Advancing computational biophysics with Virtual Reality

Modelos computacionais são ferramentas poderosas para explorar as propriedades de sistemas biológicos complexos. Na neurociência computacional, permitir fácil exploração e visualização computacional desses modelos é crucial para o progresso do campo. Nos últimos anos, os sistemas de visualização 3D e o hardware de realidade virtual tornaram-se mais acessíveis e isso abre uma janela de oportunidade para os serviços de visualização. O principal problema atual da visualização 3D diz respeito à usabilidade (ou seja, navegação e seleção). Durante esta dissertação, hipotetizaremos que a substituição do 3D por VR irá (1) superar os problemas de usabilidade mencionados e, eventualmente, (2) aumentar a eficácia dos utilizadores em relação às questões do campo de estudo (neurociência). Para avaliar os resultados do trabalho desenvolvido nesta dissertação, será realizada uma experiência de duas partes, em que um grupo de indivíduos deverá executar um conjunto de tarefas pré-determinadas e avaliar sua experiência usando 3D na primeira e VR na última parte. Além da autoavaliação da experiência, dados como tempo de conclusão e correção da tarefa também serão usados para quantificar a eficácia do método de visualização. Dada a experiência mencionada, um protótipo de uma aplicação (baseada na Web) com visualização de Realidade Virtual deve ser desenvolvido. A visualização 3D será fornecida por uma framework de código aberto baseada na Web, chamada Geppetto. Cada uma das decisões tomadas no desenvolvimento do protótipo será analisada adequadamente neste documento, bem como a literatura científica que servirá de base quando necessário. Além do estudo da Realidade Virtual propriamente dita, também serão analisados métodos padronizados para a visualização de informações (neuro) científicas. A solução proposta procurará constituir uma base de trabalho sólida e suficientemente genérica a ser aplicada, não apenas no contexto da neurociência, mas também em vários outros contextos onde a visualização de modelos através de Realidade Virtual poderá ser bem-sucedida.Computational models are powerful tools for exploring the properties of complex biological systems. In computational neuroscience, allowing easy computational exploration and visualization of this models is crucial for the progress of the field. In recent years, Virtual Reality hardware and visualization systems have become more affordable and this opens a window of opportunity for visualization services. The current major problem of 3D visualization concerns usability (i.e., navigation and selection). During this dissertation, we will hypothesize that the replacement of 3D for VR will (1) overcome the usability issues mentioned and eventually (2) boost user effectiveness regarding field of study (neuroscience) concerns. In order to evaluate the results of the work developed under this dissertation, a two-part experiment will be carried out where a group of individuals must perform a set of predetermined tasks and evaluate their experience using 3D in the first and VR in the last part. Besides the self-evaluation of the experiment, data such as completion time and task correctness will also be used to quantify the effectiveness of the visualization method. Given the aforementioned experiment, a prototype of a (web-based) application with Virtual Reality visualization shall be developed. The 3D visualization will be provided by a web-based open-sourced framework called Geppetto. Each of the decisions made in the development of the prototype will be properly analyzed in this document, as well as the scientific literature that will serve as a basis when necessary. Besides the study of Virtual Reality itself, standard methods with respect to the visualization of (neuro)scientific information will also be analyzed. The proposed solution will seek to constitute a solid and sufficiently generic work base to be applied, not only in the scope of neuroscience, but also in several other contexts where visualization through VR might be successful

Fluorescence Properties of Rare-Earth-Doped Sol-Gel Glasses

Glasses may be prepared by sol-gel processing over a wide range of compositions and thick multilayer deposits may be used as waveguides for integrated optics. Doping these layers with rare-earth (RE) ions enables the fabrication of active devices for optical amplifiers; the incorporation of these ions into nanocrystallites offers possibilities for increased dopant concentration without fluorescence quenching, improved spectroscopic performance and high quantum yields. Rare-earth (RE) ions such as erbium (Er3+), ytterbium (Yb3+), neodymium (Nd3+), thulium (Tm3+), holmium (Ho3+) and praseodymium (Pr3+) have been widely used in optical applications and cover a range of wavelengths ranging from UV-visible to the near infrared. This chapter includes basic principles of fluorescence in RE doped glasses, fluorescence lifetimes, quantum yields and Judd-Ofelt analysis. A few information is given about the preparation and characterization of glasses, thin films and glass-ceramics (nanocrystallites embedded in glass matrix) prepared by sol-gel processing. The growth of nanocrystals in glassy sol-gel films through suitable heat treatments can avoid the influence of high phonon energy of silica glasses. The characterization of such materials can be evaluated by optical techniques, namely UV-Visible, FTIR, among other additional techniques that include Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD) and Atomic Force Microscopy (AFM)

