Fourteen gene GBM prognostic signature identifies association of immune response pathway and mesenchymal subtype with high risk group

Background: Recent research on glioblastoma (GBM) has focused on deducing gene signatures predicting prognosis. The present study evaluated the mRNA expression of selected genes and correlated with outcome to arrive at a prognostic gene signature. Methods: Patients with GBM (n = 123) were prospectively recruited, treated with a uniform protocol and followed up. Expression of 175 genes in GBM tissue was determined using qRT-PCR. A supervised principal component analysis followed by derivation of gene signature was performed. Independent validation of the signature was done using TCGA data. Gene Ontology and KEGG pathway analysis was carried out among patients from TCGA cohort. Results: A 14 gene signature was identified that predicted outcome in GBM. A weighted gene (WG) score was found to be an independent predictor of survival in multivariate analysis in the present cohort (HR = 2.507; B = 0.919; p < 0.001) and in TCGA cohort. Risk stratification by standardized WG score classified patients into low and high risk predicting survival both in our cohort (p = <0.001) and TCGA cohort (p = 0.001). Pathway analysis using the most differentially regulated genes (n = 76) between the low and high risk groups revealed association of activated inflammatory/immune response pathways and mesenchymal subtype in the high risk group. Conclusion: We have identified a 14 gene expression signature that can predict survival in GBM patients. A network analysis revealed activation of inflammatory response pathway specifically in high risk group. These findings may have implications in understanding of gliomagenesis, development of targeted therapies and selection of high risk cancer patients for alternate adjuvant therapies.

Group testing based spectrum hole search using a simple sub-nyquist sampling scheme

In this paper, we consider the problem of finding a spectrum hole of a specified bandwidth in a given wide band of interest. We propose a new, simple and easily implementable sub-Nyquist sampling scheme for signal acquisition and a spectrum hole search algorithm that exploits sparsity in the primary spectral occupancy in the frequency domain by testing a group of adjacent subbands in a single test. The sampling scheme deliberately introduces aliasing during signal acquisition, resulting in a signal that is the sum of signals from adjacent sub-bands. Energy-based hypothesis tests are used to provide an occupancy decision over the group of subbands, and this forms the basis of the proposed algorithm to find contiguous spectrum holes. We extend this framework to a multi-stage sensing algorithm that can be employed in a variety of spectrum sensing scenarios, including non-contiguous spectrum hole search. Further, we provide the analytical means to optimize the hypothesis tests with respect to the detection thresholds, number of samples and group size to minimize the detection delay under a given error rate constraint. Depending on the sparsity and SNR, the proposed algorithms can lead to significantly lower detection delays compared to a conventional bin-by-bin energy detection scheme; the latter is in fact a special case of the group test when the group size is set to 1. We validate our analytical results via Monte Carlo simulations.

On the images of Sobolev spaces under the heat kernel transform on the Heisenberg group

The aim of this paper is to obtain certain characterizations for the image of a Sobolev space on the Heisenberg group under the heat kernel transform. We give three types of characterizations for the image of a Sobolev space of positive order H-m (H-n), m is an element of N-n, under the heat kernel transform on H-n, using direct sum and direct integral of Bergmann spaces and certain unitary representations of H-n which can be realized on the Hilbert space of Hilbert-Schmidt operators on L-2 (R-n). We also show that the image of Sobolev space of negative order H-s (H-n), s(> 0) is an element of R is a direct sum of two weighted Bergman spaces. Finally, we try to obtain some pointwise estimates for the functions in the image of Schwartz class on H-n under the heat kernel transform. (C) 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Revisiting the Fourier transform on the Heisenberg group

A recent theorem of S. Alesker, S. Artstein-Avidan and V. Milman characterises the Fourier transform on R-n as essentially the only transform on the space of tempered distributions which interchanges convolutions and pointwise products. In this note we study the image of the Schwartz space on the Heisenberg group under the Fourier transform and obtain a similar characterisation for the Fourier transform on the Heisenberg group.

Conserved water-mediated recognition and dynamics of NAD(+) (carboxamide group) to hIMPDH enzyme: water mimic approach toward the design of isoform-selective inhibitor

Inosine monophosphate dehydrogenase (IMPDH) enzyme involves in GMP biosynthesis pathway. Type I hIMPDH is expressed at lower levels in all cells, whereas type II is especially observed in acute myelogenous leukemia, chronic myelogenous leukemia cancer cells, and 10 ns simulation of the IMP-NAD(+) complex structures (PDB ID. 1B3O and 1JCN) have revealed the presence of a few conserved hydrophilic centers near carboxamide group of NAD(+). Three conserved water molecules (W1, W, and W1 `) in di-nucleotide binding pocket of enzyme have played a significant role in the recognition of carboxamide group (of NAD(+)) to D274 and H93 residues. Based on H-bonding interaction of conserved hydrophilic (water molecular) centers within IMP-NAD(+)-enzyme complexes and their recognition to NAD(+), some covalent modification at carboxamide group of di-nucleotide (NAD(+)) has been made by substituting the -CONH(2)group by -CONHNH2 (carboxyl hydrazide group) using water mimic inhibitor design protocol. The modeled structure of modified ligand may, though, be useful for the development of antileukemic agent or it could be act as better inhibitor for hIMPDH-II.

