Regularização e pontos conjugados Bang-bang no controlo óptimo

Doutoramento em MatemáticaConsideramos o problema de controlo óptimo de tempo mínimo para sistemas de controlo mono-entrada e controlo afim num espaço de dimensão finita com condições inicial e final fixas, onde o controlo escalar toma valores num intervalo fechado. Quando aplicamos o método de tiro a este problema, vários obstáculos podem surgir uma vez que a função de tiro não é diferenciável quando o controlo é bang-bang. No caso bang-bang os tempos conjugados são teoricamente bem definidos para este tipo de sistemas de controlo, contudo os algoritmos computacionais directos disponíveis são de difícil aplicação. Por outro lado, no caso suave o conceito teórico e prático de tempos conjugados é bem conhecido, e ferramentas computacionais eficazes estão disponíveis. Propomos um procedimento de regularização para o qual as soluções do problema de tempo mínimo correspondente dependem de um parâmetro real positivo suficientemente pequeno e são definidas por funções suaves em relação à variável tempo, facilitando a aplicação do método de tiro simples. Provamos, sob hipóteses convenientes, a convergência forte das soluções do problema regularizado para a solução do problema inicial, quando o parâmetro real tende para zero. A determinação de tempos conjugados das trajectórias localmente óptimas do problema regularizado enquadra-se na teoria suave conhecida. Provamos, sob hipóteses adequadas, a convergência do primeiro tempo conjugado do problema regularizado para o primeiro tempo conjugado do problema inicial bang-bang, quando o parâmetro real tende para zero. Consequentemente, obtemos um algoritmo eficiente para a computação de tempos conjugados no caso bang-bang.In this thesis we consider a minimal time control problem for single-input control-affine systems in finite dimension with fixed initial and final conditions, where the scalar control take values on a closed interval. When applying a shooting method for solving this problem, one may encounter numerical obstacles due to the fact that the shooting function is non smooth whenever the control is bang-bang. For these systems a theoretical concept of conjugate time has been defined in the bang-bang case, however direct algorithms of computation are difficult to apply. Besides, theoretical and practical issues for conjugate time theory are well known in the smooth case, and efficient implementation tools are available. We propose a regularization procedure for which the solutions of the minimal time problem depend on a small enough real positive parameter and are defined by smooth functions with respect to the time variable, facilitating the application of a single shooting method. Under appropriate assumptions, we prove a strong convergence result of the solutions of the regularized problem towards the solution of the initial problem, when the real parameter tends to zero. The conjugate times computation of the locally optimal trajectories for the regularized problem falls into the standard theory. We prove, under appropriate assumptions, the convergence of the first conjugate time of the regularized problem towards the first conjugate time of the initial bang-bang control problem, when the real parameter tends to zero. As a byproduct, we obtain an efficient algorithmic way to compute conjugate times in the bang-bang case.On considère le problème de contrôle optimal de temps minimal pour des systèmes affine et mono-entrée en dimension finie, avec conditions initiales et finales fixées, où le contrôle scalaire prend ses valeurs dans un intervalle fermé. Lors de l'application d'une méthode de tir pour résoudre ce problème, on peut rencontrer des obstacles numériques car la fonction de tir n'est pas lisse lorsque le contrôle est bang-bang. Pour ces systèmes, dans le cas bangbang, un concept théorique de temps conjugué a été défini, toutefois les algorithmes de calcul direct sont difficiles à appliquer. En outre, les questions théoriques et pratiques de la théorie du temps conjugué sont bien connues dans le cas lisse, et des outils efficaces de mise en oeuvre sont disponibles. On propose une procédure de régularisation pour laquelle les solutions du problème de temps minimal dépendent d’un paramètre réel positif suffisamment petit et sont définis par des fonctions lisses en temps, ce qui facilite l’application de la méthode de tir simple. Sous des hypothèses convenables, nous prouvons un résultat de convergence forte des solutions du problème régularisé vers la solution du problème initial, lorsque le paramètre réel tend vers zéro. Le calcul des temps conjugués pour les trajectoires localement optimales du problème régularisé est standard. Nous prouvons, sous des hypothèses appropriées, la convergence du premier temps conjugué du problème régularisé vers le premier temps conjugué du problème de contrôle bang-bang initial, quand le paramètre réel tend vers zéro. Ainsi, on obtient une procédure algorithmique efficace pour calculer les temps conjugués dans le cas bang-bang.FCT - SFRH/BD/27272/200

