| 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
-
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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| 11. |
- Dress, A., et al.
(författare)
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Six points suffice : How to check for metric consistency
- 2001
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Ingår i: European journal of combinatorics (Print). - : Elsevier BV. - 0195-6698 .- 1095-9971. ; 22:4, s. 465-474
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Tidskriftsartikel (refereegranskat)abstract
- In many areas of data analysis, it is desirable to have tools at hand for analyzing the structure of distance tables-or, in more mathematical terms, of finite metric spaces. One such tool, known as split decomposition theory has proven particularly useful in this respect. Tbe class of so-called totally decomposable metrics forms a cornerstone for this theory, and much work has been devoted to their study. Recently, it has become apparent that a particular subclass of these metrics, the consistent metrics, are also of fundamental importance. In this paper, we give a six-point characterization of consistent metrics amongst the totally decomposable ones.
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| 12. |
- Edvardsson, Sverker, et al.
(författare)
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A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction
- 2003
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 19:7, s. 865-873
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Tidskriftsartikel (refereegranskat)abstract
- We develop an algorithm to screen the yeast genome for novel H/ACA snoRNAs. To achieve this, we introduce some new methods for facilitating the search for noncoding RNAs in genomic sequences which are based on properties of predicted minimum free-energy (MFE) secondary structures. The algorithm has been implemented and can be generalized to enable screening of other eukaryote genomes. We find that use of primary sequence alone is insufficient for identifying novel H/ACA snoRNAs. Only the use of secondary structure filters reduces the number of candidates to a manageable size. From genomic context, we identify three strong H/ACA snoRNA candidates. These together with a further 47 candidates obtained by our analysis are being experimentally screened.
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| 13. |
- Forslund, Kristoffer, et al.
(författare)
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VisRD--visual recombination detection.
- 2004
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Ingår i: Bioinformatics. - 1367-4803 .- 1367-4811. ; 20:18, s. 3654-5
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Tidskriftsartikel (refereegranskat)
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| 14. |
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| 15. |
- Freyhult, Eva, et al.
(författare)
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Boltzmann probability of RNA structural neighbors and riboswitch detection
- 2007
-
Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 23:16, s. 2054-2062
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: We describe algorithms implemented in a new software package, RNAbor, to investigate structures in a neighborhood of an input secondary structure of an RNA sequence s. The input structure could be the minimum free energy structure, the secondary structure obtained by analysis of the X-ray structure or by comparative sequence analysis, or an arbitrary intermediate structure. Results: A secondary structure of s is called a -neighbor of if and differ by exactly base pairs. RNAbor computes the number (N), the Boltzmann partition function (Z) and the minimum free energy (MFE) and corresponding structure over the collection of all -neighbors of . This computation is done simultaneously for all m, in run time O (mn3) and memory O(mn2), where n is the sequence length. We apply RNAbor for the detection of possible RNA conformational switches, and compare RNAbor with the switch detection method paRNAss. We also provide examples of how RNAbor can at times improve the accuracy of secondary structure prediction.
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| 16. |
- Freyhult, Eva, et al.
(författare)
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Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update
- 2008
-
Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 1:49, s. 1-8
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe H/ACA family of small nucleolar RNAs (snoRNAs) plays a central role in guiding the pseudouridylation of ribosomal RNA (rRNA). In an effort to systematically identify the complete set of rRNA-modifying H/ACA snoRNAs from the genome sequence of the budding yeast, Saccharomyces cerevisiae, we developed a program - Fisher - and previously presented several candidate snoRNAs based on our analysis [1]. FindingsIn this report, we provide a brief update of this work, which was aborted after the publication of experimentally-identified snoRNAs [2] identical to candidates we had identified bioinformatically using Fisher. Our motivation for revisiting this work is to report on the status of the candidate snoRNAs described in [1], and secondly, to report that a modified version of Fisher together with the available multiple yeast genome sequences was able to correctly identify several H/ACA snoRNAs for modification sites not identified by the snoGPS program [3]. While we are no longer developing Fisher, we briefly consider the merits of the Fisher algorithm relative to snoGPS, which may be of use for workers considering pursuing a similar search strategy for the identification of small RNAs. The modified source code for Fisher is made available as supplementary material. ConclusionOur results confirm the validity of using minimum free energy (MFE) secondary structure prediction to guide comparative genomic screening for RNA families with few sequence constraints.
