Disease Localization in Multilayer Networks

We present a continuous formulation of epidemic spreading on multilayer networks using a tensorial representation, extending the models of monoplex networks to this context. We derive analytical expressions for the epidemic threshold of the SIS and SIR dynamics, as well as upper and lower bounds for the disease prevalence in the steady state for the SIS scenario. Using the quasi-stationary state method we numerically show the existence of disease localization and the emergence of two or more susceptibility peaks, which are characterized analytically and numerically through the inverse participation ratio. Furthermore, when mapping the critical dynamics to an eigenvalue problem, we observe a characteristic transition in the eigenvalue spectra of the supra-contact tensor as a function of the ratio of two spreading rates: if the rate at which the disease spreads within a layer is comparable to the spreading rate across layers, the individual spectra of each layer merge with the coupling between layers. Finally, we verified the barrier effect, i.e., for three-layer configuration, when the layer with the largest eigenvalue is located at the center of the line, it can effectively act as a barrier to the disease. The formalism introduced here provides a unifying mathematical approach to disease contagion in multiplex systems opening new possibilities for the study of spreading processes.Comment: Revised version. 25 pages and 18 figure

Fire resistance tests on concrete columns

The reinforced concrete elements are known to have enhanced fire behaviour however there are many things that can affect that performance. In the last years there have been carried out, in the University of Coimbra, Portugal, dozens of fire resistance tests on concrete columns where it was tested the influence of various parameters on the behaviour of these columns. Several parameters that might have influence on the behaviour of concrete columns in fire, were tested: cross section shape (round and square), longitudinal reinforcement ratio, slenderness of the column, stiffness of the surrounding structure (restraint level), load level and the load eccentricity. The restraining level to the thermal elongation of the columns showed not being a relevant parameter in their fire resistance probably due the increase in rotational restrain associated with the increase in the axial restraint. The first increases the fire resistance while the second reduces. The increasing of the load level lead to a reduction, while the increasing of the longitudinal reinforcement ratio or the decreasing of the slenderness of the columns lead to an increasing of the fire resistance. The spalling was also an aspect analysed in these tests. The higher load levels, the shape of the cross-section, the type of concrete with or without steel and / or polypropylene fibres, and the steel reinforcement ration was parameters that showed to have influence on concrete cracking and spalling

Exploring nutrient supplementation and bioprocess optimization to improve the production of lentiviral vectors in serum-free medium suspension cultures

Funding Information: T.A.V. acknowledges FCT for the award of the individual grant SFRH/BD/145270/2019. This work was funded by Fundação para a Ciência e Tecnologia/Ministério da Ciência, Tecnologia e Ensino Superior (FCT/MCTES, Portugal) through national funds to iNOVA4Health (UIDB/04462/2020 and UIDP/04462/2020) and the Associate Laboratory LS4FUTURE (LA/P/0087/2020). Publisher Copyright: © 2023 The Authors. Biotechnology Journal published by Wiley-VCH GmbH.The use of lentiviral vectors (LV) in gene therapy has been growing in recent years. To meet the increasing clinical demand, LV production platforms will benefit from improved productivity and scalability to enable cost-effective manufacture of LV-based therapies. Here we report the adaptation of 293T cells to serum-free suspension cultures and the improvement of LV yields through transfection parameters optimization, process intensification and medium supplementation with nutrient boosters. Cells were sequentially adapted to different serum-free culture media, transfection parameters were optimized and the two best-performing conditions were selected to explore process intensification by increasing cell density at the time of transfection. LV production at higher cell densities increased volumetric titers up to 12-fold and lipid supplementation was the most efficient metabolic optimization strategy further enhancing LV productivity by 3-fold. Furthermore, cell concentration was identified and validated as an important source of transfection variability impairing cellular uptake of DNA polyplexes, impacting transfection efficiency and reducing LV titers down to 6-fold. This work contributes to improving LV-based gene therapy by establishing new scalable manufacturing platforms and providing key metabolic insights, unveiling important bioreaction parameters to improve vector yields.publishersversionpublishe

Adaptive Optimization of Chemical Reactions with Minimal Experimental Information

