusion Using a simple approach we increased the contact prediction accuracy of a basic method by 1.5 times. Our graph approach is simple to implement, can be used with various basic prediction methods, and can provide input for further downstream analyses.

  20. HTSC-Josephson step contacts

    International Nuclear Information System (INIS)

    Herrmann, K.

    1994-03-01

    In this work the properties of josephson step contacts are investigated. After a short introduction into Josephson step contacts the structure, properties and the Josphson contacts of YBa 2 Cu 3 O 7-x high-T c superconductors is presented. The fabrication of HTSC step contacts and the microstructure is discussed. The electric properties of these contacts are measured together with the Josephson emission and the magnetic field dependence. The temperature dependence of the stationary transport properties is given. (WL)

  1. Contact dynamics math model

    Science.gov (United States)

    Glaese, John R.; Tobbe, Patrick A.

    1986-01-01

    The Space Station Mechanism Test Bed consists of a hydraulically driven, computer controlled six degree of freedom (DOF) motion system with which docking, berthing, and other mechanisms can be evaluated. Measured contact forces and moments are provided to the simulation host computer to enable representation of orbital contact dynamics. This report describes the development of a generalized math model which represents the relative motion between two rigid orbiting vehicles. The model allows motion in six DOF for each body, with no vehicle size limitation. The rotational and translational equations of motion are derived. The method used to transform the forces and moments from the sensor location to the vehicles' centers of mass is also explained. Two math models of docking mechanisms, a simple translational spring and the Remote Manipulator System end effector, are presented along with simulation results. The translational spring model is used in an attempt to verify the simulation with compensated hardware in the loop results.

  2. Contact allergy to lanolin

    DEFF Research Database (Denmark)

    Fransen, Marloes; Overgaard, Line E K; Johansen, Jeanne D

    2018-01-01

    BACKGROUND: Lanolin has been tested as lanolin alcohols (30% pet.) in baseline patch test series since 1969, and this has shown clinically relevant allergic contact dermatitis cases. OBJECTIVES: To investigate the temporal development of lanolin allergy (i.e. positive reaction to lanolin alcohols...... and/or Amerchol™ L-101), and the association between contact allergy to lanolin and patient characteristics from the MOAHLFA index. METHODS: A retrospective observational study of consecutively patch tested dermatitis patients (n = 9577) between 1 January 2004 and 31 December 2015 with lanolin...... alcohols 30% pet. and Amerchol™ L-101 50% pet. was performed. RESULTS: The prevalence of lanolin allergy increased from 0.45% in 2004 to 1.81% in 2015. In age-adjusted and sex-adjusted analyses, weak, significant associations were found between atopic dermatitis and lanolin and lanolin alcohols allergy...

  3. Management of NORM Residues

    International Nuclear Information System (INIS)

    2013-06-01

    The IAEA attaches great importance to the dissemination of information that can assist Member States in the development, implementation, maintenance and continuous improvement of systems, programmes and activities that support the nuclear fuel cycle and nuclear applications, and that address the legacy of past practices and accidents. However, radioactive residues are found not only in nuclear fuel cycle activities, but also in a range of other industrial activities, including: - Mining and milling of metalliferous and non-metallic ores; - Production of non-nuclear fuels, including coal, oil and gas; - Extraction and purification of water (e.g. in the generation of geothermal energy, as drinking and industrial process water; in paper and pulp manufacturing processes); - Production of industrial minerals, including phosphate, clay and building materials; - Use of radionuclides, such as thorium, for properties other than their radioactivity. Naturally occurring radioactive material (NORM) may lead to exposures at some stage of these processes and in the use or reuse of products, residues or wastes. Several IAEA publications address NORM issues with a special focus on some of the more relevant industrial operations. This publication attempts to provide guidance on managing residues arising from different NORM type industries, and on pertinent residue management strategies and technologies, to help Member States gain perspectives on the management of NORM residues

  4. Contact stress sensor

    Science.gov (United States)

    Kotovsky, Jack [Oakland, CA

    2012-02-07

    A contact stress sensor includes one or more MEMS fabricated sensor elements, where each sensor element of includes a thin non-recessed portion, a recessed portion and a pressure sensitive element adjacent to the recessed portion. An electric circuit is connected to the pressure sensitive element. The circuit includes a thermal compensator and a pressure signal circuit element configured to provide a signal upon movement of the pressure sensitive element.

  5. Occupational protein contact dermatitis.

    Science.gov (United States)

    Barbaud, Annick; Poreaux, Claire; Penven, Emmanuelle; Waton, Julie

    2015-01-01

    Occupational contact dermatitis is generally caused by haptens but can also be induced by proteins causing mainly immunological contact urticaria (ICU); chronic hand eczema in the context of protein contact dermatitis (PCD). In a monocentric retrospective study, from our database, only 31 (0.41%) of patients with contact dermatitis had positive skin tests with proteins: 22 had occupational PCD, 3 had non-occupational PCD, 5 occupational ICU and 1 cook had a neutrophilic fixed food eruption (NFFE) due to fish. From these results and analysis of literature, the characteristics of PCD can be summarized as follows. It is a chronic eczematous dermatitis, possibly exacerbated by work, suggestive if associated with inflammatory perionyxix and immediate erythema with pruritis, to be investigated when the patient resumes work after a period of interruption. Prick tests with the suspected protein-containing material are essential, as patch tests have negative results. In case of multisensitisation revealed by prick tests, it is advisable to analyse IgE against recombinant allergens. A history of atopy, found in 56 to 68% of the patients, has to be checked for. Most of the cases are observed among food-handlers but PCD can also be due to non-edible plants, latex, hydrolysed proteins or animal proteins. Occupational exposure to proteins can thus lead to the development of ICU. Reflecting hypersensitivity to very low concentrations of allergens, investigating ICU therefore requires caution and prick tests should be performed with a diluted form of the causative protein-containing product. Causes are food, especially fruit peel, non-edible plants, cosmetic products, latex, animals.

  6. Fragrance contact allergy

    DEFF Research Database (Denmark)

    Johansen, Jeanne D

    2003-01-01

    . This gives a positive patch-test reaction in about 10% of tested patients with eczema, and the most recent estimates show that 1.7-4.1% of the general population are sensitized to ingredients of the fragrance mix. Fragrance allergy occurs predominantly in women with facial or hand eczema. These women...... development to identify contact allergy to new allergens, reflecting the continuous developments and trends in exposure....

  7. Pediatric contact dermatitis

    Directory of Open Access Journals (Sweden)

    Sharma Vinod

    2010-01-01

    Full Text Available Allergic contact dermatitis (ACD in children, until recently, was considered rare. ACD was considered as a disorder of the adult population and children were thought to be spared due to a lack of exposure to potential allergens and an immature immune system. Prevalence of ACD to even the most common allergens in children, like poison ivy and parthenium, is relatively rare as compared to adults. However, there is now growing evidence of contact sensitization of the pediatric population, and it begins right from early childhood, including 1-week-old neonates. Vaccinations, piercing, topical medicaments and cosmetics in younger patients are potential exposures for sensitization. Nickel is the most common sensitizer in almost all studies pertaining to pediatric contact dermatitis. Other common allergens reported are cobalt, fragrance mix, rubber, lanolin, thiomersol, neomycin, gold, mercapto mix, balsum of Peru and colophony. Different factors like age, sex, atopy, social and cultural practices, habit of parents and caregivers and geographic changes affect the patterns of ACD and their variable clinical presentation. Patch testing should be considered not only in children with lesions of a morphology suggestive of ACD, but in any child with dermatitis that is difficult to control.

  8. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  9. [Sport injuries in full contact and semi-contact karate].

    Science.gov (United States)

    Greier, K; Riechelmann, H; Ziemska, J

    2014-03-01

    Karate enjoys great popularity both in professional and recreational sports and can be classified into full, half and low contact styles. The aim of this study was the analysis of sports injuries in Kyokushinkai (full contact) and traditional Karate (semi-contact). In a retrospective study design, 215 active amateur karateka (114 full contact, 101 semi-contact) were interviewed by means of a standardised questionnaire regarding typical sport injuries during the last 36 months. Injuries were categorised into severity grade I (not requiring medical treatment), grade II (single medical treatment), grade III (several outpatient medical treatments) and grade IV (requiring hospitalisation). In total, 217 injuries were reported in detail. 125 injuries (58%) occurred in full contact and 92 (42%) in semi-contact karate. The time related injury rate of full contact karateka was 1.9/1000 h compared to 1.3/1000 h of semi-contact karateka (p injuries were musculoskeletal contusions (33% full contact, 20% semi-contact), followed by articular sprains with 19% and 16%. The lower extremity was affected twice as often in full contact (40%) as in semi-contact (20%) karate. Training injuries were reported by 80% of the full contact and 77% of the semi-contact karateka. Most injuries, both in training and competition, occurred in kumite. 75% of the reported injuries of full contact and 70% of semi-contact karateka were classified as low grade (I or II). The high rate of injuries during training and kumite (sparring) points to specific prevention goals. The emphasis should be put on proprioceptive training and consistent warm-up. In the actual competition the referees play a vital role regarding prevention. © Georg Thieme Verlag KG Stuttgart · New York.

  10. Mechanical Contact Experiments and Simulations

    DEFF Research Database (Denmark)

    Nielsen, Chris Valentin; Martins, P; Zhang, W.

    2011-01-01

    Mechanical contact is studied under dynamic development by means of a combined numerical and experimental investigation. The experiments are designed to allow dynamical development of non-planar contact areas with significant expansion in all three directions as the load is increased. Different....... The overall investigation serves for testing and validating the numerical implementation of the mechanical contact, which is one of the main contributions to a system intended for 3D simulation of resistance welding. Correct modelling of contact between parts to be welded, as well as contact with electrodes......, is crucial for satisfactory modelling of the resistance welding process. The resistance heating at the contact interfaces depends on both contact area and pressure, and as the contact areas develop dynamically, the presented tests are relevant for assessing the validity and accuracy of the mechanical contact...

  11. Residual-stress measurements

    Energy Technology Data Exchange (ETDEWEB)

    Ezeilo, A N; Webster, G A [Imperial College, London (United Kingdom); Webster, P J [Salford Univ. (United Kingdom)

    1997-04-01

    Because neutrons can penetrate distances of up to 50 mm in most engineering materials, this makes them unique for establishing residual-stress distributions non-destructively. D1A is particularly suited for through-surface measurements as it does not suffer from instrumental surface aberrations commonly found on multidetector instruments, while D20 is best for fast internal-strain scanning. Two examples for residual-stress measurements in a shot-peened material, and in a weld are presented to demonstrate the attractive features of both instruments. (author).

  12. An elastic-plastic contact model for line contact structures

    Science.gov (United States)

    Zhu, Haibin; Zhao, Yingtao; He, Zhifeng; Zhang, Ruinan; Ma, Shaopeng

    2018-06-01

    Although numerical simulation tools are now very powerful, the development of analytical models is very important for the prediction of the mechanical behaviour of line contact structures for deeply understanding contact problems and engineering applications. For the line contact structures widely used in the engineering field, few analytical models are available for predicting the mechanical behaviour when the structures deform plastically, as the classic Hertz's theory would be invalid. Thus, the present study proposed an elastic-plastic model for line contact structures based on the understanding of the yield mechanism. A mathematical expression describing the global relationship between load history and contact width evolution of line contact structures was obtained. The proposed model was verified through an actual line contact test and a corresponding numerical simulation. The results confirmed that this model can be used to accurately predict the elastic-plastic mechanical behaviour of a line contact structure.

  13. Determination of contact maps in proteins: A combination of structural and chemical approaches

    Energy Technology Data Exchange (ETDEWEB)

    Wołek, Karol; Cieplak, Marek, E-mail: mc@ifpan.edu.pl [Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw (Poland); Gómez-Sicilia, Àngel [Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), Av. Doctor Arce, 37, 28002 Madrid (Spain); Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), C/Faraday 9, 28049 Cantoblanco (Madrid) (Spain)

    2015-12-28

    Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones — a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles.

  14. 40 CFR 180.435 - Deltamethrin; tolerances for residues.

    Science.gov (United States)

    2010-07-01

    ... in food handling establishments, including food service, manufacturing and processing establishments.... Contamination of food/feed or food/feed contact surfaces shall be avoided. (B) To assure safe use of the...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Specific Tolerances...

  15. 40 CFR 180.422 - Tralomethrin; tolerances for residues.

    Science.gov (United States)

    2010-07-01

    ...-handling establishments, including food service, manufacturing, and processing establishments, such as... shall be limited to a maximum of 0.06 percent active ingredient. Contamination of food and food-contact...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Specific Tolerances...

  16. 40 CFR 180.442 - Bifenthrin; tolerances for residues.

    Science.gov (United States)

    2010-07-01

    ... application of bifenthrin in food handling establishments, including food service, manufacturing and... ingredient. Contamination of food/feed or food/feed contact surfaces shall be avoided. (B) To assure safe use...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Specific Tolerances...

  17. 40 CFR 180.108 - Acephate; tolerances for residues.

    Science.gov (United States)

    2010-07-01

    ... establishments, including food service, manufacturing and processing establishments, such as restaurants... avoid atomization or splashing of the spray. Contamination of food or food-contact surfaces shall be... PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Specific Tolerances § 180.108...

  18. Hastelloy X fuel element creep relaxation and residual effects

    International Nuclear Information System (INIS)

    Castle, R.A.

    1971-01-01

    A worst case, seven element, asymmetric fuel, thermal environment was assumed and a creep relaxation analysis generated. The fuel element clad is .020 inch Hastelloy X. The contact load decreased from 11.6 pounds to 5.87 pounds in 100,000 hours. The residual stresses were then computed for various shutdown times. (U.S.)

  19. Improving the modelling of redshift-space distortions - I. A bivariate Gaussian description for the galaxy pairwise velocity distributions

    Science.gov (United States)

    Bianchi, Davide; Chiesa, Matteo; Guzzo, Luigi

    2015-01-01

    As a step towards a more accurate modelling of redshift-space distortions (RSD) in galaxy surveys, we develop a general description of the probability distribution function of galaxy pairwise velocities within the framework of the so-called streaming model. For a given galaxy separation r, such function can be described as a superposition of virtually infinite local distributions. We characterize these in terms of their moments and then consider the specific case in which they are Gaussian functions, each with its own mean μ and dispersion σ. Based on physical considerations, we make the further crucial assumption that these two parameters are in turn distributed according to a bivariate Gaussian, with its own mean and covariance matrix. Tests using numerical simulations explicitly show that with this compact description one can correctly model redshift-space distortions on all scales, fully capturing the overall linear and non-linear dynamics of the galaxy flow at different separations. In particular, we naturally obtain Gaussian/exponential, skewed/unskewed distribution functions, depending on separation as observed in simulations and data. Also, the recently proposed single-Gaussian description of RSD is included in this model as a limiting case, when the bivariate Gaussian is collapsed to a two-dimensional Dirac delta function. We also show how this description naturally allows for the Taylor expansion of 1 + ξS(s) around 1 + ξR(r), which leads to the Kaiser linear formula when truncated to second order, explicating its connection with the moments of the velocity distribution functions. More work is needed, but these results indicate a very promising path to make definitive progress in our programme to improve RSD estimators.

