Transverse single spin asymmetry in e plus p(up arrow) -> e plus J/psi plus X and transverse momentum dependent evolution of the Sivers function

We extend our analysis of transverse single spin asymmetry in electroproduction of J/psi to include the effect of the scale evolution of the transverse momentum dependent (TMD) parton distribution functions and gluon Sivers function. We estimate single spin asymmetry for JLab, HERMES, COMPASS, and eRHIC energies using the color evaporation model of charmonium production, using an analytically obtained approximate solution of TMD evolution equations discussed in the literature. We find that there is a reduction in the asymmetry compared with our predictions for the earlier case considered by us, wherein the Q(2) dependence came only from DGLAP evolution of the unpolarized gluon densities and a different parametrization of the TMD Sivers function was used.

Black hole formation in fuzzy sphere collapse

We study the collapse of a fuzzy sphere, that is a spherical membrane built out of D0-branes, in the Banks-Fischler-Shenker-Susskind model. At weak coupling, as the sphere shrinks, open strings are produced. If the initial radius is large then open string production is not important and the sphere behaves classically. At intermediate initial radius the backreaction from open string production is important but the fuzzy sphere retains its identity. At small initial radius the sphere collapses to form a black hole. The crossover between the later two regimes is smooth and occurs at the correspondence point of Horowitz and Polchinski.

Expansions of tau hadronic spectral function moments in a nonpower QCD perturbation theory with tamed large order behavior

The moments of the hadronic spectral functions are of interest for the extraction of the strong coupling alpha(s) and other QCD parameters from the hadronic decays of the tau lepton. Motivated by the recent analyses of a large class of moments in the standard fixed-order and contour-improved perturbation theories, we consider the perturbative behavior of these moments in the framework of a QCD nonpower perturbation theory, defined by the technique of series acceleration by conformal mappings, which simultaneously implements renormalization-group summation and has a tame large-order behavior. Two recently proposed models of the Adler function are employed to generate the higher-order coefficients of the perturbation series and to predict the exact values of the moments, required for testing the properties of the perturbative expansions. We show that the contour-improved nonpower perturbation theories and the renormalization-group-summed nonpower perturbation theories have very good convergence properties for a large class of moments of the so-called ``reference model,'' including moments that are poorly described by the standard expansions. The results provide additional support for the plausibility of the description of the Adler function in terms of a small number of dominant renormalons.

Single electron transfer-driven multi-dimensional signal read-out function of TCNQ as an ``off-the-shelf'' detector for cyanide

Herein we report the first applications of TCNQ as a rapid and highly sensitive off-the-shelf cyanide detector. As a proof-of-concept, we have applied a kinetically selective single-electron transfer (SET) from cyanide to deep-lying LUMO orbitals of TCNQ to generate a persistently stable radical anion (TCNQ(center dot-)), under ambient condition. In contrast to the known cyanide sensors that operate with limited signal outputs, TCNQ(center dot-) offers a unique multiple signaling platform. The signal readability is facilitated through multichannel absorption in the UV-vis-NIR region and scattering-based spectroscopic methods like Raman spectroscopy and hyper Rayleigh scattering techniques. Particularly notable is the application of the intense 840 nm NIR absorption band to detect cyanide. This can be useful for avoiding background interference in the UV-vis region predominant in biological samples. We also demonstrate the fabrication of a practical electronic device with TCNQ as a detector. The device generates multiorder enhancement in current with cyanide because of the formation of the conductive TCNQ(center dot-).

Scale-dependent relationships between tree species richness and ecosystem function in forests

1. The relationship between species richness and ecosystem function, as measured by productivity or biomass, is of long-standing theoretical and practical interest in ecology. This is especially true for forests, which represent a majority of global biomass, productivity and biodiversity. 2. Here, we conduct an analysis of relationships between tree species richness, biomass and productivity in 25 forest plots of area 8-50ha from across the world. The data were collected using standardized protocols, obviating the need to correct for methodological differences that plague many studies on this topic. 3. We found that at very small spatial grains (0.04ha) species richness was generally positively related to productivity and biomass within plots, with a doubling of species richness corresponding to an average 48% increase in productivity and 53% increase in biomass. At larger spatial grains (0.25ha, 1ha), results were mixed, with negative relationships becoming more common. The results were qualitatively similar but much weaker when we controlled for stem density: at the 0.04ha spatial grain, a doubling of species richness corresponded to a 5% increase in productivity and 7% increase in biomass. Productivity and biomass were themselves almost always positively related at all spatial grains. 4. Synthesis. This is the first cross-site study of the effect of tree species richness on forest biomass and productivity that systematically varies spatial grain within a controlled methodology. The scale-dependent results are consistent with theoretical models in which sampling effects and niche complementarity dominate at small scales, while environmental gradients drive patterns at large scales. Our study shows that the relationship of tree species richness with biomass and productivity changes qualitatively when moving from scales typical of forest surveys (0.04ha) to slightly larger scales (0.25 and 1ha). This needs to be recognized in forest conservation policy and management.

