Efficient chaining of seeds in ordered trees

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe an algorithm with complexity O(m2 log(m)) in time and O(m2) in space

Quasi Two-dimensional Transfer of Elastic Waves

A theory for multiple scattering of elastic waves is presented in a random medium bounded by two ideal free surfaces, whose horizontal size is infinite and whose transverse size is smaller than the mean free path of the waves. This geometry is relevant for seismic wave propagation in the Earth crust. We derive a time-dependent, quasi-2D radiative transfer equation, that describes the coupling of the eigenmodes of the layer (surface Rayleigh waves, SH waves, and Lamb waves). Expressions are found that relate the small-scale fluctuations to the life time of the modes and to their coupling rates. We discuss a diffusion approximation that simplifies the mathematics of this model significantly, and which should apply at large lapse times. Finally, coherent backscattering is studied within the quasi-2D radiative transfer equation for different source and detection configurations.Comment: REVTeX, 36 pages with 10 figures. Submitted to Phys. Rev.

Sarcopenia/Muscle Mass is not a Prognostic Factor for Short- and Long-Term Outcome After Esophagectomy for Cancer

Background: Recent studies have suggested that sarcopenia is a prognostic risk indicator of postoperative complications and predicts survival in cancer patients. The aim of this study is to investigate whether sarcopenia is associated with postoperative short-term outcome (morbidity and mortality) and long-term survival in patients undergoing esophagectomy for cancer after neoadjuvant chemoradiotherapy. Methods: All patients who underwent neoadjuvant chemoradiotherapy followed by esophagectomy for cancer, and of whom an adequate CT scan was available, were included in the current study. The presence of sarcopenia was defined by CT imaging using cut-off values of the total cross-sectional muscle tissue measured transversely at the third lumbar level. Results: A total number of 120 patients were eligible for analysis. Almost half of the patients (N = 54, 45 %) were classified as having sarcopenia; 24 sarcopenic patients (44 %) had overweight and 5 sarcopenic patients (9 %) were obese. Overall morbidity and mortality rate did not differ significantly between sarcopenic and non-sarcopenic patients, nor did long-term overall or disease-free survival. Also sarcopenic obesity was not associated with worse outcome. Conclusion: The presence of sarcopenia was not associated with a negative short- and long-term outcome in this selected group of esophageal cancer patients after neoadjuvant chemoradiotherapy followed by esophagectomy

Simultaneous solution of Kompaneets equation and Radiative Transfer equation in the photon energy range 1 - 125 KeV

Radiative transfer equation in plane parallel geometry and Kompaneets equation is solved simultaneously to obtain theoretical spectrum of 1-125 KeV photon energy range. Diffuse radiation field is calculated using time-independent radiative transfer equation in plane parallel geometry, which is developed using discrete space theory (DST) of radiative transfer in a homogeneous medium for different optical depths. We assumed free-free emission and absorption and emission due to electron gas to be operating in the medium. The three terms $n, n^2$ and $\displaystyle \bigg({\frac {\partial n}{\partial x_k}}\bigg)$ where $n$ is photon phase density and $\displaystyle x_k= \bigg({\frac {h \nu} {k T_e}} \bigg)$, in Kompaneets equation and those due to free-free emission are utilized to calculate the change in the photon phase density in a hot electron gas. Two types of incident radiation are considered: (1) isotropic radiation with the modified black body radiation $I^{MB}$ [1] and (2) anisotropic radiation which is angle dependent. The emergent radiation at $\tau=0$ and reflected radiation $\tau=\tau_{max}$ are calculated by using the diffuse radiation from the medium. The emergent and reflected radiation contain the free-free emission and emission from the hot electron gas. Kompaneets equation gives the changes in photon phase densities in different types of media. Although the initial spectrum is angle dependent, the Kompaneets equation gives a spectrum which is angle independent after several Compton scattering times.Comment: 31 pages, 8 figures, Accepte

In vivo and in vitro synthesis of CM-proteins (A-hordeins) from barley (Hordeum vulgare L.)