  20. Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity

    Energy Technology Data Exchange (ETDEWEB)

    Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es [Instituto de Física Fundamental (CSIC), Serrano 123, E-28006 Madrid (Spain); Fernández-Perea, Ricardo [Instituto de Estructura de la Materia (CSIC), Serrano 123, E-28006 Madrid (Spain); Madzharova, Fani; Voloshina, Elena, E-mail: elena.voloshina@hu-berlin.de [Humboldt-Universität zu Berlin, Institut für Chemie, Unter den Linden 6, 10099 Berlin (Germany)

    2016-06-28

    The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet this challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He–Mg pair potentials is also presented, as an improvement of the approximation using isolated He–Mg pairs.

  1. Acupuncture-Related Techniques for Psoriasis: A Systematic Review with Pairwise and Network Meta-Analyses of Randomized Controlled Trials.

    Science.gov (United States)

    Yeh, Mei-Ling; Ko, Shu-Hua; Wang, Mei-Hua; Chi, Ching-Chi; Chung, Yu-Chu

    2017-12-01

    There has be a large body of evidence on the pharmacological treatments for psoriasis, but whether nonpharmacological interventions are effective in managing psoriasis remains largely unclear. This systematic review conducted pairwise and network meta-analyses to determine the effects of acupuncture-related techniques on acupoint stimulation for the treatment of psoriasis and to determine the order of effectiveness of these remedies. This study searched the following databases from inception to March 15, 2016: Medline, PubMed, Cochrane Central Register of Controlled Trials, EBSCO (including Academic Search Premier, American Doctoral Dissertations, and CINAHL), Airiti Library, and China National Knowledge Infrastructure. Randomized controlled trials (RCTs) on the effects of acupuncture-related techniques on acupoint stimulation as intervention for psoriasis were independently reviewed by two researchers. A total of 13 RCTs with 1,060 participants were included. The methodological quality of included studies was not rigorous. Acupoint stimulation, compared with nonacupoint stimulation, had a significant treatment for psoriasis. However, the most common adverse events were thirst and dry mouth. Subgroup analysis was further done to confirm that the short-term treatment effect was superior to that of the long-term effect in treating psoriasis. Network meta-analysis identified acupressure or acupoint catgut embedding, compared with medication, and had a significant effect for improving psoriasis. It was noted that acupressure was the most effective treatment. Acupuncture-related techniques could be considered as an alternative or adjuvant therapy for psoriasis in short term, especially of acupressure and acupoint catgut embedding. This study recommends further well-designed, methodologically rigorous, and more head-to-head randomized trials to explore the effects of acupuncture-related techniques for treating psoriasis.

  2. The effect of fiscal incentives on market penetration of electric vehicles: A pairwise comparison of total cost of ownership

    International Nuclear Information System (INIS)

    Lévay, Petra Zsuzsa; Drossinos, Yannis; Thiel, Christian

    2017-01-01

    An important barrier to electric vehicle (EV) sales is their high purchase price compared to internal combustion engine (ICE) vehicles. We conducted total cost of ownership (TCO) calculations to study how costs and sales of EVs relate to each other and to examine the role of fiscal incentives in reducing TCO and increasing EV sales. We composed EV-ICE vehicle pairs that allowed cross-segment and cross-country comparison in eight European countries. Actual car prices were used to calculate the incentives for each model in each country. We found a negative TCO-sales relationship that differs across car segments. Compared to their ICE vehicle pair, big EVs have lower TCO, higher sales, and seem to be less price responsive than small EVs. Three country groups can be distinguished according to the level of fiscal incentives and their impact on TCO and EV sales. In Norway, incentives led to the lowest TCO for the EVs. In the Netherlands, France, and UK the TCO of EVs is close to the TCO of the ICE pairs. In the other countries the TCO of EVs exceeds that of the ICE vehicles. We found that exemptions from flat taxes favour big EVs, while lump-sum subsidies favour small EVs. - Highlights: • Pairwise comparison of EV and ICE vehicle TCO and sales in eight European countries. • In NO, EV TCO is lower than ICE TCO; in NL, FR, and UK, EV TCO is slightly higher. • Compared to ICE vehicles, big EVs have lower TCO and higher sales than small EVs. • Exemptions from flat taxes favour big EVs, lump-sum subsidies favour small EVs. • Most popular EV models: Tesla Model S, Nissan Leaf, Mitsubishi Outlander PHEV.

  3. Contacting gases and liquids

    International Nuclear Information System (INIS)

    Robinson, L.F.; Cahalan, M.J.

    1980-01-01

    A process is described for contacting substantially immiscible phases to transfer material from one phase to another, which comprises passing the phases through a contactor, while causing portions of at least one phase to be repeatedly passed through at least one other phase. One phase in the contactor is gaseous, and another liquid. A further phase can be liquid or solid The process may be used for extracting impurities from china clay, or extracting uranium values from ore with oxygen gas acting to oxidise the uranium. (author)

  4. Precision contact level gauge

    International Nuclear Information System (INIS)

    Krejci, M.; Pilat, M.; Stulik, P.

    1977-01-01

    Equipment was developed measuring the heavy water level in the TR-0 reactor core within an accuracy of several hundredths of a millimeter in a range of around 3.5 m and at a temperature of up to 90 degC. The equipment uses a vibrating needle contact as a high sensitivity level gauge and a servomechanical system with a motion screw carrying the gauge for monitoring and measuring the level in the desired range. The advantage of the unique level gauge consists in that that the transducer converts the measured level position to an electric signal, ie., pulse width, with high sensitivity and without hysteresis. (Kr)

  5. Thermal contact conductance

    CERN Document Server

    Madhusudana, Chakravarti V

    2013-01-01

    The work covers both theoretical and practical aspects of thermal contact conductance. The theoretical discussion focuses on heat transfer through spots, joints, and surfaces, as well as the role of interstitial materials (both planned and inadvertent). The practical discussion includes formulae and data that can be used in designing heat-transfer equipment for a variety of joints, including special geometries and configurations. All of the material has been updated to reflect the latest advances in the field.

  6. Contact ionization ion source

    International Nuclear Information System (INIS)

    Hashmi, N.; Van Der Houven Van Oordt, A.J.

    1975-01-01

    An ion source in which an apertured or foraminous electrode having a multiplicity of openings is spaced from one or more active surfaces of an ionisation electrode, the active surfaces comprising a material capable of ionising by contact ionization a substance to be ionized supplied during operation to the active surface or surfaces comprises means for producing during operation a magnetic field which enables a stable plasma to be formed in the space between the active surface or surfaces and the apertured electrode, the field strength of the magnetic field being preferably in the range between 2 and 8 kilogauss. (U.S.)

  7. Designing with residual materials

    NARCIS (Netherlands)

    Walhout, W.; Wever, R.; Blom, E.; Addink-Dölle, L.; Tempelman, E.

    2013-01-01

    Many entrepreneurial businesses have attempted to create value based on the residual material streams of third parties. Based on ‘waste’ materials they designed products, around which they built their company. Such activities have the potential to yield sustainable products. Many of such companies

  8. Allergic contact dermatitis from octylisothiazolinone

    DEFF Research Database (Denmark)

    Mose, Anja Pahlow; Frost, Simon; Ohlund, Ulf

    2013-01-01

    Octylisothiazolinone is a biocide that has been reported as a moderate, but rare contact allergen.......Octylisothiazolinone is a biocide that has been reported as a moderate, but rare contact allergen....

  9. Prediction of residual stress using explicit finite element method

    Directory of Open Access Journals (Sweden)

    W.A. Siswanto

    2015-12-01

    Full Text Available This paper presents the residual stress behaviour under various values of friction coefficients and scratching displacement amplitudes. The investigation is based on numerical solution using explicit finite element method in quasi-static condition. Two different aeroengine materials, i.e. Super CMV (Cr-Mo-V and Titanium alloys (Ti-6Al-4V, are examined. The usage of FEM analysis in plate under normal contact is validated with Hertzian theoretical solution in terms of contact pressure distributions. The residual stress distributions along with normal and shear stresses on elastic and plastic regimes of the materials are studied for a simple cylinder-on-flat contact configuration model subjected to normal loading, scratching and followed by unloading. The investigated friction coefficients are 0.3, 0.6 and 0.9, while scratching displacement amplitudes are 0.05 mm, 0.10 mm and 0.20 mm respectively. It is found that friction coefficient of 0.6 results in higher residual stress for both materials. Meanwhile, the predicted residual stress is proportional to the scratching displacement amplitude, higher displacement amplitude, resulting in higher residual stress. It is found that less residual stress is predicted on Super CMV material compared to Ti-6Al-4V material because of its high yield stress and ultimate strength. Super CMV material with friction coefficient of 0.3 and scratching displacement amplitude of 0.10 mm is recommended to be used in contact engineering applications due to its minimum possibility of fatigue.

  10. A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

    Science.gov (United States)

    Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

    2005-03-10

    Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

  11. A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

    Directory of Open Access Journals (Sweden)

    Maréchal Eric

    2005-03-01

    Full Text Available Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons and be the basis for a novel method of consistent and stable phylogenetic reconstruction. Results We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. Conclusion The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

  12. Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting

    Science.gov (United States)

    Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter

    2018-01-01

    Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established concepts from random survival forest (RSF) models. We introduce a novel RSF-based pairwise interaction estimator and derive a randomization method with bootstrap confidence intervals for inferring interaction significance. Using various linear and nonlinear time-to-events survival models in simulation studies, we first show the efficiency of our approach: true pairwise interaction-effects between variables are uncovered, while they may not be accompanied with their corresponding main-effects, and may not be detected by standard semi-parametric regression modeling and test statistics used in survival analysis. Moreover, using a RSF-based cross-validation scheme for generating prediction estimators, we show that informative predictors may be inferred. We applied our approach to an HIV cohort study recording key host gene polymorphisms and their association with HIV change of tropism or AIDS progression. Altogether, this shows how linear or nonlinear pairwise statistical interactions of variables may be efficiently detected with a predictive value in observational studies with time-to-event outcomes. PMID:29453930

  13. Fragrance contact allergy

    DEFF Research Database (Denmark)

    Johansen, Jeanne D

    2003-01-01

    in the same products. This means that it is difficult to avoid exposure, as products labelled as 'fragrance free' have also been shown to contain fragrance ingredients, either because of the use of fragrance ingredients as preservatives or masking perfumes, or the use of botanicals. About 2500 different...... fragrance ingredients are currently used in the composition of perfumes and at least 100 of these are known contact allergens. Therefore, it is advisable to supplement standard patch testing with the patient's own stay-on cosmetic products, as well as the fragrance chemical hydroxyisohexyl-3-cyclohexane...... carboxaldehyde, which on its own gives responses in 1-3% of tested patients. The focus in recent years on the ingredients of the fragrance mix will probably result in the fragrance industry changing the composition of perfumes, and thus make the current diagnostic test less useful. New diagnostic tests are under...

  14. Cosmetic Contact Allergens

    Directory of Open Access Journals (Sweden)

    An Goossens

    2016-02-01

    Full Text Available This article presents trends in the frequency of cosmetics as causal factors of allergic contact dermatitis during a 26-year period in 14,911 patients patch-tested between 1990 and 2014, and discusses the cosmetic allergens identified during the last six years (2010–2015 in 603 patients out of 3105 tested. The data were retrieved from, and evaluated with, a patient database developed in-house. The results show the increasing importance of cosmetic allergies, up to 25% of the patients tested during the last five-year period. As expected, fragrance materials, preservatives, and hair dyes were the most frequent culprits, but a great variety of other allergenic ingredients were involved as well. This underlines the need of additional and extensive patch testing with the patient’s products used and their ingredients.

  15. Hair dye contact allergy

    DEFF Research Database (Denmark)

    Søsted, Heidi; Rastogi, Suresh Chandra; Andersen, Klaus Ejner

    2004-01-01

    Colouring of hair can cause severe allergic contact dermatitis. The most frequently reported hair dye allergens are p-phenylenediamine (PPD) and toluene-2,5-diamine, which are included in, respectively, the patch test standard series and the hairdressers series. The aim of the present study...... was to identify dye precursors and couplers in hair dyeing products causing clinical hair dye dermatitis and to compare the data with the contents of these compounds in a randomly selected set of similar products. The patient material comprised 9 cases of characteristic clinical allergic hair dye reaction, where...... exposure history and patch testing had identified a specific hair dye product as the cause of the reaction. The 9 products used by the patients were subjected to chemical analysis. 8 hair dye products contained toluene-2,5-diamine (0.18 to 0.98%). PPD (0.27%) was found in 1 product, and m-aminophenol (0...

  16. Mechanoluminescent Contact Type Sensor

    Directory of Open Access Journals (Sweden)

    A. K. Yefremov

    2017-01-01

    Full Text Available Mechanoluminescent sensing elements convert mechanical stress into optical radiation. Advantages of such sensors are the ability to generate an optical signal, solid-state, simple structure, and resistance to electromagnetic interference. Mechanoluminescent sensor implementations can possess the concentrated and distributed sensitivity, thereby allowing us to detect the field of mechanical stresses distributed across the area and in volume. Most modern semiconductor photo-detectors can detect mechanoluminescent radiation, so there are no difficulties to provide its detection when designing the mechanoluminescent sensing devices. Mechanoluminescent substances have especial sensitivity to shock loads, and this effect can be used to create a fuse the structure of which includes a target contact type sensor with a photosensitive actuator. The paper briefly describes the theoretical basics of mechanoluminiscence: a light signal emerges from the interaction of crystalline phosphor luminescence centers with electrically charged dislocations, moving due to the deformation of the crystal. A mathematical model of the mechanoluminescent conversion is represented as a functional interaction between parameters of the mechanical shock excitation and the sensor light emission. Examples of computing the optical mechanoluminescent output signal depending on the duration and peak level of impulse load are given. It is shown that the luminous flux, generated by mechanoluminescent sensing element when there is an ammunition-target collision causes the current emerging in photo-detector (photodiode that is sufficient for a typical actuator of the fuse train to operate. The potential possibility to create a contact target type sensor based on the light-sensitive mechanoluminescent sensor was proved by the calculation and simulation results.

  17. Comparison of sputum collection methods for tuberculosis diagnosis: a systematic review and pairwise and network meta-analysis.