MPK-09, a small molecule inspired from bioactive styryllactone restores the wild-type function of mutant p53

In the search for more efficacious and less toxic cancer drugs, the tumor suppressor p53 protein has long been a desirable therapeutic target. In the recent past, few independent studies have demonstrated that the antitumor activity of wild-type p53 can be restored in cancer cells harboring mutant form of p53 using small molecule activators. In this study, we describe a novel small molecule MPK-09, which is selective and highly potent against allele specific p53 mutations mainly, R175H, R249S, R273H, R273C, and E285K. Except E285K, all other mutations tested are among the six ``hot spot'' p53 mutations reported in majority of human cancer. Furthermore, our study conclusively demonstrates that the apoptotic activity of the small molecule MPK-09 against cancer cells harboring R273C and E285K mutations is due to restoration of the wild-type conformation to the corresponding mutant form of p53.

Transition and acoustic response of recirculation structures in an unconfined co-axial isothermal swirling flow

This paper reports the first observations of transition from a pre-vortex breakdown (Pre-VB) flowreversal to a fully developed central toroidal recirculation zone in a non-reacting, double-concentric swirling jet configuration and its response to longitudinal acoustic excitation. This transition proceeds with the formation of two intermediate, critical flow regimes. First, a partially penetrated vortex breakdown bubble (VBB) is formed that indicates the first occurrence of an enclosed structure as the centre jet penetration is suppressed by the growing outer roll-up eddy; resulting in an opposed flow stagnation region. Second, a metastable transition structure is formed that marks the collapse of inner mixing vortices. In this study, the time-averaged topological changes in the coherent recirculation structures are discussed based on the non-dimensional modified Rossby number (Ro(m)) which appears to describe the spreading of the zone of swirl influence in different flow regimes. Further, the time-mean global acoustic response of pre-VB and VBB is measured as a function of pulsing frequency using the relative aerodynamic blockage factor (i.e., maximum radial width of the inner recirculation zone). It is observed that all flow modes except VBB are structurally unstable as they exhibit severe transverse radial shrinkage (similar to 20%) at the burner Helmholtz resonant modes (100-110 Hz). In contrast, all flow regimes show positional instability as seen by the large-scale, asymmetric spatial shifting of the vortex core centres. Finally, the mixing transfer function M (f) and magnitude squared coherence lambda(2)(f) analysis is presented to determine the natural couplingmodes of the system dynamic parameters (u', p'), i.e., local acoustic response. It is seen that the pre-VB flow mode exhibits a narrow-band, low pass filter behavior with a linear response window of 100-105 Hz. However, in the VBB structure, presence of critical regions such as the opposed flow stagnation region alters the linearity range with the structure showing a response even at higher pulsing frequencies (100-300 Hz). (C) 2013 AIP Publishing LLC.

Shape-function-relationship (SFR) framework for semantic interoperability of product model

The problem of semantic interoperability arises while integrating applications in different task domains across the product life cycle. A new shape-function-relationship (SFR) framework is proposed as a taxonomy based on which an ontology is developed. Ontology based on the SFR framework, that captures explicit definition of terminology and knowledge relationships in terms of shape, function and relationship descriptors, offers an attractive approach for solving semantic interoperability issue. Since all instances of terms are based on single taxonomy with a formal classification, mapping of terms requires a simple check on the attributes used in the classification. As a preliminary study, the framework is used to develop ontology of terms used in the aero-engine domain and the ontology is used to resolve the semantic interoperability problem in the integration of design and maintenance. Since the framework allows a single term to have multiple classifications, handling context dependent usage of terms becomes possible. Automating the classification of terms and establishing the completeness of the classification scheme are being addressed presently.

