A survey on compressed domain video analysis techniques

Image and video analysis requires rich features that can characterize various aspects of visual information. These rich features are typically extracted from the pixel values of the images and videos, which require huge amount of computation and seldom useful for real-time analysis. On the contrary, the compressed domain analysis offers relevant information pertaining to the visual content in the form of transform coefficients, motion vectors, quantization steps, coded block patterns with minimal computational burden. The quantum of work done in compressed domain is relatively much less compared to pixel domain. This paper aims to survey various video analysis efforts published during the last decade across the spectrum of video compression standards. In this survey, we have included only the analysis part, excluding the processing aspect of compressed domain. This analysis spans through various computer vision applications such as moving object segmentation, human action recognition, indexing, retrieval, face detection, video classification and object tracking in compressed videos.

Relaxation Labeling with Learning Automata

Relaxation labeling processes are a class of mechanisms that solve the problem of assigning labels to objects in a manner that is consistent with respect to some domain-specific constraints. We reformulate this using the model of a team of learning automata interacting with an environment or a high-level critic that gives noisy responses as to the consistency of a tentative labeling selected by the automata. This results in an iterative linear algorithm that is itself probabilistic. Using an explicit definition of consistency we give a complete analysis of this probabilistic relaxation process using weak convergence results for stochastic algorithms. Our model can accommodate a range of uncertainties in the compatibility functions. We prove a local convergence result and show that the point of convergence depends both on the initial labeling and the constraints. The algorithm is implementable in a highly parallel fashion.

Identification of Specific DNA Binding Residues in the TCP Family of Transcription Factors in Arabidopsis

The TCP transcription factors control multiple developmental traits in diverse plant species. Members of this family share an similar to 60-residue-long TCP domain that binds to DNA. The TCP domain is predicted to form a basic helix-loop-helix ( bHLH) structure but shares little sequence similarity with canonical bHLH domain. This classifies the TCP domain as a novel class of DNA binding domain specific to the plant kingdom. Little is known about how the TCP domain interacts with its target DNA. We report biochemical characterization and DNA binding properties of a TCP member in Arabidopsis thaliana, TCP4. We have shown that the 58-residue domain of TCP4 is essential and sufficient for binding to DNA and possesses DNA binding parameters comparable to canonical bHLH proteins. Using a yeast-based random mutagenesis screen and site-directed mutants, we identified the residues important for DNA binding and dimer formation. Mutants defective in binding and dimerization failed to rescue the phenotype of an Arabidopsis line lacking the endogenous TCP4 activity. By combining structure prediction, functional characterization of the mutants, and molecular modeling, we suggest a possible DNA binding mechanism for this class of transcription factors.

Tiling stencil computations to maximize parallelism

Most stencil computations allow tile-wise concurrent start, i.e., there always exists a face of the iteration space and a set of tiling hyperplanes such that all tiles along that face can be started concurrently. This provides load balance and maximizes parallelism. However, existing automatic tiling frameworks often choose hyperplanes that lead to pipelined start-up and load imbalance. We address this issue with a new tiling technique that ensures concurrent start-up as well as perfect load-balance whenever possible. We first provide necessary and sufficient conditions on tiling hyperplanes to enable concurrent start for programs with affine data accesses. We then provide an approach to find such hyperplanes. Experimental evaluation on a 12-core Intel Westmere shows that our code is able to outperform a tuned domain-specific stencil code generator by 4% to 27%, and previous compiler techniques by a factor of 2x to 10.14x.

Interaction of Sesbania mosaic virus (SeMV) RNA-dependent RNA polymerase (RdRp) with the p10 domain of polyprotein 2a and its implications in SeMV replication

Identification of viral encoded proteins that interact with RNA-dependent RNA polymerase (RdRp) is an important step towards unraveling the mechanism of replication. Sesbania mosaic virus (SeMV) RdRp was shown to interact strongly with p10 domain of polyprotein 2a and moderately with the protease domain. Mutational analysis suggested that the C-terminal disordered domain of RdRp is involved in the interaction with p10. Coexpression of full length RdRp and p10 resulted in formation of RdRp-p10 complex which showed significantly higher polymerase activity than RdRp alone. Interestingly, C Delta 43 RdRp also showed a similar increase in activity. Thus, p10 acts as a positive regulator of RdRp by interacting with the C-terminal disordered domain of RdRp. (C) 2014 The Authors. Published by Elsevier B.V.

