| 1. |
- Hellmuth, Marc, 1980-, et al.
(författare)
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Clustering systems of phylogenetic networks
- 2023
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Ingår i: Theory in biosciences. - 1431-7613 .- 1611-7530. ; :142, s. 301-358
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Tidskriftsartikel (refereegranskat)abstract
- Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set X of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization that cannot be captured by trees. A variety of classes of such networks have been discussed in the literature, including phylogenetic, level-1, tree-child, tree-based, galled tree, regular, or normal networks as models of different types of evolutionary processes. Clusters arise in models of phylogeny as the sets C(v) of descendant taxa of a vertex v. The clustering system CN comprising the clusters of a network N conveys key information on N itself. In the special case of rooted phylogenetic trees, T is uniquely determined by its clustering system CT. Although this is no longer true for networks in general, it is of interest to relate properties of N and CN. Here, we systematically investigate the relationships of several well-studied classes of networks and their clustering systems. The main results are correspondences of classes of networks and clustering systems of the following form: If N is a network of type X, then CN satisfies Y, and conversely if C is a clustering system satisfying Y, then there is network N of type X such that C⊆CN.This, in turn, allows us to investigate the mutual dependencies between the distinct types of networks in much detail.
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| 2. |
- Lansner, Anders, et al.
(författare)
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Cell assembly dynamics in detailed and abstract attractor models of cortical associative memory
- 2003
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Ingår i: Theory in biosciences. - : Springer Science and Business Media LLC. - 1431-7613 .- 1611-7530. ; 122:1, s. 19-36
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Tidskriftsartikel (refereegranskat)abstract
- During the last few decades we have seen a convergence among ideas and hypotheses regarding functional principles underlying human memory. Hebb's now more than fifty years old conjecture concerning synaptic plasticity and cell assemblies, formalized mathematically as attractor neural networks, has remained among the most viable and productive theoretical frameworks. It suggests plausible explanations for Gestalt aspects of active memory like perceptual completion, reconstruction and rivalry. We review the biological plausibility of these theories and discuss some critical issues concerning their associative memory functionality in the light of simulation studies of models with palimpsest memory properties. The focus is on memory properties and dynamics of networks modularized in terms of cortical minicolumns and hypercolumns. Biophysical compartmental models demonstrate attractor dynamics that support cell assembly operations with fast convergence and low firing rates. Using a scaling model we obtain reasonable relative connection densities and amplitudes. An abstract attractor network model reproduces systems level psychological phenomena seen in human memory experiments as the Sternberg and von Restorff effects. We conclude that there is today considerable substance in Hebb's theory of cell assemblies and its attractor network formulations, and that they have contributed to increasing our understanding of cortical associative memory function. The criticism raised with regard to biological and psychological plausibility as well as low storage capacity, slow retrieval etc has largely been disproved. Rather, this paradigm has gained further support from new experimental data as well as computational modeling.
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| 3. |
- Liljenström, Hans
(författare)
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Consciousness, decision making, and volition: freedom beyond chance and necessity
- 2022
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Ingår i: Theorie in den Biowissenschaften / Theory in Biosciences. - : Springer Science and Business Media LLC. - 1431-7613 .- 1611-7530. ; 141, s. 125-140
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Tidskriftsartikel (refereegranskat)abstract
- What is the role of consciousness in volition and decision-making? Are our actions fully determined by brain activity preceding our decisions to act, or can consciousness instead affect the brain activity leading to action? This has been much debated in philosophy, but also in science since the famous experiments by Libet in the 1980s, where the current most common interpretation is that conscious free will is an illusion. It seems that the brain knows, up to several seconds in advance what "you" decide to do. These studies have, however, been criticized, and alternative interpretations of the experiments can be given, some of which are discussed in this paper. In an attempt to elucidate the processes involved in decision-making (DM), as an essential part of volition, we have developed a computational model of relevant brain structures and their neurodynamics. While DM is a complex process, we have particularly focused on the amygdala and orbitofrontal cortex (OFC) for its emotional, and the lateral prefrontal cortex (LPFC) for its cognitive aspects. In this paper, we present a stochastic population model representing the neural information processing of DM. Simulation results seem to confirm the notion that if decisions have to be made fast, emotional processes and aspects dominate, while rational processes are more time consuming and may result in a delayed decision. Finally, some limitations of current science and computational modeling will be discussed, hinting at a future development of science, where consciousness and free will may add to chance and necessity as explanation for what happens in the world.
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| 4. |
- Monroe, Melanie J., 1982-, et al.