    Science.gov (United States)

    Datta, Sumona; Shah, Lena; Gilman, Robert H; Evans, Carlton A

    2017-08-01

    The performance of laboratory tests to diagnose pulmonary tuberculosis is dependent on the quality of the sputum sample tested. The relative merits of sputum collection methods to improve tuberculosis diagnosis are poorly characterised. We therefore aimed to investigate the effects of sputum collection methods on tuberculosis diagnosis. We did a systematic review and meta-analysis to investigate whether non-invasive sputum collection methods in people aged at least 12 years improve the diagnostic performance of laboratory testing for pulmonary tuberculosis. We searched PubMed, Google Scholar, ProQuest, Web of Science, CINAHL, and Embase up to April 14, 2017, to identify relevant experimental, case-control, or cohort studies. We analysed data by pairwise meta-analyses with a random-effects model and by network meta-analysis. All diagnostic performance data were calculated at the sputum-sample level, except where authors only reported data at the individual patient-level. Heterogeneity was assessed, with potential causes identified by logistic meta-regression. We identified 23 eligible studies published between 1959 and 2017, involving 8967 participants who provided 19 252 sputum samples. Brief, on-demand spot sputum collection was the main reference standard. Pooled sputum collection increased tuberculosis diagnosis by microscopy (odds ratio [OR] 1·6, 95% CI 1·3-1·9, pmeta-analysis confirmed these findings, and revealed that both pooled and instructed spot sputum collections were similarly effective techniques for increasing the diagnostic performance of microscopy. Tuberculosis diagnoses were substantially increased by either pooled collection or by providing instruction on how to produce a sputum sample taken at any time of the day. Both interventions had a similar effect to that reported for the introduction of new, expensive laboratory tests, and therefore warrant further exploration in the drive to end the global tuberculosis epidemic. Wellcome Trust

  18. Sharing Residual Liability

    DEFF Research Database (Denmark)

    Carbonara, Emanuela; Guerra, Alice; Parisi, Francesco

    2016-01-01

    Economic models of tort law evaluate the efficiency of liability rules in terms of care and activity levels. A liability regime is optimal when it creates incentives to maximize the value of risky activities net of accident and precaution costs. The allocation of primary and residual liability...... for policy makers and courts in awarding damages in a large number of real-world accident cases....

  19. 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/ .

  20. New encouraging developments in contact prediction: Assessment of the CASP11 results

    KAUST Repository

    Monastyrskyy, Bohdan

    2015-10-01

    © 2015 Wiley Periodicals, Inc. This article provides a report on the state-of-the-art in the prediction of intra-molecular residue-residue contacts in proteins based on the assessment of the predictions submitted to the CASP11 experiment. The assessment emphasis is placed on the accuracy in predicting long-range contacts. Twenty-nine groups participated in contact prediction in CASP11. At least eight of them used the recently developed evolutionary coupling techniques, with the top group (CONSIP2) reaching precision of 27% on target proteins that could not be modeled by homology. This result indicates a breakthrough in the development of methods based on the correlated mutation approach. Successful prediction of contacts was shown to be practically helpful in modeling three-dimensional structures; in particular target T0806 was modeled exceedingly well with accuracy not yet seen for ab initio targets of this size (>250 residues).

  1. Reducing contact resistance in graphene devices through contact area patterning.

    Science.gov (United States)

    Smith, Joshua T; Franklin, Aaron D; Farmer, Damon B; Dimitrakopoulos, Christos D

    2013-04-23

    Performance of graphene electronics is limited by contact resistance associated with the metal-graphene (M-G) interface, where unique transport challenges arise as carriers are injected from a 3D metal into a 2D-graphene sheet. In this work, enhanced carrier injection is experimentally achieved in graphene devices by forming cuts in the graphene within the contact regions. These cuts are oriented normal to the channel and facilitate bonding between the contact metal and carbon atoms at the graphene cut edges, reproducibly maximizing "edge-contacted" injection. Despite the reduction in M-G contact area caused by these cuts, we find that a 32% reduction in contact resistance results in Cu-contacted, two-terminal devices, while a 22% reduction is achieved for top-gated graphene transistors with Pd contacts as compared to conventionally fabricated devices. The crucial role of contact annealing to facilitate this improvement is also elucidated. This simple approach provides a reliable and reproducible means of lowering contact resistance in graphene devices to bolster performance. Importantly, this enhancement requires no additional processing steps.

  2. Contact angle and local wetting at contact line.

    Science.gov (United States)

    Li, Ri; Shan, Yanguang

    2012-11-06

    This theoretical study was motivated by recent experiments and theoretical work that had suggested the dependence of the static contact angle on the local wetting at the triple-phase contact line. We revisit this topic because the static contact angle as a local wetting parameter is still not widely understood and clearly known. To further clarify the relationship of the static contact angle with wetting, two approaches are applied to derive a general equation for the static contact angle of a droplet on a composite surface composed of heterogeneous components. A global approach based on the free surface energy of a thermodynamic system containing the droplet and solid surface shows the static contact angle as a function of local surface chemistry and local wetting state at the contact line. A local approach, in which only local forces acting on the contact line are considered, results in the same equation. The fact that the local approach agrees with the global approach further demonstrates the static contact angle as a local wetting parameter. Additionally, the study also suggests that the wetting described by the Wenzel and Cassie equations is also the local wetting of the contact line rather than the global wetting of the droplet.

  3. Equilibrium contact angle or the most-stable contact angle?

    Science.gov (United States)

    Montes Ruiz-Cabello, F J; Rodríguez-Valverde, M A; Cabrerizo-Vílchez, M A

    2014-04-01

    It is well-established that the equilibrium contact angle in a thermodynamic framework is an "unattainable" contact angle. Instead, the most-stable contact angle obtained from mechanical stimuli of the system is indeed experimentally accessible. Monitoring the susceptibility of a sessile drop to a mechanical stimulus enables to identify the most stable drop configuration within the practical range of contact angle hysteresis. Two different stimuli may be used with sessile drops: mechanical vibration and tilting. The most stable drop against vibration should reveal the changeless contact angle but against the gravity force, it should reveal the highest resistance to slide down. After the corresponding mechanical stimulus, once the excited drop configuration is examined, the focus will be on the contact angle of the initial drop configuration. This methodology needs to map significantly the static drop configurations with different stable contact angles. The most-stable contact angle, together with the advancing and receding contact angles, completes the description of physically realizable configurations of a solid-liquid system. Since the most-stable contact angle is energetically significant, it may be used in the Wenzel, Cassie or Cassie-Baxter equations accordingly or for the surface energy evaluation. © 2013 Elsevier B.V. All rights reserved.

  4. Contact and Non-contact Measurements of Grinding Pins

    Directory of Open Access Journals (Sweden)

    Magdziak Marek

    2015-01-01

    Full Text Available The paper presents the results of contact and non-contact measurements of external profiles of selected grinding pins. The measurements were conducted in order to choose the appropriate measuring technique in the case of the considered measurement task. In the case of contact measurements the coordinate measuring machine ACCURA II was applied. The used coordinate measuring machine was equipped with the contact scanning probe VAST XT and the Calypso inspection software. Contact coordinate measurements were performed by using of different measurement strategies. The applied strategies included different scanning velocities and distances between measured points. Non-contact measurements were conducted by means of the tool presetter produced by the Mahr company. On the basis of gained results the guidelines concerning measurements of grinding pins were formulated. The measurements of analyzed grinding pins performed by means of the non-contact measuring system are characterized by higher reproducibility than the contact measurements. The low reproducibility of contact measurements may be connected with the inaccuracy of the selected coordinate measuring machine and the measuring probe, the measurement parameters and environmental conditions in the laboratory where the coordinate measuring machine is located. Moreover, the paper presents the possible application of results of conducted investigations. The results of non-contact measurements can be used in the simulation studies of grinding processes. The simulations may reduce the costs of machining processes.

  5. Finite Element Residual Stress Analysis of Planetary Gear Tooth

    Directory of Open Access Journals (Sweden)

    Jungang Wang

    2013-01-01

    Full Text Available A method to simulate residual stress field of planetary gear is proposed. In this method, the finite element model of planetary gear is established and divided to tooth zone and profile zone, whose different temperature field is set. The gear's residual stress simulation is realized by the thermal compression stress generated by the temperature difference. Based on the simulation, the finite element model of planetary gear train is established, the dynamic meshing process is simulated, and influence of residual stress on equivalent stress of addendum, pitch circle, and dedendum of internal and external meshing planetary gear tooth profile is analyzed, according to non-linear contact theory, thermodynamic theory, and finite element theory. The results show that the equivalent stresses of planetary gear at both meshing and nonmeshing surface are significantly and differently reduced by residual stress. The study benefits fatigue cracking analysis and dynamic optimization design of planetary gear train.

  6. Process and catalysis for hydrocracking of heavy oil and residues

    Energy Technology Data Exchange (ETDEWEB)

    Morel, F.; Kressmann, S. [Centre d' Etudes et de developpement Indutriel ' Rene Navarre' , Vernaison (France); Harle, V.; Kasztelan, S. [Division Cinetique et Catalyse, Rueil-Malmaison (France)

    1997-07-01

    Atmospheric or vacuum residue can be converted into valuable distillates using reaction temperature, high hydrogen pressure and low contact time hydroprocessing units. Various residue hydrocracking processes are now commercially employed using fixed bed, moving bed or ebullated bed reactors. The choice of process type depends mainly on the amount of metals and asphaltenes in the feed and on the level of conversion required. Various improvements have been introduced in the last decade to increase run length, conversion level, products qualities and stability of the residual fuel. These improvements include on stream catalysts replacement systems, swing reactors, improved feed distribution, guard bed materials limiting pressure drop, coke resistant catalysts, complex association of catalysts using particle size, activity and pore size grading. Further improvement of the resistance of catalysts to deactivation by coke and metal deposits and of the hydrodenitrogenation activity are two major challenges for the development of new residue hydrocracking catalysts and processes. 29 refs.

  7. Contextualizing Intergroup Contact: Do Political Party Cues Enhance Contact Effects?

    DEFF Research Database (Denmark)

    Sønderskov, Kim Mannemar; Thomsen, Jens Peter Frølund

    2015-01-01

    This article examines intergroup contact effects in different political contexts. We expand on previous efforts of social psychologists by incorporating the messages of political parties as a contextual trigger of group membership awareness in contact situations. We argue that the focus among...... political parties on us-them categorizations heightens the awareness of group memberships. This focus in turn enhances the positive intergroup contact effect by stimulating majority members to perceive contacted persons as prototypical outgroup members. A multilevel analysis of 22 countries and almost 37......,000 individuals confirms that the ability of intergroup contact to reduce antiforeigner sentiment increases when political parties focus intensively on immigration issues and cultural differences. Specifically, both workplace contact and interethnic friendship become more effective in reducing antiforeigner...

  8. An analytical method for computing atomic contact areas in biomolecules.

    Science.gov (United States)

    Mach, Paul; Koehl, Patrice

    2013-01-15

    We propose a new analytical method for detecting and computing contacts between atoms in biomolecules. It is based on the alpha shape theory and proceeds in three steps. First, we compute the weighted Delaunay triangulation of the union of spheres representing the molecule. In the second step, the Delaunay complex is filtered to derive the dual complex. Finally, contacts between spheres are collected. In this approach, two atoms i and j are defined to be in contact if their centers are connected by an edge in the dual complex. The contact areas between atom i and its neighbors are computed based on the caps formed by these neighbors on the surface of i; the total area of all these caps is partitioned according to their spherical Laguerre Voronoi diagram on the surface of i. This method is analytical and its implementation in a new program BallContact is fast and robust. We have used BallContact to study contacts in a database of 1551 high resolution protein structures. We show that with this new definition of atomic contacts, we generate realistic representations of the environments of atoms and residues within a protein. In particular, we establish the importance of nonpolar contact areas that complement the information represented by the accessible surface areas. This new method bears similarity to the tessellation methods used to quantify atomic volumes and contacts, with the advantage that it does not require the presence of explicit solvent molecules if the surface of the protein is to be considered. © 2012 Wiley Periodicals, Inc. Copyright © 2012 Wiley Periodicals, Inc.

  9. Machine for compacting solid residues

    International Nuclear Information System (INIS)

    Herzog, J.

    1981-11-01

    Machine for compacting solid residues, particularly bulky radioactive residues, constituted of a horizontally actuated punch and a fixed compression anvil, in which the residues are first compacted horizontally and then vertically. Its salient characteristic is that the punch and the compression anvil have embossments on the compression side and interpenetrating plates in the compression position [fr

  10. Quaternionic contact Einstein structures and the quaternionic contact Yamabe problem

    CERN Document Server

    Ivanov, Stefan; Vassilev, Dimiter

    2014-01-01

    A partial solution of the quaternionic contact Yamabe problem on the quaternionic sphere is given. It is shown that the torsion of the Biquard connection vanishes exactly when the trace-free part of the horizontal Ricci tensor of the Biquard connection is zero and this occurs precisely on 3-Sasakian manifolds. All conformal transformations sending the standard flat torsion-free quaternionic contact structure on the quaternionic Heisenberg group to a quaternionic contact structure with vanishing torsion of the Biquard connection are explicitly described. A "3-Hamiltonian form" of infinitesimal conformal automorphisms of quaternionic contact structures is presented.

  11. Quadratic residues and non-residues selected topics

    CERN Document Server

    Wright, Steve

    2016-01-01

    This book offers an account of the classical theory of quadratic residues and non-residues with the goal of using that theory as a lens through which to view the development of some of the fundamental methods employed in modern elementary, algebraic, and analytic number theory. The first three chapters present some basic facts and the history of quadratic residues and non-residues and discuss various proofs of the Law of Quadratic Reciprosity in depth, with an emphasis on the six proofs that Gauss published. The remaining seven chapters explore some interesting applications of the Law of Quadratic Reciprocity, prove some results concerning the distribution and arithmetic structure of quadratic residues and non-residues, provide a detailed proof of Dirichlet’s Class-Number Formula, and discuss the question of whether quadratic residues are randomly distributed. The text is a valuable resource for graduate and advanced undergraduate students as well as for mathematicians interested in number theory.

  12. [Contact glass tonometer].

    Science.gov (United States)

    Dekker, P W; Kanngiesser, H; Robert, Y C

    1996-05-01

    This paper presents a tonometer built into a contactlens, which allows to measure the eye-pressure and to perform ophthalmoscopy at the same time. Artificially induced changes of the eye-pressure and their influence on the visible fundus can now be checked simultaneously. The contactlens-tonometer (CGT) also is able to record continuously the pulse-curve, which can indicate any circulatory problem. So, the device is expected to give us additional diagnostic criteria of early glaucoma. Each ophthalmologyst in the field will be able to perform with this device a oculodynamometry in an easy way. By this it is possible to estimate the pressure-tolerance of the optic disk from glaucoma-patients. There have been taken some measurements on enucleated human eyes, comparing our device with a Statham-transducer in the vitreous. We found a good correlation. In a second step, we made measurements (65) on healthy volunteers, comparing the device with Perkins-Tonometry. We found a correlation (R = 0.58). The error of the measurements was about +/- 3 mm Hg. Considering both, the deviation of the Perkins-Tonometer with which our results were compared, and the fact of a good correlation (R = 0.999) in the study with the enucleated human eyes, we found that the contact-lens-tonometer measures the intraocular pressure exactly. In future studies, we want to analyze the dynamic component of the measurements.

