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.

Fermions in synthetic non-Abelian gauge potentials: rashbon condensates to novel Hamiltonians

Recent advances in the generation of synthetic gauge fields in cold atomic systems have stimulated interest in the physics of interacting bosons and fermions in them. In this paper, we discuss interacting two-component fermionic systems in uniform non-Abelian gauge fields that produce a spin-orbit interaction and uniform spin potentials. Two classes of gauge fields discussed include those that produce a Rashba spin-orbit interaction and the type of gauge fields (SM gauge fields) obtained in experiments by the Shanxi and MIT groups. For high symmetry Rashba gauge fields, a two-particle bound state exists even for a vanishingly small attractive interaction described by a scattering length. Upon increasing the strength of a Rashba gauge field, a finite density of weakly interacting fermions undergoes a crossover from a BCS like ground state to a BEC state of a new kind of boson called the rashbon whose properties are determined solely by the gauge field and not by the interaction between the fermions. The rashbon Bose-Einstein condensate (RBEC) is a quite intriguing state with the rashbon-rashbon interactions being independent of the fermion-fermion interactions (scattering length). Furthermore, we show that the RBEC has a transition temperature of the order of the Fermi temperature, suggesting routes to enhance the transition temperatures of weakly interacting superfluids by tuning the spin-orbit coupling. For the SM gauge fields, we show that in a regime of parameters, a pair of particles with finite centre-of-mass momentum is the most strongly bound. In other regimes of centre-of-mass momenta, there is no two-body bound state, but a resonance like feature appears in the scattering continuum. In the many-body setting, this results in flow enhanced pairing. Also, strongly interacting normal states utilizing the scattering resonance can be created opening the possibility of studying properties of helical Fermi liquids. This paper contains a general discussion of the physics of Feshbach resonance in a non-Abelian gauge field, where several novel features such as centre-of-mass-momentum-dependent effective interactions are shown. It is also shown that a uniform non-Abelian gauge field in conjunction with a spatial potential can be used to generate novel Hamiltonians; we discuss an explicit example of the generation of a monopole Hamiltonian.

Splicing Functions and Global Dependency on Fission Yeast Slu7 Reveal Diversity in Spliceosome Assembly

The multiple short introns in Schizosaccharomyces pombe genes with degenerate cis sequences and atypically positioned polypyrimidine tracts make an interesting model to investigate canonical and alternative roles for conserved splicing factors. Here we report functions and interactions of the S. pombe slu7(+) (spslu7(+)) gene product, known from Saccharomyces cerevisiae and human in vitro reactions to assemble into spliceosomes after the first catalytic reaction and to dictate 3' splice site choice during the second reaction. By using a missense mutant of this essential S. pombe factor, we detected a range of global splicing derangements that were validated in assays for the splicing status of diverse candidate introns. We ascribe widespread, intron-specific SpSlu7 functions and have deduced several features, including the branch nucleotide-to-3' splice site distance, intron length, and the impact of its A/U content at the 5' end on the intron's dependence on SpSlu7. The data imply dynamic substrate-splicing factor relationships in multiintron transcripts. Interestingly, the unexpected early splicing arrest in spslu7-2 revealed a role before catalysis. We detected a salt-stable association with U5 snRNP and observed genetic interactions with spprp1(+), a homolog of human U5-102k factor. These observations together point to an altered recruitment and dependence on SpSlu7, suggesting its role in facilitating transitions that promote catalysis, and highlight the diversity in spliceosome assembly.

CFT(4) partition functions and the heat kernel on AdS(5)

We consider four-dimensional CFTs which admit a large-N expansion, and whose spectrum contains states whose conformal dimensions do not scale with N. We explicitly reorganise the partition function obtained by exponentiating the one-particle partition function of these states into a heat kernel form for the dual string spectrum on AdS(5). On very general grounds, the heat kernel answer can be expressed in terms of a convolution of the one-particle partition function of the light states in the four-dimensional CFT. (C) 2013 Elsevier B.V. All rights reserved.

Asymptotics of Harish-Chandra expansions, bounded hypergeometric functions associated with root systems, and applications

A series expansion for Heckman-Opdam hypergeometric functions phi(lambda) is obtained for all lambda is an element of alpha(C)*. As a consequence, estimates for phi(lambda) away from the walls of a Weyl chamber are established. We also characterize the bounded hypergeometric functions and thus prove an analogue of the celebrated theorem of Helgason and Johnson on the bounded spherical functions on a Riemannian symmetric space of the noncompact type. The L-P-theory for the hypergeometric Fourier transform is developed for 0 < p < 2. In particular, an inversion formula is proved when 1 <= p < 2. (C) 2013 Elsevier Inc. All rights reserved.

Effect of choice of basis functions in neural network for capturing unknown function for dynamic inversion control

The basic requirement for an autopilot is fast response and minimum steady state error for better guidance performance. The highly nonlinear nature of the missile dynamics due to the severe kinematic and inertial coupling of the missile airframe as well as the aerodynamics has been a challenge for an autopilot that is required to have satisfactory performance for all flight conditions in probable engagements. Dynamic inversion is very popular nonlinear controller for this kind of scenario. But the drawback of this controller is that it is sensitive to parameter perturbation. To overcome this problem, neural network has been used to capture the parameter uncertainty on line. The choice of basis function plays the major role in capturing the unknown dynamics. Here in this paper, many basis function has been studied for approximation of unknown dynamics. Cosine basis function has yield the best response compared to any other basis function for capturing the unknown dynamics. Neural network with Cosine basis function has improved the autopilot performance as well as robustness compared to Dynamic inversion without Neural network.

