First Steps Towards a Runtime Comparison of Natural and Artificial Evolution

Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1)EA. We show that SSWM can have a moderate advantage over the (1+1)EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1)EA by taking advantage of information on the fitness gradient

Dynamics of transcription factor binding site evolution

Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ~10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of "pre-sites" or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genetics.Comment: 28 pages, 15 figure

Desenvolvimento e otimização de sensores em fibra ótica produzidos por laser de femtosegundo

In this work, optical fibre sensors were developed and optimized using a pulsed femtosecond laser. In addition to the inherent advantages of using femtosecond pulses, by emitting radiation in the NIR band, it was possible to modify the refractive index inside dielectric materials, namely silica and polymer optical fibres. Prior to the manufacturing of optical structures, a theoretical study was carried out on the peculiarities of writing-systems based on femtosecond lasers, as well as on the most common devices inscribed in optical fibres, namely Bragg gratings, long period gratings, and Fabry-Pérot interferometers. After assembling femtosecond NIR laser system, Bragg gratings, long period gratings, Fabry-Pérot interferometers, and interferometers based on the optical Vernier effect were manufactured using the direct-writing and phase mask methods. Using the micromachining setup, different structures were created in already existing optical fibre sensors, namely channels in hollow Fabry-Pérot cavities and laser etching around Bragg gratings inscribed in polymers optical fibres. The spectral responses of all devices were extensively characterized to, mainly, variations of temperature and strain, revealing unique sensitivity values, especially for the interferometers based on the optical Vernier effect (> 1 nm/°C and 0.1 nm/µε for temperature and strain, respectively). To demystify the thermal stability of fibre Bragg gratings, a theoretical and experimental study was carried out where several Bragg gratings were inscribed by different techniques, involving different lasers as well as silica and polymer optical fibres. The experimental results corroborated the theoretical predictions, where it was concluded that the gratings inscribed by the point-to-point method using a femtosecond laser have a greater thermal stability and lifetime, even when subjected to longer and higher temperature regimes. Finally, a bridge was stablished between the fundamental research developed during the manufacture of the elementary optical fibre sensors, and possible applications. Five different sensor concepts were demonstrated and tested, capable of detecting variations in magnetic fields, fluids refractive index, temperature, strain and humidity. As results, astonishing sensitivity values were attained, and several cross-sensitivity problems were mitigated, thus establishing the foundations for the development of new prototypes for the future.Neste trabalho foram desenvolvidos e otimizados sensores em fibra ótica através de um laser pulsado de femtosegundo. Para além das vantagens inerentes de usar pulsos da ordem do femtosegundo, ao emitir radiação na banda do infravermelho foi possível modificar o índice de refração no interior de materiais dielétricos, nomeadamente fibras óticas de sílica e polímero. Antes de proceder ao fabrico das estruturas óticas, foi realizado um estudo teórico sobre as peculiaridades dos sistemas de escrita baseados em lasers de femtosegundo, bem como sobre os principais dispositivos inscritos em fibra ótica, nomeadamente redes de Bragg, redes de período longo, e interferómetros de Fabry-Pérot. Após montado o sistema laser NIR de femtosegundo, através de inscrição direta e por máscara de fase foram fabricadas redes de Bragg, redes de período longo, interferómetros de Fabry-Pérot, e interferómetros baseados no efeito ótico de Vernier. Com a montagem de micromaquinação, diferentes estruturas foram criadas em sensores já existentes, nomeadamente buracos em cavidades Fabry-Pérot e remoção de material ao redor de redes de Bragg. As respostas espetrais de todos os dispositivos foram extensivamente caracterizadas, nomeadamente a variações de temperatura e tensão, revelando elevados valores de sensibilidades, especialmente para os interferómetros baseados no efeito ótico de Vernier (> 1 nm/°C e 0.1 nm/µε para temeprature e tensão, respetivamente). Para desmistificar a estabilidade térmica de redes de Bragg em fibra ótica, foi feito um estudo teórico e experimental onde várias redes de Bragg foram gravadas por diferentes técnicas, envolvendo diferentes lasers e fibras óticas de sílica e polímero. Os resultados experimentais corroboraram as previsões teóricas, onde se concluiu que as redes gravadas pelo método de ponto-a-ponto usando um laser de femtosegundo detêm uma maior estabilidade térmica e tempo de vida, mesmo quando submetidas a regimes longos de altas temperaturas. Por fim, foi feita a ponte entre a investigação fundamental desenvolvida durante o fabrico de dispositivos elementares em fibras óticas e possíveis aplicações. Foram demonstrados e testados cinco conceitos diferentes de sensores, capazes de detetar variações de campos magnéticos, índice de refração de fluídos, temperatura, tensão e humidade. Foram atingidos valores de sensibilidade surpreendentes, bem como mitigados problemas de sensibilidade cruzada, tendo sido assim estabelecidas as fundações para o desenvolvimento de novos protótipos para o futuro.Programa Doutoral em Engenharia Físic

