Optimal Computation of Avoided Words

The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of the standard deviation of $w$, denoted by $std(w)$, effectively characterises the extent of a word by its edge contrast in the context in which it occurs. A word $w$ of length $k>2$ is a $\rho$-avoided word in $x$ if $std(w) \leq \rho$, for a given threshold $\rho < 0$. Notice that such a word may be completely absent from $x$. Hence computing all such words na\"{\i}vely can be a very time-consuming procedure, in particular for large $k$. In this article, we propose an $O(n)$-time and $O(n)$-space algorithm to compute all $\rho$-avoided words of length $k$ in a given sequence $x$ of length $n$ over a fixed-sized alphabet. We also present a time-optimal $O(\sigma n)$-time and $O(\sigma n)$-space algorithm to compute all $\rho$-avoided words (of any length) in a sequence of length $n$ over an alphabet of size $\sigma$. Furthermore, we provide a tight asymptotic upper bound for the number of $\rho$-avoided words and the expected length of the longest one. We make available an open-source implementation of our algorithm. Experimental results, using both real and synthetic data, show the efficiency of our implementation

Kinematic Effects of Tidal Interaction on Galaxy Rotation Curves

We use self-consistent N-body models, in conjunction with models of test particles moving in galaxy potentials, to explore the initial effects of interactions on the rotation curves of spiral galaxies. Using nearly self-consistent disk/bulge/halo galaxy models (Kuijken & Dubinski 1995), we simulate the first pass of galaxies on nearly parabolic orbits; we vary orbit inclinations, galaxy halo masses and impact parameters. For each simulation, we mimic observed rotation curves of the model galaxies. Transient interaction-induced features of the curves include distinctly rising or falling profiles at large radii and pronounced bumps in the central regions. Remarkably similar features occur in our statistical sample of optical emission-line rotation curves of spiral galaxies in tight pairs and n-tuples.Comment: 9 pages, 2 figures, accepted for publication in ApJ Letter

Non-linear electromagnetic interactions in thermal QED

We examine the behavior of the non-linear interactions between electromagnetic fields at high temperature. It is shown that, in general, the log(T) dependence on the temperature of the Green functions is simply related to their UV behavior at zero-temperature. We argue that the effective action describing the nonlinear thermal electromagnetic interactions has a finite limit as T tends to infinity. This thermal action approaches, in the long wavelength limit, the negative of the corresponding zero-temperature action.Comment: 7 pages, IFUSP/P-111

Hydrodynamic theory of an electron gas

The generalised hydrodynamic theory of an electron gas, which does not rely on an assumption of a local equilibrium, is derived as the long-wave limit of a kinetic equation. Apart from the common hydrodynamics variables the theory includes the tensor fields of the higher moments of the distribution function. In contrast to the Bloch hydrodynamics, the theory leads to the correct plasmon dispersion and in the low frequency limit recovers the Navies-Stocks hydrodynamics. The linear approximation to the generalised hydrodynamics is closely related to the theory of highly viscous fluids.Comment: 4 pages, revte

The structure of the graviton self-energy at finite temperature

We study the graviton self-energy function in a general gauge, using a hard thermal loop expansion which includes terms proportional to T^4, T^2 and log(T). We verify explicitly the gauge independence of the leading T^4 term and obtain a compact expression for the sub-leading T^2 contribution. It is shown that the logarithmic term has the same structure as the ultraviolet pole part of the T=0 self-energy function. We argue that the gauge-dependent part of the T^2 contribution is effectively canceled in the dispersion relations of the graviton plasma, and present the solutions of these equations.Comment: 27 pages, 6 figure

HLA-A and -B alleles and haplotypes in 240 index patients with common variable immunodeficiency and selective IgG subclass deficiency in central Alabama