The Lovasz θ function, SVMs and finding large dense subgraphs

The Lovasz θ function of a graph, is a fundamental tool in combinatorial optimization and approximation algorithms. Computing θ involves solving a SDP and is extremely expensive even for moderately sized graphs. In this paper we establish that the Lovasz θ function is equivalent to a kernel learning problem related to one class SVM. This interesting connection opens up many opportunities bridging graph theoretic algorithms and machine learning. We show that there exist graphs, which we call SVM−θ graphs, on which the Lovasz θ function can be approximated well by a one-class SVM. This leads to a novel use of SVM techniques to solve algorithmic problems in large graphs e.g. identifying a planted clique of size Θ(n√) in a random graph G(n,12). A classic approach for this problem involves computing the θ function, however it is not scalable due to SDP computation. We show that the random graph with a planted clique is an example of SVM−θ graph, and as a consequence a SVM based approach easily identifies the clique in large graphs and is competitive with the state-of-the-art. Further, we introduce the notion of a ''common orthogonal labeling'' which extends the notion of a ''orthogonal labelling of a single graph (used in defining the θ function) to multiple graphs. The problem of finding the optimal common orthogonal labelling is cast as a Multiple Kernel Learning problem and is used to identify a large common dense region in multiple graphs. The proposed algorithm achieves an order of magnitude scalability compared to the state of the art.

Examining the Effectiveness of Discriminant Function Analysis and Cluster Analysis in Species Identification of Male Field Crickets Based on Their Calling Songs

Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA) and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6-7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species classification and identification.

Structural Insights into Saccharomyces cerevisiae Msh4-Msh5 Complex Function Using Homology Modeling

The Msh4-Msh5 protein complex in eukaryotes is involved in stabilizing Holliday junctions and its progenitors to facilitate crossing over during Meiosis I. These functions of the Msh4-Msh5 complex are essential for proper chromosomal segregation during the first meiotic division. The Msh4/5 proteins are homologous to the bacterial mismatch repair protein MutS and other MutS homologs (Msh2, Msh3, Msh6). Saccharomyces cerevisiae msh4/5 point mutants were identified recently that show two fold reduction in crossing over, compared to wild-type without affecting chromosome segregation. Three distinct classes of msh4/5 point mutations could be sorted based on their meiotic phenotypes. These include msh4/5 mutations that have a) crossover and viability defects similar to msh4/5 null mutants; b) intermediate defects in crossing over and viability and c) defects only in crossing over. The absence of a crystal structure for the Msh4-Msh5 complex has hindered an understanding of the structural aspects of Msh4-Msh5 function as well as molecular explanation for the meiotic defects observed in msh4/5 mutations. To address this problem, we generated a structural model of the S. cerevisiae Msh4-Msh5 complex using homology modeling. Further, structural analysis tailored with evolutionary information is used to predict sites with potentially critical roles in Msh4-Msh5 complex formation, DNA binding and to explain asymmetry within the Msh4-Msh5 complex. We also provide a structural rationale for the meiotic defects observed in the msh4/5 point mutations. The mutations are likely to affect stability of the Msh4/5 proteins and/or interactions with DNA. The Msh4-Msh5 model will facilitate the design and interpretation of new mutational data as well as structural studies of this important complex involved in meiotic chromosome segregation.

Dielectric Function of Undoped and Doped Poly2-methoxy-5-(3 `,7 `-dimethyloctyloxy)-1,4-phenylene-vinylene] by Ellipsometry in a Wide Spectral Range

Ellipsometric measurements in a wide spectral range (from 0.05 to 6.5 eV) have been carried out on the organic semiconducting polymer, poly2-methoxy-5-(3',7'-dimethyloctyloxy)-1,4-phenylene-vinylene] (MDMO-PPV), in both undoped and doped states. The real and imaginary parts of the dielectric function and the refractive index are determined accurately, provided that the layer thickness is measured independently. After doping, the optical properties show the presence of new peaks, which could be well-resolved by spectroscopic ellipsometry. Also for the doped material, the complex refractive index, with respect to the dielectric function, has been determined. The broadening of the optical transitions is due to the delocalization of polarons at higher doping level. The detailed information about the dielectric function as well as refractive index function obtained by spectroscopic ellipsometry allows not only qualitative but also quantitative description of the optical properties of the undoped/doped polymer. For the direct characterization of the optical properties of MDMO-PPV, ellipsometry turns out to be advantageous compared to conventional reflection and transmission measurements.