  13. Contact sport and osteoarthritis.

    LENUS (Irish Health Repository)

    Molloy, Michael G

    2011-04-01

    Osteoarthritis (OA) is the most common joint disease in the world and the single largest cause of disability for those over 18 years. It affects more than twice as many people as does cardiac disease, and increases in incidence and prevalence with age. Animal and human studies have shown no evidence of increased risk of hip or knee OA with moderate exercise and in the absence of traumatic injury, sporting activity has a protective effect. One age-matched case control study found recreational runners who ran 12-14 miles per week for up to 40 years had no increase in radiological or symptomatic hip or knee OA. However, higher rates of hip OA occur in contact sports than in age-matched controls, with the highest rate in professional players. Soccer players with torn anterior cruciate ligaments (ACL) are more likely to develop knee OA than those with intact ACL. Early ACL repair reduces the risk of knee OA, but does not prevent it. Established injury prevention programmes have been refined to prevent injuries such as ACL rupture.

  14. The importance of contact quality

    DEFF Research Database (Denmark)

    van Bakel, Marian; Gerritsen, Marinel; van Oudenhoven, Jan Pieter

    Establishing contact between expatriates and a local host has been found to reap benefits with regard to Interaction Adjustment, Host National Social Support, Open-mindedness, and Social Initiative. This longitudinal study examines the role of the quality of contact for these four aspects....... Expatriates in the Netherlands were randomly divided into an experimental group (n = 33) of which 21 developed high-quality contact with their host, and a control group (n = 32) without host. The results show that contact quality plays an important role and suggest that the higher the quality of the contact......, the more benefit the expatriate experienced. Moreover, expatriates with low-quality contact did not experience a detrimental effect....

  15. Contact Lens Related Corneal Ulcer

    OpenAIRE

    Loh, KY; Agarwal, P

    2010-01-01

    A corneal ulcer caused by infection is one of the major causes of blindness worldwide. One of the recent health concerns is the increasing incidence of corneal ulcers associated with contact lens user especially if the users fail to follow specific instruction in using their contact lenses. Risk factors associated with increased risk of contact lens related corneal ulcers are: overnight wear, long duration of continuous wear, lower socio-economic classes, smoking, dry eye and poor hygiene. Th...

  16. Emotional Satisfaction of Customer Contacts

    OpenAIRE

    Güngör, Hüseyin

    2007-01-01

    For marketing and customer services researchers and professionals who are interested in customer contacts, customer satisfaction and loyalty issues. Contact centers are playing a pivotal role in customer services of the 21st century. Nevertheless, despite their growing importance and presence, contact centers are increasingly becoming the center for customer frustration, and frequently associated with negative comments in the media. Therefore, this research explores the Emotional, Cognitive, ...

  17. Non-contact ultrasound techniques

    International Nuclear Information System (INIS)

    Khazali Mohd Zin

    2001-01-01

    Non-contact ultrasound plays significant role in material characterisation and inspection. Unlike conventional ultrasonic techniques, non-contact ultrasonic is mostly applicable to areas where the former has its weaknesses and limitations. It is interesting to note that the non-contact ultrasonic technique has an important significant application in industry. The technique is signified by the fact that the object to be inspected is further away from the ultrasonic source, no couplant is needed and inconsistent pressure between the transducer and the specimen can be eliminated. The paper discusses some of the non-contact ultrasound technique and its applications. (Author)

  18. Occupational contact dermatitis in hairdressers

    DEFF Research Database (Denmark)

    Schwensen, Jakob F; Johansen, Jeanne Duus; Veien, Niels K

    2013-01-01

    BACKGROUND: Occupational contact dermatitis among hairdressers is frequent, owing to daily exposure to irritants and allergens. OBJECTIVES: To identify sensitization to the most common allergens associated with the occupation of hairdressing. METHODS: Patch test results of 399 hairdressers and 1995...... matched controls with contact dermatitis, registered by the Danish Contact Dermatitis Group between January 2002 and December 2011, were analysed. All patients were patch tested with the European baseline series, and hairdressers were additionally tested with the hairdressing series. RESULTS: Occupational...... contact dermatitis (p dermatitis was less commonly observed among hairdressers (21.3%) than among controls (29.4%) (p 

  19. Bioenergy from sisal residues

    Energy Technology Data Exchange (ETDEWEB)

    Jungersen, G. [Dansk Teknologisk Inst. (Denmark); Kivaisi, A.; Rubindamayugi, M. [Univ. of Dar es Salaam (Tanzania, United Republic of)

    1998-05-01

    The main objectives of this report are: To analyse the bioenergy potential of the Tanzanian agro-industries, with special emphasis on the Sisal industry, the largest producer of agro-industrial residues in Tanzania; and to upgrade the human capacity and research potential of the Applied Microbiology Unit at the University of Dar es Salaam, in order to ensure a scientific and technological support for future operation and implementation of biogas facilities and anaerobic water treatment systems. The experimental work on sisal residues contains the following issues: Optimal reactor set-up and performance; Pre-treatment methods for treatment of fibre fraction in order to increase the methane yield; Evaluation of the requirement for nutrient addition; Evaluation of the potential for bioethanol production from sisal bulbs. The processing of sisal leaves into dry fibres (decortication) has traditionally been done by the wet processing method, which consumes considerable quantities of water and produces large quantities of waste water. The Tanzania Sisal Authority (TSA) is now developing a dry decortication method, which consumes less water and produces a waste product with 12-15% TS, which is feasible for treatment in CSTR systems (Continously Stirred Tank Reactors). (EG)

  20. Surface contact potential patches and Casimir force measurements

    International Nuclear Information System (INIS)

    Kim, W. J.; Sushkov, A. O.; Lamoreaux, S. K.; Dalvit, D. A. R.

    2010-01-01

    We present calculations of contact potential surface patch effects that simplify previous treatments. It is shown that, because of the linearity of Laplace's equation, the presence of patch potentials does not affect an electrostatic calibration of a two-plate Casimir measurement apparatus. Using models that include long-range variations in the contact potential across the plate surfaces, a number of experimental observations can be reproduced and explained. For these models, numerical calculations show that if a voltage is applied between the plates which minimizes the force, a residual electrostatic force persists, and that the minimizing potential varies with distance. The residual force can be described by a fit to a simple two-parameter function involving the minimizing potential and its variation with distance. We show the origin of this residual force by use of a simple parallel capacitor model. Finally, the implications of a residual force that varies in a manner different from 1/d on the accuracy of previous Casimir measurements is discussed.

  1. gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.

    Science.gov (United States)

    Serçinoglu, Onur; Ozbek, Pemra

    2018-05-25

    Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

  2. Exact and Effective Pair-Wise Potential for Protein-Ligand Interactions Obtained from a Semiempirical Energy Partition

    Directory of Open Access Journals (Sweden)

    André Melo

    2008-09-01

    Full Text Available In this work, the partition method introduced by Carvalho and Melo was used to study the complex between Cucurbita maxima trypsin inhibitor (CMTI-I and glycerol at the AM1 level. An effective potential, combining non-bonding and polarization plus charge transfer (PLCT terms, was introduced to evaluate the magnitude of the interaction between each amino acid and the ligand. In this case study, the nonbonding–PLCT noncompensation characterizes the stabilization energy of the association process in study. The main residues (Gly29, Cys3 and Arg5 with net attractive effects and Arg1 (with a net repulsive effect, responsible by the stability of protein-ligand complex, are associated with large nonbonding energies non-compensated by PLCT effects. The results obtained enable us to conclude that the present decomposition scheme can be used for understanding the cohesive phenomena in proteins.

  3. Detecting phase separation of freeze-dried binary amorphous systems using pair-wise distribution function and multivariate data analysis

    DEFF Research Database (Denmark)

    Chieng, Norman; Trnka, Hjalte; Boetker, Johan

    2013-01-01

    The purpose of this study is to investigate the use of multivariate data analysis for powder X-ray diffraction-pair-wise distribution function (PXRD-PDF) data to detect phase separation in freeze-dried binary amorphous systems. Polymer-polymer and polymer-sugar binary systems at various ratios were...... freeze-dried. All samples were analyzed by PXRD, transformed to PDF and analyzed by principal component analysis (PCA). These results were validated by differential scanning calorimetry (DSC) through characterization of glass transition of the maximally freeze-concentrate solute (Tg'). Analysis of PXRD......-PDF data using PCA provides a more clear 'miscible' or 'phase separated' interpretation through the distribution pattern of samples on a score plot presentation compared to residual plot method. In a phase separated system, samples were found to be evenly distributed around the theoretical PDF profile...

  4. Fabricating customized hydrogel contact lens

    Science.gov (United States)

    Childs, Andre; Li, Hao; Lewittes, Daniella M.; Dong, Biqin; Liu, Wenzhong; Shu, Xiao; Sun, Cheng; Zhang, Hao F.

    2016-10-01

    Contact lenses are increasingly used in laboratories for in vivo animal retinal imaging and pre-clinical studies. The lens shapes often need modification to optimally fit corneas of individual test subjects. However, the choices from commercially available contact lenses are rather limited. Here, we report a flexible method to fabricate customized hydrogel contact lenses. We showed that the fabricated hydrogel is highly transparent, with refractive indices ranging from 1.42 to 1.45 in the spectra range from 400 nm to 800 nm. The Young’s modulus (1.47 MPa) and hydrophobicity (with a sessile drop contact angle of 40.5°) have also been characterized experimentally. Retinal imaging using optical coherence tomography in rats wearing our customized contact lenses has the quality comparable to the control case without the contact lens. Our method could significantly reduce the cost and the lead time for fabricating soft contact lenses with customized shapes, and benefit the laboratorial-used contact lenses in pre-clinical studies.

  5. Emotional Satisfaction of Customer Contacts

    NARCIS (Netherlands)

    Güngör, Hüseyin

    2007-01-01

    For marketing and customer services researchers and professionals who are interested in customer contacts, customer satisfaction and loyalty issues. Contact centers are playing a pivotal role in customer services of the 21st century. Nevertheless, despite their growing importance and presence,

  6. Journal of Business Research: Contact

    African Journals Online (AJOL)

    Principal Contact. Goski Alabi Mrs Institute of Professional Studies (IPS) P. 0 Box 149 Institute Of Professional Studies (IPS) Legon, Accra Ghana Phone: +233 24 64 52798. Fax: +233 21 513539. Email: goskia@yahoo.com. Support Contact. Anthony Afeadie. Phone: +233 21 500171. Email: ipsjournal@yahoo.com.

  7. Aluminum break-point contacts

    NARCIS (Netherlands)

    Heinemann, Martina; Groot, R.A. de

    1997-01-01

    Ab initio molecular dynamics is used to study the contribution of a single Al atom to an aluminum breakpoint contact during the final stages of breaking and the initial stages of the formation of such a contact. A hysteresis effect is found in excellent agreement with experiment and the form of the

  8. Contact Allergy to Neem Oil.

    NARCIS (Netherlands)

    de Groot, Anton; Jagtman, Berend A; Woutersen, Marjolijn

    2018-01-01

    A case of allergic contact dermatitis from neem oil is presented. Neem oil (synonyms: Melia azadirachta seed oil [INCI name], nim oil, margosa oil) is a vegetable (fixed) oil obtained from the seed of the neem tree Azadirachta indica by cold pressing. Contact allergy to neem oil has been described

  9. Contact dermatitis to cobalt chloride with an unusual mechanism.

    Science.gov (United States)

    Arslan, Sevket; Aksan, Serkan; Ucar, Ramazan; Caliskaner, Ahmet Zafer

    2015-10-01

    Contact dermatitis is a frequent inflammatory skin disease. A suspected diagnosis is based on clinical symptoms, a plausible contact to allergens and a suitable history of dermatitis. Therefore, careful diagnosis by patch testing is of great importance because the patch testing is important to find out which allergen/material causes the complaints. Metallic allergens such as cobalt are among the most common causes of allergic contact dermatitis, but frequencies of contact dermatitis to these allergens may vary in different skin areas. Here, we report an unusual case of cobalt allergy on the skin contact with the prosthetic leg of a 30-year-old female patient. The patient developed maculopapular and vesicular lesions on her contact region of residual limb to prosthetic leg. She underwent standard patch testing, which resulted in a strong positive reaction to cobalt chloride. This case report may serve to remind doctors to be aware of potential allergic reactions to prostheses and to enable them to recognize a metal allergy if it appears. Prosthetists should also be reminded of potential allergic reactions. Cobalt can be used as an accelerator in making a prosthetic socket. Several cases have been reported concerning allergies to components of the prosthetic socket. This is the first report of sensitization to cobalt which is used in making a prosthetic leg. © The International Society for Prosthetics and Orthotics 2014.

  10. Body contact and body language

    DEFF Research Database (Denmark)

    Winther, Helle

    2008-01-01

    and the boundaries between self and world. In western societies, the modern premises for contact are in some ways developing from close contact to virtual communication. With this breadth of perspective in mind, the ques­tion is whether conscious and experimental work with body contact and body language in move......­ment psychology and education provide potential for intense personal develop­ment as well as for social and cultural learning processes. This performative research project originates from the research project entitled, Movement Psy­chol­ogy: The Language of the Body and the Psy­chol­ogy of Movement based......Body contact and body language are unique and existential and, although culturally dependent and socially embodied, they are also universal communication forms. For small children all over the world, warm, close and nourishing body contact is fundamental to their embodied experi­ence of themselves...

  11. Reverse-contact UV nanoimprint lithography for multilayered structure fabrication

    DEFF Research Database (Denmark)

    Kehagias, N.; Reboud, V.; Chansin, G.

    2007-01-01

    In this paper, we report results on a newly developed nanofabrication technique, namely reverse-contact UV nanoimprint lithography. This technique is a combination of nanoimprint lithography and contact printing lithography. In this process, a lift-off resist and a UV cross-linkable polymer...... are spin-coated successively onto a patterned UV mask-mould. These thin polymer films are then transferred from the mould to the substrate by contact at a suitable temperature and pressure. The whole assembly is then exposed to UV light. After separation of the mould and the substrate, the unexposed...... polymer areas are dissolved in a developer solution leaving behind the negative features of the original stamp. This method delivers resist pattern transfer without a residual layer, thereby rending unnecessary the etching steps typically needed in the imprint lithography techniques for three...

  12. Reverse-contact UV nanoimprint lithography for multilayered structure fabrication

    International Nuclear Information System (INIS)

    Kehagias, N; Reboud, V; Chansin, G; Zelsmann, M; Jeppesen, C; Schuster, C; Kubenz, M; Reuther, F; Gruetzner, G; Torres, C M Sotomayor

    2007-01-01

    In this paper, we report results on a newly developed nanofabrication technique, namely reverse-contact UV nanoimprint lithography. This technique is a combination of nanoimprint lithography and contact printing lithography. In this process, a lift-off resist and a UV cross-linkable polymer are spin-coated successively onto a patterned UV mask-mould. These thin polymer films are then transferred from the mould to the substrate by contact at a suitable temperature and pressure. The whole assembly is then exposed to UV light. After separation of the mould and the substrate, the unexposed polymer areas are dissolved in a developer solution leaving behind the negative features of the original stamp. This method delivers resist pattern transfer without a residual layer, thereby rending unnecessary the etching steps typically needed in the imprint lithography techniques for three-dimensional patterning. Three-dimensional woodpile-like structures were successfully fabricated with this new technique

  13. 77 FR 50661 - Notice of Filing of Several Pesticide Petitions Filed for Residues of Pesticide Chemicals in or...

