Scalable flow-sensitive pointer analysis for fava with strong updates

The ability to perform strong updates is the main contributor to the precision of flow-sensitive pointer analysis algorithms. Traditional flow-sensitive pointer analyses cannot strongly update pointers residing in the heap. This is a severe restriction for Java programs. In this paper, we propose a new flow-sensitive pointer analysis algorithm for Java that can perform strong updates on heap-based pointers effectively. Instead of points-to graphs, we represent our points-to information as maps from access paths to sets of abstract objects. We have implemented our analysis and run it on several large Java benchmarks. The results show considerable improvement in precision over the points-to graph based flow-insensitive and flow-sensitive analyses, with reasonable running time.

Strong-coupling expansion for ultracold bosons in an optical lattice at finite temperatures in the presence of superfluidity

We develop a strong-coupling (t << U) expansion technique for calculating the density profile for bosonic atoms trapped in an optical lattice with an overall harmonic trap at finite temperature and finite on-site interaction in the presence of superfluid regions. Our results match well with quantum Monte Carlo simulations at finite temperature. We also show that the superfluid order parameter never vanishes in the trap due to the proximity effect. Our calculations for the scaled density in the vacuum-to-superfluid transition agree well with the experimental data for appropriate temperatures. We present calculations for the entropy per particle as a function of temperature which can be used to calibrate the temperature in experiments. We also discuss issues connected with the demonstration of universal quantum critical scaling in the experiments.

Computational Study of the Migration of Rhenium from One Enantioface of an Olefin to the Other Facilitated by (C-H)center dot center dot center dot Re Interactions

The migration of a metal atom in a metal olefin complex from one pi face of the olefin to the opposite pi face has been rarely documented. Gladysz and co-workers showed that such a movement is indeed possible in monosubstituted chiral Re olefin complexes, resulting in diastereomerization. Interestingly, this isomerization occurred without dissociation, and on the basis of kinetic isotope effects, the involvement of a trans C-H bond was indicated. Either oxidative addition or an agostic interaction of the vinylic C-H(D) bond with the metal could account for the experimentally observed kinetic isotope effect. In this study we compute the free energy of activation for the migration of Re from one enantioface of the olefin to the other through various pathways. On the basis of DFT calculations at the B3LYP level we show that a trans (C-H)center dot center dot center dot Re interaction and trans C-H oxidative addition provide a nondissociative path for the diastereomerization. The trans (C-H)center dot center dot center dot Re interaction path is computed to be more favorable by 2.3 kcal mol(-1) than the oxidative addition path. While direct experimental evidence was not able to discount the migration of the metal through the formation of a eta(2)-arene complex (conducted tour mechanism), computational results at the B3LYP level show that it is energetically more expensive. Surprisingly, a similar analysis carried out at the M06 level computes a lower energy path for the conducted tour mechanism and is not consistent with the experimental isotope effects observed. Metal-(C-H) interactions and oxidative additions of the metal into C-H bonds are closely separated in energy and might contribute to unusual fluxional processes such as this diastereomerization.

Protumorigenic actions of S100A2 involve regulation of PI3/Akt signaling and functional interaction with Smad3

S100 family of calcium-binding proteins is commonly upregulated in a variety of tumor types and is often associated with tumor progression. Among several S100 members, altered expression of S100A2 is a potential diagnostic and prognostic marker in cancer. Several reports suggest a role for S100A2 in metastasis. Earlier, our studies established regulation of S100A2 by transforming growth factor- (TGF-) and its involvement in TGF--mediated cancer cell invasion and migration. However, the molecular mechanisms of S100A2 protumorigenic actions remain unexplored. In the present study, we demonstrate that overexpression of S100A2 in A549 lung cancer cells induced epithelialmesenchymal transition (EMT) followed by increased invasion, loose colony morphology in soft agar and enhanced Akt phosphorylation (Ser-473). Furthermore, overexpression of S100A2 led to increased tumor growth in immunocompromised mice. In agreement, immunohistochemical examination of resected xenograft tumors established inverse correlation between S100A2 and E-cadherin expression together with activated Akt signaling. Interestingly, our study demonstrates a strong dependence of S100A2 and Smad3 in TGF--induced Hep3B cell EMT and invasion. Most importantly, we demonstrate that these effects of S100A2 are manifested through functional interaction with Smad3, which is enhanced in the presence of high calcium and TGF-. S100A2 stabilizes Smad3 and binds to its C-terminal MH2 domain. Additionally, loss of S100A2 attenuates the transcription of TGF-/Smad3 target genes involved in tumor promotion, such as PA1-1 and vimentin. Collectively, our findings present the first mechanistic details of S100A2 protumorigenic actions and its involvement in TGF--mediated cancer cell invasion and EMT.

