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Sample records for fold recognition problem

  1. Building multiclass classifiers for remote homology detection and fold recognition

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    Karypis George

    2006-10-01

    Full Text Available Abstract Background Protein remote homology detection and fold recognition are central problems in computational biology. Supervised learning algorithms based on support vector machines are currently one of the most effective methods for solving these problems. These methods are primarily used to solve binary classification problems and they have not been extensively used to solve the more general multiclass remote homology prediction and fold recognition problems. Results We present a comprehensive evaluation of a number of methods for building SVM-based multiclass classification schemes in the context of the SCOP protein classification. These methods include schemes that directly build an SVM-based multiclass model, schemes that employ a second-level learning approach to combine the predictions generated by a set of binary SVM-based classifiers, and schemes that build and combine binary classifiers for various levels of the SCOP hierarchy beyond those defining the target classes. Conclusion Analyzing the performance achieved by the different approaches on four different datasets we show that most of the proposed multiclass SVM-based classification approaches are quite effective in solving the remote homology prediction and fold recognition problems and that the schemes that use predictions from binary models constructed for ancestral categories within the SCOP hierarchy tend to not only lead to lower error rates but also reduce the number of errors in which a superfamily is assigned to an entirely different fold and a fold is predicted as being from a different SCOP class. Our results also show that the limited size of the training data makes it hard to learn complex second-level models, and that models of moderate complexity lead to consistently better results.

  2. Protein fold recognition using geometric kernel data fusion.

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    Zakeri, Pooya; Jeuris, Ben; Vandebril, Raf; Moreau, Yves

    2014-07-01

    Various approaches based on features extracted from protein sequences and often machine learning methods have been used in the prediction of protein folds. Finding an efficient technique for integrating these different protein features has received increasing attention. In particular, kernel methods are an interesting class of techniques for integrating heterogeneous data. Various methods have been proposed to fuse multiple kernels. Most techniques for multiple kernel learning focus on learning a convex linear combination of base kernels. In addition to the limitation of linear combinations, working with such approaches could cause a loss of potentially useful information. We design several techniques to combine kernel matrices by taking more involved, geometry inspired means of these matrices instead of convex linear combinations. We consider various sequence-based protein features including information extracted directly from position-specific scoring matrices and local sequence alignment. We evaluate our methods for classification on the SCOP PDB-40D benchmark dataset for protein fold recognition. The best overall accuracy on the protein fold recognition test set obtained by our methods is ∼ 86.7%. This is an improvement over the results of the best existing approach. Moreover, our computational model has been developed by incorporating the functional domain composition of proteins through a hybridization model. It is observed that by using our proposed hybridization model, the protein fold recognition accuracy is further improved to 89.30%. Furthermore, we investigate the performance of our approach on the protein remote homology detection problem by fusing multiple string kernels. The MATLAB code used for our proposed geometric kernel fusion frameworks are publicly available at http://people.cs.kuleuven.be/∼raf.vandebril/homepage/software/geomean.php?menu=5/. © The Author 2014. Published by Oxford University Press.

  3. A weighted string kernel for protein fold recognition.

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    Nojoomi, Saghi; Koehl, Patrice

    2017-08-25

    Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done before those methods provide reliable fold recognition for proteins whose sequences share little similarity. We have recently proposed an alignment-free method based on the concept of string kernels, SeqKernel (Nojoomi and Koehl, BMC Bioinformatics, 2017, 18:137). In this previous study, we have shown that while Seqkernel performs better than standard alignment-based methods, its applications are potentially limited, because of biases due mostly to sequence length effects. In this study, we propose improvements to SeqKernel that follows two directions. First, we developed a weighted version of the kernel, WSeqKernel. Second, we expand the concept of string kernels into a novel framework for deriving information on amino acids from protein sequences. Using a dataset that only contains remote homologs, we have shown that WSeqKernel performs remarkably well in fold recognition experiments. We have shown that with the appropriate weighting scheme, we can remove the length effects on the kernel values. WSeqKernel, just like any alignment-based sequence comparison method, depends on a substitution matrix. We have shown that this matrix can be optimized so that sequence similarity scores correlate well with structure similarity scores. Starting from no information on amino acid similarity, we have shown that we can derive a scoring matrix that echoes the physico-chemical properties of amino acids. We have made progress in characterizing and parametrizing string kernels as alignment-based methods for comparing protein sequences, and we have shown that they provide a framework for extracting sequence information from structure.

  4. A new tool for protein fold recognition: A Bayesian heuristic threading algorithm.

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    Crawford, O.

    1997-10-01

    This paper presents a new threading algorithm, designed to be used in protein fold recognition. Its purpose is to contribute toward the goal of predicting three-dimensional structures of proteins from knowledge of their amino-acid sequences alone. Sequences for new proteins are being discovered at a rapid rate, as a result of the Human Genome Project, and related genome research. Understanding of protein folding, and especially the ability to predict the 3D fold from the sequence, is crucial to the understanding of the function of these new proteins. This is considered by many to be the most important problem in contemporary molecular biology. Numerical tests of the speed and reliability of the algorithm are described, along with comparisons with two popular threading algorithms. For the systems examined, the new method constitutes a significant improvement.

  5. Protein-fold recognition using an improved single-source K diverse shortest paths algorithm.

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    Lhota, John; Xie, Lei

    2016-04-01

    Protein structure prediction, when construed as a fold recognition problem, is one of the most important applications of similarity search in bioinformatics. A new protein-fold recognition method is reported which combines a single-source K diverse shortest path (SSKDSP) algorithm with Enrichment of Network Topological Similarity (ENTS) algorithm to search a graphic feature space generated using sequence similarity and structural similarity metrics. A modified, more efficient SSKDSP algorithm is developed to improve the performance of graph searching. The new implementation of the SSKDSP algorithm empirically requires 82% less memory and 61% less time than the current implementation, allowing for the analysis of larger, denser graphs. Furthermore, the statistical significance of fold ranking generated from SSKDSP is assessed using ENTS. The reported ENTS-SSKDSP algorithm outperforms original ENTS that uses random walk with restart for the graph search as well as other state-of-the-art protein structure prediction algorithms HHSearch and Sparks-X, as evaluated by a benchmark of 600 query proteins. The reported methods may easily be extended to other similarity search problems in bioinformatics and chemoinformatics. The SSKDSP software is available at http://compsci.hunter.cuny.edu/~leixie/sskdsp.html. © 2016 Wiley Periodicals, Inc.

  6. A 9-state hidden Markov model using protein secondary structure information for protein fold recognition.

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    Lee, Sun Young; Lee, Jong Yun; Jung, Kwang Su; Ryu, Keun Ho

    2009-06-01

    In protein fold recognition, the main disadvantage of hidden Markov models (HMMs) is the employment of large-scale model architectures which require large data sets and high computational resources for training. Also, HMMs must consider sequential information about secondary structures of proteins, to improve prediction performance and reduce model parameters. Therefore, we propose a novel method for protein fold recognition based on a hidden Markov model, called a 9-state HMM. The method can (i) reduce the number of states using secondary structure information about proteins for each fold and (ii) recognize protein folds more accurately than other HMMs.

  7. Combining classifiers generated by multi-gene genetic programming for protein fold recognition using genetic algorithm.

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    Bardsiri, Mahshid Khatibi; Eftekhari, Mahdi; Mousavi, Reza

    2015-01-01

    In this study the problem of protein fold recognition, that is a classification task, is solved via a hybrid of evolutionary algorithms namely multi-gene Genetic Programming (GP) and Genetic Algorithm (GA). Our proposed method consists of two main stages and is performed on three datasets taken from the literature. Each dataset contains different feature groups and classes. In the first step, multi-gene GP is used for producing binary classifiers based on various feature groups for each class. Then, different classifiers obtained for each class are combined via weighted voting so that the weights are determined through GA. At the end of the first step, there is a separate binary classifier for each class. In the second stage, the obtained binary classifiers are combined via GA weighting in order to generate the overall classifier. The final obtained classifier is superior to the previous works found in the literature in terms of classification accuracy.

  8. Effective inter-residue contact definitions for accurate protein fold recognition

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    Yuan Chao

    2012-11-01

    Full Text Available Abstract Background Effective encoding of residue contact information is crucial for protein structure prediction since it has a unique role to capture long-range residue interactions compared to other commonly used scoring terms. The residue contact information can be incorporated in structure prediction in several different ways: It can be incorporated as statistical potentials or it can be also used as constraints in ab initio structure prediction. To seek the most effective definition of residue contacts for template-based protein structure prediction, we evaluated 45 different contact definitions, varying bases of contacts and distance cutoffs, in terms of their ability to identify proteins of the same fold. Results We found that overall the residue contact pattern can distinguish protein folds best when contacts are defined for residue pairs whose Cβ atoms are at 7.0 Å or closer to each other. Lower fold recognition accuracy was observed when inaccurate threading alignments were used to identify common residue contacts between protein pairs. In the case of threading, alignment accuracy strongly influences the fraction of common contacts identified among proteins of the same fold, which eventually affects the fold recognition accuracy. The largest deterioration of the fold recognition was observed for β-class proteins when the threading methods were used because the average alignment accuracy was worst for this fold class. When results of fold recognition were examined for individual proteins, we found that the effective contact definition depends on the fold of the proteins. A larger distance cutoff is often advantageous for capturing spatial arrangement of the secondary structures which are not physically in contact. For capturing contacts between neighboring β strands, considering the distance between Cα atoms is better than the Cβ−based distance because the side-chain of interacting residues on β strands sometimes point to

  9. Very low resolution face recognition problem.

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    Zou, Wilman W W; Yuen, Pong C

    2012-01-01

    This paper addresses the very low resolution (VLR) problem in face recognition in which the resolution of the face image to be recognized is lower than 16 × 16. With the increasing demand of surveillance camera-based applications, the VLR problem happens in many face application systems. Existing face recognition algorithms are not able to give satisfactory performance on the VLR face image. While face super-resolution (SR) methods can be employed to enhance the resolution of the images, the existing learning-based face SR methods do not perform well on such a VLR face image. To overcome this problem, this paper proposes a novel approach to learn the relationship between the high-resolution image space and the VLR image space for face SR. Based on this new approach, two constraints, namely, new data and discriminative constraints, are designed for good visuality and face recognition applications under the VLR problem, respectively. Experimental results show that the proposed SR algorithm based on relationship learning outperforms the existing algorithms in public face databases.

  10. Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection

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    Lee Soo-Young

    2008-07-01

    Full Text Available Abstract Background Nonnegative matrix factorization (NMF is a feature extraction method that has the property of intuitive part-based representation of the original features. This unique ability makes NMF a potentially promising method for biological sequence analysis. Here, we apply NMF to fold recognition and remote homolog detection problems. Recent studies have shown that combining support vector machines (SVM with profile-profile alignments improves performance of fold recognition and remote homolog detection remarkably. However, it is not clear which parts of sequences are essential for the performance improvement. Results The performance of fold recognition and remote homolog detection using NMF features is compared to that of the unmodified profile-profile alignment (PPA features by estimating Receiver Operating Characteristic (ROC scores. The overall performance is noticeably improved. For fold recognition at the fold level, SVM with NMF features recognize 30% of homolog proteins at > 0.99 ROC scores, while original PPA feature, HHsearch, and PSI-BLAST recognize almost none. For detecting remote homologs that are related at the superfamily level, NMF features also achieve higher performance than the original PPA features. At > 0.90 ROC50 scores, 25% of proteins with NMF features correctly detects remotely related proteins, whereas using original PPA features only 1% of proteins detect remote homologs. In addition, we investigate the effect of number of positive training examples and the number of basis vectors on performance improvement. We also analyze the ability of NMF to extract essential features by comparing NMF basis vectors with functionally important sites and structurally conserved regions of proteins. The results show that NMF basis vectors have significant overlap with functional sites from PROSITE and with structurally conserved regions from the multiple structural alignments generated by MUSTANG. The correlation between

  11. Chaotic Multiquenching Annealing Applied to the Protein Folding Problem

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    Juan Frausto-Solis

    2014-01-01

    Full Text Available The Chaotic Multiquenching Annealing algorithm (CMQA is proposed. CMQA is a new algorithm, which is applied to protein folding problem (PFP. This algorithm is divided into three phases: (i multiquenching phase (MQP, (ii annealing phase (AP, and (iii dynamical equilibrium phase (DEP. MQP enforces several stages of quick quenching processes that include chaotic functions. The chaotic functions can increase the exploration potential of solutions space of PFP. AP phase implements a simulated annealing algorithm (SA with an exponential cooling function. MQP and AP are delimited by different ranges of temperatures; MQP is applied for a range of temperatures which goes from extremely high values to very high values; AP searches for solutions in a range of temperatures from high values to extremely low values. DEP phase finds the equilibrium in a dynamic way by applying least squares method. CMQA is tested with several instances of PFP.

  12. Remote protein homology detection and fold recognition using two-layer support vector machine classifiers.

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    Muda, Hilmi M; Saad, Puteh; Othman, Razib M

    2011-08-01

    Remote protein homology detection and fold recognition refer to detection of structural homology in proteins where there are small or no similarities in the sequence. To detect protein structural classes from protein primary sequence information, homology-based methods have been developed, which can be divided to three types: discriminative classifiers, generative models for protein families and pairwise sequence comparisons. Support Vector Machines (SVM) and Neural Networks (NN) are two popular discriminative methods. Recent studies have shown that SVM has fast speed during training, more accurate and efficient compared to NN. We present a comprehensive method based on two-layer classifiers. The 1st layer is used to detect up to superfamily and family in SCOP hierarchy using optimized binary SVM classification rules. It used the kernel function known as the Bio-kernel, which incorporates the biological information in the classification process. The 2nd layer uses discriminative SVM algorithm with string kernel that will detect up to protein fold level in SCOP hierarchy. The results obtained were evaluated using mean ROC and mean MRFP and the significance of the result produced with pairwise t-test was tested. Experimental results show that our approaches significantly improve the performance of remote protein homology detection and fold recognition for all three different version SCOP datasets (1.53, 1.67 and 1.73). We achieved 4.19% improvements in term of mean ROC in SCOP 1.53, 4.75% in SCOP 1.67 and 4.03% in SCOP 1.73 datasets when compared to the result produced by well-known methods. The combination of first layer and second layer of BioSVM-2L performs well in remote homology detection and fold recognition even in three different versions of datasets. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis.

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    Liu, Bin; Wang, Xiaolong; Lin, Lei; Dong, Qiwen; Wang, Xuan

    2008-12-01

    Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate methods for solving these problems. A key step to improve the performance of the SVM-based methods is to find a suitable representation of protein sequences. In this paper, a novel building block of proteins called Top-n-grams is presented, which contains the evolutionary information extracted from the protein sequence frequency profiles. The protein sequence frequency profiles are calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into Top-n-grams. The protein sequences are transformed into fixed-dimension feature vectors by the occurrence times of each Top-n-gram. The training vectors are evaluated by SVM to train classifiers which are then used to classify the test protein sequences. We demonstrate that the prediction performance of remote homology detection and fold recognition can be improved by combining Top-n-grams and latent semantic analysis (LSA), which is an efficient feature extraction technique from natural language processing. When tested on superfamily and fold benchmarks, the method combining Top-n-grams and LSA gives significantly better results compared to related methods. The method based on Top-n-grams significantly outperforms the methods based on many other building blocks including N-grams, patterns, motifs and binary profiles. Therefore, Top-n-gram is a good building block of the protein sequences and can be widely used in many tasks of the computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the prediction of protein binding sites.

  14. Improving protein fold recognition and structural class prediction accuracies using physicochemical properties of amino acids.

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    Raicar, Gaurav; Saini, Harsh; Dehzangi, Abdollah; Lal, Sunil; Sharma, Alok

    2016-08-07

    Predicting the three-dimensional (3-D) structure of a protein is an important task in the field of bioinformatics and biological sciences. However, directly predicting the 3-D structure from the primary structure is hard to achieve. Therefore, predicting the fold or structural class of a protein sequence is generally used as an intermediate step in determining the protein's 3-D structure. For protein fold recognition (PFR) and structural class prediction (SCP), two steps are required - feature extraction step and classification step. Feature extraction techniques generally utilize syntactical-based information, evolutionary-based information and physicochemical-based information to extract features. In this study, we explore the importance of utilizing the physicochemical properties of amino acids for improving PFR and SCP accuracies. For this, we propose a Forward Consecutive Search (FCS) scheme which aims to strategically select physicochemical attributes that will supplement the existing feature extraction techniques for PFR and SCP. An exhaustive search is conducted on all the existing 544 physicochemical attributes using the proposed FCS scheme and a subset of physicochemical attributes is identified. Features extracted from these selected attributes are then combined with existing syntactical-based and evolutionary-based features, to show an improvement in the recognition and prediction performance on benchmark datasets. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

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    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.

  16. Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution.

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    Haller, Andrea; Altman, Roger B; Soulière, Marie F; Blanchard, Scott C; Micura, Ronald

    2013-03-12

    Thiamine pyrophosphate (TPP)-sensitive mRNA domains are the most prevalent riboswitches known. Despite intensive investigation, the complex ligand recognition and concomitant folding processes in the TPP riboswitch that culminate in the regulation of gene expression remain elusive. Here, we used single-molecule fluorescence resonance energy transfer imaging to probe the folding landscape of the TPP aptamer domain in the absence and presence of magnesium and TPP. To do so, distinct labeling patterns were used to sense the dynamics of the switch helix (P1) and the two sensor arms (P2/P3 and P4/P5) of the aptamer domain. The latter structural elements make interdomain tertiary contacts (L5/P3) that span a region immediately adjacent to the ligand-binding site. In each instance, conformational dynamics of the TPP riboswitch were influenced by ligand binding. The P1 switch helix, formed by the 5' and 3' ends of the aptamer domain, adopts a predominantly folded structure in the presence of Mg(2+) alone. However, even at saturating concentrations of Mg(2+) and TPP, the P1 helix, as well as distal regions surrounding the TPP-binding site, exhibit an unexpected degree of residual dynamics and disperse kinetic behaviors. Such plasticity results in a persistent exchange of the P3/P5 forearms between open and closed configurations that is likely to facilitate entry and exit of the TPP ligand. Correspondingly, we posit that such features of the TPP aptamer domain contribute directly to the mechanism of riboswitch-mediated translational regulation.

  17. A feature extraction technique using bi-gram probabilities of position specific scoring matrix for protein fold recognition.

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    Sharma, Alok; Lyons, James; Dehzangi, Abdollah; Paliwal, Kuldip K

    2013-03-07

    Discovering a three dimensional structure of a protein is a challenging task in biological science. Classifying a protein into one of its folds is an intermediate step for deciphering the three dimensional protein structure. The protein fold recognition can be done by developing feature extraction techniques to accurately extract all the relevant information from a protein sequence and then by employing a suitable classifier to label an unknown protein. Several feature extraction techniques have been developed in the past but with limited recognition accuracy only. In this work, we have developed a feature extraction technique which is based on bi-grams computed directly from Position Specific Scoring Matrices and demonstrated its effectiveness on a benchmark dataset. The proposed technique exhibits an absolute improvement of around 10% compared with existing feature extraction techniques. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. A tri-gram based feature extraction technique using linear probabilities of position specific scoring matrix for protein fold recognition.

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    Paliwal, Kuldip K; Sharma, Alok; Lyons, James; Dehzangi, Abdollah

    2014-03-01

    In biological sciences, the deciphering of a three dimensional structure of a protein sequence is considered to be an important and challenging task. The identification of protein folds from primary protein sequences is an intermediate step in discovering the three dimensional structure of a protein. This can be done by utilizing feature extraction technique to accurately extract all the relevant information followed by employing a suitable classifier to label an unknown protein. In the past, several feature extraction techniques have been developed but with limited recognition accuracy only. In this study, we have developed a feature extraction technique based on tri-grams computed directly from Position Specific Scoring Matrices. The effectiveness of the feature extraction technique has been shown on two benchmark datasets. The proposed technique exhibits up to 4.4% improvement in protein fold recognition accuracy compared to the state-of-the-art feature extraction techniques.

  19. An inverse problem approach to pattern recognition in industry

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    Ali Sever

    2015-01-01

    Full Text Available Many works have shown strong connections between learning and regularization techniques for ill-posed inverse problems. A careful analysis shows that a rigorous connection between learning and regularization for inverse problem is not straightforward. In this study, pattern recognition will be viewed as an ill-posed inverse problem and applications of methods from the theory of inverse problems to pattern recognition are studied. A new learning algorithm derived from a well-known regularization model is generated and applied to the task of reconstruction of an inhomogeneous object as pattern recognition. Particularly, it is demonstrated that pattern recognition can be reformulated in terms of inverse problems defined by a Riesz-type kernel. This reformulation can be employed to design a learning algorithm based on a numerical solution of a system of linear equations. Finally, numerical experiments have been carried out with synthetic experimental data considering a reasonable level of noise. Good recoveries have been achieved with this methodology, and the results of these simulations are compatible with the existing methods. The comparison results show that the Regularization-based learning algorithm (RBA obtains a promising performance on the majority of the test problems. In prospects, this method can be used for the creation of automated systems for diagnostics, testing, and control in various fields of scientific and applied research, as well as in industry.

  20. Some problems of geologic relations between the Amazon craton and east margins fold belts

    International Nuclear Information System (INIS)

    Almeida, F.F.M. de

    1986-01-01

    This paper deals with some geologic problems related to the limits between the Amazon craton and the fold belts developed at its margins during the Precambrian. These limits are diversified but clearly recognized. To the north, the Araguaia-Tocantins fold belt, of presumed Middle Proterozoic age, is separated from the cratonic block by a deep marginal fracture zone permeated by mafic and ultramafic rocks. The geologic, magmatic and aeromagnetic characteristics of this zone point out the presence of deep faults, supposed to be of Middle Proterozoic age. The southern Paraguay fold belt constitutes and accurated zone of linear structures supposed to be of Late Proterozoic development. Despite the great increase of knowledge during the last ten years many tectonic, stratigraphic and geochronologic problems remain unsolved. The aim of this paper is to point out some of these problems and suggest specific studies to solve them. (author)

  1. Control and Alcohol-Problem Recognition among College Students

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    Simons, Raluca M.; Hahn, Austin M.; Simons, Jeffrey S.; Gaster, Sam

    2015-01-01

    Objective: This study examined negative control (ie, perceived lack of control over life outcomes) and need for control as predictors of alcohol-problem recognition, evaluations (good/bad), and expectancies (likely/unlikely) among college students. The study also explored the interaction between the need for control and alcohol consumption in…

  2. A hybrid approach to protein folding problem integrating constraint programming with local search.

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    Ullah, Abu Dayem; Steinhöfel, Kathleen

    2010-01-18

    The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the computational hardness of this optimization problem. Heuristic search algorithms and constraint programming are two common techniques to approach this problem. The present study introduces a novel hybrid approach to simulate the protein folding problem using constraint programming technique integrated within local search. Using the face-centered-cubic lattice model and 20 amino acid pairwise interactions energy function for the protein folding problem, a constraint programming technique has been applied to generate the neighbourhood conformations that are to be used in generic local search procedure. Experiments have been conducted for a few small and medium sized proteins. Results have been compared with both pure constraint programming approach and local search using well-established local move set. Substantial improvements have been observed in terms of final energy values within acceptable runtime using the hybrid approach. Constraint programming approaches usually provide optimal results but become slow as the problem size grows. Local search approaches are usually faster but do not guarantee optimal solutions and tend to stuck in local minima. The encouraging results obtained on the small proteins show that these two approaches can be combined efficiently to obtain better quality solutions within acceptable time. It also encourages future researchers on adopting hybrid techniques to solve other hard optimization problems.

  3. The RNA folding problem: a variational problem within an adiabatic approximation.

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    Fernández, A; Niel, B; Burastero, T

    1998-08-24

    Biopolymer folding is an expeditious process taking place within timescales incommensurably shorter than ergodic times. Furthermore, its robustness suggests that the process must depend on a relatively coarse level of resolution of conformation space. To account for these features while focusing on the RNA context, we derive a variational principle formulated within an adiabatic approximation obtained by integrating out fast-relaxing molecular motions. Folding pathways are generated by means of a stochastic process which begets a least effort principle reflecting a stepwise minimization of the conformational entropy cost for each folding event with concurrent maximization of the base pairing. This economy of the process is found to have kinetic consequences if we treat base-pairing contact patterns (BPPs) adiabatically, that is, as quasi-equilibrium states: the probability distribution of overall folding timespans associated to the process resolved at the BPP level is maximized at the brachistochrone or overall least-time pathway for functionally-competent RNAs. In turn, this pathway is shown to yield all the phylogenetically-conserved structural features of the active conformation within biologically-relevant timescales.

  4. Thermodynamics of model prions and its implications for the problem of prion protein folding.

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    Harrison, P M; Chan, H S; Prusiner, S B; Cohen, F E

    1999-02-19

    Prion disease is caused by the propagation of a particle containing PrPSc, a misfolded form of the normal cellular prion protein (PrPC). PrPC can re-fold to form PrPSc with loss of alpha-helical structure and formation of extensive beta-sheet structure. Here, we model this prion folding problem with a simple, low-resolution lattice model of protein folding. If model proteins are allowed to re-fold upon dimerization, a minor proportion of them (up to approximately 17%) encrypts an alternative native state as a homodimer. The structures in this homodimeric native state re-arrange so that they are very different in conformation from the monomeric native state. We find that model proteins that are relatively less stable as monomers are more susceptible to the formation of alternative native states as homodimers. These results suggest that less-stable proteins have a greater need for a well-designed energy landscape for protein folding to overcome an increased chance of encrypting substantially different native conformations stabilized by multimeric interactions. This conceptual framework for aberrant folding should be relevant in Alzheimer's disease and other disorders associated with protein aggregation. Copyright 1999 Academic Press.

  5. Wrong capital? Problems with recognition of knowledge presented by non-native students in international education

    DEFF Research Database (Denmark)

    Wilken, Lisanne

    This paper presents research on problems of knowledge recognition among students of various nationalities at an international organisation......This paper presents research on problems of knowledge recognition among students of various nationalities at an international organisation...

  6. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

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    Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

    2011-07-01

    The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

  7. Multiphase Simulated Annealing Based on Boltzmann and Bose-Einstein Distribution Applied to Protein Folding Problem.

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    Frausto-Solis, Juan; Liñán-García, Ernesto; Sánchez-Hernández, Juan Paulo; González-Barbosa, J Javier; González-Flores, Carlos; Castilla-Valdez, Guadalupe

    2016-01-01

    A new hybrid Multiphase Simulated Annealing Algorithm using Boltzmann and Bose-Einstein distributions (MPSABBE) is proposed. MPSABBE was designed for solving the Protein Folding Problem (PFP) instances. This new approach has four phases: (i) Multiquenching Phase (MQP), (ii) Boltzmann Annealing Phase (BAP), (iii) Bose-Einstein Annealing Phase (BEAP), and (iv) Dynamical Equilibrium Phase (DEP). BAP and BEAP are simulated annealing searching procedures based on Boltzmann and Bose-Einstein distributions, respectively. DEP is also a simulated annealing search procedure, which is applied at the final temperature of the fourth phase, which can be seen as a second Bose-Einstein phase. MQP is a search process that ranges from extremely high to high temperatures, applying a very fast cooling process, and is not very restrictive to accept new solutions. However, BAP and BEAP range from high to low and from low to very low temperatures, respectively. They are more restrictive for accepting new solutions. DEP uses a particular heuristic to detect the stochastic equilibrium by applying a least squares method during its execution. MPSABBE parameters are tuned with an analytical method, which considers the maximal and minimal deterioration of problem instances. MPSABBE was tested with several instances of PFP, showing that the use of both distributions is better than using only the Boltzmann distribution on the classical SA.

  8. Multiphase Simulated Annealing Based on Boltzmann and Bose-Einstein Distribution Applied to Protein Folding Problem

    Directory of Open Access Journals (Sweden)

    Juan Frausto-Solis

    2016-01-01

    Full Text Available A new hybrid Multiphase Simulated Annealing Algorithm using Boltzmann and Bose-Einstein distributions (MPSABBE is proposed. MPSABBE was designed for solving the Protein Folding Problem (PFP instances. This new approach has four phases: (i Multiquenching Phase (MQP, (ii Boltzmann Annealing Phase (BAP, (iii Bose-Einstein Annealing Phase (BEAP, and (iv Dynamical Equilibrium Phase (DEP. BAP and BEAP are simulated annealing searching procedures based on Boltzmann and Bose-Einstein distributions, respectively. DEP is also a simulated annealing search procedure, which is applied at the final temperature of the fourth phase, which can be seen as a second Bose-Einstein phase. MQP is a search process that ranges from extremely high to high temperatures, applying a very fast cooling process, and is not very restrictive to accept new solutions. However, BAP and BEAP range from high to low and from low to very low temperatures, respectively. They are more restrictive for accepting new solutions. DEP uses a particular heuristic to detect the stochastic equilibrium by applying a least squares method during its execution. MPSABBE parameters are tuned with an analytical method, which considers the maximal and minimal deterioration of problem instances. MPSABBE was tested with several instances of PFP, showing that the use of both distributions is better than using only the Boltzmann distribution on the classical SA.

  9. Conduct Symptoms and Emotion Recognition in Adolescent Boys with Externalization Problems

    Directory of Open Access Journals (Sweden)

    Nikoletta Aspan

    2013-01-01

    Full Text Available Background. In adults with antisocial personality disorder, marked alterations in the recognition of facial affect were described. Less consistent data are available on the emotion recognition in adolescents with externalization problems. The aim of the present study was to assess the relation between the recognition of emotions and conduct symptoms in adolescent boys with externalization problems. Methods. Adolescent boys with externalization problems referred to Vadaskert Child Psychiatry Hospital participated in the study after informed consent (N=114, 11–17 years, mean = 13.4. The conduct problems scale of the strengths and difficulties questionnaire (parent and self-report was used. The performance in a facial emotion recognition test was assessed. Results. Conduct problems score (parent and self-report was inversely correlated with the overall emotion recognition. In the self-report, conduct problems score was inversely correlated with the recognition of anger, fear, and sadness. Adolescents with high conduct problems scores were significantly worse in the recognition of fear, sadness, and overall recognition than adolescents with low conduct scores, irrespective of age and IQ. Conclusions. Our results suggest that impaired emotion recognition is dimensionally related to conduct problems and might have importance in the development of antisocial behavior.

  10. Conduct symptoms and emotion recognition in adolescent boys with externalization problems.

    Science.gov (United States)

    Aspan, Nikoletta; Vida, Peter; Gadoros, Julia; Halasz, Jozsef

    2013-01-01

    In adults with antisocial personality disorder, marked alterations in the recognition of facial affect were described. Less consistent data are available on the emotion recognition in adolescents with externalization problems. The aim of the present study was to assess the relation between the recognition of emotions and conduct symptoms in adolescent boys with externalization problems. Adolescent boys with externalization problems referred to Vadaskert Child Psychiatry Hospital participated in the study after informed consent (N = 114, 11-17 years, mean = 13.4). The conduct problems scale of the strengths and difficulties questionnaire (parent and self-report) was used. The performance in a facial emotion recognition test was assessed. Conduct problems score (parent and self-report) was inversely correlated with the overall emotion recognition. In the self-report, conduct problems score was inversely correlated with the recognition of anger, fear, and sadness. Adolescents with high conduct problems scores were significantly worse in the recognition of fear, sadness, and overall recognition than adolescents with low conduct scores, irrespective of age and IQ. Our results suggest that impaired emotion recognition is dimensionally related to conduct problems and might have importance in the development of antisocial behavior.

  11. Extreme Folding

    Science.gov (United States)

    Demaine, Erik

    2012-02-01

    Our understanding of the mathematics and algorithms behind paper folding, and geometric folding in general, has increased dramatically over the past several years. These developments have found a surprisingly broad range of applications. In the art of origami, it has helped spur the technical origami revolution. In engineering and science, it has helped solve problems in areas such as manufacturing, robotics, graphics, and protein folding. On the recreational side, it has led to new kinds of folding puzzles and magic. I will give an overview of the mathematics and algorithms of folding, with a focus on new mathematics and sculpture.

  12. F-Type Lectins: A Highly Diversified Family of Fucose-Binding Proteins with a Unique Sequence Motif and Structural Fold, Involved in Self/Non-Self-Recognition

    Directory of Open Access Journals (Sweden)

    Gerardo R. Vasta

    2017-11-01

    Full Text Available The F-type lectin (FTL family is one of the most recent to be identified and structurally characterized. Members of the FTL family are characterized by a fucose recognition domain [F-type lectin domain (FTLD] that displays a novel jellyroll fold (“F-type” fold and unique carbohydrate- and calcium-binding sequence motifs. This novel lectin family comprises widely distributed proteins exhibiting single, double, or greater multiples of the FTLD, either tandemly arrayed or combined with other structurally and functionally distinct domains, yielding lectin subunits of pleiotropic properties even within a single species. Furthermore, the extraordinary variability of FTL sequences (isoforms that are expressed in a single individual has revealed genetic mechanisms of diversification in ligand recognition that are unique to FTLs. Functions of FTLs in self/non-self-recognition include innate immunity, fertilization, microbial adhesion, and pathogenesis, among others. In addition, although the F-type fold is distinctive for FTLs, a structure-based search revealed apparently unrelated proteins with minor sequence similarity to FTLs that displayed the FTLD fold. In general, the phylogenetic analysis of FTLD sequences from viruses to mammals reveals clades that are consistent with the currently accepted taxonomy of extant species. However, the surprisingly discontinuous distribution of FTLDs within each taxonomic category suggests not only an extensive structural/functional diversification of the FTLs along evolutionary lineages but also that this intriguing lectin family has been subject to frequent gene duplication, secondary loss, lateral transfer, and functional co-option.

  13. Pattern recognition in the satellite temperature retrieval problem

    Science.gov (United States)

    Thompson, O. E.; Goldberg, M. D.; Dazlich, D. A.

    1985-01-01

    Pattern recognition procedures have been developed in order to improve the first-guess fields for satellite temperature retrievals. The first procedure is used to select one or more historical radiosonde temperature profiles as analog estimates of ambient thermal structure. The second procedure is used to organize a priori data into shape-coherent pattern libraries using structural information inherent in the data itself. On the basis of independent tests of about 800 temperature retrievals, it was found that: (1) the pattern recognition techniques reduced first-guess profile errors by nearly 50 percent in comparison with traditional partitioning schemes; and (2) with regression and physical-iterative retrieval algorithms, however, the effect of pattern recognition on temperature retrieval error was insignificant. Analysis of individual retrieval errors showed that poor retrievals may outweigh the potential benefits of both pattern recognition techniques.

  14. A Computational Approach to Studying Protein Folding Problems Considering the Crucial Role of the Intracellular Environment.

    Science.gov (United States)

    González-Pérez, Pedro P; Orta, Daniel J; Peña, Irving; Flores, Eduardo C; Ramírez, José U; Beltrán, Hiram I; Alas, Salomón J

    2017-10-01

    Intracellular protein folding (PF) is performed in a highly inhomogeneous, crowded, and correlated environment. Due to this inherent complexity, the study and understanding of PF phenomena is a fundamental issue in the field of computational systems biology. In particular, it is important to use a modeled medium that accurately reflects PF in natural systems. In the current study, we present a simulation wherein PF is carried out within an inhomogeneous modeled medium. Simulation resources included a two-dimensional hydrophobic-polar (HP) model, evolutionary algorithms, and the dual site-bond model. The dual site-bond model was used to develop an environment where HP beads could be folded. Our modeled medium included correlation lengths and fractal-like behavior, which were selected according to HP sequence lengths to induce folding in a crowded environment. Analysis of three benchmark HP sequences showed that the modeled inhomogeneous space played an important role in deeper energy folding and obtained better performance and convergence compared with homogeneous environments. Our computational approach also demonstrated that our correlated network provided a better space for PF. Thus, our approach represents a major advancement in PF simulations, not only for folding but also for understanding functional chemical structure and physicochemical properties of proteins in crowded molecular systems, which normally occur in nature.

  15. Pattern Recognition as a Human Centered non-Euclidean Problem

    NARCIS (Netherlands)

    Duin, R.P.W.

    2010-01-01

    Regularities in the world are human defined. Patterns in the observed phenomena are there because we define and recognize them as such. Automatic pattern recognition tries to bridge the gap between human judgment and measurements made by artificial sensors. This is done in two steps: representation

  16. Problems with a False Recognition Paradigm for Developmental Memory Research

    Science.gov (United States)

    Lindauer, Barbara K.; Paris, Scott G.

    1976-01-01

    Developmental changes in memory organization based on synonym and antonym relationships were examined in three experiments. Subjects were 64 second graders and 64 sixth graders. Some inadequacies of a false recognition paradigm for developmental research are identified and some alternative analyses are proposed. (Author/JH)

  17. A Folded Excited State of Ligand-Free Nuclear Coactivator Binding Domain (NCBD) Underlies Plasticity in Ligand Recognition

    DEFF Research Database (Denmark)

    Kjaergaard, Magnus; Andersen, Lisbeth; Nielsen, Lau Dalby

    2013-01-01

    Intrinsically disordered proteins are renowned for their structural plasticity when they undergo coupled folding and binding to partner proteins. The nuclear coactivator binding domain of CBP is a remarkable example of this adaptability as it folds into two different conformations depending...... experience conformational exchange. The dispersion data can be described by a global two-state exchange process between a ground state and an excited state populated to 8%. The three helices are still folded in the excited state but have a different packing from the ground state; the contact between helices...... with that of NCBD in complex with the ligand IRF-3. The energy landscape of this domain is thus proposed to resemble the fold-switching proteins that have two coexisting native states, which may serve as a starting point for binding via conformational selection....

  18. Definition of new 3D invariants. Applications to pattern recognition problems with neural networks

    International Nuclear Information System (INIS)

    Proriol, J.

    1996-01-01

    We propose a definition of new 3D invariants. Usual pattern recognition methods use 2D descriptions of 3D objects, we propose a 2D approximation of the defined 3D invariants which can be used with neural networks to solve pattern recognition problems. We describe some methods to use the 2 D approximants. This work is an extension of previous 3D invariants used to solve some high energy physics problems. (author)

  19. Melody discrimination and protein fold classification

    Directory of Open Access Journals (Sweden)

    Robert P. Bywater

    2016-10-01

    Full Text Available One of the greatest challenges in theoretical biophysics and bioinformatics is the identification of protein folds from sequence data. This can be regarded as a pattern recognition problem. In this paper we report the use of a melody generation software where the inputs are derived from calculations of evolutionary information, secondary structure, flexibility, hydropathy and solvent accessibility from multiple sequence alignment data. The melodies so generated are derived from the sequence, and by inference, of the fold, in ways that give each fold a sound representation that may facilitate analysis, recognition, or comparison with other sequences.

  20. Problems in hard and soft matter: From brain folds and Levy localization to active elasticity

    Science.gov (United States)

    Mayett, David

    This thesis presents a study of condensed matter systems at different length scales. The first part presents a study of elastic instabilities in biological systems ranging from the cerebral cortex in the brain to the lining of the intestines. Such instabilities lead to a zoo of morphologies ranging from primary folds to villi and crypts to secondary folds and are brought about by growth, mechanical stresses, or a combination of the two. We propose a novel model for the description of primary folds in the cerebral cortex. Motivated by the spatial structure of the cortex, we model its elasticity as a smectic liquid crystal. With this novel description we show that vertical pulling forces via axonal tension from the brain underlying white matter can lead to buckling, which initiates the primary folds. Moreover, we are able to obtain a reasonable estimate of the critical wavelength and strain for buckling. We also model the formation of secondary folds in the cortex to obtain a more comprehensive theory. We continue this study of elastic instabilities due to growth by studying a more general system comprised of two coupled elastic membranes, one of which undergoes growth and one that does not. We employ an active formulation of growth and compare it to the one due to Rodriguez (Rodriguez). We show that different morphologies corresponding to different systems, such as the cerebral cortex and the lining of the intestines, can be obtained from our model by choosing different active stress functional forms to begin to classify the zoo of morphologies observed in seemingly different biological systems. In the second part of this thesis, to work towards a more microscopic view of biological tissues such as the brain tissue, which is composed of neurons, glial cells, and progenitor cells, we model an experiment (Theveneau) studying the dynamic interaction between neural crest cells and placodal cells in which the placodal cells run away from the neural crest cells following

  1. Recognition of Action as a Bayesian Parameter Estimation Problem over Time

    DEFF Research Database (Denmark)

    Krüger, Volker

    2007-01-01

    In this paper we will discuss two problems related to action recognition: The first problem is the one of identifying in a surveillance scenario whether a person is walking or running and in what rough direction. The second problem is concerned with the recovery of action primitives from observed...... complex actions. Both problems will be discussed within a statistical framework. Bayesian propagation over time offers a framework to treat likelihood observations at each time step and the dynamics between the time steps in a unified manner. The first problem will be approached as a patter recognition...... of the Bayesian framework for action recognition and round up our discussion....

  2. Mutational analysis of target enzyme recognition of the beta-trefoil fold barley alpha-amylase/subtilisin inhibitor

    DEFF Research Database (Denmark)

    Bønsager, Birgit Christine; Nielsen, Per K.; Abou Hachem, Maher

    2005-01-01

    The barley alpha-amylase/subtilisin inhibitor ( BASI) inhibits alpha-amylase 2 (AMY2) with subnanomolar affinity. The contribution of selected side chains of BASI to this high affinity is discerned in this study, and binding to other targets is investigated. Seven BASI residues along the AMY2-BASI...... interface and four residues in the putative protease-binding loop on the opposite side of the inhibitor were mutated. A total of 15 variants were compared with the wild type by monitoring the alpha-amylase and protease inhibitory activities using Blue Starch and azoalbumin, respectively, and the kinetics...... of binding to target enzymes by surface plasmon resonance. Generally, the mutations had little effect on k(on), whereas the k(off) values were increased up to 67-fold. The effects on the inhibitory activity, however, were far more pronounced, and the K-i values of some mutants on the AMY2-binding side...

  3. Recognition

    DEFF Research Database (Denmark)

    Gimmler, Antje

    2017-01-01

    In this article, I shall examine the cognitive, heuristic and theoretical functions of the concept of recognition. To evaluate both the explanatory power and the limitations of a sociological concept, the theory construction must be analysed and its actual productivity for sociological theory must...... be evaluated. In the first section, I will introduce the concept of recognition as a travelling concept playing a role both on the intellectual stage and in real life. In the second section, I will concentrate on the presentation of Honneth’s theory of recognition, emphasizing the construction of the concept...... and its explanatory power. Finally, I will discuss Honneth’s concept in relation to the critique that has been raised, addressing the debate between Honneth and Fraser. In a short conclusion, I will return to the question of the explanatory power of the concept of recognition....

  4. Crystal Structure of the PAC1R Extracellular Domain Unifies a Consensus Fold for Hormone Recognition by Class B G-Protein Coupled Receptors

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Shiva; Pioszak, Augen; Zhang, Chenghai; Swaminathan, Kunchithapadam; Xu, H. Eric (Van Andel); (NU Singapore)

    2012-02-21

    Pituitary adenylate cyclase activating polypeptide (PACAP) is a member of the PACAP/glucagon family of peptide hormones, which controls many physiological functions in the immune, nervous, endocrine, and muscular systems. It activates adenylate cyclase by binding to its receptor, PAC1R, a member of class B G-protein coupled receptors (GPCR). Crystal structures of a number of Class B GPCR extracellular domains (ECD) bound to their respective peptide hormones have revealed a consensus mechanism of hormone binding. However, the mechanism of how PACAP binds to its receptor remains controversial as an NMR structure of the PAC1R ECD/PACAP complex reveals a different topology of the ECD and a distinct mode of ligand recognition. Here we report a 1.9 {angstrom} crystal structure of the PAC1R ECD, which adopts the same fold as commonly observed for other members of Class B GPCR. Binding studies and cell-based assays with alanine-scanned peptides and mutated receptor support a model that PAC1R uses the same conserved fold of Class B GPCR ECD for PACAP binding, thus unifying the consensus mechanism of hormone binding for this family of receptors.

  5. Crystal structure of the PAC1R extracellular domain unifies a consensus fold for hormone recognition by class B G-protein coupled receptors.

    Science.gov (United States)

    Kumar, Shiva; Pioszak, Augen; Zhang, Chenghai; Swaminathan, Kunchithapadam; Xu, H Eric

    2011-01-01

    Pituitary adenylate cyclase activating polypeptide (PACAP) is a member of the PACAP/glucagon family of peptide hormones, which controls many physiological functions in the immune, nervous, endocrine, and muscular systems. It activates adenylate cyclase by binding to its receptor, PAC1R, a member of class B G-protein coupled receptors (GPCR). Crystal structures of a number of Class B GPCR extracellular domains (ECD) bound to their respective peptide hormones have revealed a consensus mechanism of hormone binding. However, the mechanism of how PACAP binds to its receptor remains controversial as an NMR structure of the PAC1R ECD/PACAP complex reveals a different topology of the ECD and a distinct mode of ligand recognition. Here we report a 1.9 Å crystal structure of the PAC1R ECD, which adopts the same fold as commonly observed for other members of Class B GPCR. Binding studies and cell-based assays with alanine-scanned peptides and mutated receptor support a model that PAC1R uses the same conserved fold of Class B GPCR ECD for PACAP binding, thus unifying the consensus mechanism of hormone binding for this family of receptors.

  6. Crystal structure of the PAC1R extracellular domain unifies a consensus fold for hormone recognition by class B G-protein coupled receptors.

    Directory of Open Access Journals (Sweden)

    Shiva Kumar

    Full Text Available Pituitary adenylate cyclase activating polypeptide (PACAP is a member of the PACAP/glucagon family of peptide hormones, which controls many physiological functions in the immune, nervous, endocrine, and muscular systems. It activates adenylate cyclase by binding to its receptor, PAC1R, a member of class B G-protein coupled receptors (GPCR. Crystal structures of a number of Class B GPCR extracellular domains (ECD bound to their respective peptide hormones have revealed a consensus mechanism of hormone binding. However, the mechanism of how PACAP binds to its receptor remains controversial as an NMR structure of the PAC1R ECD/PACAP complex reveals a different topology of the ECD and a distinct mode of ligand recognition. Here we report a 1.9 Å crystal structure of the PAC1R ECD, which adopts the same fold as commonly observed for other members of Class B GPCR. Binding studies and cell-based assays with alanine-scanned peptides and mutated receptor support a model that PAC1R uses the same conserved fold of Class B GPCR ECD for PACAP binding, thus unifying the consensus mechanism of hormone binding for this family of receptors.

  7. Correlates of Problem Recognition and Intentions to Change among Caregivers of Abused and Neglected Children

    Science.gov (United States)

    Littell, Julia H.; Girvin, Heather

    2006-01-01

    Objective: To identify individual, family, and caseworker characteristics associated with problem recognition (PR) and intentions to change (ITC) in a sample of caregivers who received in-home child welfare services following substantiated reports of child abuse or neglect. Methods: Caregivers were interviewed at 4 weeks, 16 weeks, and 1 year…

  8. Influence of Child Factors on Health-Care Professionals' Recognition of Common Childhood Mental-Health Problems

    NARCIS (Netherlands)

    Burke, Delia A; Koot, Hans M; de Wilde, Amber; Begeer, Sander

    2016-01-01

    Early recognition of childhood mental-health problems can help minimise long-term negative outcomes. Recognition of mental-health problems, needed for referral and diagnostic evaluation, is largely dependent on health-care professionals' (HCPs) judgement of symptoms presented by the child. This

  9. Covering folded shapes

    Directory of Open Access Journals (Sweden)

    Oswin Aichholzer

    2014-05-01

    Full Text Available Can folding a piece of paper flat make it larger? We explore whether a shape S must be scaled to cover a flat-folded copy of itself. We consider both single folds and arbitrary folds (continuous piecewise isometries \\(S\\to\\mathbb{R}^2\\. The underlying problem is motivated by computational origami, and is related to other covering and fixturing problems, such as Lebesgue's universal cover problem and force closure grasps. In addition to considering special shapes (squares, equilateral triangles, polygons and disks, we give upper and lower bounds on scale factors for single folds of convex objects and arbitrary folds of simply connected objects.

  10. Reduction of the dimension of neural network models in problems of pattern recognition and forecasting

    Science.gov (United States)

    Nasertdinova, A. D.; Bochkarev, V. V.

    2017-11-01

    Deep neural networks with a large number of parameters are a powerful tool for solving problems of pattern recognition, prediction and classification. Nevertheless, overfitting remains a serious problem in the use of such networks. A method of solving the problem of overfitting is proposed in this article. This method is based on reducing the number of independent parameters of a neural network model using the principal component analysis, and can be implemented using existing libraries of neural computing. The algorithm was tested on the problem of recognition of handwritten symbols from the MNIST database, as well as on the task of predicting time series (rows of the average monthly number of sunspots and series of the Lorentz system were used). It is shown that the application of the principal component analysis enables reducing the number of parameters of the neural network model when the results are good. The average error rate for the recognition of handwritten figures from the MNIST database was 1.12% (which is comparable to the results obtained using the "Deep training" methods), while the number of parameters of the neural network can be reduced to 130 times.

  11. A Grassmannian Approach to Address View Change Problem in Gait Recognition.

    Science.gov (United States)

    Connie, Tee; Goh, Michael Kah Ong; Teoh, Andrew Beng Jin

    2017-06-01

    Gait recognition appears to be a valuable asset when conventional biometrics cannot be employed. Nonetheless, recognizing human by gait is not a trivial task due to the complex human kinematic structure and other external factors affecting human locomotion. A major challenge in gait recognition is view variation. A large difference between the views in the query and reference sets often leads to performance deterioration. In this paper, we show how to generate virtual views to compensate the view difference in the query and reference sets, making it possible to match the query and reference sets using standardized views. The proposed method, which combines multiview matrix representation and a novel randomized kernel extreme learning machine, is an end-to-end solution for view change problem under Grassmann manifold treatment. Under the right condition, the view-tagging problem can be eliminated. Since the recording angle and walking direction of the subject are not always available, this is particularly valuable for a practical gait recognition system. We present several working scenarios for multiview recognition that have not be considered before. Rigorous experiments have been conducted on two challenging benchmark databases containing multiview gait datasets. Experiments show that the proposed approach outperforms several state-of-the-arts methods.

  12. Outcomes, moderators, and mediators of empathic-emotion recognition training for complex conduct problems in childhood.

    Science.gov (United States)

    Dadds, Mark Richard; Cauchi, Avril Jessica; Wimalaweera, Subodha; Hawes, David John; Brennan, John

    2012-10-30

    Impairments in emotion recognition skills are a trans-diagnostic indicator of early mental health problems and may be responsive to intervention. We report on a randomized controlled trial of "Emotion-recognition-training" (ERT) versus treatment-as-usual (TAU) with N=195 mixed diagnostic children (mean age 10.52 years) referred for behavioral/emotional problems measured at pre- and 6 months post-treatment. We tested overall outcomes plus moderation and mediation models, whereby diagnostic profile was tested as a moderator of change. ERT had no impact on the group as a whole. Diagnostic status of the child did not moderate outcomes; however, levels of callous-unemotional (CU) traits moderated outcomes such that children with high CU traits responded less well to TAU, while ERT produced significant improvements in affective empathy and conduct problems in these children. Emotion recognition training has potential as an adjunctive intervention specifically for clinically referred children with high CU traits, regardless of their diagnostic status. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  13. Computational Recognition of RNA Splice Sites by Exact Algorithms for the Quadratic Traveling Salesman Problem

    Directory of Open Access Journals (Sweden)

    Anja Fischer

    2015-06-01

    Full Text Available One fundamental problem of bioinformatics is the computational recognition of DNA and RNA binding sites. Given a set of short DNA or RNA sequences of equal length such as transcription factor binding sites or RNA splice sites, the task is to learn a pattern from this set that allows the recognition of similar sites in another set of DNA or RNA sequences. Permuted Markov (PM models and permuted variable length Markov (PVLM models are two powerful models for this task, but the problem of finding an optimal PM model or PVLM model is NP-hard. While the problem of finding an optimal PM model or PVLM model of order one is equivalent to the traveling salesman problem (TSP, the problem of finding an optimal PM model or PVLM model of order two is equivalent to the quadratic TSP (QTSP. Several exact algorithms exist for solving the QTSP, but it is unclear if these algorithms are capable of solving QTSP instances resulting from RNA splice sites of at least 150 base pairs in a reasonable time frame. Here, we investigate the performance of three exact algorithms for solving the QTSP for ten datasets of splice acceptor sites and splice donor sites of five different species and find that one of these algorithms is capable of solving QTSP instances of up to 200 base pairs with a running time of less than two days.

  14. A study of fuzzy logic ensemble system performance on face recognition problem

    Science.gov (United States)

    Polyakova, A.; Lipinskiy, L.

    2017-02-01

    Some problems are difficult to solve by using a single intelligent information technology (IIT). The ensemble of the various data mining (DM) techniques is a set of models which are able to solve the problem by itself, but the combination of which allows increasing the efficiency of the system as a whole. Using the IIT ensembles can improve the reliability and efficiency of the final decision, since it emphasizes on the diversity of its components. The new method of the intellectual informational technology ensemble design is considered in this paper. It is based on the fuzzy logic and is designed to solve the classification and regression problems. The ensemble consists of several data mining algorithms: artificial neural network, support vector machine and decision trees. These algorithms and their ensemble have been tested by solving the face recognition problems. Principal components analysis (PCA) is used for feature selection.

