VIP Barcoding: Composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.

Dynamics of a dilute sheared inelastic fluid. I. Hydrodynamic modes and velocity correlation functions

The hydrodynamic modes and the velocity autocorrelation functions for a dilute sheared inelastic fluid are analyzed using an expansion in the parameter epsilon=(1-e)(1/2), where e is the coefficient of restitution. It is shown that the hydrodynamic modes for a sheared inelastic fluid are very different from those for an elastic fluid in the long-wave limit, since energy is not a conserved variable when the wavelength of perturbations is larger than the ``conduction length.'' In an inelastic fluid under shear, there are three coupled modes, the mass and the momenta in the plane of shear, which have a decay rate proportional to k(2/3) in the limit k -> 0, if the wave vector has a component along the flow direction. When the wave vector is aligned along the gradient-vorticity plane, we find that the scaling of the growth rate is similar to that for an elastic fluid. The Fourier transforms of the velocity autocorrelation functions are calculated for a steady shear flow correct to leading order in an expansion in epsilon. The time dependence of the autocorrelation function in the long-time limit is obtained by estimating the integral of the Fourier transform over wave number space. It is found that the autocorrelation functions for the velocity in the flow and gradient directions decay proportional to t(-5/2) in two dimensions and t(-15/4) in three dimensions. In the vorticity direction, the decay of the autocorrelation function is proportional to t(-3) in two dimensions and t(-7/2) in three dimensions.

Composition operators on vector-valued BMOA and related function spaces

A composition operator is a linear operator between spaces of analytic or harmonic functions on the unit disk, which precomposes a function with a fixed self-map of the disk. A fundamental problem is to relate properties of a composition operator to the function-theoretic properties of the self-map. During the recent decades these operators have been very actively studied in connection with various function spaces. The study of composition operators lies in the intersection of two central fields of mathematical analysis; function theory and operator theory. This thesis consists of four research articles and an overview. In the first three articles the weak compactness of composition operators is studied on certain vector-valued function spaces. A vector-valued function takes its values in some complex Banach space. In the first and third article sufficient conditions are given for a composition operator to be weakly compact on different versions of vector-valued BMOA spaces. In the second article characterizations are given for the weak compactness of a composition operator on harmonic Hardy spaces and spaces of Cauchy transforms, provided the functions take values in a reflexive Banach space. Composition operators are also considered on certain weak versions of the above function spaces. In addition, the relationship of different vector-valued function spaces is analyzed. In the fourth article weighted composition operators are studied on the scalar-valued BMOA space and its subspace VMOA. A weighted composition operator is obtained by first applying a composition operator and then a pointwise multiplier. A complete characterization is given for the boundedness and compactness of a weighted composition operator on BMOA and VMOA. Moreover, the essential norm of a weighted composition operator on VMOA is estimated. These results generalize many previously known results about composition operators and pointwise multipliers on these spaces.

Passive vector turbulence

This thesis consists of three articles on passive vector fields in turbulence. The vector fields interact with a turbulent velocity field, which is described by the Kraichnan model. The effect of the Kraichnan model on the passive vectors is studied via an equation for the pair correlation function and its solutions. The first paper is concerned with the passive magnetohydrodynamic equations. Emphasis is placed on the so called "dynamo effect", which in the present context is understood as an unbounded growth of the pair correlation function. The exact analytical conditions for such growth are found in the cases of zero and infinite Prandtl numbers. The second paper contains an extensive study of a number of passive vector models. Emphasis is now on the properties of the (assumed) steady state, namely anomalous scaling, anisotropy and small and large scale behavior with different types of forcing or stirring. The third paper is in many ways a completion to the previous one in its study of the steady state existence problem. Conditions for the existence of the steady state are found in terms of the spatial roughness parameter of the turbulent velocity field.

Hanle-Zeeman redistribution matrix. I. Classical theory expressions in the laboratory frame

Polarized scattering in spectral lines is governed by a 4; 4 matrix that describes how the Stokes vector is scattered and redistributed in frequency and direction. Here we develop the theory for this redistribution matrix in the presence of magnetic fields of arbitrary strength and direction. This general magnetic field case is called the Hanle- Zeeman regime, since it covers both of the partially overlapping weak- and strong- field regimes in which the Hanle and Zeeman effects dominate the scattering polarization. In this general regime, the angle-frequency correlations that describe the so-called partial frequency redistribution (PRD) are intimately coupled to the polarization properties. We develop the theory for the PRD redistribution matrix in this general case and explore its detailed mathematical properties and symmetries for the case of a J = 0 -> 1 -> 0 scattering transition, which can be treated in terms of time-dependent classical oscillator theory. It is shown how the redistribution matrix can be expressed as a linear superposition of coherent and noncoherent parts, each of which contain the magnetic redistribution functions that resemble the well- known Hummer- type functions. We also show how the classical theory can be extended to treat atomic and molecular scattering transitions for any combinations of quantum numbers.

Polarisation studies on the Raman spectra of cubic crystals - Part I. Sodium chlorate

neral expressions have been derived for the intensities of the three classes of Raman lines namely totally symmetric A, doubly degenerate E and triply degenerate F, in the case of cubic crystals under the following conditions. The direction of the incident beam which is polarised with its electric vector inclined at an angle α to the normal to the scattering plane makes an angle Θ with one of the cubic axes of the crystal. The transversely scattered light is analysed by a double image prism with its principal axes inclined at angle β to the normal to the scattering plane, which is horizontal. For incident unpolarised light and Θ=22 1/2°, and the scattered light being analysed by a double image prism rotated through 45° from the position when its principal axes are vertical and horizontal ρ{variant} for A lines is equal to one, for E lines >1 and for F lines <1. This gives a method of classifying the Raman lines of a cubic crystal in a single setting. The results have been experimentally verified in sodium chlorate.