BACKGROUND: We wanted to quantify HLA-A and -B phenotype and haplotype frequencies in Alabama index patients with common variable immunodeficiency (CVID) and selective IgG subclass deficiency (IgGSD), and in control subjects. METHODS: Phenotypes were detected using DNA-based typing (index cases) and microlymphocytotoxicity typing (controls). RESULTS: A and B phenotypes were determined in 240 index cases (114 CVID, 126 IgGSD) and 1,321 controls and haplotypes in 195 index cases and 751 controls. Phenotyping revealed that the "uncorrected" frequencies of A*24, B*14, B*15, B*35, B*40, B*49, and B*50 were significantly greater in index cases, and frequencies of B*35, B*58, B*62 were significantly lower in index cases. After Bonferroni corrections, the frequencies of phenotypes A*24, B*14, and B*40 were significantly greater in index cases, and the frequency of B*62 was significantly lower in index cases. The most common haplotypes in index cases were A*02-B*44 (frequency 0.1385), A*01-B*08 (frequency 0.1308), and A*03-B*07 (frequency 0.1000), and the frequency of each was significantly greater in index cases than in control subjects ("uncorrected" values of p < 0.0001, 0.0252, and 0.0011, respectively). After performing Bonferroni corrections, however, the frequency of A*02-B*44 alone was significantly increased in probands (p < 0.0085). Three other haplotypes were also significantly more frequent in index cases (A*03-B*14, A*31-B*40, and A*32-B*14). The combined frequencies of three latter haplotypes in index patients and control subjects were 0.0411 and 0.0126, respectively ("uncorrected" value of p < 0.0002; "corrected" value of p = 0.0166). Most phenotype and haplotype frequencies in CVID and IgGSD were similar. 26.7% of index patients were HLA-haploidentical with one or more other index patients. We diagnosed CVID or IgGSD in first-degree or other relatives of 26 of 195 index patients for whom HLA-A and -B haplotypes had been ascertained; A*01-B*08, A*02-B*44, and A*29-B*44 were most frequently associated with CVID or IgGSD in these families. We conservatively estimated the combined population frequency of CVID and IgGSD to be 0.0092 in adults, based on the occurrence of CVID and IgGSD in spouses of the index cases. CONCLUSIONS: CVID and IgGSD in adults are significantly associated with several HLA haplotypes, many of which are also common in the Alabama Caucasian population. Immunoglobulin phenotype variability demonstrated in index cases and family studies herein suggests that there are multiple gene(s) on Ch6p or other chromosomes that modify immunoglobulin phenotypes of CVID and IgGSD. The estimated prevalence of CVID and IgGSD in central Alabama could be reasonably attributed to the fact that many HLA haplotypes significantly associated with these disorders are also common in the general population

Equation of motion and subsonic-transonic transitions of rectilinear edge dislocations: A collective-variable approach

A theoretical framework is proposed to derive a dynamic equation motion for rectilinear dislocations within isotropic continuum elastodynamics. The theory relies on a recent dynamic extension of the Peierls-Nabarro equation, so as to account for core-width generalized stacking-fault energy effects. The degrees of freedom of the solution of the latter equation are reduced by means of the collective-variable method, well known in soliton theory, which we reformulate in a way suitable to the problem at hand. Through these means, two coupled governing equations for the dislocation position and core width are obtained, which are combined into one single complex-valued equation of motion, of compact form. The latter equation embodies the history dependence of dislocation inertia. It is employed to investigate the motion of an edge dislocation under uniform time-dependent loading, with focus on the subsonic/transonic transition. Except in the steady-state supersonic range of velocities---which the equation does not address---our results are in good agreement with atomistic simulations on tungsten. In particular, we provide an explanation for the transition, showing that it is governed by a loading-dependent dynamic critical stress. The transition has the character of a delayed bifurcation. Moreover, various quantitative predictions are made, that could be tested in atomistic simulations. Overall, this work demonstrates the crucial role played by core-width variations in dynamic dislocation motion.Comment: v1: 11 pages, 4 figures. v2: title changed, extensive rewriting, and new material added; 19 pages, 12 figures (content as published

Improvements to the Method of Dispersion Relations for B Nonleptonic Decays

We bring some clarifications and improvements to the method of dispersion relations in the external masses variables, that we proposed recently for investigating the final state interactions in the B nonleptonic decays. We first present arguments for the existence of an additional term in the dispersion representation, which arises from an equal-time commutator in the LSZ formalism and can be approximated by the conventional factorized amplitude. The reality properties of the spectral function and the Goldberger-Treiman procedure to perform the hadronic unitarity sum are analyzed in more detail. We also improve the treatment of the strong interaction part by including the contributions of both t and u-channel trajectories in the Regge amplitudes. Applications to the $B^0\to \pi^+\pi^-$ and $B^+\to \pi^0 K^+$ decays are presented.Comment: 16 pages, 4 new figures. modifications of the dispersion representatio

Generalized forward scattering amplitudes in QCD at high temperature

We extend to a general class of covariant gauges an approach which relates the thermal Green functions to forward scattering amplitudes of thermal particles. A brief discussion of the non-transversality of the thermal gluon polarization tensor is given in this context. This method is then applied to the calculation of the ln(T) contributions associated with general configurations of 2 and 3-point gluon functions. The results are Lorentz covariant and have the same structure as the ultraviolet divergent contributions which occur at zero temperature.Comment: 10 pages, 3 figure

TarO : a target optimisation system for structural biology

This work was funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Structural Proteomics of Rational Targets (SPoRT) initiative, (Grant BBS/B/14434). Funding to pay the Open Access publication charges for this article was provided by BBSRC.TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC Structural Proteomics of Rational Targets initiative.Publisher PDFPeer reviewe