| 1. |
- Allison, J, et al.
(författare)
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Geant4 developments and applications
- 2006
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Ingår i: IEEE TRANSACTIONS ON NUCLEAR SCIENCE. - 0018-9499. ; 53:1, s. 270-278
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
- Schroter, D, et al.
(författare)
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Ecosystem service supply and vulnerability to global change in Europe
- 2005
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 310:5752, s. 1333-1337
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Tidskriftsartikel (refereegranskat)abstract
- Global change will alter the supply of ecosystem services that are vital for human well-being. To investigate ecosystem service supply during the 21st century, we used a range of ecosystem models and scenarios of climate and land-use change to conduct a Europe-wide assessment. Large changes in climate and land use typically resulted in large changes in ecosystem service supply. Some of these trends may be positive (for example, increases in forest area and productivity) or offer opportunities (for example, "surplus land" for agricultural extensification and bioenergy production). However, many changes increase vulnerability as a result of a decreasing supply of ecosystem services (for example, declining soil fertility, declining water availability, increasing risk of forest fires), especially in the Mediterranean and mountain regions.
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| 3. |
- Araújo, M.S., et al.
(författare)
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Network analysis reveals contrasting effects of intraspecific competition on individual versus population diets
- 2008
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 89:7, s. 1981-1993
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Tidskriftsartikel (refereegranskat)abstract
- Optimal foraging theory predicts that individuals should become more opportunistic when intraspecific competition is high and preferred resources are scarce. This density-dependent diet shift should result in increased diet breadth for individuals as they add previously unused prey to their repertoire. As a result, the niche breadth of the population as a whole should increase. In a recent study, R. Svanback and D. I. Bolnick confirmed that intraspecific competition led to increased population diet breadth in threespine stickleback (Gasterosteus aculeatus). However, individual diet breadth did not expand as resource levels declined. Here, we present a new method based on complex network theory that moves beyond a simple measure of diet breadth, and we use the method to reexamine the stickleback experiment. This method reveals that the population as a whole added new types of prey as stickleback density was increased. However, whereas foraging theory predicts that niche expansion is achieved by individuals accepting new prey in addition to previously preferred prey, we found that a subset of individuals ceased to use their previously preferred prey, even though other members of their population continued to specialize on the original prey types. As a result, populations were subdivided into groups of ecologically similar individuals, with diet variation among groups reflecting phenotype-dependent changes in foraging behavior as prey density declined. These results are consistent with foraging theory if we assume that quantitative trait variation among consumers affects prey preferences, and if cognitive constraints prevent individuals from continuing to use their formerly preferred prey while adding new prey.
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| 4. |
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| 5. |
- de Souto, Marcilio C P, et al.
(författare)
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Clustering cancer gene expression data: a comparative study.
- 2008
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Ingår i: BMC bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- The use of clustering methods for the discovery of cancer subtypes has drawn a great deal of attention in the scientific community. While bioinformaticians have proposed new clustering methods that take advantage of characteristics of the gene expression data, the medical community has a preference for using "classic" clustering methods. There have been no studies thus far performing a large-scale evaluation of different clustering methods in this context.We present the first large-scale analysis of seven different clustering methods and four proximity measures for the analysis of 35 cancer gene expression data sets. Our results reveal that the finite mixture of Gaussians, followed closely by k-means, exhibited the best performance in terms of recovering the true structure of the data sets. These methods also exhibited, on average, the smallest difference between the actual number of classes in the data sets and the best number of clusters as indicated by our validation criteria. Furthermore, hierarchical methods, which have been widely used by the medical community, exhibited a poorer recovery performance than that of the other methods evaluated. Moreover, as a stable basis for the assessment and comparison of different clustering methods for cancer gene expression data, this study provides a common group of data sets (benchmark data sets) to be shared among researchers and used for comparisons with new methods. The data sets analyzed in this study are available at http://algorithmics.molgen.mpg.de/Supplements/CompCancer/.
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| 6. |
- De Souto, Marcilio C P, et al.