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| 17. |
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| 18. |
- Freyhult, Eva, et al.
(författare)
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Predicting RNA structure using mutual information.
- 2005
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Ingår i: Applied Bioinformatics. - 1175-5636. ; 4:1, s. 53-59
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: With the ever-increasing number of sequenced RNAs and the establishment of new RNA databases, such as the Comparative RNA Web Site and Rfam, there is a growing need for accurately and automatically predicting RNA structures from multiple alignments. Since RNA secondary structure is often conserved in evolution, the well known, but underused, mutual information measure for identifying covarying sites in an alignment can be useful for identifying structural elements. This article presents MIfold, a MATLAB((R)) toolbox that employs mutual information, or a related covariation measure, to display and predict conserved RNA secondary structure (including pseudoknots) from an alignment. RESULTS: We show that MIfold can be used to predict simple pseudoknots, and that the performance can be adjusted to make it either more sensitive or more selective. We also demonstrate that the overall performance of MIfold improves with the number of aligned sequences for certain types of RNA sequences. In addition, we show that, for these sequences, MIfold is more sensitive but less selective than the related RNAalifold structure prediction program and is comparable with the COVE structure prediction package. CONCLUSION: MIfold provides a useful supplementary tool to programs such as RNA Structure Logo, RNAalifold and COVE, and should be useful for automatically generating structural predictions for databases such as Rfam. AVAILABILITY: MIfold is freely available from http://www.lcb.uu.se/~evaf/MIfold/
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| 19. |
- Freyhult, Eva, et al.
(författare)
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RNAbor : a web server for RNA structural neighbors
- 2007
-
Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 35:Suppl. S: Web Server issue, s. W305-W309
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Tidskriftsartikel (refereegranskat)abstract
- RNAbor provides a new tool for researchers in the biological and related sciences to explore important aspects of RNA secondary structure and folding pathways. RNAbor computes statistics concerning delta-neighbors of a given input RNA sequence and structure (the structure can, for example, be the minimum free energy (MFE) structure). A delta-neighbor is a structure that differs from the input structure by exactly delta base pairs, that is, it can be obtained from the input structure by adding and/or removing exactly d base pairs. For each distance delta RNAbor computes the density of delta-neighbors, the number of delta-neighbors, and the MFE structure, or MFEd structure, among all delta-neighbors. RNAbor can be used to study possible folding pathways, to determine alternate low-energy structures, to predict potential nucleation sites and to explore structural neighbors of an intermediate, biologically active structure. The web server is available at http://bioinformatics.bc.edu/clotelab/RNAbor.
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| 20. |
- Freyhult, Eva, et al.
(författare)
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Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling
- 2005
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 6, s. 50-
-
Tidskriftsartikel (refereegranskat)abstract
- Background Proteochemometrics is a new methodology that allows prediction of protein function directly from real interaction measurement data without the need of 3D structure information. Several reported proteochemometric models of ligand-receptor interactions have already yielded significant insights into various forms of bio-molecular interactions. The proteochemometric models are multivariate regression models that predict binding affinity for a particular combination of features of the ligand and protein. Although proteochemometric models have already offered interesting results in various studies, no detailed statistical evaluation of their average predictive power has been performed. In particular, variable subset selection performed to date has always relied on using all available examples, a situation also encountered in microarray gene expression data analysis. Results A methodology for an unbiased evaluation of the predictive power of proteochemometric models was implemented and results from applying it to two of the largest proteochemometric data sets yet reported are presented. A double cross-validation loop procedure is used to estimate the expected performance of a given design method. The unbiased performance estimates (P2) obtained for the data sets that we consider confirm that properly designed single proteochemometric models have useful predictive power, but that a standard design based on cross validation may yield models with quite limited performance. The results also show that different commercial software packages employed for the design of proteochemometric models may yield very different and therefore misleading performance estimates. In addition, the differences in the models obtained in the double CV loop indicate that detailed chemical interpretation of a single proteochemometric model is uncertain when data sets are small. Conclusion The double CV loop employed offer unbiased performance estimates about a given proteochemometric modelling procedure, making it possible to identify cases where the proteochemometric design does not result in useful predictive models. Chemical interpretations of single proteochemometric models are uncertain and should instead be based on all the models selected in the double CV loop employed here.
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| 21. |
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| 22. |
- Gill, Jonna, et al.
