--- _id: '4237' abstract: - lang: eng text: The growth function of populations is central in biomathematics. The main dogma is the existence of density-dependence mechanisms, which can be modelled with distinct functional forms that depend on the size of the Population. One important class of regulatory functions is the theta-logistic, which generalizes the logistic equation. Using this model as a motivation, this paper introduces a simple dynamical reformulation that generalizes many growth functions. The reformulation consists of two equations, one for population size, and one for the growth rate. Furthermore, the model shows that although population is density-dependent, the dynamics of the growth rate does not depend either on population size, nor on the carrying capacity. Actually, the growth equation is uncoupled from the population size equation, and the model has only two parameters, a Malthusian parameter rho and a competition coefficient theta. Distinct sign combinations of these parameters reproduce not only the family of theta-logistics, but also the van Bertalanffy, Gompertz and Potential Growth equations, among other possibilities. It is also shown that, except for two critical points, there is a general size-scaling relation that includes those appearing in the most important allometric theories, including the recently proposed Metabolic Theory of Ecology. With this model, several issues of general interest are discussed such as the growth of animal population, extinctions, cell growth and allometry, and the effect of environment over a population. (c) 2005 Elsevier Ltd. All rights reserved. article_processing_charge: No author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 citation: ama: de Vladar H. Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. 2006;238(2):245-256. doi:3802 apa: de Vladar, H. (2006). Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. Elsevier. https://doi.org/3802 chicago: Vladar, Harold de. “Density-Dependence as a Size-Independent Regulatory Mechanism.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/3802. ieee: H. de Vladar, “Density-dependence as a size-independent regulatory mechanism,” Journal of Theoretical Biology, vol. 238, no. 2. Elsevier, pp. 245–256, 2006. ista: de Vladar H. 2006. Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. 238(2), 245–256. mla: de Vladar, Harold. “Density-Dependence as a Size-Independent Regulatory Mechanism.” Journal of Theoretical Biology, vol. 238, no. 2, Elsevier, 2006, pp. 245–56, doi:3802. short: H. de Vladar, Journal of Theoretical Biology 238 (2006) 245–256. date_created: 2018-12-11T12:07:46Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:55:31Z day: '01' doi: '3802' extern: '1' intvolume: ' 238' issue: '2' language: - iso: eng month: '01' oa_version: None page: 245 - 256 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '1878' status: public title: Density-dependence as a size-independent regulatory mechanism type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 238 year: '2006' ... --- _id: '4235' author: - first_name: Harold full_name: Harold Vladar id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 - first_name: J. full_name: González,J. A last_name: González citation: ama: de Vladar H, González J. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. 2006:91-109. apa: de Vladar, H., & González, J. (2006). Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. Elsevier. chicago: Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology. Elsevier, 2006. ieee: H. de Vladar and J. González, “Dynamic response of cancer under the influence of immunological activity and therapy,” Journal of Theoretical Biology. Elsevier, pp. 91–109, 2006. ista: de Vladar H, González J. 2006. