Precise Slicing in Imperative Programs via Term-Rewriting and Abstract Interpretation

We propose a new approach for producing precise constrained slices of programs in a language such as C. We build upon a previous approach for this problem, which is based on term-rewriting, which primarily targets loop-free fragments and is fully precise in this setting. We incorporate abstract interpretation into term-rewriting, using a given arbitrary abstract lattice, resulting in a novel technique for slicing loops whose precision is linked to the power of the given abstract lattice. We address pointers in a first-class manner, including when they are used within loops to traverse and update recursive data structures. Finally, we illustrate the comparative precision of our slices over those of previous approaches using representative examples.

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background: The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better. Results: Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions. Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family. Conclusions: CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.

Compiler/Runtime Framework for Dynamic Dataflow Parallelization of Tiled Programs

Task-parallel languages are increasingly popular. Many of them provide expressive mechanisms for intertask synchronization. For example, OpenMP 4.0 will integrate data-driven execution semantics derived from the StarSs research language. Compared to the more restrictive data-parallel and fork-join concurrency models, the advanced features being introduced into task-parallelmodels in turn enable improved scalability through load balancing, memory latency hiding, mitigation of the pressure on memory bandwidth, and, as a side effect, reduced power consumption. In this article, we develop a systematic approach to compile loop nests into concurrent, dynamically constructed graphs of dependent tasks. We propose a simple and effective heuristic that selects the most profitable parallelization idiom for every dependence type and communication pattern. This heuristic enables the extraction of interband parallelism (cross-barrier parallelism) in a number of numerical computations that range from linear algebra to structured grids and image processing. The proposed static analysis and code generation alleviates the burden of a full-blown dependence resolver to track the readiness of tasks at runtime. We evaluate our approach and algorithms in the PPCG compiler, targeting OpenStream, a representative dataflow task-parallel language with explicit intertask dependences and a lightweight runtime. Experimental results demonstrate the effectiveness of the approach.

Synthesis, X-ray structure and in vitro cytotoxicity studies of Cu(I/II) complexes of thiosemicarbazone: special emphasis on their interactions with DNA

4-(p-X-phenyl)thiosemicarbazone of napthaldehyde {where X = Cl (HL1) and X = Br (HL2)}, thiosemicarbazone of quinoline-2-carbaldehyde (HL3) and 4-(p-fluorophenyl) thiosemicarbazone of salicylaldehyde (H2L4) and their copper(I) {Cu(HL1)(PPh3)(2)Br]center dot CH3CN (1) and Cu(HL2)(PPh3)(2)Cl]center dot DMSO (2)} and copper(II) {((Cu2L2Cl)-Cl-3)(2)(mu-Cl)(2)]center dot 2H(2)O (3) and Cu(L-4)(Py)] (4)} complexes are reported herein. The synthesized ligands and their copper complexes were successfully characterized by elemental analysis, cyclic voltammetry, NMR, ESI-MS, IR and UV-Vis spectroscopy. Molecular structures of all the Cu(I) and Cu(II) complexes have been determined by X-ray crystallography. All the complexes (1-4) were tested for their ability to exhibit DNA-binding and - cleavage activity. The complexes effectively interact with CT-DNA possibly by groove binding mode, with binding constants ranging from 10(4) to 10(5) M-1. Among the complexes, 3 shows the highest chemical (60%) as well as photo-induced (80%) DNA cleavage activity against pUC19 DNA. Finally, the in vitro antiproliferative activity of all the complexes was assayed against the HeLa cell line. Some of the complexes have proved to be as active as the clinical referred drugs, and the greater potency of 3 may be correlated with its aqueous solubility and the presence of the quinonoidal group in the thiosemicarbazone ligand coordinated to the metal.