| 1. |
- Allain, J. P., et al.
(författare)
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Evolutionary rate and genetic drift of hepatitis C virus are not correlated with the host immune response : Studies of infected donor-recipient clusters
- 2000
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Ingår i: Journal of Virology. - 0022-538X .- 1098-5514. ; 74:6, s. 2541-2549
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Tidskriftsartikel (refereegranskat)abstract
- Six donor-recipient clusters of hepatitis C virus (HCV)-infected individuals were studied. For five clusters the period of infection of the donor could be estimated, and for all six clusters the time of infection of the recipients from the donor via blood transfusion was also precisely known. Detailed phylogenetic analyses were carried out to investigate the genomic evolution of the viral quasispecies within infected individuals in each cluster. The molecular clock analysis showed that HCV quasispecies within a patient are evolving at the same rate and that donors that have been infected for longer time tend to have a lower evolutionary rate. Phylogenetic analysis based on the split decomposition method revealed different evolutionary patterns in different donor-recipient clusters. Reactivity of antibody against the first hypervariable region (HVR1) of HCV in donor and recipient sera was evaluated and correlated to the calculated evolutionary rate. Results indicate that anti-HVR1 reactivity was related more to the overall level of humoral immune response of the host than to the HVR1 sequence itself, suggesting that the particular sequence of the HVR1 peptides is not the determinant of reactivity. Moreover, no correlation was found between the evolutionary rate or the heterogeneity of the viral quasispecies in the patients and the strength of the immune response to HVR1 epitopes, Rather, the results seem to imply that genetic drift is less dependent on immune pressure than on the rate of evolution and that the genetic drift of HCV is independent of the host immune pressure.
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| 2. |
- Bandelt, HJ, et al.
(författare)
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Quasi-median graphs from sets of partitions
- 2002
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Ingår i: Discrete Applied Mathematics. - 0166-218X .- 1872-6771. ; 122:23-35, s. 23-35
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- In studies of molecular evolution, one is typically confronted with the task of inferring a phylogenetic tree from a set X of sequences of length n over a finite alphabet Lambda. For studies that invoke parsimony, it has been found helpful to consider the quasi-median graph generated by X in the Hamming graph Lambda(n). Although a great deal is already known about quasi-median graphs (and their algebraic counterparts), little is known about the quasi-median generation in Lambda(n) starting from a set X of vertices. We describe the vertices of the quasi-median graph generated by X in terms of the coordinatewise partitions of X. In particular, we clarify when the generated quasi-median graph is the so-called relation graph associated with X. This immediately characterizes the instances where either a block graph or the total Hamming graph is generated.
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| 3. |
- Bécoulet, A., et al.
(författare)
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Science and technology research and development in support to ITER and the Broader Approach at CEA
- 2013
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 53:10
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Tidskriftsartikel (refereegranskat)abstract
- In parallel to the direct contribution to the procurement phase of ITER and Broader Approach, CEA has initiated research & development programmes, accompanied by experiments together with a significant modelling effort, aimed at ensuring robust operation, plasma performance, as well as mitigating the risks of the procurement phase. This overview reports the latest progress in both fusion science and technology including many areas, namely the mitigation of superconducting magnet quenches, disruption-generated runaway electrons, edge-localized modes (ELMs), the development of imaging surveillance, and heating and current drive systems for steady-state operation. The WEST (W Environment for Steady-state Tokamaks) project, turning Tore Supra into an actively cooled W-divertor platform open to the ITER partners and industries, is presented.
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| 4. |
- Cieslik, D, et al.
(författare)
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Connectivity calculus
- 2003
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Ingår i: Applied Mathematics Letters. - 0893-9659 .- 1873-5452. ; 16:3, s. 395-399
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Tidskriftsartikel (refereegranskat)abstract
- Given a finite hypergraph H = (V, E) and, for each e E E, a collection of nonempty subsets pi(e) of e, Mobius inversion is used to establish a recursive formula for the number of connected components of the hypergraph H = (V, boolean OR(eis an element ofE)pi(e)). As shown elsewhere, this formula is an essential ingredient in the context of a certain divide-and-conquer strategy that allows us to define a dynamical programming scheme solving Steiner's problem for graphs in linear time (however, with a constant depending hyperexponentially on their tree width).