(författare)
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Punctuated equilibrium in a neontological context
- 2010
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Ingår i: Theory in biosciences. - : Springer. - 1431-7613 .- 1611-7530. ; 129:2-3, s. 103-111
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Tidskriftsartikel (refereegranskat)abstract
- The theory of punctuated equilibrium, which proposes that biological species evolve rapidly when they originate rather than gradually over time, has sparked intense debate between palaeontologists and evolutionary biologists about the mode of character evolution and the importance of natural selection. Difficulty in interpreting the fossil record prevented consensus, and it remains disputed as to what extent gradual change in established species is responsible for phenotypic differences between species. Against the historical background of the concept of evolution concentrated in speciation events, we review attempts to investigate tempo and mode of evolution using present-day species since the introduction of the theory of punctuated equilibrium in 1972. We discuss advantages, disadvantages, and prospects of using neontological data, methodological advances, and the findings of some recent studies.
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| 5. |
- Perseke, Marleen, et al.
(författare)
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The mitochondrial DNA of Xenoturbella bocki : genomic architecture and phylogenetic analysis
- 2007
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Ingår i: Theory in biosciences. - : Springer Science and Business Media LLC. - 1431-7613 .- 1611-7530. ; 126:1, s. 35-42
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Tidskriftsartikel (refereegranskat)abstract
- The phylogenetic position of Xenoturbella bocki has been a matter of controversy since its description in 1949. We sequenced a second complete mitochondrial genome of this species and performed phylogenetic analyses based on the amino acid sequences of all 13 mitochondrial protein-coding genes and on its gene order. Our results confirm the deuterostome relationship of Xenoturbella. However, in contrast to a recently published study (Bourlat et al. in Nature 444: 85-88, 2006), our data analysis suggests a more basal branching of Xenoturbella within the deuterostomes, rather than a sister-group relationship to the Ambulacraria (Hemichordata and Echinodermata).
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| 6. |
- Pertoldi, Cino, et al.
(författare)
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Scaling of the mean and variance of population dynamics under fluctuating regimes
- 2014
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Ingår i: Theory in Biosciences. - : Springer Science and Business Media LLC. - 1431-7613 .- 1611-7530. ; 133:3-4, s. 165-173
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Tidskriftsartikel (refereegranskat)abstract
- Theoretical ecologists have long sought to understand how the persistence of populations depends on the interactions between exogenous (biotic and abiotic) and endogenous (e.g., demographic and genetic) drivers of population dynamics. Recent work focuses on the autocorrelation structure of environmental perturbations and its effects on the persistence of populations. Accurate estimation of extinction times and especially determination of the mechanisms affecting extinction times is important for biodiversity conservation. Here we examine the interaction between environmental fluctuations and the scaling effect of the mean population size with its variance. We investigate how interactions between environmental and demographic stochasticity can affect the mean time to extinction, change optimal patch size dynamics, and how it can alter the often-assumed linear relationship between the census size and the effective population size. The importance of the correlation between environmental and demographic variation depends on the relative importance of the two types of variation. We found the correlation to be important when the two types of variation were approximately equal; however, the importance of the correlation diminishes as one source of variation dominates. The implications of these findings are discussed from a conservation and eco-evolutionary point of view.
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| 7. |
- Sumpter, David, et al.
(författare)
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Information transfer in moving animal groups
- 2008
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Ingår i: Theory in biosciences. - : Springer Science and Business Media LLC. - 1431-7613 .- 1611-7530. ; 127:2, s. 177-186
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Tidskriftsartikel (refereegranskat)abstract
- Moving animal groups provide some of the most intriguing and difficult to characterise examples of collective behaviour. We review some recent (and not so recent) empirical research on the motion of animal groups, including fish, locusts and homing pigeons. An important concept which unifies our understanding of these groups is that of transfer of directional information. Individuals which change their direction of travel in response to the direction taken by their near neighbours can quickly transfer information about the presence of a predatory threat or food source. We show that such information transfer is optimised when the density of individuals in a group is close to that at which a phase transition occurs between random and ordered motion. Similarly, we show that even relatively small differences in information possessed by group members can lead to strong collective-level decisions for one of two options. By combining the use of self-propelled particle and social force models of collective motion with thinking about the evolution of flocking we aim to better understand how complexity arises within these groups.
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| 8. |
- Bukkuri, Anuraag
(författare)
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Modeling stress-induced responses : plasticity in continuous state space and gradual clonal evolution
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Ingår i: Theory in Biosciences. - 1431-7613.
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Tidskriftsartikel (refereegranskat)abstract
- Mathematical models of cancer and bacterial evolution have generally stemmed from a gene-centric framework, assuming clonal evolution via acquisition of resistance-conferring mutations and selection of their corresponding subpopulations. More recently, the role of phenotypic plasticity has been recognized and models accounting for phenotypic switching between discrete cell states (e.g., epithelial and mesenchymal) have been developed. However, seldom do models incorporate both plasticity and mutationally driven resistance, particularly when the state space is continuous and resistance evolves in a continuous fashion. In this paper, we develop a framework to model plastic and mutational mechanisms of acquiring resistance in a continuous gradual fashion. We use this framework to examine ways in which cancer and bacterial populations can respond to stress and consider implications for therapeutic strategies. Although we primarily discuss our framework in the context of cancer and bacteria, it applies broadly to any system capable of evolving via plasticity and genetic evolution.
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