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology., 91–109. mla: de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology, Elsevier, 2006, pp. 91–109. short: H. de Vladar, J. González, Journal of Theoretical Biology (2006) 91–109. date_created: 2018-12-11T12:07:45Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:55:30Z day: '01' extern: 1 month: '01' page: 91 - 109 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '1879' quality_controlled: 0 status: public title: Dynamic response of cancer under the influence of immunological activity and therapy type: journal_article year: '2006' ... --- _id: '4248' abstract: - lang: eng text: 'In finite populations, genetic drift generates interference between selected loci, causing advantageous alleles to be found more often on different chromosomes than on the same chromosome, which reduces the rate of adaptation. This “Hill–Robertson effect” generates indirect selection to increase recombination rates. We present a new method to quantify the strength of this selection. Our model represents a new beneficial allele (A) entering a population as a single copy, while another beneficial allele (B) is sweeping at another locus. A third locus affects the recombination rate between selected loci. Using a branching process model, we calculate the probability distribution of the number of copies of A on the different genetic backgrounds, after it is established but while it is still rare. Then, we use a deterministic model to express the change in frequency of the recombination modifier, due to hitchhiking, as A goes to fixation. We show that this method can give good estimates of selection for recombination. Moreover, it shows that recombination is selected through two different effects: it increases the fixation probability of new alleles, and it accelerates selective sweeps. The relative importance of these two effects depends on the relative times of occurrence of the beneficial alleles.' author: - first_name: Denis full_name: Roze, Denis last_name: Roze - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Roze D, Barton NH. The Hill-Robertson effect and the evolution of recombination. Genetics. 2006;173(3):1793-1811. doi:10.1534/genetics.106.058586 apa: Roze, D., & Barton, N. H. (2006). The Hill-Robertson effect and the evolution of recombination. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.106.058586 chicago: Roze, Denis, and Nicholas H Barton. “The Hill-Robertson Effect and the Evolution of Recombination.” Genetics. Genetics Society of America, 2006. https://doi.org/10.1534/genetics.106.058586 . ieee: D. Roze and N. H. Barton, “The Hill-Robertson effect and the evolution of recombination,” Genetics, vol. 173, no. 3. Genetics Society of America, pp. 1793–1811, 2006. ista: Roze D, Barton NH. 2006. The Hill-Robertson effect and the evolution of recombination. Genetics. 173(3), 1793–1811. mla: Roze, Denis, and Nicholas H. Barton. “The Hill-Robertson Effect and the Evolution of Recombination.” Genetics, vol. 173, no. 3, Genetics Society of America, 2006, pp. 1793–811, doi:10.1534/genetics.106.058586 . short: D. Roze, N.H. Barton, Genetics 173 (2006) 1793–1811. date_created: 2018-12-11T12:07:50Z date_published: 2006-07-01T00:00:00Z date_updated: 2021-01-12T07:55:36Z day: '01' doi: '10.1534/genetics.106.058586 ' extern: 1 intvolume: ' 173' issue: '3' month: '07' page: 1793 - 1811 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '1854' quality_controlled: 0 status: public title: The Hill-Robertson effect and the evolution of recombination type: journal_article volume: 173 year: '2006' ... --- _id: '4250' abstract: - lang: eng text: A recent analysis has shown that divergence between human and chimpanzee varies greatly across the genome. Although this is consistent with ‘hybridisation’ between the diverging human and chimp lineages, such observations can be explained more simply by the null model of allopatric speciation. author: - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Evolutionary Biology: How did the human species form? Current Biology. 2006;16(16):647-650. doi:10.1016/j.cub.2006.07.032' apa: 'Barton, N. H. (2006). Evolutionary Biology: How did the human species form? Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2006.07.032' chicago: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?” Current Biology. Cell Press, 2006. https://doi.org/10.1016/j.cub.2006.07.032.' ieee: 'N. H. Barton, “Evolutionary Biology: How did the human species form?,” Current Biology, vol. 16, no. 16. Cell Press, pp. 647–650, 2006.' ista: 'Barton NH. 2006. Evolutionary Biology: How did the human species form? Current Biology. 