Uncovering novel plasma membrane carboxylate transporters in the yeast Cyberlindnera jadinii

The yeast Cyberlindnera jadinii has great potential in the biotechnology industry due to its ability to produce a variety of compounds of interest, including carboxylic acids. In this work, we identified genes encoding carboxylate transporters from this yeast species. The functional characterization of sixteen plasma membrane carboxylate transporters belonging to the AceTr, SHS, TDT, MCT, SSS, and DASS families was performed by heterologous expression in Saccharomyces cerevisiae. The newly identified C. jadinii transporters present specificity for mono-, di-, and tricarboxylates. The transporters CjAto5, CjJen6, CjSlc5, and CjSlc13-1 display the broadest substrate specificity; CjAto2 accepts mono- and dicarboxylates; and CjAto1,3,4, CjJen1-5, CjSlc16, and CjSlc13-2 are specific for monocarboxylic acids. A detailed characterization of these transporters, including phylogenetic reconstruction, 3D structure prediction, and molecular docking analysis is presented here. The properties presented by these transporters make them interesting targets to be explored as organic acid exporters in microbial cell factories.This study was supported by the strategic program UID/BIA/04050/2019, funded by Portuguese funds through the FCT I.P.; the projects PTDC/BIAMIC/5184/2014, funded by national funds through the FCT I.P.; and the European Regional Development Fund (ERDF) through the COMPETE 2020–Programa Operacional Competitividade e Internacionalização (POCI) and EcoAgriFood: Innovative green products and processes to promote AgriFood BioEconomy (operação NORTE-01–0145-FEDER-000009), supported by Norte Portugal Regional Operational Program (NORTE 2020) under the PORTUGAL 2020 Partnership Agreement through the European Regional Development Fund (ERDF). M.S.S. acknowledges the Norte2020 for the UMINHO/BD/25/2016 PhD grant with the reference NORTE-08–5369-FSE-000060, and J.A. acknowledges the FCT for the PD/BD/150584/2020 PhD grant. PS acknowledges FCT for contract CEECINST/0007772018. I.S-S. was supported by the program contract FCT-UMINHO/Norma transitória from the Legal Regime of Scientific Employment (RJEC)

Clinical and molecular characterization of feline mammary carcinomas overexpressing HER2 proto-oncogene (FMC-HER2+) : new strategies for effective diagnostic and cancer therapy

