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  • 1
    Publication Date: 2016-11-08
    Print ISSN: 2470-0010
    Electronic ISSN: 2470-0029
    Topics: Physics
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  • 2
    Publication Date: 2015-06-06
    Description: Author(s): I. Salazar Landea and N. Nessi We investigate the nonequilibrium dynamics of the bosonic Hubbard model starting from inhomogeneous superfluid or Mott insulator initial states using the truncated Wigner approximation (TWA). We find that the relaxation of the system develops in two steps for sufficiently large interaction strengths... [Phys. Rev. A 91, 063601] Published Tue Jun 02, 2015
    Keywords: Matter waves and collective properties of cold atoms and molecules
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 3
    Publication Date: 2013-02-01
    Description: Author(s): N. Grandi, I. Salazar Landea, and G. A. Silva We study vortexlike solutions to the Lifshitz-Chern-Simons theory. We find that such solutions exist and have a logarithmically divergent energy, which suggests that a Kostelitz-Thouless transition may occur, in which voxtex-antivortex pairs are created above a critical temperature. Following a sugg... [Phys. Rev. D 87, 025031] Published Thu Jan 31, 2013
    Keywords: Field theory, formal particle theory
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 4
    Publication Date: 2010-03-12
    Description: The relationship between the genotype and the phenotype, or the genotype-phenotype map, is generally approached with the tools of multivariate quantitative genetics and morphometrics. Whereas studies of development and mathematical models of development may offer new insights into the genotype-phenotype map, the challenge is to make them useful at the level of microevolution. Here we report a computational model of mammalian tooth development that combines parameters of genetic and cellular interactions to produce a three-dimensional tooth from a simple tooth primordia. We systematically tinkered with each of the model parameters to generate phenotypic variation and used geometric morphometric analyses to identify, or developmentally ordinate, parameters best explaining population-level variation of real teeth. To model the full range of developmentally possible morphologies, we used a population sample of ringed seals (Phoca hispida ladogensis). Seal dentitions show a high degree of variation, typically linked to the lack of exact occlusion. Our model suggests that despite the complexity of development and teeth, there may be a simple basis for dental variation. Changes in single parameters regulating signalling during cusp development may explain shape variation among individuals, whereas a parameter regulating epithelial growth may explain serial, tooth-to-tooth variation along the jaw. Our study provides a step towards integrating the genotype, development and the phenotype.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Salazar-Ciudad, Isaac -- Jernvall, Jukka -- England -- Nature. 2010 Mar 25;464(7288):583-6. doi: 10.1038/nature08838. Epub 2010 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departament de Genetica i Microbiologia, Facultat de Biociencies, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. isaac.salazar@uab.cat〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20220757" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Gene Regulatory Networks/genetics ; Genotype ; *Models, Biological ; Phenotype ; *Phoca/anatomy & histology/genetics/growth & development ; Signal Transduction ; Tooth/*anatomy & histology/growth & development/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2005-07-26
    Description: We present a global conservation analysis for an entire "flagship" taxon, land mammals. A combination of rarity, anthropogenic impacts, and political endemism has put about a quarter of terrestrial mammal species, and a larger fraction of their populations, at risk of extinction. A new global database and complementarity analysis for selecting priority areas for conservation shows that approximately 11% of Earth's land surface should be managed for conservation to preserve at least 10% of terrestrial mammal geographic ranges. Different approaches, from protection (or establishment) of reserves to countryside biogeographic enhancement of human-dominated landscapes, will be required to approach this minimal goal.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ceballos, Gerardo -- Ehrlich, Paul R -- Soberon, Jorge -- Salazar, Irma -- Fay, John P -- New York, N.Y. -- Science. 2005 Jul 22;309(5734):603-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Instituto de Ecologia, UNAM, Apdo. Postal 70-275, Mexico D.F. 04510, Mexico. gceballo@miranda.ecologia.unam.mx〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16040704" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; Animals ; Biodiversity ; *Conservation of Natural Resources ; Databases, Factual ; Developed Countries ; Developing Countries ; *Ecosystem ; Environment ; Geography ; Humans ; *Mammals ; Population Density ; Population Dynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2013-05-03
    Description: It is not known whether natural selection can encounter any given phenotype that can be produced by genetic variation. There has been a long-lasting debate about the processes that limit adaptation and, consequently, about how well adapted phenotypes are. Here we examine how development may affect adaptation, by decomposing the genotype-fitness map-the association between each genotype and its fitness-into two: one mapping genotype to phenotype by means of a computational model of organ development, and one mapping phenotype to fitness. In the map of phenotype and fitness, the fitness of each individual is based on the similarity between realized morphology and optimal morphology. We use three different simulations to map phenotype to fitness, and these differ in the way in which similarity is calculated: similarity is calculated for each trait (in terms of each cell position individually), for a large or a small number of phenotypic landmarks (the 'many-traits' and 'few-traits' phenotype-fitness maps), and by measuring the overall surface roughness of morphology (the 'roughness' phenotype-fitness map). Evolution is simulated by applying the genotype-phenotype map and one phenotype-fitness map to each individual in the population, as well as random mutation and drift. We show that the complexity of the genotype-phenotype map prevents substantial adaptation in some of the phenotype-fitness maps: sustained adaptation is only possible using 'roughness' or 'few-traits' phenotype-fitness maps. The results contribute developmental understanding to the long-standing question of which aspects of phenotype can be effectively optimized by natural selection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Salazar-Ciudad, Isaac -- Marin-Riera, Miquel -- England -- Nature. 