(författare)
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A regular decomposition of the edge-product space of phylogenetic trees
- 2008
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Ingår i: Advances in Applied Mathematics. - : Elsevier BV. - 0196-8858 .- 1090-2074. ; 41:2, s. 158-176
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the topology and combinatorics of a topological space called the edge-product space that is generated by the set of edge-weighted finite labelled trees. This space arises by multiplying the weights of edges on paths in trees, and is closely connected to tree-indexed Markov processes in molecular evolutionary biology. In particular, by considering combinatorial properties of the Tuffley poset of labelled forests, we show that the edge-product space has a regular cell decomposition with face poset equal to the Tuffley poset.
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| 23. |
- Goodman, O., et al.
(författare)
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On the tight span of an antipodal graph
- 2000
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Ingår i: Discrete Mathematics. - 0012-365X .- 1872-681X. ; 218:1-3, s. 73-96
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Tidskriftsartikel (refereegranskat)abstract
- The tight span of a finite metric space is essentially the 'smallest' path geodesic space into which the metric space embeds isometrically. In this situation, the tight span is also contractible and has a natural cell structure, so that it lends itself naturally to the study of the Cayley graph of a group. As a first step in this study, we consider the tight span of a metric space which arises from the graph metric of an antipodal graph. In particular, we develop techniques for the study of the tight span of a graph, which we then apply to antipodal graphs. In this way, we are able to find the polytopal structure of the tight span for special examples of antipodal graphs. Finally, we present computer generated examples of tight spans which were made possible by the techniques developed in this paper. (C) 2000 Elsevier Science B.V. All rights reserved.
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| 24. |
- Grünewald, Stefan, et al.
(författare)
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QNet : an agglomerative method for the construction of phylogenetic networks from weighted quartets.
- 2007
-
Ingår i: Mol Biol Evol. - 0737-4038. ; 24:2, s. 532-8
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Tidskriftsartikel (refereegranskat)abstract
- We present QNet, a method for constructing split networks from weighted quartet trees. QNet can be viewed as a quartet analogue of the distance-based Neighbor-Net (NNet) method for network construction. Just as NNet, QNet works by agglomeratively computing a collection of circular weighted splits of the taxa set which is subsequently represented by a planar split network. To illustrate the applicability of QNet, we apply it to a previously published Salmonella data set. We conclude that QNet can provide a useful alternative to NNet if distance data are not available or a character-based approach is preferred. Moreover, it can be used as an aid for determining when a quartet-based tree-building method may or may not be appropriate for a given data set. QNet is freely available for download.
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| 25. |
- Gutman, I., et al.
(författare)
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Estimating and approximating the total pi-electron energy of benzenoid hydrocarbons
- 2000
-
Ingår i: Zeitschrift fur Naturforschung A-A Journal of Physical Sciences. - 0932-0784 .- 1865-7109. ; 55:5, s. 507-512
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Tidskriftsartikel (refereegranskat)abstract
- Lower and upper bounds as well as approximate formulas for the total pi-electron energy (E) of benzenoid hydrocarbons are deduced, depending only on the number of carbon atoms (n) and number of carbon-carbon bonds (m). These are better than the several previously known (n, m)-type estimates and approximations for E.
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| 26. |
- Herrmann, Sven, et al.
(författare)
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Optimal realizations of two-dimensional, totally-decomposable metrics
- 2015
-
Ingår i: Discrete Mathematics. - : Elsevier BV. - 0012-365X .- 1872-681X. ; 338:8, s. 1289-1299
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Tidskriftsartikel (refereegranskat)abstract
- A realization of a metric d on a finite set X is a weighted graph (G, w) whose vertex set contains X such that the shortest-path distance between elements of X considered as vertices in G is equal to d. Such a realization (G, w) is called optimal if the sum of its edge weights is minimal over all such realizations. Optimal realizations always exist, although it is NP-hard to compute them in general, and they have applications in areas such as phylogenetics, electrical networks and internet tomography. A. Dress (1984) showed that the optimal realizations of a metric dare closely related to a certain polytopal complex that can be canonically associated to d called its tight-span. Moreover, he conjectured that the (weighted) graph consisting of the zero- and one-dimensional faces of the tight-span of d must always contain an optimal realization as a homeomorphic subgraph. In this paper, we prove that this conjecture does indeed hold for a certain class of metrics, namely the class of totally-decomposable metrics whose tight-span has dimension two. As a corollary, it follows that the minimum Manhattan network problem is a special case of finding optimal realizations of two-dimensional totally-decomposable metrics. (C) 2015 Elsevier B.V. All rights reserved.