Simulation of inhomogeneous distributions of ultracold atoms in an optical lattice via a massively parallel implementation of nonequilibrium strong-coupling perturbation theory

We present a nonequilibrium strong-coupling approach to inhomogeneous systems of ultracold atoms in optical lattices. We demonstrate its application to the Mott-insulating phase of a two-dimensional Fermi-Hubbard model in the presence of a trap potential. Since the theory is formulated self-consistently, the numerical implementation relies on a massively parallel evaluation of the self-energy and the Green's function at each lattice site, employing thousands of CPUs. While the computation of the self-energy is straightforward to parallelize, the evaluation of the Green's function requires the inversion of a large sparse 10(d) x 10(d) matrix, with d > 6. As a crucial ingredient, our solution heavily relies on the smallness of the hopping as compared to the interaction strength and yields a widely scalable realization of a rapidly converging iterative algorithm which evaluates all elements of the Green's function. Results are validated by comparing with the homogeneous case via the local-density approximation. These calculations also show that the local-density approximation is valid in nonequilibrium setups without mass transport.

Successful data recovery from oscillation photographs containing strong polycrystalline diffraction rings from an unknown small-molecule contaminant: preliminary structure solution of Salmonella typhimurium pyridoxal kinase (PdxK)

Pyridoxal kinase (PdxK; EC 2.7.1.35) belongs to the phosphotransferase family of enzymes and catalyzes the conversion of the three active forms of vitamin B-6, pyridoxine, pyridoxal and pyridoxamine, to their phosphorylated forms and thereby plays a key role in pyridoxal 5 `-phosphate salvage. In the present study, pyridoxal kinase from Salmonella typhimurium was cloned and overexpressed in Escherichia coli, purified using Ni-NTA affinity chromatography and crystallized. X-ray diffraction data were collected to 2.6 angstrom resolution at 100 K. The crystal belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unitcell parameters a = 65.11, b = 72.89, c = 107.52 angstrom. The data quality obtained by routine processing was poor owing to the presence of strong diffraction rings caused by a polycrystalline material of an unknown small molecule in all oscillation images. Excluding the reflections close to powder/polycrystalline rings provided data of sufficient quality for structure determination. A preliminary structure solution has been obtained by molecular replacement with the Phaser program in the CCP4 suite using E. coli pyridoxal kinase (PDB entry 2ddm) as the phasing model. Further refinement and analysis of the structure are likely to provide valuable insights into catalysis by pyridoxal kinases.

Metallic Nanoparticles Arranged in a Helical Geometry: Route Towards Strong and Broadband Chiro-optical Response

Recent advances in nanotechnology have paved ways to various techniques for designing and fabricating novel nanostructures incorporating noble metal nanoparticles, for a wide range of applications. The interaction of light with metal nanoparticles (NPs) can generate strongly localized electromagnetic fields (Localized Surface Plasmon Resonance, LSPR) at certain wavelengths of the incident beam. In assemblies or structures where the nanoparticles are placed in close proximity, the plasmons of individual metallic NPs can be strongly coupled to each other via Coulomb interactions. By arranging the metallic NPs in a chiral (e.g. helical) geometry, it is possible to induce collective excitations, which lead to differential optical response of the structures to right-and left circularly polarized light (e.g. Circular Dichroism - CD). Earlier reports in this field include novel techniques of synthesizing metallic nanoparticles on biological helical templates made from DNA, proteins etc. In the present work, we have developed new ways of fabricating chiral complexes made of metallic NPs, which demonstrate a very strong chiro-optical response in the visible region of the electromagnetic spectrum. Using DDA (Discrete Dipole Approximation) simulations, we theoretically studied the conditions responsible for large and broadband chiro-optical response. This system may be used for various applications, for example those related to polarization control of visible light, sensing of proteins and other chiral bio-molecules, and many more.

Small strong epsilon nets

Let P be a set of n points in R-d. A point x is said to be a centerpoint of P if x is contained in every convex object that contains more than dn/d+1 points of P. We call a point x a strong centerpoint for a family of objects C if x is an element of P is contained in every object C is an element of C that contains more than a constant fraction of points of P. A strong centerpoint does not exist even for halfspaces in R-2. We prove that a strong centerpoint exists for axis-parallel boxes in Rd and give exact bounds. We then extend this to small strong epsilon-nets in the plane. Let epsilon(S)(i) represent the smallest real number in 0, 1] such that there exists an epsilon(S)(i)-net of size i with respect to S. We prove upper and lower bounds for epsilon(S)(i) where S is the family of axis-parallel rectangles, halfspaces and disks. (C) 2014 Elsevier B.V. All rights reserved.

Performance analysis of FSO links under strong atmospheric turbulence conditions using various modulation schemes

Strong atmospheric turbulence is a major hindrance in wireless optical communication systems. In this paper, the performance of a wireless optical communication system is analyzed using different modulation formats such as, binary phase shift keying-subcarrier intensity modulation (BPSK-SIM), differential phase shift keying (DPSK), differential phase shift keying-subcarrier intensity modulation (DPSK-SIM), Mary pulse position modulation (M-PPM) and polarization shift keying (PoISK). The atmospheric channel is modeled for strong atmospheric turbulences with combined effect of turbulence and pointing errors. Novel closed-form analytical expressions for average bit error rate (BER), channel capacity and outage probability for the various modulation techniques, viz. BPSK-SIM, DPSK, DPSK-SIM, PoISK and M-PPM are derived. The simulated results for BER, channel capacity and outage probability of various modulation techniques are plotted and analyzed. (C) 2014 Elsevier GmbH. All rights reserved.