Dynamics of the reaction between the free end of a tethered self-avoiding polymer and a flat penetrable surface: A renormalization group study

The average time tau(r) for one end of a long, self-avoiding polymer to interact for the first time with a flat penetrable surface to which it is attached at the other end is shown here to scale essentially as the square of the chain's contour length N. This result is obtained within the framework of the Wilemski-Fixman approximation to diffusion-limited reactions, in which the reaction time is expressed as a time correlation function of a ``sink'' term. In the present work, this sink-sink correlation function is calculated using perturbation expansions in the excluded volume and the polymer-surface interactions, with renormalization group methods being used to resum the expansion into a power law form. The quadratic dependence of tau(r) on N mirrors the behavior of the average time tau(c) of a free random walk to cyclize, but contrasts with the cyclization time of a free self-avoiding walk (SAW), for which tau(r) similar to N-2.2. A simulation study by Cheng and Makarov J. Phys. Chem. B 114, 3321 (2010)] of the chain-end reaction time of an SAW on a flat impenetrable surface leads to the same N-2.2 behavior, which is surprising given the reduced conformational space a tethered polymer has to explore in order to react. (C) 2014 AIP Publishing LLC.

Digestive ripening and green synthesis of ultra-small (r < 2 nm) stable ZnO quantum dots

Given the recent reports pertaining to novel optical properties of ultra-small quantum dots (QDs) (r <2 nm), this nanomaterial is of relevance to both technology and science. However it is well known that in these size regimes most chalocogenide QD dispersions are unstable. Since applications often require use of QD dispersions (e.g. for deployment on a substrate), stabilizing these ultra-small particles is of practical relevance. In this work we demonstrate a facile, green, solution approach for synthesis of stable, ultra-small ZnO QDs having radius less than 2 nm. The particle size is calculated using Brits' equation and confirmed by transmission electron micrographs. ZnO QDs reported remain stable for > 120 days in ethanol (at similar to 298-303 K). We report digestive ripening (DR) in TEA capped ZnO QDs; this occurs rapidly over a short duration of 5 min. To explain this observation we propose a suitable mechanism based on the Lee's theory, which correlates the tendency of DR with the observed zeta potentials of the dispersed medium. To the best of our knowledge this is the (i) first report on DR in oxide QDs, as well as the first direct experimental verification of Lee's theory, and (ii) most rapid DR reported so far. The facile nature of the method presented here makes ultra-small ZnO readily accessible for fundamental exploration and technologically relevant applications. (C) 2014 Elsevier Ltd and Techna Group S.r.l. All rights reserved.

Temperature-Induced Reversible First-Order Single Crystal to Single Crystal Phase Transition in Boc-gamma(4)(R)Val-Val-OH: Interplay of Enthalpy and Entropy

Crystals of Boc-gamma y(4)(R)Val-Val-OH undergo a reversible first-order single crystal to single crystal phase transition at T-c approximate to 205 K from the orthorhombic space group P22(1)2(1) (Z' = 1) to the monoclinic space group P2(1) (Z' = 2) with a hysteresis of similar to 2.1 K. The low-temperature monoclinic form is best described as a nonmerohedral twin with similar to 50% contributions from its two components. The thermal behavior of the dipeptide crystals was characterized by differential scanning calorimetry experiments. Visual changes in birefringence of the sample during heating and cooling cycles on a hot-stage microscope with polarized light supported the phase transition. Variable-temperature unit cell check measurements from 300 to 100 K showed discontinuity in the volume and cell parameters near the transition temperature, supporting the first-order behavior. A detailed comparison of the room-temperature orthorhombic form with the low-temperature (100 K) monoclinic form revealed that the strong hydrogen-bonding motif is retained in both crystal systems, whereas the non-covalent interactions involving side chains of the dipeptide differ significantly, leading to a small change in molecular conformation in the monoclinic form as well as a small reorientation of the molecules along the ac plane. A rigid-body thermal motion analysis (translation, libration, screw; correlation of translation and libration) was performed to study the crystal entropy. The reversible nature of the phase transition is probably the result of an interplay between enthalpy and entropy: the low-temperature monoclinic form is enthalpically favored, whereas the room-temperature orthorhombic form is entropically favored.