CM-proteins from barley endosperm (CMa, CMb, CMc, CMd), which are the main components of the A-hordein fraction, are synthesized most actively 10 to 30 d after anthesis (maximum at 15–20 d). They are synthesized by membranebound polysomes as precursors of higher apparent molecular weight (13,000–21,000) than the mature proteins (12,000–16,000). The largest in vitro product (21,000) is the putative precursor of protein CMd (16,000), as it is selected with anti-CMd monospecific IgG's, and is coded by an mRNA of greater sedimentation coefficient (9 S) than those encoding the other three proteins (7.5 S). CM-proteins always appear in the soluble fraction, following different homogenization and subcellular fractionation procedures, indicating that these proteins are transferred to the soluble fraction after processing

Large Deviations for Random Trees

We consider large random trees under Gibbs distributions and prove a Large Deviation Principle (LDP) for the distribution of degrees of vertices of the tree. The LDP rate function is given explicitly. An immediate consequence is a Law of Large Numbers for the distribution of vertex degrees in a large random tree. Our motivation for this study comes from the analysis of RNA secondary structures.Comment: 10 page

Gravitation and inertia; a rearrangement of vacuum in gravity

We address the gravitation and inertia in the framework of 'general gauge principle', which accounts for 'gravitation gauge group' generated by hidden local internal symmetry implemented on the flat space. We connect this group to nonlinear realization of the Lie group of 'distortion' of local internal properties of six-dimensional flat space, which is assumed as a toy model underlying four-dimensional Minkowski space. The agreement between proposed gravitational theory and available observational verifications is satisfactory. We construct relativistic field theory of inertia and derive the relativistic law of inertia. This theory furnishes justification for introduction of the Principle of Equivalence. We address the rearrangement of vacuum state in gravity resulting from these ideas.Comment: 17 pages, no figures, revtex4, Accepted for publication in Astrophys. Space Sc

Running coupling: Does the coupling between dark energy and dark matter change sign during the cosmological evolution?

In this paper we put forward a running coupling scenario for describing the interaction between dark energy and dark matter. The dark sector interaction in our scenario is free of the assumption that the interaction term $Q$ is proportional to the Hubble expansion rate and the energy densities of dark sectors. We only use a time-variable coupling $b(a)$ (with $a$ the scale factor of the universe) to characterize the interaction $Q$. We propose a parametrization form for the running coupling $b(a)=b_0a+b_e(1-a)$ in which the early-time coupling is given by a constant $b_e$, while today the coupling is given by another constant, $b_0$. For investigating the feature of the running coupling, we employ three dark energy models, namely, the cosmological constant model ($w=-1$), the constant $w$ model ($w=w_0$), and the time-dependent $w$ model ($w(a)=w_0+w_1(1-a)$). We constrain the models with the current observational data, including the type Ia supernova, the baryon acoustic oscillation, the cosmic microwave background, the Hubble expansion rate, and the X-ray gas mass fraction data. The fitting results indicate that a time-varying vacuum scenario is favored, in which the coupling $b(z)$ crosses the noninteracting line ($b=0$) during the cosmological evolution and the sign changes from negative to positive. The crossing of the noninteracting line happens at around $z=0.2-0.3$, and the crossing behavior is favored at about 1$\sigma$ confidence level. Our work implies that we should pay more attention to the time-varying vacuum model and seriously consider the phenomenological construction of a sign-changeable or oscillatory interaction between dark sectors.Comment: 8 pages, 5 figures; refs added; to appear in EPJ

Gravitational Geometric Phase in the Presence of Torsion

We investigate the relativistic and non-relativistic quantum dynamics of a neutral spin-1/2 particle submitted an external electromagnetic field in the presence of a cosmic dislocation. We analyze the explicit contribution of the torsion in the geometric phase acquired in the dynamic of this neutral spinorial particle. We discuss the influence of the torsion in the relativistic geometric phase. Using the Foldy-Wouthuysen approximation, the non-relativistic quantum dynamics are studied and the influence of the torsion in the Aharonov-Casher and He-McKellar-Wilkens effects are discussed.Comment: 14 pages, no figur