  15. Maternal recognition of child mental health problems in two Brazilian cities

    Directory of Open Access Journals (Sweden)

    Isabel A. Bordin

    2017-06-01

    Full Text Available Objective: To identify child behaviors and types of impairment that increase the likelihood of maternal recognition of emotional/behavioral problems (EBP in children and adolescents. Methods: Maternal-reported data were obtained from two subsamples of 11-to-16-year-olds derived from cross-sectional studies conducted in two Brazilian municipalities: Itaboraí, state of Rio de Janeiro (n=480, and Embu, state of São Paulo (n=217. The Itaboraí study involved a representative sample of 6-to-16-year-olds (n=1,248; response rate = 86.0% selected from the Family Health Program registry, which covered 85.5% of the municipal population. The Embu study was based on a probabilistic sample of clusters of eligible households (women aged 15-49 years, child < 18 years, with one mother-child pair selected randomly per household (n=813; response rate = 82.4%. The outcome variable was mother’s opinion of whether her child had EBP. Potential correlates included types of child behaviors (hyperactivity/conduct/emotional problems as isolated or combined conditions and impairment, assessed using the Strengths and Difficulties Questionnaire (SDQ; child’s age and gender; maternal education and anxiety/depression (assessed using the Self-Reporting Questionnaire [SRQ]. Results: Multivariate regression models identified the following correlates of maternal perception of child EBP: comorbidity (co-occurring hyperactivity/conduct/emotional problems, emotional problems alone, and interference of problems with classroom learning and friendships. Conclusion: Comorbidity of different problem types, emotional problems alone, and interference with classroom learning and friendships increase the likelihood of maternal recognition of EBP in children.

  16. High and Low Trait Anger, Angry Thoughts, and the Recognition of Anger Problems.

    Science.gov (United States)

    Alcázar-Olán, Raúl J; Deffenbacher, Jerry L; Hernández Guzmán, Laura; Jurado Cárdenas, Samuel

    2015-10-30

    This research had two goals: (1) it tested hypotheses of the State-Trait Model of anger, and (2) it explored characteristics that may distinguish individuals with high trait anger who recognize problems with their anger from those who do not recognize anger problems. Regarding the first goal, findings supported three hypotheses tested. In particular, compared to those low in trait anger, individuals with high trait anger reported: (a) more intense anger (intensity hypothesis), p thoughts involving pejorative labeling/denigration, p thoughts of revenge, p thoughts of self-control, p positive coping hypothesis). For the second goal we employed two types of individuals, both with high trait anger: those who identified anger as a personal problem and wanted help, and those who did not identify anger as a personal issue. As a result, compared to those who did not report anger problems, those who reported anger problems demonstrated a higher overall propensity to experience anger (i.e., higher trait anger), p thoughts of self-control, p < .05, η(2) = .015, and attempts to control their angry feelings (anger-control-in), p < .05, η(2) = .016, and behavior (anger-control-out), p < .001, η(2) = .054. Gender was not associated with trait anger or anger problem recognition. Findings were discussed in terms of State-Trait Theory and implications for anger interventions.

  17. Is emotion recognition the only problem in ADHD? effects of pharmacotherapy on face and emotion recognition in children with ADHD.

    Science.gov (United States)

    Demirci, Esra; Erdogan, Ayten

    2016-12-01

    The objectives of this study were to evaluate both face and emotion recognition, to detect differences among attention deficit and hyperactivity disorder (ADHD) subgroups, to identify effects of the gender and to assess the effects of methylphenidate and atomoxetine treatment on both face and emotion recognition in patients with ADHD. The study sample consisted of 41 male, 29 female patients, 8-15 years of age, who were diagnosed as having combined type ADHD (N = 26), hyperactive/impulsive type ADHD (N = 21) or inattentive type ADHD (N = 23) but had not previously used any medication for ADHD and 35 male, 25 female healthy individuals. Long-acting methylphenidate (OROS-MPH) was prescribed to 38 patients, whereas atomoxetine was prescribed to 32 patients. The reading the mind in the eyes test (RMET) and Benton face recognition test (BFRT) were applied to all participants before and after treatment. The patients with ADHD had a significantly lower number of correct answers in child and adolescent RMET and in BFRT than the healthy controls. Among the ADHD subtypes, the hyperactive/impulsive subtype had a lower number of correct answers in the RMET than the inattentive subtypes, and the hyperactive/impulsive subtype had a lower number of correct answers in short and long form of BFRT than the combined and inattentive subtypes. Male and female patients with ADHD did not differ significantly with respect to the number of correct answers on the RMET and BFRT. The patients showed significant improvement in RMET and BFRT after treatment with OROS-MPH or atomoxetine. Patients with ADHD have difficulties in face recognition as well as emotion recognition. Both OROS-MPH and atomoxetine affect emotion recognition. However, further studies on the face and emotion recognition are needed in ADHD.

  18. HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition.

    Directory of Open Access Journals (Sweden)

    Charles Richard Bradshaw

    Full Text Available Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes. We find ∼4500 cross-species validated, remotely conserved domain predictions in the human proteome alone. As an example, we find a DNA-binding domain in the C-terminal part of the A-kinase anchor protein 10 (AKAP10, a PKA adaptor that has been implicated in cardiac arrhythmias and premature cardiac death, which upon stress likely translocates from mitochondria to the nucleus/nucleolus. Based on our prediction, we propose that with this HLH-domain, AKAP10 is involved in the transcriptional control of stress response. Further remotely conserved domains we discuss are examples from areas such as sporulation, chromosome segregation and signalling during immune response. The HMMerThread algorithm is able to automatically detect the presence of remotely conserved domains in

  19. Information behaviors and problem chain recognition effect: applying situational theory of problem solving in organ donation issues.

    Science.gov (United States)

    Kim, Jeong-Nam; Shen, Hongmei; Morgan, Susan E

    2011-03-01

    Identification of active subpopulations who are motivated to talk about, seek out, and select information about organ donation-related issues can improve health communicators' efficacy in increasing awareness of the shortage of organ and health donors. Using the Situational Theory of Problem Solving (STOPS), we segmented the general population into more meaningful subgroups (e.g., active, aware publics about an organ donation issue) and examined whether segmented public profiles could predict their likelihood of active information giving, taking, and selecting about donor shortage. We also tested whether those publics that are more active about the organ donation issue would recognize and be interested in other organ donation issues (e.g., shortage of bone marrow donors). Findings based on two survey data sets (N = 316 and N = 347) suggested that perceptual and motivation variables could predict the likelihood of information behaviors and further donation-related behavioral intentions. In addition, we found some evidence on the problem chain recognition effect-if one becomes active about an organ donation issue, she or he is likely to perceive similar or related issues as problematic. Based on the findings, we discuss the segmentation method and its utility for more strategic planning and practice of health campaigns.

  20. Mental health problems of undocumented migrants in the Netherlands: A qualitative exploration of recognition, recording, and treatment by general practitioners

    NARCIS (Netherlands)

    Teunissen, E.; Bavel, E. Van; Driessen Mareeuw, F.A. van den; Macfarlane, A.; Weel-Baumgarten, E.M. van; Muijsenbergh, M.E.T.C. van den; Weel, C. van

    2015-01-01

    OBJECTIVE: To explore the views and experiences of general practitioners (GPs) in relation to recognition, recording, and treatment of mental health problems of undocumented migrants (UMs), and to gain insight in the reasons for under-registration of mental health problems in the electronic medical

  1. Nurses' recognition and registration of depression, anxiety and diabetes-specific emotional problems in outpatients with diabetes mellitus

    DEFF Research Database (Denmark)

    Pouwer, Francois; Beekman, Aartjan T F; Lubach, Caroline

    2006-01-01

    -specific emotional distress was also found to be low, ranging from 0% (treatment-related problems) to 29% (diabetes-related emotional problems). CONCLUSION: Registration-rates of emotional problems by diabetes nurses were found to be low, but quite similar to detection rates of physicians and nurses in studies...... with non-diabetic samples. PRACTICE IMPLICATIONS: These findings suggest that recognition-rates of emotional problems in diabetes patients need to be increased. Future studies should investigate whether recognition and subsequent treatment of emotional problems in diabetes patients can be facilitated......OBJECTIVE: The aim of this study was to investigate how often emotional problems were recognized and registered by diabetes nurses. METHODS: We studied medical charts and questionnaire data of 112 diabetes patients. The hospital anxiety, depression scale and the problem areas in diabetes survey...

  2. Several Similarity Measures of Interval Valued Neutrosophic Soft Sets and Their Application in Pattern Recognition Problems

    Directory of Open Access Journals (Sweden)

    Anjan Mukherjee

    2014-12-01

    Full Text Available Interval valued neutrosophic soft set introduced by Irfan Deli in 2014[8] is a generalization of neutrosophic set introduced by F. Smarandache in 1995[19], which can be used in real scientific and engineering applications. In this paper the Hamming and Euclidean distances between two interval valued neutrosophic soft sets (IVNS sets are defined and similarity measures based on distances between two interval valued neutrosophic soft sets are proposed. Similarity measure based on set theoretic approach is also proposed. Some basic properties of similarity measures between two interval valued neutrosophic soft sets is also studied. A decision making method is established for interval valued neutrosophic soft set setting using similarity measures between IVNS sets. Finally an example is given to demonstrate the possible application of similarity measures in pattern recognition problems.

  3. The classification problem in machine learning: an overview with study cases in emotion recognition and music-speech differentiation

    OpenAIRE

    Rodríguez Cadavid, Santiago

    2015-01-01

    This work addresses the well-known classification problem in machine learning -- The goal of this study is to approach the reader to the methodological aspects of the feature extraction, feature selection and classifier performance through simple and understandable theoretical aspects and two study cases -- Finally, a very good classification performance was obtained for the emotion recognition from speech

  4. Mental Subtraction in High- and Lower Skilled Arithmetic Problem Solvers: Verbal Report versus Operand-Recognition Paradigms

    Science.gov (United States)

    Thevenot, Catherine; Castel, Caroline; Fanget, Muriel; Fayol, Michel

    2010-01-01

    The authors used the operand-recognition paradigm (C. Thevenot, M. Fanget, & M. Fayol, 2007) in order to study the strategies used by adults to solve subtraction problems. This paradigm capitalizes on the fact that algorithmic procedures degrade the memory traces of the operands. Therefore, greater difficulty in recognizing them is expected…

  5. Recognition of Psychiatric Disorders, and Self-Perceived Problems. A Follow-up Study from Age 8 to Age 18

    Science.gov (United States)

    Sourander, Andre; Haavisto, Antti; Ronning, John A.; Multimaki, Petteri; Parkkola, Kai; Santalahti, Paivi; Nikolakaros, Georgios; Helenius, Hans; Moilanen, Irma; Tamminen, Tuula; Piha, Jorma; Kumpulainen, Kirsti; Almqvist, Fredrik

    2005-01-01

    Objective: To study the rate of, and factors associated with, recognition of psychiatric disorders and self-perceived problems among 18-year-old adolescent boys. Method: The study population consisted of 2347 Finnish boys born during 1981 attending military call-up (79.7% of the original sample). At age 8, the boys were evaluated by parental and…

  6. Problems of Face Recognition in Patients with Behavioral Variant Frontotemporal Dementia.

    Science.gov (United States)

    Chandra, Sadanandavalli Retnaswami; Patwardhan, Ketaki; Pai, Anupama Ramakanth

    2017-01-01

    Faces are very special as they are most essential for social cognition in humans. It is partly understood that face processing in its abstractness involves several extra striate areas. One of the most important causes for caregiver suffering in patients with anterior dementia is lack of empathy. This apart from being a behavioral disorder could be also due to failure to categorize the emotions of the people around them. Inlusion criteria: DSM IV for Bv FTD Tested for prosopagnosia - familiar faces, famous face, smiling face, crying face and reflected face using a simple picture card (figure 1). Advanced illness and mixed causes. 46 patients (15 females, 31 males) 24 had defective face recognition. (mean age 51.5),10/15 females (70%) and 14/31males(47. Familiar face recognition defect was found in 6/10 females and 6/14 males. Total- 40%(6/15) females and 19.35%(6/31)males with FTD had familiar face recognition. Famous Face: 9/10 females and 7/14 males. Total- 60% (9/15) females with FTD had famous face recognition defect as against 22.6%(7/31) males with FTD Smiling face defects in 8/10 female and no males. Total- 53.33% (8/15) females. Crying face recognition defect in 3/10 female and 2 /14 males. Total- 20%(3/15) females and 6.5%(2/31) males. Reflected face recognition defect in 4 females. Famous face recognition and positive emotion recognition defect in 80%, only 20% comprehend positive emotions, Face recognition defects are found in only 45% of males and more common in females. Face recognition is more affected in females with FTD There is differential involvement of different aspects of the face recognition could be one of the important factor underlying decline in the emotional and social behavior of these patients. Understanding these pathological processes will give more insight regarding patient behavior.

  7. Relating dynamic brain states to dynamic machine states: Human and machine solutions to the speech recognition problem.

    Directory of Open Access Journals (Sweden)

    Cai Wingfield

    2017-09-01

    Full Text Available There is widespread interest in the relationship between the neurobiological systems supporting human cognition and emerging computational systems capable of emulating these capacities. Human speech comprehension, poorly understood as a neurobiological process, is an important case in point. Automatic Speech Recognition (ASR systems with near-human levels of performance are now available, which provide a computationally explicit solution for the recognition of words in continuous speech. This research aims to bridge the gap between speech recognition processes in humans and machines, using novel multivariate techniques to compare incremental 'machine states', generated as the ASR analysis progresses over time, to the incremental 'brain states', measured using combined electro- and magneto-encephalography (EMEG, generated as the same inputs are heard by human listeners. This direct comparison of dynamic human and machine internal states, as they respond to the same incrementally delivered sensory input, revealed a significant correspondence between neural response patterns in human superior temporal cortex and the structural properties of ASR-derived phonetic models. Spatially coherent patches in human temporal cortex responded selectively to individual phonetic features defined on the basis of machine-extracted regularities in the speech to lexicon mapping process. These results demonstrate the feasibility of relating human and ASR solutions to the problem of speech recognition, and suggest the potential for further studies relating complex neural computations in human speech comprehension to the rapidly evolving ASR systems that address the same problem domain.

  8. Mental health problems of undocumented migrants in the Netherlands: A qualitative exploration of recognition, recording, and treatment by general practitioners.

    Science.gov (United States)

    Teunissen, Erik; Van Bavel, Eric; Van Den Driessen Mareeuw, Francine; Macfarlane, Anne; Van Weel-Baumgarten, Evelyn; Van Den Muijsenbergh, Maria; Van Weel, Chris

    2015-06-01

    To explore the views and experiences of general practitioners (GPs) in relation to recognition, recording, and treatment of mental health problems of undocumented migrants (UMs), and to gain insight in the reasons for under-registration of mental health problems in the electronic medical records. Qualitative study design with semi-structured interviews using a topic guide. Sixteen GPs in the Netherlands with clinical expertise in the care of UMs. GPs recognized many mental health problems in UMs. Barriers that prevented them from recording these problems and from delivering appropriate care were their low consultation rates, physical presentation of mental health problems, high number of other problems, the UM's lack of trust towards health care professionals, and cultural differences in health beliefs and language barriers. Referrals to mental health care organizations were often seen as problematic by GPs. To overcome these barriers, GPs provided personalized care as far as possible, referred to other primary care professionals such as social workers or mental health care nurses in their practice, and were a little less restrictive in prescribing psychotropics than guidelines recommended. GPs experienced a variety of barriers in engaging with UMs when identifying or suspecting mental health problems. This explains why there is a gap between the high recognition of mental health problems and the low recording of these problems in general practice files. It is recommended that GPs address mental health problems more actively, strive for continuity of care in order to gain trust of the UMs, and look for opportunities to provide mental care that is accessible and acceptable for UMs.

  9. The Complexity of Folding Self-Folding Origami

    Directory of Open Access Journals (Sweden)

    Menachem Stern

    2017-12-01

    Full Text Available Why is it difficult to refold a previously folded sheet of paper? We show that even crease patterns with only one designed folding motion inevitably contain an exponential number of “distractor” folding branches accessible from a bifurcation at the flat state. Consequently, refolding a sheet requires finding the ground state in a glassy energy landscape with an exponential number of other attractors of higher energy, much like in models of protein folding (Levinthal’s paradox and other NP-hard satisfiability (SAT problems. As in these problems, we find that refolding a sheet requires actuation at multiple carefully chosen creases. We show that seeding successful folding in this way can be understood in terms of subpatterns that fold when cut out (“folding islands”. Besides providing guidelines for the placement of active hinges in origami applications, our results point to fundamental limits on the programmability of energy landscapes in sheets.

  10. The Complexity of Folding Self-Folding Origami

    Science.gov (United States)

    Stern, Menachem; Pinson, Matthew B.; Murugan, Arvind

    2017-10-01

    Why is it difficult to refold a previously folded sheet of paper? We show that even crease patterns with only one designed folding motion inevitably contain an exponential number of "distractor" folding branches accessible from a bifurcation at the flat state. Consequently, refolding a sheet requires finding the ground state in a glassy energy landscape with an exponential number of other attractors of higher energy, much like in models of protein folding (Levinthal's paradox) and other NP-hard satisfiability (SAT) problems. As in these problems, we find that refolding a sheet requires actuation at multiple carefully chosen creases. We show that seeding successful folding in this way can be understood in terms of subpatterns that fold when cut out ("folding islands"). Besides providing guidelines for the placement of active hinges in origami applications, our results point to fundamental limits on the programmability of energy landscapes in sheets.

  11. Problems Associated with Statistical Pattern Recognition of Acoustic Emission Signals in a Compact Tension Fatigue Specimen

    Science.gov (United States)

    Hinton, Yolanda L.

    1999-01-01

    Acoustic emission (AE) data were acquired during fatigue testing of an aluminum 2024-T4 compact tension specimen using a commercially available AE system. AE signals from crack extension were identified and separated from noise spikes, signals that reflected from the specimen edges, and signals that saturated the instrumentation. A commercially available software package was used to train a statistical pattern recognition system to classify the signals. The software trained a network to recognize signals with a 91-percent accuracy when compared with the researcher's interpretation of the data. Reasons for the discrepancies are examined and it is postulated that additional preprocessing of the AE data to focus on the extensional wave mode and eliminate other effects before training the pattern recognition system will result in increased accuracy.

  12. RNA folding: structure prediction, folding kinetics and ion electrostatics.

    Science.gov (United States)

    Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

    2015-01-01

    Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

  13. 40Ar/39Ar and K-Ar age constraints on the timing of regional deformation, south coast of New South Wales, Lachlan Fold Belt: problems and implications

    International Nuclear Information System (INIS)

    Fergusson, C.L.; Phillips, D.

    2001-01-01

    Four slate samples from subduction complex rocks exposed on the south coast of New South Wales, south of Batemans Bay, were analysed by K-Ar and 40 Ar/ 39 Ar step-heating methods, One sample contains relatively abundant detrital muscovite flakes that are locally oblique to the regional cleavage in the rock, whereas the remaining samples appear to contain sparse detrital muscovite. Separates of detrital muscovite yielded plateau ages of 505 + 3 Ma and 513 + 3 Ma indicating that inheritance has not been eliminated by metamorphism and recrystallisation. Step-heating analyses of whole-rock chips from all four slate samples produced discordant apparent age spectra with 'saddle shapes' following young apparent ages at the lowest temperature increments. Elevated apparent ages associated with the highest temperature steps are attributed to the presence of variable quantities of detrital muscovite ( 40 Ar/ 39 Ar integrated ages of ca 455Ma, which are some 15-30 million years older than K-Ar ages for the same samples. These discrepancies suggest that the slates have also been affected by recoil loss/redistribution of 39 Ar, Ieading to anomalously old 40 Ar/ 39 Ar ages. Two other samples, from slaty tectonic melange and intensely cleaved slate, yielded average 40 Ar/ 39 Ar integrated ages of ca 424Ma, which are closer to associated mean K-Ar ages of 423 + 4Ma and 409 + 16Ma, respectively. Taking into account the potential influences of recoil loss/redistribution of 39 Ar and inheritance, the results from the latter samples suggest a maximum age of ca 440 Ma for deformation/metamorphism. The current results indicate that recoil and inheritance problems may also have affected whole-rock 40 Ar/ 39 Ar data reported from other regions of the Lachlan Fold Belt. Therefore, until these effects are adequately quantified, models for the evolution of the Lachlan Fold Belt, that are based on such whole-rock 40 Ar/ 39 Ar data, should be treated with caution. Copyright (2001) Geological

  14. Self-recognition of mental health problems in a rural Australian sample.

    Science.gov (United States)

    Handley, Tonelle E; Lewin, Terry J; Perkins, David; Kelly, Brian

    2018-04-19

    Although mental health literacy has increased in recent years, mental illness is often under-recognised. There has been little research conducted on mental illness in rural areas; however, this can be most prominent in rural areas due to factors such as greater stigma and stoicism. The aim of this study is to create a profile of those who are most and least likely to self-identify mental health problems among rural residents with moderate- to-high psychological distress. Secondary analysis of a longitudinal postal survey. Rural and remote New South Wales, Australia. Four-hundred-and-seventy-two community residents. Participants completed the K10 Psychological Distress Scale, as well as the question 'In the past 12 months have you experienced any mental health problems?' The characteristics of those who reported moderate/high distress scores were explored by comparing those who did and did not experience mental health problems recently. Of the 472 participants, 319 (68%) with moderate/high distress reported a mental health problem. Reporting a mental health problem was higher among those with recent adverse life events or who perceived more stress from life events while lower among those who attributed their symptoms to a physical cause. Among a rural sample with moderate/high distress, one-third did not report a mental health problem. Results suggest a threshold effect, whereby mental health problems are more likely to be acknowledged in the context of additional life events. Ongoing public health campaigns are necessary to ensure that symptoms of mental illness are recognised in the multiple forms that they take. © 2018 National Rural Health Alliance Ltd.

  15. The Role of Initial Learning, Problem Features, Prior Knowledge, and Pattern Recognition on Transfer Success

    Science.gov (United States)

    Dinsmore, Daniel L.; Baggetta, Peter; Doyle, Stephanie; Loughlin, Sandra M.

    2014-01-01

    The purpose of this study was to demonstrate that transfer ability (positive and negative) varies depending on the nature of the problems, using the knowledge transfer matrix, as well as being dependent on the individual differences of the learner. A total of 178 participants from the United States and New Zealand completed measures of prior…

  16. Social context, social abstention, and problem recognition correlated with adult female urinary incontinence

    DEFF Research Database (Denmark)

    Lam, Gitte Wrist; Foldspang, Anders; Elving, Lisbeth Bach

    1992-01-01

    indicated the workplace and 66% the home as principal sites of UI occurrence. Thirty-one percent had experienced UI in specific situations such as during anxiety, sexual intercourse, or sleep. Nineteen percent had abstained from social activities, 17% from non-intimate social activity and 6% from sexual...... with episodes of UI occurring at home and in specific situations such as during anxiety and sleep. The experience of UI during sexual intercourse was related to all types of abstention. The perception of UI as a social or hygienic problem depended on the duration since first UI episode as well as social context...... intercourse should be further investigated also from psycho-somatic and psycho-social coping points of view....

  17. PREFACE Protein folding: lessons learned and new frontiers Protein folding: lessons learned and new frontiers

    Science.gov (United States)

    Pappu, Rohit V.; Nussinov, Ruth

    2009-03-01

    multi-scale dynamical problem when one considers the synergies between protein expression, spontaneous folding, chaperonin-assisted folding, protein targeting, the kinetics of post-translational modifications, protein degradation, and of course the drive to avoid aggregation. Further, there is growing recognition that cells not only tolerate but select for proteins that are intrinsically disordered. These proteins are essential for many crucial activities, and yet their inability to fold in isolation makes them prone to proteolytic processing and aggregation. In the series of papers that make up this special focus on protein folding in physical biology, leading researchers provide insights into diverse cross-sections of problems in protein folding. Barrick provides a concise review of what we have learned from the study of two-state folders and draws attention to how several unanswered questions are being approached using studies on large repeat proteins. Dissecting the contribution of hydration-mediated interactions to driving forces for protein folding and assembly has been extremely challenging. There is renewed interest in using hydrostatic pressure as a tool to access folding intermediates and decipher the role of partially hydrated states in folding, misfolding, and aggregation. Silva and Foguel review many of the nuances that have been uncovered by perturbing hydrostatic pressure as a thermodynamic parameter. As noted above, protein folding in vivo is expected to be considerably more complex than the folding of two-state proteins in dilute solutions. Lucent et al review the state-of-the-art in the development of quantitative theories to explain chaperonin-assisted folding in vivo. Additionally, they highlight unanswered questions pertaining to the processing of unfolded/misfolded proteins by the chaperone machinery. Zhuang et al present results that focus on the effects of surface tethering on transition state ensembles and folding mechanisms of a model two

  18. The role of pattern recognition in creative problem solving: a case study in search of new mathematics for biology.

    Science.gov (United States)

    Hong, Felix T

    2013-09-01

    Rosen classified sciences into two categories: formalizable and unformalizable. Whereas formalizable sciences expressed in terms of mathematical theories were highly valued by Rutherford, Hutchins pointed out that unformalizable parts of soft sciences are of genuine interest and importance. Attempts to build mathematical theories for biology in the past century was met with modest and sporadic successes, and only in simple systems. In this article, a qualitative model of humans' high creativity is presented as a starting point to consider whether the gap between soft and hard sciences is bridgeable. Simonton's chance-configuration theory, which mimics the process of evolution, was modified and improved. By treating problem solving as a process of pattern recognition, the known dichotomy of visual thinking vs. verbal thinking can be recast in terms of analog pattern recognition (non-algorithmic process) and digital pattern recognition (algorithmic process), respectively. Additional concepts commonly encountered in computer science, operations research and artificial intelligence were also invoked: heuristic searching, parallel and sequential processing. The refurbished chance-configuration model is now capable of explaining several long-standing puzzles in human cognition: a) why novel discoveries often came without prior warning, b) why some creators had no ideas about the source of inspiration even after the fact, c) why some creators were consistently luckier than others, and, last but not least, d) why it was so difficult to explain what intuition, inspiration, insight, hunch, serendipity, etc. are all about. The predictive power of the present model was tested by means of resolving Zeno's paradox of Achilles and the Tortoise after one deliberately invoked visual thinking. Additional evidence of its predictive power must await future large-scale field studies. The analysis was further generalized to constructions of scientific theories in general. This approach

  19. Effectiveness and Adoption of a Drawing-to-Learn Study Tool for Recall and Problem Solving: Minute Sketches with Folded Lists

    Science.gov (United States)

    Heideman, Paul D.; Flores, K. Adryan; Sevier, Lu M.; Trouton, Kelsey E.

    2017-01-01

    Drawing by learners can be an effective way to develop memory and generate visual models for higher-order skills in biology, but students are often reluctant to adopt drawing as a study method. We designed a nonclassroom intervention that instructed introductory biology college students in a drawing method, minute sketches in folded lists (MSFL),…

  20. Evidence of developmental continuity from birth to 1 year: sleep, temperament, problem solving, and recognition memory.

    Science.gov (United States)

    Judge, Michelle P; Chang, Luye; Lammi-Keefe, Carol J

    2015-04-01

    Research evidence is limited regarding developmentally appropriate care. Variations exits with respect to test procedure type, infant age at testing, and test relatedness. To assess developmental continuity using multiple developmental measures from birth to 12 months in a single cohort of term infants. A secondary analysis, longitudinal, correlational design was used to assess developmental continuity in a single cohort of infants (n 27). Measures included: sleep, using the Motility Monitoring System (first 48 hours of life); temperament, using the Infant Characteristics Questionnaire (ICQ, 6 months) and the Revised Infant Temperament Questionnaire (RITQ, 12 months); problem-solving, using the Willatts Infant Planning Test (PS, 9 and 12 months); and the Fagan Test of Infant Intelligence (FTII, 6 and 9 months). Using Spearmen correlation, significant correlations included: (1) Sleep and ICQ: transitional sleep and "unpredictable" (r 0.455, P .017), "unadaptable" (r 0.420, P .026), and "dull" (r 0.416, P .028); (2) ICQ and FTII 6 months (r -0.512, P .008); (3) RITQ "approachability" and quiet sleep (r 0.662, P .005); (4) arousals in active sleep and PS at 9 months (r -0.528, P .016). Given our reported continuity between early sleep and later developmental measures, sleep-wake state should be considered in caregiving and environmental control to support sleep. Parental education on facilitating sleep-wake regulation in the home environment is essential. These data support the existence of continuity between early sleep and later developmental milestones warranting a larger-scale investigation. Specific focus on development of care strategies for facilitating sleep immediately following birth is warranted.

  1. Methods and means of diagnostics of oncological diseases on the basis of pattern recognition: intelligent morphological systems - problems and solutions

    Science.gov (United States)

    Nikitaev, V. G.

    2017-01-01

    The development of methods of pattern recognition in modern intelligent systems of clinical cancer diagnosis are discussed. The histological (morphological) diagnosis - primary diagnosis for medical setting with cancer are investigated. There are proposed: interactive methods of recognition and structure of intellectual morphological complexes based on expert training-diagnostic and telemedicine systems. The proposed approach successfully implemented in clinical practice.

  2. Graphical symbol recognition

    OpenAIRE

    K.C. , Santosh; Wendling , Laurent

    2015-01-01

    International audience; The chapter focuses on one of the key issues in document image processing i.e., graphical symbol recognition. Graphical symbol recognition is a sub-field of a larger research domain: pattern recognition. The chapter covers several approaches (i.e., statistical, structural and syntactic) and specially designed symbol recognition techniques inspired by real-world industrial problems. It, in general, contains research problems, state-of-the-art methods that convey basic s...

  3. Investigating the genetic and environmental bases of biases in threat recognition and avoidance in children with anxiety problems

    Science.gov (United States)

    2012-01-01

    Background Adults with anxiety show biased categorization and avoidance of threats. Such biases may emerge through complex interplay between genetics and environments, occurring early in life. Research on threat biases in children has focuses on a restricted range of biases, with insufficient focus on genetic and environmental origins. Here, we explore differences between children with and without anxiety problems in under-studied areas of threat bias. We focused both on associations with anxious phenotype and the underlying gene-environmental correlates for two specific processes: the categorisation of threat faces and avoidance learning. Method Two-hundred and fifty 10-year old MZ and DZ twin pairs (500 individuals) completed tasks assessing accuracy in the labelling of threatening facial expressions and in the acquisition of avoidant responses to a card associated with a masked threatening face. To assess whether participants met criteria for an anxiety disorder, parents of twins completed a self-guided computerized version of the Development and Well-being Assessment (DAWBA). Comparison of MZ and DZ twin correlations using model-fitting were used to compute estimates of genetic, shared and non-shared environmental effects. Results Of the 500 twins assessed, 25 (5%) met diagnostic criteria for a current anxiety disorder. Children with anxiety disorders were more accurate in their ability to recognize disgust faces than those without anxiety disorders, but were commensurate on identifying other threatening face emotions (angry, fearful, sad). Children with anxiety disorders but also more strongly avoided selecting a conditioned stimulus than non-anxious children. While recognition of socially threatening faces was moderately heritable, avoidant responses were heavily influenced by the non-shared environment. Conclusion These data add to other findings on threat biases in anxious children. Specifically, we found biases in the labelling of some negative

  4. Nanodevices and a new approach to the problem of recognition and destruction of cancer cells in vivo

    Energy Technology Data Exchange (ETDEWEB)

    Namiot, V.A., E-mail: vnamiot@gmail.com

    2013-11-22

    We suggest for recognition and destruction of cancer cells in vivo to introduce into an organism simultaneously two different interacting nanodevices. Only one of the nanodevices has to be able to recognize cancer cell and mark it. The second nanodevice has to be able to destroy the marked cancer cell. Such process allows increasing the reliability of the cancer cell recognition process and making the process of their destruction rather safe for an organism.

  5. Multiview Rectification of Folded Documents.

    Science.gov (United States)

    You, Shaodi; Matsushita, Yasuyuki; Sinha, Sudipta; Bou, Yusuke; Ikeuchi, Katsushi

    2018-02-01

    Digitally unwrapping images of paper sheets is crucial for accurate document scanning and text recognition. This paper presents a method for automatically rectifying curved or folded paper sheets from a few images captured from multiple viewpoints. Prior methods either need expensive 3D scanners or model deformable surfaces using over-simplified parametric representations. In contrast, our method uses regular images and is based on general developable surface models that can represent a wide variety of paper deformations. Our main contribution is a new robust rectification method based on ridge-aware 3D reconstruction of a paper sheet and unwrapping the reconstructed surface using properties of developable surfaces via conformal mapping. We present results on several examples including book pages, folded letters and shopping receipts.

  6. MODELS OF PROTEIN FOLDING

    Directory of Open Access Journals (Sweden)

    Unnati Ahluwalia

    2012-12-01

    Full Text Available In an attempt to explore the understanding of protein folding mechanism, various models have been proposed in the literature. Advances in recent experimental and computational techniques rationalized our understanding on some of the fundamental features of the protein folding pathways. The goal of this review is to revisit the various models and outline the essential aspects of the folding reaction.

  7. The surgical anatomy of the nasolabial fold.

    Science.gov (United States)

    Pogrel, M A; Shariati, S; Schmidt, B; Faal, Z H; Regezi, J

    1998-10-01

    The purpose of this cadaver dissection study was to investigate the anatomy of the nasolabial fold with a view to explaining the problems of surgical softening or elimination of the fold. Ten formalin-fixed cadavers and 6 fresh-frozen cadavers were used for this study. In 12 cadavers (8 formalin-fixed, 4 fresh-frozen), the nasolabial fold was sectioned at right angles to the fold for histologic examination, and in 4 cadavers (2 formalin-fixed, 2 fresh-frozen) the epithelium was dissected off the fold to allow for more detailed gross examination of the underlying musculature. The fold was clearly identified on 14 of the cadavers but was indistinct on 2 on gross examination. Beneath the fold were 2 muscle bundles. The more superficial muscle runs parallel to the fold whereas a deeper muscle runs at right angles to it. The buccal fat pad lies above the fold and appears to be retained by horizontal septae in the fat pad and also by the musculature of the fold. Cadavers showing a poorly defined nasolabial fold had fewer muscle bundles to support the fat and fewer fibrous septae running through the fat. The nasolabial fold is defined by structures that support the buccal fat pad and hold it above the fold. This appears to be a combination of muscle bundles that run both across and parallel to the fold and also by fibrous septae supporting the fat pad. This has implications for the development of surgical procedures to soften or eliminate the fold, which must separate the muscles from the dermis of the fold and allow the fat to descend and soften the fold.

  8. Solving the border control problem: evidence of enhanced face matching in individuals with extraordinary face recognition skills.

    OpenAIRE

    Bobak, Anna K.; Dowsett, A.; Bate, Sarah

    2016-01-01

    Photographic identity documents (IDs) are commonly used despite clear evidence that unfamiliar face matching is a difficult and error-prone task. The current study set out to examine the performance of seven individuals with extraordinary face recognition memory, so called ?super recognisers? (SRs), on two face matching tasks resembling border control identity checks. In Experiment 1, the SRs as a group outperformed control participants on the ?Glasgow Face Matching Test?, and some case-by-ca...

  9. Prediction of protein folds: extraction of new features, dimensionality reduction, and fusion of heterogeneous classifiers.

    Science.gov (United States)

    Ghanty, Pradip; Pal, Nikhil R

    2009-03-01

    Here, we consider a two-level (four classes in level 1 and 27 folds in level 2) protein fold determination problem. We propose several new features and use some existing features including frequencies of adjacent residues, frequencies of residues separated by one residue, and triplets (trio) of amino acid compositions (AACs). The dimensionality of the trio AAC features is drastically reduced using a neural network based novel online feature selection scheme. We also propose new sets of features called trio potential computed using the hydrophobicity values considering only the selected trio AACs. We demonstrate that the proposed features including the selected trio AACs and trio potential have good discriminating power for protein fold determination. As machine learning tools, we use multilayer perceptron network, radial basis function network, and support vector machine. To improve the recognition accuracies further, we use fusion of different classifiers using the same set of features as well as different sets of features. The effectiveness of our schemes is demonstrated with a benchmark structural classification of proteins (SCOP) dataset. Our system achieves 84.9% test accuracy for the SCOP structural class (four classes) determination and 68.6% test accuracy for the fold recognition with 27 folds. In order to demonstrate the consistency of feature sets and fusion schemes, we also perform the fivefold cross-validation experiments.

  10. Vocal Fold Paralysis

    Science.gov (United States)

    ... decades-long project to develop an electrical stimulation technology to help people avoid having a tracheotomy when both vocal folds are paralyzed. The device, which currently is being tested in animals and people, uses an implanted pacemaker to stimulate ...

  11. Solving the Border Control Problem: Evidence of Enhanced Face Matching in Individuals with Extraordinary Face Recognition Skills.

    Science.gov (United States)

    Bobak, Anna Katarzyna; Dowsett, Andrew James; Bate, Sarah

    2016-01-01

    Photographic identity documents (IDs) are commonly used despite clear evidence that unfamiliar face matching is a difficult and error-prone task. The current study set out to examine the performance of seven individuals with extraordinary face recognition memory, so called "super recognisers" (SRs), on two face matching tasks resembling border control identity checks. In Experiment 1, the SRs as a group outperformed control participants on the "Glasgow Face Matching Test", and some case-by-case comparisons also reached significance. In Experiment 2, a perceptually difficult face matching task was used: the "Models Face Matching Test". Once again, SRs outperformed controls both on group and mostly in case-by-case analyses. These findings suggest that SRs are considerably better at face matching than typical perceivers, and would make proficient personnel for border control agencies.

  12. Evaluating music emotion recognition

    DEFF Research Database (Denmark)

    Sturm, Bob L.

    2013-01-01

    A fundamental problem with nearly all work in music genre recognition (MGR)is that evaluation lacks validity with respect to the principal goals of MGR. This problem also occurs in the evaluation of music emotion recognition (MER). Standard approaches to evaluation, though easy to implement, do...... not reliably differentiate between recognizing genre or emotion from music, or by virtue of confounding factors in signals (e.g., equalization). We demonstrate such problems for evaluating an MER system, and conclude with recommendations....

  13. Frnakenstein: multiple target inverse RNA folding

    Directory of Open Access Journals (Sweden)

    Lyngsø Rune B

    2012-10-01

    Full Text Available Abstract Background RNA secondary structure prediction, or folding, is a classic problem in bioinformatics: given a sequence of nucleotides, the aim is to predict the base pairs formed in its three dimensional conformation. The inverse problem of designing a sequence folding into a particular target structure has only more recently received notable interest. With a growing appreciation and understanding of the functional and structural properties of RNA motifs, and a growing interest in utilising biomolecules in nano-scale designs, the interest in the inverse RNA folding problem is bound to increase. However, whereas the RNA folding problem from an algorithmic viewpoint has an elegant and efficient solution, the inverse RNA folding problem appears to be hard. Results In this paper we present a genetic algorithm approach to solve the inverse folding problem. The main aims of the development was to address the hitherto mostly ignored extension of solving the inverse folding problem, the multi-target inverse folding problem, while simultaneously designing a method with superior performance when measured on the quality of designed sequences. The genetic algorithm has been implemented as a Python program called Frnakenstein. It was benchmarked against four existing methods and several data sets totalling 769 real and predicted single structure targets, and on 292 two structure targets. It performed as well as or better at finding sequences which folded in silico into the target structure than all existing methods, without the heavy bias towards CG base pairs that was observed for all other top performing methods. On the two structure targets it also performed well, generating a perfect design for about 80% of the targets. Conclusions Our method illustrates that successful designs for the inverse RNA folding problem does not necessarily have to rely on heavy biases in base pair and unpaired base distributions. The design problem seems to become more

  14. Vocal Fold Collision Modeling

    DEFF Research Database (Denmark)

    Granados, Alba; Brunskog, Jonas; Misztal, M. K.

    2015-01-01

    When vocal folds vibrate at normal speaking frequencies, collisions occurs. The numerics and formulations behind a position-based continuum model of contact is an active field of research in the contact mechanics community. In this paper, a frictionless three-dimensional finite element model...... of the vocal fold collision is proposed, which incorporates different procedures used in contact mechanics and mathematical optimization theories. The penalty approach and the Lagrange multiplier method are investigated. The contact force solution obtained by the penalty formulation is highly dependent...

  15. The computational measurement of apparent motion: a recurrent pattern recognition strategy as an approach to solve the correspondence problem.

    Science.gov (United States)

    Schuling, F H; Altena, P; Mastebroek, H A

    1990-01-01

    In short, the model consists of a two-dimensional set of edge detecting units, modelled according to the zero-crossing detectors introduced first by Marr and Ullman (1981). These detectors are located peripherally in our synthetic vision system and are the input elements for an intelligent recurrent network. The purpose of that network is to recognize and categorize the previously detected contrast changes in a multi-resolution representation of the original image in such a manner that the original information will be decomposed into a relatively small number N of well-defined edge primitives. The advantage of such a construction is that time-consuming pattern recognition has no longer to be done on the originally complex motion-blurred images of moving objects, but on a limited number of categorized forms. Based on a number M of elementary feature attributes for each individual edge primitive, the model is then able to decompose each edge pattern into certain features. In this way an M-dimensional vector can be constructed for each edge. For each sequence of two successive frames a tensor can be calculated containing the distances (measured in M-dimensional feature space) between all features in both images. This procedure yields a set of K-1 tensors for a sequence of K images. After cross-correlation of all N x M feature attributes from image (i) with those from image (i + 1), where i = 1,...,K-1, probability distributions can be computed. The final step is to search for maxima in these probability functions and then to construct from these extremes an optimal motion field. A number of simulation examples will be presented.

  16. The problem of the content of the recognition of the testimony of the informers towards the concept of just cause for the regular exercise of the criminal action

    Directory of Open Access Journals (Sweden)

    Walter Barbosa Bittar

    2017-03-01

    Full Text Available This article analyzes the conceptual problems regarding the legal nature of the plea bargaining and the just cause, seeking to establish limits regarding the recognition of the content of the version presented by the informers, with greater attention to the probative value, as seen in the Brazilian legal system, seeking if it is possible to include the content of what can be understood as accepted just cause, or not, as a legitimate requirement for the criminal action procedure. To fulfill this objective, we sought to establish existence and validity requirements for the beginning of a valid criminal prosecution procedure, highlighting the criminal political aspects that end up influencing in the conclusion of the inherent contours of the object of the analysis of the present study.

  17. Folds and Etudes

    Science.gov (United States)

    Bean, Robert

    2007-01-01

    In this article, the author talks about "Folds" and "Etudes" which are images derived from anonymous typing exercises that he found in a used copy of "Touch Typing Made Simple". "Etudes" refers to the musical tradition of studies for a solo instrument, which is a typewriter. Typing exercises are repetitive attempts to type words and phrases…

  18. Folding worlds between pages

    CERN Document Server

    Meier, Matthias

    2010-01-01

    "We all remember pop-up books form our childhood. As fascinated as we were back then, we probably never imagined how much engineering know-how went into these books. Pop-up engineer Anton Radevsky has even managed to fold a 27-kilometre particle accelerator into a book" (4 pages)

  19. Symmetric Circular Matchings and RNA Folding

    DEFF Research Database (Denmark)

    Hofacker, Ivo L.; Reidys, Christian; Stadler, Peter F.

    2012-01-01

    or the co-folding of two or more identical RNAs. Here, we show that the RNA folding problem with symmetry terms can still be solved with polynomial-time algorithms. Empirically, the fraction of symmetric ground state structures decreases with chain length, so that the error introduced by neglecting......RNA secondary structures can be computed as optimal solutions of certain circular matching problems. An accurate treatment of this energy minimization problem has to account for the small --- but non-negligible --- entropic destabilization of secondary structures with non-trivial automorphisms...

  20. Guiding the folding pathway of DNA origami.

    Science.gov (United States)

    Dunn, Katherine E; Dannenberg, Frits; Ouldridge, Thomas E; Kwiatkowska, Marta; Turberfield, Andrew J; Bath, Jonathan

    2015-09-03

    DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short 'staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its

  1. The Folded Horn Antenna

    Science.gov (United States)

    Farr, E. G.; Bowen, L. H.; Baum, C. E.; Prather, W. D.

    Antennas for radiating high-power mesoband (medium-bandwidth) electromagnetic signals are critical to the mission of upsetting electronics at a distance. When operated at frequencies of a few hundred megahertz, RF weapons require highly efficient antennas that can fit into a small volume. Most of the existing antennas, such as pyramidal horns, are too large to fit onto certain platforms of interest. To address this challenge, we investigate the folded horn, which has aperture dimensions of 0.5 × 2 wavelengths, and a depth of 1.5-2 wavelengths. This antenna has a nearly focused aperture field, due to a parabolic fold in the H-plane. We report here on the fabrication and testing of the first folded horn, operating at 3 GHz. After a number of iterations, we obtained a realized gain of at least 10 dBi over 3-5 GHz, an aperture efficiency of 80%, and a return loss below -10 dB over 2.8-3.35 GHz. This design could be adapted to high-voltages, and it could work well in a two-antenna array, with two antennas positioned back to back, driven by a differential source.

  2. Pattern recognition

    CERN Document Server

    Theodoridis, Sergios

    2003-01-01

    Pattern recognition is a scientific discipline that is becoming increasingly important in the age of automation and information handling and retrieval. Patter Recognition, 2e covers the entire spectrum of pattern recognition applications, from image analysis to speech recognition and communications. This book presents cutting-edge material on neural networks, - a set of linked microprocessors that can form associations and uses pattern recognition to ""learn"" -and enhances student motivation by approaching pattern recognition from the designer's point of view. A direct result of more than 10

  3. 40Ar/39Ar and K/Ar whole rock age constraints on the timing of regional deformation, South Coast of New South Wales, Lachlan Fold Belt, Southeastern Australia: problems and implications

    International Nuclear Information System (INIS)

    Phillips, D.; Fergusson, C.L.

    1999-01-01

    mellange and intensely cleaved slate have been analysed and have 40 Ar/ 39 Ar integrated ages of 422 ± 2 Ma (K/Ar: 424 ± 5 Ma) and 415 ± 2 Ma (K/Ar: 400 ± 5 Ma). The general consistency of these results accompanied by microstructural observation indicating a low abundance of detrital mica, show that in these samples recoil and inheritance problems appear to be less important. Thus they provide a more reliable upper constraint on the timing the regional deformation on the south coast of New South Wales, i.e. younger than ca. 420 Ma, consistent with previously recognised regional structural constraints. Elsewhere in the Lachlan Fold Belt 40 Ar/ 39 Ar ages on fine-grained slates have been used to provide concise constraints on the timing of deformation. The current results raise serious questions about the interpretation of these ages as representing on-going deformation and therefore tectonic models derived from these data should be treated with caution. Copyright (1999) Geological Society of Australia

  4. Applications of chaotic neurodynamics in pattern recognition

    Science.gov (United States)

    Baird, Bill; Freeman, Walter J.; Eeckman, Frank H.; Yao, Yong

    1991-08-01

    Network algorithms and architectures for pattern recognition derived from neural models of the olfactory system are reviewed. These span a range from highly abstract to physiologically detailed, and employ the kind of dynamical complexity observed in olfactory cortex, ranging from oscillation to chaos. A simple architecture and algorithm for analytically guaranteed associative memory storage of analog patterns, continuous sequences, and chaotic attractors in the same network is described. A matrix inversion determines network weights, given prototype patterns to be stored. There are N units of capacity in an N node network with 3N2 weights. It costs one unit per static attractor, two per Fourier component of each sequence, and three to four per chaotic attractor. There are no spurious attractors, and for sequences there is a Liapunov function in a special coordinate system which governs the approach of transient states to stored trajectories. Unsupervised or supervised incremental learning algorithms for pattern classification, such as competitive learning or bootstrap Widrow-Hoff can easily be implemented. The architecture can be ''folded'' into a recurrent network with higher order weights that can be used as a model of cortex that stores oscillatory and chaotic attractors by a Hebb rule. Network performance is demonstrated by application to the problem of real-time handwritten digit recognition. An effective system with on-line learning has been written by Eeckman and Baird for the Macintosh. It utilizes static, oscillatory, and/or chaotic attractors of two kinds--Lorenze attractors, or attractors resulting from chaotically interacting oscillatory modes. The successful application to an industrial pattern recognition problem of a network architecture of considerable physiological and dynamical complexity, developed by Freeman and Yao, is described. The data sets of the problem come in three classes of difficulty, and performance of the biological network is

  5. How the genome folds

    Science.gov (United States)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  6. Protein folding optimization based on 3D off-lattice model via an improved artificial bee colony algorithm.

    Science.gov (United States)

    Li, Bai; Lin, Mu; Liu, Qiao; Li, Ya; Zhou, Changjun

    2015-10-01

    Protein folding is a fundamental topic in molecular biology. Conventional experimental techniques for protein structure identification or protein folding recognition require strict laboratory requirements and heavy operating burdens, which have largely limited their applications. Alternatively, computer-aided techniques have been developed to optimize protein structures or to predict the protein folding process. In this paper, we utilize a 3D off-lattice model to describe the original protein folding scheme as a simplified energy-optimal numerical problem, where all types of amino acid residues are binarized into hydrophobic and hydrophilic ones. We apply a balance-evolution artificial bee colony (BE-ABC) algorithm as the minimization solver, which is featured by the adaptive adjustment of search intensity to cater for the varying needs during the entire optimization process. In this work, we establish a benchmark case set with 13 real protein sequences from the Protein Data Bank database and evaluate the convergence performance of BE-ABC algorithm through strict comparisons with several state-of-the-art ABC variants in short-term numerical experiments. Besides that, our obtained best-so-far protein structures are compared to the ones in comprehensive previous literature. This study also provides preliminary insights into how artificial intelligence techniques can be applied to reveal the dynamics of protein folding. Graphical Abstract Protein folding optimization using 3D off-lattice model and advanced optimization techniques.

  7. Speech Recognition

    Directory of Open Access Journals (Sweden)

    Adrian Morariu

    2009-01-01

    Full Text Available This paper presents a method of speech recognition by pattern recognition techniques. Learning consists in determining the unique characteristics of a word (cepstral coefficients by eliminating those characteristics that are different from one word to another. For learning and recognition, the system will build a dictionary of words by determining the characteristics of each word to be used in the recognition. Determining the characteristics of an audio signal consists in the following steps: noise removal, sampling it, applying Hamming window, switching to frequency domain through Fourier transform, calculating the magnitude spectrum, filtering data, determining cepstral coefficients.

  8. Evaluating music emotion recognition:Lessons from music genre recognition?

    OpenAIRE

    Sturm, Bob L.

    2013-01-01

    A fundamental problem with nearly all work in music genre recognition (MGR)is that evaluation lacks validity with respect to the principal goals of MGR. This problem also occurs in the evaluation of music emotion recognition (MER). Standard approaches to evaluation, though easy to implement, do not reliably differentiate between recognizing genre or emotion from music, or by virtue of confounding factors in signals (e.g., equalization). We demonstrate such problems for evaluating an MER syste...

  9. Evolutionary optimization of protein folding.

    Directory of Open Access Journals (Sweden)

    Cédric Debès

    Full Text Available Nature has shaped the make up of proteins since their appearance, [Formula: see text]3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last [Formula: see text]1.5 billion years that began during the "big bang" of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions.

  10. Extreme Mechanics: Self-Folding Origami

    Science.gov (United States)

    Santangelo, Christian D.

    2017-03-01

    Origami has emerged as a tool for designing three-dimensional structures from flat films. Because they can be fabricated by lithographic or roll-to-roll processing techniques, they have great potential for the manufacture of complicated geometries and devices. This article discusses the mechanics of origami and kirigami with a view toward understanding how to design self-folding origami structures. Whether an origami structure can be made to fold autonomously depends strongly on the geometry and kinematics of the origami fold pattern. This article collects some of the results on origami rigidity into a single framework, and discusses how these aspects affect the foldability of origami. Despite recent progress, most problems in origami and origami design remain completely open.

  11. Equi-Gaussian curvature folding

    Indian Academy of Sciences (India)

    have the same equi-Gaussian curvature 1/a2, where a is the radius of the sphere. Now let f : S2 → Pn be a cellular folding. Then we have the following possibilities: Firstly, there are no cellular foldings f : S2 → Pn, for any n > 3 [2]. Secondly, any cellular folding f : S2 → P3 for which Gf forms a regular graph is equivalent to ...

  12. RNA folding inside a virus capsid and dimensional reduction.

    Science.gov (United States)

    Ghafouri, Rouzbeh; Bruinsma, Robijn; Rudnick, Joseph

    2006-03-01

    As RNA folds on itself , in certain conditions, it takes the form of a branched polymer. So the problem of RNA folding in a virus capsid is essentially the problem of a branched polymer in a confined environment. In this paper we attack the problem using the technique of dimensional reduction which relates a branched polymer with self interation in D dimension to a hardcore classical gas in (D-2) dimension. We look for phase transitions and intersting physical quantities such as pressure.

  13. Teaching computers to fold proteins

    DEFF Research Database (Denmark)

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages...