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| 27. |
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| 28. |
- Huber, Katharina T, et al.
(författare)
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Pruned median networks : A technique for reducing the complexity of median networks
- 2001
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 19:2, s. 302-310
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Tidskriftsartikel (refereegranskat)abstract
- Observations from molecular marker studies on recently diverged species indicate that substitution patterns in DNA sequences can often be complex and poorly described by tree-like bifurcating evolutionary models. These observations might result from processes of-species diversification and/or processes of sequence evolution that are not tree-like. In these Cases, bifurcating tree representations provide poor visualization of phylogenetic signals in sequence data. In this paper, we use median networks to study DNA sequence substitution patterns in plant nuclear and chloroplast markers. We describe how to prune median networks to obtain so called pruned median networks. These simpler networks may help to provide a useful framework for investigating the phylogenetic complexity of recently diverged taxa with hybrid origins.
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| 29. |
- Huber, Katharina T., et al.
(författare)
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Reconstructing the evolutionary history of polyploids from multilabeled trees
- 2006
-
Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 23:9, s. 1784-1791
-
Tidskriftsartikel (refereegranskat)abstract
- In recent studies, phylogenetic networks have been derived from so-called multilabeled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were constructed using sophisticated techniques in phylogenetic analysis, the presented networks were inferred using ad hoc arguments that cannot be easily extended to larger, more complicated examples. In this paper, we present a general method for constructing such networks, which takes as input a multilabeled phylogenetic tree and outputs a phylogenetic network with certain desirable properties. To illustrate the applicability of our method, we discuss its use in reconstructing the evolutionary history of plant allopolyploids. We conclude with a discussion concerning possible future directions. The network construction method has been implemented and is freely available for use from http://www.uea.ac.uk/similar to a043878/padre.html.
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| 30. |
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| 31. |
- Huber, K. T., et al.
(författare)
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The relation graph
- 2002
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Ingår i: Discrete Mathematics. - 0012-365X .- 1872-681X. ; 244:1-3, s. 153-166
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Tidskriftsartikel (refereegranskat)abstract
- Given a set R of distinct, non-trivial partitions of a finite set, we define the relation graph G(R) of R. In case R consists only of bipartitions, G(R) is the well-known Buneman graph, a median graph that has applications in the area of phylogenetic analysis., Here we consider properties of the relation graph for general sets of partitions and, in particular, we see that it mimics the behaviour of the Buneman graph by proving the following two theorems:(i) The graph G(R) is a Hamming graph if and only if R is strongly incompatible.(ii) The graph G(R) is a block graph with #R blocks if and only if R is strongly compatible.
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| 32. |
- Joffrin, E., et al.
(författare)
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Overview of the JET preparation for deuterium-tritium operation with the ITER like-wall
- 2019
-
Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 59:11
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Forskningsöversikt (refereegranskat)abstract
- For the past several years, the JET scientific programme (Pamela et al 2007 Fusion Eng. Des. 82 590) has been engaged in a multi-campaign effort, including experiments in D, H and T, leading up to 2020 and the first experiments with 50%/50% D-T mixtures since 1997 and the first ever D-T plasmas with the ITER mix of plasma-facing component materials. For this purpose, a concerted physics and technology programme was launched with a view to prepare the D-T campaign (DTE2). This paper addresses the key elements developed by the JET programme directly contributing to the D-T preparation. This intense preparation includes the review of the physics basis for the D-T operational scenarios, including the fusion power predictions through first principle and integrated modelling, and the impact of isotopes in the operation and physics of D-T plasmas (thermal and particle transport, high confinement mode (H-mode) access, Be and W erosion, fuel recovery, etc). This effort also requires improving several aspects of plasma operation for DTE2, such as real time control schemes, heat load control, disruption avoidance and a mitigation system (including the installation of a new shattered pellet injector), novel ion cyclotron resonance heating schemes (such as the three-ions scheme), new diagnostics (neutron camera and spectrometer, active Alfven eigenmode antennas, neutral gauges, radiation hard imaging systems...) and the calibration of the JET neutron diagnostics at 14 MeV for accurate fusion power measurement. The active preparation of JET for the 2020 D-T campaign provides an incomparable source of information and a basis for the future D-T operation of ITER, and it is also foreseen that a large number of key physics issues will be addressed in support of burning plasmas.
