Search results for "COD"

Stable maps from surfaces to the plane with prescribed branching data

2007

Abstract We consider the problem of constructing stable maps from surfaces to the plane with branch set a given set of curves immersed (except possibly with cusps) in the plane. Various constructions are used (1) piecing together regions immersed in the plane (2) modifying an existing stable map by a sequence of codimension one transitions (swallowtails etc) or by surgeries. In (1) the way the regions are pieced together is described by a bipartite graph (an edge C* corresponds to a branch curve C with the vertices of C* corresponding to the two regions containing C). We show that any bipartite graph may be realized by a stable map and we consider the question of realizing graphs by fold ma…

FLP estimation of semi-parametric models for space-time point processes and diagnostic tools

2015

Abstract The conditional intensity function of a space–time branching model is defined by the sum of two main components: the long-run term intensity and short-run term one. Their simultaneous estimation is a complex issue that usually requires the use of hard computational techniques. This paper deals with a new mixed estimation approach for a particular space–time branching model, the Epidemic Type Aftershock Sequence model. This approach uses a simultaneous estimation of the different model components, alternating a parametric step for estimating the induced component by Maximum Likelihood and a non-parametric estimation step, for the background intensity, by FLP (Forward Predictive Like…

Step-by-Step Control of the Dynamics of a Superconducting QED-like System

2007

We discuss the modus operandi of a theoretical scalable coupling scheme to control step by step the time evolution of a pair of flux qubits embedded in a lossy resonant cavity. The sequential interaction of each qubit with the quantized cavity mode is controlled by externally applied magnetic fluxes. Our analysis indicates that indirect qubit-qubit interactions, with the electromagnetic mode acting as a data bus, can be selectively performed and exploited both for the implementation of entangling gates and for the generation of states with a priori known characteristics.

Dans quelle mesure les préférences individuelles contraignent-elles le développement du marché de l'assurance dépendance ?

2015

Dans un contexte de vieillissement de la population, différents scenarii sont envisagés pour réformer l’organisation et le financement de la prise en charge des personnes âgées dépendantes. La place de la prévoyance individuelle dans le financement de la dépendance est à ce titre largement débattue. À l’heure actuelle, malgré des restes à charge potentiellement conséquents, peu d’individus disposent d’une couverture assurantielle. Cet article vise à enrichir la littérature existante en évaluant dans quelle mesure les préférences observées dans la population limitent cette couverture. Nous mobilisons pour cela l’enquête Patrimoine et préférences vis-à-vis du temps et du risque (Pater) de 201…

Adaptive reference-free compression of sequence quality scores

2014

Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are assigned to each sequence, even though these scores may be harder to compress than the sequences themselves. By aggregating a set of reads into a compressed index, we find that the majority of bases can be predicted from the sequence of bases that are adjacent to them and hence are likely to be less informative for variant calling or other applications. The quality scores for such bases are aggressively compressed, leaving a relatively small number at full reso…

2021

Abstract We prove the existence of a smoothing for a toroidal crossing space under mild assumptions. By linking log structures with infinitesimal deformations, the result receives a very compact form for normal crossing spaces. The main approach is to study log structures that are incoherent on a subspace of codimension 2 and prove a Hodge–de Rham degeneration theorem for such log spaces that also settles a conjecture by Danilov. We show that the homotopy equivalence between Maurer–Cartan solutions and deformations combined with Batalin–Vilkovisky theory can be used to obtain smoothings. The construction of new Calabi–Yau and Fano manifolds as well as Frobenius manifold structures on moduli…

On the dimerization of the primitive tRNAs: implications in the origin of genetic code.

2002

RNAs that catalyse their own aminoacylation have been recently selected in vitro. These findings support the notion that the primitive aminoacyl-tRNA synthetases may have been RNAs. In this paper, we propose a structural model for the first aminoacyl-tRNA synthetase consisting of an RNA complex formed between two primitive tRNA molecules through two intermolecular loop-strand interactions, and with implications in the origin of the genetic code.

Topological Minimally Entangled States via Geometric Measure

2014

Here we show how the Minimally Entangled States (MES) of a 2d system with topological order can be identified using the geometric measure of entanglement. We show this by minimizing this measure for the doubled semion, doubled Fibonacci and toric code models on a torus with non-trivial topological partitions. Our calculations are done either quasi-exactly for small system sizes, or using the tensor network approach in [R. Orus, T.-C. Wei, O. Buerschaper, A. Garcia-Saez, arXiv:1406.0585] for large sizes. As a byproduct of our methods, we see that the minimisation of the geometric entanglement can also determine the number of Abelian quasiparticle excitations in a given model. The results in …

kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.

2018

Abstract Motivation K-mers along with their frequency have served as an elementary building block for error correction, repeat detection, multiple sequence alignment, genome assembly, etc., attracting intensive studies in k-mer counting. However, the output of k-mer counters itself is large; very often, it is too large to fit into main memory, leading to highly narrowed usability. Results We introduce a novel idea of encoding k-mers as well as their frequency, achieving good memory saving and retrieval efficiency. Specifically, we propose a Bloom filter-like data structure to encode counted k-mers by coupled-bit arrays—one for k-mer representation and the other for frequency encoding. Exper…

ArtiFuse—computational validation of fusion gene detection tools without relying on simulated reads

2019

Abstract Motivation Gene fusions are an important class of transcriptional variants that can influence cancer development and can be predicted from RNA sequencing (RNA-seq) data by multiple existing tools. However, the real-world performance of these tools is unclear due to the lack of known positive and negative events, especially with regard to fusion genes in individual samples. Often simulated reads are used, but these cannot account for all technical biases in RNA-seq data generated from real samples. Results Here, we present ArtiFuse, a novel approach that simulates fusion genes by sequence modification to the genomic reference, and therefore, can be applied to any RNA-seq dataset wit…