  14. Side-View Face Recognition

    NARCIS (Netherlands)

    Santemiz, P.; Spreeuwers, Lieuwe Jan; Veldhuis, Raymond N.J.

    2010-01-01

    Side-view face recognition is a challenging problem with many applications. Especially in real-life scenarios where the environment is uncontrolled, coping with pose variations up to side-view positions is an important task for face recognition. In this paper we discuss the use of side view face

  15. Recognition of fractal graphs

    NARCIS (Netherlands)

    Perepelitsa, VA; Sergienko, [No Value; Kochkarov, AM

    1999-01-01

    Definitions of prefractal and fractal graphs are introduced, and they are used to formulate mathematical models in different fields of knowledge. The topicality of fractal-graph recognition from the point of view, of fundamental improvement in the efficiency of the solution of algorithmic problems

  16. Neutron structural biology. Beyond the folding structure

    International Nuclear Information System (INIS)

    Niimura, Nobuo

    2009-01-01

    Hydrogen atoms and water molecules around proteins and nucleic acids play a crucial role in many physiological functions. Neutron diffraction provides an experimental method of directly locating hydrogen atoms. (a) Since almost all the H atom positions can be identified experimentally, the geometrical details of certain types of H-bonds can be visualized and (b) as far as mechanistic implications are concerned, the identification of protonation and deprotonation states of certain important amino acid residues can be carried out. (c) The hydration structure around proteins and the hydration networks around DNA oligomers have been successfully characterized in several outstanding cases. These will open the new field beyond the folding structure of bio-macromolecules such as: 1) Recognition of proteins and nucleic acids through the network structure of water molecules surrounding bio-macromolecules, and 2) The nature of chemical bond in proteins and nucleic acids elucidated by the accumulation of accurate structural information of hydrogen atoms. (author)

  17. Markov Models for Handwriting Recognition

    CERN Document Server

    Plotz, Thomas

    2011-01-01

    Since their first inception, automatic reading systems have evolved substantially, yet the recognition of handwriting remains an open research problem due to its substantial variation in appearance. With the introduction of Markovian models to the field, a promising modeling and recognition paradigm was established for automatic handwriting recognition. However, no standard procedures for building Markov model-based recognizers have yet been established. This text provides a comprehensive overview of the application of Markov models in the field of handwriting recognition, covering both hidden

  18. On the Folded Normal Distribution

    Directory of Open Access Journals (Sweden)

    Michail Tsagris

    2014-02-01

    Full Text Available The characteristic function of the folded normal distribution and its moment function are derived. The entropy of the folded normal distribution and the Kullback–Leibler from the normal and half normal distributions are approximated using Taylor series. The accuracy of the results are also assessed using different criteria. The maximum likelihood estimates and confidence intervals for the parameters are obtained using the asymptotic theory and bootstrap method. The coverage of the confidence intervals is also examined.

  19. FRAN and RBF-PSO as two components of a hyper framework to recognize protein folds.

    Science.gov (United States)

    Abbasi, Elham; Ghatee, Mehdi; Shiri, M E

    2013-09-01

    In this paper, an intelligent hyper framework is proposed to recognize protein folds from its amino acid sequence which is a fundamental problem in bioinformatics. This framework includes some statistical and intelligent algorithms for proteins classification. The main components of the proposed framework are the Fuzzy Resource-Allocating Network (FRAN) and the Radial Bases Function based on Particle Swarm Optimization (RBF-PSO). FRAN applies a dynamic method to tune up the RBF network parameters. Due to the patterns complexity captured in protein dataset, FRAN classifies the proteins under fuzzy conditions. Also, RBF-PSO applies PSO to tune up the RBF classifier. Experimental results demonstrate that FRAN improves prediction accuracy up to 51% and achieves acceptable multi-class results for protein fold prediction. Although RBF-PSO provides reasonable results for protein fold recognition up to 48%, it is weaker than FRAN in some cases. However the proposed hyper framework provides an opportunity to use a great range of intelligent methods and can learn from previous experiences. Thus it can avoid the weakness of some intelligent methods in terms of memory, computational time and static structure. Furthermore, the performance of this system can be enhanced throughout the system life-cycle. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Pattern recognition in speech and language processing

    CERN Document Server

    Chou, Wu

    2003-01-01

    Minimum Classification Error (MSE) Approach in Pattern Recognition, Wu ChouMinimum Bayes-Risk Methods in Automatic Speech Recognition, Vaibhava Goel and William ByrneA Decision Theoretic Formulation for Adaptive and Robust Automatic Speech Recognition, Qiang HuoSpeech Pattern Recognition Using Neural Networks, Shigeru KatagiriLarge Vocabulary Speech Recognition Based on Statistical Methods, Jean-Luc GauvainToward Spontaneous Speech Recognition and Understanding, Sadaoki FuruiSpeaker Authentication, Qi Li and Biing-Hwang JuangHMMs for Language Processing Problems, Ri

  1. ETIOLOGICAL FACTORS FOR VOCAL FOLD POLYP FORMATION

    Directory of Open Access Journals (Sweden)

    DAŠA GLUVAJIĆ

    2016-05-01

    Full Text Available Background: Vocal fold polyp is one of the most common causes for hoarseness. Many different etiological factors contribute to vocal fold polyp formation. The aim of the study was to find out whether the etiological factors for polyp formation have changed in the last 30 years.Methods: Eighty-one patients with unilateral vocal fold polyp were included in the study. A control group was composed of 50 volunteers without voice problems who matched the patients by age and gender. The data about etiological factors and the findings of phoniatric examination were obtained from the patients' medical documentation and from the questionnaires for the control group. The incidence of etiological factors was compared between the two groups. The program SPSS, Version 18 was used for statistical analysis.Results: The most frequent etiological factors were occupational voice load, GER, allergy and smoking. In 79% of patients 2 – 6 contemporary acting risk factors were found. Occupational voice load (p=0,018 and GER (p=0,004 were significantly more frequent in the patients than in the controls. The other factors did not significantly influence the polyp formation.Conclusions: There are several factors involved simultaneously in the formation of vocal fold polyps both nowadays and 30 years ago. Some of the most common factors remain the same (voice load, smoking, others are new (GER, allergy, which is probably due to the different lifestyle and working conditions than 30 years ago. Occupational voice load and GER were significantly more frequently present in the patients with polyp than in the control group. Regarding the given results it is important to instruct workers with professional vocal load about etiological factors for vocal fold polyp formation.

  2. Speaker Recognition

    DEFF Research Database (Denmark)

    Mølgaard, Lasse Lohilahti; Jørgensen, Kasper Winther

    2005-01-01

    Speaker recognition is basically divided into speaker identification and speaker verification. Verification is the task of automatically determining if a person really is the person he or she claims to be. This technology can be used as a biometric feature for verifying the identity of a person...

  3. NoFold: RNA structure clustering without folding or alignment.

    Science.gov (United States)

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. © 2014 Middleton and Kim; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  4. MARATHON DESPITE UNILATERAL VOCAL FOLD PARALYSIS

    Directory of Open Access Journals (Sweden)

    Matthias Echternach

    2008-06-01

    Full Text Available The principal symptoms of unilateral vocal fold paralysis are hoarseness and difficulty in swallowing. Dyspnea is comparatively rare (Laccourreye et al., 2003. The extent to which unilateral vocal fold paralysis may lead to respiratory problems at all - in contrast to bilateral vocal fold paralysis- has not yet well been determined. On the one hand, inspiration is impaired with unilateral vocal fold paralysis; on the other hand, neither the position of the vocal fold paralysis nor the degree of breathiness correlates with respiratory parameters (Cantarella et al., 2003; 2005. The question of what respiratory stress a patient with a vocal fold paresis can endure has not yet been dealt with.A 43 year-old female patient was suffering from recurrent unspecific respiratory complaints for four months after physical activity. During training for a marathon, she experienced no difficulty in breathing. These unspecific respiratory complaints occurred only after athletic activity and persisted for hours. The patient observed neither an increased coughing nor a stridor. Her voice remained unaltered during the attacks, nor were there any signs of a symptomatic gastroesophageal reflux or infectious disease. A cardio-pulmonary and a radiological examination by means of an X-ray of the thorax also revealed no pathological phenomena. As antiallergic and antiobstructive therapy remained unsuccessful, a laryngological examination was performed in order to exclude a vocal cord dysfunction.Surprisingly enough, the laryngostroboscopy showed, as an initial description, a vocal fold paralysis of the left vocal fold in median position (Figure 1. The anamnestic background for the cause was unclear. The only clue was a thoracotomy on the left side due to a pleuritis in childhood. A subsequent laryngoscopic examination had never been performed. Good mucosa waves and amplitudes were shown bilateral with complete glottal closure. Neither in the acoustic analysis, nor in the

  5. Pattern recognition in calorimeters

    International Nuclear Information System (INIS)

    Della Negra, M.

    1980-07-01

    It is probable that LEP detectors will often include 4π calorimeters. Since this is a novel technique, not much expertise exists yet in the field of pattern recognition for large calorimeter systems. A fast method to simulate calorimeter signals, based on an analytical parametrization of electromagnetic and hadronic showers, developped by the UAl software group on calorimetry, is presented. Some reconstruction problems are discussed, in particular the question of disentangling individual showers within an energetic jet

  6. Conceptual Transformation and Cognitive Processes in Origami Paper Folding

    Science.gov (United States)

    Tenbrink, Thora; Taylor, Holly A.

    2015-01-01

    Research on problem solving typically does not address tasks that involve following detailed and/or illustrated step-by-step instructions. Such tasks are not seen as cognitively challenging problems to be solved. In this paper, we challenge this assumption by analyzing verbal protocols collected during an Origami folding task. Participants…

  7. Folded supersymmetry with a twist

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, Timothy [Department of Physics, Princeton University,Princeton, NJ 08544 (United States); School of Natural Sciences, Institute for Advanced Study,Princeton, NJ 08540 (United States); Institute of Theoretical Science, University of Oregon,Eugene, OR 97403 (United States); Craig, Nathaniel [Department of Physics, University of California,Santa Barbara, CA 93106 (United States); Lou, Hou Keong [Department of Physics, Princeton University,Princeton, NJ 08544 (United States); Pinner, David [Princeton Center for Theoretical Science, Princeton University,Princeton, NJ 08544 (United States)

    2016-03-30

    Folded supersymmetry (f-SUSY) stabilizes the weak scale against radiative corrections from the top sector via scalar partners whose gauge quantum numbers differ from their Standard Model counterparts. This non-trivial pairing of states can be realized in extra-dimensional theories with appropriate supersymmetry-breaking boundary conditions. We present a class of calculable f-SUSY models that are parametrized by a non-trivial twist in 5D boundary conditions and can accommodate the observed Higgs mass and couplings. Although the distinctive phenomenology associated with the novel folded states should provide strong evidence for this mechanism, the most stringent constraints are currently placed by conventional supersymmetry searches. These models remain minimally fine-tuned in light of LHC8 data and provide a range of both standard and exotic signatures accessible at LHC13.

  8. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested...... that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...... of proteins) are natural consequences of the suggested wring mode model. Native (folded) proteins are found to possess an intrinsic standing wring mode....

  9. Compression induced folding of a sheet: An integrable system

    Science.gov (United States)

    Diamant, Haim; Witten, Thomas A.

    2012-02-01

    The apparently intractable shape of a fold in a compressed elastic film lying on a fluid substrate is found to have an exact solution. Such systems buckle at a nonzero wave vector set by the bending stiffness of the film and the weight of the substrate fluid. Our solution describes the entire progression from a weakly displaced sinusoidal buckling to a single large fold that contacts itself. The pressure decrease is exactly quadratic in the lateral displacement. We demonstrate a subtle connection to the sine-Gordon problem, which reveals a new symmetry in the folding phenomenon.

  10. Equi-Gaussian curvature folding

    Indian Academy of Sciences (India)

    curvature kf (p) i.e., kp = kf (p). In this case f will map curves to curves with equal equi-. Gaussian curvature at corresponding points. It will also map area with sectional curvature k(σ, p) into areas with the same sectional curvature, and so on. The set of all equi-Gaussian curvature foldings of M into N will be denoted by.

  11. Synovial folds in equine articular process joints

    DEFF Research Database (Denmark)

    Thomsen, Line Nymann; Berg, Lise Charlotte; Markussen, Bo

    2013-01-01

    Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses.......Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses....

  12. Old fold in a new X-ray diffraction dataset? Low-resolution molecular replacement using representative structural templates can provide phase information.

    Science.gov (United States)

    Rajavel, M; Warrier, Thulasi; Gopal, B

    2006-09-01

    The advent of structural genomics has led to a dramatic increase in the number of structures deposited in the Protein Data Bank. The number of new folds, however, still remains a very small fraction of the total number of deposited structures. Recent data on the progress of the structural genomics initiative reveals that more than 85% of target proteins that progress to the stage of data collection and structure determination have a known fold. Enzymes, which tend to exploit reaction space while adopting a common stable scaffold, contribute significantly to this observation. Herein, we evaluate a method to examine the "old fold in a new dataset" scenario likely to be encountered in the structural genomics pipeline. We demonstrate that a fold detection strategy based on secondary structure signatures followed by molecular replacement using a minimalist model can be effectively used to solve the phase problem in X-ray crystallography without further recourse to heavy atom derivatives or multiple anomalous dispersion techniques. Three common folds-the triosephosphate isomerase (TIM), adenine nucleotide alpha hydrolase-like (HUP), and RNA recognition motif (RRM)-were examined using this approach. The results presented herein also provide an estimate of the extent of phase information that can be derived from a single domain in a large multidomain structure. (c) 2006 Wiley-Liss, Inc.

  13. Recognition of Disorders and Emotional Problems of Deaf Children Using House-Tree-Person and Draw-A-Person Tests in Comparison with Normal Children of Hamadan Province

    Directory of Open Access Journals (Sweden)

    D. Amini

    2013-04-01

    Full Text Available Introduction & Objective: Deaf children have special emotional reactions, Understanding these characteristics and problems can help medical and paramedical professionals, parents and teachers to reach the purpose of behavioral adaptability.The present study was performed in order to recognize disorders, emotional problems and functions of deaf children compared with normal children in emotional components of anxiety, depression, aggression, impulsiv-ity and lack of compromise. Materials & Methods: In order to recognize emotional disorders and problems of deaf children, sample groups of 120 male and female patients (60 deaf children and 60 children with nor-mal hearing with equal number of male and female enrolled in primary schools of Hamadan province were selected by multi stage randomly sampling in this casual_comparative study. House-Tree-Person (HTP and Draw-A-Person tests (DAP were used to determine their emotional problems. Results:Our results indicate that in terms of parameters related to the two tests (distance of three components of each other ,anxiety, aggression, depression and impulsivity and lack of compromise, participants' overall scores in two tests by major scales such as anxiety (?=0.01, P< 0.05; 3.48, 3.13 aggression (?= 0.05 , 0.01, P< 0.05; 6.12 ,3.97 depression (?=0.05 P<0.05 ; 3.75,3.81 , impulsivity (?=0.05, 0.01, P<0.05 ; 3.47, 3.01 and lack of compromise (?=0.05, 0.01, P<0.05; 4.89, 4.95 are significantly different from each other. Conclusion:The deaf children in terms of denotative parameters related to the two tests are sig-nificantly different from normal children; and the overall scores obtained on each of the scales generally show a significant difference with normal children,In the deaf group with regard to gender variable (male and female significant differences in some of the scales such as distance of three components of each other ,anxiety, aggression, depression and lack of compromise iare observed between

  14. Recognition tunneling

    International Nuclear Information System (INIS)

    Lindsay, Stuart; He Jin; Zhang Peiming; Chang Shuai; Huang Shuo; Sankey, Otto; Hapala, Prokop; Jelinek, Pavel

    2010-01-01

    Single molecules in a tunnel junction can now be interrogated reliably using chemically functionalized electrodes. Monitoring stochastic bonding fluctuations between a ligand bound to one electrode and its target bound to a second electrode ('tethered molecule-pair' configuration) gives insight into the nature of the intermolecular bonding at a single molecule-pair level, and defines the requirements for reproducible tunneling data. Simulations show that there is an instability in the tunnel gap at large currents, and this results in a multiplicity of contacts with a corresponding spread in the measured currents. At small currents (i.e. large gaps) the gap is stable, and functionalizing a pair of electrodes with recognition reagents (the 'free-analyte' configuration) can generate a distinct tunneling signal when an analyte molecule is trapped in the gap. This opens up a new interface between chemistry and electronics with immediate implications for rapid sequencing of single DNA molecules. (topical review)

  15. Recognition tunneling

    Energy Technology Data Exchange (ETDEWEB)

    Lindsay, Stuart; He Jin; Zhang Peiming; Chang Shuai; Huang Shuo [Biodesign Institute, Arizona State University, Tempe, AZ 85287 (United States); Sankey, Otto [Department of Physics, Arizona State University, Tempe, AZ 85287 (United States); Hapala, Prokop; Jelinek, Pavel [Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnicka 10, 1862 53, Prague (Czech Republic)

    2010-07-02

    Single molecules in a tunnel junction can now be interrogated reliably using chemically functionalized electrodes. Monitoring stochastic bonding fluctuations between a ligand bound to one electrode and its target bound to a second electrode ('tethered molecule-pair' configuration) gives insight into the nature of the intermolecular bonding at a single molecule-pair level, and defines the requirements for reproducible tunneling data. Simulations show that there is an instability in the tunnel gap at large currents, and this results in a multiplicity of contacts with a corresponding spread in the measured currents. At small currents (i.e. large gaps) the gap is stable, and functionalizing a pair of electrodes with recognition reagents (the 'free-analyte' configuration) can generate a distinct tunneling signal when an analyte molecule is trapped in the gap. This opens up a new interface between chemistry and electronics with immediate implications for rapid sequencing of single DNA molecules. (topical review)

  16. Indirect recognition

    DEFF Research Database (Denmark)

    Lund, Christian; Rachman, Noer Fauzi

    2018-01-01

    Government institutions and local people in Indonesia have entrenched, resurrected, and reinvented space through their different territorial and property claims. From colonial times, onward, government institutions have dissolved local political orders and territorialized and reordered spatial...... categories are struggled over, and groups of actors seek to legitimate their presence, their activities, and their resource use by occupation, mapping, and construction of "public" infrastructure. In the case of conservation in the Mount Halimun-Salak National Park, we find that rather than one overarching...... important legal and political work. After the authoritarian New Order regime, in particular, claims to citizenship worked as indirect property claims, and indirect recognition of such claims are important because they serve as pragmatic proxies for formal property rights. Two case studies examine how people...

  17. Genetic Algorithms and Their Application to the Protein Folding Problem

    Science.gov (United States)

    1993-12-01

    Example of a Mutation ............................................................................. 16 Figure 4. A Three Amino Acid ProteinA ...given its primary structure. HH Figure 4. A Three Amino Acid ProteinA 28 3.1 Background Proteins are an integral part of everyday life. The function of

  18. Non-symmetric localized fold of a floating sheet

    Science.gov (United States)

    Rivetti, Marco

    2013-03-01

    An elastic sheet lying on the surface of a liquid, if axially compressed, shows a transition from a smooth sinusoidal pattern to a well-localized fold. This wrinkle-to-fold transition is a manifestation of a localized buckling. The symmetric and antisymmetric shapes of the fold have recently been described by Diamant and Witten (2011), who found two exact solutions of the nonlinear equilibrium equations. In this Note, we show that these solutions can be generalized to a continuous family of solutions, which yields non-symmetric shapes of the fold. We prove that non-symmetric solutions also describe the shape of a soft strip withdrawn from a liquid bath, a physical problem that allows us to easily observe portions of non-symmetric profiles.

  19. Criteria for folding in structure-based models of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Wołek, Karol; Cieplak, Marek, E-mail: mc@ifpan.edu.pl [Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw (Poland)

    2016-05-14

    In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very low thermodynamic stability, especially when the contact map used is too sparse. We consider six different structure-based models and show that allowing for a small, but model-dependent, percentage of the native contacts not being established boosts the folding temperature substantially while affecting the time scales of folding only in a minor way. We also compare other properties of the six models. We show that the choice of the description of the backbone stiffness has a substantial effect on the values of characteristic temperatures that relate both to equilibrium and kinetic properties. Models without any backbone stiffness (like the self-organized polymer) are found to perform similar to those with the stiffness, including in the studies of stretching.

  20. Improving decoy databases for protein folding algorithms

    KAUST Repository

    Lindsey, Aaron

    2014-01-01

    Copyright © 2014 ACM. Predicting protein structures and simulating protein folding are two of the most important problems in computational biology today. Simulation methods rely on a scoring function to distinguish the native structure (the most energetically stable) from non-native structures. Decoy databases are collections of non-native structures used to test and verify these functions. We present a method to evaluate and improve the quality of decoy databases by adding novel structures and removing redundant structures. We test our approach on 17 different decoy databases of varying size and type and show significant improvement across a variety of metrics. We also test our improved databases on a popular modern scoring function and show that they contain a greater number of native-like structures than the original databases, thereby producing a more rigorous database for testing scoring functions.

  1. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested that prot......The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested...... that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...

  2. Bodies Folded in Migrant Crypts

    DEFF Research Database (Denmark)

    Galis, Vasilis; Tzokas, Spyros; Tympas, Aristotle

    2016-01-01

    , and to performing mobility in general. Dis/ability and migration have not been associated in the literature. We adopt an analytical symmetry between humans and non-humans, in this case between bodies and crypts. By suggesting an infected, ambivalent, and hybrid approach to the human subject, the body......This article considers media narratives that suggest that hiding in trucks, buses, and other vehicles to cross borders has, in fact, been a common practice in the context of migration to, and within, Europe. We aim to problematize how the tension between the materiality of bordering practices...... and human migrants generates a dis/abled subject. In this context, dis/ability may be a cause or consequence of migration, both in physical/material (the folding of bodies in the crypt) and cultural/semiotic terms, and may become a barrier to accessing protection, to entering and/or crossing a country...

  3. Fluoroangiographic picture of chorioretinal folds

    International Nuclear Information System (INIS)

    Kalvodova, B.; Karel, I.

    1988-01-01

    Fluoroangiographic pictures of chorioretinal folds (CRF) were analyzed in 13 eyes of 12 patients. The orbital origin of CRF was present in 8 eyes (orbital tumors in 7 eyes and thyroid ophthalmopathy in one eye), the intraocular origin in 5 eyes (hypotonic postoperative syndrome caused by the detachment of the choroid in 3 eyes, Irwine-Gass syndrome in 2 eyes, scleral bucle used for retinal detachment repair in one eye). The fluoroangiographic findings of CRF were determined by changes in the pigmented epithelium and choroid of a different degree, which modified the clinical picture of the basic disease. Fluorescein angiography is a very useful method for the differentiation of retinal and choroid detachments but with a limited possibility to determine the etiological factor of the disease. (author). 6 figs., 2 tabs., 32 refs

  4. Dynamic Programming Algorithms in Speech Recognition

    Directory of Open Access Journals (Sweden)

    Titus Felix FURTUNA

    2008-01-01

    Full Text Available In a system of speech recognition containing words, the recognition requires the comparison between the entry signal of the word and the various words of the dictionary. The problem can be solved efficiently by a dynamic comparison algorithm whose goal is to put in optimal correspondence the temporal scales of the two words. An algorithm of this type is Dynamic Time Warping. This paper presents two alternatives for implementation of the algorithm designed for recognition of the isolated words.

  5. Optical syntactic pattern recognition by fuzzy scoring

    Energy Technology Data Exchange (ETDEWEB)

    Srinivasan, R.; Kinser, J.; Schamschula, M.; Shamir, J.; Caulfield, H.J. [Center for Applied Optical Sciences, Department of Physics, Alabama A& M University, Normal, Alabama 35762 (United States)

    1996-06-01

    A novel syntactic approach is introduced to treat particular problems in pattern recognition. The procedure is implemented by the use of optical correlation methods for identifying the various primitives that appear in the input pattern, and their importance is determined by fuzzy relational scoring. Robust pattern recognition with tolerance to normal variations is demonstrated, indicating an efficient new approach for optical pattern recognition. {copyright} {ital 1996 Optical Society of America.}

  6. Mathematical symbol hypothesis recognition with rejection option

    OpenAIRE

    Julca-Aguilar , Frank; Hirata , Nina ,; Viard-Gaudin , Christian; Mouchère , Harold; Medjkoune , Sofiane

    2014-01-01

    International audience; In the context of handwritten mathematical expressions recognition, a first step consist on grouping strokes (segmentation) to form symbol hypotheses: groups of strokes that might represent a symbol. Then, the symbol recognition step needs to cope with the identification of wrong segmented symbols (false hypotheses). However, previous works on symbol recognition consider only correctly segmented symbols. In this work, we focus on the problem of mathematical symbol reco...

  7. A Bayesian classifier for symbol recognition

    OpenAIRE

    Barrat , Sabine; Tabbone , Salvatore; Nourrissier , Patrick

    2007-01-01

    URL : http://www.buyans.com/POL/UploadedFile/134_9977.pdf; International audience; We present in this paper an original adaptation of Bayesian networks to symbol recognition problem. More precisely, a descriptor combination method, which enables to improve significantly the recognition rate compared to the recognition rates obtained by each descriptor, is presented. In this perspective, we use a simple Bayesian classifier, called naive Bayes. In fact, probabilistic graphical models, more spec...

  8. Exemplar-based Face Recognition from Video

    DEFF Research Database (Denmark)

    Krüger, Volker; Zhou, Shaohua; Chellappa, Rama

    2005-01-01

    The ability to integrate information over time in order to come to a conclusion is a strength of a cognitive system. It allows the cognitive system to verify insecure observations: This is the case when the data is noisy or the conditions are non-optimal exploit general knowledge about spatio......-temporal relations: This allows the system to use dynamics as well as to generate warnings when 'implausible' situations occur or to circumvent these altogether. We have studied the effectiveness of temporal integration for recognition purposes by using the face recognition as an example problem. Face recognition...... is a prominent problem and has been studied more extensively than almost any other recognition problem. An observation is that face recognition works well in ideal conditions. If those conditions, however, are not met, then all present algorithms break down disgracefully. This probelm appears to be general...

  9. The parallel universe of RNA folding.

    Science.gov (United States)

    Batey, R T; Doudna, J A

    1998-05-01

    How do large RNA molecules find their active conformations among a universe of possible structures? Two recent studies reveal that RNA folding is a rapid and ordered process, with surprising similarities to protein folding mechanisms.

  10. A New Heuristic Algorithm for Protein Folding in the HP Model.

    Science.gov (United States)

    Traykov, Metodi; Angelov, Slav; Yanev, Nicola

    2016-08-01

    This article presents an efficient heuristic for protein folding. The protein folding problem is to predict the compact three-dimensional structure of a protein based on its amino acid sequence. The focus is on an original integer programming model derived from a platform used for Contact Map Overlap problem.

  11. Ear recognition: a complete system

    Science.gov (United States)

    Abaza, Ayman; Harrison, Mary Ann F.

    2013-05-01

    Ear Recognition has recently received significant attention in the literature. Even though current ear recognition systems have reached a certain level of maturity, their success is still limited. This paper presents an efficient complete ear-based biometric system that can process five frames/sec; Hence it can be used for surveillance applications. The ear detection is achieved using Haar features arranged in a cascaded Adaboost classifier. The feature extraction is based on dividing the ear image into several blocks from which Local Binary Pattern feature distributions are extracted. These feature distributions are then fused at the feature level to represent the original ear texture in the classification stage. The contribution of this paper is three fold: (i) Applying a new technique for ear feature extraction, and studying various optimization parameters for that technique; (ii) Presenting a practical ear recognition system and a detailed analysis about error propagation in that system; (iii) Studying the occlusion effect of several ear parts. Detailed experiments show that the proposed ear recognition system achieved better performance (94:34%) compared to other shape-based systems as Scale-invariant feature transform (67:92%). The proposed approach can also handle efficiently hair occlusion. Experimental results show that the proposed system can achieve about (78%) rank-1 identification, even in presence of 60% occlusion.

  12. View based approach to forensic face recognition

    NARCIS (Netherlands)

    Dutta, A.; van Rootseler, R.T.A.; Veldhuis, Raymond N.J.; Spreeuwers, Lieuwe Jan

    Face recognition is a challenging problem for surveillance view images commonly encountered in a forensic face recognition case. One approach to deal with a non-frontal test image is to synthesize the corresponding frontal view image and compare it with frontal view reference images. However, it is

  13. The Army word recognition system

    Science.gov (United States)

    Hadden, David R.; Haratz, David

    1977-01-01

    The application of speech recognition technology in the Army command and control area is presented. The problems associated with this program are described as well as as its relevance in terms of the man/machine interactions, voice inflexions, and the amount of training needed to interact with and utilize the automated system.

  14. Selective Search for Object Recognition

    NARCIS (Netherlands)

    Uijlings, J.R.; van de Sande, K.E.A.; Gevers, T.; Smeulders, A.W.M.

    This paper addresses the problem of generating possible object locations for use in object recognition. We introduce selective search which combines the strength of both an exhaustive search and segmentation. Like segmentation, we use the image structure to guide our sampling process. Like

  15. Diagnosing plant problems

    Science.gov (United States)

    Cheryl A. Smith

    2008-01-01

    Diagnosing Christmas tree problems can be a challenge, requiring a basic knowledge of plant culture and physiology, the effect of environmental influences on plant health, and the ability to identify the possible causes of plant problems. Developing a solution or remedy to the problem depends on a proper diagnosis, a process that requires recognition of a problem and...

  16. ALGORITHM OF OBJECT RECOGNITION

    Directory of Open Access Journals (Sweden)

    Loktev Alexey Alexeevich

    2012-10-01

    Full Text Available The second important problem to be resolved to the algorithm and its software, that comprises an automatic design of a complex closed circuit television system, represents object recognition, by virtue of which an image is transmitted by the video camera. Since imaging of almost any object is dependent on many factors, including its orientation in respect of the camera, lighting conditions, parameters of the registering system, static and dynamic parameters of the object itself, it is quite difficult to formalize the image and represent it in the form of a certain mathematical model. Therefore, methods of computer-aided visualization depend substantially on the problems to be solved. They can be rarely generalized. The majority of these methods are non-linear; therefore, there is a need to increase the computing power and complexity of algorithms to be able to process the image. This paper covers the research of visual object recognition and implementation of the algorithm in the view of the software application that operates in the real-time mode

  17. Solitons and protein folding: An In Silico experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ilieva, N., E-mail: nevena.ilieva@parallel.bas.bg [Institute of Information and Communication Technologies, Bulgarian Aacademy of Sciences, Sofia (Bulgaria); Dai, J., E-mail: daijing491@gmail.com [School of Physics, Beijing Institute of Technology, Beijing (China); Sieradzan, A., E-mail: adams86@wp.pl [Faculty of Chemistry, University of Gdańsk, Gdańsk (Poland); Niemi, A., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, Uppsala (Sweden); LMPT–CNRS, Université de Tours, Tours (France)

    2015-10-28

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

  18. Laser induced temperature jump investigations of fast protein folding dynamics

    Science.gov (United States)

    Qiu, Linlin

    Protein folding has a large parameter space, diverse mechanism, and multipath kinetics. However, there are some common features many proteins share in their folding processes: all seem to fold at the rates much faster than the random conformation search, and all fold into the structures which have the highly regular motifs like alpha-helices, beta-sheets and turns. Understanding how fast proteins can fold is one of the central issues in solving the protein folding problem. Ultrafast folding kinetics had not been accessible until a few sub-millisecond probes were invented and applied lately. We constructed a laser induced temperature jump spectrometer which is a great utility in identifying the local structure and tertiary contact formation of proteins on the time scale from 10 -8 to 10-3 s with time resolution of 10 -9 s. With this spectrometer we studied the fast folding mini-protein, TrpCage and a few short stable beta-hairpins, the TrpZip series. Studying TrpCage was a major breakthrough it was a pioneer protein model which brought experiment and simulation very close: its structures measured by NMR and predicted by the molecular dynamics were amazingly alike. Our kinetic results showed that it folds in 4 mus at room temperature which turned out to be the fastest ever known for protein-like molecules. Also this folding time constant is consistent with what was later on simulated by distributed computation. TrpZips are among the smallest and stablest polypeptide chains which form secondary structures. They are slightly different from each other based on structural stability and by forming various types of beta-hairpins which are the minimum units of beta tertiary structure. The beta-hairpins form in the time range of 1--10 mus that confirms the theory that loop formation is controlled by the diffusion process (˜mus). We also investigated the kinetics of the protein chain collapse, a very controversial problem. By comparing the collapse of the foldable 104

  19. A High Performance Banknote Recognition System Based on a One-Dimensional Visible Light Line Sensor.

    Science.gov (United States)

    Park, Young Ho; Kwon, Seung Yong; Pham, Tuyen Danh; Park, Kang Ryoung; Jeong, Dae Sik; Yoon, Sungsoo

    2015-06-15

    An algorithm for recognizing banknotes is required in many fields, such as banknote-counting machines and automatic teller machines (ATM). Due to the size and cost limitations of banknote-counting machines and ATMs, the banknote image is usually captured by a one-dimensional (line) sensor instead of a conventional two-dimensional (area) sensor. Because the banknote image is captured by the line sensor while it is moved at fast speed through the rollers inside the banknote-counting machine or ATM, misalignment, geometric distortion, and non-uniform illumination of the captured images frequently occur, which degrades the banknote recognition accuracy. To overcome these problems, we propose a new method for recognizing banknotes. The experimental results using two-fold cross-validation for 61,240 United States dollar (USD) images show that the pre-classification error rate is 0%, and the average error rate for the final recognition of the USD banknotes is 0.114%.

  20. Anatomy and Histology of an Epicanthal Fold.

    Science.gov (United States)

    Park, Jae Woo; Hwang, Kun

    2016-06-01

    The aim of this study is to elucidate the precise anatomical and histological detail of the epicanthal fold.Thirty-two hemifaces of 16 Korean adult cadavers were used in this study (30 hemifaces with an epicanthal fold, 2 without an epicanthal fold). In 2 patients who had an epicanthoplasty, the epicanthal folds were sampled.In a dissection, the periorbital skin and subcutaneous tissues were removed and the epicanthal fold was observed in relation to each part of the orbicularis oculi muscle. Specimens including the epicanthal fold were embeddedin in paraffin, sectioned at 10 um, and stained with Hematoxylin-Eosin. The horizontal section in the level of the paplebral fissure was made and the prepared slides were observed under a light microscope.In the specimens without an epicanthal fold, no connection between the upper preseptal muscle and the lower preseptal muscle was found. In the specimens with an epicanthal fold, a connection of the upper preseptal muscle to the lower preseptal muscle was observed. It was present in all 15 hemifaces (100%). There was no connection between the pretarsal muscles. In a horizontal section, the epicanthal fold was composed of 3 compartments: an outer skin lining, a core structure, and an innerskin lining. The core structure was mainly composed of muscular fibers and fibrotic tissue and they were intermingled.Surgeons should be aware of the anatomical details of an epicanthal fold. In removing or reconstructing an epicanthal fold, the fibromuscular core band should also be removed or reconstructed.

  1. Simultaneous tracking and activity recognition

    DEFF Research Database (Denmark)

    Manfredotti, Cristina Elena; Fleet, David J.; Hamilton, Howard J.

    2011-01-01

    Many tracking problems involve several distinct objects interacting with each other. We develop a framework that takes into account interactions between objects allowing the recognition of complex activities. In contrast to classic approaches that consider distinct phases of tracking and activity...... recognition, our framework performs these two tasks simultaneously. In particular, we adopt a Bayesian standpoint where the system maintains a joint distribution of the positions, the interactions and the possible activities. This turns out to be advantegeous, as information about the ongoing activities can...

  2. Viscoelastic properties of the false vocal fold

    Science.gov (United States)

    Chan, Roger W.

    2004-05-01

    The biomechanical properties of vocal fold tissues have been the focus of many previous studies, as vocal fold viscoelasticity critically dictates the acoustics and biomechanics of phonation. However, not much is known about the viscoelastic response of the ventricular fold or false vocal fold. It has been shown both clinically and in computer simulations that the false vocal fold may contribute significantly to the aerodynamics and sound generation processes of human voice production, with or without flow-induced oscillation of the false fold. To better understand the potential role of the false fold in phonation, this paper reports some preliminary measurements on the linear and nonlinear viscoelastic behavior of false vocal fold tissues. Linear viscoelastic shear properties of human false fold tissue samples were measured by a high-frequency controlled-strain rheometer as a function of frequency, and passive uniaxial tensile stress-strain response of the tissue samples was measured by a muscle lever system as a function of strain and loading rate. Elastic moduli (Young's modulus and shear modulus) of the false fold tissues were calculated from the measured data. [Work supported by NIH.

  3. Face Recognition using Approximate Arithmetic

    DEFF Research Database (Denmark)

    Marso, Karol

    Face recognition is image processing technique which aims to identify human faces and found its use in various different fields for example in security. Throughout the years this field evolved and there are many approaches and many different algorithms which aim to make the face recognition as effective...... as possible. The use of different approaches such as neural networks and machine learning can lead to fast and efficient solutions however, these solutions are expensive in terms of hardware resources and power consumption. A possible solution to this problem can be use of approximate arithmetic. In many image...... processing applications the results do not need to be completely precise and use of the approximate arithmetic can lead to reduction in terms of delay, space and power consumption. In this paper we examine possible use of approximate arithmetic in face recognition using Eigenfaces algorithm....

  4. A comparison of RNA folding measures

    DEFF Research Database (Denmark)

    Freyhult, E.; Gardner, P. P.; Moulton, V.

    2005-01-01

    Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare...... the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. Results Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE) than...... random sequences with the same dinucleotide frequency. Moreover, even when the MFE is significant, many ncRNAs appear to not have a unique fold, but rather several alternative folds, at least when folded in silico. Furthermore, we find that the six investigated measures are correlated to varying degrees...

  5. Adaptive Origami for Efficiently Folded Structures

    Science.gov (United States)

    2016-02-01

    AFRL-RQ-WP-TR-2016-0020 ADAPTIVE ORIGAMI FOR EFFICIENTLY FOLDED STRUCTURES James J. Joo and Greg Reich Design and Analysis Branch... ORIGAMI FOR EFFICIENTLY FOLDED STRUCTURES 5a. CONTRACT NUMBER In-house 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 61102F 6. AUTHOR(S) James J...NOTES PA Case Number: 88ABW-2016-0843; Clearance Date: 25 February 2016. 14. ABSTRACT Origami , the art of paper folding, transforms a flat sheet into

  6. Spherical images and inextensible curved folding

    Science.gov (United States)

    Seffen, Keith A.

    2018-02-01

    In their study, Duncan and Duncan [Proc. R. Soc. London A 383, 191 (1982), 10.1098/rspa.1982.0126] calculate the shape of an inextensible surface folded in two about a general curve. They find the analytical relationships between pairs of generators linked across the fold curve, the shape of the original path, and the fold angle variation along it. They present two special cases of generator layouts for which the fold angle is uniform or the folded curve remains planar, for simplifying practical folding in sheet-metal processes. We verify their special cases by a graphical treatment according to a method of Gauss. We replace the fold curve by a piecewise linear path, which connects vertices of intersecting pairs of hinge lines. Inspired by the d-cone analysis by Farmer and Calladine [Int. J. Mech. Sci. 47, 509 (2005), 10.1016/j.ijmecsci.2005.02.013], we construct the spherical images for developable folding of successive vertices: the operating conditions of the special cases in Duncan and Duncan are then revealed straightforwardly by the geometric relationships between the images. Our approach may be used to synthesize folding patterns for novel deployable and shape-changing surfaces without need of complex calculation.

  7. Fold maps and positive topological quantum field theories

    Energy Technology Data Exchange (ETDEWEB)

    Wrazidlo, Dominik Johannes

    2017-04-12

    The notion of positive TFT as coined by Banagl is specified by an axiomatic system based on Atiyah's original axioms for TFTs. By virtue of a general framework that is based on the concept of Eilenberg completeness of semirings from computer science, a positive TFT can be produced rigorously via quantization of systems of fields and action functionals - a process inspired by Feynman's path integral from classical quantum field theory. The purpose of the present dissertation thesis is to investigate a new differential topological invariant for smooth manifolds that arises as the state sum of the fold map TFT, which has been constructed by Banagl as a example of a positive TFT. By eliminating an internal technical assumption on the fields of the fold map TFT, we are able to express the informational content of the state sum in terms of an extension problem for fold maps from cobordisms into the plane. Next, we use the general theory of generic smooth maps into the plane to improve known results about the structure of the state sum in arbitrary dimensions, and to determine it completely in dimension two. The aggregate invariant of a homotopy sphere, which is derived from the state sum, naturally leads us to define a filtration of the group of homotopy spheres in order to understand the role of indefinite fold lines beyond a theorem of Saeki. As an application, we show how Kervaire spheres can be characterized by indefinite fold lines in certain dimensions.

  8. Modeling and imaging of the vocal fold vibration for voice health

    DEFF Research Database (Denmark)

    Granados, Alba

    of vibration, showing dierent characteristics in normal and abnormal phonation. In the last part of this thesis research, the optical ow algorithm for data acquisition as well as the biomechanical model of the vocal fold are used to formulate a nonstationary statistical inverse problem for vocal fold features......, analysis and inference. This thesis deals with biomechanical models of the vocal fold, specially of the collision, and laryngeal videoendoscopic analysis procedures suitable for the inference of the underlying vocal fold characteristics. The rst part of this research is devoted to frictionless contact...... modeling during asymmetric vocal fold vibration. The prediction problem is numerically addressed with a self-sustained three-dimensional nite element model of the vocal fold with position-based contact constraints. A novel contact detection mechanism is shown to successfully detect collision in asymmetric...

  9. INFO-RNA--a fast approach to inverse RNA folding.

    Science.gov (United States)

    Busch, Anke; Backofen, Rolf

    2006-08-01

    The structure of RNA molecules is often crucial for their function. Therefore, secondary structure prediction has gained much interest. Here, we consider the inverse RNA folding problem, which means designing RNA sequences that fold into a given structure. We introduce a new algorithm for the inverse folding problem (INFO-RNA) that consists of two parts; a dynamic programming method for good initial sequences and a following improved stochastic local search that uses an effective neighbor selection method. During the initialization, we design a sequence that among all sequences adopts the given structure with the lowest possible energy. For the selection of neighbors during the search, we use a kind of look-ahead of one selection step applying an additional energy-based criterion. Afterwards, the pre-ordered neighbors are tested using the actual optimization criterion of minimizing the structure distance between the target structure and the mfe structure of the considered neighbor. We compared our algorithm to RNAinverse and RNA-SSD for artificial and biological test sets. Using INFO-RNA, we performed better than RNAinverse and in most cases, we gained better results than RNA-SSD, the probably best inverse RNA folding tool on the market. www.bioinf.uni-freiburg.de?Subpages/software.html.

  10. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

    Science.gov (United States)

    Das, Payel; Moll, Mark; Stamati, Hernán; Kavraki, Lydia E.; Clementi, Cecilia

    2006-01-01

    The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the “simple” case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear dimensionality reduction. We validate the usefulness of this method by characterizing the folding landscape associated with a coarse-grained protein model of src homology 3 as sampled by molecular dynamics simulations. The folding free-energy landscape projected on the few relevant coordinates emerging from the dimensionality reduction can correctly identify the transition-state ensemble of the reaction. The first embedding dimension efficiently captures the evolution of the folding process along the main folding route. These results clearly show that the proposed method can efficiently find a low-dimensional representation of a complex process such as protein folding. PMID:16785435

  11. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

    OpenAIRE

    Das, Payel; Moll, Mark; Stamati, Hernán; Kavraki, Lydia E.; Clementi, Cecilia

    2006-01-01

    The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the “simple” case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear dimensionality reduction. We validate the usefulness of this method by characterizing the folding landscape associated with a coarse-grained protein mo...

  12. Merging monads and folds for functional programming

    NARCIS (Netherlands)

    Meijer, E.; Jeuring, J.T.

    1995-01-01

    These notes discuss the simultaneous use of generalised fold operators and monads to structure functional programs. Generalised fold operators structure programs after the decomposition of the value they consume. Monads structure programs after the computation of the value they produce. Our programs

  13. Folded tandem ion accelerator facility at Trombay

    Indian Academy of Sciences (India)

    Keywords. Folded tandem ion accelerator; carbon beam; magnets; electrostatic deflector; quadrupole lenses; foil/gas strippers; Rutherford back scattering. Abstract. The folded tandem ion accelerator (FOTIA) project at BARC has been commissioned. The analysed carbon beams of 40 nA(3+) and 25 nA(4+), at terminal ...

  14. Accelerated molecular dynamics simulations of protein folding.

    Science.gov (United States)

    Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew

    2015-07-30

    Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.

  15. THE ALPHA/BETA-HYDROLASE FOLD

    NARCIS (Netherlands)

    OLLIS, DL; CHEAH, E; CYGLER, M; FROLOW, F; FRANKEN, SM; HAREL, M; REMINGTON, SJ; SILMAN, [No Value; SCHRAG, J; SUSSMAN, JL; VERSCHUEREN, KHG; GOLDMAN, A

    We have identified a new protein fold-the alpha/beta-hydrolase fold-that is common to several hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is similar: an alpha/beta-sheet, not barrel, of eight beta-sheets connected by alpha-helices. These

  16. Graph-representation of oxidative folding pathways

    Directory of Open Access Journals (Sweden)

    Kaján László

    2005-01-01

    Full Text Available Abstract Background The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS which can also be isolated and characterized. Each DIS corresponds to a family of folding states (conformations that the given DIS can adopt in three dimensions. Results The oxidative folding space can be represented as a network of DIS states interconnected by disulfide interchange reactions that can either create/abolish or rearrange disulfide bridges. We propose a simple 3D representation wherein the states having the same number of disulfide bridges are placed on separate planes. In this representation, the shuffling transitions are within the planes, and the redox edges connect adjacent planes. In a number of experimentally studied cases (bovine pancreatic trypsin inhibitor, insulin-like growth factor and epidermal growth factor, the observed intermediates appear as part of contiguous oxidative folding pathways. Conclusions Such networks can be used to visualize folding pathways in terms of the experimentally observed intermediates. A simple visualization template written for the Tulip package http://www.tulip-software.org/ can be obtained from V.A.

  17. Simultaneous Indoor Tracking and Activity Recognition Using Pyroelectric Infrared Sensors

    Directory of Open Access Journals (Sweden)

    Xiaomu Luo

    2017-07-01

    Full Text Available Indoor human tracking and activity recognition are fundamental yet coherent problems for ambient assistive living. In this paper, we propose a method to address these two critical issues simultaneously. We construct a wireless sensor network (WSN, and the sensor nodes within WSN consist of pyroelectric infrared (PIR sensor arrays. To capture the tempo-spatial information of the human target, the field of view (FOV of each PIR sensor is modulated by masks. A modified partial filter algorithm is utilized to decode the location of the human target. To exploit the synergy between the location and activity, we design a two-layer random forest (RF classifier. The initial activity recognition result of the first layer is refined by the second layer RF by incorporating various effective features. We conducted experiments in a mock apartment. The mean localization error of our system is about 0.85 m. For five kinds of daily activities, the mean accuracy for 10-fold cross-validation is above 92%. The encouraging results indicate the effectiveness of our system.

  18. Fold and Fit: Space Conserving Shape Editing

    KAUST Repository

    Ibrahim, Mohamed

    2017-09-01

    We present a framework that folds man-made objects in a structure-aware manner for space-conserving storage and transportation. Given a segmented 3D mesh of a man-made object, our framework jointly optimizes for joint locations, the folding order, and folding angles for each part of the model, enabling it to transform into a spatially efficient configuration while keeping its original functionality as intact as possible. That is, if a model is supposed to withstand several forces in its initial state to serve its functionality, our framework places the joints between the parts of the model such that the model can withstand forces with magnitudes that are comparable to the magnitudes applied on the unedited model. Furthermore, if the folded shape is not compact, our framework proposes further segmentation of the model to improve its compactness in its folded state.

  19. Geometric U-folds in four dimensions

    Science.gov (United States)

    Lazaroiu, C. I.; Shahbazi, C. S.

    2018-01-01

    We describe a general construction of geometric U-folds compatible with a non-trivial extension of the global formulation of four-dimensional extended supergravity on a differentiable spin manifold. The topology of geometric U-folds depends on certain flat fiber bundles which encode how supergravity fields are globally glued together. We show that smooth non-trivial U-folds of this type can exist only in theories where both the scalar and space-time manifolds have non-trivial fundamental group and in addition the scalar map of the solution is homotopically non-trivial. Consistency with string theory requires smooth geometric U-folds to be glued using subgroups of the effective discrete U-duality group, implying that the fundamental group of the scalar manifold of such solutions must be a subgroup of the latter. We construct simple examples of geometric U-folds in a generalization of the axion-dilaton model of \

  20. Fan-fold shielded electrical leads

    Science.gov (United States)

    Rohatgi, Rajeev R.; Cowan, Thomas E.

    1996-01-01

    Fan-folded electrical leads made from copper cladded Kapton, for example, with the copper cladding on one side serving as a ground plane and the copper cladding on the other side being etched to form the leads. The Kapton is fan folded with the leads located at the bottom of the fan-folds. Electrical connections are made by partially opening the folds of the fan and soldering, for example, the connections directly to the ground plane and/or the lead. The fan folded arrangement produces a number of advantages, such as electrically shielding the leads from the environment, is totally non-magnetic, and has a very low thermal conductivity, while being easy to fabricate.

  1. Face Detection and Recognition

    National Research Council Canada - National Science Library

    Jain, Anil K

    2004-01-01

    This report describes research efforts towards developing algorithms for a robust face recognition system to overcome many of the limitations found in existing two-dimensional facial recognition systems...

  2. The Main Cognitive Model of Visual Recognition: Contour Recognition

    OpenAIRE

    Chen, YongHong

    2017-01-01

    In this paper, we will study the following pattern recognition problem: Every pattern is a 3-dimensional graph, its surface can be split up into some regions, every region is composed of the pixels with the approximately same colour value and the approximately same depth value that is distance to eyes, and there may also be some contours, e.g., literal contours, on a surface of every pattern. For this problem we reveal the inherent laws. Moreover, we establish a cognitive model to reflect the...

  3. Stretched versus compressed exponential kinetics in α-helix folding

    International Nuclear Information System (INIS)

    Hamm, Peter; Helbing, Jan; Bredenbeck, Jens

    2006-01-01

    In a recent paper (J. Bredenbeck, J. Helbing, J.R. Kumita, G.A. Woolley, P. Hamm, α-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time resolved IR spectroscopy, Proc. Natl. Acad. Sci USA 102 (2005) 2379), we have investigated the folding of a photo-switchable α-helix with a kinetics that could be fit by a stretched exponential function exp(-(t/τ) β ). The stretching factor β became smaller as the temperature was lowered, a result which has been interpreted in terms of activated diffusion on a rugged energy surface. In the present paper, we discuss under which conditions diffusion problems occur with stretched exponential kinetics (β 1). We show that diffusion problems do have a strong tendency to yield stretched exponential kinetics, yet, that there are conditions (strong perturbation from equilibrium, performing the experiment in the folding direction) under which compressed exponential kinetics would be expected instead. We discuss the kinetics on free energy surfaces predicted by simple initiation-propagation models (zipper models) of α-helix folding, as well as by folding funnel models. We show that our recent experiment has been performed under condition for which models with strong downhill driving force, such as the zipper model, would predict compressed, rather than stretched exponential kinetics, in disagreement with the experimental observation. We therefore propose that the free energy surface along a reaction coordinate that governs the folding kinetics must be relatively flat and has a shape similar to a 1D golf course. We discuss how this conclusion can be unified with the thermodynamically well established zipper model by introducing an additional kinetic reaction coordinate

  4. Performance of isolated and folded footings

    Directory of Open Access Journals (Sweden)

    Mahmoud Samir El-kady

    2017-04-01

    Full Text Available Folded foundations have been used as an alternative to the conventional flat shallow foundations, in situations involving heavy loads or weak soils. They can be geometrically shaped in many forms especially for isolated footings. The purpose of this paper is introducing an alternative foundation shape that reduces the cost of foundations by reducing the amount of reinforcing steel by minimizing or even eliminating the tension zones in the folded isolated footings. Also, achieving lower soil stresses through changing the isolated footing shape will consequently reduce the expected settlements and the footing stresses. Experimental and numerical studies are performed on five (5 quarter scale footings of which one (1 footing of flat shape is tested as a reference sample and four (4 footings are of folded shape by folding angles of 10°, 20°, 30°, and 40° with the horizontal. Results showed that the folded isolated footings achieve economic design by decreasing the quantities of reinforcement. It also induced less soil settlements, and stresses. In addition, the tensile stresses in the reinforced concrete footing body are also less in folded isolated footings than the flat one. Results show that the folded isolated footing have a better load carrying capacity when compared with the conventional slab/flat footing of similar cross sectional area for both cases of experimental and numerical analysis.