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| 33. |
- Koolen, J., et al.
(författare)
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A classification of the six-point prime metrics
- 2000
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Ingår i: European journal of combinatorics (Print). - 0195-6698 .- 1095-9971. ; 21:6, s. 815-829
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Tidskriftsartikel (refereegranskat)abstract
- The notion of a coherent decomposition of a metric on a finite set has proven fruitful, with applications to areas such as the geometry of metric cones and bioinformatics. In order to obtain a deeper insight into these decompositions it is important to improve our knowledge of those metrics which cannot be coherently decomposed in a non-trivial way, i.e.,the prime metrics. In this paper we classify the prime metrics on six points. (C) 2000 Academic Press.
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| 34. |
- Koolen, Jack, et al.
(författare)
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Concerning the relationship between realizations and tight spans of finite metrics
- 2007
-
Ingår i: Discrete & Computational Geometry. - : Springer Science and Business Media LLC. - 0179-5376 .- 1432-0444. ; 38:3, s. 605-614
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Tidskriftsartikel (refereegranskat)abstract
- Given a metric d on a finite set X, a realization of d is a weighted graph $G=(V,E,w\colon \ E \to {\Bbb R}_{>0})$ with $X \subseteq V$ such that for all $x,y \in X$ the length of any shortest path in G between x and y equals d(x,y). In this paper we consider two special kinds of realizations, optimal realizations and hereditarily optimal realizations, and their relationship with the so-called tight span. In particular, we present an infinite family of metrics {dk}k≥1, and—using a new characterization for when the so-called underlying graph of a metric is an optimal realization that we also present—we prove that dk has (as a function of k) exponentially many optimal realizations with distinct degree sequences. We then show that this family of metrics provides counter-examples to a conjecture made by Dress in 1984 concerning the relationship between optimal realizations and the tight span, and a negative reply to a question posed by Althofer in 1988 on the relationship between optimal and hereditarily optimal realizations.
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| 35. |
- Koolen, J. H., et al.
(författare)
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Improving the McClelland inequality for total pi-electron energy
- 2000
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Ingår i: Chemical Physics Letters. - 0009-2614 .- 1873-4448. ; 320:3-4, s. 213-216
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Tidskriftsartikel (refereegranskat)abstract
- The McClelland inequality, E less than or equal to root 2mn, estimates the total pi-electron energy (E) of a conjugated hydrocarbon by means of the number of carbon atoms (n) and the number of carbon-carbon bonds (m). We now show that in the general case 2m/n + root(n - 1)(2m - 4m(2)/n(2)) is a better (n,m)-type upper bound for E. An even better estimate, 4m/n + root(n - 2)(2m - 8m(2)/n(2)), holds for alternant hydrocarbons. (C) 2000 Elsevier Science B.V. All rights reserved.
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| 36. |
- Koolen, Jack H., et al.
(författare)
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Injective optimal realizations of finite metric spaces
- 2012
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Ingår i: Discrete Mathematics. - : Elsevier BV. - 0012-365X .- 1872-681X. ; 312:10, s. 1602-1610
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Tidskriftsartikel (refereegranskat)abstract
- A realization of a finite metric space (X, d) is a weighted graph (G, w) whose vertex set contains X such that the distances between the elements of X in G correspond to those given by d. Such a realization is called optimal if it has minimal total edge weight. Optimal realizations have applications in fields such as phylogenetics, psychology, compression software and Internet tomography. Given an optimal realization (G, w) of (X, d), there always exist certain "proper" maps from the vertex set of G into the so-called tight span of d. In [A. Dress, Trees, tight extensions of metric spaces, and the cohomological dimension of certain groups: a note on combinatorial properties of metric spaces, Adv. Math. 53 (1984) 321-402], Dress conjectured that any such map must be injective. Although this conjecture was recently disproven, in this paper we show that it is possible to characterize those optimal realizations (G, w) for which certain generalizations of proper maps - that map the geometric realization of (G, w) into the tight span instead of its vertex set - must always be injective. We also prove that these "injective" optimal realizations always exist, and show how they may be constructed from non-injective ones. Ultimately it is hoped that these results will contribute towards developing new ways to compute optimal realizations from tight spans.