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| 5. |
- Dress, A., et al.
(författare)
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Affine maps that induce polyhedral complex isomorphisms
- 2000
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Ingår i: Discrete & Computational Geometry. - 0179-5376 .- 1432-0444. ; 24:1, s. 49-60
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we show that an affine bijection f: T-1 --> T-2 between two polyhedral complexes T-1, T-2, both of which consist of a union of faces of two convex polyhedra P-1 and P-2, necessarily respects the cell-complex structure of T-1 and T-2 inherited from P-1 and P-2, respectively, provided f extends to an affine map from P-1 into P-2. In addition, we present an application of this result within the area of T-theory to obtain a far-reaching generalization of previous results regarding the equivalence of two distinct constructions of the phylogenetic tree associated to "perfect" (that is, treelike) distance data.
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| 6. |
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| 7. |
- Dress, A, et al.
(författare)
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Antipodal metrics and split systems
- 2002
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Ingår i: European Journal of Combinatorics. - : Elsevier BV. - 0195-6698 .- 1095-9971. ; 23:2, s. 187-200
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Tidskriftsartikel (refereegranskat)abstract
- Recall that a metric d on a finite set X is called antipodal if there exists a map sigma : X --> X: x --> (x) over bar so that d(x, (x) over bar) = d(x, y) + d(y, (x) over bar) holds for all x, y epsilon X. Antipodal metrics canonically arise as metrics induced on specific weighted graphs, although their abundance becomes clearer in light of the fact that any finite metric space can be isometrically embedded in a more or less canonical way into an antipodal metric space called its full antipodal extension. In this paper, we examine in some detail antipodal metrics that are, in addition, totally split decomposable. In particular, we give an explicit characterization of such metrics, and prove that-somewhat surprisingly-the full antipodal extension of a proper metric d on a finite set X is totally split decomposable if and only if d is linear or #X = 3 holds.
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| 8. |
- Dress, Andreas, et al.
(författare)
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Hereditarily Optimal Realizations of Consistent Metrics.
- 2006
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Ingår i: Annals of Combinatorics. - : Springer Science and Business Media LLC. - 0218-0006 .- 0219-3094. ; 10:1, s. 63-76
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Tidskriftsartikel (refereegranskat)abstract
- One of the main problems in phylogenetics is to find good approximations of metrics by weighted trees. As an aid to solving this problem, it could be tempting to consider optimal realizations of metrics—the guiding principle being that, the (necessarily unique) optimal realization of a tree metric is the weighted tree that realizes this metric. And, although optimal realizations of arbitrary metrics are, in general, not trees, but rather weighted networks, one could still hope to obtain a phylogenetically informative representation of a given metric, maybe even more informative than the best approximating tree. However, optimal realizations are not only difficult to compute, they may also be non-unique. Here we focus on one possible way out of this dilemma: hereditarily optimal realizations. These are essentially unique, and can be described in a rather explicit way. In this paper, we recall what a hereditarily optimal realization of a metric is and how it is related to the 1-skeleton of the tight span of that metric, and we investigate under what conditions it coincides with this 1-skeleton. As a consequence, we will show that hereditarily optimal realizations for consistent metrics, a large class of phylogentically relevant metrics, can be computed in a straight-forward fashion.
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| 9. |
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| 10. |
- Dress, A., et al.
(författare)
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On line arrangements in the hyperbolic plane
- 2002
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Ingår i: European journal of combinatorics (Print). - : Elsevier BV. - 0195-6698 .- 1095-9971. ; 23:5, s. 549-557
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Tidskriftsartikel (refereegranskat)abstract
- Given a finite collection L of lines in the hyperbolic plane H, we denote by k = k(L) its Karzanov number, i.e., the maximal number of pairwise intersecting lines in L, and by C(L) and n = n(L) the set and the number, respectively, of those points at infinity that are incident with at least one line from L. By using purely combinatorial properties of cyclic seta:, it is shown that #L less than or equal to 2nk - ((2k+1)(2)) always holds and that #L equals 2nk - ((2k+1)(2)) if and only if there is no collection L' of lines in H with L subset of or equal to L', k(L') = k(L) and C(L') = C(L).
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