A transient detection algorithm for audio using iterative analysis of STFT

We propose an iterative algorithm to detect transient segments in audio signals. Short time Fourier transform(STFT) is used to detect rapid local changes in the audio signal. The algorithm has two steps that iteratively - (a) calculate a function of the STFT and (b) build a transient signal. A dynamic thresholding scheme is used to locate the potential positions of transients in the signal. The iterative procedure ensures that genuine transients are built up while the localised spectral noise are suppressed by using an energy criterion. The extracted transient signal is later compared to a ground truth dataset. The algorithm performed well on two databases. On the EBU-SQAM database of monophonic sounds, the algorithm achieved an F-measure of 90% while on our database of polyphonic audio an F-measure of 91% was achieved. This technique is being used as a preprocessing step for a tempo analysis algorithm and a TSR (Transients + Sines + Residue) decomposition scheme.

Method of designing an access mechanism for social networks

The rapid development of communication and networking has lessened geographical boundaries among actors in social networks. In social networks, actors often want to access databases depending upon their access rights, privacy, context, privileges, etc. Managing and handling knowledge based access of actors is complex and hard for which broad range of technologies need to be called. Access based on dynamic access rights and circumstances of actors impose major tasks on access systems. In this paper, we present an Access Mechanism for Social Networks (AMSN) to render access to actors over databases taking privacy and status of actors into consideration. The designed AMSN model is tested over an Agriculture Social Network (ASN) which utilises distinct access rights and privileges of actors related to the agriculture occupation, and provides access to actors over databases.

DoSA: Database of Structural Alignments

Protein structure alignment is a crucial step in protein structure-function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159 780 conformationally similar and 56 140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function.

A naturally occurring amino acid substitution in the voltage-dependent sodium channel selectivity filter affects channel gating

The pore of sodium channels contains a selectivity filter made of 4 amino acids, D/E/K/A. In voltage sensitive sodium channel (Nav) channels from jellyfish to human the fourth amino acid is Ala. This Ala, when mutated to Asp, promotes slow inactivation. In some Nav channels of pufferfishes, the Ala is replaced with Gly. We studied the biophysical properties of an Ala-to-Gly substitution (A1529G) in rat Nav1.4 channel expressed in Xenopus oocytes alone or with a beta 1 subunit. The Ala-to-Gly substitution does not affect monovalent cation selectivity and positively shifts the voltage-dependent inactivation curve, although co-expression with a beta 1 subunit eliminates the difference between A1529G and WT. There is almost no difference in channel fast inactivation, but the beta 1 subunit accelerates WT current inactivation significantly more than it does the A1529G channels. The Ala-to-Gly substitution mainly influences the rate of recovery from slow inactivation. Again, the beta 1 subunit is less effective on speeding recovery of A1529G than the WT. We searched Nav channels in numerous databases and noted at least four other independent Ala-to-Gly substitutions in Nav channels in teleost fishes. Thus, the Ala-to-Gly substitution occurs more frequently than previously realized, possibly under selection for alterations of channel gating.

Epoch extraction based on integrated linear prediction residual using plosion index

Epoch is defined as the instant of significant excitation within a pitch period of voiced speech. Epoch extraction continues to attract the interest of researchers because of its significance in speech analysis. Existing high performance epoch extraction algorithms require either dynamic programming techniques or a priori information of the average pitch period. An algorithm without such requirements is proposed based on integrated linear prediction residual (ILPR) which resembles the voice source signal. Half wave rectified and negated ILPR (or Hilbert transform of ILPR) is used as the pre-processed signal. A new non-linear temporal measure named the plosion index (PI) has been proposed for detecting `transients' in speech signal. An extension of PI, called the dynamic plosion index (DPI) is applied on pre-processed signal to estimate the epochs. The proposed DPI algorithm is validated using six large databases which provide simultaneous EGG recordings. Creaky and singing voice samples are also analyzed. The algorithm has been tested for its robustness in the presence of additive white and babble noise and on simulated telephone quality speech. The performance of the DPI algorithm is found to be comparable or better than five state-of-the-art techniques for the experiments considered.