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| 37. |
- Koolen, J H, et al.
(författare)
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Maximal energy bipartite graphs
- 2003
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Ingår i: Graphs and Combinatorics. - : Springer Science and Business Media LLC. - 0911-0119 .- 1435-5914. ; 19:1, s. 131-135
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Tidskriftsartikel (refereegranskat)abstract
- Given a graph G, its energy E(G) is defined to be the sum of the absolute values of the eigenvalues of G. This quantity is used in chemistry to approximate the total pi-electron energy of molecules and in particular, in case G is bipartite, alternant hydrocarbons. Here we show that if G is a bipartite graph with n vertices, thenE(G) less than or equal to n/(root8 (root2 + n)must hold, characterize those bipartite graphs for which this bound is sharp, and provide an infinite family of maximal energy bipartite graphs.Given a graph G, define the energy of G, denoted E(G), by[GRAPHICS]where the eigenvalues of, G are simply those of the adjacency matrix of G. In chemistry, the energy of a graph is intensively studied since it can be used to approximate, the total pi-electron energy of a molecule (see, for example, [3, 6, 8]). In [12], we considered maximal energy graphs (see also [9, 10, 13, 14, 17] for related results). In particular, for any graph G with n vertices, we derived an improvement of the well-known McClelland bound [15] for the energy of a graph, showing thatE(G) less than or equal to n/2(1 + rootn)must hold. We also characterized those graphs for which this bound is sharp, i.e. the maximal energy graphs, and provided an infinite family of such graphs.
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| 38. |
- Koolen, J H, et al.
(författare)
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Maximal energy graphs
- 2001
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Ingår i: Advances in Applied Mathematics. - : Elsevier BV. - 0196-8858 .- 1090-2074. ; 26:1, s. 47-52
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Tidskriftsartikel (refereegranskat)abstract
- Given a graph G, its energy E(G) is defined as the sum of the absolute values of the eigenvalues of G. The concept of the energy of a graph was introduced in the subject of chemistry by I. Gutman. due to its relevance to the total pi -elrctron energy of certain molecules. In this paper, we show that if G is a graph on n vertices, then E(G) less than or equal to (n/2)(1 + rootn) must hold, and we give an infinite family of graphs for which this bound is sharp.
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| 39. |
- Koolen, J. H., et al.
(författare)
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More hyperenergetic molecular graphs
- 2000
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Ingår i: Journal of the Serbian Chemical Society. - 0352-5139 .- 1820-7421. ; 65:8, s. 571-575
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Tidskriftsartikel (refereegranskat)abstract
- If G is a molecular graph and lambda(1), lambda(2),... lambda(n) are its eigenvalues, then the energy of G is equal to E(G) = \lambda(1)\+ \lambda(2)\+... + \lambda(n)\. This energy cannot exceed the value n root(n - 1) approximate to n(3/2). The graph G is said to be hyperenergetic if E(G) > 2n - 2. We describe the construction of hyperenergetic graphs G for which E(G) approximate to 1/2 n(3/2).
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| 40. |
- Koolen, JH, et al.
(författare)
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Hyperbolic bridged graphs
- 2002
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Ingår i: European Journal of Combinatorics. - : Elsevier BV. - 0195-6698 .- 1095-9971. ; 23:6, s. 683-699
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Tidskriftsartikel (refereegranskat)abstract
- Given a connected graph G, we take, as usual, the distance xy between any two vertices x, y of G to be the length of some geodesic between x and y. The graph G is said to be delta-hyperbolic, for some 3 : 0, if for all vertices x, y, u, v in G the inequality xy + uv :5 max{xu + yv, xv + yu} + delta holds, and G is bridged if it contains no finite isometric cycles of length four or more. In this paper, we will show that a finite connected bridged graph is 1-hyperbolic if and only if it does not contain any of a list of six graphs as an isometric subgraph.
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| 41. |
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| 42. |
- Koolen, Jack, et al.