Optimizing reaction conditions depends on expert chemistry knowledge and laborious exploration of reaction parameters. To automate this task and augment chemical intuition, we here report a computational tool to navigate search spaces. Our approach (LabMate.ML) integrates random sampling of 0.03%–0.04% of all search space as input data with an interpretable, adaptive machine-learning algorithm. LabMate.ML can optimize many real-valued and categorical reaction parameters simultaneously, with minimal computational resources and time. In nine prospective proof-of-concept studies pursuing distinctive objectives, we demonstrate how LabMate.ML can identify optimal goal-oriented conditions for several different chemistries and substrates. Double-blind competitions and the conducted expert surveys reveal that its performance is competitive with that of human experts. LabMate.ML does not require specialized hardware, affords quantitative and interpretable reactivity insights, and autonomously formalizes chemical intuition, thereby providing an innovative framework for informed, automated experiment selection toward the democratization of synthetic chemistry.D.R. is a Swiss National Science Foundation Fellow (grant nos. P2EZP3_168827 and P300P2_177833). E.A.H. is supported by the Herchel Smith Fellowship awarded by Williams College. G.J.L.B. is a Royal Society URF (URF\R\180019). T.R. is an Investigador Auxiliar supported by FCT Portugal (CEECIND/00887/2017). T.R. acknowledges the H2020 (TWINN-2017 ACORN, grant no. 807281), FCT/FEDER (02/SAICT/2017, grant no. 28333). D.R. acknowledges the MIT-IBM Watson AI Lab and the MIT SenseTime coalition for funding. The authors are extremely grateful to several colleagues for suggesting Ugi reaction conditions, and to Prof. R. Langer and Prof. G. Traverso, who provided invaluable comments on the research and manuscript. The authors are indebted to Prof. R. Moreira for access to the CEM microwave reactor; Dr. F. Corzana for technical assistance with HRMS; and the 13 graduate students, 17 postdoctoral researchers, and eight principal investigators across Austria, Denmark, Portugal, Spain, the United Kingdom, and the United States who took part in the survey. We thank R. Rodrigues for help in producing Figure 1. The survey was approved by the iMM and MIT (COUHES protocol 1809514426). The authors also thank the four anonymous reviewers for their most insightful comments.info:eu-repo/semantics/publishedVersio

TV WPN : programa de cálculo automático para análise da vulnerabilidade de redes de abastecimento de água

A aplicação da teoria da vulnerabilidade a redes de abastecimento de água reais é um procedimento complexo e moroso, tornando imperativo o desenvolvimento de ferramentas informáticas que agilizem e automatizem esse processo. O programa de cálculo automático que está a ser desenvolvido, designado por TV WPN (Theory of Vulnerability of Water Pipe Networks), constitui um importante estímulo à inclusão do estudo da vulnerabilidade e da avaliação do risco na conceção, dimensionamento e reabilitação de sistemas de abastecimento de água. Até à data, a aplicação desta teoria restringia-se apenas a exemplos de teste correspondentes a redes fictícias de abastecimento de água, com geometria simples e um limitado número de troços. Com esta nova ferramenta, tais limitações podem ser ultrapassadas, pois o tempo de computação torna-se significativamente mais rápido, mesmo considerando redes reais complexas. Deste modo, o aprofundamento e validação dos fundamentos desta teoria podem ganhar um forte e decisivo impulso, permitindo explorar o seu promissor potencial de aplicação às redes hidráulicas em geral, assumindo-se o novo paradigma da gestão do risco em sistemas urbanos de águas

Exploiting non-conventional yeasts for low-alcohol beer production

Non-Saccharomyces yeasts represent a very appealing alternative to producing beers with zero or low ethanol content. The current study explores the potential of seven non-Saccharomyces yeasts to produce low-alcohol or non-alcoholic beer, in addition to engineered/selected Saccharomyces yeasts for low-alcohol production. The yeasts were first screened for their sugar consumption and ethanol production profiles, leading to the selection of strains with absent or inefficient maltose consumption and consequently with low-to-null ethanol production. The selected yeasts were then used in larger-scale fermentations for volatile and sensory evaluation. Overall, the yeasts produced beers with ethanol concentrations below 1.2% in which fusel alcohols and esters were also detected, making them eligible to produce low-alcohol beers. Among the lager beers produced in this study, beers produced using Saccharomyces yeast demonstrated a higher acceptance by taster panelists. This study demonstrates the suitability of non-conventional yeasts for producing low-alcohol or non-alcoholic beers and opens perspectives for the development of non-conventional beers.This research was supported by European Structural and Investment Funds in the ESIF component, through the Operational Competitiveness and Internationalization Program (COM‐ PETE 2020), in the framework of the project YES (project reference POCI‐01‐0247‐FEDER‐070135), and by the Portuguese Foundation for Science and Technology (FCT, Portugal) under the scope of the strategic funding of UIDB/04469/2020.info:eu-repo/semantics/publishedVersio