16(16), 647–650.' mla: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?” Current Biology, vol. 16, no. 16, Cell Press, 2006, pp. 647–50, doi:10.1016/j.cub.2006.07.032.' short: N.H. Barton, Current Biology 16 (2006) 647–650. date_created: 2018-12-11T12:07:51Z date_published: 2006-08-22T00:00:00Z date_updated: 2019-04-26T07:22:41Z day: '22' doi: 10.1016/j.cub.2006.07.032 extern: 1 intvolume: ' 16' issue: '16' month: '08' page: 647 - 650 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '1850' quality_controlled: 0 status: public title: 'Evolutionary Biology: How did the human species form?' type: review volume: 16 year: '2006' ... --- _id: '4359' alternative_title: - LNCS 3855 author: - first_name: Thomas full_name: Thomas Wies id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies - first_name: Viktor full_name: Kuncak, Viktor last_name: Kuncak - first_name: Patrick full_name: Lam,Patrick last_name: Lam - first_name: Andreas full_name: Podelski,Andreas last_name: Podelski - first_name: Martin full_name: Rinard,Martin last_name: Rinard citation: ama: 'Wies T, Kuncak V, Lam P, Podelski A, Rinard M. Field Constraint Analysis. In: Springer; 2006:157-173. doi:1551' apa: 'Wies, T., Kuncak, V., Lam, P., Podelski, A., & Rinard, M. (2006). Field Constraint Analysis (pp. 157–173). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Springer. https://doi.org/1551' chicago: Wies, Thomas, Viktor Kuncak, Patrick Lam, Andreas Podelski, and Martin Rinard. “Field Constraint Analysis,” 157–73. Springer, 2006. https://doi.org/1551. ieee: 'T. Wies, V. Kuncak, P. Lam, A. Podelski, and M. Rinard, “Field Constraint Analysis,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, 2006, pp. 157–173.' ista: 'Wies T, Kuncak V, Lam P, Podelski A, Rinard M. 2006. Field Constraint Analysis. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS 3855, , 157–173.' mla: Wies, Thomas, et al. Field Constraint Analysis. Springer, 2006, pp. 157–73, doi:1551. short: T. Wies, V. Kuncak, P. Lam, A. Podelski, M. Rinard, in:, Springer, 2006, pp. 157–173. conference: name: 'VMCAI: Verification, Model Checking and Abstract Interpretation' date_created: 2018-12-11T12:08:27Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:56:23Z day: '01' doi: '1551' extern: 1 month: '01' page: 157 - 173 publication_status: published publisher: Springer publist_id: '1097' quality_controlled: 0 status: public title: Field Constraint Analysis type: conference year: '2006' ... --- _id: '4373' alternative_title: - LNCS author: - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Dejan Nickovic id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Amir full_name: Pnueli,Amir last_name: Pnueli citation: ama: 'Maler O, Nickovic D, Pnueli A. Real Time Temporal Logic: Past, Present, Future. In: Springer; 2006:2-16. doi:1571' apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2006). Real Time Temporal Logic: Past, Present, Future (pp. 2–16). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/1571' chicago: 'Maler, Oded, Dejan Nickovic, and Amir Pnueli. “Real Time Temporal Logic: Past, Present, Future,” 2–16. Springer, 2006. https://doi.org/1571.' ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “Real Time Temporal Logic: Past, Present, Future,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, pp. 2–16.' ista: 'Maler O, Nickovic D, Pnueli A. 2006. Real Time Temporal Logic: Past, Present, Future. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 2–16.' mla: 'Maler, Oded, et al. Real Time Temporal Logic: Past, Present, Future. Springer, 2006, pp. 2–16, doi:1571.' short: O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 2–16. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:08:31Z date_published: 2006-01-23T00:00:00Z date_updated: 2021-01-12T07:56:29Z day: '23' doi: '1571' extern: 1 month: '01' page: 2 - 16 publication_status: published publisher: Springer publist_id: '1084' quality_controlled: 0 status: public title: 'Real Time Temporal Logic: Past, Present, Future' type: conference year: '2006' ... --- _id: '4374' alternative_title: - LNCS author: - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Dejan Nickovic id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Amir full_name: Pnueli,Amir last_name: Pnueli citation: ama: 'Maler O, Nickovic D, Pnueli A. From MITL to Timed Automata. In: Springer; 2006:274-289. doi:1570' apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2006). From MITL to Timed Automata (pp. 274–289). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/1570' chicago: Maler, Oded, Dejan Nickovic, and Amir Pnueli. “From MITL to Timed Automata,” 274–89. Springer, 2006. https://doi.org/1570. ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “From MITL to Timed Automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, pp. 274–289.' ista: 'Maler O, Nickovic D, Pnueli A. 2006. From MITL to Timed Automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 274–289.' mla: Maler, Oded, et al. From MITL to Timed Automata. Springer, 2006, pp. 274–89, doi:1570. short: O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 274–289. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:08:31Z date_published: 2006-10-19T00:00:00Z date_updated: 2021-01-12T07:56:30Z day: '19' doi: '1570' extern: 1 month: '10' page: 274 - 289 publication_status: published publisher: Springer publist_id: '1085' quality_controlled: 0 status: public title: From MITL to Timed Automata type: conference year: '2006' ... --- _id: '4406' abstract: - lang: eng text: We propose and evaluate a new algorithm for checking the universality of nondeterministic finite automata. In contrast to the standard algorithm, which uses the subset construction to explicitly determinize the automaton, we keep the determinization step implicit. Our algorithm computes the least fixed point of a monotone function on the lattice of antichains of state sets. We evaluate the performance of our algorithm experimentally using the random automaton model recently proposed by Tabakov and Vardi. We show that on the difficult instances of this probabilistic model, the antichain algorithm outperforms the standard one by several orders of magnitude. We also show how variations of the antichain method can be used for solving the language-inclusion problem for nondeterministic finite automata, and the emptiness problem for alternating finite automata. acknowledgement: This research was supported in part by the NSF grants CCR-0234690 and CCR-0225610, and the Belgian FNRS grant 2.4530.02 of the FRFC project “Centre Fédéré en Vérification.” alternative_title: - LNCS author: - first_name: Martin full_name: De Wulf, Martin last_name: De Wulf - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jean full_name: Raskin, Jean-François last_name: Raskin citation: ama: 'De Wulf M, Doyen L, Henzinger TA, Raskin J. Antichains: A new algorithm for checking universality of finite automata. In: Vol 4144. Springer; 2006:17-30. doi:10.1007/11817963_5' apa: 'De Wulf, M., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Antichains: A new algorithm for checking universality of finite automata (Vol. 4144, pp. 17–30). Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/11817963_5' chicago: 'De Wulf, Martin, Laurent Doyen, Thomas A Henzinger, and Jean Raskin. “Antichains: A New Algorithm for Checking Universality of Finite Automata,” 4144:17–30. Springer, 2006. https://doi.org/10.1007/11817963_5.' ieee: 'M. De Wulf, L. Doyen, T. A. Henzinger, and J. Raskin, “Antichains: A new algorithm for checking universality of finite automata,” presented at the CAV: Computer Aided Verification, 2006, vol. 4144, pp. 17–30.' ista: 'De Wulf M, Doyen L, Henzinger TA, Raskin J. 2006. Antichains: A new algorithm for checking universality of finite automata. CAV: Computer Aided Verification, LNCS, vol. 4144, 17–30.' mla: 'De Wulf, Martin, et al. Antichains: A New Algorithm for Checking Universality of Finite Automata. Vol. 4144, Springer, 2006, pp. 17–30, doi:10.1007/11817963_5.' short: M. De Wulf, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006, pp. 17–30. conference: name: 'CAV: Computer Aided Verification' date_created: 2018-12-11T12:08:41Z date_published: 2006-08-08T00:00:00Z date_updated: 2021-01-12T07:56:45Z day: '08' doi: 10.1007/11817963_5 extern: 1 intvolume: ' 4144' month: '08' page: 17 - 30 publication_status: published publisher: Springer publist_id: '326' quality_controlled: 0 status: public title: 'Antichains: A new algorithm for checking universality of finite automata' type: conference volume: 4144 year: '2006' ... --- _id: '4401' alternative_title: - LNCS author: - first_name: Rajeev full_name: Alur, Rajeev last_name: Alur - first_name: Pavol full_name: Pavol Cerny id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Steve full_name: Zdancewic,Steve last_name: Zdancewic citation: ama: 'Alur R, Cerny P, Zdancewic S. Preserving Secrecy Under Refinement. In: Springer; 2006:107-118. doi:1543' apa: 'Alur, R., Cerny, P., & Zdancewic, S. (2006). Preserving Secrecy Under Refinement (pp. 107–118). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/1543' chicago: Alur, Rajeev, Pavol Cerny, and Steve Zdancewic. “Preserving Secrecy Under Refinement,” 107–18. Springer, 2006. https://doi.org/1543. ieee: 'R. Alur, P. Cerny, and S. Zdancewic, “Preserving Secrecy Under Refinement,” presented at the ICALP: Automata, Languages and Programming, 2006, pp. 107–118.' ista: 'Alur R, Cerny P, Zdancewic S. 2006. Preserving Secrecy Under Refinement. ICALP: Automata, Languages and Programming, LNCS, , 107–118.' mla: Alur, Rajeev, et al. Preserving Secrecy Under Refinement. Springer, 2006, pp. 107–18, doi:1543. short: R. Alur, P. Cerny, S. Zdancewic, in:, Springer, 2006, pp. 107–118. conference: name: 'ICALP: Automata, Languages and Programming' date_created: 2018-12-11T12:08:40Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:56:42Z day: '01' doi: '1543' extern: 1 month: '01' page: 107 - 118 publication_status: published publisher: Springer publist_id: '1054' quality_controlled: 0 status: public title: Preserving Secrecy Under Refinement type: conference year: '2006' ... --- _id: '4437' abstract: - lang: eng text: The synthesis of reactive systems requires the solution of two-player games on graphs with ω-regular objectives. When the objective is specified by a linear temporal logic formula or nondeterministic Büchi automaton, then previous algorithms for solving the game require the construction of an equivalent deterministic automaton. However, determinization for automata on infinite words is extremely complicated, and current implementations fail to produce deterministic automata even for relatively small inputs. We show how to construct, from a given nondeterministic Büchi automaton, an equivalent nondeterministic parity automaton that is good for solving games with objective . The main insight is that a nondeterministic automaton is good for solving games if it fairly simulates the equivalent deterministic automaton. In this way, we omit the determinization step in game solving and reactive synthesis. The fact that our automata are nondeterministic makes them surprisingly simple, amenable to symbolic implementation, and allows an incremental search for winning strategies. acknowledgement: This research was supported in part by the Swiss National Science Foundation. alternative_title: - LNCS author: - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Nir full_name: Piterman, Nir last_name: Piterman citation: ama: 'Henzinger TA, Piterman N. Solving games without determinization. In: Vol 4207. Springer; 2006:395-410. doi:10.1007/11874683_26' apa: 'Henzinger, T. A., & Piterman, N. (2006). Solving games without determinization (Vol. 4207, pp. 395–410). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_26' chicago: Henzinger, Thomas A, and Nir Piterman. “Solving Games without Determinization,” 4207:395–410. Springer, 2006. https://doi.org/10.1007/11874683_26. ieee: 'T. A. Henzinger and N. Piterman, “Solving games without determinization,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 395–410.' ista: 'Henzinger TA, Piterman N. 2006. Solving games without determinization. CSL: Computer Science Logic, LNCS, vol. 4207, 395–410.' mla: Henzinger, Thomas A., and Nir Piterman. Solving Games without Determinization. Vol. 4207, Springer, 2006, pp. 395–410, doi:10.1007/11874683_26. short: T.A. Henzinger, N. Piterman, in:, Springer, 2006, pp. 395–410. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:08:51Z date_published: 2006-09-20T00:00:00Z date_updated: 2021-01-12T07:56:58Z day: '20' doi: 10.1007/11874683_26 extern: 1 intvolume: ' 4207' month: '09' page: 395 - 410 publication_status: published publisher: Springer publist_id: '295' quality_controlled: 0 status: public title: Solving games without determinization type: conference volume: 4207 year: '2006' ...