Approximate Nearest Neighbour Field based Optic Disk Detection

Approximate Nearest Neighbour Field maps are commonly used by computer vision and graphics community to deal with problems like image completion, retargetting, denoising, etc. In this paper, we extend the scope of usage of ANNF maps to medical image analysis, more specifically to optic disk detection in retinal images. In the analysis of retinal images, optic disk detection plays an important role since it simplifies the segmentation of optic disk and other retinal structures. The proposed approach uses FeatureMatch, an ANNF algorithm, to find the correspondence between a chosen optic disk reference image and any given query image. This correspondence provides a distribution of patches in the query image that are closest to patches in the reference image. The likelihood map obtained from the distribution of patches in query image is used for optic disk detection. The proposed approach is evaluated on five publicly available DIARETDB0, DIARETDB1, DRIVE, STARE and MESSIDOR databases, with total of 1540 images. We show, experimentally, that our proposed approach achieves an average detection accuracy of 99% and an average computation time of 0.2 s per image. (C) 2013 Elsevier Ltd. All rights reserved.

Detection of the closure-burst transitions of stops and affricates in continuous speech using the plosion index

Automatic and accurate detection of the closure-burst transition events of stops and affricates serves many applications in speech processing. A temporal measure named the plosion index is proposed to detect such events, which are characterized by an abrupt increase in energy. Using the maxima of the pitch-synchronous normalized cross correlation as an additional temporal feature, a rule-based algorithm is designed that aims at selecting only those events associated with the closure-burst transitions of stops and affricates. The performance of the algorithm, characterized by receiver operating characteristic curves and temporal accuracy, is evaluated using the labeled closure-burst transitions of stops and affricates of the entire TIMIT test and training databases. The robustness of the algorithm is studied with respect to global white and babble noise as well as local noise using the TIMIT test set and on telephone quality speech using the NTIMIT test set. For these experiments, the proposed algorithm, which does not require explicit statistical training and is based on two one-dimensional temporal measures, gives a performance comparable to or better than the state-of-the-art methods. In addition, to test the scalability, the algorithm is applied on the Buckeye conversational speech corpus and databases of two Indian languages. (C) 2014 Acoustical Society of America.

Filling-in Void and Sparse Regions in Protein Sequence Space by Protein-Like Artificial Sequences Enables Remarkable Enhancement in Remote Homology Detection Capability

Protein functional annotation relies on the identification of accurate relationships, sequence divergence being a key factor. This is especially evident when distant protein relationships are demonstrated only with three-dimensional structures. To address this challenge, we describe a computational approach to purposefully bridge gaps between related protein families through directed design of protein-like ``linker'' sequences. For this, we represented SCOP domain families, integrated with sequence homologues, as multiple profiles and performed HMM-HMM alignments between related domain families. Where convincing alignments were achieved, we applied a roulette wheel-based method to design 3,611,010 protein-like sequences corresponding to 374 SCOP folds. To analyze their ability to link proteins in homology searches, we used 3024 queries to search two databases, one containing only natural sequences and another one additionally containing designed sequences. Our results showed that augmented database searches showed up to 30% improvement in fold coverage for over 74% of the folds, with 52 folds achieving all theoretically possible connections. Although sequences could not be designed between some families, the availability of designed sequences between other families within the fold established the sequence continuum to demonstrate 373 difficult relationships. Ultimately, as a practical and realistic extension, we demonstrate that such protein-like sequences can be ``plugged-into'' routine and generic sequence database searches to empower not only remote homology detection but also fold recognition. Our richly statistically supported findings show that complementary searches in both databases will increase the effectiveness of sequence-based searches in recognizing all homologues sharing a common fold. (C) 2013 Elsevier Ltd. All rights reserved.