Internship report: A guide to structured products – Reverse convertible on S&P500

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Finance from the NOVA – School of Business and EconomicsThe purpose of this report is to describe the main characteristics of structured products. These products can be divided in Capital Guaranteed products and Non Capital guaranteed products, having these two types of products different risk profiles and potential returns. In the final part of the report a Reverse Convertible on the S&P500 is created, which offers 8.57% return per year subject to a capital loss in case the underlying goes below 70% initial level, in one year

Ability of Gordonia alkanivorans strain 1B for high added value carotenoids production

Currently, carotenoids are valuable bioactive molecules for several industries, such as chemical, pharmaceutical, food and cosmetics, due to their multiple benefits as natural colorants, antioxidants and vitamin precursors. Hence, the increasing interest on these high added-value products has led to the search of alternatives, more cost-effective and with better yields, towards their industrial production. Indeed, microbial metabolism offers a promising option for carotenoids production. Herein it is shown the potential of the dibenzothiophene desulfurizing bacterium Gordonia alkanivorans strain 1B as a high carotenoid-producer microorganism. The novel carotenoids, produced under different culture conditions, were extracted with DMSO and then further analyzed both through spectrophotometry and HPLC. When grown in glucose-sulfate-light, strain 1B was able of achieving 2015 g carotenoids per g DCW in shake-flask assays, with about 60% corresponding to lutein, canthaxanthin and astaxanthin. Further optimization studies open a new focus of research aiming to get a hyper pigment-producer strain that may be applied towards different industrial sectors

Production of carotenoids and biosurfactants by Gordonia Alkanivorans Strain 1B using food residues and derivatives [Poster]

ABSTRACT: Through different bioprocesses, microorganisms, such as yeasts and bacteria, ferment and transform residue streams into high added value products, such as carotenoids and biosurfactants. Gordonia alkanivorans strain 1B is one of such bacteria, capable of consuming and transforming many types of residues. It is mostly known for its biodesulfurizing ability and it was recently described as a producer of both carotenoids and biosurfactants. In previous works, strain 1B has been cultivated on different sugar rich alternative carbon sources. However, it was shown, that in order to promote surfactant production, the microorganisms should be exposed to inducing factors, such as lipids and alcohols. This work focusses on valorisation of residues from the restaurant and food industry, and derivatives from their processing, by using them as carbon sources to grow the bacterium and produce carotenoids and surfactants.N/

Helmintofauna gastrointestinal em aves de rapina no Estado do Pará.