  5. Mapping the Universe of RNA Tetraloop Folds.

    Science.gov (United States)

    Bottaro, Sandro; Lindorff-Larsen, Kresten

    2017-07-25

    We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG folds. We identify clusters corresponding to known tetraloop folds such as GGUG, RNYA, AGNN, and CUUG. These clusters are represented in a simple two-dimensional projection that recapitulates the relationship among the different folds. The cluster analysis also identifies 20 novel tetraloop folds that are peculiar to specific positions in ribosomal RNAs and that are stabilized by tertiary interactions. In our RNA tetraloop database we find a significant number of non-GNRA and non-UNCG sequences adopting the canonical GNRA and UNCG folds. Conversely, we find a significant number of GNRA and UNCG sequences adopting non-GNRA and non-UNCG folds. Our analysis demonstrates that there is not a simple one-to-one, but rather a many-to-many mapping between tetraloop sequence and tetraloop fold. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  6. Coarsely resolved topography along protein folding pathways

    Science.gov (United States)

    Fernández, Ariel; Kostov, Konstantin S.; Berry, R. Stephen

    2000-03-01

    The kinetic data from the coarse representation of polypeptide torsional dynamics described in the preceding paper [Fernandez and Berry, J. Chem. Phys. 112, 5212 (2000), preceding paper] is inverted by using detailed balance to obtain a topographic description of the potential-energy surface (PES) along the dominant folding pathway of the bovine pancreatic trypsin inhibitor (BPTI). The topography is represented as a sequence of minima and effective saddle points. The dominant folding pathway displays an overall monotonic decrease in energy with a large number of staircaselike steps, a clear signature of a good structure-seeker. The diversity and availability of alternative folding pathways is analyzed in terms of the Shannon entropy σ(t) associated with the time-dependent probability distribution over the kinetic ensemble of contact patterns. Several stages in the folding process are evident. Initially misfolded states form and dismantle revealing no definite pattern in the topography and exhibiting high Shannon entropy. Passage down a sequence of staircase steps then leads to the formation of a nativelike intermediate, for which σ(t) is much lower and fairly constant. Finally, the structure of the intermediate is refined to produce the native state of BPTI. We also examine how different levels of tolerance to mismatches of side chain contacts influence the folding kinetics, the topography of the dominant folding pathway, and the Shannon entropy. This analysis yields upper and lower bounds of the frustration tolerance required for the expeditious and robust folding of BPTI.

  7. Folded Plate Structures as Building Envelopes

    DEFF Research Database (Denmark)

    Falk, Andreas; Buelow, Peter von; Kirkegaard, Poul Henning

    2012-01-01

    This paper treats applications of cross-laminated timber (CLT) in structural systems for folded façade solutions. Previous work on CLT-based systems for folded roofs has shown a widening range of structural possibilities to develop timber-based shells. Geometric and material properties play...... CLT-based systems, which are studied and analysed by using a combination of digital tools for structural and environmental design and analysis. The results show gainful, rational properties of folded systems and beneficial effects from an integration of architectural and environmental performance...... criteria in the design of CLT-based façades....

  8. A bidirectional shape memory alloy folding actuator

    International Nuclear Information System (INIS)

    Paik, Jamie K; Wood, Robert J

    2012-01-01

    This paper presents a low-profile bidirectional folding actuator based on annealed shape memory alloy sheets applicable for meso- and microscale systems. Despite the advantages of shape memory alloys—high strain, silent operation, and mechanical simplicity—their application is often limited to unidirectional operation. We present a bidirectional folding actuator that produces two opposing 180° motions. A laser-patterned nickel alloy (Inconel 600) heater localizes actuation to the folding sections. The actuator has a thin ( < 1 mm) profile, making it appropriate for use in robotic origami. Various design parameters and fabrication variants are described and experimentally explored in the actuator prototype. (paper)

  9. Mechanical Models of Fault-Related Folding

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  10. Recognition and Toleration

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2010-01-01

    Recognition and toleration are ways of relating to the diversity characteristic of multicultural societies. The article concerns the possible meanings of toleration and recognition, and the conflict that is often claimed to exist between these two approaches to diversity. Different forms...... or interpretations of recognition and toleration are considered, confusing and problematic uses of the terms are noted, and the compatibility of toleration and recognition is discussed. The article argues that there is a range of legitimate and importantly different conceptions of both toleration and recognition...

  11. COMMERCIAL FUND, RECOGNITION AND ASSESSMENT

    Directory of Open Access Journals (Sweden)

    VIOREL TRIF

    2010-01-01

    Full Text Available The importance of the immaterial investments within companies nowadays urges the specialists in accounting to find the ways to present more in the elements. In their studies researchers face the controversy reinvestments, as an asset in the balance sheet or an expense in the profit or loss account. The main goal of this paper is to analyze the difficulties in commercial fund. In the first part we will analyze various definitions of the problems concerning the commercial fund’s recognition and assessment. The paper also suggests that investments are really social and economic problems.

  12. Quantum Nuclear Extension of Electron Nuclear Dynamics on Folded Effective-Potential Surfaces

    DEFF Research Database (Denmark)

    Hall, B.; Deumens, E.; Ohrn, Y.

    2014-01-01

    A perennial problem in quantum scattering calculations is accurate theoretical treatment of low energy collisions. We propose a method of extracting a folded, nonadiabatic, effective potential energy surface from electron nuclear dynamics (END) trajectories; we then perform nuclear wave packet...

  13. Gait recognition based on integral outline

    Science.gov (United States)

    Ming, Guan; Fang, Lv

    2017-02-01

    Biometric identification technology replaces traditional security technology, which has become a trend, and gait recognition also has become a hot spot of research because its feature is difficult to imitate and theft. This paper presents a gait recognition system based on integral outline of human body. The system has three important aspects: the preprocessing of gait image, feature extraction and classification. Finally, using a method of polling to evaluate the performance of the system, and summarizing the problems existing in the gait recognition and the direction of development in the future.

  14. Robust recognition via information theoretic learning

    CERN Document Server

    He, Ran; Yuan, Xiaotong; Wang, Liang

    2014-01-01

    This Springer Brief represents a comprehensive review of information theoretic methods for robust recognition. A variety of information theoretic methods have been proffered in the past decade, in a large variety of computer vision applications; this work brings them together, attempts to impart the theory, optimization and usage of information entropy.The?authors?resort to a new information theoretic concept, correntropy, as a robust measure and apply it to solve robust face recognition and object recognition problems. For computational efficiency,?the brief?introduces the additive and multip

  15. Purposive recognition: an active and qualitative approach

    Science.gov (United States)

    Rivlin, Ehud; Aloimonos, Yiannis; Rosenfeld, Azriel

    1992-04-01

    We propose an alternative way to study the problem of visual recognition which is closer to the spirit emerging from Brooks' work on building robots than to Marr's reconstructive approach. Our theory is purposive in the sense that recognition is considered in the context of an agent performing it in an environment, along with the agent's intentions that translate into a set of behaviors; it is qualitative in the sense that only partial recovery is needed; it is active in the sense that various partial recovery tasks need for recognition are achieved through active vision; and it is opportunistic in the sense that every available cue is used.

  16. Matching Algorithms and Feature Match Quality Measures for Model-Based Object Recognition with Applications to Automatic Target Recognition

    National Research Council Canada - National Science Library

    Keller, Martin G

    1999-01-01

    In the fields of computational vision and image understanding, the object recognition problem can be formulated as a problem of matching a collection of model features to features extracted from an observed scene...

  17. Object Recognition and Segmentation of Wounds

    OpenAIRE

    Wåsjø, Robin

    2015-01-01

    Object recognition and segmentation of objects is a complex task. Our goal is to develop an algorithm that can recognize and segment wound objects in images. We attempt to solve the object recognition and segmentation problem by using a hypothesis optimization framework. This method optimizes the object segmentation by assigning objective function values to the object segmentation hypotheses. The optimization algorithm is a genetic algorithm. The objective function relies on textural and shap...

  18. Learning Hierarchical Feature Extractors for Image Recognition

    Science.gov (United States)

    2012-09-01

    recognition, but the analysis applies to all tasks which incorporate some form 48 of pooling (e.g., text processing from which the bag-of-features method ...performance rely on solving an `1-regularized optimization. Several efficient algorithms have been devised for this problem. Homotopy methods such as the...recent advances in image recognition. First, we recast many methods into a common unsupervised feature extraction framework based on an alternation of

  19. Self-folding miniature elastic electric devices

    International Nuclear Information System (INIS)

    Miyashita, Shuhei; Meeker, Laura; Rus, Daniela; Tolley, Michael T; Wood, Robert J

    2014-01-01

    Printing functional materials represents a considerable impact on the access to manufacturing technology. In this paper we present a methodology and validation of print-and-self-fold miniature electric devices. Polyvinyl chloride laminated sheets based on metalized polyester film show reliable self-folding processes under a heat application, and it configures 3D electric devices. We exemplify this technique by fabricating fundamental electric devices, namely a resistor, capacitor, and inductor. Namely, we show the development of a self-folded stretchable resistor, variable resistor, capacitive strain sensor, and an actuation mechanism consisting of a folded contractible solenoid coil. Because of their pre-defined kinematic design, these devices feature elasticity, making them suitable as sensors and actuators in flexible circuits. Finally, an RLC circuit obtained from the integration of developed devices is demonstrated, in which the coil based actuator is controlled by reading a capacitive strain sensor. (paper)

  20. Folded Resonant Horns for Power Ultrasonic Applications

    Science.gov (United States)

    Sherrit, Stewart; Askins, Stephen; Gradziel, Michael; Bao, Xiaoqi; Chang, Zensheu; Dolgin, Benjamin; Bar-Cohen, Yoseph; Peterson, Tom

    2003-01-01

    Folded horns have been conceived as alternatives to straight horns used as resonators and strain amplifiers in power ultrasonic systems. Such systems are used for cleaning, welding, soldering, cutting, and drilling in a variety of industries. In addition, several previous NASA Tech Briefs articles have described instrumented drilling, coring, and burrowing machines that utilize combinations of sonic and ultrasonic vibrational actuation. The main advantage of a folded horn, relative to a straight horn of the same resonance frequency, is that the folded horn can be made shorter (that is, its greatest linear dimension measured from the outside can be made smaller). Alternatively, for a given length, the resonance frequency can be reduced. Hence, the folded-horn concept affords an additional degree of design freedom for reducing the length of an ultrasonic power system that includes a horn.

  1. Cycle 24 COS/NUV Fold Distribution

    Science.gov (United States)

    Wheeler, Thomas; Welty, Alan

    2018-02-01

    We summarize the Cycle 24 COS/NUV Fold Distribution for the Cosmic Origins Spectrograph's (COS) MAMA detector on the Hubble Space Telescope. The detector micro-channel plate's health state is determined and the results presented.

  2. Topology Explains Why Automobile Sunshades Fold Oddly

    Science.gov (United States)

    Feist, Curtis; Naimi, Ramin

    2009-01-01

    Automobile sunshades always fold into an "odd" number of loops. The explanation why involves elementary topology (braid theory and linking number, both explained in detail here with definitions and examples), and an elementary fact from algebra about symmetric group.

  3. Origami: Paper Folding--The Algorithmic Way.

    Science.gov (United States)

    Heukerott, Pamela Beth

    1988-01-01

    Describes origami, the oriental art of paper folding as an activity to teach upper elementary students concepts and skills in geometry involving polygons, angles, measurement, symmetry, and congruence. (PK)

  4. Chondroitin sulphate-mediated fusion of brain neural folds in rat embryos.

    Science.gov (United States)

    Alonso, M I; Moro, J A; Martín, C; de la Mano, A; Carnicero, E; Martínez-Alvarez, C; Navarro, N; Cordero, J; Gato, A

    2009-01-01

    Previous studies have demonstrated that during neural fold fusion in different species, an apical extracellular material rich in glycoconjugates is involved. However, the composition and the biological role of this material remain undetermined. In this paper, we show that this extracellular matrix in rat increases notably prior to contact between the neural folds, suggesting the dynamic behaviour of the secretory process. Immunostaining has allowed us to demonstrate that this extracellular matrix contains chondroitin sulphate proteoglycan (CSPG), with a spatio-temporal distribution pattern, suggesting a direct relationship with the process of adhesion. The degree of CSPG involvement in cephalic neural fold fusion in rat embryos was determined by treatment with specific glycosidases.In vitro rat embryo culture and microinjection techniques were employed to carry out selective digestion, with chondroitinase AC, of the CSPG on the apical surface of the neural folds; this was done immediately prior to the bonding of the cephalic neural folds. In all the treated embryos, cephalic defects of neural fold fusion could be detected. These results show that CSPG plays an important role in the fusion of the cephalic neural folds in rat embryos, which implies that this proteoglycan could be involved in cellular recognition and adhesion. (c) 2008 S. Karger AG, Basel.

  5. "Wet" Versus "Dry" Folding of Polyproline

    Science.gov (United States)

    Shi, Liuqing; Holliday, Alison E.; Bohrer, Brian C.; Kim, Doyong; Servage, Kelly A.; Russell, David H.; Clemmer, David E.

    2016-06-01

    When the all- cis polyproline-I helix (PPI, favored in 1-propanol) of polyproline-13 is introduced into water, it folds into the all- trans polyproline-II (PPII) helix through at least six intermediates [Shi, L., Holliday, A.E., Shi, H., Zhu, F., Ewing, M.A., Russell, D.H., Clemmer, D.E.: Characterizing intermediates along the transition from PPI to PPII using ion mobility-mass spectrometry. J. Am. Chem. Soc. 136, 12702-12711 (2014)]. Here, we show that the solvent-free intermediates refold into the all- cis PPI helix with high (>90%) efficiency. Moreover, in the absence of solvent, each intermediate appears to utilize the same small set of pathways observed for the solution-phase PPII → PPI transition upon immersion of PPIIaq in 1-propanol. That folding in solution (under conditions where water is displaced by propanol) and folding in vacuo (where energy required for folding is provided by collisional activation) occur along the same pathway is remarkable. Implicit in this statement is that 1-propanol mimics a "dry" environment, similar to the gas phase. We note that intermediates with structures that are similar to PPIIaq can form PPII under the most gentle activation conditions—indicating that some transitions observed in water (i.e. , "we t" folding, are accessible (albeit inefficient) in vacuo. Lastly, these "dry" folding experiments show that PPI (all cis) is favored under "dry" conditions, which underscores the role of water as the major factor promoting preference for trans proline.

  6. Gyral Folding Pattern Analysis via Surface Profiling

    Science.gov (United States)

    Li, Kaiming; Guo, Lei; Li, Gang; Nie, Jingxin; Faraco, Carlos; Cui, Guangbin; Zhao, Qun; Miller, L. Stephen; Liu, Tianming

    2010-01-01

    Folding is an essential shape characteristic of the human cerebral cortex. Descriptors of cortical folding patterns have been studied for decades. However, many previous studies are either based on local shape descriptors such as curvature, or based on global descriptors such as gyrification index or spherical wavelets. This paper proposes a gyrus-scale folding pattern analysis technique via cortical surface profiling. Firstly, we sample the cortical surface into 2D profiles and model them using a power function. This step provides both the flexibility of representing arbitrary shape by profiling and the compactness of representing shape by parametric modeling. Secondly, based on the estimated model parameters, we extract affine-invariant features on the cortical surface, and apply the affinity propagation clustering algorithm to parcellate the cortex into cortical regions with strict hierarchy and smooth transitions among them. Finally, a second-round surface profiling is performed on the parcellated cortical surface, and the number of hinges is detected to describe the gyral folding pattern. We have applied the surface profiling method to two normal brain datasets and a Schizophrenia patient dataset. The experimental results demonstrate that the proposed method can accurately classify human gyri into 2-hinge, 3-hinge and 4-hinge patterns. The distribution of these folding patterns on brain lobes and the relationship between fiber density and gyral folding patterns are further investigated. Results from the Schizophrenia dataset are consistent with commonly found abnormality in former studies by others, which demonstrates the potential clinical applications of the proposed technique. PMID:20472071

  7. Large gastric folds arising in polyposis syndromes

    Directory of Open Access Journals (Sweden)

    Xiang-Yang Wangz

    2013-08-01

    Full Text Available Large gastric folds (LGF can be caused by benign conditions as well as malignancies. Unfortunately, endoscopic features and biopsy results are often equivocal, making the diagnosis and management of large gastric folds difficult. Polyposis syndromes encompass a group of conditions in which multiple gastrointestinal polyps occur in the lumen of the gut. Large gastric folds are extremely rare in these syndromes. We present the case of a patient with polyposis who was found to have large gastric folds in the entire gastric fundus and body, mimicking malignancy. The patient's medical history and endoscopic ultrasonography (EUS with mucosal resection confirmed the diagnosis of a pre-malignant disease. The lesion was monitored by serial endoscopic ultrasonography and biopsy, abdominal computed tomography (CT, and positron emission and computed tomography (PET-CT for 6 years. The lesion remained stable, with the exception of abnormal fluorodeoxyglucose uptake on PET-CT in the gastric folds, which was determined to be a false-positive sign. To date, the patient remains healthy. We further discuss the mechanisms underlying the formation of large gastric folds caused by polyposis syndromes. Helicobacter pylori (H. pylori or cytomegalovirus (CMV is unnecessary for this progression. Immunohistochemistry (IHC staining suggested that overexpression of transforming growth factor alpha (TGF-α and down-regulation of myocyte enhancer-binding factor 2 (MEF2 may be involved in this case.

  8. Upright folding during extensional and transtensional tectonics

    Science.gov (United States)

    Teyssier, Christian; Fossen, Haakon; Rey, Patrice F.; Whitney, Donna L.

    2017-04-01

    Upright folds are common structures that develop in response to horizontal shortening in layered material, for example in foreland basins that surround orogens. While the contractional nature of these folds is not in doubt, interpretation of their tectonic setting needs careful consideration. Here we focus on two examples: (1) folds developed in transtension; and (2) folds developed during the flow of deep crust in response to lithospheric extension. In both cases we consider folding of nearly horizontal layers that are either primary (bedding) or secondary (foliation). Strain theory inspired by John Ramsay's work makes predictions for the behavior of material lines and planes as well as strain axes (instantaneous, finite) during transtensional deformation. Results show: folds can form in transtension; fold hinges rotate toward the direction of divergence (and not the shear zone boundary as they do in transpression), providing unique insight into ancient plate motions; fold tightness is controlled by the obliquity of divergence and not finite strain; hinge parallel stretching is always greater than hinge-perpendicular shortening, resulting in constriction strain and boudinage of fold hinges. Taken together these results provide a rigorous framework for interpreting field observations where structures are complex and boundary conditions unclear. These principles are applied to various tectonic settings ranging from active tectonic regions of oblique divergence in western North America to ancient folding that developed during oblique extension of the Western Gneiss Region, deposition of Devonian basins, and exhumation of ultrahigh-pressure rocks in the Norwegian Caledonides. The other class of upright folds that form during extension may require revision of the tectonic interpretation of structural overprints in orogenic cores, for example in gneiss/migmatite domes. Dynamic modeling of extension of thick/hot crust predicts a positive feedback between extension of

  9. Folding of DsbB in mixed micelles

    DEFF Research Database (Denmark)

    Otzen, Daniel

    2003-01-01

    is sensitive to changes in lipid and detergent composition. As an attempt to overcome this problem, I present a kinetic analysis of the folding of a membrane protein, disulfide bond reducing protein B (DsbB), in a mixed micelle system consisting of varying molar ratios of sodium dodecyl sulfate (SDS......, when monitored by conventional stopped-flow. The kinetic data indicate that denaturation occurs around 0.3 mole fraction of SDS, in agreement with CD analysis and acrylamide quenching data. The rate constants have been fit to a three-state folding scheme involving the SDS-denatured state, the native...... state and an unfolding intermediate that accumulates only under unfolding conditions at high mole fractions of SDS. The stability of DsbB is around 4.4 kcal/mol in DM, and this is halved upon reduction of the two periplasmic disulfide bonds, and is sensitive to mutagenesis. With the caveat that kinetic...

  10. Multimodal eye recognition

    Science.gov (United States)

    Zhou, Zhi; Du, Yingzi; Thomas, N. L.; Delp, Edward J., III

    2010-04-01

    Multimodal biometrics use more than one means of biometric identification to achieve higher recognition accuracy, since sometimes a unimodal biometric is not good enough used to do identification and classification. In this paper, we proposed a multimodal eye recognition system, which can obtain both iris and sclera patterns from one color eye image. Gabor filter and 1-D Log-Gabor filter algorithms have been applied as the iris recognition algorithms. In sclera recognition, we introduced automatic sclera segmentation, sclera pattern enhancement, sclera pattern template generation, and sclera pattern matching. We applied kernelbased matching score fusion to improve the performance of the eye recognition system. The experimental results show that the proposed eye recognition method can achieve better performance compared to unimodal biometric identification, and the accuracy of our proposed kernel-based matching score fusion method is higher than two classic linear matching score fusion methods: Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA).

  11. Viral infections of the folds (intertriginous areas).

    Science.gov (United States)

    Adışen, Esra; Önder, Meltem

    2015-01-01

    Viruses are considered intracellular obligates with a nucleic acid, either RNA or DNA. They have the ability to encode proteins involved in viral replication and production of the protective coat within the host cells but require host cell ribosomes and mitochondria for translation. The members of the families Herpesviridae, Poxviridae, Papovaviridae, and Picornaviridae are the most commonly known agents for the cutaneous viral diseases, but other virus families, such as Adenoviridae, Togaviridae, Parvoviridae, Paramyxoviridae, Flaviviridae, and Hepadnaviridae, can also infect the skin. Though the cutaneous manifestations of viral infections are closely related to the type and the transmission route of the virus, viral skin diseases may occur in almost any part of the body. In addition to friction caused by skin-to-skin touch, skin folds are warm and moist areas of the skin that have limited air circulation. These features provide a fertile breeding ground for many kinds of microorganisms, including bacteria and fungi. In contrast to specific bacterial and fungal agents that have an affinity for the skin folds, except for viral diseases of the anogenital area, which have well-known presentations, viral skin infections that have a special affinity to the skin folds are not known. Many viral exanthems may affect the skin folds during the course of the infection, but here we focus only on the ones that usually affect the fold areas and also on the less well-known conditions or recently described associations. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Bifurcation of self-folded polygonal bilayers

    Science.gov (United States)

    Abdullah, Arif M.; Braun, Paul V.; Hsia, K. Jimmy

    2017-09-01

    Motivated by the self-assembly of natural systems, researchers have investigated the stimulus-responsive curving of thin-shell structures, which is also known as self-folding. Self-folding strategies not only offer possibilities to realize complicated shapes but also promise actuation at small length scales. Biaxial mismatch strain driven self-folding bilayers demonstrate bifurcation of equilibrium shapes (from quasi-axisymmetric doubly curved to approximately singly curved) during their stimulus-responsive morphing behavior. Being a structurally instable, bifurcation could be used to tune the self-folding behavior, and hence, a detailed understanding of this phenomenon is appealing from both fundamental and practical perspectives. In this work, we investigated the bifurcation behavior of self-folding bilayer polygons. For the mechanistic understanding, we developed finite element models of planar bilayers (consisting of a stimulus-responsive and a passive layer of material) that transform into 3D curved configurations. Our experiments with cross-linked Polydimethylsiloxane samples that change shapes in organic solvents confirmed our model predictions. Finally, we explored a design scheme to generate gripper-like architectures by avoiding the bifurcation of stimulus-responsive bilayers. Our research contributes to the broad field of self-assembly as the findings could motivate functional devices across multiple disciplines such as robotics, artificial muscles, therapeutic cargos, and reconfigurable biomedical devices.

  13. Kinetics and Thermodynamics of Membrane Protein Folding

    Directory of Open Access Journals (Sweden)

    Ernesto A. Roman

    2014-03-01

    Full Text Available Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field.

  14. Pattern recognition & machine learning

    CERN Document Server

    Anzai, Y

    1992-01-01

    This is the first text to provide a unified and self-contained introduction to visual pattern recognition and machine learning. It is useful as a general introduction to artifical intelligence and knowledge engineering, and no previous knowledge of pattern recognition or machine learning is necessary. Basic for various pattern recognition and machine learning methods. Translated from Japanese, the book also features chapter exercises, keywords, and summaries.

  15. Three-dimensional fingerprint recognition by using convolution neural network

    Science.gov (United States)

    Tian, Qianyu; Gao, Nan; Zhang, Zonghua

    2018-01-01

    With the development of science and technology and the improvement of social information, fingerprint recognition technology has become a hot research direction and been widely applied in many actual fields because of its feasibility and reliability. The traditional two-dimensional (2D) fingerprint recognition method relies on matching feature points. This method is not only time-consuming, but also lost three-dimensional (3D) information of fingerprint, with the fingerprint rotation, scaling, damage and other issues, a serious decline in robustness. To solve these problems, 3D fingerprint has been used to recognize human being. Because it is a new research field, there are still lots of challenging problems in 3D fingerprint recognition. This paper presents a new 3D fingerprint recognition method by using a convolution neural network (CNN). By combining 2D fingerprint and fingerprint depth map into CNN, and then through another CNN feature fusion, the characteristics of the fusion complete 3D fingerprint recognition after classification. This method not only can preserve 3D information of fingerprints, but also solves the problem of CNN input. Moreover, the recognition process is simpler than traditional feature point matching algorithm. 3D fingerprint recognition rate by using CNN is compared with other fingerprint recognition algorithms. The experimental results show that the proposed 3D fingerprint recognition method has good recognition rate and robustness.

  16. Statistical Pattern Recognition

    CERN Document Server

    Webb, Andrew R

    2011-01-01

    Statistical pattern recognition relates to the use of statistical techniques for analysing data measurements in order to extract information and make justified decisions.  It is a very active area of study and research, which has seen many advances in recent years. Applications such as data mining, web searching, multimedia data retrieval, face recognition, and cursive handwriting recognition, all require robust and efficient pattern recognition techniques. This third edition provides an introduction to statistical pattern theory and techniques, with material drawn from a wide range of fields,

  17. Timing of isoclinal folds in multiply deformed high metamorphic grade region using FIA succession

    Science.gov (United States)

    Cao, Hui; Cai, Zhihui

    2013-04-01

    Multiply deformed and isoclinally folded interlayered high metamorphic grade gneisses and schists can be very difficult rocks for resolving early formed stratigraphic and structural relationships. When such rocks contain porphyroblasts a new approach is possible because of the way in which porphyroblast growth is affected by crenulation versus reactivation of compositional layering. The asymmetries of the overprinting foliations preserved as inclusion trails that define the FIAs can be used to investigate whether an enigmatic isoclinal fold is an antiform or synform. This approach also reveals when the fold first formed during the tectonic history of the region. Isoclinally folded rocks in the Arkansas River region of Central Colorado contain relics of fold hinges that have been very difficult to ascertain whether they are antiforms or synforms because of younger refolding effects and the locally truncated nature of coarse compositional layering. With the realization that rocks with a schistosity parallel to bedding (S0 parallel S1) have undergone lengthy histories of deformation that predate the obvious first deformation came recognition that large scale regional folds can form early during this process and be preserved throughout orogenesis. This extensive history is lost within the matrix because of reactivational shear on the compositional layering. However, it can be extracted by measuring FIAs. Recent work using this approach has revealed that the trends of axial planes of all map scale folds, when plotted on a rose diagram, strikingly reflect the FIA trends. That is, although it was demonstrated that the largest scale regional folds commonly form early in the total history, other folds can form and be preserved from subsequent destruction in the strain shadows of plutons or through the partitioning of deformation due to heterogeneities at depth.

  18. SDEM modelling of fault-propagation folding

    DEFF Research Database (Denmark)

    Clausen, O.R.; Egholm, D.L.; Poulsen, Jane Bang

    2009-01-01

    Understanding the dynamics and kinematics of fault-propagation-folding is important for evaluating the associated hydrocarbon play, for accomplishing reliable section balancing (structural reconstruction), and for assessing seismic hazards. Accordingly, the deformation style of fault-propagation-......Understanding the dynamics and kinematics of fault-propagation-folding is important for evaluating the associated hydrocarbon play, for accomplishing reliable section balancing (structural reconstruction), and for assessing seismic hazards. Accordingly, the deformation style of fault......-propagation-folding has already been the topic of a large number of empirical studies as well as physical and computational model experiments. However, with the newly developed Stress-based Discrete Element Method (SDEM), we have, for the first time, explored computationally the link between self-emerging fault patterns...

  19. Improvement of a Vocal Fold Imaging System

    Energy Technology Data Exchange (ETDEWEB)

    Krauter, K. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-02-01

    Medical professionals can better serve their patients through continual update of their imaging tools. A wide range of pathologies and disease may afflict human vocal cords or, as they’re also known, vocal folds. These diseases can affect human speech hampering the ability of the patient to communicate. Vocal folds must be opened for breathing and the closed to produce speech. Currently methodologies to image markers of potential pathologies are difficult to use and often fail to detect early signs of disease. These current methodologies rely on a strobe light and slower frame rate camera in an attempt to obtain images as the vocal folds travel over the full extent of their motion.

  20. Kinetics of Peptide Folding in Lipid Membranes

    Science.gov (United States)

    Oh, Kwang-Im; Smith-Dupont, Kathryn B.; Markiewicz, Beatrice N.; Gai, Feng

    2015-01-01

    Despite our extensive understanding of water-soluble protein folding kinetics, much less is known about the folding dynamics and mechanisms of membrane proteins. However, recent studies have shown that for relatively simple systems, such as peptides that form a transmembrane α-helix, helical dimer, or helix-turn-helix, it is possible to assess the kinetics of several important steps, including peptide binding to the membrane from aqueous solution, peptide folding on the membrane surface, helix insertion into the membrane, and helix-helix association inside the membrane. Herein, we provide a brief review of these studies and also suggest new initiation and probing methods that could lead to improved temporal and structural resolution in future experiments. PMID:25808575

  1. Non-cylindrical fold growth in the Zagros fold and thrust belt (Kurdistan, NE-Iraq)

    Science.gov (United States)

    Bartl, Nikolaus; Bretis, Bernhard; Grasemann, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros mountains extends over 1800 km from Kurdistan in N-Iraq to the Strait of Hormuz in Iran and is one of the world most promising regions for the future hydrocarbon exploration. The Zagros Mountains started to form as a result of the collision between the Eurasian and Arabian Plates, whose convergence began in the Late Cretaceous as part of the Alpine-Himalayan orogenic system. Geodetic and seismological data document that both plates are still converging and that the fold and thrust belt of the Zagros is actively growing. Extensive hydrocarbon exploration mainly focuses on the antiforms of this fold and thrust belt and therefore the growth history of the folds is of great importance. This work investigates by means of structural field work and quantitative geomorphological techniques the progressive fold growth of the Permam, Bana Bawi- and Safeen- Anticlines located in the NE of the city of Erbil in the Kurdistan region of Northern Iraq. This part of the Zagros fold and thrust belt belongs to the so-called Simply Folded Belt, which is dominated by gentle to open folding. Faults or fault related folds have only minor importance. The mechanical anisotropy of the formations consisting of a succession of relatively competent (massive dolomite and limestone) and incompetent (claystone and siltstone) sediments essentially controls the deformation pattern with open to gentle parallel folding of the competent layers and flexural flow folding of the incompetent layers. The characteristic wavelength of the fold trains is around 10 km. Due to faster erosion of the softer rock layers in the folded sequence, the more competent lithologies form sharp ridges with steeply sloping sides along the eroded flanks of the anticlines. Using an ASTER digital elevation model in combination with geological field data we quantified 250 drainage basins along the different limbs of the subcylindrical Permam, Bana Bawi- and Safeen- Anticlines. Geomorphological indices of the drainage

  2. Towards a systematic classification of protein folds

    DEFF Research Database (Denmark)

    Lindgård, Per-Anker; Bohr, Henrik

    1997-01-01

    structures are given a unique name, which simultaneously represent a linear string of physical coupling constants describing hinge spin interactions. We have defined a metric and a precise distance measure between the fold classes. An automated procedure is constructed in which any protein structure...... magic number of secondary structures. Thermodynamic arguments for the increased abundance and a phase diagram for the folding scenario are given. This includes an intermediate high symmetry phase, the parent structures, between the molten globule and the native states. We have made an exhaustive...

  3. Stretching and folding mechanism in foams

    Energy Technology Data Exchange (ETDEWEB)

    Tufaile, Alberto [Escola de Artes, Ciencias e Humanidades, Soft Matter Laboratory, Universidade de Sao Paulo, 03828-000 Sao Paulo, SP (Brazil)], E-mail: tufaile@usp.br; Pedrosa Biscaia Tufaile, Adriana [Escola de Artes, Ciencias e Humanidades, Soft Matter Laboratory, Universidade de Sao Paulo, 03828-000 Sao Paulo, SP (Brazil)

    2008-10-13

    We have described the stretching and folding of foams in a vertical Hele-Shaw cell containing air and a surfactant solution, from a sequence of upside-down flips. Besides the fractal dimension of the foam, we have observed the logistic growth for the soap film length. The stretching and folding mechanism is present during the foam formation, and this mechanism is observed even after the foam has reached its respective maximum fractal dimension. Observing the motion of bubbles inside the foam, large bubbles present power spectrum associated with random walk motion in both directions, while the small bubbles are scattered like balls in a Galton board.

  4. Hand Gesture Recognition Using Particle Swarm Movement

    Directory of Open Access Journals (Sweden)

    Clementine Nyirarugira

    2016-01-01

    Full Text Available We present a gesture recognition method derived from particle swarm movement for free-air hand gesture recognition. Online gesture recognition remains a difficult problem due to uncertainty in vision-based gesture boundary detection methods. We suggest an automated process of segmenting meaningful gesture trajectories based on particle swarm movement. A subgesture detection and reasoning method is incorporated in the proposed recognizer to avoid premature gesture spotting. Evaluation of the proposed method shows promising recognition results: 97.6% on preisolated gestures, 94.9% on stream gestures with assistive boundary indicators, and 94.2% for blind gesture spotting on digit gesture vocabulary. The proposed recognizer requires fewer computation resources; thus it is a good candidate for real-time applications.

  5. Parametric HMMs for Movement Recognition and Synthesis

    DEFF Research Database (Denmark)

    Herzog, Dennis; Krüger, Volker

    2009-01-01

    combine our PHMM approach with a 3D body tracker. Experiments are performed with pointing and grasping movements parameterized by their target positions at a table-top. A systematical evaluation of synthesis and recognition shows the use of our approach. In case of recognition, our approach is able...... to recover the movement type, and, e.g., the object position a human is pointing at. Our experiments show the flexibility of the PHMMs in terms of the amount of training data and its robustness in terms of noisy observation data. In addition, we compare our PHMM to an other kind of PHMM, which has been......A common problem in human movement recognition is the recognition of movements of a particular type (semantic). E.g., grasping movements have a particular semantic (grasping) but the actual movements usually have very different appearances due to, e.g., different grasping directions. In this paper...

  6. Accessing Specific Peptide Recognition by Combinatorial Chemistry

    DEFF Research Database (Denmark)

    Li, Ming

    in recognition, a hook peptide library was built as sequence blocks containing two L-prolines, facilitating peptide back-bones to organize into a bend “hook” shape. Selection of pairs recognizing each other by entanglement with the conformational shape as a fundamental mechanism of molecular recognition...... was studied with this hook peptide library via the beadbead adhesion screening approach. The recognition pairs interlocked and formed a complex. (chapter 8) During accessing peptide molecular recognition by combinatorial chemistry, we faced several problems, which were solved by a range of analytical...... separation of is developed and used to select the best hits from the “hook” peptide library. The association strength of complex was also evaluated by MS-MS analysis. (chapter 8) a microchannel flow device was designed and utilized to measure binding constants on a single bead. (chapter 5) An important...

  7. Review of holographic-based three-dimensional object recognition techniques [invited].

    Science.gov (United States)

    Tsang, P W M; Poon, T-C; Liu, J-P; Situ, W C

    2014-09-20

    With the advancement of computing and optical technologies, it is now possible to capture digital holograms of real-life object scenes. Theoretically, through the analysis of a hologram, the three-dimensional (3D) objects coded on the hologram can be identified. However, being different from an optical image, a hologram is composed of complicated fringes that cannot be analyzed easily with traditional computer vision methods. Over the years, numerous important research investigations have been attempted to provide viable solutions to this problem. The aim of this work is three-fold. First, we provide a quick walkthrough on the overall development of holographic-based 3D object recognition (H3DOR) in the past five decades, from film-based approaches to digital-based innovation. Second, we describe in more detail a number of selected H3DOR methods that are introduced at different timelines, starting from the late sixties and then from the seventies, where viable digital holographic-based 3D recognition methods began to emerge. Finally, we present our work on digital holographic, pose-invariant 3D object recognition that is based on a recently introduced virtual diffraction plane framework. As our method has not been reported elsewhere, we have included some experimental results to demonstrate the feasibility of the approach.

  8. Engineering antibody fitness and function using membrane-anchored display of correctly folded proteins.

    Science.gov (United States)

    Karlsson, Amy J; Lim, Hyung-Kwon; Xu, Hansen; Rocco, Mark A; Bratkowski, Matthew A; Ke, Ailong; DeLisa, Matthew P

    2012-02-10

    A hallmark of the bacterial twin-arginine translocation (Tat) pathway is its ability to export folded proteins. Here, we discovered that overexpressed Tat substrate proteins form two distinct, long-lived translocation intermediates that are readily detected by immunolabeling methods. Formation of the early translocation intermediate Ti-1, which exposes the N- and C-termini to the cytoplasm, did not require an intact Tat translocase, a functional Tat signal peptide, or a correctly folded substrate. In contrast, formation of the later translocation intermediate, Ti-2, which exhibits a bitopic topology with the N-terminus in the cytoplasm and C-terminus in the periplasm, was much more particular, requiring an intact translocase, a functional signal peptide, and a correctly folded substrate protein. The ability to directly detect Ti-2 intermediates was subsequently exploited for a new protein engineering technology called MAD-TRAP (membrane-anchored display for Tat-based recognition of associating proteins). Through the use of just two rounds of mutagenesis and screening with MAD-TRAP, the intracellular folding and antigen-binding activity of a human single-chain antibody fragment were simultaneously improved. This approach has several advantages for library screening, including the unique involvement of the Tat folding quality control mechanism that ensures only native-like proteins are displayed, thus eliminating poorly folded sequences from the screening process. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. Self-organization and mismatch tolerance in protein folding: General theory and an application

    Science.gov (United States)

    Fernández, Ariel; Berry, R. Stephen

    2000-03-01

    The folding of a protein is a process both expeditious and robust. The analysis of this process presented here uses a coarse, discretized representation of the evolving form of the backbone chain, based on its torsional states. This coarse description consists of discretizing the torsional coordinates modulo the Ramachandran basins in the local softmode dynamics. Whenever the representation exhibits "contact patterns" that correspond to topological compatibilities with particular structural forms, secondary and then tertiary, the elements constituting the pattern are effectively entrained by a reduction of their rates of exploration of their discretized configuration space. The properties "expeditious and robust" imply that the folding protein must have some tolerance to both torsional "frustrated" and side-chain contact mismatches which may occur during the folding process. The energy-entropy consequences of the staircase or funnel topography of the potential surface should allow the folding protein to correct these mismatches, eventually. This tolerance lends itself to an iterative pattern-recognition-and-feedback description of the folding process that reflects mismatched local torsional states and hydrophobic/polar contacts. The predictive potential of our algorithm is tested by application to the folding of bovine pancreatic trypsin inhibitor (BPTI), a protein whose ability to form its active structure is contingent upon its frustration tolerance.

  10. Pattern recognition principles

    Science.gov (United States)

    Tou, J. T.; Gonzalez, R. C.

    1974-01-01

    The present work gives an account of basic principles and available techniques for the analysis and design of pattern processing and recognition systems. Areas covered include decision functions, pattern classification by distance functions, pattern classification by likelihood functions, the perceptron and the potential function approaches to trainable pattern classifiers, statistical approach to trainable classifiers, pattern preprocessing and feature selection, and syntactic pattern recognition.

  11. Paradigms in object recognition

    International Nuclear Information System (INIS)

    Mutihac, R.; Mutihac, R.C.

    1999-09-01

    A broad range of approaches has been proposed and applied for the complex and rather difficult task of object recognition that involves the determination of object characteristics and object classification into one of many a priori object types. Our paper revises briefly the three main different paradigms in pattern recognition, namely Bayesian statistics, neural networks, and expert systems. (author)

  12. Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins.

    Directory of Open Access Journals (Sweden)

    Yunxiang Sun

    Full Text Available Energetic frustration is becoming an important topic for understanding the mechanisms of protein folding, which is a long-standing big biological problem usually investigated by the free energy landscape theory. Despite the significant advances in probing the effects of folding frustrations on the overall features of protein folding pathways and folding intermediates, detailed characterizations of folding frustrations at an atomic or residue level are still lacking. In addition, how and to what extent folding frustrations interact with protein topology in determining folding mechanisms remains unclear. In this paper, we tried to understand energetic frustrations in the context of protein topology structures or native-contact networks by comparing the energetic frustrations of five homologous Im9 alpha-helix proteins that share very similar topology structures but have a single hydrophilic-to-hydrophobic mutual mutation. The folding simulations were performed using a coarse-grained Gō-like model, while non-native hydrophobic interactions were introduced as energetic frustrations using a Lennard-Jones potential function. Energetic frustrations were then examined at residue level based on φ-value analyses of the transition state ensemble structures and mapped back to native-contact networks. Our calculations show that energetic frustrations have highly heterogeneous influences on the folding of the four helices of the examined structures depending on the local environment of the frustration centers. Also, the closer the introduced frustration is to the center of the native-contact network, the larger the changes in the protein folding. Our findings add a new dimension to the understanding of protein folding the topology determination in that energetic frustrations works closely with native-contact networks to affect the protein folding.

  13. Glueballs as rotating folded closed strings

    Science.gov (United States)

    Sonnenschein, Jacob; Weissman, Dorin

    2015-12-01

    In previous papers [1, 2] we argued that mesons and baryons can be described as rotating open strings in holographic backgrounds. Now we turn to closed strings, which should be the duals of glueballs. We look at the rotating folded closed string in both flat and curved backgrounds.

  14. Vocal fold nodules: morphological and immunohistochemical investigations.

    Science.gov (United States)

    Martins, Regina Helena Garcia; Defaveri, Julio; Custódio Domingues, Maria Aparecida; de Albuquerque E Silva, Rafael; Fabro, Alexandre

    2010-09-01

    The objective of this study was to investigate the morphological and immunohistochemical characteristics of vocal fold nodules. The study design was prospective and retrospective. For the histological study, we reviewed 15 slides from the surgical cases of vocal fold nodules, in which we analyzed epithelium, basal membrane (bm), and lamina propria. For the transmission and scanning electron microscopy (TEM, SEM) studies, five new cases on vocal fold nodules were included. Immunohistochemistry study was carried out in the 15 specimens, using antifibronectin, antilaminin, and anticollagen IV antibodies. The main histological alterations were epithelial hyperplasia (73.33%), basement membrane thickening (86.66%), edema, and fibrosis (93.33%). SEM--reduction in mucous lacing and increase in the desquamating cells, without epithelial erosion. TEM--hyperplasia of the epithelium, enlargement of the intercellular junctions, which was filled by fluid, subepithelial thickening of the lamina reticularis, and break points in the basal membrane. Immunohistochemistry--we identified greater immunoexpression of fibronectin on the basal membrane, on the lamina propria, and around the vessels. Antilaminin and anticollagen IV antibodies showed higher pigmentation on the endothelium of the vessels than that on the basal membrane. In vocal fold nodules, combined assessment using light microscopy, electron microscopy, and immunohistochemistry can reveal important morphological details useful in characterizing these lesions. 2010 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

  15. Assessment of thyroplasty for vocal fold paralysis

    DEFF Research Database (Denmark)

    Grøntved, Ågot Møller; Faber, Christian; Jakobsen, John

    2009-01-01

    INTRODUCTION: Thyroplasty with silicone rubber implantation is a surgical procedure for treatment of patients with vocal fold paralysis. The aim of the present study was to evaluate the outcome of the operation and to monitor which of the analyses were the more beneficial. MATERIAL AND METHODS...

  16. Self-folding graphene-polymer bilayers

    International Nuclear Information System (INIS)

    Deng, Tao; Yoon, ChangKyu; Jin, Qianru; Li, Mingen; Liu, Zewen; Gracias, David H.

    2015-01-01

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting

  17. Engineering Biology by Controlling Tissue Folding.

    Science.gov (United States)

    Hookway, Tracy A

    2018-04-01

    Achieving complex self-organization in vitro has remained a fundamental challenge in tissue engineering. A recent study in Developmental Cell by Hughes and colleagues uses computational and experimental approaches to understand and control the morphogenic process of tissue folding. These approaches provide an engineering framework to reproducibly control tissue shape. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. Mapping the universe of RNA tetraloop folds

    DEFF Research Database (Denmark)

    Bottaro, Sandro; Lindorff-Larsen, Kresten

    2017-01-01

    We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG fold...

  19. Fold in Origami and Unfold Math

    Science.gov (United States)

    Georgeson, Joseph

    2011-01-01

    Students enjoy origami and like making everything from paper cranes to footballs out of small, colorful squares of paper. They can invent their own shapes and are intrigued by the polyhedrons that they can construct. Paper folding is fun, but where is the math? Unless teachers develop lessons that address mathematical objectives, origami could be…

  20. Challenging ocular image recognition

    Science.gov (United States)

    Pauca, V. Paúl; Forkin, Michael; Xu, Xiao; Plemmons, Robert; Ross, Arun A.

    2011-06-01

    Ocular recognition is a new area of biometric investigation targeted at overcoming the limitations of iris recognition performance in the presence of non-ideal data. There are several advantages for increasing the area beyond the iris, yet there are also key issues that must be addressed such as size of the ocular region, factors affecting performance, and appropriate corpora to study these factors in isolation. In this paper, we explore and identify some of these issues with the goal of better defining parameters for ocular recognition. An empirical study is performed where iris recognition methods are contrasted with texture and point operators on existing iris and face datasets. The experimental results show a dramatic recognition performance gain when additional features are considered in the presence of poor quality iris data, offering strong evidence for extending interest beyond the iris. The experiments also highlight the need for the direct collection of additional ocular imagery.

  1. Recognition and Justice

    Directory of Open Access Journals (Sweden)

    Charles Reagan

    2016-01-01

    The complexities of the meanings of “to recognize” and “recognition” are important in their roles in the realm of justice. I include in the concept of justice, the judiciary, both civil and criminal; distributive justice; and, social and political justice. For each one of these, there are multiple meanings of recognition that are important to understanding their foundation and their scope. There are meanings of recognition that are relevant to other aspects of social justice as the recognition of marginal, oppressed, devalued, groups as deserving of being treated as equals. The structure of my paper is to go through the various meanings and categories of meanings of “to recognize” and “recognition.” I give an account of each of the types of justice and show how various kinds of recognition are relevant to each kind of justice.

  2. ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles.

    Science.gov (United States)

    Ghouzam, Yassine; Postic, Guillaume; Guerin, Pierre-Edouard; de Brevern, Alexandre G; Gelly, Jean-Christophe

    2016-06-20

    Protein structure prediction based on comparative modeling is the most efficient way to produce structural models when it can be performed. ORION is a dedicated webserver based on a new strategy that performs this task. The identification by ORION of suitable templates is performed using an original profile-profile approach that combines sequence and structure evolution information. Structure evolution information is encoded into profiles using structural features, such as solvent accessibility and local conformation -with Protein Blocks-, which give an accurate description of the local protein structure. ORION has recently been improved, increasing by 5% the quality of its results. The ORION web server accepts a single protein sequence as input and searches homologous protein structures within minutes. Various databases such as PDB, SCOP and HOMSTRAD can be mined to find an appropriate structural template. For the modeling step, a protein 3D structure can be directly obtained from the selected template by MODELLER and displayed with global and local quality model estimation measures. The sequence and the predicted structure of 4 examples from the CAMEO server and a recent CASP11 target from the 'Hard' category (T0818-D1) are shown as pertinent examples. Our web server is accessible at http://www.dsimb.inserm.fr/ORION/.

  3. Folding of multidomain proteins: biophysical consequences of tethering even in apparently independent folding.

    Science.gov (United States)

    Arviv, Oshrit; Levy, Yaakov

    2012-12-01

    Most eukaryotic and a substantial fraction of prokaryotic proteins are composed of more than one domain. The tethering of these evolutionary, structural, and functional units raises, among others, questions regarding the folding process of conjugated domains. Studying the folding of multidomain proteins in silico enables one to identify and isolate the tethering-induced biophysical determinants that govern crosstalks generated between neighboring domains. For this purpose, we carried out coarse-grained and atomistic molecular dynamics simulations of two two-domain constructs from the immunoglobulin-like β-sandwich fold. Each of these was experimentally shown to behave as the "sum of its parts," that is, the thermodynamic and kinetic folding behavior of the constituent domains of these constructs seems to occur independently, with the folding of each domain uncoupled from the folding of its partner in the two-domain construct. We show that the properties of the individual domains can be significantly affected by conjugation to another domain. The tethering may be accompanied by stabilizing as well as destabilizing factors whose magnitude depends on the size of the interface, the length, and the flexibility of the linker, and the relative stability of the domains. Accordingly, the folding of a multidomain protein should not be viewed as the sum of the folding patterns of each of its parts, but rather, it involves abrogating several effects that lead to this outcome. An imbalance between these effects may result in either stabilization or destabilization owing to the tethering. Copyright © 2012 Wiley Periodicals, Inc.

  4. Convolutional Neural Networks for Handwritten Javanese Character Recognition

    OpenAIRE

    Dewa, Chandra Kusuma; Fadhilah, Amanda Lailatul; Afiahayati, A

    2018-01-01

    Convolutional neural network (CNN) is state-of-the-art method in object recognition task. Specialized for spatial input data type, CNN has special convolutional and pooling layers which enable hierarchical feature learning from the input space. For offline handwritten character recognition problem such as classifying character in MNIST database, CNN shows better classification result than any other methods. By leveraging the advantages of CNN over character recognition task, in this paper we ...

  5. Inverse folding of RNA pseudoknot structures

    Directory of Open Access Journals (Sweden)

    Li Linda YM

    2010-06-01

    Full Text Available Abstract Background RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms, RNAinverse, RNA-SSD as well as INFO-RNA are limited to RNA secondary structures, we present in this paper the inverse folding algorithm Inv which can deal with 3-noncrossing, canonical pseudoknot structures. Results In this paper we present the inverse folding algorithm Inv. We give a detailed analysis of Inv, including pseudocodes. We show that Inv allows to design in particular 3-noncrossing nonplanar RNA pseudoknot 3-noncrossing RNA structures-a class which is difficult to construct via dynamic programming routines. Inv is freely available at http://www.combinatorics.cn/cbpc/inv.html. Conclusions The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures. In comparison with RNAinverse it uses new ideas, for instance by considering sets of competing structures. As a result, Inv is not only able to find novel sequences even for RNA secondary structures, it does so in the context of competing structures that potentially exhibit cross-serial interactions.

  6. Folding and Fracturing of Rocks: the background

    Science.gov (United States)

    Ramsay, John G.

    2017-04-01

    This book was generated by structural geology teaching classes at Imperial College. I was appointed lecturer during 1957 and worked together with Dr Gilbert Wilson teaching basic structural geology at B.Sc level. I became convinced that the subject, being essentially based on geometric field observations, required a firm mathematical basis for its future development. In particular it seemed to me to require a very sound understanding of stress and strain. My field experience suggested that a knowledge of two- and three-demensional strain was critical in understanding natural tectonic processes. I found a rich confirmation for this in early publications of deformed fossils, oolitic limestones and spotted slates made by several geologists around the beginning of the 20th century (Sorby, Philips, Haughton, Harker) often using surprisingly sophisticated mathematical methods. These methods were discussed and elaborated in Folding and Fracturing of Rocks in a practical way. The geometric features of folds were related to folding mechanisms and the fold related small scale structures such as cleavage, schistosity and lineation explained in terms of rock strain. My work in the Scottish Highlands had shown just how repeated fold superposition could produce very complex geometric features, while further work in other localities suggested that such geometric complications are common in many orogenic zones. From the development of structural geological studies over the past decades it seems that the readers of this book have found many of the ideas set out are still of practical application. The mapping of these outcrop-scale structures should be emphasised in all field studies because they can be seen as ''fingerprints'' of regional scale tectonic processes. My own understanding of structural geology has been inspired by field work and I am of the opinion that future progress in understanding will be likewise based on careful observation and measurement of the features of

  7. Radar automatic target recognition (ATR) and non-cooperative target recognition (NCTR)

    CERN Document Server

    Blacknell, David

    2013-01-01

    The ability to detect and locate targets by day or night, over wide areas, regardless of weather conditions has long made radar a key sensor in many military and civil applications. However, the ability to automatically and reliably distinguish different targets represents a difficult challenge. Radar Automatic Target Recognition (ATR) and Non-Cooperative Target Recognition (NCTR) captures material presented in the NATO SET-172 lecture series to provide an overview of the state-of-the-art and continuing challenges of radar target recognition. Topics covered include the problem as applied to th

  8. Post processing for offline Chinese handwritten character string recognition

    Science.gov (United States)

    Wang, YanWei; Ding, XiaoQing; Liu, ChangSong

    2012-01-01

    Offline Chinese handwritten character string recognition is one of the most important research fields in pattern recognition. Due to the free writing style, large variability in character shapes and different geometric characteristics, Chinese handwritten character string recognition is a challenging problem to deal with. However, among the current methods over-segmentation and merging method which integrates geometric information, character recognition information and contextual information, shows a promising result. It is found experimentally that a large part of errors are segmentation error and mainly occur around non-Chinese characters. In a Chinese character string, there are not only wide characters namely Chinese characters, but also narrow characters like digits and letters of the alphabet. The segmentation error is mainly caused by uniform geometric model imposed on all segmented candidate characters. To solve this problem, post processing is employed to improve recognition accuracy of narrow characters. On one hand, multi-geometric models are established for wide characters and narrow characters respectively. Under multi-geometric models narrow characters are not prone to be merged. On the other hand, top rank recognition results of candidate paths are integrated to boost final recognition of narrow characters. The post processing method is investigated on two datasets, in total 1405 handwritten address strings. The wide character recognition accuracy has been improved lightly and narrow character recognition accuracy has been increased up by 10.41% and 10.03% respectively. It indicates that the post processing method is effective to improve recognition accuracy of narrow characters.