Tese de Doutoramento em Ciências Veterinárias na Especialidade de Ciências Biológicas e Biomé[email protected] the scarce data available in feline mammary carcinoma (FMC) and despite its importance in veterinary clinical practice, this thesis emerges in order to increase the knowledge of this tumor type, especially the FMC-HER2 positive. In the first two studies, the protocols for detection and quantification of the fHER2 and Ki-67 biomarkers were optimized and validated. These studies demonstrated that, in cats, the incidence of fHER2 overexpression were similar to women (about 30%), although no gene amplification was detected. It was also demonstrated that high levels of Ki-67 index were associated with a worse prognosis. Using a panel of protein biomarkers, the FMC were divided into six different groups that demonstrated prognostic value, similarly to what is described in women. In fact, cats with triple negative basal-like or HER2-positive subtypes were associated with shorter overall survival, contrasting with cats presenting luminal A tumors. Moreover, these studies also indicated that luminal B and triple negative basal-like subtypes are the most common in cats. When the metastatic lesions were evaluated, a marked loss of receptor expression was found, which was associated with an increase of the triple negative basal-like subtype, highlighting the importance of immunophenotyping all lesions (primary and metastatic) in cats. Considering these results, the development of diagnostic methodologies that allows the continuous follow-up of the patients would be very useful. Therefore, the last study presented in this thesis evaluates the fHER2 serum levels in cats with FMC using two different immunoassays (ELISA and dot blot). The serum levels of fHER2 were significantly associated with the fHER2 in tissue samples of FMC (assessed by IHC). This is consistent to what is described for humans and suggests that serum quantification could be an important tool for monitoring cats after the surgery. In sum, the results presented herein provide new diagnostic and prognostic tools for veterinary oncology. Considering the high prevalence and similarities with the human counterpart, cat can also represent a potential animal model for the study of luminal B and triple negative subtypes. Considering fHER2-positive FMC more studies are required in order to determine the aetiology of the protein overexpression.RESUMO - Os tumores mamários felinos (TMF) são umas das neoplasias mais comuns em Oncologia Felina, com uma incidência que pode atingir os 40%, pelo que assumem um papel relevante na prática clínica veterinária. Estes tumores apresentam habitualmente uma etiologia maligna (carcinomas) e um comportamento agressivo, estando associados a um prognóstico reservado. Atualmente, existem poucas opções terapêuticas que permitam aumentar a qualidade e a esperança média de vida dos animais afectados por esta neoplasia. Assim, estudos que permitam uma melhor caracterização dos tumores, identificando potenciais biomarcadores que possam ser utilizados como factores de prognóstico ou preditivos, são fundamentais para o desenvolvimento da Medicina Felina. Por outro lado, os carcinomas mamários que ocorrem espontaneamente nos animais de companhia têm sido sugeridos como potenciais modelos biológicos para o estudo do Cancro da Mama, com vantagens, comparativamente aos animais de laboratório que são atualmente utilizados. De facto, nesses animais, os tumores são quimicamente induzidos ou xenotransplantados, pelo que são considerados modelos mais artificiais. Deste modo, esta tese de doutoramento surge com o objetivo de aumentar o conhecimento sobre os tumores mamários felinos, com especial interesse no recetor transmembranar para o fator de crescimento epidérmico de tipo 2 (HER2), quer numa perspetiva clínica, de forma a melhorar a qualidade de vida destes animais de companhia, abrindo portas a novos meios de diagnóstico e potenciais novos alvos terapêuticos, quer no sentido de investigar a viabilidade de a Gata ser um bom modelo animal para o estudo do Cancro da Mama na Mulher. Relativamente à Mulher, a investigação oncológica desenvolveu grandes esforços para encontrar biomarcadores que permitam otimizar o diagnóstico e o tratamento do cancro da mama. Entre estes, encontra-se a proteína HER2, uma oncoproteína que pode estar sobreexpressa em vários tumores da espécie humana (mama, pâncreas, cólon, próstata, bexiga, entre outros) e que lhes confere elevada agressividade e prognóstico reservado. No Cancro da Mama, estima-se que entre 10 a 40% dos tumores apresentem amplificação do gene HER2, o que se traduz na sobreexpressão da proteína. Estas alterações são rotineiramente detetadas através de duas técnicas moleculares, a hibridação in situ (ISH) e a imunohistoquímica (IHC), respetivamente. A avaliação do status da proteína HER2 é importante, não só pelo seu valor de prognóstico, mas também como fator preditivo, já que pacientes com sobreexpressão desta proteína são elegíveis para tratamento com terapêuticas específicas dirigidas contra o HER2, tais como os anticorpos anti-HER2 (sendo o trastuzumab o mais conhecido), o que veio aumentar consideravelmente a sobrevida destas doentes. Contrastando com a medicina humana, a literatura disponível em medicina veterinária apresenta ainda escassos estudos sobre a importância da proteína HER2 nos TMF, ou sobre os novos sistemas de classificação que subdividem os tumores mamários conforme o seu perfil imunofenotípico.(...