    Science.gov (United States)

    2012-08-22

    ... purposes. Contact: Thomas Harris, (703) 308-9423, email address: harris.thomas@epa.gov . 4. PP 2E8025. (EPA... submitted. Since there is no reasonable expectation of finding residues of dodine in livestock or poultry...

  14. Immobilization of acid digestion residue

    International Nuclear Information System (INIS)

    Greenhalgh, W.O.; Allen, C.R.

    1983-01-01

    Acid digestion treatment of nuclear waste is similar to incineration processes and results in the bulk of the waste being reduced in volume and weight to some residual solids termed residue. The residue is composed of various dispersible solid materials and typically contains the resultant radioactivity from the waste. This report describes the immobilization of the residue in portland cement, borosilicate glass, and some other waste forms. Diagrams showing the cement and glass virtification parameters are included in the report as well as process steps and candidate waste product forms. Cement immobilization is simplest and probably least expensive; glass vitrification exhibits the best overall volume reduction ratio

  15. Leaf habit does not determine the investment in both physical and chemical defences and pair-wise correlations between these defensive traits.

    Science.gov (United States)

    Moreira, X; Pearse, I S

    2017-05-01

    Plant life-history strategies associated with resource acquisition and economics (e.g. leaf habit) are thought to be fundamental determinants of the traits and mechanisms that drive herbivore pressure, resource allocation to plant defensive traits, and the simultaneous expression (positive correlations) or trade-offs (negative correlations) between these defensive traits. In particular, it is expected that evergreen species - which usually grow slower and support constant herbivore pressure in comparison with deciduous species - will exhibit higher levels of both physical and chemical defences and a higher predisposition to the simultaneous expression of physical and chemical defensive traits. Here, by using a dataset which included 56 oak species (Quercus genus), we investigated whether leaf habit of plant species governs the investment in both physical and chemical defences and pair-wise correlations between these defensive traits. Our results showed that leaf habit does not determine the production of most leaf physical and chemical defences. Although evergreen oak species had higher levels of leaf toughness and specific leaf mass (physical defences) than deciduous oak species, both traits are essentially prerequisites for evergreenness. Similarly, our results also showed that leaf habit does not determine pair-wise correlations between defensive traits because most physical and chemical defensive traits were simultaneously expressed in both evergreen and deciduous oak species. Our findings indicate that leaf habit does not substantially contribute to oak species differences in plant defence investment. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

  16. CNNcon: improved protein contact maps prediction using cascaded neural networks.

    Directory of Open Access Journals (Sweden)

    Wang Ding

    Full Text Available BACKGROUNDS: Despite continuing progress in X-ray crystallography and high-field NMR spectroscopy for determination of three-dimensional protein structures, the number of unsolved and newly discovered sequences grows much faster than that of determined structures. Protein modeling methods can possibly bridge this huge sequence-structure gap with the development of computational science. A grand challenging problem is to predict three-dimensional protein structure from its primary structure (residues sequence alone. However, predicting residue contact maps is a crucial and promising intermediate step towards final three-dimensional structure prediction. Better predictions of local and non-local contacts between residues can transform protein sequence alignment to structure alignment, which can finally improve template based three-dimensional protein structure predictors greatly. METHODS: CNNcon, an improved multiple neural networks based contact map predictor using six sub-networks and one final cascade-network, was developed in this paper. Both the sub-networks and the final cascade-network were trained and tested with their corresponding data sets. While for testing, the target protein was first coded and then input to its corresponding sub-networks for prediction. After that, the intermediate results were input to the cascade-network to finish the final prediction. RESULTS: The CNNcon can accurately predict 58.86% in average of contacts at a distance cutoff of 8 Å for proteins with lengths ranging from 51 to 450. The comparison results show that the present method performs better than the compared state-of-the-art predictors. Particularly, the prediction accuracy keeps steady with the increase of protein sequence length. It indicates that the CNNcon overcomes the thin density problem, with which other current predictors have trouble. This advantage makes the method valuable to the prediction of long length proteins. As a result, the effective

  17. Nordic project food contact materials

    DEFF Research Database (Denmark)

    Li, Ågot; Tesdal Håland, Julie; Petersen, Jens Højslev

    Denmark, Finland, Faroe Islands, Iceland, Norway and Sweden have in 2013––2015 conducted a Nordic project on food contact materials. Food contact materials are used in all stages of food production and can be a general source of contamination. The food safety authorities in most of the Nordic...... countries have had a limited focus on the FCM area with the exception of Denmark and Finland. The aim of the project was therefore to control establishments producing, importing or using plastic food contact materials as well as to increase the knowledge of the inspectors performing these controls....... The focus of the inspections was to control the declaration of compliance (DoC) for plastic food contact materials. The requirement for a Doc is mandatory in order to ensure that the FCM complies with the legislation. In addition some products were analyzed for phthalates....

  18. Scalable algorithms for contact problems

    CERN Document Server

    Dostál, Zdeněk; Sadowská, Marie; Vondrák, Vít

    2016-01-01

    This book presents a comprehensive and self-contained treatment of the authors’ newly developed scalable algorithms for the solutions of multibody contact problems of linear elasticity. The brand new feature of these algorithms is theoretically supported numerical scalability and parallel scalability demonstrated on problems discretized by billions of degrees of freedom. The theory supports solving multibody frictionless contact problems, contact problems with possibly orthotropic Tresca’s friction, and transient contact problems. It covers BEM discretization, jumping coefficients, floating bodies, mortar non-penetration conditions, etc. The exposition is divided into four parts, the first of which reviews appropriate facets of linear algebra, optimization, and analysis. The most important algorithms and optimality results are presented in the third part of the volume. The presentation is complete, including continuous formulation, discretization, decomposition, optimality results, and numerical experimen...

  19. Research in Hospitality Management: Contact

    African Journals Online (AJOL)

    Principal Contact. Dr Sjoerd A Gehrels Editor-in-Chief Stenden Hotel Management School, Academy of International Hospitality Research, Leeuwarden, The Netherlands Email: sjoerd.gehrels@stenden.com ...

  20. EPA Alternative Dispute Resolution Contacts

    Science.gov (United States)

    The success of EPA's ADR efforts depends on a network of talented and experienced professionals in Headquarters offices and EPA Regions. For Agency-wide ADR information, please contact the Conflict Prevention and Resolution Center.

  1. Metal semiconductor contacts and devices

    CERN Document Server

    Cohen, Simon S; Einspruch, Norman G

    1986-01-01

    VLSI Electronics Microstructure Science, Volume 13: Metal-Semiconductor Contacts and Devices presents the physics, technology, and applications of metal-semiconductor barriers in digital integrated circuits. The emphasis is placed on the interplay among the theory, processing, and characterization techniques in the development of practical metal-semiconductor contacts and devices.This volume contains chapters that are devoted to the discussion of the physics of metal-semiconductor interfaces and its basic phenomena; fabrication procedures; and interface characterization techniques, particularl

  2. Embodied Archives as Contact Zones

    Directory of Open Access Journals (Sweden)

    Judit Vidiella

    2015-02-01

    Full Text Available This article proposes a reflection about affective politics from locating some theoretical and conceptual genealogies like «emotion», «affection», «zones of contact»…, that understand them as action and force fields. These contributions allow us to rethink the relation of affects with politics and strategies of archive linked to performance, and understood as zones of friction, collision, circulation and contact: performative writing, repertoire, memes…

  3. Landfilling of waste incineration residues

    DEFF Research Database (Denmark)

    Christensen, Thomas Højlund; Astrup, Thomas; Cai, Zuansi

    2002-01-01

    Residues from waste incineration are bottom ashes and air-pollution-control (APC) residues including fly ashes. The leaching of heavy metals and salts from the ashes is substantial and a wide spectrum of leaching tests and corresponding criteria have been introduced to regulate the landfilling...

  4. Accumulation of {sup 14}C-trinitrotoluene and related nonextractable (bound) residues in Eisenia fetida

    Energy Technology Data Exchange (ETDEWEB)

    Belden, Jason B., E-mail: jbelden@okstate.edu [Department of Zoology, Oklahoma State University, Stillwater, OK 74078 (United States); Lotufo, Guillerme R. [US Army Engineer Research and Development Center, Vicksburg, MS 39180 (United States); Chambliss, C. Kevin [Department of Chemistry, Baylor University, Waco, TX 76798 (United States); Fisher, Jonathan C. [Department of Zoology, Oklahoma State University, Stillwater, OK 74078 (United States); Johnson, Dave R.; Boyd, Robert E.; Sims, Jerre G. [US Army Engineer Research and Development Center, Vicksburg, MS 39180 (United States)

    2011-05-15

    To determine if trinitrotoluene (TNT) forms nonextractable residues in earthworms and to measure the relative degree of accumulation as compared to TNT and its deaminated metabolites, Eisenia fetida was exposed to {sup 14}C-TNT using dermal contact to filter paper or exposure to soil. Nonextractable residues made up 32-68% of total body burden depending on exposure media and depuration time. Parent TNT accounted for less than 3% of radioactivity, while ADNTs accounted for 7-38%. Elimination half-lives were 61-120 h for TNT, ADNTs, and DANTs, which was significantly lower than the half-lives found for nonextractable residues, 201-240 h. However, over 80% of the nonextractable residue was solubilized using weak acid (pH 2). Based on our findings that TNT accumulation occurs primarily as nonextractable residues, which have a longer half-life, and that nonextractable residues can be solubilized, we propose that nonextractable residues could be used as a selective biomarker for assessing TNT contamination. - Highlights: > Trinitrotoluene accumulation in earthworms primarily occurs as nonextractable residues. > Nonextractable residues have a significantly longer half life in the worm as compared to TNT and its solvent-extractable deaminated metabolites. > Nonextractable residue may be useful as a biomarker for exposure to TNT. - The majority of trinitrotoluene accumulation in earthworms occurs as nonextractable residues that have a significantly longer half life in the worm as compared to TNT and its solvent-extractable deaminated metabolites.

  5. [Contact allergy to henna tattoos].

    Science.gov (United States)

    Steinkjer, Bjarte; Stangeland, Katarina Zak; Mikkelsen, Carsten Sauer

    2011-03-18

    Tattoos with henna colours have become very popular and the prevalence of contact allergy seems to increase. This is a short review article based on our own clinical experience and literature identified through a search in PubMed with the words "henna", "paraphenylendiamin" and "allergic contact dermatitis." A case report is included. It is well documented that many experience skin reactions after henna tattoos. The cause is almost always contact allergy to the azo compound paraphenylendiamin, which is added to speed up the process and make the colour darker. Most people, including children, get henna tattoos during vacations in Asia or the Mediterranean. Established contact allergy is permanent. Many hair-colour products contain paraphenylendiamin, and persons with contact allergy against the product may develop a very strong contact allergic eczema by use of such substances. Acute reactions are treated with local cortisone products, or with systemic steroids. Cross reaction to substances with a similar chemical structure may occur. Tattoos with paraphenylendiamin-containing henna colours should be avoided.

  6. Hazardous properties of paint residues from the furniture industry.

    Science.gov (United States)

    Vaajasaari, Kati; Kulovaara, Maaret; Joutti, Anneli; Schultz, Eija; Soljamo, Kari

    2004-01-30

    The objective of this study was to screen nine excess paint residues for environmental hazard and to evaluate their disposability in a non-hazardous or hazardous-waste landfill. These residues were produced in the process of spray-painting furniture. Residues were classified according to their leaching and ecotoxicological properties. Leaching properties were determined with the European standard SFS-EN 12457-2 leaching-test. The toxicity of the leaching-test eluates was measured with plant-, bacteria- and enzyme-inhibition bioassays. Total organic carbon, formaldehyde and solvent concentrations in the solid wastes and in the leaching-test eluates were analysed. It seemed likely that leached formaldehyde caused very high acute toxicity in leaching-test eluates of the dry-booth residues. This hypothesis was based on the fact that the formaldehyde concentrations in the leaching-test eluates of the dry-booth residues were 62-75 times higher than the EC50 value reported in the literature for formaldehyde. The results of the water-curtain booth residues showed that the samples with the highest TOC and aromatic solvent concentrations were also the most toxic. The studied excess paint residues were complex organic mixtures and contained large amounts of compounds not identifiable from chemical data. Therefore, the evaluation of the hazard based solely on available chemical data is unlikely to be sufficient, as evidenced by our study. Our results show that harmful compounds remain in the solid waste and the toxicity results of their leaching-test eluates show that toxicity may leach from residues in contact with water at landfill sites. They also confirm the benefit of combining chemical and ecotoxicological assays in assessing the potential environmental hazard of complex organic mixtures found in wastes. Copyright 2003 Elsevier B.V.

  7. Statistical inference on residual life

    CERN Document Server

    Jeong, Jong-Hyeon

    2014-01-01

    This is a monograph on the concept of residual life, which is an alternative summary measure of time-to-event data, or survival data. The mean residual life has been used for many years under the name of life expectancy, so it is a natural concept for summarizing survival or reliability data. It is also more interpretable than the popular hazard function, especially for communications between patients and physicians regarding the efficacy of a new drug in the medical field. This book reviews existing statistical methods to infer the residual life distribution. The review and comparison includes existing inference methods for mean and median, or quantile, residual life analysis through medical data examples. The concept of the residual life is also extended to competing risks analysis. The targeted audience includes biostatisticians, graduate students, and PhD (bio)statisticians. Knowledge in survival analysis at an introductory graduate level is advisable prior to reading this book.

  8. Contact isotopic- and contact ion-exchange between two adsorbents

    International Nuclear Information System (INIS)

    Bunzl, K.; Mohan, R.; Haimerl, M.