(författare)
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Optimal realizations of generic 5-point metrics
- 2009
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Ingår i: European journal of combinatorics (Print). - : Elsevier BV. - 0195-6698 .- 1095-9971. ; 30:5, s. 1164-1171
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Tidskriftsartikel (refereegranskat)abstract
- Given a metric cl oil a finite set X, a realization of d is a triple (G, phi, omega) consisting of a graph G = (V, E), a labeling phi : X -> V, and a weighting omega : E -> R->0 such that for all x, y is an element of X the length of any shortest path in G between phi(x) and phi(y) equals d(x, y). Such a realization is called optimal if parallel to G parallel to := Sigma(e is an element of E) omega(e) is minimal amongst all realizations of d. In this paper we will consider optimal realizations of generic five-point metric spaces. In particular, we show that there is a canonical subdivision C Of the metric fail of five-point metrics into cones such that (i) every metric d in the interior of a cone C is an element of C has a unique optimal realization (G, phi, omega), (ii) if d' is also in the interior of C with optimal realization (G', phi', omega') then (G, phi) and (G', phi') are isomorphic as labeled graphs, and (iii) any labeled graph that underlies all optimal realizations of the metrics in the interior of some cone C e C must belong to one of three isomorphism classes.
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| 43. |
- Kutalic, Zoltan, et al.
(författare)
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S-system parameter estimation for noisy metabolic profiles using Newton-flow analysis
- 2007
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Ingår i: IET Systems Biology. - : Institution of Engineering and Technology (IET). - 1751-8849 .- 1751-8857. ; 1:3, s. 174-180
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Tidskriftsartikel (refereegranskat)abstract
- Biochemical systems are commonly modelled by systems of ordinary differentialequations (ODEs). A particular class of such models called S-systems have recently gained popu-larity in biochemical system modelling. The parameters of an S-system are usually estimated fromtime-course profiles. However, finding these estimates is a difficult computational problem.Moreover, although several methods have been recently proposed to solve this problem for idealprofiles, relatively little progress has been reported for noisy profiles. We describe a specialfeature of a Newton-flow optimisation problem associated with S-system parameter estimation.This enables us to significantly reduce the search space, and also lends itself to parameter esti-mation for noisy data. We illustrate the applicability of our method by applying it to noisy time-course data synthetically produced from previously published 4- and 30-dimensional S-systems.In addition, we propose an extension of our method that allows the detection of network topologiesfor small S-systems. We introduce a new method for estimating S-system parameters from time-course profiles. We show that the performance of this method compares favorably with competingmethods for ideal profiles, and that it also allows the determination of parameters for noisy profiles.
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| 44. |
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| 45. |
- Lesser, Alice, 1977-
(författare)
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Optimal and Hereditarily Optimal Realizations of Metric Spaces
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This PhD thesis, consisting of an introduction, four papers, and some supplementary results, studies the problem of finding an optimal realization of a given finite metric space: a weighted graph which preserves the metric's distances and has minimal total edge weight. This problem is known to be NP-hard, and solutions are not necessarily unique.It has been conjectured that extremally weighted optimal realizations may be found as subgraphs of the hereditarily optimal realization Γd, a graph which in general has a higher total edge weight than the optimal realization but has the advantages of being unique, and possible to construct explicitly via the tight span of the metric.In Paper I, we prove that the graph Γd is equivalent to the 1-skeleton of the tight span precisely when the metric considered is totally split-decomposable. For the subset of totally split-decomposable metrics known as consistent metrics this implies that Γd is isomorphic to the easily constructed Buneman graph.In Paper II, we show that for any metric on at most five points, any optimal realization can be found as a subgraph of Γd.In Paper III we provide a series of counterexamples; metrics for which there exist extremally weighted optimal realizations which are not subgraphs of Γd. However, for these examples there also exists at least one optimal realization which is a subgraph.Finally, Paper IV examines a weakened conjecture suggested by the above counterexamples: can we always find some optimal realization as a subgraph in Γd? Defining extremal optimal realizations as those having the maximum possible number of shortest paths, we prove that any embedding of the vertices of an extremal optimal realization into Γd is injective. Moreover, we prove that this weakened conjecture holds for the subset of consistent metrics which have a 2-dimensional tight span
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| 46. |
- Lott, Martin, et al.
(författare)
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Inferring polyploid phylogenies from multiply-labeled gene trees.