  9. Automatic Recognition of Road Signs

    Science.gov (United States)

    Inoue, Yasuo; Kohashi, Yuuichirou; Ishikawa, Naoto; Nakajima, Masato

    2002-11-01

    The increase in traffic accidents is becoming a serious social problem with the recent rapid traffic increase. In many cases, the driver"s carelessness is the primary factor of traffic accidents, and the driver assistance system is demanded for supporting driver"s safety. In this research, we propose the new method of automatic detection and recognition of road signs by image processing. The purpose of this research is to prevent accidents caused by driver"s carelessness, and call attention to a driver when the driver violates traffic a regulation. In this research, high accuracy and the efficient sign detecting method are realized by removing unnecessary information except for a road sign from an image, and detect a road sign using shape features. At first, the color information that is not used in road signs is removed from an image. Next, edges except for circular and triangle ones are removed to choose sign shape. In the recognition process, normalized cross correlation operation is carried out to the two-dimensional differentiation pattern of a sign, and the accurate and efficient method for detecting the road sign is realized. Moreover, the real-time operation in a software base was realized by holding down calculation cost, maintaining highly precise sign detection and recognition. Specifically, it becomes specifically possible to process by 0.1 sec(s)/frame using a general-purpose PC (CPU: Pentium4 1.7GHz). As a result of in-vehicle experimentation, our system could process on real time and has confirmed that detection and recognition of a sign could be performed correctly.

  10. Pattern recognition with discrete and mixed data : theory and practice

    NARCIS (Netherlands)

    C.E.A. Queiros (Carlos)

    1988-01-01

    textabstractThis thesis is devoted to aspects related to the analysis of medical data bases in the context of pattern recognition. It contains both theoretical aspects and practical applications and its scope includes questions and problems that arise when applying pattern recognition methods and

  11. Recognition of Pitman shorthand text using tangent feature values at ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Keywords. Pitman shorthand; pitman word (stroke); consonant primitives; vowel markers; tangents; contour traversal; thinning. 1. Introduction. Recognition of Pitman shorthand is a challenging pattern recognition problem because of the variety of pattern shapes involved with it (Chen & Lee 1992; Leedham & Nair 1992;.

  12. Regression-based Multi-View Facial Expression Recognition

    NARCIS (Netherlands)

    Rudovic, Ognjen; Patras, Ioannis; Pantic, Maja

    2010-01-01

    We present a regression-based scheme for multi-view facial expression recognition based on 2蚠D geometric features. We address the problem by mapping facial points (e.g. mouth corners) from non-frontal to frontal view where further recognition of the expressions can be performed using a

  13. Devnagari numeral recognition by combining decision of multiple ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Generic techniques cannot, in general, tackle problems associated with script specific peculiarities. In this paper, we present a neural network–based architecture for recognition of handwritten numerals. Although the architecture is generic, it has been found to be useful for recognition of hand- written Devnagari numerals.

  14. Speech Recognition Technology for Disabilities Education

    Science.gov (United States)

    Tang, K. Wendy; Kamoua, Ridha; Sutan, Victor; Farooq, Omer; Eng, Gilbert; Chu, Wei Chern; Hou, Guofeng

    2005-01-01

    Speech recognition is an alternative to traditional methods of interacting with a computer, such as textual input through a keyboard. An effective system can replace or reduce the reliability on standard keyboard and mouse input. This can especially assist dyslexic students who have problems with character or word use and manipulation in a textual…

  15. Pronunciation Modeling for Large Vocabulary Speech Recognition

    Science.gov (United States)

    Kantor, Arthur

    2010-01-01

    The large pronunciation variability of words in conversational speech is one of the major causes of low accuracy in automatic speech recognition (ASR). Many pronunciation modeling approaches have been developed to address this problem. Some explicitly manipulate the pronunciation dictionary as well as the set of the units used to define the…

  16. Ribosome binding site recognition using neural networks

    Directory of Open Access Journals (Sweden)

    Márcio Ferreira da Silva Oliveira

    2004-01-01

    Full Text Available Pattern recognition is an important process for gene localization in genomes. The ribosome binding sites are signals that can help in the identification of a gene. It is difficult to find these signals in the genome through conventional methods because they are highly degenerated. Artificial Neural Networks is the approach used in this work to address this problem.

  17. RECOGNITION AND VERIFICATION OF TOUCHING HANDWRITTEN NUMERALS

    NARCIS (Netherlands)

    Zhou, J.; Kryzak, A.; Suen, C.Y.

    2004-01-01

    In the field of financial document processing, recognition of touching handwritten numerals has been limited by lack of good benchmarking databases and low reliability of algorithms. This paper addresses the efforts toward solving the two problems. Two databases IRIS-Bell\\\\\\'98 and TNIST are

  18. Pattern Recognition by Retina-Like Devices.

    Science.gov (United States)

    Weiman, Carl F. R.; Rothstein, Jerome

    This study has investigated some pattern recognition capabilities of devices consisting of arrays of cooperating elements acting in parallel. The problem of recognizing straight lines in general position on the quadratic lattice has been completely solved by applying parallel acting algorithms to a special code for lines on the lattice. The…

  19. A rough set approach to speech recognition

    Science.gov (United States)

    Zhao, Zhigang

    1992-09-01

    Speech recognition is a very difficult classification problem due to the variations in loudness, speed, and tone of voice. In the last 40 years, many methodologies have been developed to solve this problem, but most lack learning ability and depend fully on the knowledge of human experts. Systems of this kind are hard to develop and difficult to maintain and upgrade. A study was conducted to investigate the feasibility of using a machine learning approach in solving speech recognition problems. The system is based on rough set theory. It first generates a set of decision rules using a set of reference words called training samples, and then uses the decision rules to recognize new words. The main feature of this system is that, under the supervision of human experts, the machine learns and applies knowledge on its own to the designated tasks. The main advantages of this system over a traditional system are its simplicity and adaptiveness, which suggest that it may have significant potential in practical applications of computer speech recognition. Furthermore, the studies presented demonstrate the potential application of rough-set based learning systems in solving other important pattern classification problems, such as character recognition, system fault detection, and trainable robotic control.

  20. Material Recognition for Content Based Image Retrieval

    NARCIS (Netherlands)

    Geusebroek, J.M.

    2002-01-01

    One of the open problems in content-based Image Retrieval is the recognition of material present in an image. Knowledge about the set of materials present gives important semantic information about the scene under consideration. For example, detecting sand, sky, and water certainly classifies the

  1. Folding pathways explored with artificial potential functions

    International Nuclear Information System (INIS)

    Ulutaş, B; Bozma, I; Haliloglu, T

    2009-01-01

    This paper considers the generation of trajectories to a given protein conformation and presents a novel approach based on artificial potential functions—originally proposed for multi-robot navigation. The artificial potential function corresponds to a simplified energy model, but with the novelty that—motivated by work on robotic navigation—a nonlinear compositional scheme of constructing the energy model is adapted instead of an additive formulation. The artificial potential naturally gives rise to a dynamic system for the protein structure that ensures collision-free motion to an equilibrium point. In cases where the equilibrium point is the native conformation, the motion trajectory corresponds to the folding pathway. This framework is used to investigate folding in a variety of protein structures, and the results are compared with those of other approaches including experimental studies

  2. Ca-Dependent Folding of Human Calumenin

    Science.gov (United States)

    Mazzorana, Marco; Hussain, Rohanah; Sorensen, Thomas

    2016-01-01

    Human calumenin (hCALU) is a six EF-hand protein belonging to the CREC family. As other members of the family, it is localized in the secretory pathway and regulates the activity of SERCA2a and of the ryanodine receptor in the endoplasmic reticulum (ER). We have studied the effects of Ca2+ binding to the protein and found it to attain a more compact structure upon ion binding. Circular Dichroism (CD) measurements suggest a major rearrangement of the protein secondary structure, which reversibly switches from disordered at low Ca2+ concentrations to predominantly alpha-helical when Ca2+ is added. SAXS experiments confirm the transition from an unfolded to a compact structure, which matches the structural prediction of a trilobal fold. Overall our experiments suggest that calumenin is a Ca2+ sensor, which folds into a compact structure, capable of interacting with its molecular partners, when Ca2+ concentration within the ER reaches the millimolar range. PMID:26991433

  3. Thermostable exoshells fold and stabilize recombinant proteins.

    Science.gov (United States)

    Deshpande, Siddharth; Masurkar, Nihar D; Girish, Vallerinteavide Mavelli; Desai, Malan; Chakraborty, Goutam; Chan, Juliana M; Drum, Chester L

    2017-11-13

    The expression and stabilization of recombinant proteins is fundamental to basic and applied biology. Here we have engineered a thermostable protein nanoparticle (tES) to improve both expression and stabilization of recombinant proteins using this technology. tES provides steric accommodation and charge complementation to green fluorescent protein (GFPuv), horseradish peroxidase (HRPc), and Renilla luciferase (rLuc), improving the yields of functional in vitro folding by ~100-fold. Encapsulated enzymes retain the ability to metabolize small-molecule substrates, presumably via four 4.5-nm pores present in the tES shell. GFPuv exhibits no spectral shifts in fluorescence compared to a nonencapsulated control. Thermolabile proteins internalized by tES are resistant to thermal, organic, chaotropic, and proteolytic denaturation and can be released from the tES assembly with mild pH titration followed by proteolysis.

  4. Cutting and Folding for Tunable Materials Properties

    Science.gov (United States)

    Damasceno, Pablo; Dodd, Paul; Shyu, Terry; Shlian, Matthew; Shtein, Max; Kotov, Nicholas; Glotzer, Sharon

    2014-03-01

    Despite the small set of building blocks used for their assembly, naturally occurring materials such as proteins show remarkable diversity in their mechanical properties ranging from something resembling rubber-low stiffness, high resilience and extensibility-to silk-high stiffness and strength. Moreover, their self-folding properties inspire the design of structures capable of tunable reconfiguration. Motivated by such versatility, we report on simulations and experiments for the design of nanocomposites sheets whose mechanical properties can be made tunable via ``secondary structures'' patterning. Our simulations reveal the main cutting features needed to obtain desired material extensibility. Additionally, we study how similar sheets could self-fold into their desired ``native'' structure via stochastic forces. Our results open the possibilities for manufacture of flexible and reconfigurable materials with targeted strength and extensibility. Research supported by the National Science Foundation, Emerging Frontiers in Research and Innovation Award # EFRI-1240264.

  5. Self-folding micropatterned polymeric containers.

    Science.gov (United States)

    Azam, Anum; Laflin, Kate E; Jamal, Mustapha; Fernandes, Rohan; Gracias, David H

    2011-02-01

    We demonstrate self-folding of precisely patterned, optically transparent, all-polymeric containers and describe their utility in mammalian cell and microorganism encapsulation and culture. The polyhedral containers, with SU-8 faces and biodegradable polycaprolactone (PCL) hinges, spontaneously assembled on heating. Self-folding was driven by a minimization of surface area of the liquefying PCL hinges within lithographically patterned two-dimensional (2D) templates. The strategy allowed for the fabrication of containers with variable polyhedral shapes, sizes and precisely defined porosities in all three dimensions. We provide proof-of-concept for the use of these polymeric containers as encapsulants for beads, chemicals, mammalian cells and bacteria. We also compare accelerated hinge degradation rates in alkaline solutions of varying pH. These optically transparent containers resemble three-dimensional (3D) micro-Petri dishes and can be utilized to sustain, monitor and deliver living biological components.

  6. Unit operations of tissue development: epithelial folding.

    Science.gov (United States)

    Zartman, Jeremiah J; Shvartsman, Stanislav Y

    2010-01-01

    The development of multicellular organisms relies on a small set of construction techniques-assembly, sculpting, and folding-that are spatially and temporally regulated in a combinatorial manner to produce the diversity of tissues within the body. These basic processes are well conserved across tissue types and species at the level of both genes and mechanisms. Here we review the signaling, patterning, and biomechanical transformations that occur in two well-studied model systems of epithelial folding to illustrate both the complexity and modularity of tissue development. In particular, we discuss the possibility of a spatial code specifying morphogenesis. To decipher this code, engineers and scientists need to establish quantitative experimental systems and to develop models that address mechanisms at multiple levels of organization, from gene sequence to tissue biomechanics. In turn, quantitative models of embryogenesis can inspire novel methods for creating synthetic organs and treating degenerative tissue diseases.

  7. Protein folding simulations by generalized-ensemble algorithms.

    Science.gov (United States)

    Yoda, Takao; Sugita, Yuji; Okamoto, Yuko

    2014-01-01

    In the protein folding problem, conventional simulations in physical statistical mechanical ensembles, such as the canonical ensemble with fixed temperature, face a great difficulty. This is because there exist a huge number of local-minimum-energy states in the system and the conventional simulations tend to get trapped in these states, giving wrong results. Generalized-ensemble algorithms are based on artificial unphysical ensembles and overcome the above difficulty by performing random walks in potential energy, volume, and other physical quantities or their corresponding conjugate parameters such as temperature, pressure, etc. The advantage of generalized-ensemble simulations lies in the fact that they not only avoid getting trapped in states of energy local minima but also allows the calculations of physical quantities as functions of temperature or other parameters from a single simulation run. In this article we review the generalized-ensemble algorithms. Four examples, multicanonical algorithm, replica-exchange method, replica-exchange multicanonical algorithm, and multicanonical replica-exchange method, are described in detail. Examples of their applications to the protein folding problem are presented.

  8. Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Gorodkin, Jan; Backofen, Rolf

    2008-01-01

    Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both. However, there is currently no approach that combines both sources of information in a single...... the corresponding probability of being single stranded. Furthermore, we found that structurally conserved RNA motifs are mostly supported by folding energies. Other problems (e.g. RNA-folding kinetics) may also benefit from employing the principles of the model we introduce. Our implementation, PETfold, was tested...

  9. Protein Folding: Search for Basic Physical Models

    Directory of Open Access Journals (Sweden)

    Ivan Y. Torshin

    2003-01-01

    Full Text Available How a unique three-dimensional structure is rapidly formed from the linear sequence of a polypeptide is one of the important questions in contemporary science. Apart from biological context of in vivo protein folding (which has been studied only for a few proteins, the roles of the fundamental physical forces in the in vitro folding remain largely unstudied. Despite a degree of success in using descriptions based on statistical and/or thermodynamic approaches, few of the current models explicitly include more basic physical forces (such as electrostatics and Van Der Waals forces. Moreover, the present-day models rarely take into account that the protein folding is, essentially, a rapid process that produces a highly specific architecture. This review considers several physical models that may provide more direct links between sequence and tertiary structure in terms of the physical forces. In particular, elaboration of such simple models is likely to produce extremely effective computational techniques with value for modern genomics.

  10. Folding Membrane Proteins by Deep Transfer Learning

    KAUST Repository

    Wang, Sheng

    2017-08-29

    Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here, we describe a high-throughput deep transfer learning method that first predicts MP contacts by learning from non-MPs and then predicts 3D structure models using the predicted contacts as distance restraints. Tested on 510 non-redundant MPs, our method has contact prediction accuracy at least 0.18 better than existing methods, predicts correct folds for 218 MPs, and generates 3D models with root-mean-square deviation (RMSD) less than 4 and 5 Å for 57 and 108 MPs, respectively. A rigorous blind test in the continuous automated model evaluation project shows that our method predicted high-resolution 3D models for two recent test MPs of 210 residues with RMSD ∼2 Å. We estimated that our method could predict correct folds for 1,345–1,871 reviewed human multi-pass MPs including a few hundred new folds, which shall facilitate the discovery of drugs targeting at MPs.

  11. Araguaia fold belt, new geochronological data

    International Nuclear Information System (INIS)

    Lafon, J.M.; Macambira, J.B.; Macambira, M.J.B.; Moura, C.A.V.; Souza, A.C.C.

    1990-01-01

    The northern part of the Araguaia Fold Belt (AFB) outcrops in a N-S direction for about 400 km in the state of Tocantins. Dome-like structures occur in this fold belt also in a N-S direction. Both deformation and metamorphism increase from the West to the East. The basement of the AFB consist of Colmeia complex and Cantao gneiss, which crop out mainly in the core of the dome-like structures. The supracrustals rocks of the fold belt belongs to the Baixo Araguaia supergroup which is divided into the lower Estrondo group and the upper Tocantins group. Preliminary Sm-Nd data from the Colmeia complex (Grota Rica dome) gave Archean model ages of 2.8 Ga (TNd sub(DM)) while Rb-Sr data in the same rocks give an age of 2530 ± 200 Ma. In the others dome-like structures, the Rb-Sr systematics gave ages for the Colmeia a complex of 2239 ± 47 Ma (Colmeia structure) and 1972 ± 46 Ma (Lontra structure). These younger ages are believed to represent partial to total isotopic resetting of the Rb-Sr system during the Transamazonian Event. The Rb-Sr studies of the Cantao gneiss gave an age of 1774 ± 31 Ma. (author)

  12. Learned image representations for visual recognition

    DEFF Research Database (Denmark)

    Larsen, Anders Boesen Lindbo

    This thesis addresses the problem of extracting image structures for representing images effectively in order to solve visual recognition tasks. Problems from diverse research areas (medical imaging, material science and food processing) have motivated large parts of the methodological development...... the ability to learn high-level concepts in images of faces. The thesis argues in favor of learning features and presents new methods for domains with limited amounts of labeled data allowing feature learning to be applied more broadly....

  13. Face recognition using ensemble string matching.

    Science.gov (United States)

    Chen, Weiping; Gao, Yongsheng

    2013-12-01

    In this paper, we present a syntactic string matching approach to solve the frontal face recognition problem. String matching is a powerful partial matching technique, but is not suitable for frontal face recognition due to its requirement of globally sequential representation and the complex nature of human faces, containing discontinuous and non-sequential features. Here, we build a compact syntactic Stringface representation, which is an ensemble of strings. A novel ensemble string matching approach that can perform non-sequential string matching between two Stringfaces is proposed. It is invariant to the sequential order of strings and the direction of each string. The embedded partial matching mechanism enables our method to automatically use every piece of non-occluded region, regardless of shape, in the recognition process. The encouraging results demonstrate the feasibility and effectiveness of using syntactic methods for face recognition from a single exemplar image per person, breaking the barrier that prevents string matching techniques from being used for addressing complex image recognition problems. The proposed method not only achieved significantly better performance in recognizing partially occluded faces, but also showed its ability to perform direct matching between sketch faces and photo faces.

  14. Work and Recognition

    DEFF Research Database (Denmark)

    Willig, Rasmus

    2004-01-01

    individual and collective identity formation and has led to an increase in social pathological illnesses such as stress and depression. By juxtaposing these analyses with Honneth’s theory on recognition, we conclude that the contemporary logic of work is unable to provide adequate forms of recognition......The article deals with the relationship between work and recognition, taking Axel Honneth’s social-philosophical theory of the struggle for recognition as its point of departure. In order to give sociological substance to Honneth’s theory, we turn to three contemporary social theorists - Jean......-Pierre Le Goff, Christophe Dejours and Emmanuel Renault. In spite of many differences, their work is united by a critical description of the logic of work and its consequences for individual individuation. These theorists agree that the growth of autonomy, flexibility and mobility has destabilised...

  15. Forensic speaker recognition

    NARCIS (Netherlands)

    Meuwly, Didier

    2013-01-01

    The aim of forensic speaker recognition is to establish links between individuals and criminal activities, through audio speech recordings. This field is multidisciplinary, combining predominantly phonetics, linguistics, speech signal processing, and forensic statistics. On these bases, expert-based

  16. Very deep recurrent convolutional neural network for object recognition

    Science.gov (United States)

    Brahimi, Sourour; Ben Aoun, Najib; Ben Amar, Chokri

    2017-03-01

    In recent years, Computer vision has become a very active field. This field includes methods for processing, analyzing, and understanding images. The most challenging problems in computer vision are image classification and object recognition. This paper presents a new approach for object recognition task. This approach exploits the success of the Very Deep Convolutional Neural Network for object recognition. In fact, it improves the convolutional layers by adding recurrent connections. This proposed approach was evaluated on two object recognition benchmarks: Pascal VOC 2007 and CIFAR-10. The experimental results prove the efficiency of our method in comparison with the state of the art methods.

  17. The Recognition Of Fatigue

    DEFF Research Database (Denmark)

    Elsass, Peter; Jensen, Bodil; Mørup, Rikke

    2007-01-01

    Elsass P., Jensen B., Morup R., Thogersen M.H. (2007). The Recognition Of Fatigue: A qualitative study of life-stories from rehabilitation clients. International Journal of Psychosocial Rehabilitation. 11 (2), 75-87......Elsass P., Jensen B., Morup R., Thogersen M.H. (2007). The Recognition Of Fatigue: A qualitative study of life-stories from rehabilitation clients. International Journal of Psychosocial Rehabilitation. 11 (2), 75-87...

  18. Wood Species Recognition System

    OpenAIRE

    Bremananth R; Nithya B; Saipriya R

    2009-01-01

    The proposed system identifies the species of the wood using the textural features present in its barks. Each species of a wood has its own unique patterns in its bark, which enabled the proposed system to identify it accurately. Automatic wood recognition system has not yet been well established mainly due to lack of research in this area and the difficulty in obtaining the wood database. In our work, a wood recognition system has been designed based on pre-processing te...

  19. Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios

    Science.gov (United States)

    Fernández, Ariel; Colubri, Andrés; Berry, R. Stephen

    2001-04-01

    This work presents a method to portray protein folding dynamics at a coarse resolution, based on a pattern-recognition-and-feedback description of the evolution of torsional motions of the backbone chain in the hydrophobic collapse of the protein. The approach permits theory and computation to treat the search of conformation space from picoseconds to the millisecond time scale or longer, the time scales of adiabatic evolution of soft-mode dynamics. The procedure tracks the backbone torsional coordinates modulo the basins of attraction to which they belong in the Ramachandran maps. The state and history of the backbone are represented in a map of local torsional states and hydrophobicity/hydrophilicity matching of the residues comprising the chain, the local topology matrix (LTM). From this map, we infer allowable structural features by recognizing patterns in the LTM as topologically compatible with particular structural forms within a level of frustration tolerance. Each such 3D realization of an LTM leads to a contact map, from which one can infer one or more structures. Introduction of energetic and entropic terms allow elimination of all but the most favored of these structures at each new juncture. The method's predictive power is first established by comparing "final," stable LTMs for natural sequences of intermediate length (N⩽120) with PDB data. The method is extended further to β-lactoglobulin (β-LG, N=162), the quintessential nonhierarchical folder.

  20. Dynamics of folding: Impact of fault bend folds on earthquake cycles

    Science.gov (United States)

    Sathiakumar, S.; Barbot, S.; Hubbard, J.

    2017-12-01

    Earthquakes in subduction zones and subaerial convergent margins are some of the largest in the world. So far, forecasts of future earthquakes have primarily relied on assessing past earthquakes to look for seismic gaps and slip deficits. However, the roles of fault geometry and off-fault plasticity are typically overlooked. We use structural geology (fault-bend folding theory) to inform fault modeling in order to better understand how deformation is accommodated on the geological time scale and through the earthquake cycle. Fault bends in megathrusts, like those proposed for the Nepal Himalaya, will induce folding of the upper plate. This introduces changes in the slip rate on different fault segments, and therefore on the loading rate at the plate interface, profoundly affecting the pattern of earthquake cycles. We develop numerical simulations of slip evolution under rate-and-state friction and show that this effect introduces segmentation of the earthquake cycle. In crustal dynamics, it is challenging to describe the dynamics of fault-bend folds, because the deformation is accommodated by small amounts of slip parallel to bedding planes ("flexural slip"), localized on axial surface, i.e. folding axes pinned to fault bends. We use dislocation theory to describe the dynamics of folding along these axial surfaces, using analytic solutions that provide displacement and stress kernels to simulate the temporal evolution of folding and assess the effects of folding on earthquake cycles. Studies of the 2015 Gorkha earthquake, Nepal, have shown that fault geometry can affect earthquake segmentation. Here, we show that in addition to the fault geometry, the actual geology of the rocks in the hanging wall of the fault also affect critical parameters, including the loading rate on parts of the fault, based on fault-bend folding theory. Because loading velocity controls the recurrence time of earthquakes, these two effects together are likely to have a strong impact on the

  1. Why recognition is rational

    Directory of Open Access Journals (Sweden)

    Clintin P. Davis-Stober

    2010-07-01

    Full Text Available The Recognition Heuristic (Gigerenzer and Goldstein, 1996; Goldstein and Gigerenzer, 2002 makes the counter-intuitive prediction that a decision maker utilizing less information may do as well as, or outperform, an idealized decision maker utilizing more information. We lay a theoretical foundation for the use of single-variable heuristics such as the Recognition Heuristic as an optimal decision strategy within a linear modeling framework. We identify conditions under which over-weighting a single predictor is a mini-max strategy among a class of a priori chosen weights based on decision heuristics with respect to a measure of statistical lack of fit we call ``risk''. These strategies, in turn, outperform standard multiple regression as long as the amount of data available is limited. We also show that, under related conditions, weighting only one variable and ignoring all others produces the same risk as ignoring the single variable and weighting all others. This approach has the advantage of generalizing beyond the original environment of the Recognition Heuristic to situations with more than two choice options, binary or continuous representations of recognition, and to other single variable heuristics. We analyze the structure of data used in some prior recognition tasks and find that it matches the sufficient conditions for optimality in our results. Rather than being a poor or adequate substitute for a compensatory model, the Recognition Heuristic closely approximates an optimal strategy when a decision maker has finite data about the world.

  2. Multi-thread Parallel Speech Recognition for Mobile Applications

    Directory of Open Access Journals (Sweden)

    LOJKA Martin

    2014-05-01

    Full Text Available In this paper, the server based solution of the multi-thread large vocabulary automatic speech recognition engine is described along with the Android OS and HTML5 practical application examples. The basic idea was to bring speech recognition available for full variety of applications for computers and especially for mobile devices. The speech recognition engine should be independent of commercial products and services (where the dictionary could not be modified. Using of third-party services could be also a security and privacy problem in specific applications, when the unsecured audio data could not be sent to uncontrolled environments (voice data transferred to servers around the globe. Using our experience with speech recognition applications, we have been able to construct a multi-thread speech recognition serverbased solution designed for simple applications interface (API to speech recognition engine modified to specific needs of particular application.

  3. Understanding the folding process of synthetic polymers by small ...

    Indian Academy of Sciences (India)

    This two-point interaction between the folding agent and the polymer backbone leads to a folding of the polymer chain, which was readily monitored by NMR titrations. The effect of various parameters, such as structures of the folding agent and polymer, and the solvent composition, on the folding propensities of the polymer ...

  4. Psychosociale problemen bij peuters: Onderkenning en ingesteld beleid door artsen en verpleegkundigen in de jeugdgezondheidszorg [Psychosocial problems in pre-school children: Recognition and strategy applied by doctors and nurses in child health care

    NARCIS (Netherlands)

    Reijneveld, S.A.; Brugman, E.; Verhulst, F.C.; Verloove-Vanhorick, S.P.

    2005-01-01

    Objective. To assess the degree to which preventive child health professionals (CHPs) identify and manage psychosocial problems among pre-school children in the general population, and to determine its association with parent-reported behavioral and emotional problems, sociodemographic factors and

  5. Human recognition at a distance in video

    CERN Document Server

    Bhanu, Bir

    2010-01-01

    Most biometric systems employed for human recognition require physical contact with, or close proximity to, a cooperative subject. Far more challenging is the ability to reliably recognize individuals at a distance, when viewed from an arbitrary angle under real-world environmental conditions. Gait and face data are the two biometrics that can be most easily captured from a distance using a video camera. This comprehensive and logically organized text/reference addresses the fundamental problems associated with gait and face-based human recognition, from color and infrared video data that are

  6. Convolutional neural networks and face recognition task

    Science.gov (United States)

    Sochenkova, A.; Sochenkov, I.; Makovetskii, A.; Vokhmintsev, A.; Melnikov, A.

    2017-09-01

    Computer vision tasks are remaining very important for the last couple of years. One of the most complicated problems in computer vision is face recognition that could be used in security systems to provide safety and to identify person among the others. There is a variety of different approaches to solve this task, but there is still no universal solution that would give adequate results in some cases. Current paper presents following approach. Firstly, we extract an area containing face, then we use Canny edge detector. On the next stage we use convolutional neural networks (CNN) to finally solve face recognition and person identification task.

  7. Comparison of fault-related folding algorithms to restore a fold-and-thrust-belt

    Science.gov (United States)

    Brandes, Christian; Tanner, David

    2017-04-01

    Fault-related folding means the contemporaneous evolution of folds as a consequence of fault movement. It is a common deformation process in the upper crust that occurs worldwide in accretionary wedges, fold-and-thrust belts, and intra-plate settings, in either strike-slip, compressional, or extensional regimes. Over the last 30 years different algorithms have been developed to simulate the kinematic evolution of fault-related folds. All these models of fault-related folding include similar simplifications and limitations and use the same kinematic behaviour throughout the model (Brandes & Tanner, 2014). We used a natural example of fault-related folding from the Limón fold-and-thrust belt in eastern Costa Rica to test two different algorithms and to compare the resulting geometries. A thrust fault and its hanging-wall anticline were restored using both the trishear method (Allmendinger, 1998; Zehnder & Allmendinger, 2000) and the fault-parallel flow approach (Ziesch et al. 2014); both methods are widely used in academia and industry. The resulting hanging-wall folds above the thrust fault are restored in substantially different fashions. This is largely a function of the propagation-to-slip ratio of the thrust, which controls the geometry of the related anticline. Understanding the controlling factors for anticline evolution is important for the evaluation of potential hydrocarbon reservoirs and the characterization of fault processes. References: Allmendinger, R.W., 1998. Inverse and forward numerical modeling of trishear fault propagation folds. Tectonics, 17, 640-656. Brandes, C., Tanner, D.C. 2014. Fault-related folding: a review of kinematic models and their application. Earth Science Reviews, 138, 352-370. Zehnder, A.T., Allmendinger, R.W., 2000. Velocity field for the trishear model. Journal of Structural Geology, 22, 1009-1014. Ziesch, J., Tanner, D.C., Krawczyk, C.M. 2014. Strain associated with the fault-parallel flow algorithm during kinematic fault

  8. Robust Face Recognition by Computing Distances from Multiple Histograms of Oriented Gradients

    NARCIS (Netherlands)

    Karaaba, Mahir; Surinta, Olarik; Schomaker, Lambertus; Wiering, Marco

    2015-01-01

    The Single Sample per Person Problem is a challenging problem for face recognition algorithms. Patch-based methods have obtained some promising results for this problem. In this paper, we propose a new face recognition algorithm that is based on a combination of different histograms of oriented

  9. Image pattern recognition supporting interactive analysis and graphical visualization

    Science.gov (United States)

    Coggins, James M.

    1992-01-01

    Image Pattern Recognition attempts to infer properties of the world from image data. Such capabilities are crucial for making measurements from satellite or telescope images related to Earth and space science problems. Such measurements can be the required product itself, or the measurements can be used as input to a computer graphics system for visualization purposes. At present, the field of image pattern recognition lacks a unified scientific structure for developing and evaluating image pattern recognition applications. The overall goal of this project is to begin developing such a structure. This report summarizes results of a 3-year research effort in image pattern recognition addressing the following three principal aims: (1) to create a software foundation for the research and identify image pattern recognition problems in Earth and space science; (2) to develop image measurement operations based on Artificial Visual Systems; and (3) to develop multiscale image descriptions for use in interactive image analysis.

  10. Page Recognition: Quantum Leap In Recognition Technology

    Science.gov (United States)

    Miller, Larry

    1989-07-01

    No milestone has proven as elusive as the always-approaching "year of the LAN," but the "year of the scanner" might claim the silver medal. Desktop scanners have been around almost as long as personal computers. And everyone thinks they are used for obvious desktop-publishing and business tasks like scanning business documents, magazine articles and other pages, and translating those words into files your computer understands. But, until now, the reality fell far short of the promise. Because it's true that scanners deliver an accurate image of the page to your computer, but the software to recognize this text has been woefully disappointing. Old optical-character recognition (OCR) software recognized such a limited range of pages as to be virtually useless to real users. (For example, one OCR vendor specified 12-point Courier font from an IBM Selectric typewriter: the same font in 10-point, or from a Diablo printer, was unrecognizable!) Computer dealers have told me the chasm between OCR expectations and reality is so broad and deep that nine out of ten prospects leave their stores in disgust when they learn the limitations. And this is a very important, very unfortunate gap. Because the promise of recognition -- what people want it to do -- carries with it tremendous improvements in our productivity and ability to get tons of written documents into our computers where we can do real work with it. The good news is that a revolutionary new development effort has led to the new technology of "page recognition," which actually does deliver the promise we've always wanted from OCR. I'm sure every reader appreciates the breakthrough represented by the laser printer and page-makeup software, a combination so powerful it created new reasons for buying a computer. A similar breakthrough is happening right now in page recognition: the Macintosh (and, I must admit, other personal computers) equipped with a moderately priced scanner and OmniPage software (from Caere

  11. Gauge Theory and Calibrated Geometry for Calabi-Yau 4-folds

    Science.gov (United States)

    Cao, Yalong

    This thesis is devoted to the study of gauge theory and calibrated geometry for Calabi-Yau 4-folds. More specifically, our study is along the following five directions. 1. We develop Donaldson-Thomas type theory on Calabi-Yau 4-folds. Let X be a compact complex Calabi-Yau 4-fold. We define Donaldson-Thomas type deformation invariants (DT4 invariants) by studying moduli spaces of solutions to the Donaldson- Thomas equations on X. We also study sheaves counting problems on local Calabi-Yau 4-folds. We relate DT4 invariants of KY to the Donaldson-Thomas invariants of the associated Fano 3-fold Y. When the Calabi-Yau 4-fold is toric, we adapt the virtual localization formula to define the corresponding equivariant DT4 invariants. We also discuss the non-commutative version of DT4 invariants for quivers with relations. Finally, we compute DT4 invariants for certain Calabi-Yau 4-folds when moduli spaces are smooth and find a DT 4/GW correspondence for X. Examples of wall-crossing phenomenon in DT4 theory are also given. 2. Given a complex 4-fold X with an (Calabi-Yau 3-fold) anti-canonical divisor Y, we study relative Donaldson-Thomas invariants for this pair, which are elements in the Donaldson-Thomas cohomologies of Y. We also discuss gluing formulas which relate relative invariants and DT4 invariants for Calabi-Yau 4-folds. 3. We study orientability issues of moduli spaces from gauge theories on Calabi-Yau manifolds. Our results generalize and strengthen those for Donaldson-Thomas theory on Calabi-Yau manifolds of dimensions 3 and 4. We also prove a corresponding result in the relative situation which is relevant to the gluing formula in DT theory. 4. Motivated by Strominger-Yau-Zaslow's mirror symmetry proposal and Kontsevich's homological mirror symmetry conjecture, we study mirror phenomena (in A-model) of certain results from Donaldson-Thomas theory for Calabi-Yau 4-folds. More precisely, we study calibrated geometry in the sense of Harvey-Lawson and Lagrangian

  12. Image analysis of vocal fold histology

    Science.gov (United States)

    Reinisch, Lou; Garrett, C. Gaelyn

    2001-05-01

    To visualize the concentration gradients of collagen, elastin and ground substance in histologic sections of vocal folds, an image enhancement scheme was devised. Slides stained with Movat's solution were viewed on a light microscope. The image was digitally photographed. Using commercially available software, all pixels within a color range are selected from the mucosa presented on the image. Using the Movat's pentachrome stain, yellow to yellow-brown pixels represented mature collagen, blue to blue-green pixels represented young collagen (collagen that is not fully cross-linked) and black to dark violet pixels represented elastin. From each of the color range selections, a black and white image was created. The pixels not within the color range were black. The selected pixels within the color range were white. The image was averaged and smoothed to produce 256 levels of gray with less spatial resolution. This new grey-scale image showed the concentration gradient. These images were further enhanced with contour lines surrounding equivalent levels of gray. This technique is helpful to compare the micro-anatomy of the vocal folds. For instance, we find large concentration of the collagen deep in the mucosa and adjacent to the vocalis muscle.

  13. Numerical modeling of fold-and-thrust belts: Applications to Kuqa foreland fold belt, China

    Science.gov (United States)

    Yin, H.; Morgan, J. K.; Zhang, J.; Wang, Z.

    2009-12-01

    We constructed discrete element models to simulate the evolution of fold-and-thrust belts. The impact of rock competence and decollement strength on the geometric pattern and deformation mechanics of fold-and-thrust belts has been investigated. The models reproduced some characteristic features of fold-and-thrust belts, such as faulted detachment folds, pop-ups, far-traveled thrust sheets, passive-roof duplexes, and back thrusts. In general, deformation propagates farther above a weak decollement than above a strong decollement. Our model results confirm that fold-and-thrust belts with strong frictional decollements develop relatively steep and narrow wedges formed by closely spaced imbricate thrust slices, whereas fold belts with weak decollements form wide low-taper wedges composed of faulted detachment folds, pop-ups, and back thrusts. Far-traveled thrust sheets and passive-roof duplexes are observed in the model with a strong lower decollement and a weak upper detachment. Model results also indicate that the thickness of the weak layer is critical. If it is thick enough, it acts as a ductile layer that is able to flow under differential stress, which helps to partition deformation above and below it. The discrete element modeling results were used to interpret the evolution of Kuqa Cenozoic fold-and-thrust belt along northern Tarim basin, China. Seismic and well data show that the widely distributed Paleogene rock salt has a significant impact on the deformation in this area. Structures beneath salt are closely spaced imbricate thrust and passive-roof duplex systems. Deformation above salt propagates much farther than below the salt. Faults above salt are relatively wide spaced. A huge controversy over the Kuqa fold-and-thrust belt is whether it is thin-skinned or thick-skinned. With the insights from DEM results, we suggest that Kuqa structures are mostly thin-skinned with Paleogene salt as decollement, except for the rear part near the backstop, where the

  14. 2nd International Conference on Pattern Recognition

    CERN Document Server

    Marsico, Maria

    2015-01-01

    This book contains the extended and revised versions of a set of selected papers from the 2nd International Conference on Pattern Recognition (ICPRAM 2013), held in Barcelona, Spain, from 15 to 18 February, 2013. ICPRAM was organized by the Institute for Systems and Technologies of Information, Control and Communication (INSTICC) and was held in cooperation with the Association for the Advancement of Artificial Intelligence (AAAI). The hallmark of this conference was to encourage theory and practice to meet in a single venue. The focus of the book is on contributions describing applications of Pattern Recognition techniques to real-world problems, interdisciplinary research, experimental and/or theoretical studies yielding new insights that advance Pattern Recognition methods.

  15. Circuit topology of self-interacting chains: implications for folding and unfolding dynamics.

    Science.gov (United States)

    Mugler, Andrew; Tans, Sander J; Mashaghi, Alireza

    2014-11-07

    Understanding the relationship between molecular structure and folding is a central problem in disciplines ranging from biology to polymer physics and DNA origami. Topology can be a powerful tool to address this question. For a folded linear chain, the arrangement of intra-chain contacts is a topological property because rearranging the contacts requires discontinuous deformations. Conversely, the topology is preserved when continuously stretching the chain while maintaining the contact arrangement. Here we investigate how the folding and unfolding of linear chains with binary contacts is guided by the topology of contact arrangements. We formalize the topology by describing the relations between any two contacts in the structure, which for a linear chain can either be in parallel, in series, or crossing each other. We show that even when other determinants of folding rate such as contact order and size are kept constant, this 'circuit' topology determines folding kinetics. In particular, we find that the folding rate increases with the fractions of parallel and crossed relations. Moreover, we show how circuit topology constrains the conformational phase space explored during folding and unfolding: the number of forbidden unfolding transitions is found to increase with the fraction of parallel relations and to decrease with the fraction of series relations. Finally, we find that circuit topology influences whether distinct intermediate states are present, with crossed contacts being the key factor. The approach presented here can be more generally applied to questions on molecular dynamics, evolutionary biology, molecular engineering, and single-molecule biophysics.

  16. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

    Science.gov (United States)

    Das, Payel; Moll, Mark; Stamati, Hernán; Kavraki, Lydia E.; Clementi, Cecilia

    2006-06-01

    The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the "simple" case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear dimensionality reduction. We validate the usefulness of this method by characterizing the folding landscape associated with a coarse-grained protein model of src homology 3 as sampled by molecular dynamics simulations. The folding free-energy landscape projected on the few relevant coordinates emerging from the dimensionality reduction can correctly identify the transition-state ensemble of the reaction. The first embedding dimension efficiently captures the evolution of the folding process along the main folding route. These results clearly show that the proposed method can efficiently find a low-dimensional representation of a complex process such as protein folding. reaction coordinate | transition state | manifold | embedding | ISOMAP

  17. AN ILLUMINATION INVARIANT TEXTURE BASED FACE RECOGNITION

    Directory of Open Access Journals (Sweden)

    K. Meena

    2013-11-01

    Full Text Available Automatic face recognition remains an interesting but challenging computer vision open problem. Poor illumination is considered as one of the major issue, since illumination changes cause large variation in the facial features. To resolve this, illumination normalization preprocessing techniques are employed in this paper to enhance the face recognition rate. The methods such as Histogram Equalization (HE, Gamma Intensity Correction (GIC, Normalization chain and Modified Homomorphic Filtering (MHF are used for preprocessing. Owing to great success, the texture features are commonly used for face recognition. But these features are severely affected by lighting changes. Hence texture based models Local Binary Pattern (LBP, Local Derivative Pattern (LDP, Local Texture Pattern (LTP and Local Tetra Patterns (LTrPs are experimented under different lighting conditions. In this paper, illumination invariant face recognition technique is developed based on the fusion of illumination preprocessing with local texture descriptors. The performance has been evaluated using YALE B and CMU-PIE databases containing more than 1500 images. The results demonstrate that MHF based normalization gives significant improvement in recognition rate for the face images with large illumination conditions.

  18. Contemporary deep recurrent learning for recognition

    Science.gov (United States)

    Iftekharuddin, K. M.; Alam, M.; Vidyaratne, L.

    2017-05-01

    Large-scale feed-forward neural networks have seen intense application in many computer vision problems. However, these networks can get hefty and computationally intensive with increasing complexity of the task. Our work, for the first time in literature, introduces a Cellular Simultaneous Recurrent Network (CSRN) based hierarchical neural network for object detection. CSRN has shown to be more effective to solving complex tasks such as maze traversal and image processing when compared to generic feed forward networks. While deep neural networks (DNN) have exhibited excellent performance in object detection and recognition, such hierarchical structure has largely been absent in neural networks with recurrency. Further, our work introduces deep hierarchy in SRN for object recognition. The simultaneous recurrency results in an unfolding effect of the SRN through time, potentially enabling the design of an arbitrarily deep network. This paper shows experiments using face, facial expression and character recognition tasks using novel deep recurrent model and compares recognition performance with that of generic deep feed forward model. Finally, we demonstrate the flexibility of incorporating our proposed deep SRN based recognition framework in a humanoid robotic platform called NAO.

  19. Factors associated with alcohol consumption, problem drinking, and related consequences among high school students in Taiwan.

    Science.gov (United States)

    Yeh, Mei-Yu

    2006-02-01

    This research evaluated the risk factors associated with alcohol consumption, problem drinking, and related consequences among high school students in Taiwan. A total of 779 10th grade students from four randomly selected high schools in eastern Taiwan were included in the survey. Survey data were self-reported by students and analyzed using logistic regression methods. The results showed that alcohol consumption and problem drinking was 2.22-2.71-fold greater in male than in female adolescents. Parents and peer groups were the determinants influencing alcohol consumption, and these influences could be enhanced particularly by the drinking behaviors of fathers and peer groups, and the relationship of students with their peer groups. The probability of developing adolescent problem drinking was fourfold greater in students whose fathers had habits of drinking. Ethnicity had a notable impact on the risk of problem drinking. The occurrence of problem drinking among indigenous adolescents was 2.98-fold higher than among Hans, indicating a diversity of biological factors, social norms, and expectation for alcohol drinking between these two ethnic groups. This study suggests that a policy for preventing alcohol abuse among high school students should start by addressing the two major associated problems: a need to earn peer group recognition, and the lack of family support among at-risk students.

  20. FUNDAMENTALS OF SPEAKER RECOGNITION

    Directory of Open Access Journals (Sweden)

    Figen ERTAŞ

    2000-02-01

    Full Text Available The explosive growth of information technology in the last decade has made a considerable impact on the design and construction of systems for human-machine communication, which is becoming increasingly important in many aspects of life. Amongst other speech processing tasks, a great deal of attention has been devoted to developing procedures that identify people from their voices, and the design and construction of speaker recognition systems has been a fascinating enterprise pursued over many decades. This paper introduces speaker recognition in general and discusses its relevant parameters in relation to system performance.

  1. Touchless palmprint recognition systems

    CERN Document Server

    Genovese, Angelo; Scotti, Fabio

    2014-01-01

    This book examines the context, motivation and current status of biometric systems based on the palmprint, with a specific focus on touchless and less-constrained systems. It covers new technologies in this rapidly evolving field and is one of the first comprehensive books on palmprint recognition systems.It discusses the research literature and the most relevant industrial applications of palmprint biometrics, including the low-cost solutions based on webcams. The steps of biometric recognition are described in detail, including acquisition setups, algorithms, and evaluation procedures. Const

  2. A Survey on Sentiment Classification in Face Recognition

    Science.gov (United States)

    Qian, Jingyu

    2018-01-01

    Face recognition has been an important topic for both industry and academia for a long time. K-means clustering, autoencoder, and convolutional neural network, each representing a design idea for face recognition method, are three popular algorithms to deal with face recognition problems. It is worthwhile to summarize and compare these three different algorithms. This paper will focus on one specific face recognition problem-sentiment classification from images. Three different algorithms for sentiment classification problems will be summarized, including k-means clustering, autoencoder, and convolutional neural network. An experiment with the application of these algorithms on a specific dataset of human faces will be conducted to illustrate how these algorithms are applied and their accuracy. Finally, the three algorithms are compared based on the accuracy result.

  3. Applications of evolutionary computation in image processing and pattern recognition

    CERN Document Server

    Cuevas, Erik; Perez-Cisneros, Marco

    2016-01-01

    This book presents the use of efficient Evolutionary Computation (EC) algorithms for solving diverse real-world image processing and pattern recognition problems. It provides an overview of the different aspects of evolutionary methods in order to enable the reader in reaching a global understanding of the field and, in conducting studies on specific evolutionary techniques that are related to applications in image processing and pattern recognition. It explains the basic ideas of the proposed applications in a way that can also be understood by readers outside of the field. Image processing and pattern recognition practitioners who are not evolutionary computation researchers will appreciate the discussed techniques beyond simple theoretical tools since they have been adapted to solve significant problems that commonly arise on such areas. On the other hand, members of the evolutionary computation community can learn the way in which image processing and pattern recognition problems can be translated into an...

  4. Noise Folding in Completely Perturbed Compressed Sensing

    Directory of Open Access Journals (Sweden)

    Limin Zhou

    2016-01-01

    Full Text Available This paper first presents a new generally perturbed compressed sensing (CS model y=(A+E(x+u+e, which incorporated a general nonzero perturbation E into sensing matrix A and a noise u into signal x simultaneously based on the standard CS model y=Ax+e and is called noise folding in completely perturbed CS model. Our construction mainly will whiten the new proposed CS model and explore in restricted isometry property (RIP and coherence of the new CS model under some conditions. Finally, we use OMP to give a numerical simulation which shows that our model is feasible although the recovered value of signal is not exact compared with original signal because of measurement noise e, signal noise u, and perturbation E involved.

  5. Electrotransfection of Polyamine Folded DNA Origami Structures.

    Science.gov (United States)

    Chopra, Aradhana; Krishnan, Swati; Simmel, Friedrich C

    2016-10-12

    DNA origami structures are artificial molecular nanostructures in which DNA double helices are forced into a closely packed configuration by a multitude of DNA strand crossovers. We show that three different types of origami structures (a flat sheet, a hollow tube, and a compact origami block) can be formed in magnesium-free buffer solutions containing low (origami folding is proportional to the DNA concentration. At excessive amounts, the structures aggregate and precipitate. In contrast to origami structures formed in conventional buffers, the resulting structures are stable in the presence of high electric field pulses, such as those commonly used for electrotransfection experiments. We demonstrate that spermidine-stabilized structures are stable in cell lysate and can be delivered into mammalian cells via electroporation.

  6. Microscopic Phonosurgery in Benign Vocal Fold Lesions

    Directory of Open Access Journals (Sweden)

    Sukamal Das

    2014-06-01

    Thirty out of 32 patients showed objective improvement in fibreoptic laryngoscopy post treatment. Two patients were noncompliant to voice therapy and showed recurrence of their pathologies.Mean VHI 10 score showed significant improvement from 8 in the preoperative period to 3 in the postoperative period. Conclusion : Phonosurgery is a quick and effective treatment with uncommon and transient post-operative complications. Pre and postoperative voice therapy plays an integral role in combination with phono-micro surgery enhances the outcome in patients with benign vocal fold lesions. Objective assessment of the voice pre- and postoperatively should be used consistently to evaluate the additional impact of pre- and postoperative voice therapy.

  7. Unfolding a Problem

    Science.gov (United States)

    Currier, Sarah Cox

    2015-01-01

    In this article, Sarah Currier, a math specialist at Elizabeth Hall International School in Minnesota, describes how she used origami in a deliberate manner to teach content. She shares how she uses paper folding to teach mathematical concepts, reinforce vocabulary, and as a problem-solving model. She also offers ideas for using origami in other…

  8. Hybrid gesture recognition system for short-range use

    Science.gov (United States)

    Minagawa, Akihiro; Fan, Wei; Katsuyama, Yutaka; Takebe, Hiroaki; Ozawa, Noriaki; Hotta, Yoshinobu; Sun, Jun

    2012-03-01

    In recent years, various gesture recognition systems have been studied for use in television and video games[1]. In such systems, motion areas ranging from 1 to 3 meters deep have been evaluated[2]. However, with the burgeoning popularity of small mobile displays, gesture recognition systems capable of operating at much shorter ranges have become necessary. The problems related to such systems are exacerbated by the fact that the camera's field of view is unknown to the user during operation, which imposes several restrictions on his/her actions. To overcome the restrictions generated from such mobile camera devices, and to create a more flexible gesture recognition interface, we propose a hybrid hand gesture system, in which two types of gesture recognition modules are prepared and with which the most appropriate recognition module is selected by a dedicated switching module. The two recognition modules of this system are shape analysis using a boosting approach (detection-based approach)[3] and motion analysis using image frame differences (motion-based approach)(for example, see[4]). We evaluated this system using sample users and classified the resulting errors into three categories: errors that depend on the recognition module, errors caused by incorrect module identification, and errors resulting from user actions. In this paper, we show the results of our investigations and explain the problems related to short-range gesture recognition systems.

  9. Recognition of Face and Emotional Facial Expressions in Autism

    Directory of Open Access Journals (Sweden)

    Muhammed Tayyib Kadak

    2013-03-01

    Full Text Available Autism is a genetically transferred neurodevelopmental disorder characterized by severe and permanent deficits in many interpersonal relation areas like communication, social interaction and emotional responsiveness. Patients with autism have deficits in face recognition, eye contact and recognition of emotional expression. Both recognition of face and expression of facial emotion carried on face processing. Structural and functional impairment in fusiform gyrus, amygdala, superior temporal sulcus and other brain regions lead to deficits in recognition of face and facial emotion. Therefore studies suggest that face processing deficits resulted in problems in areas of social interaction and emotion in autism. Studies revealed that children with autism had problems in recognition of facial expression and used mouth region more than eye region. It was also shown that autistic patients interpreted ambiguous expressions as negative emotion. In autism, deficits related in various stages of face processing like detection of gaze, face identity, recognition of emotional expression were determined, so far. Social interaction impairments in autistic spectrum disorders originated from face processing deficits during the periods of infancy, childhood and adolescence. Recognition of face and expression of facial emotion could be affected either automatically by orienting towards faces after birth, or by “learning” processes in developmental periods such as identity and emotion processing. This article aimed to review neurobiological basis of face processing and recognition of emotional facial expressions during normal development and in autism.

  10. On the folding of graphs-theory and application

    International Nuclear Information System (INIS)

    Nada, S.I.; Hamouda, E.H.