2013 May 16;497(7449):361-4. doi: 10.1038/nature12142. Epub 2013 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Evolutionary phenomics group. Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland. isaac.salazar@uab.cat〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23636325" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Algorithms ; Biological Evolution ; Computer Simulation ; Genetic Fitness/genetics ; *Genotype ; *Models, Biological ; *Phenotype ; Population Density ; Principal Component Analysis ; Selection, Genetic ; Tooth/anatomy & histology/*growth & development
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2014-08-01
    Description: The evolutionary relationships of extinct species are ascertained primarily through the analysis of morphological characters. Character inter-dependencies can have a substantial effect on evolutionary interpretations, but the developmental underpinnings of character inter-dependence remain obscure because experiments frequently do not provide detailed resolution of morphological characters. Here we show experimentally and computationally how gradual modification of development differentially affects characters in the mouse dentition. We found that intermediate phenotypes could be produced by gradually adding ectodysplasin A (EDA) protein in culture to tooth explants carrying a null mutation in the tooth-patterning gene Eda. By identifying development-based character inter-dependencies, we show how to predict morphological patterns of teeth among mammalian species. Finally, in vivo inhibition of sonic hedgehog signalling in Eda null teeth enabled us to reproduce characters deep in the rodent ancestry. Taken together, evolutionarily informative transitions can be experimentally reproduced, thereby providing development-based expectations for character-state transitions used in evolutionary studies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252015/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252015/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harjunmaa, Enni -- Seidel, Kerstin -- Hakkinen, Teemu -- Renvoise, Elodie -- Corfe, Ian J -- Kallonen, Aki -- Zhang, Zhao-Qun -- Evans, Alistair R -- Mikkola, Marja L -- Salazar-Ciudad, Isaac -- Klein, Ophir D -- Jernvall, Jukka -- DP2 OD007191/OD/NIH HHS/ -- DP2-OD007191/OD/NIH HHS/ -- K99 DE024214/DE/NIDCR NIH HHS/ -- R01 DE021420/DE/NIDCR NIH HHS/ -- R01-DE021420/DE/NIDCR NIH HHS/ -- England -- Nature. 2014 Aug 7;512(7512):44-8. doi: 10.1038/nature13613. Epub 2014 Jul 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Developmental Biology Program, Institute of Biotechnology, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki, Finland. ; 1] Program in Craniofacial and Mesenchymal Biology, University of California, San Francisco, San Francisco, California 94114, USA [2] Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California 94114, USA. ; Division of Materials Physics, Department of Physics, University of Helsinki, P.O. Box 64, FIN-00014 Helsinki, Finland. ; Key Laboratory of Evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. ; 1] School of Biological Sciences, Monash University, Victoria 3800, Australia [2] Geosciences, Museum Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia. ; 1] Developmental Biology Program, Institute of Biotechnology, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki, Finland [2] Genomics, Bioinformatics and Evolution Group. Department de Genetica i Microbiologia, Universitat Autonoma de Barcelona, Cerdanyola del Valles 08193, Spain. ; 1] Program in Craniofacial and Mesenchymal Biology, University of California, San Francisco, San Francisco, California 94114, USA [2] Department of Orofacial Sciences, University of California, San Francisco, San Francisco, California 94114, USA [3] Department of Pediatrics, University of California, San Francisco, San Francisco, California 94114, USA [4] Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25079326" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Computer Simulation ; Ectodysplasins/deficiency/genetics/pharmacology ; Female ; *Fossils ; Gene Deletion ; Hedgehog Proteins/antagonists & inhibitors/genetics ; In Vitro Techniques ; Male ; Mice ; Molar/anatomy & histology/drug effects/growth & development ; Phenotype ; Signal Transduction/drug effects ; Tooth/*anatomy & histology/drug effects/*growth & development
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2016-11-09
    Description: Author(s): D. Areán, L. A. Pando Zayas, I. Salazar Landea, and A. Scardicchio We implement the effects of disorder on a holographic superconductor by introducing a random chemical potential on the boundary. We demonstrate explicitly that increasing disorder leads to the formation of islands where the superconducting order is enhanced and subsequently to the transition to a me… [Phys. Rev. D 94, 106003] Published Tue Nov 08, 2016
    Keywords: String theory, quantum gravity, gauge/gravity duality
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 9
    Publication Date: 2014-05-14
    Description: Author(s): D. Areán, A. Farahi, L. A. Pando Zayas, I. Salazar Landea, and A. Scardicchio We study the effects of disorder on a holographic superconductor by introducing a random chemical potential on the boundary. We consider various realizations of disorder and find that the critical temperature for superconductivity is enhanced. We also present evidence for a precise form of renormali... [Phys. Rev. D 89, 106003] Published Tue May 13, 2014
    Keywords: String Theory
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 10
    Publication Date: 2014-05-13
    Print ISSN: 1550-7998
    Electronic ISSN: 1550-2368
    Topics: Physics
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