Group Testing-Based Spectrum Hole Search for Cognitive Radios

This paper investigates the use of adaptive group testing to find a spectrum hole of a specified bandwidth in a given wideband of interest. We propose a group testing-based spectrum hole search algorithm that exploits sparsity in the primary spectral occupancy by testing a group of adjacent subbands in a single test. This is enabled by a simple and easily implementable sub-Nyquist sampling scheme for signal acquisition by the cognitive radios (CRs). The sampling scheme deliberately introduces aliasing during signal acquisition, resulting in a signal that is the sum of signals from adjacent subbands. Energy-based hypothesis tests are used to provide an occupancy decision over the group of subbands, and this forms the basis of the proposed algorithm to find contiguous spectrum holes of a specified bandwidth. We extend this framework to a multistage sensing algorithm that can be employed in a variety of spectrum sensing scenarios, including noncontiguous spectrum hole search. Furthermore, we provide the analytical means to optimize the group tests with respect to the detection thresholds, number of samples, group size, and number of stages to minimize the detection delay under a given error probability constraint. Our analysis allows one to identify the sparsity and SNR regimes where group testing can lead to significantly lower detection delays compared with a conventional bin-by-bin energy detection scheme; the latter is, in fact, a special case of the group test when the group size is set to 1 bin. We validate our analytical results via Monte Carlo simulations.

Efficient density matrix renormalization group algorithm to study Y junctions with integer and half-integer spin

An efficient density matrix renormalization group (DMRG) algorithm is presented and applied to Y junctions, systems with three arms of n sites that meet at a central site. The accuracy is comparable to DMRG of chains. As in chains, new sites are always bonded to the most recently added sites and the superblock Hamiltonian contains only new or once renormalized operators. Junctions of up to N = 3n + 1 approximate to 500 sites are studied with antiferromagnetic (AF) Heisenberg exchange J between nearest-neighbor spins S or electron transfer t between nearest neighbors in half-filled Hubbard models. Exchange or electron transfer is exclusively between sites in two sublattices with N-A not equal N-B. The ground state (GS) and spin densities rho(r) = < S-r(z)> at site r are quite different for junctions with S = 1/2, 1, 3/2, and 2. The GS has finite total spin S-G = 2S(S) for even (odd) N and for M-G = S-G in the S-G spin manifold, rho(r) > 0(< 0) at sites of the larger (smaller) sublattice. S = 1/2 junctions have delocalized states and decreasing spin densities with increasing N. S = 1 junctions have four localized S-z = 1/2 states at the end of each arm and centered on the junction, consistent with localized states in S = 1 chains with finite Haldane gap. The GS of S = 3/2 or 2 junctions of up to 500 spins is a spin density wave with increased amplitude at the ends of arms or near the junction. Quantum fluctuations completely suppress AF order in S = 1/2 or 1 junctions, as well as in half-filled Hubbard junctions, but reduce rather than suppress AF order in S = 3/2 or 2 junctions.

Heterotic string on the CHL orbifold of K3

We study N = 2 compactifications of heterotic string theory on the CHL orbifold (K3 x T-2)/Z(N) with N = 2, 3, 5, 7. Z(N) acts as an automorphism on K3 together with a shift of 1/N along one of the circles of T-2. These compactifications generalize the example of the heterotic string on K3 x T-2 studied in the context of dualities in string theories. We evaluate the new supersymmetric index for these theories and show that their expansion can be written in terms of the McKay-Thompson series associated with the Z(N) automorphism embedded in the Mathieu group M-24. We then evaluate the difference in one-loop threshold corrections to the non-Abelian gauge couplings with Wilson lines and show that their moduli dependence is captured by Siegel modular forms related to dyon partition functions of N = 4 string theories.

Heterotic string on the CHL orbifold of K3

We study N = 2 compactifications of heterotic string theory on the CHL orbifold (K3 x T-2)/Z(N) with N = 2, 3, 5, 7. Z(N) acts as an automorphism on K3 together with a shift of 1/N along one of the circles of T-2. These compactifications generalize the example of the heterotic string on K3 x T-2 studied in the context of dualities in string theories. We evaluate the new supersymmetric index for these theories and show that their expansion can be written in terms of the McKay-Thompson series associated with the Z(N) automorphism embedded in the Mathieu group M-24. We then evaluate the difference in one-loop threshold corrections to the non-Abelian gauge couplings with Wilson lines and show that their moduli dependence is captured by Siegel modular forms related to dyon partition functions of N = 4 string theories.