    2009-01-01

    In this article, we recall the definition of graph folding in the sense of El-kholy and El-Esawy [El-kholy E, El-Esawy A. Graph folding of some special graphs. J Math Stat 2005;1(1):66-70.] and study the limit of folding of some graphs. Also we define the folding number and give a formula to compute the number of folding maps f: P n → P n , where P n is a path with n edges. We also discuss application of folding from Orgami to buckling and high energy physics.

  11. CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.

    Directory of Open Access Journals (Sweden)

    Oliver C Redfern

    2007-11-01

    Full Text Available We present CATHEDRAL, an iterative protocol for determining the location of previously observed protein folds in novel multidomain protein structures. CATHEDRAL builds on the features of a fast secondary-structure-based method (using graph theory to locate known folds within a multidomain context and a residue-based, double-dynamic programming algorithm, which is used to align members of the target fold groups against the query protein structure to identify the closest relative and assign domain boundaries. To increase the fidelity of the assignments, a support vector machine is used to provide an optimal scoring scheme. Once a domain is verified, it is excised, and the search protocol is repeated in an iterative fashion until all recognisable domains have been identified. We have performed an initial benchmark of CATHEDRAL against other publicly available structure comparison methods using a consensus dataset of domains derived from the CATH and SCOP domain classifications. CATHEDRAL shows superior performance in fold recognition and alignment accuracy when compared with many equivalent methods. If a novel multidomain structure contains a known fold, CATHEDRAL will locate it in 90% of cases, with <1% false positives. For nearly 80% of assigned domains in a manually validated test set, the boundaries were correctly delineated within a tolerance of ten residues. For the remaining cases, previously classified domains were very remotely related to the query chain so that embellishments to the core of the fold caused significant differences in domain sizes and manual refinement of the boundaries was necessary. To put this performance in context, a well-established sequence method based on hidden Markov models was only able to detect 65% of domains, with 33% of the subsequent boundaries assigned within ten residues. Since, on average, 50% of newly determined protein structures contain more than one domain unit, and typically 90% or more of these

  12. Galeotti on recognition as inclusion

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2008-01-01

    Anna Elisabetta Galeotti's theory of 'toleration as recognition' has been criticised by Peter Jones for being conceptually incoherent, since liberal toleration presupposes a negative attitude to differences, whereas multicultural recognition requires positive affirmation hereof. The paper spells...... out Galeotti's justification for recognition as a requirement of liberal justice in detail and asks in what sense the policies supported by Galeotti are policies of recognition. It is argued that Jones misrepresents Galeotti's theory, insofar as this sense of recognition actually is compatible...... in respects that need to be filled out in order to secure compatibility with liberalism, and that this may prove problematic. Keywords: liberalism; multiculturalism; recognition; toleration...

  13. Identification of novel restriction endonuclease-like fold families among hypothetical proteins.

    Science.gov (United States)

    Kinch, Lisa N; Ginalski, Krzysztof; Rychlewski, Leszek; Grishin, Nick V

    2005-01-01

    Restriction endonucleases and other nucleic acid cleaving enzymes form a large and extremely diverse superfamily that display little sequence similarity despite retaining a common core fold responsible for cleavage. The lack of significant sequence similarity between protein families makes homology inference a challenging task and hinders new family identification with traditional sequence-based approaches. Using the consensus fold recognition method Meta-BASIC that combines sequence profiles with predicted protein secondary structure, we identify nine new restriction endonuclease-like fold families among previously uncharacterized proteins and predict these proteins to cleave nucleic acid substrates. Application of transitive searches combined with gene neighborhood analysis allow us to confidently link these unknown families to a number of known restriction endonuclease-like structures and thus assign folds to the uncharacterized proteins. Finally, our method identifies a novel restriction endonuclease-like domain in the C-terminus of RecC that is not detected with structure-based searches of the existing PDB database.

  14. Protein folding: Over half a century lasting quest. Comment on "There and back again: Two views on the protein folding puzzle" by Alexei V. Finkelstein et al.

    Science.gov (United States)

    Krokhotin, Andrey; Dokholyan, Nikolay V.

    2017-07-01

    Most proteins fold into unique three-dimensional (3D) structures that determine their biological functions, such as catalytic activity or macromolecular binding. Misfolded proteins can pose a threat through aberrant interactions with other proteins leading to a number of diseases including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis [1,2]. What does determine 3D structure of proteins? The first clue to this question came more than fifty years ago when Anfinsen demonstrated that unfolded proteins can spontaneously fold to their native 3D structures [3,4]. Anfinsen's experiments lead to the conclusion that proteins fold to unique native structure corresponding to the stable and kinetically accessible free energy minimum, and protein native structure is solely determined by its amino acid sequence. The question of how exactly proteins find their free energy minimum proved to be a difficult problem. One of the puzzles, initially pointed out by Levinthal, was an inconsistency between observed protein folding times and theoretical estimates. A self-avoiding polymer model of a globular protein of 100-residues length on a cubic lattice can sample at least 1047 states. Based on the assumption that conformational sampling occurs at the highest vibrational mode of proteins (∼picoseconds), predicted folding time by searching among all the possible conformations leads to ∼1027 years (much larger than the age of the universe) [5]. In contrast, observed protein folding time range from microseconds to minutes. Due to tremendous theoretical progress in protein folding field that has been achieved in past decades, the source of this inconsistency is currently understood that is thoroughly described in the review by Finkelstein et al. [6].

  15. Fine-grained recognition of plants from images.

    Science.gov (United States)

    Šulc, Milan; Matas, Jiří

    2017-01-01

    Fine-grained recognition of plants from images is a challenging computer vision task, due to the diverse appearance and complex structure of plants, high intra-class variability and small inter-class differences. We review the state-of-the-art and discuss plant recognition tasks, from identification of plants from specific plant organs to general plant recognition "in the wild". We propose texture analysis and deep learning methods for different plant recognition tasks. The methods are evaluated and compared them to the state-of-the-art. Texture analysis is only applied to images with unambiguous segmentation (bark and leaf recognition), whereas CNNs are only applied when sufficiently large datasets are available. The results provide an insight in the complexity of different plant recognition tasks. The proposed methods outperform the state-of-the-art in leaf and bark classification and achieve very competitive results in plant recognition "in the wild". The results suggest that recognition of segmented leaves is practically a solved problem, when high volumes of training data are available. The generality and higher capacity of state-of-the-art CNNs makes them suitable for plant recognition "in the wild" where the views on plant organs or plants vary significantly and the difficulty is increased by occlusions and background clutter.

  16. Glycoprotein folding and quality-control mechanisms in protein-folding diseases

    Directory of Open Access Journals (Sweden)

    Sean P. Ferris

    2014-03-01

    Full Text Available Biosynthesis of proteins – from translation to folding to export – encompasses a complex set of events that are exquisitely regulated and scrutinized to ensure the functional quality of the end products. Cells have evolved to capitalize on multiple post-translational modifications in addition to primary structure to indicate the folding status of nascent polypeptides to the chaperones and other proteins that assist in their folding and export. These modifications can also, in the case of irreversibly misfolded candidates, signal the need for dislocation and degradation. The current Review focuses on the glycoprotein quality-control (GQC system that utilizes protein N-glycosylation and N-glycan trimming to direct nascent glycopolypeptides through the folding, export and dislocation pathways in the endoplasmic reticulum (ER. A diverse set of pathological conditions rooted in defective as well as over-vigilant ER quality-control systems have been identified, underlining its importance in human health and disease. We describe the GQC pathways and highlight disease and animal models that have been instrumental in clarifying our current understanding of these processes.

  17. Optical Character Recognition.

    Science.gov (United States)

    Converso, L.; Hocek, S.

    1990-01-01

    This paper describes computer-based optical character recognition (OCR) systems, focusing on their components (the computer, the scanner, the OCR, and the output device); how the systems work; and features to consider in selecting a system. A list of 26 questions to ask to evaluate systems for potential purchase is included. (JDD)

  18. Tolerance and recognition

    Directory of Open Access Journals (Sweden)

    Hans Marius Hansteen

    2014-12-01

    Full Text Available Even though “toleration” and “recognition” designate opposing attitudes (to tolerate something, implies a negative stance towards it, whereas recognition seems to imply a positive one, the concepts do not constitute mutually exclusive alternatives. However, “toleration” is often associated with liberal universalism, focusing on individual rights, whereas “recognition” often connotes communitarian perspectives, focusing on relations and identity. This paper argues that toleration may be founded on recognition, and that recognition may imply toleration. In outlining a differentiated understanding of the relationship between toleration and recognition, it seems apt to avoid an all-to-general dichotomy between universalism and particularism or, in other words, to reach beyond the debate between liberalism and communitarianism in political philosophy.The paper takes as its starting point the view that the discussion on toleration and diversity in intercultural communication is one of the contexts where it seems important to get beyond the liberal/communitarian dichotomy. Some basic features of Rainer Forst’s theory of toleration and Axel Honneth’s theory of the struggle for recognition are presented, in order to develop a more substantial understanding of the relationship between the concepts of toleration and recognition. One lesson from Forst is that toleration is a normatively dependent concept, i.e., that it is impossible to deduce principles for toleration and its limits from a theory of toleration as such. A central lesson from Honneth is that recognition – understood as a basic human need – is always conflictual and therefore dynamic.Accordingly, a main point in the paper is that the theory of struggles for and about recognition (where struggles for designates struggles within an established order of recognition, and struggles about designates struggles that challenge established orders of recognition may clarify what

  19. Importance of ECM recognition

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Importance of ECM recognition. Leishmaniasis transmitted by parasite injection into blood during blood meal of insect vector. Parasites home in macrophages of liver and spleen - adhere, penetrate, transform and replicate. Macrophage lysis - attack of neighbouring ...

  20. Facial Expression Recognition

    NARCIS (Netherlands)

    Pantic, Maja; Li, S.; Jain, A.

    2009-01-01

    Facial expression recognition is a process performed by humans or computers, which consists of: 1. Locating faces in the scene (e.g., in an image; this step is also referred to as face detection), 2. Extracting facial features from the detected face region (e.g., detecting the shape of facial

  1. The review on tessellation origami inspired folded structure

    Science.gov (United States)

    Chu, Chai Chen; Keong, Choong Kok

    2017-10-01

    Existence of folds enhances the load carrying capacity of a folded structure which makes it suitable to be used for application where large open space is required such as large span roof structures and façade. Folded structure is closely related to origami especially the tessellation origami. Tessellation origami provides a folded configuration with facetted surface as a result from repeated folding pattern. Besides that, tessellation origami has flexible folding mechanism that produced a variety of 3-dimensional folded configurations. Despite the direct relationship between fold in origami and folded structure, the idea of origami inspired folded structure is not properly reviewed in the relevant engineering field. Hence, this paper aims to present the current studies from related discipline which has direct relation with application of tessellation origami in folded structure. First, tessellation origami is properly introduced and defined. Then, the review covers the topic on the origami tessellation design suitable for folded structure, its modeling and simulation method, and existing studies and applications of origami as folded structure is presented. The paper also includes the discussion on the current issues related to each topic.

  2. PATTER, Pattern Recognition Data Analysis

    International Nuclear Information System (INIS)

    Cox, L.C. Jr.; Bender, C.F.

    1986-01-01

    1 - Description of program or function: PATTER is an interactive program with extensive facilities for modeling analytical processes and solving complex data analysis problems using statistical methods, spectral analysis, and pattern recognition techniques. PATTER addresses the type of problem generally stated as follows: given a set of objects and a list of measurements made on these objects, is it possible to find or predict a property of the objects which is not directly measurable but is known to define some unknown relationship? When employed intelligently, PATTER will act upon a data set in such a way it becomes apparent if useful information, beyond that already discerned, is contained in the data. 2 - Method of solution: In order to solve the general problem, PATTER contains preprocessing techniques to produce new variables that are related to the values of the measurements which may reduce the number of variables and/or reveal useful information about the 'obscure' property; display techniques to represent the variable space in some way that can be easily projected onto a two- or three-dimensional plot for human observation to see if any significant clustering of points occurs; and learning techniques based on both unsupervised and supervised methods, to extract as much information from the data as possible so that the optimum solution can be found

  3. A High Performance Banknote Recognition System Based on a One-Dimensional Visible Light Line Sensor

    Directory of Open Access Journals (Sweden)

    Young Ho Park

    2015-06-01

    Full Text Available An algorithm for recognizing banknotes is required in many fields, such as banknote-counting machines and automatic teller machines (ATM. Due to the size and cost limitations of banknote-counting machines and ATMs, the banknote image is usually captured by a one-dimensional (line sensor instead of a conventional two-dimensional (area sensor. Because the banknote image is captured by the line sensor while it is moved at fast speed through the rollers inside the banknote-counting machine or ATM, misalignment, geometric distortion, and non-uniform illumination of the captured images frequently occur, which degrades the banknote recognition accuracy. To overcome these problems, we propose a new method for recognizing banknotes. The experimental results using two-fold cross-validation for 61,240 United States dollar (USD images show that the pre-classification error rate is 0%, and the average error rate for the final recognition of the USD banknotes is 0.114%.

  4. Self-folding origami at any energy scale

    Science.gov (United States)

    Pinson, Matthew B.; Stern, Menachem; Carruthers Ferrero, Alexandra; Witten, Thomas A.; Chen, Elizabeth; Murugan, Arvind

    2017-05-01

    Programmable stiff sheets with a single low-energy folding motion have been sought in fields ranging from the ancient art of origami to modern meta-materials research. Despite such attention, only two extreme classes of crease patterns are usually studied; special Miura-Ori-based zero-energy patterns, in which crease folding requires no sheet bending, and random patterns with high-energy folding, in which the sheet bends as much as creases fold. We present a physical approach that allows systematic exploration of the entire space of crease patterns as a function of the folding energy. Consequently, we uncover statistical results in origami, finding the entropy of crease patterns of given folding energy. Notably, we identify three classes of Mountain-Valley choices that have widely varying `typical' folding energies. Our work opens up a wealth of experimentally relevant self-folding origami designs not reliant on Miura-Ori, the Kawasaki condition or any special symmetry in space.

  5. Phonosurgery of vocal fold polyps, cysts and nodules is beneficial

    DEFF Research Database (Denmark)

    Jensen, Jane Bjerg; Rasmussen, Niels

    2013-01-01

    This study reports our experience with microscopic phonosurgery (PS) of benign lesions of the vocal folds.......This study reports our experience with microscopic phonosurgery (PS) of benign lesions of the vocal folds....

  6. School IPM Recognition and Certification

    Science.gov (United States)

    Schools and school districts can get support and recognition for implementation of school IPM. EPA is developing a program to provide recognition for school districts that are working towards or have achieved a level of success with school IPM programs.

  7. 3D fold growth rates in transpressional tectonic settings

    Science.gov (United States)

    Frehner, Marcel

    2015-04-01

    Geological folds are inherently three-dimensional (3D) structures; hence, they also grow in 3D. In this study, fold growth in all three dimensions is quantified numerically using a finite-element algorithm for simulating deformation of Newtonian media in 3D. The presented study is an extension and generalization of the work presented in Frehner (2014), which only considered unidirectional layer-parallel compression. In contrast, the full range from strike slip settings (i.e., simple shear) to unidirectional layer-parallel compression is considered here by varying the convergence angle of the boundary conditions; hence the results are applicable to general transpressional tectonic settings. Only upright symmetrical single-layer fold structures are considered. The horizontal higher-viscous layer exhibits an initial point-like perturbation. Due to the mixed pure- and simple shear boundary conditions a mechanical buckling instability grows from this perturbation in all three dimensions, described by: Fold amplification (vertical growth): Fold amplification describes the growth from a fold shape with low limb-dip angle to a shape with higher limb-dip angle. Fold elongation (growth parallel to fold axis): Fold elongation describes the growth from a dome-shaped (3D) structure to a more cylindrical fold (2D). Sequential fold growth (growth perpendicular to fold axial plane): Sequential fold growth describes the growth of secondary (and further) folds adjacent to the initial isolated fold. The term 'lateral fold growth' is used as an umbrella term for both fold elongation and sequential fold growth. In addition, the orientation of the fold axis is tracked as a function of the convergence angle. Even though the absolute values of all three growth rates are markedly reduced with increasing simple-shear component at the boundaries, the general pattern of the quantified fold growth under the studied general-shear boundary conditions is surprisingly similar to the end

  8. Factors that affect coseismic folds in an overburden layer

    Science.gov (United States)

    Zeng, Shaogang; Cai, Yongen

    2018-03-01

    Coseismic folds induced by blind thrust faults have been observed in many earthquake zones, and they have received widespread attention from geologists and geophysicists. Numerous studies have been conducted regarding fold kinematics; however, few have studied fold dynamics quantitatively. In this paper, we establish a conceptual model with a thrust fault zone and tectonic stress load to study the factors that affect coseismic folds and their formation mechanisms using the finite element method. The numerical results show that the fault dip angle is a key factor that controls folding. The greater the dip angle is, the steeper the fold slope. The second most important factor is the overburden thickness. The thicker the overburden is, the more gradual the fold. In this case, folds are difficult to identify in field surveys. Therefore, if a fold can be easily identified with the naked eye, the overburden is likely shallow. The least important factors are the mechanical parameters of the overburden. The larger the Young's modulus of the overburden is, the smaller the displacement of the fold and the fold slope. Strong horizontal compression and vertical extension in the overburden near the fault zone are the main mechanisms that form coseismic folds.

  9. 76 FR 74704 - Folded Self-Mailers and Unenveloped Mailpieces

    Science.gov (United States)

    2011-12-01

    ... as an oblong. The final folded edge of an oblong folded self-mailer must be the leading (right) edge... POSTAL SERVICE 39 CFR Part 111 Folded Self-Mailers and Unenveloped Mailpieces AGENCY: Postal... self-mailers (FSM) and unenveloped mailpieces that are mailed at automation or machinable prices. To...

  10. Folds in multilayered rocks of Proterozoic age, Rajasthan, India

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Johnson and Johnson 2002 etc) shows that the fold shape modification may be brought about by buckling and flattening operating simultaneously throughout the development of fold. In the present paper a series of F1 folds devel- oped in slates with interlayered alternations with quartzite of Proterozoic age and unaffected ...

  11. Kinematics of large scale asymmetric folds and associated smaller ...

    Indian Academy of Sciences (India)

    active-hinge folding (involving lateral migration of active axial surfaces, e.g., Suppe 1983) are invoked to explain finite fold development. Any inference about fold kinematics is based on the analysis of distributions of diagnostic deformation features (Stewart and Alvarez 1991; Fischer et al. Keywords. Kinematic history ...

  12. Nomenclature proposal to describe vocal fold motion impairment

    NARCIS (Netherlands)

    Rosen, Clark A.; Mau, Ted; Remacle, Marc; Hess, Markus; Eckel, Hans E.; Young, VyVy N.; Hantzakos, Anastasios; Yung, Katherine C.; Dikkers, Frederik G.

    2016-01-01

    The terms used to describe vocal fold motion impairment are confusing and not standardized. This results in a failure to communicate accurately and to major limitations of interpreting research studies involving vocal fold impairment. We propose standard nomenclature for reporting vocal fold

  13. Nomenclature proposal to describe vocal fold motion impairment

    NARCIS (Netherlands)

    Rosen, Clark A.; Mau, Ted; Remacle, Marc; Hess, Markus; Eckel, Hans E.; Young, VyVy N.; Hantzakos, Anastasios; Yung, Katherine C.; Dikkers, Frederik G.

    The terms used to describe vocal fold motion impairment are confusing and not standardized. This results in a failure to communicate accurately and to major limitations of interpreting research studies involving vocal fold impairment. We propose standard nomenclature for reporting vocal fold

  14. α/β Hydrolase fold enzymes: the family keeps growing

    NARCIS (Netherlands)

    Nardini, Marco; Dijkstra, B W

    1999-01-01

    The alpha/beta hydrolase fold is a typical example of a tertiary fold adopted by proteins that have no obvious sequence similarity, but nevertheless, in the course of evolution, diverged from a common ancestor. Recently solved structures demonstrate a considerably increased variability in fold

  15. Probing folding free energy landscape of small proteins through ...

    Indian Academy of Sciences (India)

    Unknown

    lattice and off-lattice models of proteins have been used to study the statistical and dynamical aspects of folding.12,13 Levitt pioneered in the computational studies of protein folding using off-lattice protein models.14 A recent off-lattice model study of HP-36 based on hydrophobicity tried to correlate the folding with many ...

  16. 77 FR 74513 - Folding Gift Boxes From China

    Science.gov (United States)

    2012-12-14

    ... COMMISSION Folding Gift Boxes From China Determination On the basis of the record \\1\\ developed in the... antidumping duty order on folding gift boxes from China would be likely to lead to continuation or recurrence... Commission are contained in USITC Publication 4365 (November 2012), entitled Folding Gift Boxes from China...

  17. Kinetics of folding of the myosin rod.

    Science.gov (United States)

    Bechet, J J; Nozais, M

    1997-02-15

    The kinetics of the unfolding and refolding of the myosin rod have been studied by fluorescence and circular dichroism techniques, at different concentrations of protein and guanidine hydrochloride. The unfolding of the myosin rod was fast and at least biphasic in 2-3 M denaturant, with an initial immediate phase followed by a slower low-amplitude first-order phase. The refolding of the rod in 0.4-2 M guanidine hydrochloride was also at least biphasic; an initial immediate phase preceded a slow second-order phase. At the final denaturant concentration of 0.8 M, the amplitude of the burst phase was weakly dependent on the protein concentration and the rate constant of the refolding slow phase was optimal. These data are incorporated into a folding mechanism with at least three states. The high rates of the first steps of unfolding and refolding may be relevant for the functioning of the native myosin molecule by allowing a transient separation of the two strands of the myosin tail.

  18. Amyloid Beta Peptide Folding in Reverse Micelles.

    Science.gov (United States)

    Eskici, Gözde; Axelsen, Paul H

    2017-07-19

    Previously published experimental studies have suggested that when the 40-residue amyloid beta peptide is encapsulated in a reverse micelle, it folds into a structure that may nucleate amyloid fibril formation (Yeung, P. S.-W.; Axelsen, P. H. J. Am. Chem. Soc. 2012, 134, 6061 ). The factors that induce the formation of this structure have now been identified in a multi-microsecond simulation of the same reverse micelle system that was studied experimentally. Key features of the polypeptide-micelle interaction include the anchoring of a hydrophobic residue cluster into gaps in the reverse micelle surface, the formation of a beta turn at the anchor point that brings N- and C-terminal segments of the polypeptide into proximity, high ionic strength that promotes intramolecular hydrogen bond formation, and deformation of the reverse micelle surface to facilitate interactions with the surface along the entire length of the polypeptide. Together, these features cause the simulation-derived vibrational spectrum to red shift in a manner that reproduces the red-shift previously reported experimentally. On the basis of these findings, a new mechanism is proposed whereby membranes nucleate fibril formation and facilitate the in-register alignment of polypeptide strands that is characteristic of amyloid fibrils.

  19. Hydrophobic-hydrophilic forces in protein folding.

    Science.gov (United States)

    Durell, Stewart R; Ben-Naim, Arieh

    2017-08-01

    The process of protein folding is obviously driven by forces exerted on the atoms of the amino-acid chain. These forces arise from interactions with other parts of the protein itself (direct forces), as well as from interactions with the solvent (solvent-induced forces). We present a statistical-mechanical formalism that describes both these direct and indirect, solvent-induced thermodynamic forces on groups of the protein. We focus on 2 kinds of protein groups, commonly referred to as hydrophobic and hydrophilic. Analysis of this result leads to the conclusion that the forces on hydrophilic groups are in general stronger than on hydrophobic groups. This is then tested and verified by a series of molecular dynamics simulations, examining both hydrophobic alkanes of different sizes and hydrophilic moieties represented by polar-neutral hydroxyl groups. The magnitude of the force on assemblies of hydrophilic groups is dependent on their relative orientation: with 2 to 4 times larger forces on groups that are able to form one or more direct hydrogen bonds. © 2017 Wiley Periodicals, Inc.

  20. Folding very short peptides using molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Bosco K Ho

    2006-04-01

    Full Text Available Peptides often have conformational preferences. We simulated 133 peptide 8-mer fragments from six different proteins, sampled by replica-exchange molecular dynamics using Amber7 with a GB/SA (generalized-Born/solvent-accessible electrostatic approximation to water implicit solvent. We found that 85 of the peptides have no preferred structure, while 48 of them converge to a preferred structure. In 85% of the converged cases (41 peptides, the structures found by the simulations bear some resemblance to their native structures, based on a coarse-grained backbone description. In particular, all seven of the beta hairpins in the native structures contain a fragment in the turn that is highly structured. In the eight cases where the bioinformatics-based I-sites library picks out native-like structures, the present simulations are largely in agreement. Such physics-based modeling may be useful for identifying early nuclei in folding kinetics and for assisting in protein-structure prediction methods that utilize the assembly of peptide fragments.

  1. A Markov Random Field Groupwise Registration Framework for Face Recognition.

    Science.gov (United States)

    Liao, Shu; Shen, Dinggang; Chung, Albert C S

    2014-04-01

    In this paper, we propose a new framework for tackling face recognition problem. The face recognition problem is formulated as groupwise deformable image registration and feature matching problem. The main contributions of the proposed method lie in the following aspects: (1) Each pixel in a facial image is represented by an anatomical signature obtained from its corresponding most salient scale local region determined by the survival exponential entropy (SEE) information theoretic measure. (2) Based on the anatomical signature calculated from each pixel, a novel Markov random field based groupwise registration framework is proposed to formulate the face recognition problem as a feature guided deformable image registration problem. The similarity between different facial images are measured on the nonlinear Riemannian manifold based on the deformable transformations. (3) The proposed method does not suffer from the generalizability problem which exists commonly in learning based algorithms. The proposed method has been extensively evaluated on four publicly available databases: FERET, CAS-PEAL-R1, FRGC ver 2.0, and the LFW. It is also compared with several state-of-the-art face recognition approaches, and experimental results demonstrate that the proposed method consistently achieves the highest recognition rates among all the methods under comparison.

  2. Type-2 fuzzy graphical models for pattern recognition

    CERN Document Server

    Zeng, Jia

    2015-01-01

    This book discusses how to combine type-2 fuzzy sets and graphical models to solve a range of real-world pattern recognition problems such as speech recognition, handwritten Chinese character recognition, topic modeling as well as human action recognition. It covers these recent developments while also providing a comprehensive introduction to the fields of type-2 fuzzy sets and graphical models. Though primarily intended for graduate students, researchers and practitioners in fuzzy logic and pattern recognition, the book can also serve as a valuable reference work for researchers without any previous knowledge of these fields. Dr. Jia Zeng is a Professor at the School of Computer Science and Technology, Soochow University, China. Dr. Zhi-Qiang Liu is a Professor at the School of Creative Media, City University of Hong Kong, China.

  3. Comparing word and face recognition: an insoluble conundrum

    DEFF Research Database (Denmark)

    Robotham, Ro Julia; Starrfelt, Randi

    2017-01-01

    Abstract The relationship between face recognition and visual word recognition/reading has received increasing attention lately. A core question is whether face and word recognition rely on cognitive and cerebral processes that are largely independent, or rather processes that are distributed...... included, as a control, which makes designing experiments all the more challenging. Three main strategies have been used to overcome this problem, each of which has limitations: 1) Compare performances on typical tests of the three stimulus types (e.g., a Face Memory Test, an Object recognition test......). None of these methods, however, has provided measurements that enable direct comparison of performances across categories. We propose a simple framework for classifying tests of face, object, and word recognition according to the level of perceptual processing required to perform each test. Using...

  4. Recognition of knowledge – A step towards optimization of education

    Directory of Open Access Journals (Sweden)

    Vanda Rebolj

    2011-03-01

    In her presentation of the knowledge recognition procedures, the author relies on constructivist theories on knowledge and highlights the importance of the achieved levels of knowledge, paying equal attention to the low levels (skills, higher levels and the highest levels (problem­solving, none of which should be omitted in the assessment and recognition procedures. The author then presents the experience in knowledge recognition gained in the last five years by several colleges providing part­time studies, starting with a course in accounting and proceeding with other programmes. It is essential that knowledge recognition should not be pushed into the domain of experts or become an administrative procedure; it must remain part of the regular teaching procedure and under control of the teacher. This requires implementation of appropriate teacher training. Despite the fact that the recognition procedures developed so far have proved to be valid and have gained on credibility, numerous new research issues are being raised in this field.

  5. Cost-Sensitive Learning for Emotion Robust Speaker Recognition

    Science.gov (United States)

    Li, Dongdong; Yang, Yingchun

    2014-01-01

    In the field of information security, voice is one of the most important parts in biometrics. Especially, with the development of voice communication through the Internet or telephone system, huge voice data resources are accessed. In speaker recognition, voiceprint can be applied as the unique password for the user to prove his/her identity. However, speech with various emotions can cause an unacceptably high error rate and aggravate the performance of speaker recognition system. This paper deals with this problem by introducing a cost-sensitive learning technology to reweight the probability of test affective utterances in the pitch envelop level, which can enhance the robustness in emotion-dependent speaker recognition effectively. Based on that technology, a new architecture of recognition system as well as its components is proposed in this paper. The experiment conducted on the Mandarin Affective Speech Corpus shows that an improvement of 8% identification rate over the traditional speaker recognition is achieved. PMID:24999492

  6. Feature based sliding window technique for face recognition

    Science.gov (United States)

    Javed, Muhammad Younus; Mohsin, Syed Maajid; Anjum, Muhammad Almas

    2010-02-01

    Human beings are commonly identified by biometric schemes which are concerned with identifying individuals by their unique physical characteristics. The use of passwords and personal identification numbers for detecting humans are being used for years now. Disadvantages of these schemes are that someone else may use them or can easily be forgotten. Keeping in view of these problems, biometrics approaches such as face recognition, fingerprint, iris/retina and voice recognition have been developed which provide a far better solution when identifying individuals. A number of methods have been developed for face recognition. This paper illustrates employment of Gabor filters for extracting facial features by constructing a sliding window frame. Classification is done by assigning class label to the unknown image that has maximum features similar to the image stored in the database of that class. The proposed system gives a recognition rate of 96% which is better than many of the similar techniques being used for face recognition.

  7. Word Recognition in Auditory Cortex

    Science.gov (United States)

    DeWitt, Iain D. J.

    2013-01-01

    Although spoken word recognition is more fundamental to human communication than text recognition, knowledge of word-processing in auditory cortex is comparatively impoverished. This dissertation synthesizes current models of auditory cortex, models of cortical pattern recognition, models of single-word reading, results in phonetics and results in…

  8. Face recognition using Krawtchouk moment

    Indian Academy of Sciences (India)

    Artificial Intelligence 17(1): 41–62. Hu M K 1962 Visual pattern recognition by moment invariants. IRE Trans. on Information Theory, IT-8,. 179–187. Huang F T, Zhou Z, Zhang H-J and Chen T 2000 Pose invariant face recognition, Proc. Fourth IEEE. International Conference on Automatic Face and Gesture Recognition, ...

  9. Forensic Face Recognition: A Survey

    NARCIS (Netherlands)

    Ali, Tauseef; Spreeuwers, Lieuwe Jan; Veldhuis, Raymond N.J.; Quaglia, Adamo; Epifano, Calogera M.

    2012-01-01

    The improvements of automatic face recognition during the last 2 decades have disclosed new applications like border control and camera surveillance. A new application field is forensic face recognition. Traditionally, face recognition by human experts has been used in forensics, but now there is a

  10. Visual Recognition Memory across Contexts

    Science.gov (United States)

    Jones, Emily J. H.; Pascalis, Olivier; Eacott, Madeline J.; Herbert, Jane S.

    2011-01-01

    In two experiments, we investigated the development of representational flexibility in visual recognition memory during infancy using the Visual Paired Comparison (VPC) task. In Experiment 1, 6- and 9-month-old infants exhibited recognition when familiarization and test occurred in the same room, but showed no evidence of recognition when…

  11. Maximum Correntropy Criterion for Robust Face Recognition.

    Science.gov (United States)

    He, Ran; Zheng, Wei-Shi; Hu, Bao-Gang

    2011-08-01

    In this paper, we present a sparse correntropy framework for computing robust sparse representations of face images for recognition. Compared with the state-of-the-art l(1)norm-based sparse representation classifier (SRC), which assumes that noise also has a sparse representation, our sparse algorithm is developed based on the maximum correntropy criterion, which is much more insensitive to outliers. In order to develop a more tractable and practical approach, we in particular impose nonnegativity constraint on the variables in the maximum correntropy criterion and develop a half-quadratic optimization technique to approximately maximize the objective function in an alternating way so that the complex optimization problem is reduced to learning a sparse representation through a weighted linear least squares problem with nonnegativity constraint at each iteration. Our extensive experiments demonstrate that the proposed method is more robust and efficient in dealing with the occlusion and corruption problems in face recognition as compared to the related state-of-the-art methods. In particular, it shows that the proposed method can improve both recognition accuracy and receiver operator characteristic (ROC) curves, while the computational cost is much lower than the SRC algorithms.

  12. Gesture recognition for smart home applications using portable radar sensors.

    Science.gov (United States)

    Wan, Qian; Li, Yiran; Li, Changzhi; Pal, Ranadip

    2014-01-01

    In this article, we consider the design of a human gesture recognition system based on pattern recognition of signatures from a portable smart radar sensor. Powered by AAA batteries, the smart radar sensor operates in the 2.4 GHz industrial, scientific and medical (ISM) band. We analyzed the feature space using principle components and application-specific time and frequency domain features extracted from radar signals for two different sets of gestures. We illustrate that a nearest neighbor based classifier can achieve greater than 95% accuracy for multi class classification using 10 fold cross validation when features are extracted based on magnitude differences and Doppler shifts as compared to features extracted through orthogonal transformations. The reported results illustrate the potential of intelligent radars integrated with a pattern recognition system for high accuracy smart home and health monitoring purposes.

  13. Cricothyroid muscle dysfunction impairs vocal fold vibration in unilateral vocal fold paralysis.

    Science.gov (United States)

    Pei, Yu-Cheng; Fang, Tuan-Jen; Li, Hsueh-Yu; Wong, Alice M K

    2014-01-01

    The relevance of the cricothyroid (CT) muscle in patients with unilateral vocal fold paralysis (UVFP) remains controversial. To clarify the functional significance of the CT muscle in patients with UVFP, the confounding effect of the severity of recurrent laryngeal nerve injury should be taken into consideration. In the present study, quantitative laryngeal electromyography (LEMG) was used to measure the severity of paralysis of the thyroarytenoid-lateral cricoarytenoid (TA-LCA) muscle complex to allow the functional contribution of the CT muscle to be determined. Cross-sectional study performed in an otolaryngology outpatient clinic. Thirty-one patients with a main diagnosis of UVFP were recruited. The main outcome measures included LEMG examination, quantitative LEMG analysis of the TA-LCA muscle complex, UVFP-related quality-of-life questionnaire (Voice Outcome Survey [VOS]), voice acoustics analysis, videolaryngostroboscopy, and general quality-of-life questionnaire (Short Form-36 Health Survey [SF-36]) assessments. The vocal cord position did not differ between patients with and without CT muscle impairment. Patients with both TA-LCA and CT paralysis showed poorer vocal fold vibration (P = .048) and higher fundamental frequency (P = .02), and the VOS and SF-36 were both poorer compared with patients with only TA-LCA paralysis. Although the vocal cord position was not influenced by CT muscle function, coexisting CT muscle paralysis may damage the voice by impairing vocal fold vibration in UVFP patients. © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

  14. Harmonization versus Mutual Recognition

    DEFF Research Database (Denmark)

    Jørgensen, Jan Guldager; Schröder, Philipp

    with the opportunity to start export sales. In contrast, harmonization, in particular the prospect that one’s own national (but not the foreign) standard becomes the only globally accepted standard, opens the foreign market without balancing entry at home. We study these scenarios in a reduced form lobby game with two......, harmonized standards may fail to harvest the full pro-competitive effects from trade liberalization compared to mutual recognition; moreover, the issue is most pronounced in markets featuring price competition....

  15. Making 2D face recognition more robust using AAMs for pose compensation

    NARCIS (Netherlands)

    Huisman, Peter; Munster, Ruud; Moro-Ellenberger, Stephanie; Veldhuis, Raymond N.J.; Bazen, A.M.

    2006-01-01

    The problem of pose in 2D face recognition is widely acknowledged. Commercial systems are limited to near frontal face images and cannot deal with pose deviations larger than 15 degrees from the frontal view. This is a problem, when using face recognition for surveillance applications in which

  16. Kinetic Dissection of the Pre-existing Conformational Equilibrium in the Trypsin Fold*

    Science.gov (United States)

    Vogt, Austin D.; Chakraborty, Pradipta; Di Cera, Enrico

    2015-01-01

    Structural biology has recently documented the conformational plasticity of the trypsin fold for both the protease and zymogen in terms of a pre-existing equilibrium between closed (E*) and open (E) forms of the active site region. How such plasticity is manifested in solution and affects ligand recognition by the protease and zymogen is poorly understood in quantitative terms. Here we dissect the E*-E equilibrium with stopped-flow kinetics in the presence of excess ligand or macromolecule. Using the clotting protease thrombin and its zymogen precursor prethrombin-2 as relevant models we resolve the relative distribution of the E* and E forms and the underlying kinetic rates for their interconversion. In the case of thrombin, the E* and E forms are distributed in a 1:4 ratio and interconvert on a time scale of 45 ms. In the case of prethrombin-2, the equilibrium is shifted strongly (10:1 ratio) in favor of the closed E* form and unfolds over a faster time scale of 4.5 ms. The distribution of E* and E forms observed for thrombin and prethrombin-2 indicates that zymogen activation is linked to a significant shift in the pre-existing equilibrium between closed and open conformations that facilitates ligand binding to the active site. These findings broaden our mechanistic understanding of how conformational transitions control ligand recognition by thrombin and its zymogen precursor prethrombin-2 and have direct relevance to other members of the trypsin fold. PMID:26216877

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

    Science.gov (United States)

    Zhao, Chunchun; Sahni, Sartaj

    2017-12-06

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

  18. Pose-Invariant Face Recognition via RGB-D Images.

    Science.gov (United States)

    Sang, Gaoli; Li, Jing; Zhao, Qijun

    2016-01-01

    Three-dimensional (3D) face models can intrinsically handle large pose face recognition problem. In this paper, we propose a novel pose-invariant face recognition method via RGB-D images. By employing depth, our method is able to handle self-occlusion and deformation, both of which are challenging problems in two-dimensional (2D) face recognition. Texture images in the gallery can be rendered to the same view as the probe via depth. Meanwhile, depth is also used for similarity measure via frontalization and symmetric filling. Finally, both texture and depth contribute to the final identity estimation. Experiments on Bosphorus, CurtinFaces, Eurecom, and Kiwi databases demonstrate that the additional depth information has improved the performance of face recognition with large pose variations and under even more challenging conditions.

  19. Statistical pattern recognition for automatic writer identification and verification

    NARCIS (Netherlands)

    Bulacu, Marius Lucian

    2007-01-01

    The thesis addresses the problem of automatic person identification using scanned images of handwriting.Identifying the author of a handwritten sample using automatic image-based methods is an interesting pattern recognition problem with direct applicability in the forensic and historic document

  20. Learning Driving Behavior by Timed Syntactic Pattern Recognition

    NARCIS (Netherlands)

    Verwer, S.E.; De Weerdt, M.M.; Witteveen, C.

    2011-01-01

    We advocate the use of an explicit time representation in syntactic pattern recognition because it can result in more succinct models and easier learning problems. We apply this approach to the real-world problem of learning models for the driving behavior of truck drivers. We discretize the values

  1. Enhancing emotion recognition in VIPs with haptic feedback

    NARCIS (Netherlands)

    Buimer, Hendrik; Bittner, Marian; Kostelijk, Tjerk; van der Geest, Thea; van Wezel, Richard Jack Anton; Zhao, Yan; Stephanidis, Constantine

    2016-01-01

    The rise of smart technologies has created new opportunities to support blind and visually impaired persons (VIPs). One of the biggest problems we identified in our previous research on problems VIPs face during activities of daily life concerned the recognition of persons and their facial

  2. Pattern Recognition Control Design

    Science.gov (United States)

    Gambone, Elisabeth A.

    2018-01-01

    Spacecraft control algorithms must know the expected vehicle response to any command to the available control effectors, such as reaction thrusters or torque devices. Spacecraft control system design approaches have traditionally relied on the estimated vehicle mass properties to determine the desired force and moment, as well as knowledge of the effector performance to efficiently control the spacecraft. A pattern recognition approach was used to investigate the relationship between the control effector commands and spacecraft responses. Instead of supplying the approximated vehicle properties and the thruster performance characteristics, a database of information relating the thruster ring commands and the desired vehicle response was used for closed-loop control. A Monte Carlo simulation data set of the spacecraft dynamic response to effector commands was analyzed to establish the influence a command has on the behavior of the spacecraft. A tool developed at NASA Johnson Space Center to analyze flight dynamics Monte Carlo data sets through pattern recognition methods was used to perform this analysis. Once a comprehensive data set relating spacecraft responses with commands was established, it was used in place of traditional control methods and gains set. This pattern recognition approach was compared with traditional control algorithms to determine the potential benefits and uses.

  3. Audio-visual gender recognition

    Science.gov (United States)

    Liu, Ming; Xu, Xun; Huang, Thomas S.

    2007-11-01

    Combining different modalities for pattern recognition task is a very promising field. Basically, human always fuse information from different modalities to recognize object and perform inference, etc. Audio-Visual gender recognition is one of the most common task in human social communication. Human can identify the gender by facial appearance, by speech and also by body gait. Indeed, human gender recognition is a multi-modal data acquisition and processing procedure. However, computational multimodal gender recognition has not been extensively investigated in the literature. In this paper, speech and facial image are fused to perform a mutli-modal gender recognition for exploring the improvement of combining different modalities.

  4. Protein-Folding Landscapes in Multi-Chain Systems

    Energy Technology Data Exchange (ETDEWEB)

    Cellmer, Troy; Bratko, Dusan; Prausnitz, John M.; Blanch, Harvey

    2005-06-20

    Computational studies of proteins have significantly improved our understanding of protein folding. These studies are normally carried out using chains in isolation. However, in many systems of practical interest, proteins fold in the presence of other molecules. To obtain insight into folding in such situations, we compare the thermodynamics of folding for a Miyazawa-Jernigan model 64-mer in isolation to results obtained in the presence of additional chains. The melting temperature falls as the chain concentration increases. In multi-chain systems, free-energy landscapes for folding show an increased preference for misfolded states. Misfolding is accompanied by an increase in inter-protein interactions; however, near the folding temperature, the transition from folded chains to misfolded and associated chains isentropically driven. A majority of the most probable inter-protein contacts are also native contacts, suggesting that native topology plays a role in early stages of aggregation.

  5. Structured neural networks for pattern recognition.

    Science.gov (United States)

    Murino, V

    1998-01-01

    This paper proposes a novel approach for the design of structures of neural networks for pattern recognition. The basic idea lies in subdividing the whole classification problem in smaller and simpler problems at different levels, each managed by appropriate components of a complex neural architecture. Three neural structures are presented and applied in a surveillance system aimed at monitoring a railway waiting room classifying potential dangerous situations. Each architecture is composed by nodes, which are actual multilayer perceptrons trained to discriminate between subsets of classes until a complete separation among the classes is achieved. This approach showed better performances with respect to a classical statistical classification procedures and to a single neural network.

  6. Iris recognition in the presence of ocular disease.

    Science.gov (United States)

    Aslam, Tariq Mehmood; Tan, Shi Zhuan; Dhillon, Baljean

    2009-05-06

    Iris recognition systems are among the most accurate of all biometric technologies with immense potential for use in worldwide security applications. This study examined the effect of eye pathology on iris recognition and in particular whether eye disease could cause iris recognition systems to fail. The experiment involved a prospective cohort of 54 patients with anterior segment eye disease who were seen at the acute referral unit of the Princess Alexandra Eye Pavilion in Edinburgh. Iris camera images were obtained from patients before treatment was commenced and again at follow-up appointments after treatment had been given. The principal outcome measure was that of mathematical difference in the iris recognition templates obtained from patients' eyes before and after treatment of the eye disease. Results showed that the performance of iris recognition was remarkably resilient to most ophthalmic disease states, including corneal oedema, iridotomies (laser puncture of iris) and conjunctivitis. Problems were, however, encountered in some patients with acute inflammation of the iris (iritis/anterior uveitis). The effects of a subject developing anterior uveitis may cause current recognition systems to fail. Those developing and deploying iris recognition should be aware of the potential problems that this could cause to this key biometric technology.

  7. Recognition of misfolded proteins by Lon, a AAA(+) protease.

    Science.gov (United States)

    Gur, Eyal; Sauer, Robert T

    2008-08-15

    Proteins unfold constantly in cells, especially under stress conditions. Degradation of denatured polypeptides by Lon and related ATP-dependent AAA(+) proteases helps prevent toxic aggregates formation and other deleterious consequences, but how these destructive enzymatic machines distinguish between damaged and properly folded proteins is poorly understood. Here, we show that Escherichia coli Lon recognizes specific sequences -- rich in aromatic residues -- that are accessible in unfolded polypeptides but hidden in most native structures. Denatured polypeptides lacking such sequences are poor substrates. Lon also unfolds and degrades stably folded proteins with accessible recognition tags. Thus, protein architecture and the positioning of appropriate targeting sequences allow Lon degradation to be dependent or independent of the folding status of a protein. Our results suggest that Lon can recognize multiple signals in unfolded polypeptides synergistically, resulting in nanomolar binding and a mechanism for discriminating irreversibly damaged proteins from transiently unfolded elements of structure.

  8. Action Recognition in Semi-synthetic Images using Motion Primitives

    DEFF Research Database (Denmark)

    Fihl, Preben; Holte, Michael Boelstoft; Moeslund, Thomas B.

    This technical report describes an action recognition approach based on motion primitives. A few characteristic time instances are found in a sequence containing an action and the action is classified from these instances. The characteristic instances are defined solely on the human motion, hence...... motion primitives. The motion primitives are extracted by double difference images and represented by four features. In each frame the primitive, if any, that best explains the observed data is identified. This leads to a discrete recognition problem since a video sequence will be converted into a string...... achieving a recognition rate of 96.5%....

  9. Deep Learning based Super-Resolution for Improved Action Recognition

    DEFF Research Database (Denmark)

    Nasrollahi, Kamal; Guerrero, Sergio Escalera; Rasti, Pejman

    2015-01-01

    and cameras, people are pictured very small and hence challenge action recognition algorithms. Simple upsampling methods, like bicubic interpolation, cannot retrieve all the detailed information that can help the recognition. To deal with this problem, in this paper we combine results of bicubic interpolation...... with results of a state-of- the-art deep learning-based super-resolution algorithm, through an alpha-blending approach. The experimental results obtained on down-sampled version of a large subset of Hoolywood2 benchmark database show the importance of the proposed system in increasing the recognition rate...

  10. Object recognition of real targets using modelled SAR images

    Science.gov (United States)

    Zherdev, D. A.

    2017-12-01

    In this work the problem of recognition is studied using SAR images. The algorithm of recognition is based on the computation of conjugation indices with vectors of class. The support subspaces for each class are constructed by exception of the most and the less correlated vectors in a class. In the study we examine the ability of a significant feature vector size reduce that leads to recognition time decrease. The images of targets form the feature vectors that are transformed using pre-trained convolutional neural network (CNN).

  11. Application Of t-Cherry Junction Trees in Pattern Recognition

    Directory of Open Access Journals (Sweden)

    Edith Kovacs

    2010-06-01

    Full Text Available Pattern recognition aims to classify data (patterns based ei-
    ther on a priori knowledge or on statistical information extracted from the data. In this paper we will concentrate on statistical pattern recognition using a new probabilistic approach which makes possible to select the so called 'informative' features. We develop a pattern recognition algorithm which is based on the conditional independence structure underlying the statistical data. Our method was succesfully applied on a real problem of recognizing Parkinson's disease on the basis of voice disorders.

  12. Audio Data Augmentation with respect to Musical Instrument Recognition

    OpenAIRE

    Siddharth Bhardwaj

    2017-01-01

    Identifying musical instruments in a polyphonic music recording is a difficult yet crucial problem in music information retrieval. It helps in auto-tagging of a musical piece by instrument, consequently enabling searching music databases by instrument. Other useful applications of instrument recognition are source separation, genre recognition, music transcription, and instrument specific equalizations. We review the state of the art methods for the task, including the recent Convolutional Ne...

  13. Race, Ethnicity, and Eating Disorder Recognition by Peers

    OpenAIRE

    Sala, Margarita; Reyes-Rodríguez, Mae Lynn; Bulik, Cynthia M.; Bardone-Cone, Anna

    2013-01-01

    We investigated racial/ethnic stereotyping in the recognition and referral of eating disorders with 663 university students. We explored responses to problem and eating disorder recognition, and health care referral after reading a vignette concerning a patient of different race/ethnic background presenting with eating disorders. A series of three 4 × 3 ANOVAs revealed significant main effects for eating disorder across all three outcome variables. There were no significant main effects acros...

  14. Towards The Deep Model : Understanding Visual Recognition Through Computational Models

    OpenAIRE

    Wang, Panqu

    2017-01-01

    Understanding how visual recognition is achieved in the human brain is one of the most fundamental questions in vision research. In this thesis I seek to tackle this problem from a neurocomputational modeling perspective. More specifically, I build machine learning-based models to simulate and explain cognitive phenomena related to human visual recognition, and I improve computational models using brain-inspired principles to excel at computer vision tasks.I first describe how a neurocomputat...

  15. ORNL Biometric Eye Model for Iris Recognition

    Energy Technology Data Exchange (ETDEWEB)

    Santos-Villalobos, Hector J [ORNL; Barstow, Del R [ORNL; Karakaya, Mahmut [ORNL; Chaum, Edward [University of Tennessee, Knoxville (UTK); Boehnen, Chris Bensing [ORNL

    2012-01-01

    Iris recognition has been proven to be an accurate and reliable biometric. However, the recognition of non-ideal iris images such as off angle images is still an unsolved problem. We propose a new biometric targeted eye model and a method to reconstruct the off-axis eye to its frontal view allowing for recognition using existing methods and algorithms. This allows for existing enterprise level algorithms and approaches to be largely unmodified by using our work as a pre-processor to improve performance. In addition, we describe the `Limbus effect' and its importance for an accurate segmentation of off-axis irides. Our method uses an anatomically accurate human eye model and ray-tracing techniques to compute a transformation function, which reconstructs the iris to its frontal, non-refracted state. Then, the same eye model is used to render a frontal view of the reconstructed iris. The proposed method is fully described and results from synthetic data are shown to establish an upper limit on performance improvement and establish the importance of the proposed approach over traditional linear elliptical unwrapping methods. Our results with synthetic data demonstrate the ability to perform an accurate iris recognition with an image taken as much as 70 degrees off-axis.

  16. Facial affect recognition deficits in bipolar disorder.

    Science.gov (United States)

    Getz, Glen E; Shear, Paula K; Strakowski, Stephen M

    2003-05-01

    Patients diagnosed with bipolar disorder (BPD), by definition, have problems with emotional regulation. However, it remains uncertain whether these patients are also deficient at processing other people's emotions, particularly while manic. The present study examined the ability of 25 manic bipolar patients and 25 healthy participants on tasks of facial recognition and facial affect recognition at three different presentation durations: 500 ms, 750 ms, and 1000 ms. The groups did not differ in terms of age, education, sex, ethnicity, or estimated IQ. The groups did not differ significantly on either a novel computerized facial recognition task or the Benton Facial Recognition Test. In contrast, the bipolar group performed significantly more poorly than did the comparison group on a novel facial affect labeling task. Although the patient group had slower reaction times on all 3 computerized tasks, the presentation duration did not have an effect on performance in the patients. This study suggests that patients with bipolar disorder are able to recognize faces, but have difficulty processing facial affective cues.

  17. Is tropopause folding promoting or suppressing deep convection? First results from TROSIAD

    Science.gov (United States)

    Antonescu, B.; Vaughan, G.; Schultz, D. M.