Carbon Dots as a Fluorescence pH Nanosensor by Application of an Active Surface Preservation Strategy

In the environmental, industrial, and biomedical fields, pH monitorization is of the upmost importance. However, the most used type of pH sensors, glass pH-electrodes, still present limitations in their application in low volume samples and in cellular pH sensing, due to their size and invasive nature. Fluorescence-based sensors present a solution to such issues, providing a non-invasive solution to pH sensing. Herein, we report the rational development of carbon dots (CDs) as a pH nanosensor via an active surface preservation (ASP) method. Carbon dots (CDs) are carbon-based fluorescent nanoparticles with valuable properties such as high aqueous solubility, low cost and good biocompatibility, with remarkable fluorescence performance, been increasingly used as fluorescent nanosensors. Namely, these nanomaterials present advantages over molecular probes in terms of (photo)stability and water solubility, among others. By employing ASP strategies, the CDs will be prepared by using precursors with known active functional features. The ASP method allows the nanoparticles to retain the structural features of precursors, thus retaining their properties, without the need for costly and time-consuming post-synthesis functionalization procedures. In this work, we intend to provide a proof-of-concept of this type of strategy by utilizing the known pH-sensitivity of fluorescein to provide a pH-based response to CDs. The resulting CDs presented reversible response by fluorescence enhancement in the range of pH from 4 to 12. The nanoparticles exhibited excellent photostability, in different pH solutions. The studied CDs were also unaffected by, either variation of ionic strength or the presence of interferent species, while being compatible with human cancer cells. Finally, CDs were able to determine the pH of real samples. Thus, a selective pH fluorescent CDs-based nanosensor was developed.</jats:p

DESTA ÁGUA (não) BEBEREI? : modelos de correlação identificados entre dados biológicos e meteorológicos - lagoas de S. Miguel

A secção UAciência é coordenada pelo Professor Universitário Armindo Rodrigues.[…]. Neste trabalho foram identificados modelos de correlação de forma exploratória entre os diversos parâmetros biológicos (fitoplâncton) e meteorológicos, durante o período de 2003 a 2017, nas lagoas do Fogo, Furnas e Sete Cidades (site GRA). Neste estudo, com muitas amostras e variáveis de diversas naturezas, a melhor forma de avaliar globalmente os dados foi a metodologia estatística multivariada, como a análise de componentes principais (ACP), onde as variáveis podem ser analisadas em conjunto. Os dados disponíveis permitiram obter correlações por lagoa, profundidades de recolha, ano de recolha e por temporada (primavera, verão, outono e inverno), no período temporal considerado. As comunidades biológicas nas lagoas dos Açores estão representadas pelas divisões mais comuns do fitoplâncton. […].info:eu-repo/semantics/publishedVersio

Um novo sistema de clonagem baseado na lipoproteína OprI para obtenção de formulações imunogénicas derivadas da parede celular bacteriana

Tese de Doutoramento em Ciências Veterinárias. Especialidade de Sanidade AnimalA modulação de imunidade específica por conjugação de antigénios com ligandos de receptores de reconhecimento de padrão (PRR) constitui uma estratégia emergente para o desenvolvimento de vacinas subunitárias. Neste trabalho, desenvolve-se um novo sistema de clonagem em Escherichia coli para expressão de antigénios em fusão com a lipoproteína OprI, um ligando TLR da membrana externa de Pseudomonas aeruginosa. O sistema permite um controlo apertado da expressão proteica e a purificação por cromatografia de afinidade com iões metálicos, ultrapassando as principais limitações de versões anteriores. Confirmou-se o processamento, translocação e triacilação da lipoproteína e desenvolveram-se protocolos para a produção de outras formulações recombinantes derivadas da parede bacteriana (fragmentos e vesículas de membrana externa) com potencial distinto para activação PRR. Como modelo, clonaram-se as sequências dos antigénios A104R do vírus da peste suína africana (VPSA), ovalbumina e EGFP. Demonstrou-se a capacidade adjuvante das três formulações, avaliando a resposta humoral e a indução de linfócitos T CD8+ in vivo e o perfil de citocinas e quimiocinas induzidas em células dendríticas estimuladas in vitro. Os resultados observados validam o sistema para a obtenção de formulações imunogénicas com aplicação no desenvolvimento de vacinas subunitárias experimentais e em estudos de modulação de resposta adaptativa.ABSTRACT - A new cloning system based on the OprI lipoprotein for the production of bacterial cell wall-derived immunogenic formulations - The modulation of specific immunity through the conjugation of antigens with ligands of pattern recognition receptors (PRR) is emerging as a promising strategy for the development of subunit vaccines. Here, a new Escherichia coli cloning system for the expression of antigens in fusion with the OprI lipoprotein, a TLR ligand from the Pseudomonas aeruginosa outer membrane, is described. The system offers tight regulation of expression and allows for purification by metal affinity chromatography, circumventing the major drawbacks of former versions. Lipoprotein processing, translocation and triacylation were confirmed and protocols for the productions of other recombinant bacterial cell wall-derived formulations (outer membrane fragments and vesicles) with distinct potential for PRR activation were developed. As models, the sequences coding for the antigens A104R from African swine fever virus (ASFV), ovalbumin and EGFP were cloned. The adjuvant capacity of the three formulations was demonstrated evaluating the induction of humoral and CD8+ T cells responses in vivo and the cytokine and chemokine profile induced in dendritic cells stimulated in vitro. The results observed validate the system for the production of immunogenic formulations suitable for the development of experimental subunit vaccines and for studies on the modulation of adaptive immunity.FCT-Fundação para a Ciência e Tecnologia. CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal da Faculdade de Medicina Veterinária-UTL