Segregating Discourse Segments from Engineering Documents for Knowledge Acquisition

The broader goal of the research being described here is to automatically acquire diagnostic knowledge from documents in the domain of manual and mechanical assembly of aircraft structures. These documents are treated as a discourse used by experts to communicate with others. It therefore becomes possible to use discourse analysis to enable machine understanding of the text. The research challenge addressed in the paper is to identify documents or sections of documents that are potential sources of knowledge. In a subsequent step, domain knowledge will be extracted from these segments. The segmentation task requires partitioning the document into relevant segments and understanding the context of each segment. In discourse analysis, the division of a discourse into various segments is achieved through certain indicative clauses called cue phrases that indicate changes in the discourse context. However, in formal documents such language may not be used. Hence the use of a domain specific ontology and an assembly process model is proposed to segregate chunks of the text based on a local context. Elements of the ontology/model, and their related terms serve as indicators of current context for a segment and changes in context between segments. Local contexts are aggregated for increasingly larger segments to identify if the document (or portions of it) pertains to the topic of interest, namely, assembly. Knowledge acquired through such processes enables acquisition and reuse of knowledge during any part of the lifecycle of a product.

Immunological cross-reactivity of mycobacterial topoisomerase I and divergence from other bacteria

Mycobacterium smegmatis topoisomerase I exhibits several distinctive characteristics among all topoisomerases. The enzyme is devoid of Zn2+fingers found typically in other bacterial type I topoisomerases and binds DNA in a site-specific manner. Using polyclonal antibodies, we demonstrate the high degree of relatedness of the enzyme across mycobacteria but not other bacteria. This absence of cross-reactivity from other bacteria indicates that mycobacterial topoisomerase I has diverged from Escherichia coli and other bacteria. We have investigated further the immunological properties of the enzyme by raising a panel of monoclonal antibodies that recognises different antigenically active regions of the enzyme and binds it with widely varied affinity. Inhibition of a C-terminal domain-specific antibody binding by enzyme-specific and non-specific oligonucleotides suggests the possibility of using these monoclonal antibodies to probe the structure, function and in vivo role of the enzyme.

Critical behavior of the aqueous electrolytic system 3-methylpyridine+D2O+NaBr

The system 3-methylpyridine(3MP)+water(H2O)+NaBr has been the subject of an intense scientific debate since the work of Jacob [Phys. Rev. E. 58, 2188 (1988)] and Anisimov [Phys. Rev. Lett. 85, 2336 (2000)]. The crossover critical behavior of this system seemed to show remarkable sensitivity to the weight fraction (X) of the ionic impurity NaBr. In the range X <= 0.10 the system displayed Ising behavior and a pronounced crossover to mean-field behavior in the range 0.10 <= X <= 0.16. A complete mean-field behavior was observed at X=0.17, a result that was later attributed to the existence of long-living nonequilibrium states in this system [Kostko , Phys. Rev. E. 70, 026118 (2004)]. In this paper, we report the near-critical behavior of osmotic susceptibility in the isotopically related ternary system, 3MP+heavy water(D2O)+NaBr. Detailed light-scattering experiments performed at exactly the same NaBr concentrations as investigated by Jacob reveal that the system 3MP+D2O+NaBr shows a simple Ising-type critical behavior with gamma similar or equal to 1.24 and nu similar or equal to 0.63 over the entire NaBr concentration range 0 <= X <= 0.1900. The crossover behavior is predominantly nonmonotonic and is completed well outside the critical domain. An analysis in terms of the effective susceptibility exponent (gamma(eff)) reveals that the crossover behavior is nonmonotonic for 0 <= X <= 0.1793 and tends to become monotonic for X > 0.1793. The correlation length amplitude xi(o), has a value of similar or equal to 2 A for 0.0250 <= X <= 0.1900, whereas for X=0, xi(o)similar or equal to 3.179 A. Since isotopic H -> D substitution is not expected to change the critical behavior of the system, our results support the recent results obtained by Kostko [Phys. Rev. E. 70, 026118 (2004)] that 3MP+H2O+NaBr exhibits universal Ising-type critical behavior typical for other aqueous solutions.