Short-term wind forecasting for energy resources scheduling

This paper proposes a wind power forecasting methodology based on two methods: direct wind power forecasting and wind speed forecasting in the first phase followed by wind power forecasting using turbines characteristics and the aforementioned wind speed forecast. The proposed forecasting methodology aims to support the operation in the scope of the intraday resources scheduling model, namely with a time horizon of 5 minutes. This intraday model supports distribution network operators in the short-term scheduling problem, in the smart grid context. A case study using a real database of 12 months recorded from a Portuguese wind power farm was used. The results show that the straightforward methodology can be applied in the intraday model with high wind speed and wind power accuracy. The wind power forecast direct method shows better performance than wind power forecast using turbine characteristics and wind speed forecast obtained in first phase

Structural characterization of the Aspergillus niger citrate transporter CexA uncovers the role of key residues S75, R192 and Q196

Supplementary data associated with this article can be found in the online version at doi:10.1016/j.csbj.2023.04.025.The Aspergillus niger CexA transporter belongs to the DHA1 (Drug-H+ antiporter) family. CexA homologs are exclusively found in eukaryotic genomes, and CexA is the sole citrate exporter to have been functionally characterized in this family so far. In the present work, we expressed CexA in Saccharomyces cerevisiae, demonstrating its ability to bind isocitric acid, and import citrate at pH 5.5 with low affinity. Citrate uptake was independent of the proton motive force and compatible with a facilitated diffusion mechanism. To unravel the structural features of this transporter, we then targeted 21 CexA residues for site-directed mutagenesis. Residues were identified by a combination of amino acid residue conservation among the DHA1 family, 3D structure prediction, and substrate molecular docking analysis. S. cerevisiae cells expressing this library of CexA mutant alleles were evaluated for their capacity to grow on carboxylic acid-containing media and transport of radiolabeled citrate. We also determined protein subcellular localization by GFP tagging, with seven amino acid substitutions affecting CexA protein expression at the plasma membrane. The substitutions P200A, Y307A, S315A, and R461A displayed loss-of-function phenotypes. The majority of the substitutions affected citrate binding and translocation. The S75 residue had no impact on citrate export but affected its import, as the substitution for alanine increased the affinity of the transporter for citrate. Conversely, expression of CexA mutant alleles in the Yarrowia lipolytica cex1Δ strain revealed the involvement of R192 and Q196 residues in citrate export. Globally, we uncovered a set of relevant amino acid residues involved in CexA expression, export capacity and import affinity.This work was supported by the Strategic Programme UID/BIA/04050/2020 and the project LA/P/0069/2020 granted to the Associate Laboratory ARNET, both funded by Portuguese funds through the FCT-IP. J.A. acknowledges the FCT and the Doctoral Program in Applied and Environmental Microbiology for the PD/BD/150584/2020 PhD grant and a COST Action CA18113 Short-Term Scientific Mission grant (EuroMicropH). M.S.S. acknowledges the Norte2020 for the UMINHO/BD/25/2016 PhD grant with the re ference NORTE-08-5369-FSE-000060. I.S-S. was supported by the program contract FCTUMINHO/Norma transitória from the Legal Regime of Scientific Employment (RJEC)

DO DYNAMIC TARIFFS PROMOTE INVESTMENT IN RENEWABLES? THE CASE OF A NON-REGULATED MONOPOLY

We consider a non-regulated monopolist supplier of electricity that may use renewable and/or non-renewable resources to produce electricity. Renewable resources require an ex ante investment and generate an uncertain output with fixed operating costs. Non-renewable resources are perfectly dispatchable and have variable operating costs proportional to output. We find that dynamic tariffs promote investment in renewables in all scenarios except one where output from renewables when weather conditions are favorable is so large that the monopolist prefers to curtail excess energy. Only in that scenario, dynamic tariffs decrease investment in renewables. In any case, dynamic tariffs are welfare-improving in that both the monopolist and consumers become better off

