A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombinationdetecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of postrecombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.Comment: 5 pages, 3 figures. Chan CX, Beiko RG and Ragan MA (2007). A two-phase approach for detecting recombination in nucleotide sequences. In Hazelhurst S and Ramsay M (Eds) Proceedings of the First Southern African Bioinformatics Workshop, 28-30 January, Johannesburg, 9-1

Classification of unitary highest weight representations for non compact real forms

Using Jakobsen theorems, unitarizability in Hermitian Symmetric Spaces is discussed. The set of all missing highest weights is explicitly calculated and the construction of their corresponding highest weights vectors is studied.Comment: PDF, 35 pages (late submission

Quantized Dirac Operators

We determine what should correspond to the Dirac operator on certain quantized hermitian symmetric spaces and what its properties are. A new insight into the quantized wave operator is obtained.Comment: To appear in the Proceedings of the Quantum Groups And Integrable Systems meeting in Prag, June 22-24 2000. To be published with the Czechoslovak Journal of Physi

Indecomposable finite-dimensional representations of a class of Lie algebras and Lie superalgebras

In the article at hand, we sketch how, by utilizing nilpotency to its fullest extent (Engel, Super Engel) while using methods from the theory of universal enveloping algebras, a complete description of the indecomposable representations may be reached. In practice, the combinatorics is still formidable, though. It turns out that the method applies to both a class of ordinary Lie algebras and to a similar class of Lie superalgebras. Besides some examples, due to the level of complexity we will only describe a few precise results. One of these is a complete classification of which ideals can occur in the enveloping algebra of the translation subgroup of the Poincar\'e group. Equivalently, this determines all indecomposable representations with a single, 1-dimensional source. Another result is the construction of an infinite-dimensional family of inequivalent representations already in dimension 12. This is much lower than the 24-dimensional representations which were thought to be the lowest possible. The complexity increases considerably, though yet in a manageable fashion, in the supersymmetric setting. Besides a few examples, only a subclass of ideals of the enveloping algebra of the super Poincar\'e algebra will be determined in the present article.Comment: LaTeX 14 page

The Borrowers: Researching the cognitive aspects of translation

The paper considers the interdisciplinary interaction of research on the cognitive aspects of translation. Examples of influence from linguistics, psychology, neuroscience, cognitive science, reading and writing research and language technology are given, with examples from specific sub-disciplines within each one. The breadth of borrowing by researchers in cognitive translatology is made apparent, but the minimal influence of cognitive translatology on the respective disciplines themselves is also highlighted. Suggestions for future developments are made, including ways in which the domain of cognitive translatology might exert greater influence on other disciplines

Agriculture and Co-operativism, a Persistent Duality: The Case of Denmark

The paper argues that co-operativism in Danish agriculture represents both continuity and strong changes from the start of the movement as the economic branch of a comprehensive social and political movement to the large agro-industrial enterprises of today, and that co-operativism still is a necessary tool for both large scale production and for innovation within the agro-industrial sector. After a short description of the role of co-operative thinking and organising in the Danish context historically, the paper presents a statistical overview of the current position of co-operative societies in Danish agriculture on the background of the structural changes that have occurred in primary agriculture and agro-industry during the last generation and a half. The third section presents historical conditions and experiences of co-operativism that have paved the way for the characteristics of the current relation between agriculture and co-operativism. Finally, challenges to this relation are discussed in the context of market trends within the established sectors and new areas of agricultural activities – using the example of organic production.Agribusiness,

Observations of the diffuse UV radiation field

Spectra are presented for the diffuse UV radiation field between 1250 to 3100 A from eight different regions of the sky, which were obtained with the Johns Hopkins UVX experiment. UVX flew aboard the Space Shuttle Columbia (STS-61C) in January 1986 as part of the Get-Away Special project. The experiment consisted of two 1/4 m Ebert-Fastie spectrometers, covering the spectral range 1250 to 1700 A at 17 A resolution and 1600 to 3100 A at 27 A resolution, respectively, with a field of view of 4 x .25 deg, sufficiently small to pick out regions of the sky with no stars in the line of sight. Values were found for the diffuse cosmic background ranging in intensity from 300 to 900 photons/sq cm/sec/sr/A. The cosmic background is spectrally flat from 1250 to 3100 A, within the uncertainties of each spectrometer. The zodiacal light begins to play a significant role in the diffuse radiation field above 2000 A, and its brightness was determined relative to the solar emission. Observed brightnesses of the zodiacal light in the UV remain almost constant with ecliptic latitude, unlike the declining visible brightnesses, possibly indicating that those (smaller) grains responsible for the UV scattering have a much more uniform distribution with distance from the ecliptic plane than do those grains responsible for the visible scattering

Endlessly single-mode holey fibers: the influence of core design

In this paper we evaluate the cut-off properties of holey fibers (HFs) with a triangular lattice of air holes and the core formed by the removal of a single (HF1) or more air holes (HF3 and HF7). With the aid of finite-element simulations we determine the single-mode and multi-mode phases and also find the air hole diameters limiting the endlessly single-mode regime. From calculations of V and W parameters we find that in general HF1 is less susceptible to longitudinal non-uniformities compared to the other designs for equivalent effective areas. As an example we illustrate this general property for the particular case of a macro-bending induced loss.Comment: 7 pages including 4 figures. Accepted for Opt. Expres