PLIC: protein-ligand interaction clusters

Most of the biological processes are governed through specific protein-ligand interactions. Discerning different components that contribute toward a favorable protein-ligand interaction could contribute significantly toward better understanding protein function, rationalizing drug design and obtaining design principles for protein engineering. The Protein Data Bank (PDB) currently hosts the structure of similar to 68 000 protein-ligand complexes. Although several databases exist that classify proteins according to sequence and structure, a mere handful of them annotate and classify protein-ligand interactions and provide information on different attributes of molecular recognition. In this study, an exhaustive comparison of all the biologically relevant ligand-binding sites (84 846 sites) has been conducted using PocketMatch: a rapid, parallel, in-house algorithm. PocketMatch quantifies the similarity between binding sites based on structural descriptors and residue attributes. A similarity network was constructed using binding sites whose PocketMatch scores exceeded a high similarity threshold (0.80). The binding site similarity network was clustered into discrete sets of similar sites using the Markov clustering (MCL) algorithm. Furthermore, various computational tools have been used to study different attributes of interactions within the individual clusters. The attributes can be roughly divided into (i) binding site characteristics including pocket shape, nature of residues and interaction profiles with different kinds of atomic probes, (ii) atomic contacts consisting of various types of polar, hydrophobic and aromatic contacts along with binding site water molecules that could play crucial roles in protein-ligand interactions and (iii) binding energetics involved in interactions derived from scoring functions developed for docking. For each ligand-binding site in each protein in the PDB, site similarity information, clusters they belong to and description of site attributes are provided as a relational database-protein-ligand interaction clusters (PLIC).

Some Thermodynamic Aspects of the Oxides of Chromium

To understand Cr emissions from slag melts to a vapor phase, an assessment of the stabilities of the chromium oxides at high temperatures has been carried out. The objective of the present study is to present a set of consistent data corresponding to the thermodynamic properties of the oxides of chromium, with special reference to the emission of hexavalent chromium from slags. In the current work, critical analysis of the experimental data available and a third analysis in the case of Cr2O3 have been carried out. Commercial databases, Fact Sage and ThermoCalc along with NIST-JANAF Thermochemical Tables, have been used for the analysis and comparisons of the results that are presented. The significant discrepancies in the available data have been pointed out. The data from NIST-JANAF Thermochemical Tables have been found to provide a set of consistent data for the various chromium oxides. An Ellingham diagram and the equations for the Delta G degrees (standard Gibbs free energy change) of formation of CrOx have been proposed. The present analysis shows that CrO3(g) is likely to be emitted from slag melts at high oxygen partial pressures. (C) The Minerals, Metals & Materials Society and ASM International 2014

Ontology analysis of global gene expression differences of human bone marrow stromal cells cultured on 3D scaffolds or 2D films

Differences in gene expression of human bone marrow stromal cells (hBMSCs) during culture in three-dimensional (3D) nanofiber scaffolds or on two-dimensional (2D) films were investigated via pathway analysis of microarray mRNA expression profiles. Previous work has shown that hBMSC culture in nanofiber scaffolds can induce osteogenic differentiation in the absence of osteogenic supplements (OS). Analysis using ontology databases revealed that nanofibers and OS regulated similar pathways and that both were enriched for TGF-beta and cell-adhesion/ECM-receptor pathways. The most notable difference between the two was that nanofibers had stronger enrichment for cell-adhesion/ECM-receptor pathways. Comparison of nanofibers scaffolds with flat films yielded stronger differences in gene expression than comparison of nanofibers made from different polymers, suggesting that substrate structure had stronger effects on cell function than substrate polymer composition. These results demonstrate that physical (nanofibers) and biochemical (OS) signals regulate similar ontological pathways, suggesting that these cues use similar molecular mechanisms to control hBMSC differentiation. Published by Elsevier Ltd.