    1975-01-01

    The kinetics of contact ion exchange processes between an ion exchange membrane and resin ion exchange beads, stirred in pure water, was investigated. A general criterion was derived, which indicates whether diffusion of the ions between the intermingling electric double layers or the collision frequency between the two adsorbents is the rate dermining step. Since the latter process proved to be rate controlling under our experimental conditions, the corresponding rate equations were derived under various initial and boundary conditions. Experimentally, the kinetics of contact isotopic exchange of Cs + - and Na + -ions as well as of the reverse contact ion exchange process of Cs + -versus Na + -ions were investigated by using Na 22 and Cs 137 radioisotopes. The experiments reveal in quantitative accord with the theory that the rate of collision controlled contact ion exchange processes depends mainly on the 'exchange coefficient', the separation factor and the collision frequency. While the latter two quantities were determined independently by separate experiments, the 'exchange coefficient' was evaluated from a contact isotopic exchange experiment. (orig.) [de

  9. Co-Occurring Atomic Contacts for the Characterization of Protein Binding Hot Spots

    Science.gov (United States)

    Liu, Qian; Ren, Jing; Song, Jiangning; Li, Jinyan

    2015-01-01

    A binding hot spot is a small area at a protein-protein interface that can make significant contribution to binding free energy. This work investigates the substantial contribution made by some special co-occurring atomic contacts at a binding hot spot. A co-occurring atomic contact is a pair of atomic contacts that are close to each other with no more than three covalent-bond steps. We found that two kinds of co-occurring atomic contacts can play an important part in the accurate prediction of binding hot spot residues. One is the co-occurrence of two nearby hydrogen bonds. For example, mutations of any residue in a hydrogen bond network consisting of multiple co-occurring hydrogen bonds could disrupt the interaction considerably. The other kind of co-occurring atomic contact is the co-occurrence of a hydrophobic carbon contact and a contact between a hydrophobic carbon atom and a π ring. In fact, this co-occurrence signifies the collective effect of hydrophobic contacts. We also found that the B-factor measurements of several specific groups of amino acids are useful for the prediction of hot spots. Taking the B-factor, individual atomic contacts and the co-occurring contacts as features, we developed a new prediction method and thoroughly assessed its performance via cross-validation and independent dataset test. The results show that our method achieves higher prediction performance than well-known methods such as Robetta, FoldX and Hotpoint. We conclude that these contact descriptors, in particular the novel co-occurring atomic contacts, can be used to facilitate accurate and interpretable characterization of protein binding hot spots. PMID:26675422

  10. Wounds caused by tight contact with the barrel-cylinder gap of revolvers.

    Science.gov (United States)

    Rogers, D R

    1984-06-01

    A case is presented in which the recognition of a tight cylinder gap contact wound was crucial. Experiments were carried out to reproduce the wound which was noted on the hand of a robbery suspect. Tight contact with the cylinder gap of a revolver produces a characteristic, readily recognizable wound. It is characterized by an L-shaped pattern of powder residue. Along one axis a searing burn may occur which may be deep and which may lead to significant tissue destruction.

  11. Solar cell with back side contacts

    Science.gov (United States)

    Nielson, Gregory N; Okandan, Murat; Cruz-Campa, Jose Luis; Resnick, Paul J; Wanlass, Mark Woodbury; Clews, Peggy J

    2013-12-24

    A III-V solar cell is described herein that includes all back side contacts. Additionally, the positive and negative electrical contacts contact compoud semiconductor layers of the solar cell other than the absorbing layer of the solar cell. That is, the positive and negative electrical contacts contact passivating layers of the solar cell.

  12. Measuring The Contact Resistances Of Photovoltaic Cells

    Science.gov (United States)

    Burger, D. R.

    1985-01-01

    Simple method devised to measure contact resistances of photovoltaic solar cells. Method uses readily available equipment and applicable at any time during life of cell. Enables evaluation of cell contact resistance, contact-end resistance, contact resistivity, sheet resistivity, and sheet resistivity under contact.

  13. Residual stress by repair welds

    International Nuclear Information System (INIS)

    Mochizuki, Masahito; Toyoda, Masao

    2003-01-01

    Residual stress by repair welds is computed using the thermal elastic-plastic analysis with phase-transformation effect. Coupling phenomena of temperature, microstructure, and stress-strain fields are simulated in the finite-element analysis. Weld bond of a plate butt-welded joint is gouged and then deposited by weld metal in repair process. Heat source is synchronously moved with the deposition of the finite-element as the weld deposition. Microstructure is considered by using CCT diagram and the transformation behavior in the repair weld is also simulated. The effects of initial stress, heat input, and weld length on residual stress distribution are studied from the organic results of numerical analysis. Initial residual stress before repair weld has no influence on the residual stress after repair treatment near weld metal, because the initial stress near weld metal releases due to high temperature of repair weld and then stress by repair weld regenerates. Heat input has an effect for residual stress distribution, for not its magnitude but distribution zone. Weld length should be considered reducing the magnitude of residual stress in the edge of weld bead; short bead induces high tensile residual stress. (author)

  14. 76 FR 55329 - Receipt of Several Pesticide Petitions Filed for Residues of Pesticide Chemicals in or on Various...

    Science.gov (United States)

    2011-09-07

    ... quantified after HPLC separation by tandem mass spectrometry (MS/MS) detection. Contact: Sidney Jackson, (703... ultraviolet (UV) detection or confirmatory LC/MS. Contact: Rose Mary Kearns, (703) 305- 5611, e-mail address... from the requirement of a tolerance for residues of the antimicrobial dimethyl didecyl ammonium...

  15. Where is the line? Phylogeography and secondary contact of western Palearctic coal tits (Periparus ater: Aves, Passeriformes, Paridae)

    DEFF Research Database (Denmark)

    Pentzold, Stefan; Tritsch, Christian; Martens, Jochen

    2013-01-01

    -European delimitation of a postulated secondary contact zone among coal tits from the north-eastern Palearctic ater subspecies group and those from the south-western Palearctic abietum group. Generally, between population differentiation was greatest in the Mediterranean range, which was explained by a greater...... separation in multiple Pleistocene refuge areas compared to the lower differentiation across the northeastern Palearctic range. Genetic diversity indices were lowest on Mediterranean island populations as compared to continental populations. Pairwise ˚ST values were highest among island populations....... At the same time, at least four distinct genetic lineages emerged in eastern Eurasia, the nominate ater subspecies group being one of them. Finally, during the Holocene extant wide-range secondary contact in Europe was established via rapid westward range expansion from an East Asian refuge and via...

  16. Antibacterial surface design - Contact kill

    Science.gov (United States)

    Kaur, Rajbir; Liu, Song

    2016-08-01

    Designing antibacterial surfaces has become extremely important to minimize Healthcare Associated Infections which are a major cause of mortality worldwide. A previous biocide-releasing approach is based on leaching of encapsulated biocides such as silver and triclosan which exerts negative impacts on the environment and potentially contributes to the development of bacterial resistance. This drawback of leachable compounds led to the shift of interest towards a more sustainable and environmentally friendly approach: contact-killing surfaces. Biocides that can be bound onto surfaces to give the substrates contact-active antibacterial activity include quaternary ammonium compounds (QACs), quaternary phosphoniums (QPs), carbon nanotubes, antibacterial peptides, and N-chloramines. Among the above, QACs and N-chloramines are the most researched contact-active biocides. We review the engineering of contact-active surfaces using QACs or N-chloramines, the modes of actions as well as the test methods. The charge-density threshold of cationic surfaces for desired antibacterial efficacy and attempts to combine various biocides for the generation of new contact-active surfaces are discussed in detail. Surface positive charge density is identified as a key parameter to define antibacterial efficacy. We expect that this research field will continue to attract more research interest in view of the potential impact of self-disinfective surfaces on healthcare-associated infections, food safety and corrosion/fouling resistance required on industrial surfaces such as oil pipes and ship hulls.

  17. A pairwise unit-root-test based approach to investigating convergence of household debts in South Africa and the United States

    Directory of Open Access Journals (Sweden)

    Ntebogang Dinah Moroke

    2015-05-01

    Full Text Available The purpose of this paper was to test convergence of household debts in the United States and South Africa taking a pairwise unit root tests based approaches into account. Substantial number of studies dealt with convergence of several macroeconomic variables but to my knowledge no study considered this subject with respect to household debts of the identified countries. Quarterly data on household debts consisting of 88 observations in the South Africa and United States spanning the period 1990 to 2013 was collected from the South African and St. Louis Federal Reserve Banks. Focused on the absolute value of household debts, this study proved that South Africa is far from catching-up with the United States in terms of overcoming household debts for the selected period. The findings of this study can be used by relevant authorities to help improve ways and means of dealing with household debts South Africa

  18. A spreadsheet template compatible with Microsoft Excel and iWork Numbers that returns the simultaneous confidence intervals for all pairwise differences between multiple sample means.

    Science.gov (United States)

    Brown, Angus M

    2010-04-01

    The objective of the method described in this paper is to develop a spreadsheet template for the purpose of comparing multiple sample means. An initial analysis of variance (ANOVA) test on the data returns F--the test statistic. If F is larger than the critical F value drawn from the F distribution at the appropriate degrees of freedom, convention dictates rejection of the null hypothesis and allows subsequent multiple comparison testing to determine where the inequalities between the sample means lie. A variety of multiple comparison methods are described that return the 95% confidence intervals for differences between means using an inclusive pairwise comparison of the sample means. 2009 Elsevier Ireland Ltd. All rights reserved.

  19. RESIDUAL RISK ASSESSMENT: ETHYLENE OXIDE ...

    Science.gov (United States)

    This document describes the residual risk assessment for the Ethylene Oxide Commercial Sterilization source category. For stationary sources, section 112 (f) of the Clean Air Act requires EPA to assess risks to human health and the environment following implementation of technology-based control standards. If these technology-based control standards do not provide an ample margin of safety, then EPA is required to promulgate addtional standards. This document describes the methodology and results of the residual risk assessment performed for the Ethylene Oxide Commercial Sterilization source category. The results of this analyiss will assist EPA in determining whether a residual risk rule for this source category is appropriate.

  20. Contact-impact algorithms on parallel computers

    International Nuclear Information System (INIS)

    Zhong Zhihua; Nilsson, Larsgunnar

    1994-01-01

    Contact-impact algorithms on parallel computers are discussed within the context of explicit finite element analysis. The algorithms concerned include a contact searching algorithm and an algorithm for contact force calculations. The contact searching algorithm is based on the territory concept of the general HITA algorithm. However, no distinction is made between different contact bodies, or between different contact surfaces. All contact segments from contact boundaries are taken as a single set. Hierarchy territories and contact territories are expanded. A three-dimensional bucket sort algorithm is used to sort contact nodes. The defence node algorithm is used in the calculation of contact forces. Both the contact searching algorithm and the defence node algorithm are implemented on the connection machine CM-200. The performance of the algorithms is examined under different circumstances, and numerical results are presented. ((orig.))

  1. Enthalpic pairwise self-association of L-carnitine in aqueous solutions of some alkali halides at T = 298.15 K

    International Nuclear Information System (INIS)

    Wang, Hua-Qin; Cheng, Wei-Na; Zhu, Li-Yuan; Hu, Xin-Gen

    2016-01-01

    Highlights: • Dilution enthalpies of L-carnitine in aqueous alkali halide solutions by ITC. • The second virial coefficients of enthalpy (h_2) have been calculated. • The values of h_2 increase with increasing molalities of aqueous salt solutions. • The signs of h_2 turn from negative in pure water to positive in salt solutions. • The trends is ascribed to the salt effects on pairwise self-associations. - Abstract: Knowledge of the influence of ions of various nature on intermolecular hydrophilic and hydrophobic interactions in solutions is required in many research fields. In this paper, dilution enthalpies of zwitterion L-carnitine in aqueous NaCl, KCl and NaBr solutions of various molalities (b = 0 to 3.0 mol · kg"−"1) have been determined respectively at T = (298.15 ± 0.01) K and p = (0.100 ± 0.005) MPa by isothermal titration calorimetry (ITC). In light of the MacMillan–Mayer theory, the 2nd virial enthalpic coefficients (h_2) have been calculated. The h_2 coefficients increase gradually with increasing molality (b) of the three aqueous alkali halides solutions, from small negative values in pure water to relatively larger positive values in solution. The trends of h_2 coefficients are ascribed to the salt effects on the balance between hydrophilic and hydrophobic interactions in pairwise self-associations. It is considered that the size of cations and anions exert influences on h_2 coefficients through their surface charge densities and hydration (or dehydration) abilities.

  2. Fast-GPU-PCC: A GPU-Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Time Series Data-fMRI Study.

    Science.gov (United States)

    Eslami, Taban; Saeed, Fahad

    2018-04-20

    Functional magnetic resonance imaging (fMRI) is a non-invasive brain imaging technique, which has been regularly used for studying brain’s functional activities in the past few years. A very well-used measure for capturing functional associations in brain is Pearson’s correlation coefficient. Pearson’s correlation is widely used for constructing functional network and studying dynamic functional connectivity of the brain. These are useful measures for understanding the effects of brain disorders on connectivities among brain regions. The fMRI scanners produce huge number of voxels and using traditional central processing unit (CPU)-based techniques for computing pairwise correlations is very time consuming especially when large number of subjects are being studied. In this paper, we propose a graphics processing unit (GPU)-based algorithm called Fast-GPU-PCC for computing pairwise Pearson’s correlation coefficient. Based on the symmetric property of Pearson’s correlation, this approach returns N ( N − 1 ) / 2 correlation coefficients located at strictly upper triangle part of the correlation matrix. Storing correlations in a one-dimensional array with the order as proposed in this paper is useful for further usage. Our experiments on real and synthetic fMRI data for different number of voxels and varying length of time series show that the proposed approach outperformed state of the art GPU-based techniques as well as the sequential CPU-based versions. We show that Fast-GPU-PCC runs 62 times faster than CPU-based version and about 2 to 3 times faster than two other state of the art GPU-based methods.

  3. Device including a contact detector

    DEFF Research Database (Denmark)

    2011-01-01

    arms (12) may extend from the supporting body in co-planar relationship with the first surface. The plurality of cantilever arms (12) may extend substantially parallel to each other and each of the plurality of cantilever arms (12) may include an electrical conductive tip for contacting the area......The present invention relates to a probe for determining an electrical property of an area of a surface of a test sample, the probe is intended to be in a specific orientation relative to the test sample. The probe may comprise a supporting body defining a first surface. A plurality of cantilever...... of the test sample by movement of the probe relative to the surface of the test sample into the specific orientation.; The probe may further comprise a contact detector (14) extending from the supporting body arranged so as to contact the surface of the test sample prior to any one of the plurality...

  4. All-graphene edge contacts

    DEFF Research Database (Denmark)

    Jacobsen, Kåre Wedel; Falkenberg, Jesper Toft; Papior, Nick Rübner

    2016-01-01

    Using ab-initio methods we investigate the possibility of three-terminalgraphene "T-junction" devices and show that these all-graphene edge contactsare energetically feasible when the 1D interface itself is free from foreignatoms. We examine the energetics of various junction structures as a func......Using ab-initio methods we investigate the possibility of three-terminalgraphene "T-junction" devices and show that these all-graphene edge contactsare energetically feasible when the 1D interface itself is free from foreignatoms. We examine the energetics of various junction structures...... to be in therange of 1-10 kΩμm which is comparable to the best contact resistance reportedfor edge-contacted graphene-metal contacts. We conclude that conductingall-carbon T-junctions should be feasible....

  5. Contact Lenses for Color Blindness.

    Science.gov (United States)

    Badawy, Abdel-Rahman; Hassan, Muhammad Umair; Elsherif, Mohamed; Ahmed, Zubair; Yetisen, Ali K; Butt, Haider

    2018-06-01

    Color vision deficiency (color blindness) is an inherited genetic ocular disorder. While no cure for this disorder currently exists, several methods can be used to increase the color perception of those affected. One such method is the use of color filtering glasses which are based on Bragg filters. While these glasses are effective, they are high cost, bulky, and incompatible with other vision correction eyeglasses. In this work, a rhodamine derivative is incorporated in commercial contact lenses to filter out the specific wavelength bands (≈545-575 nm) to correct color vision blindness. The biocompatibility assessment of the dyed contact lenses in human corneal fibroblasts and human corneal epithelial cells shows no toxicity and cell viability remains at 99% after 72 h. This study demonstrates the potential of the dyed contact lenses in wavelength filtering and color vision deficiency management. © 2018 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Methylisothiazolinone contact allergy - A review

    DEFF Research Database (Denmark)

    Lundov, M D; Krongaard, Teddy; L Menné, T

    2011-01-01

    In the early 2000s the preservative methylisothiazolinone (MI) was released as an individual preservative for industrial products and in 2005 permitted for use in cosmetic products. Up till then MI had only been used in combination with methylcholoroisthiazolinone (MCI). MCI/MI is one of the most...... frequent causes of preservative contact allergy and early studies showed that both MI and MCI are sensitizers. The prevalence of MI contact allergy is already around 1·5% and sources of exposure are associated with occupation, cosmetic products or household products. Use of MI in industrial products...... is not restricted and cases of occupational contact allergy to MI e.g. in painters are reported. The frequency of use of MI in cosmetics is low, around 1%, while up to 16·5% of household products were preserved with MI. We found 19 (1·5%) out of 1272 cosmetic products labelled with MI, primarily rinse-off products...