- 2009
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Ingår i: BMC evolutionary biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Gene trees that arise in the context of reconstructing the evolutionary history of polyploid species are often multiply-labeled, that is, the same leaf label can occur several times in a single tree. This property considerably complicates the task of forming a consensus of a collection of such trees compared to usual phylogenetic trees. RESULTS: We present a method for computing a consensus tree of multiply-labeled trees. As with the well-known greedy consensus tree approach for phylogenetic trees, our method first breaks the given collection of gene trees into a set of clusters. It then aims to insert these clusters one at a time into a tree, starting with the clusters that are supported by most of the gene trees. As the problem to decide whether a cluster can be inserted into a multiply-labeled tree is computationally hard, we have developed a heuristic method for solving this problem. CONCLUSION: We illustrate the applicability of our method using two collections of trees for plants of the genus Silene, that involve several allopolyploids at different levels.
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| 47. |
- Mock, Thomas, et al.
(författare)
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Multiomics in the central Arctic Ocean for benchmarking biodiversity change
- 2022
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 20:10
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Tidskriftsartikel (refereegranskat)abstract
- Multiomics approaches need to be applied in the central Arctic Ocean to benchmark biodiversity change and to identify novel species and their genes. As part of MOSAiC, EcoOmics will therefore be essential for conservation and sustainable bioprospecting in one of the least explored ecosystems on Earth.
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| 48. |
- Moulton, Vincent, et al.
(författare)
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Metrics on RNA secondary structures
- 2000
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Ingår i: Journal of Computational Biology. - : Mary Ann Liebert Inc. - 1066-5277 .- 1557-8666. ; 7:1-2, s. 277-292
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Tidskriftsartikel (refereegranskat)abstract
- Many different programs have been developed for the prediction of the secondary structure of an RNA sequence, Some of these programs generate an ensemble of structures, all of which have free energy close to that of the optimal structure, making it important to be able to quantify how similar these different structures are. To deal with this problem, we define a new class of metrics, the mountain metrics, on the set of RNA secondary structures of a fixed length, We compare properties of these metrics with other well known metrics on RNA secondary structures. We also study some global and local properties of these metrics.
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| 49. |
- Moulton, Vincent, et al.
(författare)
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RNA folding argues against a hot-start origin of life
- 2000
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Ingår i: Journal of Molecular Evolution. - 0022-2844 .- 1432-1432. ; 51:4, s. 416-421
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Opinion is strongly divided on whether life arose on earth under hot or cold conditions, the hot-start and cold-start Scenarios, respectively. The origin of life close to deep thermal vents appears as the majority opinion among biologists, but there is considerable biochemical evidence that high temperatures are incompatible with an RNA world. To be functional, RNA has to fold into a three-dimensional structure. We report both theoretical and experimental results on RNA folding and show that las expected) hot conditions strongly reduce RNA folding. The theoretical results come from energy-minimization calculations of the average extent of folding of RNA, mainly from 0-90 degreesC, for both random sequences and tRNA sequences. The experimental results are from circular-dichroism measurements of tRNA over a similar range of temperatures. The quantitative agreement between calculations and experiment is remarkable, even to the shape of the curves indicating the cooperative nature of RNA folding and unfolding. These results provide additional evidence for a lower temperature stage being necessary in the origin of life.
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| 50. |
- Reimerdes, H., et al.
(författare)
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Overview of the TCV tokamak experimental programme
- 2022
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 62:4
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Tidskriftsartikel (refereegranskat)abstract
- The tokamak a configuration variable (TCV) continues to leverage its unique shaping capabilities, flexible heating systems and modern control system to address critical issues in preparation for ITER and a fusion power plant. For the 2019-20 campaign its configurational flexibility has been enhanced with the installation of removable divertor gas baffles, its diagnostic capabilities with an extensive set of upgrades and its heating systems with new dual frequency gyrotrons. The gas baffles reduce coupling between the divertor and the main chamber and allow for detailed investigations on the role of fuelling in general and, together with upgraded boundary diagnostics, test divertor and edge models in particular. The increased heating capabilities broaden the operational regime to include T (e)/T (i) similar to 1 and have stimulated refocussing studies from L-mode to H-mode across a range of research topics. ITER baseline parameters were reached in type-I ELMy H-modes and alternative regimes with 'small' (or no) ELMs explored. Most prominently, negative triangularity was investigated in detail and confirmed as an attractive scenario with H-mode level core confinement but an L-mode edge. Emphasis was also placed on control, where an increased number of observers, actuators and control solutions became available and are now integrated into a generic control framework as will be needed in future devices. The quantity and quality of results of the 2019-20 TCV campaign are a testament to its successful integration within the European research effort alongside a vibrant domestic programme and international collaborations.
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