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

End point estimates for Radon transform of radial functions on non-Euclidean spaces

We prove end point estimate for Radon transform of radial functions on affine Grasamannian and real hyperbolic space. We also discuss analogs of these results on the sphere.

The Ginibre Ensemble and Gaussian Analytic Functions

We show that as n changes, the characteristic polynomial of the n x n random matrix with i.i.d. complex Gaussian entries can be described recursively through a process analogous to Polya's urn scheme. As a result, we get a random analytic function in the limit, which is given by a mixture of Gaussian analytic functions. This suggests another reason why the zeros of Gaussian analytic functions and the Ginibre ensemble exhibit similar local repulsion, but different global behavior. Our approach gives new explicit formulas for the limiting analytic function.

Feshbach resonance in a synthetic non-Abelian gauge field

We study the Feshbach resonance of spin-1/2 particles in a uniform synthetic non-Abelian gauge field that produces spin-orbit coupling and constant spin potentials. We develop a renormalizable quantum field theory including the closed-channel boson which engenders the resonance. We show that the gauge field shifts the Feshbach field where the low-energy scattering length diverges. In addition the Feshbach field is shown to depend on the center-of-mass momentum of the particles. For high-symmetry gauge fields which produce a Rashba spin coupling, we show that the system supports two bound states over a regime of magnetic fields when the background scattering length is negative and the resonance width is comparable to the energy scale of the spin-orbit coupling. We discuss interesting consequences useful for future theoretical and experimental studies, even while our predictions are in agreement with recent experiments.

Analytical test functions for free vibration analysis of rotating non-homogeneous Timoshenko beams

In this paper, the governing equations for free vibration of a non-homogeneous rotating Timoshenko beam, having uniform cross-section, is studied using an inverse problem approach, for both cantilever and pinned-free boundary conditions. The bending displacement and the rotation due to bending are assumed to be simple polynomials which satisfy all four boundary conditions. It is found that for certain polynomial variations of the material mass density, elastic modulus and shear modulus, along the length of the beam, the assumed polynomials serve as simple closed form solutions to the coupled second order governing differential equations with variable coefficients. It is found that there are an infinite number of analytical polynomial functions possible for material mass density, shear modulus and elastic modulus distributions, which share the same frequency and mode shape for a particular mode. The derived results are intended to serve as benchmark solutions for testing approximate or numerical methods used for the vibration analysis of rotating non-homogeneous Timoshenko beams.

Model domains in C-3 with abelian automorphism group

It is shown that every hyperbolic rigid polynomial domain in C-3 of finite-type, with abelian automorphism group is equivalent to a domain that is balanced with respect to some weight.

The HORMA domain: an evolutionarily conserved domain discovered in chromatin-associated proteins, has unanticipated diverse functions

The HORMA domain (for Hop1p, Rev7p and MAD2) was discovered in three chromatin-associated proteins in the budding yeast Saccharomyces cerevisiae. This domain has also been found in proteins with similar functions in organisms including plants, animals and nematodes. The HORMA domain containing proteins are thought to function as adaptors for meiotic checkpoint protein signaling and in the regulation of meiotic recombination. Surprisingly, new work has disclosed completely unanticipated and diverse functions for the HORMA domain containing proteins. A. M. Villeneuve and colleagues (Schvarzstein et al., 2013) show that meiosis-specific HORMA domain containing proteins plays a vital role in preventing centriole disengagement during Caenorhabditis elegans spermatocyte meiosis. Another recent study reveals that S. cerevisiae Atg13 HORMA domain acts as a phosphorylation-dependent conformational switch in the cellular autophagic process. (C) 2014 Elsevier B.V. All rights reserved.

Fermions in Synthetic Non-Abelian Gauge Fields

Quantum emulation property of the cold atoms has generated a lot of interest in studying systems with synthetic gauge fields. In this article, we describe the physics of two component Fermi gas in the presence of synthetic non-Abelian SU(2) gauge fields. Even for the non-interacting system with the gauge fields, there is an interesting change in the topology of the Fermi surface by tuning only the gauge field strength. When a trapping potential is used in conjunction with the gauge fields, the non-interacting system has the ability to produce novel Hamiltonians and show characteristic change in the density profile of the cloud. Without trap, the gauge fields act as an attractive interaction amplifier and for special kinds of gauge field configurations, there are two-body bound states for any attraction even in three dimensions. For a many body system, the gauge fields can induce a crossover from a weak superfluid to a strong superfluid with transition temperature as high as the Fermi temperature. The superfluid state obtained for a very large gauge field strength is a superfluid of new kind of bosons, called ``rashbons'', the properties of which are independent of its constituent two component fermions and are solely determined by the gauge field strength. We also discuss the collective excitations over the superfluid ground states and the experimental relevance of the physics.