Mining Unit Tests for Discovery and Migration of Math APIs

Today's programming languages are supported by powerful third-party APIs. For a given application domain, it is common to have many competing APIs that provide similar functionality. Programmer productivity therefore depends heavily on the programmer's ability to discover suitable APIs both during an initial coding phase, as well as during software maintenance. The aim of this work is to support the discovery and migration of math APIs. Math APIs are at the heart of many application domains ranging from machine learning to scientific computations. Our approach, called MATHFINDER, combines executable specifications of mathematical computations with unit tests (operational specifications) of API methods. Given a math expression, MATHFINDER synthesizes pseudo-code comprised of API methods to compute the expression by mining unit tests of the API methods. We present a sequential version of our unit test mining algorithm and also design a more scalable data-parallel version. We perform extensive evaluation of MATHFINDER (1) for API discovery, where math algorithms are to be implemented from scratch and (2) for API migration, where client programs utilizing a math API are to be migrated to another API. We evaluated the precision and recall of MATHFINDER on a diverse collection of math expressions, culled from algorithms used in a wide range of application areas such as control systems and structural dynamics. In a user study to evaluate the productivity gains obtained by using MATHFINDER for API discovery, the programmers who used MATHFINDER finished their programming tasks twice as fast as their counterparts who used the usual techniques like web and code search, IDE code completion, and manual inspection of library documentation. For the problem of API migration, as a case study, we used MATHFINDER to migrate Weka, a popular machine learning library. Overall, our evaluation shows that MATHFINDER is easy to use, provides highly precise results across several math APIs and application domains even with a small number of unit tests per method, and scales to large collections of unit tests.

Strain-induced electronic phase transition and strong enhancement of thermopower of TiS2

Using first-principles density functional theory calculations, we show a semimetal to semiconducting electronic phase transition for bulk TiS2 by applying uniform biaxial tensile strain. This electronic phase transition is triggered by charge transfer from Ti to S, which eventually reduces the overlap between Ti-(d) and S-(p) orbitals. The electronic transport calculations show a large anisotropy in electrical conductivity and thermopower, which is due to the difference in the effective masses along the in-plane and out-of-plane directions. Strain-induced opening of band gap together with changes in dispersion of bands lead to threefold enhancement in thermopower for both p-and n-type TiS2. We further demonstrate that the uniform tensile strain, which enhances the thermoelectric performance, can be achieved by doping TiS2 with larger iso-electronic elements such as Zr or Hf at Ti sites.

On strong centerpoints

Let P be a set of n points in R-d and F be a family of geometric objects. We call a point x is an element of P a strong centerpoint of P w.r.t..F if x is contained in all F is an element of F that contains more than cn points of P, where c is a fixed constant. A strong centerpoint does not exist even when F is the family of halfspaces in the plane. We prove the existence of strong centerpoints with exact constants for convex polytopes defined by a fixed set of orientations. We also prove the existence of strong centerpoints for abstract set systems with bounded intersection. (C) 2014 Elsevier B.V. All rights reserved.

Novel anti IGFBP2 single chain variable fragment inhibits glioma cell migration and invasion

Insulin like growth factor binding protein 2 (IGFBP2) is highly up regulated in glioblastoma (GBM) tissues and has been one of the prognostic indicators. There are compelling evidences suggesting important roles for IGFBP2 in glioma cell proliferation, migration and invasion. Extracellular IGFBP2 through its carboxy terminal arginine glycine aspartate (RGD) motif can bind to cell surface alpha 5 beta 1 integrins and activate pathways downstream to integrin signaling. This IGFBP2 activated integrin signaling is known to play a crucial role in IGFBP2 mediated invasion of glioma cells. Hence a molecular inhibitor of carboxy terminal domain of IGFBP2 which can inhibit IGFBP2-cell surface interaction is of great therapeutic importance. In an attempt to develop molecular inhibitors of IGFBP2, we screened single chain variable fragment (scFv) phage display libraries, Tomlinson I (Library size 1.47 x 10(8)) and Tomlinson J (Library size 1.37 x 10(8)) using human recombinant IGFBP2. After screening we obtained three IGFBP2 specific binders out of which one scFv B7J showed better binding to IGFBP2 at its carboxy terminal domain, blocked IGFBP2-cell surface association, reduced activity of matrix metalloprotease 2 in the conditioned medium of glioma cells and inhibited IGFBP2 induced migration and invasion of glioma cells. We demonstrate for the first time that in vitro inhibition of extracellular IGFBP2 activity by using human scFv results in significant reduction of glioma cell migration and invasion. Therefore, the inhibition of IGFBP2 can serve as a potential therapeutic strategy in the management of GBM.