Expanding the knowledge on the skillful yeast Cyberlindnera jadinii

Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. The emerging applications of this yeast reinforce its potential in the white biotechnology sector. Nonetheless, it is necessary to expand the knowledge on its metabolism, regulatory networks, and transport mechanisms, as well as to develop more robust genetic manipulation systems and synthetic biology tools to promote the full exploitation of C. jadinii.This work was supported by the strategic program UID/BIA/04050/2019, funded by Portuguese funds through the FCT I.P., the projects: PTDC/BIAMIC/5184/2014, funded by national funds through the Fundação para a Ciência e Tecnologia (FCT) I.P. and by the European Regional Development Fund (ERDF) through the COMPETE 2020–Programa Operacional Competitividade e Internacionalização (POCI), and EcoAgriFood: Innovative green products and processes to promote AgriFood BioEconomy (operação NORTE-01–0145-FEDER-000009), supported by Norte Portugal Regional Operational Program (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). M.S.S. acknowledges the Norte2020 for the UMINHO/BD/25/2016 PhD grant with the reference NORTE-08–5369-FSE-000060

Engineering the activity and specificity of Saccharomyces cerevisiae Acetate Transporter Ady2/Ato1

Organic acids are industrially relevant chemicals with application in polymer, food, agricultural and pharmaceutical sectors. Yeasts commonly represent the organisms of choice for production of organic acids, namely due to their tolerance of low pH environments since such production conditions allow for direct formation of the desired protonated form of the acid and thus cut downstream processing costs. Since organic acid export over the plasma membrane represents one of the key steps in microbial production of these compounds, organic acid transporters started receiving greater attention in metabolic engineering strategies. Ato1 is the main transporter responsible for uptake of acetic acid into the cytosol in S. cerevisiae, while also being able to mediate organic acid transport in the opposite direction, as it was shown to be involved in the export of lactic acid from S. cerevisiae cells engineered for lactic acid production. Ato1 is a member of the Acetate Uptake Transporter Family (AceTR), with several functionally characterized homologues in yeast, fungi, and bacteria. Recently solved crystal structure of its bacterial homologue, SatP, depicts a hexameric anion channel. In this work, we studied the relationship between structure and function of Ato1 via rational mutagenesis and identified residues critical for Ato1 substrate specificity and transport activity. By utilizing computer-assisted three-dimensional modelling tools, we provide possible explanations of acquired features. Our final goal is to test applicability of these transporters in yeast cell factories that produce organic acids.Supported by strategic program UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) and TransAcids (PTDC/BIAMIC/5184/2014) funded by national funds, FCT-IP and ERDF by COMPETE 2020-POCI; EcoAgriFood (NORTE-01-0145-FEDER-000009), supported by NORTE-2020, under the PORTUGAL 2020 Partnership Agreement. TC acknowledges Yeastdoc European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 764927

A ocupação do Neolítico Antigo do povoado do Carrascal (Leceia, Oeiras)

Do período de quase 500 anos em que se observou coexistência sem sobreposição territorial entre os grupos neolíticos de cerâmica predominantemente impressa (incluindo, naturalmente, a cardial) da Estremadura e os grupos mesolíticos do vale do Tejo, entre cerca de 5400 e cerca de 5000 anos a.C., evoluiu-se para outra realidade, em que as cerâmicas incisas se desenvolvem, situável entre finais do VI e abarcando todo o V milénio a.C. É nessa altura que, finalmente, se deverá ter produzido interacção entre as comunidades neolitizadas e as derradeiras comunidades mesolíticas sedeadas nos concheiros, conforme atestam as cerâmicas do Neolítico Antigo Evolucionado encontradas nas camadas superiores dos concheiros do vale do Tejo (FERREIRA, 1974), bem como nos concheiros do vale do Sado, de que é exemplo o concheiro do Cabeço do Pez (SANTOS, SOARES & SILVA., 1974). Resta, contudo, saber se não se trata de simples reocupações dos mesmos sítios, depois de intervalos de abandono mais ou menos longos.info:eu-repo/semantics/publishedVersio