  7. Methylisothiazolinone contact allergy: a review

    DEFF Research Database (Denmark)

    Lundov, M D; Krongaard, T; Menné, T L

    2011-01-01

    In the early 2000s the preservative methylisothiazolinone (MI) was released as an individual preservative for industrial products and in 2005 permitted for use in cosmetic products. Up till then MI had only been used in combination with methylcholoroisthiazolinone (MCI). MCI/MI is one of the most...... frequent causes of preservative contact allergy and early studies showed that both MI and MCI are sensitizers. The prevalence of MI contact allergy is already around 1·5% and sources of exposure are associated with occupation, cosmetic products or household products. Use of MI in industrial products...... is not restricted and cases of occupational contact allergy to MI e.g. in painters are reported. The frequency of use of MI in cosmetics is low, around 1%, while up to 16·5% of household products were preserved with MI. We found 19 (1·5%) out of 1272 cosmetic products labelled with MI, primarily rinse-off products...

  8. Variable reluctance switch avoids contact corrosion and contact bounce

    Science.gov (United States)

    Watson, P. C.

    1967-01-01

    Variable reluctance switch avoids contact corrosion and bounce in a hostile environment. It consists of a wire-wound magnetic core and moveable bridge piece that alters the core flux pattern to produce an electrical output useful for switching control media.

  9. Homotopy classification of contact foliations on open contact manifolds

    Indian Academy of Sciences (India)

    64

    Let ξt, t ∈ [0, 1] be a continuous family of contact structures defined by the ... here is based on ideas that can be found in [5] and [8] and may be known to experts. ..... the bigger rectangle represents the set U ×Iε1 and the central dotted line.

  10. Contact Dynamics of EHL Contacts under Time Varying Conditions

    NARCIS (Netherlands)

    Venner, Cornelis H.; Popovici, G.; Wijnant, Ysbrand H.; Dalmaz, G.; Lubrecht, A.A.; Priest, M

    2004-01-01

    By means of numerical simulations of two situations with time varying operating conditions it is shown that the dynamic behaviour of Elasto-Hydrodynamically Lubricated contacts in terms of vibrations can be characterized as: Changes in the mutual approach lead to film thickness changes in the inlet

  11. Reactive boundary layers in metallic rolling contacts

    Energy Technology Data Exchange (ETDEWEB)

    Burbank, John

    2016-05-01

    more thorough investigation into the effects of residual austenite on the properties of this material. The high-performance alternative steels, 36NiCrMoV1-5-7 (hot working steel) and 45SiCrMo6 (spring steel), were heat treated as recommended by their respective manufacturers, and were not case-hardened. The selection of materials with and materials without case-hardening allows for an investigation into whether or not case-hardening is even necessary to deliver acceptable friction behaviour and wear performance. Elemental analyses were conducted by multiple methods to ensure accurate results. Residual austenite contents of the steels and the depth profiles of residual stresses were determined by X-Ray diffraction (XRD), for 20MnCr5 ranging from approximately 6 - 14 vol.%, and under 2 vol.% for the alternative alloys. Hardness profiles were taken from the testing surfaces into the material core. The carburization of 20MnCr5 led to higher hardness and the greater concentration of carbon in the carburization zone more representative of a hardened SAE E52100, or 100Cr6/102Cr6, than of a non-case-hardened 20MnCr5. Residual stresses from machining and case-hardening were measured directly at the sample surface. The high-performance steels fulfilled manufacturer expectations in terms of elemental content, with hardness values between 50 - 55 HRC and strongly martensitic microstructure character. With characterization of the chosen materials complete, the materials could then be subjected to pre-conditioning. The first pre-conditioning method involved targeted generation of cold work hardening as induced boundary layers to protect the contact zone against wear. Work hardening was identified both by variations in residual stress profiles, i.e. the introduction of beneficial compressive residual stresses, and hardness increases in the contact zone, providing enhanced wear resistance. Parameters for work hardening were further optimized to reduce damage to the surface substrates

  12. Reactive boundary layers in metallic rolling contacts

    International Nuclear Information System (INIS)

    Burbank, John

    2016-01-01

    thorough investigation into the effects of residual austenite on the properties of this material. The high-performance alternative steels, 36NiCrMoV1-5-7 (hot working steel) and 45SiCrMo6 (spring steel), were heat treated as recommended by their respective manufacturers, and were not case-hardened. The selection of materials with and materials without case-hardening allows for an investigation into whether or not case-hardening is even necessary to deliver acceptable friction behaviour and wear performance. Elemental analyses were conducted by multiple methods to ensure accurate results. Residual austenite contents of the steels and the depth profiles of residual stresses were determined by X-Ray diffraction (XRD), for 20MnCr5 ranging from approximately 6 - 14 vol.%, and under 2 vol.% for the alternative alloys. Hardness profiles were taken from the testing surfaces into the material core. The carburization of 20MnCr5 led to higher hardness and the greater concentration of carbon in the carburization zone more representative of a hardened SAE E52100, or 100Cr6/102Cr6, than of a non-case-hardened 20MnCr5. Residual stresses from machining and case-hardening were measured directly at the sample surface. The high-performance steels fulfilled manufacturer expectations in terms of elemental content, with hardness values between 50 - 55 HRC and strongly martensitic microstructure character. With characterization of the chosen materials complete, the materials could then be subjected to pre-conditioning. The first pre-conditioning method involved targeted generation of cold work hardening as induced boundary layers to protect the contact zone against wear. Work hardening was identified both by variations in residual stress profiles, i.e. the introduction of beneficial compressive residual stresses, and hardness increases in the contact zone, providing enhanced wear resistance. Parameters for work hardening were further optimized to reduce damage to the surface substrates of the

  13. Fragrance contact allergy in Iran.

    Science.gov (United States)

    Firooz, A; Nassiri-Kashani, M; Khatami, A; Gorouhi, F; Babakoohi, S; Montaser-Kouhsari, L; Davari, P; Dowlati, Y

    2010-12-01

    Fragrances are considered as one of the most common causes of allergic contact dermatitis. About 1-4% of the general population suffer from fragrance contact allergy (FCA). To determine the frequency of FCA and its clinical relevance in a sample of Iranian patients with history of contact and/or atopic dermatitis from January 2004 to December 2008. Standardized patch testing with 28-allergen screening series recommended by the German Contact Dermatitis Research Group and European Standard Series was used at six dermatological clinics in Iran. Fragrance allergens comprised of fragrance mix I (FM I), Myroxylon pereirae (MP; balsam of Peru), Lyral, turpentine and FM II. Fragrance contact allergy was detected in 7.2% of the patients. The frequency of positive reactions to FM I, MP and FM II were 3.7% (41/1105), 2.8% (32/1135) and 1.1% (3/267) respectively. 82.4% of the reactions to fragrance allergens were clinically relevant. The most common involved areas were hands (68.4%) and face (35.4%). Fragrance allergy predominantly affected women aged more than 40 years (P=0.008). Positive reaction to more than two allergens was significantly higher in FCA patients compared with other contact dermatitis patients (P<0.0001), and FM I, nickel and MP were the most frequent allergens in these patients. Despite less frequency of FCA in comparison with some European countries, its clinical relevance in Iranian patients seems to be high. It mostly affects the hands and the face predominantly in women aged more than 40 years. © 2010 The Authors. Journal compilation © 2010 European Academy of Dermatology and Venereology.

  14. Metal Contacts to Gallium Arsenide.

    Science.gov (United States)

    Ren, Fan

    1991-07-01

    While various high performance devices fabricated from the gallium arsenide (GaAs) and related materials have generated considerable interest, metallization are fundamental components to all semiconductor devices and integrated circuits. The essential roles of metallization systems are providing the desired electrical paths between the active region of the semiconductor and the external circuits through the metal interconnections and contacts. In this work, in-situ clean of native oxide, high temperature n-type, low temperature n-type and low temperature p-type ohmic metal systems have been studied. Argon ion mill was used to remove the native oxide prior to metal deposition. For high temperature process n-type GaAs ohmic contacts, Tungsten (W) and Tungsten Silicide (WSi) were used with an epitaxial grown graded Indium Gallium Arsenide (InGaAs) layer (0.2 eV) on GaAs. In addition, refractory metals, Molybdenum (Mo), was incorporated in the Gold-Germanium (AuGe) based on n-type GaAs ohmic contacts to replace conventional silver as barrier to prevent the reaction between ohmic metal and chlorine based plasma as well as the ohmic metallization intermixing which degrades the device performance. Finally, Indium/Gold-Beryllium (In/Au-Be) alloy has been developed as an ohmic contact for p-type GaAs to reduce the contact resistance. The Fermi-level pinning of GaAs has been dominated by the surface states. The Schottky barrier height of metal contacts are about 0.8 V regardless of the metal systems. By using p-n junction approach, barrier height of pulsed C-doped layers was achieved as high as 1.4 V. Arsenic implantation into GaAs method was also used to enhance the barrier height of 1.6 V.

  15. Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns

    International Nuclear Information System (INIS)

    Huang, Yingying; Triscari, Joseph M.; Tseng, George C.; Pasa-Tolic, Ljiljana; Lipton, Mary S.; Smith, Richard D.; Wysocki, Vicki H.

    2005-01-01

    Data mining was performed on 28 330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pairwise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly charged Arg- and Lys-ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides, a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from peptides that have a localized proton and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton. When Pro is absent from peptides that have a mobile or partially mobile proton, cleavage at each peptide bond becomes much more prominent. Whether the above patterns can be found in b ions, y ions, or both depends on the location of the proton holder(s). Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and should be useful in algorithm development that employs improved models to predict fragment ion

  16. Superstring amplitudes and contact interactions

    International Nuclear Information System (INIS)

    Greensite, J.

    1987-08-01

    We show that scattering amplitudes computed from light-cone superstring field theory are divergent at tree level. The divergences can be eliminated, and supersymmetry restored, by the addition of certain counter terms to the light-cone Hamiltonian. These counter terms have the form of local contact interactions, whose existence we had previously deduced on grounds of vacuum stability, and closure of the super-Poincare algebra. The quartic contact interactions required in Type I and Type IIB superstring theories are constructed in detail. (orig.)

  17. Clinical update on contact allergy

    DEFF Research Database (Denmark)

    Uter, Wolfgang; Johansen, Jeanne Duus; Orton, David I

    2005-01-01

    PURPOSE OF REVIEW: The aim of this article is to review recent findings in contact allergy, regarding clinical research. RECENT FINDINGS: The biocide methyldibromo glutaronitrile was identified to be an important sensitizer. Subsequently, it was banned from leave-on cosmetics in the European Union...... a classification of newly introduced chemicals; increasingly, the local lymph node assay is supplementing and potentially replacing the guinea pig maximization test. Recent advances in occupational contact allergy include, for example, some attempts to improve diagnostics for epoxy resin and other plastic, glue...

  18. CONTACT DERMATITIS AMONG CONSTRUCTION WORKERS

    Directory of Open Access Journals (Sweden)

    Ida Ayu Diah Purnama Sari

    2013-02-01

    Full Text Available Contact dermatitis is a form of skin inflammation with spongiosis or intercellular edema of the epidermis due to the interaction of irritants and allergens. While occupational contact dermatitis is an inflammation of the skin due to exposure to irritants or allergens in the workplace. One of the jobs that have a high risk of the disease are construction workers. Although the disease is rarely-threatening but can cause high morbidity and suffering for workers, so it can affect the economy and quality of life of patients.

  19. Nitrogen availability of biogas residues

    Energy Technology Data Exchange (ETDEWEB)

    El-Sayed Fouda, Sara

    2011-09-07

    The objectives of this study were to characterize biogas residues either unseparated or separated into a liquid and a solid phase from the fermentation of different substrates with respect to their N and C content. In addition, short and long term effects of the application of these biogas residues on the N availability and N utilization by ryegrass was investigated. It is concluded that unseparated or liquid separated biogas residues provide N at least corresponding to their ammonium content and that after the first fertilizer application the C{sub org}:N{sub org} ratio of the biogas residues was a crucial factor for the N availability. After long term application, the organic N accumulated in the soil leads to an increased release of N.

  20. Vesícula residual

    Directory of Open Access Journals (Sweden)

    Júlio C. U. Coelho

    Full Text Available Our objective is to report three patients with recurrent severe upper abdominal pain secondary to residual gallbladder. All patients had been subjected to cholecystectomy from 1 to 20 years before. The diagnosis was established after several episodes of severe upper abdominal pain by imaging exams: ultrasonography, tomography, or endoscopic retrograde cholangiography. Removal of the residual gallbladder led to complete resolution of symptoms. Partial removal of the gallbladder is a very rare cause of postcholecystectomy symptoms.

  1. Residual number processing in dyscalculia ?

    OpenAIRE

    Cappelletti, Marinella; Price, Cathy J.

    2013-01-01

    Developmental dyscalculia – a congenital learning disability in understanding numerical concepts – is typically associated with parietal lobe abnormality. However, people with dyscalculia often retain some residual numerical abilities, reported in studies that otherwise focused on abnormalities in the dyscalculic brain. Here we took a different perspective by focusing on brain regions that support residual number processing in dyscalculia. All participants accurately performed semantic and ca...

  2. Americium recovery from reduction residues

    Science.gov (United States)

    Conner, W.V.; Proctor, S.G.

    1973-12-25

    A process for separation and recovery of americium values from container or bomb'' reduction residues comprising dissolving the residues in a suitable acid, adjusting the hydrogen ion concentration to a desired level by adding a base, precipitating the americium as americium oxalate by adding oxalic acid, digesting the solution, separating the precipitate, and thereafter calcining the americium oxalate precipitate to form americium oxide. (Official Gazette)

  3. Characterisation of silica surfaces III: Characterisation of aerosil samples through ethanol adsorption and contact angle studies

    Directory of Open Access Journals (Sweden)

    M.S. Nadiye–Tabbiruka

    2009-12-01

    Full Text Available Aerosil samples, heat treated and then silylated with various silanes at various temperatures have been characterised by adsorption of ethanol at 293 K. Adsorption isotherms were plotted and the BET specific surface areas were determined. Contact angles were measured by the captive bubble method at the three phase contact line in ethanol, on glass slides similarly modified. Silylation was found to alter the ethanol adsorptive properties on aerosil and increase the contact angles on the glass slides to extents that depend on the silane used as well as the concentration of residual silanols and that of surface silyl groups.