Inference on Cointegration in Vector Autoregressive Models (summary section only)

In the thesis we consider inference for cointegration in vector autoregressive (VAR) models. The thesis consists of an introduction and four papers. The first paper proposes a new test for cointegration in VAR models that is directly based on the eigenvalues of the least squares (LS) estimate of the autoregressive matrix. In the second paper we compare a small sample correction for the likelihood ratio (LR) test of cointegrating rank and the bootstrap. The simulation experiments show that the bootstrap works very well in practice and dominates the correction factor. The tests are applied to international stock prices data, and the .nite sample performance of the tests are investigated by simulating the data. The third paper studies the demand for money in Sweden 1970—2000 using the I(2) model. In the fourth paper we re-examine the evidence of cointegration between international stock prices. The paper shows that some of the previous empirical results can be explained by the small-sample bias and size distortion of Johansen’s LR tests for cointegration. In all papers we work with two data sets. The first data set is a Swedish money demand data set with observations on the money stock, the consumer price index, gross domestic product (GDP), the short-term interest rate and the long-term interest rate. The data are quarterly and the sample period is 1970(1)—2000(1). The second data set consists of month-end stock market index observations for Finland, France, Germany, Sweden, the United Kingdom and the United States from 1980(1) to 1997(2). Both data sets are typical of the sample sizes encountered in economic data, and the applications illustrate the usefulness of the models and tests discussed in the thesis.

Global, Local and Vector-Valued Tb Theorems on Non-Homogeneous Metric Spaces

Various Tb theorems play a key role in the modern harmonic analysis. They provide characterizations for the boundedness of Calderón-Zygmund type singular integral operators. The general philosophy is that to conclude the boundedness of an operator T on some function space, one needs only to test it on some suitable function b. The main object of this dissertation is to prove very general Tb theorems. The dissertation consists of four research articles and an introductory part. The framework is general with respect to the domain (a metric space), the measure (an upper doubling measure) and the range (a UMD Banach space). Moreover, the used testing conditions are weak. In the first article a (global) Tb theorem on non-homogeneous metric spaces is proved. One of the main technical components is the construction of a randomization procedure for the metric dyadic cubes. The difficulty lies in the fact that metric spaces do not, in general, have a translation group. Also, the measures considered are more general than in the existing literature. This generality is genuinely important for some applications, including the result of Volberg and Wick concerning the characterization of measures for which the analytic Besov-Sobolev space embeds continuously into the space of square integrable functions. In the second article a vector-valued extension of the main result of the first article is considered. This theorem is a new contribution to the vector-valued literature, since previously such general domains and measures were not allowed. The third article deals with local Tb theorems both in the homogeneous and non-homogeneous situations. A modified version of the general non-homogeneous proof technique of Nazarov, Treil and Volberg is extended to cover the case of upper doubling measures. This technique is also used in the homogeneous setting to prove local Tb theorems with weak testing conditions introduced by Auscher, Hofmann, Muscalu, Tao and Thiele. This gives a completely new and direct proof of such results utilizing the full force of non-homogeneous analysis. The final article has to do with sharp weighted theory for maximal truncations of Calderón-Zygmund operators. This includes a reduction to certain Sawyer-type testing conditions, which are in the spirit of Tb theorems and thus of the dissertation. The article extends the sharp bounds previously known only for untruncated operators, and also proves sharp weak type results, which are new even for untruncated operators. New techniques are introduced to overcome the difficulties introduced by the non-linearity of maximal truncations.

A maximal operator, Carleson's embedding, and tent spaces for vector-valued functions

This thesis is concerned with the area of vector-valued Harmonic Analysis, where the central theme is to determine how results from classical Harmonic Analysis generalize to functions with values in an infinite dimensional Banach space. The work consists of three articles and an introduction. The first article studies the Rademacher maximal function that was originally defined by T. Hytönen, A. McIntosh and P. Portal in 2008 in order to prove a vector-valued version of Carleson's embedding theorem. The boundedness of the corresponding maximal operator on Lebesgue-(Bochner) -spaces defines the RMF-property of the range space. It is shown that the RMF-property is equivalent to a weak type inequality, which does not depend for instance on the integrability exponent, hence providing more flexibility for the RMF-property. The second article, which is written in collaboration with T. Hytönen, studies a vector-valued Carleson's embedding theorem with respect to filtrations. An earlier proof of the dyadic version assumed that the range space satisfies a certain geometric type condition, which this article shows to be also necessary. The third article deals with a vector-valued generalizations of tent spaces, originally defined by R. R. Coifman, Y. Meyer and E. M. Stein in the 80's, and concerns especially the ones related to square functions. A natural assumption on the range space is then the UMD-property. The main result is an atomic decomposition for tent spaces with integrability exponent one. In order to suit the stochastic integrals appearing in the vector-valued formulation, the proof is based on a geometric lemma for cones and differs essentially from the classical proof. Vector-valued tent spaces have also found applications in functional calculi for bisectorial operators. In the introduction these three themes come together when studying paraproduct operators for vector-valued functions. The Rademacher maximal function and Carleson's embedding theorem were applied already by Hytönen, McIntosh and Portal in order to prove boundedness for the dyadic paraproduct operator on Lebesgue-Bochner -spaces assuming that the range space satisfies both UMD- and RMF-properties. Whether UMD implies RMF is thus an interesting question. Tent spaces, on the other hand, provide a method to study continuous time paraproduct operators, although the RMF-property is not yet understood in the framework of tent spaces.