    2012-04-01

    The occurrence, timing, and location of deep, moist convection remains a problem for operational weather forecasting, despite the rapid development of the numerical weather prediction models and implementation of new observational techniques. One impediment to better forecasting of deep convection is the role played by tropopause folds. How deep convection is modulated by tropopause folding, which brings stratospheric air into the troposphere, is not well understood. Three ingredients are required for deep moist, convection- moisture, instability, and lift-and all three ingredients associated with tropopause folds can either promote or suppress convection. For example, the dry air associated with the descent of upper-tropospheric air may limit the vertical development of buoyant thermals, yet this dry air may also create potential instability. The purpose of the research project TROSIAD is to assess the importance for convection forecasting of correctly representing tropopause folds in numerical weather forecasting models and to disentangle the conflicting paradigms that tropopause folds both promote and suppress convection. The work plan of the project involves the analysis of existing data from the Mesosphere-Stratosphere-Troposphere (MST) Radar at Aberystwyth, UK, which can measure both tropopause folds and convection, a number of cases studies from measurement campaigns, and numerical modelling experiments. The project begins with building 5-year (2006-2010) climatologies of radar data, and wind-profiling data to determine the relationship between tropopause folds and deep moist convection. Using data from Met Office NIMROD radar network, a climatology of all convective storms with the track in study region was developed. To be included in the climatology, a convective storm must persist for at least 30 minutes with a maximum radar reflectivity greater than 30 dBZ. A total of 663 convective storms were identified. A climatology of the tropopause folds over

  18. Structural Analysis of Protein Folding by the Long-Chain Archaeal Chaperone FKBP26

    Energy Technology Data Exchange (ETDEWEB)

    E Martinez-Hackert; W Hendrickson

    2011-12-31

    In the cell, protein folding is mediated by folding catalysts and chaperones. The two functions are often linked, especially when the catalytic module forms part of a multidomain protein, as in Methanococcus jannaschii peptidyl-prolyl cis/trans isomerase FKBP26. Here, we show that FKBP26 chaperone activity requires both a 50-residue insertion in the catalytic FKBP domain, also called 'Insert-in-Flap' or IF domain, and an 80-residue C-terminal domain. We determined FKBP26 structures from four crystal forms and analyzed chaperone domains in light of their ability to mediate protein-protein interactions. FKBP26 is a crescent-shaped homodimer. We reason that folding proteins are bound inside the large crescent cleft, thus enabling their access to inward-facing peptidyl-prolyl cis/trans isomerase catalytic sites and ipsilateral chaperone domain surfaces. As these chaperone surfaces participate extensively in crystal lattice contacts, we speculate that the observed lattice contacts reflect a proclivity for protein associations and represent substrate interactions by FKBP26 chaperone domains. Finally, we find that FKBP26 is an exceptionally flexible molecule, suggesting a mechanism for nonspecific substrate recognition.

  19. 3-D anatomy of an active fault-propagation fold: A multidisciplinary case study from Tsaishi, western Caucasus (Georgia)

    Science.gov (United States)

    Tibaldi, A.; Russo, E.; Bonali, F. L.; Alania, V.; Chabukiani, A.; Enukidze, O.; Tsereteli, N.

    2017-10-01

    Ongoing deformation processes combining fault propagation and folding are the cause of diffuse seismicity in many areas of the world. A detailed understanding of the structural evolution of tectonically active folds is crucial for the evaluation of seismic hazard. This paper proposes an integrated analysis of an active fold, consisting in the development of a 3D model by combination of geomorphological observations, field geological-structural data and seismic reflection sections. Our case study is the Tsaishi anticline, located at the southwestern tip of the Rioni Basin uplifted area, at the foothill of Greater Caucasus (Western Georgia). We recognized that the fold started to form since the beginning of the middle Miocene, although preliminary data suggest the possibility of initial local uplift in the Oligocene. Folding process continues up to nowadays giving rise to a south-vergent anticline, as shown by upwarped late Quaternary river deposits. The fold backlimb is affected by three main back-thrusts, whereas at the foot of the forelimb a main north-dipping thrust comes very close to the surface based on seismic sections. Here, field data show the presence of a 13-km-long fault scarp (or fold scarp). Along the scarp is located the epicenter of the strongest earthquake to date: the MS 6.0 Tsaishi earthquake that struck the area in 1614 CE. Based on our results, we propose that the overall structure can be classified as an active fault-propagation fold. The recognition of its very recent growing associated with a major, underlying active fault, represents also a major contribution to the seismic hazard assessment of this populated area.

  20. Re-thinking employee recognition: understanding employee experiences of recognition

    OpenAIRE

    Smith, Charlotte

    2013-01-01

    Despite widespread acceptance of the importance of employee recognition for both individuals and organisations and evidence of its increasing use in organisations, employee recognition has received relatively little focused attention from academic researchers. Particularly lacking is research exploring the lived experience of employee recognition and the interpretations and meanings which individuals give to these experiences. Drawing on qualitative interviews conducted as part of my PhD rese...

  1. Mexican sign language recognition using normalized moments and artificial neural networks

    Science.gov (United States)

    Solís-V., J.-Francisco; Toxqui-Quitl, Carina; Martínez-Martínez, David; H.-G., Margarita

    2014-09-01

    This work presents a framework designed for the Mexican Sign Language (MSL) recognition. A data set was recorded with 24 static signs from the MSL using 5 different versions, this MSL dataset was captured using a digital camera in incoherent light conditions. Digital Image Processing was used to segment hand gestures, a uniform background was selected to avoid using gloved hands or some special markers. Feature extraction was performed by calculating normalized geometric moments of gray scaled signs, then an Artificial Neural Network performs the recognition using a 10-fold cross validation tested in weka, the best result achieved 95.83% of recognition rate.

  2. Restrictions to protein folding determined by the protein size.

    Science.gov (United States)

    Finkelstein, Alexei V; Bogatyreva, Natalya S; Garbuzynskiy, Sergiy O

    2013-06-27

    Experimentally measured rates of spontaneous folding of single-domain globular proteins range from microseconds to hours: the difference (11 orders of magnitude!) is akin to the difference between the life span of a mosquito and the age of the Universe. We show that physical theory with biological constraints outlines the possible range of folding rates for single-domain globular proteins of various size and stability, and that the experimentally measured folding rates fall within this narrow "golden triangle" built without any adjustable parameters, filling it almost completely. This "golden triangle" also successfully predicts the maximal allowed size of the "foldable" protein domains, as well as the maximal size of protein domains that fold under solely thermodynamic (rather than kinetic) control. In conclusion, we give a phenomenological formula for dependence of the folding rate on the size, shape and stability of the protein fold. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  3. Cotranslational Protein Folding inside the Ribosome Exit Tunnel

    Directory of Open Access Journals (Sweden)

    Ola B. Nilsson

    2015-09-01

    Full Text Available At what point during translation do proteins fold? It is well established that proteins can fold cotranslationally outside the ribosome exit tunnel, whereas studies of folding inside the exit tunnel have so far detected only the formation of helical secondary structure and collapsed or partially structured folding intermediates. Here, using a combination of cotranslational nascent chain force measurements, inter-subunit fluorescence resonance energy transfer studies on single translating ribosomes, molecular dynamics simulations, and cryoelectron microscopy, we show that a small zinc-finger domain protein can fold deep inside the vestibule of the ribosome exit tunnel. Thus, for small protein domains, the ribosome itself can provide the kind of sheltered folding environment that chaperones provide for larger proteins.

  4. Sparse RNA folding revisited: space-efficient minimum free energy structure prediction.

    Science.gov (United States)

    Will, Sebastian; Jabbari, Hosna

    2016-01-01

    RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to improve the time efficiency of various structure prediction algorithms while guaranteeing the same result; however, for many such folding problems, space efficiency is of even greater concern, particularly for long RNA sequences. So far, space-efficient sparsified RNA folding with fold reconstruction was solved only for simple base-pair-based pseudo-energy models. Here, we revisit the problem of space-efficient free energy minimization. Whereas the space-efficient minimization of the free energy has been sketched before, the reconstruction of the optimum structure has not even been discussed. We show that this reconstruction is not possible in trivial extension of the method for simple energy models. Then, we present the time- and space-efficient sparsified free energy minimization algorithm SparseMFEFold that guarantees MFE structure prediction. In particular, this novel algorithm provides efficient fold reconstruction based on dynamically garbage-collected trace arrows. The complexity of our algorithm depends on two parameters, the number of candidates Z and the number of trace arrows T; both are bounded by [Formula: see text], but are typically much smaller. The time complexity of RNA folding is reduced from [Formula: see text] to [Formula: see text]; the space complexity, from [Formula: see text] to [Formula: see text]. Our empirical results show more than 80 % space savings over RNAfold [Vienna RNA package] on the long RNAs from the RNA STRAND database (≥2500 bases). The presented technique is intentionally generalizable to complex prediction algorithms; due to their high space demands, algorithms like pseudoknot prediction and RNA-RNA-interaction prediction are expected to profit even stronger than "standard" MFE folding. SparseMFEFold is free

  5. Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a beta-Hairpin.

    Directory of Open Access Journals (Sweden)

    2005-06-01

    Full Text Available The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a combinatorial pattern discovery approach toward understanding the global state changes during the folding process. This is a first step toward an unsupervised (and perhaps eventually automated approach toward identification of global states. The approach is based on computing biclusters (or patterned clusters-each cluster is a combination of various reaction coordinates, and its signature pattern facilitates the computation of the Z-score for the cluster. For this discovery process, we present an algorithm of time complexity cinRO((N + nm log n, where N is the size of the output patterns and (n x m is the size of the input with n time frames and m reaction coordinates. To date, this is the best time complexity for this problem. We next apply this to a beta-hairpin folding trajectory and demonstrate that this approach extracts crucial information about protein folding intermediate states and mechanism. We make three observations about the approach: (1 The method recovers states previously obtained by visually analyzing free energy surfaces. (2 It also succeeds in extracting meaningful patterns and structures that had been overlooked in previous works, which provides a better understanding of the folding mechanism of the beta-hairpin. These new patterns also interconnect various states in existing free energy surfaces versus different reaction coordinates. (3 The approach does not require calculating the free energy values, yet it offers an analysis comparable to, and sometimes better than, the methods that use free energy landscapes, thus validating the

  6. TERRAIN TECTONICS OF THE CENTRAL ASIAN FOLDED BELT

    Directory of Open Access Journals (Sweden)

    M. M. Buslov

    2014-01-01

    Full Text Available The terrain analysis concept envisages primarily a possibility of approximation of fragments / terrains of various geodynamic settings which belong to different plates. The terrain analysis can supplement the theory of plate tectonics in solving problems of geodynamics and tectonics of regions of the crust with complex structures. The Central Asian belt is among such complicated regions. Terrain structures occurred as a result of combined movements in the system of 'frontal' and/or oblique subduction – collision. In studies of geological objects, it is required first of all to prove their (vertical and horizontal autochthony in relations to each other and then proceed to paleogeodynamic, paleotectonic and paleogeographic reconstructions. Obviously, such a complex approach needs data to be obtained by a variety of research methods, including those applied to study geologic structures, stratigraphy, paleontology, paleogeography, lithothlogy, geochemistry, geochronology, paleomagnetism etc. Only by correlating such data collected from inter-disciplinary studies of the regions, it is possible to establish reliable characteristics of the geological settings and avoid mistakes and misinterpretations that may be associated with the 'stratigraphic' approach to solutions of both regional and global problems of geodynamics and tectonics of folded areas. The terrain analysis of the Central Asian folded belt suggests that its tectonic structure combines marginal continental rock complexes that were formed by the evolution of two major oceanic plates. One of them is the plate of the Paleo-Asian Ocean. As the analogue of the current Indo-Atlantic segment of Earth, it is characterised by the presence of continental blocks in the composition of the oceanic crust and the formation of oceanic basins resulting from the breakup of Rodinia and Gondvana. In the course of its evolution, super-continents disintegrated, and the blocks were reunited into the Kazakhstan

  7. The Complex Kinetics of Protein Folding in Wide Temperature Ranges

    OpenAIRE

    Wang, Jin

    2004-01-01

    The complex protein folding kinetics in wide temperature ranges is studied through diffusive dynamics on the underlying energy landscape. The well-known kinetic chevron rollover behavior is recovered from the mean first passage time, with the U-shape dependence on temperature. The fastest folding temperature T0 is found to be smaller than the folding transition temperature Tf. We found that the fluctuations of the kinetics through the distribution of first passage time show rather universal b...

  8. Iterative Controller Tuning for Process with Fold Bifurcations

    DEFF Research Database (Denmark)

    Huusom, Jakob Kjøbsted; Poulsen, Niels Kjølstad; Jørgensen, Sten Bay

    2007-01-01

    Processes involving fold bifurcation are notoriously difficult to control in the vicinity of the fold where most often optimal productivity is achieved . In cases with limited process insight a model based control synthesis is not possible. This paper uses a data driven approach with an improved...... version of iterative feedback tuning to optimizing a closed loop performance criterion, as a systematic tool for tuning process with fold bifurcations....

  9. The Ventricular-Fold Dynamics in Human Phonation

    OpenAIRE

    Bailly , Lucie; Henrich Bernardoni , Nathalie; Müller , Frank; Rohlfs , Anna-Katharina; Hess , Markus

    2014-01-01

    International audience; Purpose: In this study, the authors aimed (a) to provide a classification of the ventricular-fold dynamics during voicing, (b) to study the aerodynamic impact of these motions on vocal-fold vibrations, and (c) to assess whether ventricularfold oscillations could be sustained by aerodynamic coupling with the vocal folds. Method: A 72-sample database of vocal gestures accompanying different acoustical events comprised highspeed cinematographic, audio, and electroglottogr...

  10. Extended Target Recognition in Cognitive Radar Networks

    Directory of Open Access Journals (Sweden)

    Xiqin Wang

    2010-11-01

    Full Text Available We address the problem of adaptive waveform design for extended target recognition in cognitive radar networks. A closed-loop active target recognition radar system is extended to the case of a centralized cognitive radar network, in which a generalized likelihood ratio (GLR based sequential hypothesis testing (SHT framework is employed. Using Doppler velocities measured by multiple radars, the target aspect angle for each radar is calculated. The joint probability of each target hypothesis is then updated using observations from different radar line of sights (LOS. Based on these probabilities, a minimum correlation algorithm is proposed to adaptively design the transmit waveform for each radar in an amplitude fluctuation situation. Simulation results demonstrate performance improvements due to the cognitive radar network and adaptive waveform design. Our minimum correlation algorithm outperforms the eigen-waveform solution and other non-cognitive waveform design approaches.

  11. The program complex for vocal recognition

    Science.gov (United States)

    Konev, Anton; Kostyuchenko, Evgeny; Yakimuk, Alexey

    2017-01-01

    This article discusses the possibility of applying the algorithm of determining the pitch frequency for the note recognition problems. Preliminary study of programs-analogues were carried out for programs with function “recognition of the music”. The software package based on the algorithm for pitch frequency calculation was implemented and tested. It was shown that the algorithm allows recognizing the notes in the vocal performance of the user. A single musical instrument, a set of musical instruments, and a human voice humming a tune can be the sound source. The input file is initially presented in the .wav format or is recorded in this format from a microphone. Processing is performed by sequentially determining the pitch frequency and conversion of its values to the note. According to test results, modification of algorithms used in the complex was planned.

  12. Multicultural medicine and the politics of recognition.

    Science.gov (United States)

    Kirmayer, Laurence J

    2011-08-01

    Health care services increasingly face patient populations with high levels of ethnic and cultural diversity. Cultures are associated with distinctive ways of life; concepts of personhood; value systems; and visions of the good that affect illness experience, help seeking, and clinical decision-making. Cultural differences may impede access to health care, accurate diagnosis, and effective treatment. The clinical encounter, therefore, must recognize relevant cultural differences, negotiate common ground in terms of problem definition and potential solutions, accommodate differences that are associated with good clinical outcomes, and manage irresolvable differences. Clinical attention to and respect for cultural difference (a) can provide experiences of recognition that increase trust in and commitment to the institutions of the larger society, (b) can help sustain a cultural community through recognition of its distinct language, knowledge, values, and healing practices, and (c) to the extent that it is institutionalized, can contribute to building a pluralistic civil society.

  13. Artificial intelligence tools for pattern recognition

    Science.gov (United States)

    Acevedo, Elena; Acevedo, Antonio; Felipe, Federico; Avilés, Pedro

    2017-06-01

    In this work, we present a system for pattern recognition that combines the power of genetic algorithms for solving problems and the efficiency of the morphological associative memories. We use a set of 48 tire prints divided into 8 brands of tires. The images have dimensions of 200 x 200 pixels. We applied Hough transform to obtain lines as main features. The number of lines obtained is 449. The genetic algorithm reduces the number of features to ten suitable lines that give thus the 100% of recognition. Morphological associative memories were used as evaluation function. The selection algorithms were Tournament and Roulette wheel. For reproduction, we applied one-point, two-point and uniform crossover.

  14. Action Recognition Using Discriminative Structured Trajectory Groups

    KAUST Repository

    Atmosukarto, Indriyati

    2015-01-06

    In this paper, we develop a novel framework for action recognition in videos. The framework is based on automatically learning the discriminative trajectory groups that are relevant to an action. Different from previous approaches, our method does not require complex computation for graph matching or complex latent models to localize the parts. We model a video as a structured bag of trajectory groups with latent class variables. We model action recognition problem in a weakly supervised setting and learn discriminative trajectory groups by employing multiple instance learning (MIL) based Support Vector Machine (SVM) using pre-computed kernels. The kernels depend on the spatio-temporal relationship between the extracted trajectory groups and their associated features. We demonstrate both quantitatively and qualitatively that the classification performance of our proposed method is superior to baselines and several state-of-the-art approaches on three challenging standard benchmark datasets.

  15. Ear Problems

    Science.gov (United States)

    ... Infants and Children Chest Pain, Acute Chest Pain, Chronic Cold and Flu Cough Diarrhea Ear Problems Elimination Problems Elimination Problems in Infants and Children Eye Problems Facial Swelling Feeding Problems in Infants ...

  16. Urination Problems

    Science.gov (United States)

    ... Infants and Children Chest Pain, Acute Chest Pain, Chronic Cold and Flu Cough Diarrhea Ear Problems Elimination Problems Elimination Problems in Infants and Children Eye Problems Facial Swelling Feeding Problems in Infants ...

  17. Human activity recognition and prediction

    CERN Document Server

    2016-01-01

    This book provides a unique view of human activity recognition, especially fine-grained human activity structure learning, human-interaction recognition, RGB-D data based action recognition, temporal decomposition, and causality learning in unconstrained human activity videos. The techniques discussed give readers tools that provide a significant improvement over existing methodologies of video content understanding by taking advantage of activity recognition. It links multiple popular research fields in computer vision, machine learning, human-centered computing, human-computer interaction, image classification, and pattern recognition. In addition, the book includes several key chapters covering multiple emerging topics in the field. Contributed by top experts and practitioners, the chapters present key topics from different angles and blend both methodology and application, composing a solid overview of the human activity recognition techniques. .

  18. Folding System for the Clothes by a Robot and Tools

    OpenAIRE

    大澤, 文明; 関, 啓明; 神谷, 好承

    2004-01-01

    The works of a home robot has the laundering. The purpose of this study is to find a means of folding of the clothes and store the clothes in a drawer by a home robot. Because the shape of cloth tends to change in various ways depending on the situation, it is difficult for robot hands to fold the clothes. In this paper, we propose a realistic folding system for the clothes by a robot and tools. The function of a tool is folding the clothes in half by inserting the clothes using two plates. T...

  19. Specific features of vocal fold paralysis in functional computed tomography

    International Nuclear Information System (INIS)

    Laskowska, K.; Mackiewicz-Nartowicz, H.; Serafin, Z.; Nawrocka, E.

    2008-01-01

    Vocal fold paralysis is usually recognized in laryngological examination, and detailed vocal fold function may be established based on laryngovideostroboscopy. Additional imaging should exclude any morphological causes of the paresis, which should be treated pharmacologically or surgically. The aim of this paper was to analyze the computed tomography (CT) images of the larynx in patients with unilateral vocal fold paralysis. CT examinations of the larynx were performed in 10 patients with clinically defined unilateral vocal fold paralysis. The examinations consisted of unenhanced acquisition and enhanced 3-phased acquisition: during free breathing, Valsalva maneuver, and phonation. The analysis included the following morphologic features of the paresis.the deepened epiglottic vallecula, the deepened piriform recess, the thickened and medially positioned aryepiglottic fold, the widened laryngeal pouch, the anteriorly positioned arytenoid cartilage, the thickened vocal fold, and the filled infraglottic space in frontal CT reconstruction. CT images were compared to laryngovideostroboscopy. The most common symptoms of vocal cord paralysis in CT were the deepened epiglottic vallecula and piriform recess, the widened laryngeal pouch with the filled infraglottic space, and the thickened aryepiglottic fold. Regarding the efficiency of the paralysis determination, the three functional techniques of CT larynx imaging used did not differ significantly, and laryngovideostroboscopy demonstrated its advantage over CT. CT of the larynx is a supplementary examination in the diagnosis of vocal fold paralysis, which may enable topographic analysis of the fold dysfunction. The knowledge of morphological CT features of the paralysis may help to prevent false-positive diagnosis of laryngeal cancer. (author)

  20. Protein folding and the organization of the protein topology universe

    DEFF Research Database (Denmark)

    Lindorff-Larsen,, Kresten; Røgen, Peter; Paci, Emanuele

    2005-01-01

    of protein folds that is based on the topological features of the polypeptide backbone, rather than the conventional view that depends on the arrangement of different types of secondary-structure elements. By linking the folding process to the organization of the protein structure universe, we propose......The mechanism by which proteins fold to their native states has been the focus of intense research in recent years. The rate-limiting event in the folding reaction is the formation of a conformation in a set known as the transition-state ensemble. The structural features present within...

  1. Fracture Toughness of Vocal Fold Tissue: A Preliminary Study.

    Science.gov (United States)

    Miri, Amir K; Chen, Lei Xi; Mongrain, Rosaire; Mongeau, Luc

    2016-05-01

    A customized mechanical tester that slices thin, soft samples was used to measure the fracture toughness of vocal fold tissue. Porcine vocal fold lamina propria was subjected to quasi-static, guillotine-like tests at three equally distanced regions along the anterior-posterior direction. The central one-third where high-velocity collisions between vocal folds occur was found to have the maximum fracture toughness. In contrast, the anterior one-third featured a lower toughness. Fracture toughness can be indicative of the risk of benign and malignant lesions in vocal fold tissue. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  2. Apply lightweight recognition algorithms in optical music recognition

    Science.gov (United States)

    Pham, Viet-Khoi; Nguyen, Hai-Dang; Nguyen-Khac, Tung-Anh; Tran, Minh-Triet

    2015-02-01

    The problems of digitalization and transformation of musical scores into machine-readable format are necessary to be solved since they help people to enjoy music, to learn music, to conserve music sheets, and even to assist music composers. However, the results of existing methods still require improvements for higher accuracy. Therefore, the authors propose lightweight algorithms for Optical Music Recognition to help people to recognize and automatically play musical scores. In our proposal, after removing staff lines and extracting symbols, each music symbol is represented as a grid of identical M ∗ N cells, and the features are extracted and classified with multiple lightweight SVM classifiers. Through experiments, the authors find that the size of 10 ∗ 12 cells yields the highest precision value. Experimental results on the dataset consisting of 4929 music symbols taken from 18 modern music sheets in the Synthetic Score Database show that our proposed method is able to classify printed musical scores with accuracy up to 99.56%.

  3. Xerostomia: recognition and management.

    Science.gov (United States)

    Fox, Philip C

    2008-01-01

    Awareness and recognition of xerostomia are essential in order to help patients minimize dryness symptoms, to institute preventive measures and to limit oral complications. The dental professional has the opportunity to ask every patient if they are experiencing dry mouth. In particular, complaints of dryness while eating, or difficulty swallowing dry foods, or the necessity of using liquids to ease swallowing are important clues that salivary function may be impaired. As part of a routine oral examination, one should examine the oral cavity carefully for signs of salivary gland dysfunction. Findings such as an increase in caries activity, mucosal alterations, infection or salivary gland enlargement may indicate salivary dysfunction. Evaluation should be conducted proactively at each patient visit. Early recognition will minimize damage and dysfunction and allow appropriate management to begin. Although the salivary dysfunction may be irreversible, preventive measures and conservative treatments can avoid or limit mucosal breakdown, infections and permanent damage to teeth. Adequate symptomatic relief is possible with local palliative and systemic measures in many patients. Appropriate management of symptoms and increasing saliva output may help patients feel more comfortable and improve their quality of life.

  4. Complex Event Recognition Architecture

    Science.gov (United States)

    Fitzgerald, William A.; Firby, R. James

    2009-01-01

    Complex Event Recognition Architecture (CERA) is the name of a computational architecture, and software that implements the architecture, for recognizing complex event patterns that may be spread across multiple streams of input data. One of the main components of CERA is an intuitive event pattern language that simplifies what would otherwise be the complex, difficult tasks of creating logical descriptions of combinations of temporal events and defining rules for combining information from different sources over time. In this language, recognition patterns are defined in simple, declarative statements that combine point events from given input streams with those from other streams, using conjunction, disjunction, and negation. Patterns can be built on one another recursively to describe very rich, temporally extended combinations of events. Thereafter, a run-time matching algorithm in CERA efficiently matches these patterns against input data and signals when patterns are recognized. CERA can be used to monitor complex systems and to signal operators or initiate corrective actions when anomalous conditions are recognized. CERA can be run as a stand-alone monitoring system, or it can be integrated into a larger system to automatically trigger responses to changing environments or problematic situations.

  5. Radically enhanced molecular recognition

    KAUST Repository

    Trabolsi, Ali

    2009-12-17

    The tendency for viologen radical cations to dimerize has been harnessed to establish a recognition motif based on their ability to form extremely strong inclusion complexes with cyclobis(paraquat-p-phenylene) in its diradical dicationic redox state. This previously unreported complex involving three bipyridinium cation radicals increases the versatility of host-guest chemistry, extending its practice beyond the traditional reliance on neutral and charged guests and hosts. In particular, transporting the concept of radical dimerization into the field of mechanically interlocked molecules introduces a higher level of control within molecular switches and machines. Herein, we report that bistable and tristable [2]rotaxanes can be switched by altering electrochemical potentials. In a tristable [2]rotaxane composed of a cyclobis(paraquat-p-phenylene) ring and a dumbbell with tetrathiafulvalene, dioxynaphthalene and bipyridinium recognition sites, the position of the ring can be switched. On oxidation, it moves from the tetrathiafulvalene to the dioxynaphthalene, and on reduction, to the bipyridinium radical cation, provided the ring is also reduced simultaneously to the diradical dication. © 2010 Macmillan Publishers Limited. All rights reserved.

  6. Travelling waves and fold localization in hovercraft seals

    Science.gov (United States)

    Wiggins, Andrew; Zalek, Steve; Perlin, Marc; Ceccio, Steve

    2013-11-01

    The seal system on hovercraft consists of a series of open-ended fabric cylinders that contact the free surface and, when inflated, form a compliant pressure barrier. Due to a shortening constraint imposed by neighboring seals, bow seals operate in a post-buckled state. We present results from large-scale experiments on these structures. These experiment show the hydroelastic response of seals to be characterized by striking stable and unstable post-buckling behavior. Using detailed 3-d measurements of the deformed seal shape, dominant response regimes are identified. These indicate that mode number decreases with wetted length, and that the form of the buckling packet becomes localized with increased velocity and decreased bending stiffness. Eventually, at a critical pressure, travelling waves emerge. To interpret the wide range of observed behavior, a 2-d nonlinear post-buckling model is developed and compared with the experimental studies. The model shows the importance of seal shortening and the buckling length, which is driven by the balance of hydrodynamic and bending energies. Preliminary scaling laws for the fold amplitude and mode number are presented. The experiments may ultimately provide insight into the bedeviling problem of seal wear. Sponsored by the Office of Naval Research under grant N00014-10-1-0302, Ms. Kelly B. Cooper, program manager.

  7. Bio-recognitive photonics of a DNA-guided organic semiconductor

    Science.gov (United States)

    Back, Seung Hyuk; Park, Jin Hyuk; Cui, Chunzhi; Ahn, Dong June

    2016-01-01

    Incorporation of duplex DNA with higher molecular weights has attracted attention for a new opportunity towards a better organic light-emitting diode (OLED) capability. However, biological recognition by OLED materials is yet to be addressed. In this study, specific oligomeric DNA-DNA recognition is successfully achieved by tri (8-hydroxyquinoline) aluminium (Alq3), an organic semiconductor. Alq3 rods crystallized with guidance from single-strand DNA molecules show, strikingly, a unique distribution of the DNA molecules with a shape of an `inverted' hourglass. The crystal's luminescent intensity is enhanced by 1.6-fold upon recognition of the perfect-matched target DNA sequence, but not in the case of a single-base mismatched one. The DNA-DNA recognition forming double-helix structure is identified to occur only in the rod's outer periphery. This study opens up new opportunities of Alq3, one of the most widely used OLED materials, enabling biological recognition.

  8. Product Grammars for Alignment and Folding.

    Science.gov (United States)

    Höner Zu Siederdissen, Christian; Hofacker, Ivo L; Stadler, Peter F

    2015-01-01

    We develop a theory of algebraic operations over linear and context-free grammars that makes it possible to combine simple "atomic" grammars operating on single sequences into complex, multi-dimensional grammars. We demonstrate the utility of this framework by constructing the search spaces of complex alignment problems on multiple input sequences explicitly as algebraic expressions of very simple one-dimensional grammars. In particular, we provide a fully worked frameshift-aware, semiglobal DNA-protein alignment algorithm whose grammar is composed of products of small, atomic grammars. The compiler accompanying our theory makes it easy to experiment with the combination of multiple grammars and different operations. Composite grammars can be written out in L(A)T(E)X for documentation and as a guide to implementation of dynamic programming algorithms. An embedding in Haskell as a domain-specific language makes the theory directly accessible to writing and using grammar products without the detour of an external compiler. Software and supplemental files available here: http://www.bioinf. uni-leipzig.de/Software/gramprod/.

  9. Learning generative models for protein fold families.

    Science.gov (United States)

    Balakrishnan, Sivaraman; Kamisetty, Hetunandan; Carbonell, Jaime G; Lee, Su-In; Langmead, Christopher James

    2011-04-01

    We introduce a new approach to learning statistical models from multiple sequence alignments (MSA) of proteins. Our method, called GREMLIN (Generative REgularized ModeLs of proteINs), learns an undirected probabilistic graphical model of the amino acid composition within the MSA. The resulting model encodes both the position-specific conservation statistics and the correlated mutation statistics between sequential and long-range pairs of residues. Existing techniques for learning graphical models from MSA either make strong, and often inappropriate assumptions about the conditional independencies within the MSA (e.g., Hidden Markov Models), or else use suboptimal algorithms to learn the parameters of the model. In contrast, GREMLIN makes no a priori assumptions about the conditional independencies within the MSA. We formulate and solve a convex optimization problem, thus guaranteeing that we find a globally optimal model at convergence. The resulting model is also generative, allowing for the design of new protein sequences that have the same statistical properties as those in the MSA. We perform a detailed analysis of covariation statistics on the extensively studied WW and PDZ domains and show that our method out-performs an existing algorithm for learning undirected probabilistic graphical models from MSA. We then apply our approach to 71 additional families from the PFAM database and demonstrate that the resulting models significantly out-perform Hidden Markov Models in terms of predictive accuracy. Copyright © 2011 Wiley-Liss, Inc.

  10. Protein folding and protein metallocluster studies using synchrotron small angler X-ray scattering

    International Nuclear Information System (INIS)

    Eliezer, D.

    1994-06-01

    Proteins, biological macromolecules composed of amino-acid building blocks, possess unique three dimensional shapes or conformations which are intimately related to their biological function. All of the information necessary to determine this conformation is stored in a protein's amino acid sequence. The problem of understanding the process by which nature maps protein amino-acid sequences to three-dimensional conformations is known as the protein folding problem, and is one of the central unsolved problems in biophysics today. The possible applications of a solution are broad, ranging from the elucidation of thousands of protein structures to the rational modification and design of protein-based drugs. The scattering of X-rays by matter has long been useful as a tool for the characterization of physical properties of materials, including biological samples. The high photon flux available at synchrotron X-ray sources allows for the measurement of scattering cross-sections of dilute and/or disordered samples. Such measurements do not yield the detailed geometrical information available from crystalline samples, but do allow for lower resolution studies of dynamical processes not observable in the crystalline state. The main focus of the work described here has been the study of the protein folding process using time-resolved small-angle x-ray scattering measurements. The original intention was to observe the decrease in overall size which must accompany the folding of a protein from an extended conformation to its compact native state. Although this process proved too fast for the current time-resolution of the technique, upper bounds were set on the probable compaction times of several small proteins. In addition, an interesting and unexpected process was detected, in which the folding protein passes through an intermediate state which shows a tendency to associate. This state is proposed to be a kinetic molten globule folding intermediate

  11. Protein folding and protein metallocluster studies using synchrotron small angler X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Eliezer, D.

    1994-06-01

    Proteins, biological macromolecules composed of amino-acid building blocks, possess unique three dimensional shapes or conformations which are intimately related to their biological function. All of the information necessary to determine this conformation is stored in a protein`s amino acid sequence. The problem of understanding the process by which nature maps protein amino-acid sequences to three-dimensional conformations is known as the protein folding problem, and is one of the central unsolved problems in biophysics today. The possible applications of a solution are broad, ranging from the elucidation of thousands of protein structures to the rational modification and design of protein-based drugs. The scattering of X-rays by matter has long been useful as a tool for the characterization of physical properties of materials, including biological samples. The high photon flux available at synchrotron X-ray sources allows for the measurement of scattering cross-sections of dilute and/or disordered samples. Such measurements do not yield the detailed geometrical information available from crystalline samples, but do allow for lower resolution studies of dynamical processes not observable in the crystalline state. The main focus of the work described here has been the study of the protein folding process using time-resolved small-angle x-ray scattering measurements. The original intention was to observe the decrease in overall size which must accompany the folding of a protein from an extended conformation to its compact native state. Although this process proved too fast for the current time-resolution of the technique, upper bounds were set on the probable compaction times of several small proteins. In addition, an interesting and unexpected process was detected, in which the folding protein passes through an intermediate state which shows a tendency to associate. This state is proposed to be a kinetic molten globule folding intermediate.

  12. Speech Recognition on Mobile Devices

    DEFF Research Database (Denmark)

    Tan, Zheng-Hua; Lindberg, Børge

    2010-01-01

    The enthusiasm of deploying automatic speech recognition (ASR) on mobile devices is driven both by remarkable advances in ASR technology and by the demand for efficient user interfaces on such devices as mobile phones and personal digital assistants (PDAs). This chapter presents an overview of ASR...... in the mobile context covering motivations, challenges, fundamental techniques and applications. Three ASR architectures are introduced: embedded speech recognition, distributed speech recognition and network speech recognition. Their pros and cons and implementation issues are discussed. Applications within...... command and control, text entry and search are presented with an emphasis on mobile text entry....

  13. Sudden Event Recognition: A Survey

    Directory of Open Access Journals (Sweden)

    Mohd Asyraf Zulkifley

    2013-08-01

    Full Text Available Event recognition is one of the most active research areas in video surveillance fields. Advancement in event recognition systems mainly aims to provide convenience, safety and an efficient lifestyle for humanity. A precise, accurate and robust approach is necessary to enable event recognition systems to respond to sudden changes in various uncontrolled environments, such as the case of an emergency, physical threat and a fire or bomb alert. The performance of sudden event recognition systems depends heavily on the accuracy of low level processing, like detection, recognition, tracking and machine learning algorithms. This survey aims to detect and characterize a sudden event, which is a subset of an abnormal event in several video surveillance applications. This paper discusses the following in detail: (1 the importance of a sudden event over a general anomalous event; (2 frameworks used in sudden event recognition; (3 the requirements and comparative studies of a sudden event recognition system and (4 various decision-making approaches for sudden event recognition. The advantages and drawbacks of using 3D images from multiple cameras for real-time application are also discussed. The paper concludes with suggestions for future research directions in sudden event recognition.

  14. Molecular Mechanisms of Odor Recognition

    National Research Council Canada - National Science Library

    Anholt, Robert

    2000-01-01

    .... We characterized the transduction pathway for the recognition of pheromones in the vomeronasal organ and also characterized subpopulations of olfactory neurons expressing different axonal G proteins...

  15. Sudden Event Recognition: A Survey

    Science.gov (United States)

    Suriani, Nor Surayahani; Hussain, Aini; Zulkifley, Mohd Asyraf

    2013-01-01

    Event recognition is one of the most active research areas in video surveillance fields. Advancement in event recognition systems mainly aims to provide convenience, safety and an efficient lifestyle for humanity. A precise, accurate and robust approach is necessary to enable event recognition systems to respond to sudden changes in various uncontrolled environments, such as the case of an emergency, physical threat and a fire or bomb alert. The performance of sudden event recognition systems depends heavily on the accuracy of low level processing, like detection, recognition, tracking and machine learning algorithms. This survey aims to detect and characterize a sudden event, which is a subset of an abnormal event in several video surveillance applications. This paper discusses the following in detail: (1) the importance of a sudden event over a general anomalous event; (2) frameworks used in sudden event recognition; (3) the requirements and comparative studies of a sudden event recognition system and (4) various decision-making approaches for sudden event recognition. The advantages and drawbacks of using 3D images from multiple cameras for real-time application are also discussed. The paper concludes with suggestions for future research directions in sudden event recognition. PMID:23921828

  16. Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

    Science.gov (United States)

    Chu, Xiakun; Gan, Linfeng; Wang, Erkang; Wang, Jin

    2013-01-01

    Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding–folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative “coupled binding–folding” and three-state noncooperative “folding prior to binding” scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding–folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding–folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found “U-shape” temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments. PMID:23754431

  17. A Multi-Modal Person Recognition System for Social Robots

    Directory of Open Access Journals (Sweden)

    Mohammad K. Al-Qaderi

    2018-03-01

    Full Text Available The paper presents a solution to the problem of person recognition by social robots via a novel brain-inspired multi-modal perceptual system. The system employs spiking neural network to integrate face, body features, and voice data to recognize a person in various social human-robot interaction scenarios. We suggest that, by and large, most reported multi-biometric person recognition algorithms require active participation by the subject and as such are not appropriate for social human-robot interactions. However, the proposed algorithm relaxes this constraint. As there are no public datasets for multimodal systems, we designed a hybrid dataset by integration of the ubiquitous FERET, RGB-D, and TIDIGITS datasets for face recognition, person recognition, and speaker recognition, respectively. The combined dataset facilitates association of facial features, body shape, and speech signature for multimodal person recognition in social settings. This multimodal dataset is employed for testing the algorithm. We assess the performance of the algorithm and discuss its merits against related methods. Within the context of the social robotics, the results suggest the superiority of the proposed method over other reported person recognition algorithms.

  18. Amino acid alphabet reduction preserves fold information contained in contact interactions in proteins.

    Science.gov (United States)

    Solis, Armando D

    2015-12-01

    To reduce complexity, understand generalized rules of protein folding, and facilitate de novo protein design, the 20-letter amino acid alphabet is commonly reduced to a smaller alphabet by clustering amino acids based on some measure of similarity. In this work, we seek the optimal alphabet that preserves as much of the structural information found in long-range (contact) interactions among amino acids in natively-folded proteins. We employ the Information Maximization Device, based on information theory, to partition the amino acids into well-defined clusters. Numbering from 2 to 19 groups, these optimal clusters of amino acids, while generated automatically, embody well-known properties of amino acids such as hydrophobicity/polarity, charge, size, and aromaticity, and are demonstrated to maintain the discriminative power of long-range interactions with minimal loss of mutual information. Our measurements suggest that reduced alphabets (of less than 10) are able to capture virtually all of the information residing in native contacts and may be sufficient for fold recognition, as demonstrated by extensive threading tests. In an expansive survey of the literature, we observe that alphabets derived from various approaches-including those derived from physicochemical intuition, local structure considerations, and sequence alignments of remote homologs-fare consistently well in preserving contact interaction information, highlighting a convergence in the various factors thought to be relevant to the folding code. Moreover, we find that alphabets commonly used in experimental protein design are nearly optimal and are largely coherent with observations that have arisen in this work. © 2015 Wiley Periodicals, Inc.

  19. A model of traffic signs recognition with convolutional neural network

    Science.gov (United States)

    Hu, Haihe; Li, Yujian; Zhang, Ting; Huo, Yi; Kuang, Wenqing

    2016-10-01

    In real traffic scenes, the quality of captured images are generally low due to some factors such as lighting conditions, and occlusion on. All of these factors are challengeable for automated recognition algorithms of traffic signs. Deep learning has provided a new way to solve this kind of problems recently. The deep network can automatically learn features from a large number of data samples and obtain an excellent recognition performance. We therefore approach this task of recognition of traffic signs as a general vision problem, with few assumptions related to road signs. We propose a model of Convolutional Neural Network (CNN) and apply the model to the task of traffic signs recognition. The proposed model adopts deep CNN as the supervised learning model, directly takes the collected traffic signs image as the input, alternates the convolutional layer and subsampling layer, and automatically extracts the features for the recognition of the traffic signs images. The proposed model includes an input layer, three convolutional layers, three subsampling layers, a fully-connected layer, and an output layer. To validate the proposed model, the experiments are implemented using the public dataset of China competition of fuzzy image processing. Experimental results show that the proposed model produces a recognition accuracy of 99.01 % on the training dataset, and yield a record of 92% on the preliminary contest within the fourth best.

  20. Quantification of fold growth of frontal antiforms in the Zagros fold and thrust belt (Kurdistan, NE Iraq)

    Science.gov (United States)

    Bretis, Bernhard; Bartl, Nikolaus; Graseman, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros fold and thrust belt is a seismically active orogen, where actual kinematic models based on GPS networks suggest a north-south shortening between Arabian and Eurasian in the order of 1.5-2.5 cm/yr. Most of this deformation is partitioned in south-southwest oriented folding and thrusting with northwest-southeast to north-south trending dextral strike slip faults. The Zagros fold and thrust belt is of great economic interest because it has been estimated that this area contains about 15% of the global recoverable hydrocarbons. Whereas the SE parts of the Zagros have been investigated by detailed geological studies, the NW extent being part of the Republic of Iraq have experienced considerably less attention. In this study we combine field work and remote sensing techniques in order to investigate the interaction of erosion and fold growth in the area NE of Erbil (Kurdistan, Iraq). In particular we focus on the interaction of the transient development of drainage patterns along growing antiforms, which directly reflects the kinematics of progressive fold growth. Detailed geomorphological studies of the Bana Bawi-, Permam- and Safeen fold trains show that these anticlines have not developed from subcylindrical embryonic folds but they have merged from different fold segments that joined laterally during fold amplification. This fold segments with length between 5 and 25 km have been detected by mapping ancient and modern river courses that initially cut the nose of growing folds and eventually got defeated leaving behind a wind gap. Fold segments, propagating in different directions force rivers to join resulting in steep gorges, which dissect the merging fold noses. Along rapidly lateral growing folds (e.g. at the SE end of the Bana Bawi Anticline) we observed "curved wind gaps", a new type of abandoned river course, where form of the wind gap mimics a formed nose of a growing antiform. The inherited curved segments of uplifted curved river courses strongly

  1. The problem of automatic identification of concepts

    International Nuclear Information System (INIS)

    Andreewsky, Alexandre

    1975-11-01

    This paper deals with the problem of the automatic recognition of concepts and describes an important language tool, the ''linguistic filter'', which facilitates the construction of statistical algorithms. Certain special filters, of prepositions, conjunctions, negatives, logical implication, compound words, are presented. This is followed by a detailed description of a statistical algorithm allowing recognition of pronoun referents, and finally the problem of the automatic treatment of negatives in French is discussed [fr

  2. Sugar recognition by human galactokinase

    Directory of Open Access Journals (Sweden)

    Timson David J

    2003-11-01

    Full Text Available Abstract Background Galactokinase catalyses the first committed step of galactose catabolism in which the sugar is phosphorylated at the expense of MgATP. Recent structural studies suggest that the enzyme makes several contacts with galactose – five side chain and two main chain hydrogen bonds. Furthermore, it has been suggested that inhibition of galactokinase may help sufferers of the genetic disease classical galactosemia which is caused by defects in another enzyme of the pathway galactose-1-phosphate uridyl transferase. Galactokinases from different sources have a range of substrate specificities and a diversity of kinetic mechanisms. Therefore only studies on the human enzyme are likely to be of value in the design of therapeutically useful inhibitors. Results Using recombinant human galactokinase expressed in and purified from E. coli we have investigated the sugar specificity of the enzyme and the kinetic consequences of mutating residues in the sugar-binding site in order to improve our understanding of substrate recognition by this enzyme. D-galactose and 2-deoxy-D-galactose are substrates for the enzyme, but N-acetyl-D-galactosamine, L-arabinose, D-fucose and D-glucose are all not phosphorylated. Mutation of glutamate-43 (which forms a hydrogen bond to the hydroxyl group attached to carbon 6 of galactose to alanine results in only minor changes in the kinetic parameters of the enzyme. Mutation of this residue to glycine causes a ten-fold drop in the turnover number. In contrast, mutation of histidine 44 to either alanine or isoleucine results in insoluble protein following expression in E. coli. Alteration of the residue that makes hydrogen bonds to the hydroxyl attached to carbons 3 and 4 (aspartate 46 results in an enzyme that although soluble is essentially inactive. Conclusions The enzyme is tolerant to small changes at position 2 of the sugar ring, but not at positions 4 and 6. The results from site directed mutagenesis could

  3. Understanding the folding process of synthetic polymers by small ...

    Indian Academy of Sciences (India)

    WINTEC

    Understanding the folding process of synthetic polymers by small-molecule folding agents. S G RAMKUMAR and S RAMAKRISHNAN*. Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012 e-mail: raman@ipc.iisc.ernet.in. Abstract. Two acceptor containing polyimides PDI and NDI ...

  4. Spatially confined folding of chromatin in the interphase nucleus

    NARCIS (Netherlands)

    Mateos-Langerak, J.; Bohn, M.; de Leeuw, W.; Giromus, O.; Manders, E.M.M.; Verschure, P.J.; Indemans, M.H.G.; Gierman, H.J.; Heermann, D.W.; van Driel, R.; Goetze, S.

    2009-01-01

    Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Polymer models have been used to describe chromatin folding. However, none of the proposed models gives a

  5. Landforms along transverse faults parallel to axial zone of folded ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Earth System Science; Volume 126; Issue 1. Landforms along transverse faults parallel to axial zone of folded mountain front, north-eastern Kumaun Sub-Himalaya, India. Khayingshing ... Keywords. Himalayan Frontal Thrust; outer Kumaun Himalaya; transverse structure; folded mountain front.

  6. Co-transcriptional folding is encoded within RNA genes

    Directory of Open Access Journals (Sweden)

    Miklós István

    2004-08-01

    Full Text Available Abstract Background Most of the existing RNA structure prediction programs fold a completely synthesized RNA molecule. However, within the cell, RNA molecules emerge sequentially during the directed process of transcription. Dedicated experiments with individual RNA molecules have shown that RNA folds while it is being transcribed and that its correct folding can also depend on the proper speed of transcription. Methods The main aim of this work is to study if and how co-transcriptional folding is encoded within the primary and secondary structure of RNA genes. In order to achieve this, we study the known primary and secondary structures of a comprehensive data set of 361 RNA genes as well as a set of 48 RNA sequences that are known to differ from the originally transcribed sequence units. We detect co-transcriptional folding by defining two measures of directedness which quantify the extend of asymmetry between alternative helices that lie 5' and those that lie 3' of the known helices with which they compete. Results We show with statistical significance that co-transcriptional folding strongly influences RNA sequences in two ways: (1 alternative helices that would compete with the formation of the functional structure during co-transcriptional folding are suppressed and (2 the formation of transient structures which may serve as guidelines for the co-transcriptional folding pathway is encouraged. Conclusions These findings have a number of implications for RNA secondary structure prediction methods and the detection of RNA genes.

  7. Analysis of protein folds using protein contact networks

    Indian Academy of Sciences (India)

    Proteins are important biomolecules, which perform diverse structural and functional roles in living systems. Starting from a linear chain of amino acids, proteins fold to different secondary structures, which then fold through short- and long-range interactions to give rise to the final three-dimensional shapes useful to carry out ...

  8. Competition between folding and glycosylation in the endoplasmic reticulum

    DEFF Research Database (Denmark)

    Holst, B; Bruun, A W; Kielland-Brandt, Morten

    1996-01-01

    Using carboxypeptidase Y in Saccharomyces cerevisiae as a model system, the in vivo relationship between protein folding and N-glycosylation was studied. Seven new sites for N-glycosylation were introduced at positions buried in the folded protein structure. The level of glycosylation of such new...

  9. Analyses of fold profiles by changing weight parameters of NURB ...

    Indian Academy of Sciences (India)

    Manash Pratim Gogoi

    2017-10-06

    Oct 6, 2017 ... try was not simulated earlier from linear viscous rheology, as per Cruikshank and Johnson (1993). Doming of fluid/ductile deforming rocks with a. Newtonian viscous rheology produces parabolic fold morphology (Johnson and Fletcher 1994). On the other hand, the parabolic fold profiles simu- lated in figure ...

  10. Status report on the folded tandem ion accelerator at BARC

    Indian Academy of Sciences (India)

    Folded tandem ion accelerator; charged particle beams; voltage stability; Rutherford backscattering; ion optics; beam lines. Abstract. The folded tandem ion accelerator (FOTIA) facility set up at BARC has become operational. At present, it is used for elemental analysis studies using the Rutherford backscattering technique.

  11. The dominant folding route minimizes backbone distortion in SH3.

    Directory of Open Access Journals (Sweden)

    Heiko Lammert

    Full Text Available Energetic frustration in protein folding is minimized by evolution to create a smooth and robust energy landscape. As a result the geometry of the native structure provides key constraints that shape protein folding mechanisms. Chain connectivity in particular has been identified as an essential component for realistic behavior of protein folding models. We study the quantitative balance of energetic and geometrical influences on the folding of SH3 in a structure-based model with minimal energetic frustration. A decomposition of the two-dimensional free energy landscape for the folding reaction into relevant energy and entropy contributions reveals that the entropy of the chain is not responsible for the folding mechanism. Instead the preferred folding route through the transition state arises from a cooperative energetic effect. Off-pathway structures are penalized by excess distortion in local backbone configurations and contact pair distances. This energy cost is a new ingredient in the malleable balance of interactions that controls the choice of routes during protein folding.

  12. Surfing the free energy landscape of flavodoxin folding

    NARCIS (Netherlands)

    Bollen, Y.J.M.

    2004-01-01

    The research described in this thesis has been carried out to obtain a better understanding of the fundamental rules describing protein folding. Protein folding is the process in which a linear chain of amino acids contracts to a compact state in which it is active. Flavodoxin from Azotobacter

  13. Vocal Fold Mucus Aggregation in Persons with Voice Disorders

    Science.gov (United States)

    Bonilha, Heather Shaw; White, Lisa; Kuckhahn, Kelsey; Gerlach, Terri Treman; Deliyski, Dimitar D.

    2012-01-01

    Mucus aggregation on the vocal folds is a common finding from laryngeal endoscopy. Patients with voice disorders report the presence of mucus aggregation. Patients also report that mucus aggregation causes them to clear their throat, a behavior believed to be harmful to vocal fold mucosa. Even though clinicians and patients report and discuss…

  14. Double folding model analysis of elastic scattering of halo nucleus ...

    Indian Academy of Sciences (India)

    barrier energy have been performed using a potential obtained from the double folding model and are compared with the ... In double folding (DF) model, the real nucleus–nucleus optical potential is given by the expression [9]. V DF(r) = ∫ dr1. ∫ ... expressed as a sum of three Yukawa terms. It is obtained from the fitting of ...

  15. BENIGN LESIONS OF THE VOCAL FOLDS - HISTOPATHOLOGY AND PHONOTRAUMA

    NARCIS (Netherlands)

    DIKKERS, FG; NIKKELS, PGJ

    Benign lesions of the vocal folds have various appearances. Histopathologic examination might provide the true diagnosis. Therefore, histologic slides of 74 patients (92 vocal folds) with clinically well-defined diagnoses were single-blind examined by a pathologist. Single histologic features did

  16. Analyses of fold profiles by changing weight parameters of NURB ...

    Indian Academy of Sciences (India)

    56

    Department of Geology, Sibsagar College, Joysagar, Sivasagar-785665, Assam, INDIA. 2. Department of Earth Sciences, Indian ..... 3rd degree (n=3) cubic NURB folds generated by increasing value of w1=w2=w from 0.1 to 9.9 and increasing R = hL-1. In all cases, h remains constant. 7*4 possibilities of fold geometries ...

  17. Fluorescence of Alexa Fluor dye tracks protein folding

    NARCIS (Netherlands)

    Lindhoud, S.; Westphal, A.H.; Borst, J.W.; Visser, A.J.W.G.; Mierlo, van C.P.M.

    2012-01-01

    Fluorescence spectroscopy is an important tool for the characterization of protein folding. Often, a protein is labeled with appropriate fluorescent donor and acceptor probes and folding-induced changes in Förster Resonance Energy Transfer (FRET) are monitored. However, conformational changes of the

  18. Chemical recognition software

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, J.S.; Trahan, M.W.; Nelson, W.E.; Hargis, P.J. Jr.; Tisone, G.C.

    1994-12-01

    We have developed a capability to make real time concentration measurements of individual chemicals in a complex mixture using a multispectral laser remote sensing system. Our chemical recognition and analysis software consists of three parts: (1) a rigorous multivariate analysis package for quantitative concentration and uncertainty estimates, (2) a genetic optimizer which customizes and tailors the multivariate algorithm for a particular application, and (3) an intelligent neural net chemical filter which pre-selects from the chemical database to find the appropriate candidate chemicals for quantitative analyses by the multivariate algorithms, as well as providing a quick-look concentration estimate and consistency check. Detailed simulations using both laboratory fluorescence data and computer synthesized spectra indicate that our software can make accurate concentration estimates from complex multicomponent mixtures. even when the mixture is noisy and contaminated with unknowns.

  19. Chemical recognition software

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, J.S.; Trahan, M.W.; Nelson, W.E.; Hargis, P.H. Jr.; Tisone, G.C.

