The Treewidth of MDS and Reed-Muller Codes

The constraint complexity of a graphical realization of a linear code is the maximum dimension of the local constraint codes in the realization. The treewidth of a linear code is the least constraint complexity of any of its cycle-free graphical realizations. This notion provides a useful parameterization of the maximum-likelihood decoding complexity for linear codes. In this paper, we show the surprising fact that for maximum distance separable codes and Reed-Muller codes, treewidth equals trelliswidth, which, for a code, is defined to be the least constraint complexity (or branch complexity) of any of its trellis realizations. From this, we obtain exact expressions for the treewidth of these codes, which constitute the only known explicit expressions for the treewidth of algebraic codes.

IgG2 subclass isotype antibody and intrauterine infections

The foetus is dependent on its mother for passive immunity involving receptor-mediated specific transport of antibodies. IgG antibody is present in highest concentration in serum and is the only antibody type that can cross the placenta efficiently, except for its IgG2 subclass. Most of the pathogenic manifestations affecting the foetus involve capsular antigens and polysaccharides of pathogens and it is known that immune response to these antigens is primed to the predominant production of IgG2 type of antibody. Paradoxically, the IgG2 subclass cannot cross the placenta and neutralize such antigens; therefore, infections related to these antigens may persist and can lead to serious conditions like miscarriage and stillbirth. This article describes in brief the properties of IgG subclasses, intrauterine infections seen during pregnancy and discusses possible IgG-based strategies to manage infections to afford protection to the foetus.

On maximum entropy and minimum KL-divergence optimization by Grobner basis methods

In this paper we study constrained maximum entropy and minimum divergence optimization problems, in the cases where integer valued sufficient statistics exists, using tools from computational commutative algebra. We show that the estimation of parametric statistical models in this case can be transformed to solving a system of polynomial equations. We give an implicit description of maximum entropy models by embedding them in algebraic varieties for which we give a Grobner basis method to compute it. In the cases of minimum KL-divergence models we show that implicitization preserves specialization of prior distribution. This result leads us to a Grobner basis method to embed minimum KL-divergence models in algebraic varieties. (C) 2012 Elsevier Inc. All rights reserved.

ENTANGLEMENT IN A 3-SPIN HEISENBERG-XY CHAIN WITH NEAREST-NEIGHBOR INTERACTIONS, SIMULATED IN AN NMR QUANTUM SIMULATOR

The evolution of entanglement in a 3-spin chain with nearest-neighbor Heisenberg-XY interactions for different initial states is investigated here. In an NMR experimental implementation, we generate multipartite entangled states starting from initial separable pseudo-pure states by simulating nearest-neighbor XY interactions in a 3-spin linear chain of nuclear spin qubits. For simulating XY interactions, we follow algebraic method of Zhang et al. Phys. Rev. A 72 (2005) 012331]. Bell state between end qubits has been generated by using only the unitary evolution of the XY Hamiltonian. For generating W-state and GHZ-state a single qubit rotation is applied on second and all the three qubits, respectively after the unitary evolution of the XY Hamiltonian.

Automatic energy-momentum conserving time integrators for hyperelastic waves

An energy-momentum conserving time integrator coupled with an automatic finite element algorithm is developed to study longitudinal wave propagation in hyperelastic layers. The Murnaghan strain energy function is used to model material nonlinearity and full geometric nonlinearity is considered. An automatic assembly algorithm using algorithmic differentiation is developed within a discrete Hamiltonian framework to directly formulate the finite element matrices without recourse to an explicit derivation of their algebraic form or the governing equations. The algorithm is illustrated with applications to longitudinal wave propagation in a thin hyperelastic layer modeled with a two-mode kinematic model. Solution obtained using a standard nonlinear finite element model with Newmark time stepping is provided for comparison. (C) 2012 Elsevier B.V. All rights reserved.

Salmonella enterica serovars Typhimurium and Typhi as model organisms Revealing paradigm of host-pathogen interactions

The lifestyle of intracellular pathogens has always questioned the skill of a microbiologist in the context of finding the permanent cure to the diseases caused by them. The best tool utilized by these pathogens is their ability to reside inside the host cell, which enables them to easily bypass the humoral immunity of the host, such as the complement system. They further escape from the intracellular immunity, such as lysosome and inflammasome, mostly by forming a protective vacuole-bound niche derived from the host itself. Some of the most dreadful diseases are caused by these vacuolar pathogens, for example, tuberculosis by Mycobacterium or typhoid fever by Salmonella. To deal with such successful pathogens therapeutically, the knowledge of a host-pathogen interaction system becomes primarily essential, which further depends on the use of a model system. A well characterized pathogen, namely Salmonella, suits the role of a model for this purpose, which can infect a wide array of hosts causing a variety of diseases. This review focuses on various such aspects of research on Salmonella which are useful for studying the pathogenesis of other intracellular pathogens.