Expression and function of cyclooxygenase-2 is necessary for hamster blastocyst hatching

Blastocyst hatching is critical for successful implantation leading to pregnancy. Its failure causes infertility. The phenomenon of blastocyst hatching in humans is poorly understood and the available information on this stems from studies of rodents such as mice and hamsters. We and others showed that hamster blastocyst hatching is characterized by firstly blastocyst deflation followed by a dissolution of the zona pellucida (zona) and accompanied by trophectodermal projections (TEPs). We also showed that embryo-derived cathepsins (Cat) proteases, specifically Cat-L, -B and -P act as zonalysins and are responsible for hatching. In this study, we show the expression and function of one of the potential regulators of embryogenesis, cyclooxygenase (COX)-2 during blastocyst development and hatching. The expression of COX-2 mRNA and protein was observed in 8-cell through hatched blastocyst stages and it was also localized to blastocysts TEPs. Specific COX-2 inhibitors, NS-398 and CAY-10404, inhibited blastocyst hatching; percentages achieved were only 28.4 5.3 and 32.3 5.4, respectively, compared with 90 with untreated embryos. Interestingly, inhibitor-treated blastocysts failed to deflate, normally observed during hatching. Supplementation of prostaglandins (PGs)-E-2 or -I-2 to cultured embryos reversed the inhibitors effect on hatching and also the deflation behavior. Importantly, the levels of mRNA and protein of Cat-L, -B and -P showed a significant reduction in the inhibitor-treated embryos compared with untreated embryos, although its mechanism remains to be examined. These data provide the first evidence that COX-2 is critical for blastocyst hatching in the golden hamster.

Solid-solid collapse transition in a two dimensional model molecular system

Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different energy and length scales involved in molecular systems, often mediated through a solvent. In this work we employ Monte-Carlo simulation to study the collapse transition in a model molecular system interacting via both isotropic as well as anisotropic interactions having different length and energy scales. The model we use is known as Mercedes-Benz (MB), which, for a specific set of parameters, sustains two solid phases: honeycomb and oblique. In order to study the temperature induced collapse transition, we start with a metastable honeycomb solid and induce transition by increasing temperature. High density oblique solid so formed has two characteristic length scales corresponding to isotropic and anisotropic parts of interaction potential. Contrary to the common belief and classical nucleation theory, interestingly, we find linear strip-like nucleating clusters having significantly different order and average coordination number than the bulk stable phase. In the early stage of growth, the cluster grows as a linear strip, followed by branched and ring-like strips. The geometry of growing cluster is a consequence of the delicate balance between two types of interactions, which enables the dominance of stabilizing energy over destabilizing surface energy. The nucleus of stable oblique phase is wetted by intermediate order particles, which minimizes the surface free energy. In the case of pressure induced transition at low temperature the collapsed state is a disordered solid. The disordered solid phase has diverse local quasi-stable structures along with oblique-solid like domains. (C) 2013 AIP Publishing LLC.

Form and Function of Proteins. Historical Background and the Indian Effort in Macromolecular Crystallography

Global efforts in macromolecular crystallography started in the thirties of the last century. However, definitive results began to emerge only in the late fifties and the early sixties. India has a long tradition in crystallography. The country had a head start in theoretical and computational structural biology, thanks to the efforts of G.N. Ramachandran and his colleagues in the fifties and the sixties. However, macromolecular crystallography got off the ground in India only in the eighties, particularly after the Bangalore group received adequate support from the Department of Science and Technology under their Thrust Area Programme. The Bangalore centre was also identified as a national nucleus for the development of the area in the country. Since then work in the area has spread widely and is being carried out by several groups, mainly led by scientists trained at Bangalore or their descendents, in about thirty institutions in India. In addition to the Department of Science and Technology, the effort is now supported by other agencies like the Department of Biotechnology and the Council of Scientific and Industrial Research. The problems addressed by macromolecular crystallographers in India encompass almost all aspects of modern biology. Indian efforts in macromolecular crystallography have also become an important component of the international efforts in the area.