Phylogenetic relationships and classification of thiolases and thiolase-like proteins of Mycobacterium tuberculosis and Mycobacterium smegmatis

Thiolases are enzymes involved in lipid metabolism. Thiolases remove the acetyl-CoA moiety from 3-ketoacyl-CoAs in the degradative reaction. They can also catalyze the reverse Claisen condensation reaction, which is the first step of biosynthetic processes such as the biosynthesis of sterols and ketone bodies. In human, six distinct thiolases have been identified. Each of these thiolases is different from the other with respect to sequence, oligomeric state, substrate specificity and subcellular localization. Four sequence fingerprints, identifying catalytic loops of thiolases, have been described. In this study genome searches of two mycobacterial species (Mycobacterium tuberculosis and Mycobacterium smegmatis), were carried out, using the six human thiolase sequences as queries. Eight and thirteen different thiolase sequences were identified in M. tuberculosis and M. smegmatis, respectively. In addition, thiolase-like proteins (one encoded in the Mtb and two in the Msm genome) were found. The purpose of this study is to classify these mostly uncharacterized thiolases and thiolase-like proteins. Several other sequences obtained by searches of genome databases of bacteria, mammals and the parasitic protist family of the Trypanosomatidae were included in the analysis. Thiolase-like proteins were also found in the trypanosomatid genomes, but not in those of mammals. In order to study the phylogenetic relationships at a high confidence level, additional thiolase sequences were included such that a total of 130 thiolases and thiolase-like protein sequences were used for the multiple sequence alignment. The resulting phylogenetic tree identifies 12 classes of sequences, each possessing a characteristic set of sequence fingerprints for the catalytic loops. From this analysis it is now possible to assign the mycobacterial thiolases to corresponding homologues in other kingdoms of life. The results of this bioinformatics analysis also show interesting differences between the distributions of M. tuberculosis and M. smegmatis thiolases over the 12 different classes. (C) 2014 Elsevier Ltd. All rights reserved.

Performance enhancement of online handwritten Tamil symbol recognition with reevaluation techniques

In this article, we aim at reducing the error rate of the online Tamil symbol recognition system by employing multiple experts to reevaluate certain decisions of the primary support vector machine classifier. Motivated by the relatively high percentage of occurrence of base consonants in the script, a reevaluation technique has been proposed to correct any ambiguities arising in the base consonants. Secondly, a dynamic time-warping method is proposed to automatically extract the discriminative regions for each set of confused characters. Class-specific features derived from these regions aid in reducing the degree of confusion. Thirdly, statistics of specific features are proposed for resolving any confusions in vowel modifiers. The reevaluation approaches are tested on two databases (a) the isolated Tamil symbols in the IWFHR test set, and (b) the symbols segmented from a set of 10,000 Tamil words. The recognition rate of the isolated test symbols of the IWFHR database improves by 1.9 %. For the word database, the incorporation of the reevaluation step improves the symbol recognition rate by 3.5 % (from 88.4 to 91.9 %). This, in turn, boosts the word recognition rate by 11.9 % (from 65.0 to 76.9 %). The reduction in the word error rate has been achieved using a generic approach, without the incorporation of language models.

Key challenges for the creation and maintenance of specialist protein resources

As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with professional staff and long-term funding. Specialist protein resources fill an important middle ground, providing interactive web interfaces to their databases for a focused topic or family of proteins, using specialized approaches that are not feasible in the major reference databases. Many are labors of love, run by a single lab with little or no dedicated funding and there are many challenges to building and maintaining them. This perspective arose from a meeting of several specialist protein resources and major reference databases held at the Wellcome Trust Genome Campus (Cambridge, UK) on August 11 and 12, 2014. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. In laying out these challenges, we aim to inform users about how these issues impact our resources and illustrate ways in which our working together could enhance their accuracy, currency, and overall value. Proteins 2015; 83:1005-1013. (c) 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Voice source characterization using pitch synchronous discrete cosine transform for speaker identification

A characterization of the voice source (VS) signal by the pitch synchronous (PS) discrete cosine transform (DCT) is proposed. With the integrated linear prediction residual (ILPR) as the VS estimate, the PS DCT of the ILPR is evaluated as a feature vector for speaker identification (SID). On TIMIT and YOHO databases, using a Gaussian mixture model (GMM)-based classifier, it performs on par with existing VS-based features. On the NIST 2003 database, fusion with a GMM-based classifier using MFCC features improves the identification accuracy by 12% in absolute terms, proving that the proposed characterization has good promise as a feature for SID studies. (C) 2015 Acoustical Society of America