(författare)
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Comparative study on normalization procedures for cluster analysis of gene expression datasets
- 2008
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Ingår i: Proceedings of the International Joint Conference on Neural Networks.
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Konferensbidrag (refereegranskat)abstract
- Normalization before clustering is often needed for proximity indices, such as Euclidian distance, which are sensitive to differences in the magnitude or scales of the attributes. The goal is to equalize the size or magnitude and the variability of these features. This can also be seen as a way to adjust the relative weighting of the attributes. In this context, we present a first large scale data driven comparative study of three normalization procedures applied to cancer gene expression data. The results are presented in terms of the recovering of the true cluster structure as found by five different clustering algorithms. ©2008 IEEE.
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| 7. |
- De Souto, Marcilio C P, et al.
(författare)
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Ranking and selecting clustering algorithms using a meta-learning approach
- 2008
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Ingår i: Proceedings of the International Joint Conference on Neural Networks.
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Konferensbidrag (refereegranskat)abstract
- We present a novel framework that applies a meta-learning approach to clustering algorithms. Given a dataset, our meta-learning approach provides a ranking for the candidate algorithms that could be used with that dataset. This ranking could, among other things, support non-expert users in the algorithm selection task. In order to evaluate the framework proposed, we implement a prototype that employs regression support vector machines as the meta-learner. Our case study is developed in the context of cancer gene expression microarray datasets. © 2008 IEEE.
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| 8. |
- Kim, Duck Young, et al.
(författare)
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Structurally induced insulator-metal transition in solid oxygen : A quasiparticle investigation
- 2008
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 77:9, s. 092104-
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Tidskriftsartikel (refereegranskat)abstract
- Structural phase transition of solid oxygen has been investigated by using ab initio calculations based on density functional theory. We found sudden jumps in structural parameters at the transition pressure, which confirm that the epsilon (epsilon) phase undergoes a first-order isostructural phase transformation to the zeta (zeta) phase. In particular, this happens without any molecular dissociation. Using the GW approximation to calculate the band-gap closure under high pressure, we show that the structural transition is accompanied by an insulator-metal transition, contrary to a standard density functional calculation which predicts a metallization at a much lower pressure in the epsilon phase.
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| 9. |
- Kühn, Ingolf, et al.
(författare)
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MACIS: Minimisation of and Adaptation to Climate Change Impacts on BiodiverSity
- 2008
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Ingår i: GAIA. - 0940-5550. ; 17:4, s. 393-395
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Tidskriftsartikel (refereegranskat)abstract
- The recently finished EU funded project MACIS reviewed observed and projected climate change impacts on biodiversity. It assessed mitigation and adaptation options. It also reviewed and developed methods to assess future impacts of climate change on biodiversity including the identification of policy options to prevent and minimise these impacts.
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| 10. |
- Thuiller, W, et al.
(författare)
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Climate change threats to plant diversity in Europe
- 2005
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 102:23, s. 8245-8250
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Tidskriftsartikel (refereegranskat)abstract
- Climate change has already triggered species distribution shifts in many parts of the world. Increasing impacts are expected for the future, yet few studies have aimed for a general understanding of the regional basis for species vulnerability. We projected late 21st century distributions for 1,350 European plants species under seven climate change scenarios. Application of the International Union for Conservation of Nature and Natural Resources Red List criteria to our projections shows that many European plant species could become severely threatened. More than half of the species we studied could be vulnerable or threatened by 2080. Expected species loss and turnover per pixel proved to be highly variable across scenarios (27-42% and 45-63% respectively, averaged over Europe) and across regions (2.5-86% and 17-86%, averaged over scenarios). Modeled species loss and turnover were found to depend strongly on the degree of change in just two climate variables describing temperature and moisture conditions. Despite the coarse scale of the analysis, species from mountains could be seen to be disproportionably sensitive to climate change (approximate to 60% species loss). The boreal region was projected to lose few species, although gaining many others from immigration. The greatest changes are expected in the transition between the Mediterranean and Euro-Siberian regions. We found that risks of extinction for European plants may be large, even in moderate scenarios of climate change and despite inter-model variability.
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