Order independent structural alignment of circularly permuted proteins

Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because current detection methods can miss many occurances, mistaking random repeats as circular permutation. Here we develop a method for detecting circularly permuted proteins from structural comparison. Sequence order independent alignment of protein structures can be regarded as a special case of the maximum-weight independent set problem, which is known to be computationally hard. We develop an efficient approximation algorithm by repeatedly solving relaxations of an appropriate intermediate integer programming formulation, we show that the approximation ratio is much better then the theoretical worst case ratio of $r = 1/4$. Circularly permuted proteins reported in literature can be identified rapidly with our method, while they escape the detection by publicly available servers for structural alignment.Comment: 5 pages, 3 figures, Accepted by IEEE-EMBS 2004 Conference Proceeding

Theoretical Procedures and Elder-Vass's Critical Realist Ontology

This article scrutinizes some theoretical procedures prevalent in the philosophy of social science. These procedures are exemplified in Elder-Vass’s critical realism, which promises to place the social sciences on a sound ontological footing. The article focuses on the way that Elder-Vass’s general emergentist ontology is constituted and on the methods through which it is applied to society. It is contended that the ontology is not and could not be grounded in science and that its philosophical use distorts what it is applied to. The incoherent methods that social ontological projects constitutionally rely on entail that they cannot ground social scientific explanation

Modification of the Unitarity Relation for sin2beta-Vub in Supersymmetric Models

Recently, a more than 2sigma discrepancy has been observed between the well measured inclusive value of Vub and the predicted value of Vub from the unitarity triangle fit using the world average value of sin2beta. We attempt to resolve this tension in the context of grand unified SO(10) and SU(5) models where the neutrino mixing matrix is responsible for flavor changing neutral current at the weak scale and the models with non-proportional A-terms (can be realized simply in the context of intersecting D-brane models) and investigate the interplay between the constraints arising from B_{s,d}-\bar B_{s,d} mixings, epsilon_K, Br(tau -> mu gamma), Br(mu -> e gamma) and a fit of this new discrepancy. We also show that the ongoing measurement of the phase of Bs mixing will be able to identify the grand unified model. The measurement of Br(tau -> e gamma) will also be able to test these scenarios, especially the models with non-proportional A-terms.Comment: 20 pages, 4 figures. Minor corrections, references adde

Correlation between direct dark matter detection and Br(B_s -> mu mu) with a large phase of B_s - anti-B_s mixing

We combine the analyses for flavor changing neutral current processes and dark matter solutions in minimal-type supersymmetric grand unified theory (GUT) models, SO(10) and SU(5), with a large B_s - anti-B_s mixing phase and large tan beta. For large tan beta, the double penguin diagram dominates the SUSY contribution to the B_s - anti-B_s mixing amplitude. Also, the Br(B_s -> mu mu) constraint becomes important as it grows as tan^6 beta, although it can still be suppressed by large pseudoscalar Higgs mass m_A. We investigate the correlation between B_s -> mu mu and the dark matter direct detection cross-section through their dependence on m_A. In the minimal-type of SU(5) with type I seesaw, the large mixing in neutrino Dirac couplings results in large lepton flavor violating decay process tau to mu gamma, which in turn sets upper bound on m_A. In the SO(10) case, the large mixing can be chosen to be in the Majorana couplings instead, and the constraint from Br(tau -> mu gamma) can be avoided. The heavy Higgs funnel region turns out to be an interesting possibility in both cases and the direct dark matter detection should be possible in the near future in these scenarios.Comment: 19 pages, 8 figure

The co-pyrolysis of flame retarded high impact polystyrene and polyolefins

The co-pyrolysis of brominated high impact polystyrene (Br-HIPS) with polyolefins using a fixed bed reactor has been investigated, in particular, the effect that different types brominated aryl compounds and antimony trioxide have on the pyrolysis products. The pyrolysis products were analysed using FT-IR, GC-FID, GC-MS, and GC-ECD. Liquid chromatography was used to separate the oils/waxes so that a more detailed analysis of the aliphatic, aromatic, and polar fractions could be carried out. It was found that interaction occurs between Br-HIPS and polyolefins during co-pyrolysis and that the presence of antimony trioxide influences the pyrolysis mass balance. Analysis of the Br-HIPS + polyolefin co-pyrolysis products showed that the presence of polyolefins led to an increase in the concentration of alkyl and vinyl mono-substituted benzene rings in the pyrolysis oil/wax resulting from Br-HIPS pyrolysis. The presence of Br-HIPS also had an impact on the oil/wax products of polyolefin pyrolysis, particularly on the polyethylene oil/wax composition which converted from being a mixture of 1-alkenes and n-alkanes to mostly n-alkanes. Antimony trioxide had very little impact on the polyolefin wax/oil composition but it did suppress the formation of styrene and alpha-methyl styrene and increase the formation of ethylbenzene and cumene during the pyrolysis of the Br-HIPS

Minimal SUGRA Model and Collider Signals

The SUSY signals in the dominant stau-neutralino coannihilation region at a 500(800) GeV linear collider are investigated. The region is consistent with the WMAP measurement of the cold dark matter relic density as well as all other current experimental bounds within the mSUGRA framework. The signals are characterized by an existence of very low-energy tau leptons in the final state due to small mass difference between stau_1 and chi_1 (5-15 GeV). We study the accuracy of the mass difference measurement with a 1^deg active mask to reduce a huge SM two-photon background.Comment: 4 pages, 3 figures, Talk presented at ICHEP04, Aug.16-22, Beijing, China, Numerical typos in Table 5 and 6 are corrected, no changes in figures and in other numerical result

Rectified Gaussian Scale Mixtures and the Sparse Non-Negative Least Squares Problem

In this paper, we develop a Bayesian evidence maximization framework to solve the sparse non-negative least squares (S-NNLS) problem. We introduce a family of probability densities referred to as the Rectified Gaussian Scale Mixture (R- GSM) to model the sparsity enforcing prior distribution for the solution. The R-GSM prior encompasses a variety of heavy-tailed densities such as the rectified Laplacian and rectified Student- t distributions with a proper choice of the mixing density. We utilize the hierarchical representation induced by the R-GSM prior and develop an evidence maximization framework based on the Expectation-Maximization (EM) algorithm. Using the EM based method, we estimate the hyper-parameters and obtain a point estimate for the solution. We refer to the proposed method as rectified sparse Bayesian learning (R-SBL). We provide four R- SBL variants that offer a range of options for computational complexity and the quality of the E-step computation. These methods include the Markov chain Monte Carlo EM, linear minimum mean-square-error estimation, approximate message passing and a diagonal approximation. Using numerical experiments, we show that the proposed R-SBL method outperforms existing S-NNLS solvers in terms of both signal and support recovery performance, and is also very robust against the structure of the design matrix.Comment: Under Review by IEEE Transactions on Signal Processin