Development of a monitoring system for electrical energy consumption and power quality analysis

This paper presents the development of a monitoring system for electrical energy consumption and power quality analysis, also known as power quality analyser (PQA). The internal architecture of the developed monitoring system is described in detail along the paper, highlighting the signal conditioning circuit and analogue to digital conversion (ADC) stage, the advanced RISC machine (ARM) processor, and the digital signal processor (DSP), which are used, respectively, for data acquisition, data communication and power quality calculations. This paper also describes the software developed for a Raspberry Pi, which receives the processed information from the ARM processor and presents it in real-time using a touch screen user-friendly interface. Among all the available features of the developed system, the paper presents the most relevant experimental results obtained with linear and nonlinear loads, showing the main functionalities of the different menus available in the developed user interface, mainly the menus “Scope”, “Harmonics” and “Data”.This work is supported by FCT with the reference project UID/EEA/04436/2013, by FEDER funds through the COMPETE 2020 – Programa Operacional Competitividade e Internacionalização (POCI) with the reference project POCI-01-0145-FEDER-006941.info:eu-repo/semantics/publishedVersio

Análise e melhoria dos processos de produção de uma empresa do setor da ourivesaria

Atualmente, as empresas deparam-se com um mercado cada vez mais competitivo e exigente. Surge assim, a necessidade de produzir mais e melhor, com capacidade de resposta rápida, consumindo cada vez menos recursos. O projeto em estudo foi desenvolvido numa empresa do setor da ourivesaria, Flamingo – Indústria da Ourivesaria SA, no departamento de joalharia inserido na área de produção. Este estudo, tem como objetivos a melhoria dos processos produtivos, a redução de custos e aumento da produtividade. Após uma análise aos processos existentes, foram detetados vários problemas e oportunidades de melhoria nos processos de gestão e controlo da produção e orçamentação. Com o intuito de colmatar os problemas diagnosticados, foram sugeridas e implementadas diversas propostas de melhoria, como: elaboração do dossier do produto, organização do setor produtivo com base na metodologia 5S, elaboração de documentos pró-forma, elaboração de um método para a determinação de prioridade de produção, desenvolvimento de uma ferramenta de gestão e controlo da produção, determinação do ponto de encomenda com base em históricos de venda e lead time produtivo e alteração dos modus operandi do processo de orçamentação. A propostas de melhoria implementadas permitiram à empresa obter como ganhos a redução de lead time produtivo, redução de custos de produção, aumento da produtividade, redução da variabilidade entre lotes de produção, aumento da qualidade do produto final, entres outros. Estes ganhos possibilitaram um aumento de 83% de informação documentada, uma redução de 37% de lead time e de 51% do desvio-padrão do mesmo, assim como um aumento de 148% na faturação mensal de uma marca produzida no departamento.Nowadays, companies face an increasingly competitive and demanding market. Thus, the need to produce more and better rises, with fast response capability, consuming less and less resources. The project in study, was developed in a company inserted in the jewellery sector, Flamingo – Indústria da Ourivesaria SA, in the production area. This study aims to improve production processes, reduce costs and increase productivity. After analysing the existing processes, several problems and improvement opportunities in production management and control and budgeting processes were detected. In order to overcome the problems diagnosed, several proposals for improvement were suggested and implemented, such as: elaboration of the product dossier, organization of the productive sector based on 5S methodology, elaboration of proforma documents, elaboration of a method for determinating manufacturing priorities, development of a production management and control tool, setting the order point based on sales history and productive lead time and changing the budgeting process modus operandi. The improvement proposals implemented allowed the company to obtain profits as reduction of productive lead time, reduction of production costs, increase of productivity, reduction of variability between batches of production, increase of final product quality, among others. These gains enabled an increase of 83% in documented information, a lead time reduction of 37% and 51% of the standard deviation, as well as a 148% increase in monthly invoicing for a brand produced in the department