    1994-06-01

    We have developed a capability to make real time concentration measurements of individual chemicals in a complex mixture using a multispectral laser remote sensing system. Our chemical recognition and analysis software consists of three parts: (1) a rigorous multivariate analysis package for quantitative concentration and uncertainty estimates, (2) a genetic optimizer which customizes and tailors the multivariate algorithm for a particular application, and (3) an intelligent neural net chemical filter which pre-selects from the chemical database to find the appropriate candidate chemicals for quantitative analyses by the multivariate algorithms, as well as providing a quick-look concentration estimate and consistency check. Detailed simulations using both laboratory fluorescence data and computer synthesized spectra indicate that our software can make accurate concentration estimates from complex multicomponent mixtures, even when the mixture is noisy and contaminated with unknowns.

  20. Iris Recognition Using Wavelet

    Directory of Open Access Journals (Sweden)

    Khaliq Masood

    2013-08-01

    Full Text Available Biometric systems are getting more attention in the present era. Iris recognition is one of the most secure and authentic among the other biometrics and this field demands more authentic, reliable and fast algorithms to implement these biometric systems in real time. In this paper, an efficient localization technique is presented to identify pupil and iris boundaries using histogram of the iris image. Two small portions of iris have been used for polar transformation to reduce computational time and to increase the efficiency of the system. Wavelet transform is used for feature vector generation. Rotation of iris is compensated without shifts in the iris code. System is tested on Multimedia University Iris Database and results show that proposed system has encouraging performance.

  1. SAR: Stroke Authorship Recognition

    KAUST Repository

    Shaheen, Sara

    2015-10-15

    Are simple strokes unique to the artist or designer who renders them? If so, can this idea be used to identify authorship or to classify artistic drawings? Also, could training methods be devised to develop particular styles? To answer these questions, we propose the Stroke Authorship Recognition (SAR) approach, a novel method that distinguishes the authorship of 2D digitized drawings. SAR converts a drawing into a histogram of stroke attributes that is discriminative of authorship. We provide extensive classification experiments on a large variety of data sets, which validate SAR\\'s ability to distinguish unique authorship of artists and designers. We also demonstrate the usefulness of SAR in several applications including the detection of fraudulent sketches, the training and monitoring of artists in learning a particular new style and the first quantitative way to measure the quality of automatic sketch synthesis tools. © 2015 The Eurographics Association and John Wiley & Sons Ltd.

  2. A numerical strategy for finite element modeling of frictionless asymmetric vocal fold collision

    DEFF Research Database (Denmark)

    Granados, Alba; Misztal, Marek Krzysztof; Brunskog, Jonas

    2016-01-01

    . Theoretical background and numerical analysis of the finite-element position-based contact model are presented, along with validation. A novel contact detection mechanism capable to detect collision in asymmetric oscillations is developed. The effect of inexact contact constraint enforcement on vocal fold...... dynamics is examined by different variational methods for inequality constrained minimization problems, namely the Lagrange multiplier method and the penalty method. In contrast to the penalty solution, which is related to classical spring-like contact forces, numerical examples show that the parameter......-independent Lagrange multiplier solution is more robust and accurate in the estimation of dynamical and mechanical features at vocal fold contact. Furthermore, special attention is paid to the temporal integration schemes in relation to the contact problem, the results suggesting an advantage of highly diffusive...

  3. Are Haar-like Rectangular Features for Biometric Recognition Reducible?

    DEFF Research Database (Denmark)

    Nasrollahi, Kamal; Moeslund, Thomas B.

    2013-01-01

    Biometric recognition is still a very difficult task in real-world scenarios wherein unforeseen changes in degradations factors like noise, occlusion, blurriness and illumination can drastically affect the extracted features from the biometric signals. Very recently Haar-like rectangular features...... which have usually been used for object detection were introduced for biometric recognition resulting in systems that are robust against most of the mentioned degradations [9]. The problem with these features is that one can define many different such features for a given biometric signal...... and it is not clear whether all of these features are required for the actual recognition or not. This is exactly what we are dealing with in this paper: How can an initial set of Haar-like rectangular features, that have been used for biometric recognition, be reduced to a set of most influential features...

  4. Finger vein recognition based on finger crease location

    Science.gov (United States)

    Lu, Zhiying; Ding, Shumeng; Yin, Jing

    2016-07-01

    Finger vein recognition technology has significant advantages over other methods in terms of accuracy, uniqueness, and stability, and it has wide promising applications in the field of biometric recognition. We propose using finger creases to locate and extract an object region. Then we use linear fitting to overcome the problem of finger rotation in the plane. The method of modular adaptive histogram equalization (MAHE) is presented to enhance image contrast and reduce computational cost. To extract the finger vein features, we use a fusion method, which can obtain clear and distinguishable vein patterns under different conditions. We used the Hausdorff average distance algorithm to examine the recognition performance of the system. The experimental results demonstrate that MAHE can better balance the recognition accuracy and the expenditure of time compared with three other methods. Our resulting equal error rate throughout the total procedure was 3.268% in a database of 153 finger vein images.

  5. Multimodal recognition based on face and ear using local feature

    Science.gov (United States)

    Yang, Ruyin; Mu, Zhichun; Chen, Long; Fan, Tingyu

    2017-06-01

    The pose issue which may cause loss of useful information has always been a bottleneck in face and ear recognition. To address this problem, we propose a multimodal recognition approach based on face and ear using local feature, which is robust to large facial pose variations in the unconstrained scene. Deep learning method is used for facial pose estimation, and the method of a well-trained Faster R-CNN is used to detect and segment the region of face and ear. Then we propose a weighted region-based recognition method to deal with the local feature. The proposed method has achieved state-of-the-art recognition performance especially when the images are affected by pose variations and random occlusion in unconstrained scene.

  6. Method of generating ploynucleotides encoding enhanced folding variants

    Energy Technology Data Exchange (ETDEWEB)

    Bradbury, Andrew M.; Kiss, Csaba; Waldo, Geoffrey S.

    2017-05-02

    The invention provides directed evolution methods for improving the folding, solubility and stability (including thermostability) characteristics of polypeptides. In one aspect, the invention provides a method for generating folding and stability-enhanced variants of proteins, including but not limited to fluorescent proteins, chromophoric proteins and enzymes. In another aspect, the invention provides methods for generating thermostable variants of a target protein or polypeptide via an internal destabilization baiting strategy. Internally destabilization a protein of interest is achieved by inserting a heterologous, folding-destabilizing sequence (folding interference domain) within DNA encoding the protein of interest, evolving the protein sequences adjacent to the heterologous insertion to overcome the destabilization (using any number of mutagenesis methods), thereby creating a library of variants. The variants in the library are expressed, and those with enhanced folding characteristics selected.

  7. Co- and post-translational protein folding in the ER

    DEFF Research Database (Denmark)

    Ellgaard, Lars; McCaul, Nicholas; Chatsisvili, Anna

    2016-01-01

    The biophysical rules that govern folding of small, single-domain proteins in dilute solutions are now quite well understood. The mechanisms underlying co-translational folding of multidomain and membrane-spanning proteins in complex cellular environments are often less clear. The endoplasmic...... and the variety of ER-specific protein modifications. Here, we review chaperone-assisted co- and post-translational folding and assembly in the ER and underline the influence of protein modifications on these processes. We emphasize how method development has helped advance the field by allowing researchers...... to monitor the progression of folding as it occurs inside living cells, while at the same time probing the intricate relationship between protein modifications during folding....

  8. Folding propensity of intrinsically disordered proteins by osmotic stress

    International Nuclear Information System (INIS)

    Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.

    2016-01-01

    Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR). Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scattering (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.

  9. The Legal Recognition of Sign Languages

    Science.gov (United States)

    De Meulder, Maartje

    2015-01-01

    This article provides an analytical overview of the different types of explicit legal recognition of sign languages. Five categories are distinguished: constitutional recognition, recognition by means of general language legislation, recognition by means of a sign language law or act, recognition by means of a sign language law or act including…

  10. Methods of Teaching Speech Recognition

    Science.gov (United States)

    Rader, Martha H.; Bailey, Glenn A.

    2010-01-01

    Objective: This article introduces the history and development of speech recognition, addresses its role in the business curriculum, outlines related national and state standards, describes instructional strategies, and discusses the assessment of student achievement in speech recognition classes. Methods: Research methods included a synthesis of…

  11. Iris Recognition - Beyond One Meter

    Science.gov (United States)

    Matey, James R.; Kennell, Lauren R.

    Iris recognition Iris recognition is, arguably, the most robust form of biometric Biometrics identification. It has been deployed in large-scale systems that have been very effective. The systems deployed to date make use of iris Remote Biometric cameras that require significant user cooperation; that in turn imposes significant constraints on the deployment scenarios that are practical.

  12. Side-View Face Recognition

    NARCIS (Netherlands)

    Santemiz, P.; Spreeuwers, Lieuwe Jan; Veldhuis, Raymond N.J.; van den Biggelaar, Olivier

    As a widely used biometrics, face recognition has many advantages such as being non-intrusive, natural and passive. On the other hand, in real-life scenarios with uncontrolled environment, pose variation up to side-view positions makes face recognition a challenging work. In this paper we discuss

  13. Forensic Face Recognition: A Survey

    NARCIS (Netherlands)

    Ali, Tauseef; Veldhuis, Raymond N.J.; Spreeuwers, Lieuwe Jan

    2010-01-01

    Beside a few papers which focus on the forensic aspects of automatic face recognition, there is not much published about it in contrast to the literature on developing new techniques and methodologies for biometric face recognition. In this report, we review forensic facial identification which is

  14. Computer image processing and recognition

    Science.gov (United States)

    Hall, E. L.

    1979-01-01

    A systematic introduction to the concepts and techniques of computer image processing and recognition is presented. Consideration is given to such topics as image formation and perception; computer representation of images; image enhancement and restoration; reconstruction from projections; digital television, encoding, and data compression; scene understanding; scene matching and recognition; and processing techniques for linear systems.

  15. Problems in problem analysis

    DEFF Research Database (Denmark)

    Almegaard, Henrik

    2014-01-01

    The majority of literature on engineering design methods is focused on the processes of fulfilling the design goals as efficiently as possible. This paper will focus on - and discuss - the processes of determining the design goals: the specifications. The purpose is to draw attention to the inher...... to the inherent problems, dilemmas and possibilities in these processes bearing in mind that that the most important decisions in a design project are taken in the beginning of the project....

  16. Face Detection and Recognition

    National Research Council Canada - National Science Library

    Jain, Anil K

    2004-01-01

    .... Specifically, the report addresses the problem of detecting faces in color images in the presence of various lighting conditions and complex backgrounds as well as recognizing faces under variations...

  17. Intrusion detection using pattern recognition methods

    Science.gov (United States)

    Jiang, Nan; Yu, Li

    2007-09-01

    Today, cyber attacks such as worms, scanning, active attackers are pervasive in Internet. A number of security approaches are proposed to address this problem, among which the intrusion detection system (IDS) appears to be one of the major and most effective solutions for defending against malicious users. Essentially, intrusion detection problem can be generalized as a classification problem, whose goal is to distinguish normal behaviors and anomalies. There are many well-known pattern recognition algorithms for classification purpose. In this paper we describe the details of applying pattern recognition methods to the intrusion detection research field. Experimenting on the KDDCUP 99 data set, we first use information gain metric to reduce the dimensionality of the original feature space. Two supervised methods, the support vector machine as well as the multi-layer neural network have been tested and the results display high detection rate and low false alarm rate, which is promising for real world applications. In addition, three unsupervised methods, Single-Linkage, K-Means, and CLIQUE, are also implemented and evaluated in the paper. The low computational complexity reveals their application in initial data reduction process.

  18. Balance Problems

    Science.gov (United States)

    ... often, it could be a sign of a balance problem. Balance problems can make you feel unsteady. You may ... related injuries, such as a hip fracture. Some balance problems are due to problems in the inner ...

  19. Entropic formulation for the protein folding process: Hydrophobic stability correlates with folding rates

    Science.gov (United States)

    Dal Molin, J. P.; Caliri, A.

    2018-01-01

    Here we focus on the conformational search for the native structure when it is ruled by the hydrophobic effect and steric specificities coming from amino acids. Our main tool of investigation is a 3D lattice model provided by a ten-letter alphabet, the stereochemical model. This minimalist model was conceived for Monte Carlo (MC) simulations when one keeps in mind the kinetic behavior of protein-like chains in solution. We have three central goals here. The first one is to characterize the folding time (τ) by two distinct sampling methods, so we present two sets of 103 MC simulations for a fast protein-like sequence. The resulting sets of characteristic folding times, τ and τq were obtained by the application of the standard Metropolis algorithm (MA), as well as by an enhanced algorithm (Mq A). The finding for τq shows two things: (i) the chain-solvent hydrophobic interactions {hk } plus a set of inter-residues steric constraints {ci,j } are able to emulate the conformational search for the native structure. For each one of the 103MC performed simulations, the target is always found within a finite time window; (ii) the ratio τq / τ ≅ 1 / 10 suggests that the effect of local thermal fluctuations, encompassed by the Tsallis weight, provides to the chain an innate efficiency to escape from energetic and steric traps. We performed additional MC simulations with variations of our design rule to attest this first result, both algorithms the MA and the Mq A were applied to a restricted set of targets, a physical insight is provided. Our second finding was obtained by a set of 600 independent MC simulations, only performed with the Mq A applied to an extended set of 200 representative targets, our native structures. The results show how structural patterns should modulate τq, which cover four orders of magnitude; this finding is our second goal. The third, and last result, was obtained with a special kind of simulation performed with the purpose to explore a

  20. ACTION RECOGNITION USING SALIENT NEIGHBORING HISTOGRAMS

    DEFF Research Database (Denmark)

    Ren, Huamin; Moeslund, Thomas B.

    2013-01-01

    Combining spatio-temporal interest points with Bag-of-Words models achieves state-of-the-art performance in action recognition. However, existing methods based on “bag-ofwords” models either are too local to capture the variance in space/time or fail to solve the ambiguity problem in spatial...... and temporal dimensions. Instead, we propose a salient vocabulary construction algorithm to select visual words from a global point of view, and form compact descriptors to represent discriminative histograms in the neighborhoods. Those salient neighboring histograms are then trained to model different actions...

  1. Recognition memory impairments caused by false recognition of novel objects.

    Science.gov (United States)

    Yeung, Lok-Kin; Ryan, Jennifer D; Cowell, Rosemary A; Barense, Morgan D

    2013-11-01

    A fundamental assumption underlying most current theories of amnesia is that memory impairments arise because previously studied information either is lost rapidly or is made inaccessible (i.e., the old information appears to be new). Recent studies in rodents have challenged this view, suggesting instead that under conditions of high interference, recognition memory impairments following medial temporal lobe damage arise because novel information appears as though it has been previously seen. Here, we developed a new object recognition memory paradigm that distinguished whether object recognition memory impairments were driven by previously viewed objects being treated as if they were novel or by novel objects falsely recognized as though they were previously seen. In this indirect, eyetracking-based passive viewing task, older adults at risk for mild cognitive impairment showed false recognition to high-interference novel items (with a significant degree of feature overlap with previously studied items) but normal novelty responses to low-interference novel items (with a lower degree of feature overlap). The indirect nature of the task minimized the effects of response bias and other memory-based decision processes, suggesting that these factors cannot solely account for false recognition. These findings support the counterintuitive notion that recognition memory impairments in this memory-impaired population are not characterized by forgetting but rather are driven by the failure to differentiate perceptually similar objects, leading to the false recognition of novel objects as having been seen before. PsycINFO Database Record (c) 2013 APA, all rights reserved.

  2. Multimodal approaches for emotion recognition: a survey

    Science.gov (United States)

    Sebe, Nicu; Cohen, Ira; Gevers, Theo; Huang, Thomas S.

    2005-01-01

    Recent technological advances have enabled human users to interact with computers in ways previously unimaginable. Beyond the confines of the keyboard and mouse, new modalities for human-computer interaction such as voice, gesture, and force-feedback are emerging. Despite important advances, one necessary ingredient for natural interaction is still missing-emotions. Emotions play an important role in human-to-human communication and interaction, allowing people to express themselves beyond the verbal domain. The ability to understand human emotions is desirable for the computer in several applications. This paper explores new ways of human-computer interaction that enable the computer to be more aware of the user's emotional and attentional expressions. We present the basic research in the field and the recent advances into the emotion recognition from facial, voice, and physiological signals, where the different modalities are treated independently. We then describe the challenging problem of multimodal emotion recognition and we advocate the use of probabilistic graphical models when fusing the different modalities. We also discuss the difficult issues of obtaining reliable affective data, obtaining ground truth for emotion recognition, and the use of unlabeled data.

  3. Emotion Pattern Recognition Using Physiological Signals

    Directory of Open Access Journals (Sweden)

    Xiaowei Niu

    2014-06-01

    Full Text Available In this paper, we first regard emotion recognition as a pattern recognition problem, a novel feature selection method was presented to recognize human emotional state from four physiological signals. Electrocardiogram (ECG, electromyogram (EMG, skin conductance (SC and respiration (RSP. The raw training data was collected from four sensors, ECG, EMG, SC, RSP, when a single subject intentionally expressed four different affective states, joy, anger, sadness, pleasure. The total 193 features were extracted for the recognition. A music induction method was used to elicit natural emotional reactions from the subject, after calculating a sufficient amount of features from the raw signals, the genetic algorithm and the K-neighbor methods were tested to extract a new feature set consisting of the most significant features which represents exactly the relevant emotional state for improving classification performance. The numerical results demonstrate that there is significant information in physiological signals for recognizing the affective state. It also turned out that it was much easier to separate emotions along the arousal axis than along the valence axis.

  4. A Review of Human Activity Recognition Methods

    Directory of Open Access Journals (Sweden)

    Michalis eVrigkas

    2015-11-01

    Full Text Available Recognizing human activities from video sequences or still images is a challenging task due to problems such as background clutter, partial occlusion, changes in scale, viewpoint, lighting, and appearance. Many applications, including video surveillance systems, human-computer interaction, and robotics for human behavior characterization, require a multiple activity recognition system. In this work, we provide a detailed review of recent and state-of-the-art research advances in the field of human activity classification. We propose a categorization of human activity methodologies and discuss their advantages and limitations. In particular, we divide human activity classification methods into two large categories according to whether they use data from different modalities or not. Then, each of these categories is further analyzed into sub-categories, which reflect how they model human activities and what type of activities they are interested in. Moreover, we provide a comprehensive analysis of the existing, publicly available human activity classification datasets and examine the requirements for an ideal human activity recognition dataset. Finally, we report the characteristics of future research directions and present some open issues on human activity recognition.

  5. A Leaf Recognition Of Vegetables Using Matlab

    Directory of Open Access Journals (Sweden)

    Nadine Jaan D. Caldito

    2015-08-01

    Full Text Available Recognizing plants is a vital problem especially for biologists agricultural researchers and environmentalists. Plant recognition can be performed by human experts manually but it is a time consuming and low-efficiency process. Automation of plant recognition is an important process for the fields working with plants. This paper presents an approach for plant recognition using leaf images. In this study the proponents demonstrated the development of the system that gives users the ability to identify vegetables based on photographs of the leaves taken with a high definition camera. At the heart of this system is a modernize process of identification so as to automate the way of identifying the vegetable plants through leaf image and digital image processing. The system used the Gabor Filter Edge Detection RGB Color and Grayscale Image to acquire the physical parameter of the leaves. The output parameters are used to compute well documented metrics for the statistical and shape. Base on the study the following conclusion are drawn The system can extract the physical parameters from the leafs image that will be used in identifying Vegetables. From the extracted leaf parameters the system provides the statistical analysis and general information of the identified leaf. The used algorithm can organize data and information to useful resources to the future researchers.

  6. Sleep promotes analogical transfer in problem solving.

    Science.gov (United States)

    Monaghan, Padraic; Sio, Ut Na; Lau, Sum Wai; Woo, Hoi Kei; Linkenauger, Sally A; Ormerod, Thomas C

    2015-10-01

    Analogical problem solving requires using a known solution from one problem to apply to a related problem. Sleep is known to have profound effects on memory and information restructuring, and so we tested whether sleep promoted such analogical transfer, determining whether improvement was due to subjective memory for problems, subjective recognition of similarity across related problems, or by abstract generalisation of structure. In Experiment 1, participants were exposed to a set of source problems. Then, after a 12-h period involving sleep or wake, they attempted target problems structurally related to the source problems but with different surface features. Experiment 2 controlled for time of day effects by testing participants either in the morning or the evening. Sleep improved analogical transfer, but effects were not due to improvements in subjective memory or similarity recognition, but rather effects of structural generalisation across problems. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Effect of sugarcane biopolymer gel injected in rabbit vocal fold

    Directory of Open Access Journals (Sweden)

    Rodrigo Augusto de Souza Leão

    2014-06-01

    Full Text Available INTRODUCTION: Alterations in the vocal folds that involve volume reduction and glottal closure failure result in exaggerated air escape during speech. For such situations, the use of implants or grafts of different materials has been proposed. OBJECTIVE: To define the effect of sugarcane biopolymer gel when implanted in the vocal folds of rabbits. METHODS: This was an experimental study. The vocal folds of rabbits injected with sugarcane biopolymer and saline solution were histologically evaluated after 21 and 90 days. RESULTS: Mild to moderate inflammation and increased volume were observed in all vocal folds injected with biopolymer, when compared to controls. There were no cases of necrosis or calcification. DISCUSSION: This study showed higher inflammatory reaction in cases than in controls and biopolymer biointegration to the vocal fold. This fibrogenic response with absence of epithelial repercussions suggests that the biopolymer in its gel form can be bioactive and preserve the normal vibratory function of the epithelium. CONCLUSION: We show that in spite of producing an inflammatory reaction in vocal fold tissues, the material remained in vocal fold throughout the study period.

  8. Analyzing the effect of homogeneous frustration in protein folding.

    Science.gov (United States)

    Contessoto, Vinícius G; Lima, Debora T; Oliveira, Ronaldo J; Bruni, Aline T; Chahine, Jorge; Leite, Vitor B P

    2013-10-01

    The energy landscape theory has been an invaluable theoretical framework in the understanding of biological processes such as protein folding, oligomerization, and functional transitions. According to the theory, the energy landscape of protein folding is funneled toward the native state, a conformational state that is consistent with the principle of minimal frustration. It has been accepted that real proteins are selected through natural evolution, satisfying the minimum frustration criterion. However, there is evidence that a low degree of frustration accelerates folding. We examined the interplay between topological and energetic protein frustration. We employed a Cα structure-based model for simulations with a controlled nonspecific energetic frustration added to the potential energy function. Thermodynamics and kinetics of a group of 19 proteins are completely characterized as a function of increasing level of energetic frustration. We observed two well-separated groups of proteins: one group where a little frustration enhances folding rates to an optimal value and another where any energetic frustration slows down folding. Protein energetic frustration regimes and their mechanisms are explained by the role of non-native contact interactions in different folding scenarios. These findings strongly correlate with the protein free-energy folding barrier and the absolute contact order parameters. These computational results are corroborated by principal component analysis and partial least square techniques. One simple theoretical model is proposed as a useful tool for experimentalists to predict the limits of improvements in real proteins. Copyright © 2013 Wiley Periodicals, Inc.

  9. The role of the mesenchyme in cranial neural fold elevation

    Energy Technology Data Exchange (ETDEWEB)

    Morris-Wiman, J.A.

    1988-01-01

    It has been previously postulated that the expansion of an hyaluronate-rich extracellular matrix in the fold mesenchyme is responsible for neural fold elevation. In this study we provide evidence that such expansions may play an important role in cranial neural fold elevation by pushing the folds towards the dorsal midline to assist in their elevation. For mesenchymal expansion to result in fold elevation, hyaluronate (HA) and mesenchymal cells must be non-randomly distributed within the mesenchyme. Patterns of mesenchymal cell distribution and cell proliferation were analyzed using the computer-assisted method of smoothed spatial averaging. The distribution of Alcian blue-stained and {sup 3}H-glucosamine-labelled HA was also analyzed during cranial neural fold elevation using established image processing techniques. Analysis of the distribution of {sup 3}H-thymidine-labelled mesenchymal cells indicated that differential mitotic activity was not responsible for decreased mesenchymal cell density. Likewise, analysis of distribution patterns of {sup 3}H-glucosamine-labelled HA indicated that decreased HA concentration was not produced by regional differences in HA synthesis. These results suggest that decreases in mesenchymal cell density and HA concentration that occur during neural fold elevation are produced by mesenchymal expansion.

  10. The role of the mesenchyme in cranial neural fold elevation

    International Nuclear Information System (INIS)

    Morris-Wiman, J.A.

    1988-01-01

    It has been previously postulated that the expansion of an hyaluronate-rich extracellular matrix in the fold mesenchyme is responsible for neural fold elevation. In this study we provide evidence that such expansions may play an important role in cranial neural fold elevation by pushing the folds towards the dorsal midline to assist in their elevation. For mesenchymal expansion to result in fold elevation, hyaluronate (HA) and mesenchymal cells must be non-randomly distributed within the mesenchyme. Patterns of mesenchymal cell distribution and cell proliferation were analyzed using the computer-assisted method of smoothed spatial averaging. The distribution of Alcian blue-stained and 3 H-glucosamine-labelled HA was also analyzed during cranial neural fold elevation using established image processing techniques. Analysis of the distribution of 3 H-thymidine-labelled mesenchymal cells indicated that differential mitotic activity was not responsible for decreased mesenchymal cell density. Likewise, analysis of distribution patterns of 3 H-glucosamine-labelled HA indicated that decreased HA concentration was not produced by regional differences in HA synthesis. These results suggest that decreases in mesenchymal cell density and HA concentration that occur during neural fold elevation are produced by mesenchymal expansion

  11. Origami-Inspired Folding of Thick, Rigid Panels

    Science.gov (United States)

    Trease, Brian P.; Thomson, Mark W.; Sigel, Deborah A.; Walkemeyer, Phillip E.; Zirbel, Shannon; Howell, Larry; Lang, Robert

    2014-01-01

    To achieve power of 250 kW or greater, a large compression ratio of stowed-to-deployed area is needed. Origami folding patterns were used to inspire the folding of a solar array to achieve synchronous deployment; however, origami models are generally created for near-zero-thickness material. Panel thickness is one of the main challenges of origami-inspired design. Three origami-inspired folding techniques (flasher, square twist, and map fold) were created with rigid panels and hinges. Hinge components are added to the model to enable folding of thick, rigid materials. Origami models are created assuming zero (or near zero) thickness. When a material with finite thickness is used, the panels are required to bend around an increasingly thick fold as they move away from the center of the model. The two approaches for dealing with material thickness are to use membrane hinges to connect the panels, or to add panel hinges, or hinges of the same thickness, at an appropriate width to enable folding.

  12. Fluorescence of Alexa fluor dye tracks protein folding.

    Directory of Open Access Journals (Sweden)

    Simon Lindhoud

    Full Text Available Fluorescence spectroscopy is an important tool for the characterization of protein folding. Often, a protein is labeled with appropriate fluorescent donor and acceptor probes and folding-induced changes in Förster Resonance Energy Transfer (FRET are monitored. However, conformational changes of the protein potentially affect fluorescence properties of both probes, thereby profoundly complicating interpretation of FRET data. In this study, we assess the effects protein folding has on fluorescence properties of Alexa Fluor 488 (A488, which is commonly used as FRET donor. Here, A488 is covalently attached to Cys69 of apoflavodoxin from Azotobacter vinelandii. Although coupling of A488 slightly destabilizes apoflavodoxin, the three-state folding of this protein, which involves a molten globule intermediate, is unaffected. Upon folding of apoflavodoxin, fluorescence emission intensity of A488 changes significantly. To illuminate the molecular sources of this alteration, we applied steady state and time-resolved fluorescence techniques. The results obtained show that tryptophans cause folding-induced changes in quenching of Alexa dye. Compared to unfolded protein, static quenching of A488 is increased in the molten globule. Upon populating the native state both static and dynamic quenching of A488 decrease considerably. We show that fluorescence quenching of Alexa Fluor dyes is a sensitive reporter of conformational changes during protein folding.

  13. Fluorescence of Alexa fluor dye tracks protein folding.

    Science.gov (United States)

    Lindhoud, Simon; Westphal, Adrie H; Visser, Antonie J W G; Borst, Jan Willem; van Mierlo, Carlo P M

    2012-01-01

    Fluorescence spectroscopy is an important tool for the characterization of protein folding. Often, a protein is labeled with appropriate fluorescent donor and acceptor probes and folding-induced changes in Förster Resonance Energy Transfer (FRET) are monitored. However, conformational changes of the protein potentially affect fluorescence properties of both probes, thereby profoundly complicating interpretation of FRET data. In this study, we assess the effects protein folding has on fluorescence properties of Alexa Fluor 488 (A488), which is commonly used as FRET donor. Here, A488 is covalently attached to Cys69 of apoflavodoxin from Azotobacter vinelandii. Although coupling of A488 slightly destabilizes apoflavodoxin, the three-state folding of this protein, which involves a molten globule intermediate, is unaffected. Upon folding of apoflavodoxin, fluorescence emission intensity of A488 changes significantly. To illuminate the molecular sources of this alteration, we applied steady state and time-resolved fluorescence techniques. The results obtained show that tryptophans cause folding-induced changes in quenching of Alexa dye. Compared to unfolded protein, static quenching of A488 is increased in the molten globule. Upon populating the native state both static and dynamic quenching of A488 decrease considerably. We show that fluorescence quenching of Alexa Fluor dyes is a sensitive reporter of conformational changes during protein folding.

  14. [Population problem, comprehension problem].

    Science.gov (United States)

    Tallon, F

    1993-08-01

    Overpopulation of developing countries in general, and Rwanda in particular, is not just their problem but a problem for developed countries as well. Rapid population growth is a key factor in the increase of poverty in sub-Saharan Africa. Population growth outstrips food production. Africa receives more and more foreign food, economic, and family planning aid each year. The Government of Rwanda encourages reduced population growth. Some people criticize it, but this criticism results in mortality and suffering. One must combat this ignorance, but attitudes change slowly. Some of these same people find the government's acceptance of family planning an invasion of their privacy. Others complain that rich countries do not have campaigns to reduce births, so why should Rwanda do so? The rate of schooling does not increase in Africa, even though the number of children in school increases, because of rapid population growth. Education is key to improvements in Africa's socioeconomic growth. Thus, Africa, is underpopulated in terms of potentiality but overpopulated in terms of reality, current conditions, and possibilities of overexploitation. Africa needs to invest in human resources. Families need to save, and to so, they must refrain from having many children. Africa should resist the temptation to waste, as rich countries do, and denounce it. Africa needs to become more independent of these countries, but structural adjustment plans, growing debt, and rapid population growth limit national independence. Food aid is a means for developed countries to dominate developing countries. Modernization through foreign aid has had some positive effects on developing countries (e.g., improved hygiene, mortality reduction), but these also sparked rapid population growth. Rwandan society is no longer traditional, but it is also not yet modern. A change in mentality to fewer births, better quality of life for living infants, better education, and less burden for women must occur

  15. A Taxonomy of 3D Occluded Objects Recognition Techniques

    Science.gov (United States)

    Soleimanizadeh, Shiva; Mohamad, Dzulkifli; Saba, Tanzila; Al-ghamdi, Jarallah Saleh

    2016-03-01

    The overall performances of object recognition techniques under different condition (e.g., occlusion, viewpoint, and illumination) have been improved significantly in recent years. New applications and hardware are shifted towards digital photography, and digital media. This faces an increase in Internet usage requiring object recognition for certain applications; particularly occulded objects. However occlusion is still an issue unhandled, interlacing the relations between extracted feature points through image, research is going on to develop efficient techniques and easy to use algorithms that would help users to source images; this need to overcome problems and issues regarding occlusion. The aim of this research is to review recognition occluded objects algorithms and figure out their pros and cons to solve the occlusion problem features, which are extracted from occluded object to distinguish objects from other co-existing objects by determining the new techniques, which could differentiate the occluded fragment and sections inside an image.

  16. Data analysis and pattern recognition in multiple databases

    CERN Document Server

    Adhikari, Animesh; Pedrycz, Witold

    2014-01-01

    Pattern recognition in data is a well known classical problem that falls under the ambit of data analysis. As we need to handle different data, the nature of patterns, their recognition and the types of data analyses are bound to change. Since the number of data collection channels increases in the recent time and becomes more diversified, many real-world data mining tasks can easily acquire multiple databases from various sources. In these cases, data mining becomes more challenging for several essential reasons. We may encounter sensitive data originating from different sources - those cannot be amalgamated. Even if we are allowed to place different data together, we are certainly not able to analyse them when local identities of patterns are required to be retained. Thus, pattern recognition in multiple databases gives rise to a suite of new, challenging problems different from those encountered before. Association rule mining, global pattern discovery, and mining patterns of select items provide different...

  17. Audio signal recognition for speech, music, and environmental sounds

    Science.gov (United States)

    Ellis, Daniel P. W.

    2003-10-01

    Human listeners are very good at all kinds of sound detection and identification tasks, from understanding heavily accented speech to noticing a ringing phone underneath music playing at full blast. Efforts to duplicate these abilities on computer have been particularly intense in the area of speech recognition, and it is instructive to review which approaches have proved most powerful, and which major problems still remain. The features and models developed for speech have found applications in other audio recognition tasks, including musical signal analysis, and the problems of analyzing the general ``ambient'' audio that might be encountered by an auditorily endowed robot. This talk will briefly review statistical pattern recognition for audio signals, giving examples in several of these domains. Particular emphasis will be given to common aspects and lessons learned.

  18. Soft Computing Applications in Optimization, Control, and Recognition

    CERN Document Server

    Castillo, Oscar

    2013-01-01

    Soft computing includes several intelligent computing paradigms, like fuzzy logic, neural networks, and bio-inspired optimization algorithms. This book describes the application of soft computing techniques to intelligent control, pattern recognition, and optimization problems. The book is organized in four main parts. The first part deals with nature-inspired optimization methods and their applications. Papers included in this part propose new models for achieving intelligent optimization in different application areas. The second part discusses hybrid intelligent systems for achieving control. Papers included in this part make use of nature-inspired techniques, like evolutionary algorithms, fuzzy logic and neural networks, for the optimal design of intelligent controllers for different kind of applications. Papers in the third part focus on intelligent techniques for pattern recognition and propose new methods to solve complex pattern recognition problems. The fourth part discusses new theoretical concepts ...

  19. Endoscopic Anatomy of the Tensor Fold and Anterior Attic.

    Science.gov (United States)

    Li, Bin; Doan, Phi; Gruhl, Robert R; Rubini, Alessia; Marchioni, Daniele; Fina, Manuela

    2018-02-01

    Objectives The objectives of the study were to (1) study the anatomical variations of the tensor fold and its anatomic relation with transverse crest, supratubal recess, and anterior epitympanic space and (2) explore the most appropriate endoscopic surgical approach to each type of the tensor fold variants. Study Design Cadaver dissection study. Setting Temporal bone dissection laboratory. Subjects and Methods Twenty-eight human temporal bones (26 preserved and 2 fresh) were dissected through an endoscopic transcanal approach between September 2016 and June 2017. The anatomical variations of the tensor fold, transverse crest, supratubal recess, and anterior epitympanic space were studied before and after removing ossicles. Results Three different tensor fold orientations were observed: vertical (type A, 11/28, 39.3%) with attachment to the transverse crest, oblique (type B, 13/28, 46.4%) with attachment to the anterior tegmen tympani, and horizontal (type C, 4/28, 14.3%) with attachment to the tensor tympani canal. The tensor fold was a complete membrane in 20 of 28 (71.4%) specimens, preventing direct ventilation between the supratubal recess and anterior epitympanic space. We identified 3 surgical endoscopic approaches, which allowed visualization of the tensor fold without removing the ossicles. Conclusions The orientation of the tensor fold is the determining structure that dictates the conformation and limits of the epitympanic space. We propose a classification of the tensor fold based on 3 anatomical variants. We also describe 3 different minimally invasive endoscopic approaches to identify the orientation of the tensor fold while maintaining ossicular chain continuity.

  20. A nomenclature paradigm for benign midmembranous vocal fold lesions.

    Science.gov (United States)

    Rosen, Clark A; Gartner-Schmidt, Jackie; Hathaway, Bridget; Simpson, C Blake; Postma, Gregory N; Courey, Mark; Sataloff, Robert T

    2012-06-01

    There is a significant lack of uniform agreement regarding nomenclature for benign vocal fold lesions (BVFLs). This confusion results in difficulty for clinicians communicating with their patients and with each other. In addition, BVFL research and comparison of treatment methods are hampered by the lack of a detailed and uniform BVFL nomenclature. Clinical consensus conferences were held to develop an initial BVFL nomenclature paradigm. Perceptual video analysis was performed to validate the stroboscopy component of the paradigm. The culmination of the consensus conferences and the video-perceptual analysis was used to evaluate the BVFL nomenclature paradigm using a retrospective review of patients with BVFL. An initial BVFL nomenclature paradigm was proposed utilizing detailed definitions relating to vocal fold lesion morphology, stroboscopy, response to voice therapy and intraoperative findings. Video-perceptual analysis of stroboscopy demonstrated that the proposed binary stroboscopy system used in the BVFL nomenclature paradigm was valid and widely applicable. Retrospective review of 45 patients with BVFL followed to the conclusion of treatment demonstrated that slight modifications of the initial BVFL nomenclature paradigm were required. With the modified BVFL nomenclature paradigm, 96% of the patients fit into the predicted pattern and definitions of the BVFL nomenclature system. This study has validated a multidimensional BVFL nomenclature paradigm. This vocal fold nomenclature paradigm includes nine distinct vocal fold lesions: vocal fold nodules, vocal fold polyp, pseudocyst, vocal fold cyst (subepithelial or ligament), nonspecific vocal fold lesion, vocal fold fibrous mass (subepithelial or ligament), and reactive lesion. Copyright © 2011 The American Laryngological, Rhinological, and Otological Society, Inc.

  1. Speech Recognition: How Do We Teach It?

    Science.gov (United States)

    Barksdale, Karl

    2002-01-01

    States that growing use of speech recognition software has made voice writing an essential computer skill. Describes how to present the topic, develop basic speech recognition skills, and teach speech recognition outlining, writing, proofreading, and editing. (Contains 14 references.) (SK)

  2. Automatic music genres classification as a pattern recognition problem

    Science.gov (United States)

    Ul Haq, Ihtisham; Khan, Fauzia; Sharif, Sana; Shaukat, Arsalan

    2013-12-01

    Music genres are the simplest and effect descriptors for searching music libraries stores or catalogues. The paper compares the results of two automatic music genres classification systems implemented by using two different yet simple classifiers (K-Nearest Neighbor and Naïve Bayes). First a 10-12 second sample is selected and features are extracted from it, and then based on those features results of both classifiers are represented in the form of accuracy table and confusion matrix. An experiment carried out on test 60 taken from middle of a song represents the true essence of its genre as compared to the samples taken from beginning and ending of a song. The novel techniques have achieved an accuracy of 91% and 78% by using Naïve Bayes and KNN classifiers respectively.

  3. Molecular dynamics studies of protein folding and aggregation

    Science.gov (United States)

    Ding, Feng

    This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism

  4. Adjustable thermal resistor by reversibly folding a graphene sheet.

    Science.gov (United States)

    Song, Qichen; An, Meng; Chen, Xiandong; Peng, Zhan; Zang, Jianfeng; Yang, Nuo

    2016-08-11

    Phononic (thermal) devices such as thermal diodes, thermal transistors, thermal logic gates, and thermal memories have been studied intensively. However, tunable thermal resistors have not been demonstrated yet. Here, we propose an instantaneously adjustable thermal resistor based on folded graphene. Through theoretical analysis and molecular dynamics simulations, we study the phonon-folding scattering effect and the dependence of thermal resistivity on the length between two folds and the overall length. Furthermore, we discuss the possibility of realizing instantaneously adjustable thermal resistors in experiment. Our studies bring new insights into designing thermal resistors and understanding the thermal modulation of 2D materials by adjusting basic structure parameters.

  5. Anisotropic Liquid Microcapsules from Biomimetic Self-Folding Polymer Films.

    Science.gov (United States)

    Zakharchenko, Svetlana; Ionov, Leonid

    2015-06-17

    We demonstrated a novel approach for the fabrication of anisotropic capsules with liquid content using biomimetic self-folding thermoresponsive polymer films. The behavior of self-folding films is very similar to actuation in plants, where nonhomogenous swelling results in complex movements such as twisting, bending, or folding. This approach allows the design of anisotropic liquid capsules with rodlike and dumbbell-like morphologies. We found that these capsules are able to assemble into different complex structures, such as nematic-like one and 3D network depending on their morphology.

  6. Towards a geomechanics classification of folded layered rock masses

    Science.gov (United States)

    Agliardi, Federico; Zanchi, Andrea; Bianchi, Federico; Crosta, Giovanni B.

    2016-04-01

    Several schemes have been proposed in the last decades to account for the effects of structure and alteration of rock masses on their geo-mechanical properties. Among these, the Geological Strength Index (GSI) turned out as the most effective to account for complex geological conditions, including heavily fractured, heterogeneous (e.g. flysch-like) or tectonically disturbed rock masses. It is well known that folding has a direct impact on the type and degree of fracturing. Nevertheless, no classification scheme has been developed to introduce explicitly the effects of folding and associated fracturing on rock mass strength and deformability. In this perspective, we carried out an exploratory study aimed at establishing relationships between outcrop-scale folding and GSI in layered carbonate rock masses, exceptionally well exposed in a quarry near Bergamo (Lombardia, Southern Alps). A N-S trending, 350m long and 115m high benched rock face exposes a complete cross section of a sub-horizontal inclined fold involving Lower Jurassic cherty mudstones (Moltrasio Lms.) and marly limestones successions (Domaro Lms.). The main fold has an axial surface moderately dipping to the north and is characterised by polyharmonic folds at scales of metres to tens of metres. The site was documented by producing a digital outcrop through a high-resolution terrestrial photogrammetric survey from distances ranging from 70 to 130 m (18 camera stations, 395 pictures), using RTK GNSS measurements for camera station geo-referencing. Data processing by Structure-from-Motion (SfM) techniques resulted in detailed point clouds covering the entire slope with a cm-scale accuracy. In order to establish relationships between lithology, folding styles, and geomechanical properties of folded rock masses we performed a detailed structural analysis at 25 survey stations spread over all the different fold sectors. These surveys include: lithology, bedding attitude and thickness, brittle structures (e

  7. Miniaturization of Multiple-Layer Folded Patch Antennas

    DEFF Research Database (Denmark)

    Zhang, Jiaying; Breinbjerg, Olav

    2009-01-01

    layer patch is fabricated and measured to validate the design method. The theoretical analysis, design and simulations, fabrications, as well as the measurements are presented in this paper. All the results show that the folded patch antenna is a good candidate in making a highly miniaturized compact......A new folded patch antenna with multiple layers was developed in this paper, by folding the patch in a proper way, and a highly miniaturized antenna can be realized. The multiple layer patch with 4-layer and 6-layer are designed and evaluated at 2.4 GHz, 915 MHz, and 415 MHz respectively. Then a 4...

  8. Large sonic band gaps in 12-fold quasicrystals

    Science.gov (United States)

    Lai, Yun; Zhang, Xiangdong; Zhang, Zhao-Qing

    2002-05-01

    The sonic band-gap structures of 12-fold symmetry quasicrystals consisting of rigid cylinders in air are investigated by using the multiple scattering method. Large full gaps are found in this system owing to its high symmetry. At filling fractions between 0.2 and 0.4, this 12-fold square-triangle tiling is much better for the realization of sonic band gaps than the square or triangular lattice. This makes the 12-fold quasicrystal a promising structure for acoustic-wave band-gap materials.

  9. Water dynamics clue to key residues in protein folding

    International Nuclear Information System (INIS)

    Gao, Meng; Zhu, Huaiqiu; Yao, Xin-Qiu; She, Zhen-Su

    2010-01-01

    A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.

  10. Competition between folding and glycosylation in the endoplasmic reticulum

    DEFF Research Database (Denmark)

    Holst, B; Bruun, A W; Kielland-Brandt, Morten

    1996-01-01

    Using carboxypeptidase Y in Saccharomyces cerevisiae as a model system, the in vivo relationship between protein folding and N-glycosylation was studied. Seven new sites for N-glycosylation were introduced at positions buried in the folded protein structure. The level of glycosylation of such new...... acceptor sites was analysed by pulse-labelling under two sets of conditions that are known to reduce the rate of folding: (i) addition of dithiothreitol to the growth medium and (ii) introduction of deletions in the propeptide. A variety of effects was observed, depending on the position of the new...

  11. Autonomy, recognition and education

    Directory of Open Access Journals (Sweden)

    Angelo Vitório Cenci

    2015-01-01

    Full Text Available This paper addresses Honneth’s concept of autonomy from two dimensions of his work, distinct, though inseparable. The first one is suggested through the subject’s positive practical self-relation linked to the patterns of reciprocal recognition of love, right and social esteem; the second is formulated as non-centered autonomy opposed to the present-day criticism of the modern autonomous subject encompassing three levels, namely: the capacity of linguistic articulation, the narrative coherence of life and the complementation of being guided by principles with some criteria of moral sensitivity to the context. We defend the position that, by metaphysically anchoring the concept of autonomy onto the intersubjective assumptions of his/her theory of the subject, and exploring it linked to the subject’s positive practical self-relation and to a non-centered meaning, Honneth has managed to renew it, which allows drawing important consequences of such effort to the field of education.

  12. Pattern recognition in spectra

    Science.gov (United States)

    Gebran, M.; Paletou, F.

    2017-06-01

    We present a new automated procedure that simultaneously derives the effective temperature Teff, surface gravity log g, metallicity [Fe/H], and equatorial projected rotational velocity ve sin i for stars. The procedure is inspired by the well-known PCA-based inversion of spectropolarimetric full-Stokes solar data, which was used both for Zeeman and Hanle effects. The efficiency and accuracy of this procedure have been proven for FGK, A, and late type dwarf stars of K and M spectral types. Learning databases are generated from the Elodie stellar spectra library using observed spectra for which fundamental parameters were already evaluated or with synthetic data. The synthetic spectra are calculated using ATLAS9 model atmospheres. This technique helped us to detect many peculiar stars such as Am, Ap, HgMn, SiEuCr and binaries. This fast and efficient technique could be used every time a pattern recognition is needed. One important application is the understanding of the physical properties of planetary surfaces by comparing aboard instrument data to synthetic ones.

  13. Pattern recognition in spectra

    International Nuclear Information System (INIS)

    Gebran, M; Paletou, F

    2017-01-01

    We present a new automated procedure that simultaneously derives the effective temperature T eff , surface gravity log g , metallicity [ Fe/H ], and equatorial projected rotational velocity v e sin i for stars. The procedure is inspired by the well-known PCA-based inversion of spectropolarimetric full-Stokes solar data, which was used both for Zeeman and Hanle effects. The efficiency and accuracy of this procedure have been proven for FGK, A, and late type dwarf stars of K and M spectral types. Learning databases are generated from the Elodie stellar spectra library using observed spectra for which fundamental parameters were already evaluated or with synthetic data. The synthetic spectra are calculated using ATLAS9 model atmospheres. This technique helped us to detect many peculiar stars such as Am, Ap, HgMn, SiEuCr and binaries. This fast and efficient technique could be used every time a pattern recognition is needed. One important application is the understanding of the physical properties of planetary surfaces by comparing aboard instrument data to synthetic ones. (paper)

  14. Investigation on Optimization in Segmentation Phase of Iris Recognition

    Directory of Open Access Journals (Sweden)

    Selvamuthukumaran Shanmugam

    2010-01-01

    Full Text Available In a progressively more digital society, the demandfor secure identification has led to amplified development ofbiometric systems. Iris biometric systems are becoming widelyadopted and accepted as one of the most effective ways topositively identify people. In this paper, the Segmentation phasesof Iris recognition has been examined. The performance of theSegmentation phase could be amplified by the proposedoptimization technique- Optimized Iris Segmentation using SobelEdge Detection. By the proposed method, the overall rank-onerecognition rate of 90% is being achieved which is much betterthan reported accuracies for iris recognition in the literature.Also the proposed approach makes the overall iris recognitionsystem performance by the improvement factor of 10 fold as well.

  15. Iris Recognition Using Feature Extraction of Box Counting Fractal Dimension

    Science.gov (United States)

    Khotimah, C.; Juniati, D.

    2018-01-01

    Biometrics is a science that is now growing rapidly. Iris recognition is a biometric modality which captures a photo of the eye pattern. The markings of the iris are distinctive that it has been proposed to use as a means of identification, instead of fingerprints. Iris recognition was chosen for identification in this research because every human has a special feature that each individual is different and the iris is protected by the cornea so that it will have a fixed shape. This iris recognition consists of three step: pre-processing of data, feature extraction, and feature matching. Hough transformation is used in the process of pre-processing to locate the iris area and Daugman’s rubber sheet model to normalize the iris data set into rectangular blocks. To find the characteristics of the iris, it was used box counting method to get the fractal dimension value of the iris. Tests carried out by used k-fold cross method with k = 5. In each test used 10 different grade K of K-Nearest Neighbor (KNN). The result of iris recognition was obtained with the best accuracy was 92,63 % for K = 3 value on K-Nearest Neighbor (KNN) method.

  16. Protein structure prediction using a docking-based hierarchical folding scheme.

    Science.gov (United States)

    Kifer, Ilona; Nussinov, Ruth; Wolfson, Haim J

    2011-06-01

    The pathways by which proteins fold into their specific native structure are still an unsolved mystery. Currently, many methods for protein structure prediction are available, and most of them tackle the problem by relying on the vast amounts of data collected from known protein structures. These methods are often not concerned with the route the protein follows to reach its final fold. This work is based on the premise that proteins fold in a hierarchical manner. We present FOBIA, an automated method for predicting a protein structure. FOBIA consists of two main stages: the first finds matches between parts of the target sequence and independently folding structural units using profile-profile comparison. The second assembles these units into a 3D structure by searching and ranking their possible orientations toward each other using a docking-based approach. We have previously reported an application of an initial version of this strategy to homology based targets. Since then we have considerably enhanced our method's abilities to allow it to address the more difficult template-based target category. This allows us to now apply FOBIA to the template-based targets of CASP8 and to show that it is both very efficient and promising. Our method can provide an alternative for template-based structure prediction, and in particular, the docking-basedranking technique presented here can be incorporated into any profile-profile comparison based method. Copyright © 2011 Wiley-Liss, Inc.

  17. Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding.

    Directory of Open Access Journals (Sweden)

    Wayne K Dawson

    Full Text Available Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem. Yet neglecting pseudoknots limits the utility of such approaches. Here, an algorithm utilizing structure mapping and thermodynamics is introduced for RNA pseudoknot prediction that finds the minimum free energy and identifies information about the flexibility of the RNA. The heuristic approach takes advantage of the 5' to 3' folding direction of many biological RNA molecules and is consistent with the hierarchical folding hypothesis and the contact order model. Mapping methods are used to build and analyze the folded structure for pseudoknots and to add important 3D structural considerations. The program can predict some well known pseudoknot structures correctly. The results of this study suggest that many functional RNA sequences are optimized for proper folding. They also suggest directions we can proceed in the future to achieve even better results.

  18. Quality of the voice after injection of hyaluronic acid into the vocal fold.

    Science.gov (United States)

    Szkiełkowska, Agata; Miaśkiewicz, Beata; Remacle, Marc; Krasnodębska, Paulina; Skarżyński, Henryk

    2013-04-17

    Voice disorders resulting from glottic insufficiency are a significant clinical problem in everyday phoniatric practice. One method of treatment is injection laryngoplasty. Our study aimed to assess the voice quality of patients treated with hyaluronic acid injection into the vocal fold. We studied 25 patients suffering from dysphonia, conducting laryngological and phoniatric examination, including videostroboscopy and acoustic voice analysis, before the operation and 1, 3, and 6 months later. In all cases there was complete or almost complete glottic closure after the operation. One month after the procedure, videostroboscopic examination revealed reappearance of vocal fold vibration in 8 cases; after 3 months this had risen to 15 cases. Perceptual voice quality (as assessed by the GRBAS scale) in patients with glottic insufficiency was improved. The most significant improvement was obtained 1 month after surgery (p=0.0002), and within the next months further statistically significant improvements (p=0.000002) were noted. Multidimensional voice analysis showed statistically significant and rapid improvement in frequency parameters, especially vFo. Other parameters were also improved 3 and 6 months after surgery. Injection of hyaluronic acid into the vocal fold improves phonatory functions of the larynx and the quality of voice in patients with glottic insufficiency. It may be a safe and conservative method for treatment of voice disorders. Hyaluronic acid injection to the vocal fold is an easy, effective, and fast method for restoration of good voice quality.

  19. Binding-induced folding of prokaryotic ubiquitin-like protein on the mycobacterium proteasomal ATPase targets substrates for degradation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, T.; Li, H.; Darwin, K. H.

    2010-11-01

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.

  20. Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation

    Science.gov (United States)

    Wang, Tao; Darwin, K. Heran; Li, Huilin

    2010-01-01

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analogue of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein bearing little sequence or structural resemblance to the highly structured ubiquitin. Thus it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled-coils that recognize Pup. Mpa binds unstructured Pup via hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an α-helix in Pup. Our work revealed a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This critical difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment of tuberculosis. PMID:20953180