Parasitos do trato digestório são frequentemente detectados nestas aves, porém o conhecimento da helmintofauna em aves de rapina no Brasil ainda é incipiente. Portanto, o objetivo deste trabalho é investigar a helmintofauna gastrointestinal de aves de rapina que ocorrem no Estado do Pará, Brasil. Foram utilizadas 33 carcaças e helmintos regurgitados por um indivíduo, totalizando 34 indivíduos de 14 espécies: Megascops choliba (n=10), Rupornis magnirostris (n=8), Tyto furcata (n=5), Megascops usta (n=1), Athene cunicularia (n=1), Ibycter americanus (n=1), Asio clamator (n=1), Geranoaetus albicaudatus (n=1), Caracara plancus (n=1), Gampsonyx swainsonii (n=1), Buteogallus schistaceus (n=1), Micrastur ruficollis (n=1), Falco rufigularis (n=1) e Elanoides forficatus (n=1). Foi verificado 73,5% (n=20) de parasitismo nos exemplares analisados. A helmintofauna gastrointestinal apresentou grande riqueza de espécies, totalizando 12 táxons: os nematódeos Porrocaecum angusticolle em C. plancus, Subulura forcipata e Dispharynx sp. em M. choliba, Microtetrameres sp. em R. magnirostris e Procyrnea sp. em B. schistaceus; os trematódeos Platynosomum illiciens em M. choliba, T. furcata e G. swainsonii, Athesmia sp. em G. albicaudatus e Strigea sp. em R. magnirostris; e os acantocéfalos Centrorhynchus kuntzi em R. magnirostris, Centrorhynchus millerae em E. furficatus, Centrorhynchus guira e Centrorhynchus sp. em M. choliba. Nenhum cestódeo foi encontrado. As carcaças de M. usta, A. clamator, A. cunicularia, I. americanus, M. ruficollis e F. rufigularis não apresentaram helmintos gastrointestinais. C. guira e P. angusticolle representam novas ocorrências no território brasileiro e no Estado do Pará, estendendo seu alcance geográfico. São considerados novos hospedeiros: M. choliba para C. guira e S. forcipata; E. forficatus para C. millerae; B. schistaceus para Procyrnea sp.; C. plancus para P. angusticolle; G. albicaudatus para Athesmia sp.; e M. choliba e G. swainsonii para P. illiciens. Estes resultados reforçam a necessidade de ampliar as pesquisas no campo da parasitologia de aves de rapina no Brasil e, particularmente, no Estado do Pará.Parasites of digestive tract are frequently detected in these birds, but the knowledge of helminthofauna in birds of prey in Brazil is still incipient. Therefore the objective of this work is to investigate the gastrointestinal helminthofauna of birds of prey that occur in the State of Pará, Brazil. 33 carcasses and helminths regurgitated by one individual were used, totaling 34 individuals of 14 species: Megascops choliba (n = 10), Rupornis magnirostris (n = 8), Tyto furcata (n = 5), Megascops usta (n = 1), Athene cunicularia (n = 1), Ibycter americanus (n =1), Asio clamator (n = 1), Geranoaetus albicaudatus (n = 1), Caracara plancus (n = 1), Gampsonyx swainsonii (n = 1), Buteogallus schistaceus (n = 1), Micrastur ruficollis (n = 1), Falco rufigularis (n = 1) and Elanoides forficatus (n = 1). There was 73.5% (n = 20) of parasitism in the analyzed specimens. The gastrointestinal helminthofauna presented a great richness of species, totaling 12 taxa: the nematodes Porrocaecum angusticolle in C. plancus, Subulura forcipata and Dispharynx sp. in M. choliba, Microtetrameres sp. in R. magnirostris and Procyrnea sp. in B. schistaceus; the trematodes Platynosomum illiciens in M. choliba, T. furcata and G. swainsonii, Athesmia sp. in G. albicaudatus and Strigea sp. in R. magnirostris; and the acanthocephalans Centrorhynchus kuntzi in R. magnirostris, Centrorhynchus millerae in E. furficatus, Centrorhynchus guira and Centrorhynchus sp. in M. choliba. No cestodes were found. The carcasses of M. usta, A. clamator, A. cunicularia, I. americanus, M. ruficollis and F. rufigularis did not show gastrointestinal helminths. C. guira and P. angusticolle represent new occurrences in the Brazilian territory and in the State of Pará, extending their geographic reach. New hosts are considered: M. choliba for C. guira and S. forcipata; E. forficatus for C. millerae; B. schistaceus for Procyrnea sp.; C. plancus for P. angusticolle; G. albicaudatus for Athesmia sp .; and M. choliba and G. swainsonii for P. illiciens. These results reinforce the need to expand research in the field of birds of prey parasitology in Brazil and, particularly, in the State of Pará

Nonlinear pharmacokinetics of imipramine and its active metabolite, desipramine

研究科: 千葉大学大学院薬学研究院学位:千大院薬博乙第80

Estabilidade térmica de redes de Bragg fabricadas por laser femtosegundo

Mestrado em Engenharia FísicaNo presente trabalho é descrito e apresentado o estudo da estabilidade térmica de redes de Bragg em fibra ótica de sílica, fabricadas por um laser de femtosegundo. O plano de trabalhos começou por uma pesquisa bibliográfica relacionada com as diferentes técnicas de gravação de redes de Bragg em fibras óticas e o estado de arte em estudos de estabilidade térmica das mesmas redes. Foram desenvolvidos e produzidos (em ambiente empresarial) um total de 8 sondas de temperatura cujo princípio de funcionamento baseia-se no comportamento típico de redes de Bragg em fibra ótica, quando submetidas a variações de temperatura. Estas sondas foram posteriormente calibradas termicamente. Implementaram-se dois regimes de testes a dois conjuntos de 4 sondas: um regime isotérmico e outro isócrono. Ambos foram desenvolvidos tanto no Departamento de Física da Universidade de Aveiro como nas instalações da HBM FiberSensing, S.A., no Porto. Os resultados obtidos relativos à variação do comprimento de onda de Bragg e refletividade do pico máximo de cada sonda em função do tempo e da temperatura permitiram aplicar um modelo teórico e concluir quanto à estabilidade térmica das redes de Bragg.In this thesis is presented a study of the thermal stability of Bragg gratings in optical silica fiber fabricated by a femtosecond laser. The work plan began with a literature review related to the different Bragg gratings recording techniques in optical fiber and the state of the art of thermal stability studies. A total of eight temperature sensors were developed and produced, whose operating principle is based on typical behaviour of Bragg gratings when submitted to temperature variations. These probes were thereafter thermally calibrated. Two types of tests were implemented for two different sets of four probes each: an isothermal and an isochronous regime. Both tests were developed in the Department of Physics at the University of Aveiro and at HBM FiberSensing, SA in Porto. A theoretical model was applied to the results relating to the variation of Bragg wavelength and to the reflectivity peak of each probe (as a function of time and temperature). With the application of this method it was possible to conclude about the thermal stability of the Bragg gratings