Purification and characterization of prophenoloxidase from cotton bollworm, Helicoverpa armigera

Phenoloxidases are oxidative enzymes, which play an important role in both cell mediated and humoral immunity. Purification and biochemical characterization of prophenoloxidase from cotton bollworm, Helicoverpa armigera (Hubner) were carried out to study its biochemical properties. Prophenoloxidase consists of a single polypeptide chain with a relative molecular weight of 85 kDa as determined by SDSPAGE, MALDITOF MS and LCESI MS. After the final step, the enzyme showed 71.7 fold of purification with a recovery of 49.2%. Purified prophenoloxidase showed high specific activity and homology with phenoloxidase subunit-1 of Bombyx mori and the conserved regions of copper binding (B) site of phenoloxidase. Purified prophenoloxidase has pH optima of 6.8 and has high catalytic efficiency towards the dopamine as a substrate in comparison to catechol and L-Dopa. The PO activity was strongly inhibited by phenylthiourea, thiourea, dithiothreitol and kojic acid.

An Adaptive Conditional Zero-Forcing Decoder With Full-Diversity, Least Complexity and Essentially-ML Performance for STBCs

A low complexity, essentially-ML decoding technique for the Golden code and the three antenna Perfect code was introduced by Sirianunpiboon, Howard and Calderbank. Though no theoretical analysis of the decoder was given, the simulations showed that this decoding technique has almost maximum-likelihood (ML) performance. Inspired by this technique, in this paper we introduce two new low complexity decoders for Space-Time Block Codes (STBCs)-the Adaptive Conditional Zero-Forcing (ACZF) decoder and the ACZF decoder with successive interference cancellation (ACZF-SIC), which include as a special case the decoding technique of Sirianunpiboon et al. We show that both ACZF and ACZF-SIC decoders are capable of achieving full-diversity, and we give a set of sufficient conditions for an STBC to give full-diversity with these decoders. We then show that the Golden code, the three and four antenna Perfect codes, the three antenna Threaded Algebraic Space-Time code and the four antenna rate 2 code of Srinath and Rajan are all full-diversity ACZF/ACZF-SIC decodable with complexity strictly less than that of their ML decoders. Simulations show that the proposed decoding method performs identical to ML decoding for all these five codes. These STBCs along with the proposed decoding algorithm have the least decoding complexity and best error performance among all known codes for transmit antennas. We further provide a lower bound on the complexity of full-diversity ACZF/ACZF-SIC decoding. All the five codes listed above achieve this lower bound and hence are optimal in terms of minimizing the ACZF/ACZF-SIC decoding complexity. Both ACZF and ACZF-SIC decoders are amenable to sphere decoding implementation.

Border basis detection is NP-complete

Border basis detection (BBD) is described as follows: given a set of generators of an ideal, decide whether that set of generators is a border basis of the ideal with respect to some order ideal. The motivation for this problem comes from a similar problem related to Grobner bases termed as Grobner basis detection (GBD) which was proposed by Gritzmann and Sturmfels (1993). GBD was shown to be NP-hard by Sturmfels and Wiegelmann (1996). In this paper, we investigate the computational complexity of BBD and show that it is NP-complete.

Loop transformations: convexity, pruning, and optimization

High-level loop transformations are a key instrument in mapping computational kernels to effectively exploit the resources in modern processor architectures. Nevertheless, selecting required compositions of loop transformations to achieve this remains a significantly challenging task; current compilers may be off by orders of magnitude in performance compared to hand-optimized programs. To address this fundamental challenge, we first present a convex characterization of all distinct, semantics-preserving, multidimensional affine transformations. We then bring together algebraic, algorithmic, and performance analysis results to design a tractable optimization algorithm over this highly expressive space. Our framework has been implemented and validated experimentally on a representative set of benchmarks running on state-of-the-art multi-core platforms.

On the treewidth of MDS and Reed-Muller codes

The treewidth of a linear code is the least constraint complexity of any of its cycle-free graphical realizations. This notion provides a useful parametrization of the maximum-likelihood decoding complexity for linear codes. In this paper, we compute exact expressions for the treewidth of maximum distance separable codes, and first- and second-order Reed-Muller codes. These results constitute the only known explicit expressions for the treewidth of algebraic codes.