LentiPro stable producer cells: Delivering scalable and reliable lentiviral vector manufacturing

Lentiviral vectors are one of the most currently used viral vectors for gene and cell therapies. Their use in clinical protocols has significantly increased in the past 5 years with the approval of several gene therapeutic products relying on lentiviral vector gene delivery. Capable of transducing non-dividing cells and presenting safer integration profiles as self-inactivating vectors, lentiviral vectors have progressively undertaken gammaretroviral vector use in gene therapies. However the knowledge on lentiviral vector manufacture is far more immature than that of gammaretroviral vectors. While the production of gammaretrovirus rely on stable producer cell lines and perfusion systems, enabling high cell density and longer term productions, most of the bioprocesses for lentiviral bioproducts rely on transient transfections and short term batch productions. At the upstream process, many of the challenges lentiviral bioproducts present in their manufacturing are related to the apoptosis leading cytotoxicity of some of the vector components. Supported on our long track experience and enabling tools developed for gammaretrovirus manufacturing, we carried out the challenge of establishing a constitutive stable lentiviral producer cell line. To surpass the challenges we proposed to eliminate or reduce the cytotoxicity of the lentiviral vector expression components1. Several strategic novelties were introduced in the development of the cell line namely: (i) the use of a modified gag-pro-pol, (ii) introduction of all the third generation lentiviral expression cassettes by chemical transfection instead of viral transduction and (iii) performing only one clone screening step (enabling the use on the ‘Single step cloning screening’ protocol developed by our group2). After establishing a stable producer cell line the culture conditions were developed with the main aim of extending bioreaction culture time and viral vector total yields. A lentiviral producer cell line constitutively producing infective titers above 106 TU.mL-1.day-1 was established. Moreover the new protocol to generate the cell line enabled its development in less than six months. The cell line showed to be stable, consistently maintaining vector productivity over one month in the absence of antibiotics. At the bioreaction process it was possible to maintain the cells continuously producing over 10 days1. These results validate the transition to continuous or perfusion large-scale production systems qualifying the strengths and advantages of the strategies followed. This work to be presented will discuss the challenges on the manufacture and scale-up of lentiviral vectors as well the strategies and novel technologies to be adopted to enable effective upstream processes. 1Tomás et al. (2018) ‘LentiPro26: novel stable cell lines for constitutive lentiviral vector production\u27 Sci Rep. 8(1):5271 2 Rodrigues et al. (2015) ‘Single step cloning-screening method: a new tool for developing and studying high-titer viral vector producer cells\u27 Gene Ther. 22(9):6

Design optimization of conformal cooling channels for injection molds: 3D transient heat transfer analysis

This research aims to enhance the design of an injection mold in order to minimize ejection time and increase temperature uniformity by repositioning cooling channels. For 3D transient thermal simulations, the ANSYS finite element method (FEM) program was employed, while the MATLAB program was used for optimization. It was discovered that the method could be used successfully to optimize the design of Conformal Cooling Channels (CCCs) in injection molds. The objective function value of the optimized model represents a near 40% improvement in relation to the initial model. The combined parameterization, simulation, and optimization method has proven beneficial for enhancing the arrangement of channels in an injection machine mold. The methodology is generalizable. As such, it can be employed in any industrial applications involving injection molding machines, for the improvement of the quality of the manufactured part.PORTUGAL 2020 Partnership Agreement, through the European Social Fund (ESF) European Regional Development Fund, by the Operational Programme "Competitiveness and Internationalization”, in the scope of “Portugal 2020”.European Regional Development Fund, by the Operational Programme "Competitiveness and Internationalization”, in the scope of “Portugal 2020”