Falcon: A Graph Manipulation Language for Heterogeneous Systems

Graph algorithms have been shown to possess enough parallelism to keep several computing resources busy-even hundreds of cores on a GPU. Unfortunately, tuning their implementation for efficient execution on a particular hardware configuration of heterogeneous systems consisting of multicore CPUs and GPUs is challenging, time consuming, and error prone. To address these issues, we propose a domain-specific language (DSL), Falcon, for implementing graph algorithms that (i) abstracts the hardware, (ii) provides constructs to write explicitly parallel programs at a higher level, and (iii) can work with general algorithms that may change the graph structure (morph algorithms). We illustrate the usage of our DSL to implement local computation algorithms (that do not change the graph structure) and morph algorithms such as Delaunay mesh refinement, survey propagation, and dynamic SSSP on GPU and multicore CPUs. Using a set of benchmark graphs, we illustrate that the generated code performs close to the state-of-the-art hand-tuned implementations.

PolyMage: Automatic Optimization for Image Processing Pipelines

This paper presents the design and implementation of PolyMage, a domain-specific language and compiler for image processing pipelines. An image processing pipeline can be viewed as a graph of interconnected stages which process images successively. Each stage typically performs one of point-wise, stencil, reduction or data-dependent operations on image pixels. Individual stages in a pipeline typically exhibit abundant data parallelism that can be exploited with relative ease. However, the stages also require high memory bandwidth preventing effective utilization of parallelism available on modern architectures. For applications that demand high performance, the traditional options are to use optimized libraries like OpenCV or to optimize manually. While using libraries precludes optimization across library routines, manual optimization accounting for both parallelism and locality is very tedious. The focus of our system, PolyMage, is on automatically generating high-performance implementations of image processing pipelines expressed in a high-level declarative language. Our optimization approach primarily relies on the transformation and code generation capabilities of the polyhedral compiler framework. To the best of our knowledge, this is the first model-driven compiler for image processing pipelines that performs complex fusion, tiling, and storage optimization automatically. Experimental results on a modern multicore system show that the performance achieved by our automatic approach is up to 1.81x better than that achieved through manual tuning in Halide, a state-of-the-art language and compiler for image processing pipelines. For a camera raw image processing pipeline, our performance is comparable to that of a hand-tuned implementation.

C2 domain is responsible for targeting rice phosphoinositide specific phospholipase C

Phosphoinositide-specific phospholipase C (PLC) is involved in Ca2+ mediated signalling events that lead to altered cellular status. Using various sequence-analysis methods, we identified two conserved motifs in known PLC sequences. The identified motifs are located in the C2 domain of plant PLCs and are not found in any other protein. These motifs are specifically found in the Ca2+ binding loops and form adjoining beta strands. Further, we identified certain conserved residues that are highly distinct from corresponding residues of animal PLCs. The motifs reported here could be used to annotate plant-specific phospholipase C sequences. Furthermore, we demonstrated that the C2 domain alone is capable of targeting PLC to the membrane in response to a Ca2+ signal. We also showed that the binding event results from a change in the hydrophobicity of the C2 domain upon Ca2+ binding. Bioinformatic analyses revealed that all PLCs from Arabidopsis and rice lack a transmembrane domain, myristoylation and GPI-anchor protein modifications. Our bioinformatic study indicates that plant PLCs are located in the cytoplasm, the nucleus and the mitochondria. Our results suggest that there are no distinct isoforms of plant PLCs, as have been proposed to exist in the soluble and membrane associated fractions. The same isoform could potentially be present in both subcellular fractions, depending on the calcium level of the cytosol. Overall, these data suggest that the C2 domain of PLC plays a vital role in calcium signalling.

Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families

Background: Disulphide bridges are well known to play key roles in stability, folding and functions of proteins. Introduction or deletion of disulphides by site-directed mutagenesis have produced varying effects on stability and folding depending upon the protein and location of disulphide in the 3-D structure. Given the lack of complete understanding it is worthwhile to learn from an analysis of extent of conservation of disulphides in homologous proteins. We have also addressed the question of what structural interactions replaces a disulphide in a homologue in another homologue. Results: Using a dataset involving 34,752 pairwise comparisons of homologous protein domains corresponding to 300 protein domain families of known 3-D structures, we provide a comprehensive analysis of extent of conservation of disulphide bridges and their structural features. We report that only 54% of all the disulphide bonds compared between the homologous pairs are conserved, even if, a small fraction of the non-conserved disulphides do include cytoplasmic proteins. Also, only about one fourth of the distinct disulphides are conserved in all the members in protein families. We note that while conservation of disulphide is common in many families, disulphide bond mutations are quite prevalent. Interestingly, we note that there is no clear relationship between sequence identity between two homologous proteins and disulphide bond conservation. Our analysis on structural features at the sites where cysteines forming disulphide in one homologue are replaced by non-Cys residues show that the elimination of a disulphide in a homologue need not always result in stabilizing interactions between equivalent residues. Conclusion: We observe that in the homologous proteins, disulphide bonds are conserved only to a modest extent. Very interestingly, we note that extent of conservation of disulphide in homologous proteins is unrelated to the overall sequence identity between homologues. The non-conserved disulphides are often associated with variable structural features that were recruited to be associated with differentiation or specialisation of protein function.

Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations

Background: Phosphorylation by protein kinases is a common event in many cellular processes. Further, many kinases perform specialized roles and are regulated by non-kinase domains tethered to kinase domain. Perturbation in the regulation of kinases leads to malignancy. We have identified and analysed putative protein kinases encoded in the genome of chimpanzee which is a close evolutionary relative of human. Result: The shared core biology between chimpanzee and human is characterized by many orthologous protein kinases which are involved in conserved pathways. Domain architectures specific to chimp/human kinases have been observed. Chimp kinases with unique domain architectures are characterized by deletion of one or more non-kinase domains in the human kinases. Interestingly, counterparts of some of the multi-domain human kinases in chimp are characterized by identical domain architectures but with kinase-like non-kinase domain. Remarkably, out of 587 chimpanzee kinases no human orthologue with greater than 95% sequence identity could be identified for 160 kinases. Variations in chimpanzee kinases compared to human kinases are brought about also by differences in functions of domains tethered to the catalytic kinase domain. For example, the heterodimer forming PB1 domain related to the fold of ubiquitin/Ras-binding domain is seen uniquely tethered to PKC-like chimpanzee kinase. Conclusion: Though the chimpanzee and human are evolutionary very close, there are chimpanzee kinases with no close counterpart in the human suggesting differences in their functions. This analysis provides a direction for experimental analysis of human and chimpanzee protein kinases in order to enhance our understanding on their specific biological roles.

The Evolution of Guanylyl Cyclases as Multidomain Proteins: Conserved Features of Kinase-Cyclase Domain Fusions

Guanylyl cyclases (GCs) are enzymes that generate cyclic GMP and regulate different physiologic and developmental processes in a number of organisms. GCs possess sequence similarity to class III adenylyl cyclases (ACs) and are present as either membrane-bound receptor GCs or cytosolic soluble GCs. We sought to determine the evolution of GCs using a large-scale bioinformatic analysis and found multiple lineage-specific expansions of GC genes in the genomes of many eukaryotes. Moreover, a few GC-like proteins were identified in prokaryotes, which come fused to a number of different domains, suggesting allosteric regulation of nucleotide cyclase activity Eukaryotic receptor GCs are associated with a kinase homology domain (KHD), and phylogenetic analysis of these proteins suggest coevolution of the KHD and the associated cyclase domain as well as a conservation of the sequence and the size of the linker region between the KHD and the associated cyclase domain. Finally, we also report the existence of mimiviral proteins that contain putative active kinase domains associated with a cyclase domain, which could suggest early evolution of the fusion of these two important domains involved in signa transduction.

Analysis-By-Synthesis Based Switched Transform Domain Split Vq Using Gaussian Mixture Model

Using analysis-by-synthesis (AbS) approach, we develop a soft decision based switched vector quantization (VQ) method for high quality and low complexity coding of wideband speech line spectral frequency (LSF) parameters. For each switching region, a low complexity transform domain split VQ (TrSVQ) is designed. The overall rate-distortion (R/D) performance optimality of new switched quantizer is addressed in the Gaussian mixture model (GMM) based parametric framework. In the AbS approach, the reduction of quantization complexity is achieved through the use of nearest neighbor (NN) TrSVQs and splitting the transform domain vector into higher number of subvectors. Compared to the current LSF quantization methods, the new method is shown to provide competitive or better trade-off between R/D performance and complexity.