Isolation of a High Affinity Neutralizing Monoclonal Antibody against 2009 Pandemic H1N1 Virus That Binds at the `Sa' Antigenic Site

Influenza virus evades host immunity through antigenic drift and shift, and continues to circulate in the human population causing periodic outbreaks including the recent 2009 pandemic. A large segment of the population was potentially susceptible to this novel strain of virus. Historically, monoclonal antibodies (MAbs) have been fundamental tools for diagnosis and epitope mapping of influenza viruses and their importance as an alternate treatment option is also being realized. The current study describes isolation of a high affinity (K-D = 2.1 +/- 0.4 pM) murine MAb, MA2077 that binds specifically to the hemagglutinin (HA) surface glycoprotein of the pandemic virus. The antibody neutralized the 2009 pandemic H1N1 virus in an in vitro microneutralization assay (IC50 = 0.08 mu g/ml). MA2077 also showed hemagglutination inhibition activity (HI titre of 0.50 mu g/ml) against the pandemic virus. In a competition ELISA, MA2077 competed with the binding site of the human MAb, 2D1 (isolated from a survivor of the 1918 Spanish flu pandemic) on pandemic H1N1 HA. Epitope mapping studies using yeast cell-surface display of a stable HA1 fragment, wherein `Sa' and `Sb' sites were independently mutated, localized the binding site of MA2077 within the `Sa' antigenic site. These studies will facilitate our understanding of antigen antibody interaction in the context of neutralization of the pandemic influenza virus.

Bactericidal/permeability increasing protein: A multifaceted protein with functions beyond LPS neutralization

Bactericidal permeability increasing protein (BPI), a 55-60kDa protein, first reported in 1975, has gone a long way as a protein with multifunctional roles. Its classical role in neutralizing endotoxin (LPS) raised high hopes among septic shock patients. Today, BPI is not just a LPS-neutralizing protein, but a protein with diverse functions. These functions can be as varied as inhibition of endothelial cell growth and inhibition of dendritic cell maturation, or as an anti-angiogenic, chemoattractant or opsonization agent. Though the literature available is extremely limited, it is fascinating to look into how BPI is gaining major importance as a signalling molecule. In this review, we briefly summarize the recent research focused on the multiple roles of BPI and its use as a therapeutic.

Wide Voltage Input Receiver with Hysteresis Characteristic to Reduce Input Signal Noise Effect

In this paper, an input receiver with a hysteresis characteristic that can work at voltage levels between 0.9 V and 5 V is proposed. The input receiver can be used as a wide voltage range Schmitt trigger also. At the same time, reliable circuit operation is ensured. According to the research findings, this is the first time a wide voltage range Schmitt trigger is being reported. The proposed circuit is compared with previously reported input receivers, and it is shown that the circuit has better noise immunity. The proposed input receiver ends the need for a separate Schmitt trigger and input buffer. The frequency of operation is also higher than that of the previously reported receiver. The circuit is simulated using HSPICE at 035-mu m standard thin oxide technology. Monte Carlo analysis is conducted at different process conditions, showing that the proposed circuit works well for different process conditions at different voltage levels of operation. A noise impulse of (V-CC/2) magnitude is added to the input voltage to show that the receiver receives the correct logic level even in the presence of noise. Here, V-CC is the fixed voltage supply of 3.3 V.

A transform approach to linear network coding for acyclic networks with delay

The algebraic formulation for linear network coding in acyclic networks with each link having an integer delay is well known. Based on this formulation, for a given set of connections over an arbitrary acyclic network with integer delay assumed for the links, the output symbols at the sink nodes at any given time instant is a Fq-linear combination of the input symbols across different generations, where Fq denotes the field over which the network operates. We use finite-field discrete Fourier transform (DFT) to convert the output symbols at the sink nodes at any given time instant into a Fq-linear combination of the input symbols generated during the same generation. We call this as transforming the acyclic network with delay into n-instantaneous networks (n is sufficiently large). We show that under certain conditions, there exists a network code satisfying sink demands in the usual (non-transform) approach if and only if there exists a network code satisfying sink demands in the transform approach. Furthermore, assuming time invariant local encoding kernels, we show that the transform method can be employed to achieve half the rate corresponding to the individual source-destination mincut (which are assumed to be equal to 1) for some classes of three-source three-destination multiple unicast network with delays using alignment strategies when the zero-interference condition is not satisfied.