Multivariate Statistical Analysis of the Phytoplankton Interactions with Physicochemical and Meteorological Parameters in Volcanic Crater Lakes from Azores

Publisher Copyright: © 2022 by the authors.This study aimed to identify the key factors influencing the phytoplankton development in four lakes on the island of São Miguel (Azores). We used a multivariate analysis of biological parameters (phytoplankton), physicochemical parameters, and meteorological data. Data were collected between 2003 and 2018 in the volcanic Lakes of Sete Cidades (Green and Blue), Fogo, and Furnas. The ecosystems of these bodies of water are increasingly vulnerable to anthropogenic activities (increasing human pressure) as well as to changing climate patterns. This analysis is the first exploratory approach to this dataset to explore trends and patterns of evolution from a multivariate perspective. This approach is also intended to improve understanding of the conditions that favor the emergence of different Cyanobacterial divisions. For this purpose, several statistical and chemometric methods were used, such as analysis of variance (ANOVA) and principal component analysis (PCA). Multivariate models combining biological and meteorological data focused from 2010 to 2012. The results from the PCA models showed that the abundance of Bacillariophyta, Dinophyta, and Cryptophyta phyla are correlated and appear to be influenced by high levels of precipitation, evaporation, and wind speed. On the other hand, the Cyanophyta, Chlorophyta, and Chrysophyta phyla appear to be more correlated with high values of air temperature, water temperature, and radiation. Also, the Euglenophyta phylum appears to be associated with low levels of precipitation, evaporation and wind speed, and high temperatures. Finally, we can conclude that these lakes have endured physicochemical parameters over the past 15 years, meaning that the measures adopted to monitor and protect the lakes are effective.publishersversionpublishe

Design of an intrinsically safe series-series compensation WPT system for automotive LiDAR

The earliest and simplest impedance compensation technique used in inductive wireless power transfer (WPT) design is the series-series (SS) compensation circuit, which uses capacitors in series with both primary and secondary coils of an air-gapped transformer. Despite of its simplicity at the resonant condition, this configuration exhibits a major sensitivity to variations of the load attached to the secondary, especially when higher coupling coefficients are used in the design. In the extreme situation that the secondary coil is left at open circuit, the current at the primary coil may increase above the safety limits for either the power converter driving the primary coil or the components in the primary circuit, including the coil itself. An approach often used to minimize this problem is detuning, but this also reduces the electrical efficiency of the power transfer. In low power, fixed-distance stationary WPT, a fair trade-off between efficiency and safety must be verified. This paper aims to consolidate a simple design procedure for such a SS-compensation, exemplifying its use in the prototype of a WPT system for automotive light detection and ranging (LiDAR) equipment. The guidelines herein provided should equally apply to other low power applications.This work has been supported by national funds through FCT—Fundação para a Ciência e Tecnologia within the Project Scope: UID/CEC/00319/2019, and also European Structural and Investment Funds in the FEDER component, through the Operational Competitiveness and Internationalization Programme (COMPETE 2020) [Project nº 037902; Funding Reference: POCI-01-0247-FEDER-037902]

In vivo anticancer activity of AZD3965: a systematic review

Proliferating cancer cells have high energy demands, which is mainly obtained through glycolysis. The transmembrane trafficking of lactate, a major metabolite produced by glycolytic cancer cells, relies on monocarboxylate transporters (MCTs). MCT1 optimally imports lactate, although it can work bidirectionally, and its activity has been linked to cancer aggressiveness and poor outcomes. AZD3965, a specific MCT1 inhibitor, was tested both in vitro and in vivo, with encouraging results; a phase I clinical trial has already been undertaken. Thus, analysis of the experimental evidence using AZD3965 in different cancer types could give valuable information for its clinical use. This systematic review aimed to assess the in vivo anticancer activity of AZD3965 either alone (monotherapy) or with other interventions (combination therapy). Study search was performed in nine different databases using the keywords “AZD3965 in vivo” as search terms. The results show that AZD3965 successfully decreased tumor growth and promoted intracellular lactate accumulation, which confirmed its effectiveness, especially in combined therapy. These results support the setup of clinical trials, but other important findings, namely AZD3965 enhanced activity when given in combination with other therapies, or MCT4-induced treatment resistance, should be further considered in the clinical trial design to improve therapy response.This work has been funded by National funds, through the Foundation for Science and Technology (FCT)-project UIDB/50026/2020 and UIDP/50026/2020 and by the project NORTE-01- 0145-FEDER-000055, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). J.A. received a fellowship from FCT, ref. SFRH/BPD/116784/2016