  4. Highly reproducible and reliable metal/graphene contact by ultraviolet-ozone treatment

    Energy Technology Data Exchange (ETDEWEB)

    Li, Wei [Key Laboratory for the Physics and Chemistry of Nanodevices and Department of Electronics, Peking University, Beijing 100871 (China); Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States); Hacker, Christina A.; Cheng, Guangjun; Hight Walker, A. R.; Richter, Curt A.; Gundlach, David J., E-mail: david.gundlach@nist.gov, E-mail: liangxl@pku.edu.cn [Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States); Liang, Yiran; Tian, Boyuan; Liang, Xuelei, E-mail: david.gundlach@nist.gov, E-mail: liangxl@pku.edu.cn; Peng, Lianmao [Key Laboratory for the Physics and Chemistry of Nanodevices and Department of Electronics, Peking University, Beijing 100871 (China)

    2014-03-21

    Resist residue from the device fabrication process is a significant source of contamination at the metal/graphene contact interface. Ultraviolet Ozone (UVO) treatment is proven here, by X-ray photoelectron spectroscopy and Raman measurement, to be an effective way of cleaning the metal/graphene interface. Electrical measurements of devices that were fabricated by using UVO treatment of the metal/graphene contact region show that stable and reproducible low resistance metal/graphene contacts are obtained and the electrical properties of the graphene channel remain unaffected.

  5. Highly reproducible and reliable metal/graphene contact by ultraviolet-ozone treatment

    International Nuclear Information System (INIS)

    Li, Wei; Hacker, Christina A.; Cheng, Guangjun; Hight Walker, A. R.; Richter, Curt A.; Gundlach, David J.; Liang, Yiran; Tian, Boyuan; Liang, Xuelei; Peng, Lianmao

    2014-01-01

    Resist residue from the device fabrication process is a significant source of contamination at the metal/graphene contact interface. Ultraviolet Ozone (UVO) treatment is proven here, by X-ray photoelectron spectroscopy and Raman measurement, to be an effective way of cleaning the metal/graphene interface. Electrical measurements of devices that were fabricated by using UVO treatment of the metal/graphene contact region show that stable and reproducible low resistance metal/graphene contacts are obtained and the electrical properties of the graphene channel remain unaffected

  6. CONTACT LENS RELATED CORNEAL ULCER

    Directory of Open Access Journals (Sweden)

    AGARWAL P

    2010-01-01

    Full Text Available A corneal ulcer caused by infection is one of the major causes of blindness worldwide. One of the recent health concerns is the increasing incidence of corneal ulcers associated with contact lens user especially if the users fail to follow specific instruction in using their contact lenses. Risk factors associated with increased risk of contact lens related corneal ulcers are:overnight wear, long duration of continuous wear, lower socio-economic classes, smoking, dry eye and poor hygiene. The presenting symptoms of contact lens related corneal ulcers include eye discomfort, foreign body sensation and lacrimation. More serious symptoms are redness (especially circum-corneal injection, severe pain, photophobia, eye discharge and blurring of vision. The diagnosis is established by a thorough slit lamp microscopic examination with fluorescein staining and corneal scraping for Gram stain and culture of the infective organism. Delay in diagnosing and treatment can cause permanent blindness, therefore an early referral to ophthalmologist and commencing of antimicrobial therapy can prevent visual loss.

  7. Contact symmetries and Hamiltonian thermodynamics

    International Nuclear Information System (INIS)

    Bravetti, A.; Lopez-Monsalvo, C.S.; Nettel, F.

    2015-01-01

    It has been shown that contact geometry is the proper framework underlying classical thermodynamics and that thermodynamic fluctuations are captured by an additional metric structure related to Fisher’s Information Matrix. In this work we analyse several unaddressed aspects about the application of contact and metric geometry to thermodynamics. We consider here the Thermodynamic Phase Space and start by investigating the role of gauge transformations and Legendre symmetries for metric contact manifolds and their significance in thermodynamics. Then we present a novel mathematical characterization of first order phase transitions as equilibrium processes on the Thermodynamic Phase Space for which the Legendre symmetry is broken. Moreover, we use contact Hamiltonian dynamics to represent thermodynamic processes in a way that resembles the classical Hamiltonian formulation of conservative mechanics and we show that the relevant Hamiltonian coincides with the irreversible entropy production along thermodynamic processes. Therefore, we use such property to give a geometric definition of thermodynamically admissible fluctuations according to the Second Law of thermodynamics. Finally, we show that the length of a curve describing a thermodynamic process measures its entropy production

  8. An improved diagnostic contact lens.

    Science.gov (United States)

    Smith, R J

    1979-01-01

    Modification of a standard Goldmann goniolens by reducing the curvature of the contact surface to 8.5 mm radius of curvature (from the standard curvature of 7.4 mm) enabled gonioscopy to be carried out without the nuisance of air bubbles. Images PMID:465424

  9. Stellenbosch Papers in Linguistics: Contact

    African Journals Online (AJOL)

    Mailing Address. Editors SPiL. Department of General Linguistics University of Stellenbosch Private Bag X1 Matieland, 7602. Stellenbosch South Africa. Principal Contact. Dr Kate Huddlestone Journal Manager Department of General Linguistics. University of Stellenbosch. Private Bag X1. Matieland, 7602. Stellenbosch.

  10. Ohmic contacts to semiconducting diamond

    Science.gov (United States)

    Zeidler, James R.; Taylor, M. J.; Zeisse, Carl R.; Hewett, C. A.; Delahoussaye, Paul R.

    1990-10-01

    Work was carried out to improve the electron beam evaporation system in order to achieve better deposited films. The basic system is an ion pumped vacuum chamber, with a three-hearth, single-gun e-beam evaporator. Four improvements were made to the system. The system was thoroughly cleaned and new ion pump elements, an e-gun beam adjust unit, and a more accurate crystal monitor were installed. The system now has a base pressure of 3 X 10(exp -9) Torr, and can easily deposit high-melting-temperature metals such as Ta with an accurately controlled thickness. Improved shadow masks were also fabricated for better alignment and control of corner contacts for electrical transport measurements. Appendices include: A Thermally Activated Solid State Reaction Process for Fabricating Ohmic Contacts to Semiconducting Diamond; Tantalum Ohmic Contacts to Diamond by a Solid State Reaction Process; Metallization of Semiconducting Diamond: Mo, Mo/Au, and Mo/Ni/Au; Specific Contact Resistance Measurements of Ohmic Contracts to Diamond; and Electrical Activation of Boron Implanted into Diamond.

  11. Sandia National Laboratories: Contact Us

    Science.gov (United States)

    Employment (VOE) - New Mexico and California Please submit your requests by fax OR email - not both. Fax Number: (505) 845-0097, ATTN: HR Records Email Address: HR-Records@sandia.gov HR Records' Hotline: (505 in Writing Requester's Contact Information: Requester's name, company name (if applicable), phone

  12. Contact Hwersensitaity to Mustard Khal and Mustard Oil

    OpenAIRE

    J S Pasricha; Ramji Gupta; S K Gupta

    1985-01-01

    This report describes 2 females patients having contact dermatitis due to mustard khal the residue of,mustard seeds after the oil hasbeen extracted out. The dermatitis was caused by mbdng mustard khal with the cattle feed and was occurring on the hands and forearms, though the face, ear lobules and neck were also mvolved because of the practice of applying mustard oil on the hair. Patch tests were positive with the mustard khal and its fractionation products in both the patients and with must...

  13. Contact Hwersensitaity to Mustard Khal and Mustard Oil

    Directory of Open Access Journals (Sweden)

    J S Pasricha

    1985-01-01

    Full Text Available This report describes 2 females patients having contact dermatitis due to mustard khal the residue of,mustard seeds after the oil hasbeen extracted out. The dermatitis was caused by mbdng mustard khal with the cattle feed and was occurring on the hands and forearms, though the face, ear lobules and neck were also mvolved because of the practice of applying mustard oil on the hair. Patch tests were positive with the mustard khal and its fractionation products in both the patients and with mustard oil in one patient.

  14. Computational stress and damage modelling for rolling contact fatigue

    DEFF Research Database (Denmark)

    Cerullo, Michele

    Rolling contact fatigue in radial roller bearings is studied by means of a 2D plane strain nite element program. The Dang Van multiaxial fatigue criterion is firstly used, in a macroscopic study modeling the bearing raceway, to investigate the region where fatigue cracks are more likely to nucleate...... and of compressive residual stresses are also analyzed. The stress history of a material point at the depth where the maximum Dang Van damage factor is reached is then recorded and used in a subsequent micro-mechanical analysis. The stress history is applied as periodic boundary conditions in a representative volume...

  15. ConKit: a python interface to contact predictions.

    Science.gov (United States)

    Simkovic, Felix; Thomas, Jens M H; Rigden, Daniel J

    2017-07-15

    Recent advances in protein residue contact prediction algorithms have led to the emergence of many new methods and a variety of file formats. We present ConKit , an open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions. ConKit is available via the Python Package Index. The documentation can be found at http://www.conkit.org . ConKit is licensed under the BSD 3-Clause. hlfsimko@liverpool.ac.uk or drigden@liverpool.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  16. Conflicting selective forces affect T cell receptor contacts in an immunodominant human immunodeficiency virus epitope

    DEFF Research Database (Denmark)

    Iversen, Astrid K N; Stewart-Jones, Guillaume; Learn, Gerald H

    2006-01-01

    two principal, diametrically opposed evolutionary pathways that exclusively affect T cell-receptor contact residues. One pathway was characterized by acquisition of CTL escape mutations and the other by selection for wild-type amino acids. The pattern of CTL responses to epitope variants shaped which...

  17. Improving consensus contact prediction via server correlation reduction.

    Science.gov (United States)

    Gao, Xin; Bu, Dongbo; Xu, Jinbo; Li, Ming

    2009-05-06

    Protein inter-residue contacts play a crucial role in the determination and prediction of protein structures. Previous studies on contact prediction indicate that although template-based consensus methods outperform sequence-based methods on targets with typical templates, such consensus methods perform poorly on new fold targets. However, we find out that even for new fold targets, the models generated by threading programs can contain many true contacts. The challenge is how to identify them. In this paper, we develop an integer linear programming model for consensus contact prediction. In contrast to the simple majority voting method assuming that all the individual servers are equally important and independent, the newly developed method evaluates their correlation by using maximum likelihood estimation and extracts independent latent servers from them by using principal component analysis. An integer linear programming method is then applied to assign a weight to each latent server to maximize the difference between true contacts and false ones. The proposed method is tested on the CASP7 data set. If the top L/5 predicted contacts are evaluated where L is the protein size, the average accuracy is 73%, which is much higher than that of any previously reported study. Moreover, if only the 15 new fold CASP7 targets are considered, our method achieves an average accuracy of 37%, which is much better than that of the majority voting method, SVM-LOMETS, SVM-SEQ, and SAM-T06. These methods demonstrate an average accuracy of 13.0%, 10.8%, 25.8% and 21.2%, respectively. Reducing server correlation and optimally combining independent latent servers show a significant improvement over the traditional consensus methods. This approach can hopefully provide a powerful tool for protein structure refinement and prediction use.

  18. Improving consensus contact prediction via server correlation reduction

    Directory of Open Access Journals (Sweden)

    Xu Jinbo

    2009-05-01

    Full Text Available Abstract Background Protein inter-residue contacts play a crucial role in the determination and prediction of protein structures. Previous studies on contact prediction indicate that although template-based consensus methods outperform sequence-based methods on targets with typical templates, such consensus methods perform poorly on new fold targets. However, we find out that even for new fold targets, the models generated by threading programs can contain many true contacts. The challenge is how to identify them. Results In this paper, we develop an integer linear programming model for consensus contact prediction. In contrast to the simple majority voting method assuming that all the individual servers are equally important and independent, the newly developed method evaluates their correlation by using maximum likelihood estimation and extracts independent latent servers from them by using principal component analysis. An integer linear programming method is then applied to assign a weight to each latent server to maximize the difference between true contacts and false ones. The proposed method is tested on the CASP7 data set. If the top L/5 predicted contacts are evaluated where L is the protein size, the average accuracy is 73%, which is much higher than that of any previously reported study. Moreover, if only the 15 new fold CASP7 targets are considered, our method achieves an average accuracy of 37%, which is much better than that of the majority voting method, SVM-LOMETS, SVM-SEQ, and SAM-T06. These methods demonstrate an average accuracy of 13.0%, 10.8%, 25.8% and 21.2%, respectively. Conclusion Reducing server correlation and optimally combining independent latent servers show a significant improvement over the traditional consensus methods. This approach can hopefully provide a powerful tool for protein structure refinement and prediction use.

  19. Contact topical anesthesia for strabismus surgery in adult patients.

    Science.gov (United States)

    Vallés-Torres, J; García-Martín, E; Peña-Calvo, P; Sanjuan-Villarreal, A; Gil-Arribas, L M; Fernández-Tirado, F J

    2015-05-01

    To analyze the effectiveness and usefulness of contact topical anesthesia in strabismus surgery in adult patients. A prospective study was conducted on 20 patients undergoing strabismus surgery using contact topical anesthesia and sedation with remifentanil. The intensity of pain was recorded using a numeric pain rating scale at the time of anesthesia implementation, during the surgical procedure, 30 min afterwards, and during the first postoperative day. The incidence of oculocardiac reflex, postoperative nausea and vomiting, corneal ulcers, patient satisfaction (numerically from 0 to 10) and the degree of residual ocular deviation were also assessed. The operation was performed successfully in all patients. Average pain intensity was 1.40 ± 1.73 during anesthesia implementation, 4.20 ± 2.57 during the surgical procedure, 2.50 ± 2.54 30 min after surgery, and 3.55 ± 2.89 during the first postoperative day. Oculocardiac reflex was observed in 7 patients (35%), postoperative nausea and vomiting in 4 (20%), and corneal ulcer in 4 (20%). The patient satisfaction was 9.53 ± 2.51. More than two-thirds (70%) of patients had a residual ocular deviation less than 10 prism diopters. Contact topical anesthesia is a safe and effective alternative for strabismus surgery in adult patients. Contact topical anesthesia provides adequate pain control, lower incidence of postoperative nausea and vomiting and oculocardiac reflex, and optimal setting of ocular alignment. Copyright © 2014 Sociedad Española de Anestesiología, Reanimación y Terapéutica del Dolor. Publicado por Elsevier España, S.L.U. All rights reserved.

  20. Contact metallurgy optimization for ohmic contacts to InP

    DEFF Research Database (Denmark)

    Clausen, Thomas; Pedersen, Arne Skyggebjerg; Leistiko, Otto

    1991-01-01

    AuGeNi and AuZnNi metallizations to n- and p-InP were studied as a function of the annealing temperature in a Rapid Thermal Annealing (RTA) system. For n-InP (S:8×1018cm-3) a broad minimum existed from 385°C to 500°C, in which the specific contact resistance, rc, was about 10-7 ¿cm2. The lowe...