Alvira : comparative genomics of viral strains

The Alvira tool is a general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. This new tool has been devised specifically to address the problem of the simultaneous analysis of a large number of viral strains. The multiple alignment is embedded in a graph that can be explored at different levels of resolution

Weighted Bergman kernels and virtual Bergman kernels

We introduce the notion of "virtual Bergman kernel" and apply it to the computation of the Bergman kernel of "domains inflated by Hermitian balls", in particular when the base domain is a bounded symmetric domain.Comment: 12 pages. One-hour lecture for graduate students, SCV 2004, August 2004, Beijing, P.R. China. V2: typo correcte

Frequency of Drug Resistance Gene Amplification in Clinical Leishmania Strains

Experimental studies about Leishmania resistance to metal and antifolates have pointed out that gene amplification is one of the main mechanisms of drug detoxification. Amplified genes code for adenosine triphosphate-dependent transporters (multidrug resistance and P-glycoproteins P), enzymes involved in trypanothione pathway, particularly gamma glutamyl cysteine synthase, and others involved in folates metabolism, such as dihydrofolate reductase and pterine reductase. The aim of this study was to detect and quantify the amplification of these genes in clinical strains of visceral leishmaniasis agents: Leishmania infantum, L. donovani, and L. archibaldi. Relative quantification experiments by means of real-time polymerase chain reaction showed that multidrug resistance gene amplification is the more frequent event. For P-glycoproteins P and dihydrofolate reductase genes, level of amplification was comparable to the level observed after in vitro selection of resistant clones. Gene amplification is therefore a common phenomenon in wild strains concurring to Leishmania genomic plasticity. This finding, which corroborates results of experimental studies, supports a better understanding of metal resistance selection and spreading in endemic areas

Balanced metrics on Cartan and Cartan-Hartogs domains

This paper consists of two results dealing with balanced metrics (in S. Donaldson terminology) on nonconpact complex manifolds. In the first one we describe all balanced metrics on Cartan domains. In the second one we show that the only Cartan-Hartogs domain which admits a balanced metric is the complex hyperbolic space. By combining these results with those obtained in [13] (Kaehler-Einstein submanifolds of the infinite dimensional projective space, to appear in Mathematische Annalen) we also provide the first example of complete, Kaehler-Einstein and projectively induced metric g such that $\alpha g$ is not balanced for all $\alpha >0$.Comment: 11 page

Metric trees of generalized roundness one

Every finite metric tree has generalized roundness strictly greater than one. On the other hand, some countable metric trees have generalized roundness precisely one. The purpose of this paper is to identify some large classes of countable metric trees that have generalized roundness precisely one. At the outset we consider spherically symmetric trees endowed with the usual combinatorial metric (SSTs). Using a simple geometric argument we show how to determine decent upper bounds on the generalized roundness of finite SSTs that depend only on the downward degree sequence of the tree in question. By considering limits it follows that if the downward degree sequence $(d_{0}, d_{1}, d_{2}...)$ of a SST $(T,\rho)$ satisfies $|\{j \, | \, d_{j} > 1 \}| = \aleph_{0}$, then $(T,\rho)$ has generalized roundness one. Included among the trees that satisfy this condition are all complete $n$-ary trees of depth $\infty$ ($n \geq 2$), all $k$-regular trees ($k \geq 3$) and inductive limits of Cantor trees. The remainder of the paper deals with two classes of countable metric trees of generalized roundness one whose members are not, in general, spherically symmetric. The first such class of trees are merely required to spread out at a sufficient rate (with a restriction on the number of leaves) and the second such class of trees resemble infinite combs.Comment: 14 pages, 2 figures, 2 table

A second order cone formulation of continuous CTA model

The final publication is available at link.springer.comIn this paper we consider a minimum distance Controlled Tabular Adjustment (CTA) model for statistical disclosure limitation (control) of tabular data. The goal of the CTA model is to find the closest safe table to some original tabular data set that contains sensitive information. The measure of closeness is usually measured using l1 or l2 norm; with each measure having its advantages and disadvantages. Recently, in [4] a regularization of the l1 -CTA using Pseudo-Huber func- tion was introduced in an attempt to combine positive characteristics of both l1 -CTA and l2 -CTA. All three models can be solved using appro- priate versions of Interior-Point Methods (IPM). It is known that IPM in general works better on well structured problems such as conic op- timization problems, thus, reformulation of these CTA models as conic optimization problem may be advantageous. We present reformulation of Pseudo-Huber-CTA, and l1 -CTA as Second-Order Cone (SOC) op- timization problems and test the validity of the approach on the small example of two-dimensional tabular data set.Peer ReviewedPostprint (author's final draft

Notes on Stein-Sahi representations and some problems of non L2L^2 harmonic analysis

We discuss one natural class of kernels on pseudo-Riemannian symmetric spaces.Comment: 40p

VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Background: Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. Findings: A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. Conclusions: We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies

Stein--Sahi complementary series and their degenerations

The aim of the paper is an introduction to Stein--Sahi complementary series, holomorphic series, and 'unipotent representations'. We also discuss some open problems related to these objects. For the sake of simplicity, we consider only the groups U(n,n).Comment: 40pp, 7fig, revised versio

Meromorphic tensor equivalence for Yangians and quantum loop algebras

Let ${\mathfrak g}$ be a complex semisimple Lie algebra, and $Y_h({\mathfrak g})$, $U_q(L{\mathfrak g})$ the corresponding Yangian and quantum loop algebra, with deformation parameters related by $q=\exp(\pi i h)$. When $h$ is not a rational number, we constructed in arXiv:1310.7318 a faithful functor $\Gamma$ from the category of finite-dimensional representations of $Y_h ({\mathfrak g})$ to those of $U_q(L{\mathfrak g})$. The functor $\Gamma$ is governed by the additive difference equations defined by the commuting fields of the Yangian, and restricts to an equivalence on a subcategory of $Y_h({\mathfrak g})$ defined by choosing a branch of the logarithm. In this paper, we construct a tensor structure on $\Gamma$ and show that, if $|q|\neq 1$, it yields an equivalence of meromorphic braided tensor categories, when $Y_h({\mathfrak g})$ and $U_q(L{\mathfrak g})$ are endowed with the deformed Drinfeld coproducts and the commutative part of the universal $R$-matrix. This proves in particular the Kohno-Drinfeld theorem for the abelian $q$KZ equations defined by $Y_h({\mathfrak g})$. The tensor structure arises from the abelian $q$KZ equations defined by a appropriate regularisation of the commutative $R$-matrix of $Y_h({\mathfrak g})$.Comment: Title changed, details added. 67 pages, 1 figure. Final version, to appear in Publ. Math IHE