Contribution to the development of methods and systems for the automatization during the early stages of bioprocess development

This thesis is framed within the field of red biotechnology and more specifically in the development of bioprocesses for cell species that feature some therapeutical interest, either for the production of vaccines and monoclonal antibodies or stem cell experimental research. The main objective was the development and application of different instrumental techniques for the control and online monitorization of cell cultures. Oxygen consumption OUR (Oxygen Uptake Rate) was chosen as the central theme since this parameter has often been referenced as the most straighforward indicator of metabolic activity in animal cell culture. This thesis was carried out in the context of a Spin-Off project (Hexascreen Culture Technologies) whose objective was the development of disposable Minibioreactors intended for biopharmaceutical research. Obviously, this has led to a number of important trade-offs, as well as the proposal of several imaginative solutions to solve various technological challenges. For this reason and in order to offer a better idea of the work's scope, it was decided to include in the thesis not only the description of the method and results related to the OUR estimation but a detailed description of the systems developed. Results demonstrate the feasibility of a simplified procedure for estimating the oxygen consumption. This is a review of the Stationary liquid phase mass balance method which allows reducing the implementation cost and unlike the Dynamic method (The most usual thechnique) prevents changes on the oxygen tension that could affect the cell's normal arctivity. The proposed method is based on the accurate control of the oxygen concentration by means of PWM driven electrovalves and using the control loop internal signals to estimate the OUR.Aquesta Tesi doctoral està enquadrada en l'àmbit de la Biotecnologia vermella i més concretament en el desenvolupament de Bioprocessos relacionats amb espècies cel·lulars d’interès terapèutic, bé sigui per a la producció de vacunes, anticossos monoclonals o bé per a la recerca experimental amb cèl·lules mare. L'objectiu general ha estat el desenvolupament i aplicació de diferents tècniques instrumentals per al control i monitorització en línia de cultius cel·lulars, tant mateix d'entre les diferents tècniques emprades es va escollir la monitorització de la demanda d'oxigen O.U.R. (Oxygen Uptake Rate) com a tema central de la tesi degut a que aquest paràmetre ha estat referenciat sovint com un dels millors indicadors de l'activitat metabòlica en cultius de cèl·lules animals. Cal mencionar que la Tesi ha estat duta a terme en el context d'un projecte empresarial (HexaScreen Culture Technologies) l'objectiu del qual ha estat el desenvolupament de Minibioreactors d'un sol ús orientats al mon de la recerca Biofarmacèutica. Òbviament això ha comportant un número important de compromisos a l'hora d'abordar les diferents tasques, així com el plantejament de solucions imaginatives per a la resolució dels diferents reptes tecnològic. Per aquest motiu i per tal de transmetre una millor idea de l'abast del treball realitzat, es va decidir incloure en la tesi no només la descripció del mètode i resultats relacionats amb l'estimació de la O.U.R. sinó amés una descripció prou detallada dels sistemes desenvolupats. Pel que fa al tema central de la tesi, es demostra la viabilitat d'un procediment simplificat per a l'estimació de la demanda d’oxigen. Es tracta d'una revisió del procediment d'estimació de la OUR en condicions de concentració estacionària en la fase líquida que permet reduir-ne el cost de implementació tot prescindint de l'ús de cabalímetres màssics, així com a diferència del mètode dinàmic (Tècnica més habitual) evitar cap mena de canvi en la tensió d’oxigen que pogués afectar l’activitat normal de les cèl·lules. El mètode proposat, es basa en el control de la concentració d’oxigen mitjançant actuació PWM de les vàlvules d'aereació i l’ús dels propis senyals del llaç de control per tal d'estimar la O.U.R.Postprint (published version

Experimental study of optimal measurements for quantum state tomography

Quantum tomography is a critically important tool to evaluate quantum hardware, making it essential to develop optimized measurement strategies that are both accurate and efficient. We compare a variety of strategies using nearly pure test states. Those that are informationally complete for all states are found to be accurate and reliable even in the presence of errors in the measurements themselves, while those designed to be complete only for pure states are far more efficient but highly sensitive to such errors. Our results highlight the unavoidable tradeoffs inherent to quantum tomography.Comment: 5 pages, 3 figure

Introduction: Examined Live – An Epistemological Exchange Between Philosophy and Cultural Psychology on Reflection

Besides the general agreement about the human capability of reflection, there is a large area of disagreement and debate about the nature and value of “reflective scrutiny” and the role of “second-order states” in everyday life. This problem has been discussed in a vast and heterogeneous literature about topics such as epistemic injustice, epistemic norms, agency, understanding, meta-cognition etc. However, there is not yet any extensive and interdisciplinary work, specifically focused on the topic of the epistemic value of reflection. This volume is one of the first attempts aimed at providing an innovative contribution, an exchange between philosophy, epistemology and psychology about the place and value of reflection in everyday life. Our goal in the next sections is not to offer an exhaustive overview of recent work on epistemic reflection, nor to mimic all of the contributions made by the chapters in this volume. We will try to highlight some topics that have motivated a new resumption of this field and, with that, drawing on chapters from this volume where relevant. Two elements defined the scope and content of this volume, on the one hand, the crucial contribution of Ernest Sosa, whose works provide original and thought-provoking contributions to contemporary epistemology in setting a new direction for old dilemmas about the nature and value of knowledge, giving a central place to reflection. On the other hand, the recent developments of cultural psychology, in the version of the “Aalborg approach”, reconsider the object and scope of psychological sciences, stressing that “[h]uman conduct is purposeful”

Web-based visualisation of the transcriptional control network of Escherichia coli

Transcription is one of the basic processes of gene expression, controlled by a complex network of biochemical reactions. Despite its importance, most work on the visualisation of biochemical networks focuses on the representation of metabolic pathways. The visualisation of the complex networks controlling transcription requires the implementation of a hierarchical approach that allows the display of the structure of each regulatory region with its transcription factors and regulated operons. This paper presents a web-based application for the visualisation of transcriptional control networks. It takes as case study the organism Escherichia coli. The definition of the visual components implemented is mainly based on those proposed by Shen-Orr et al., 2002, slightly extended to visualise complex networks. © 2004 - IOS Press and Bioinformation Systems e.V. and the authors. All rights reserved. [accessed 2014 October 15

Quantum state tomography by continuous measurement and compressed sensing

The need to perform quantum state tomography on ever larger systems has spurred a search for methods that yield good estimates from incomplete data. We study the performance of compressed sensing (CS) and least squares (LS) estimators in a fast protocol based on continuous measurement on an ensemble of cesium atomic spins. Both efficiently reconstruct nearly pure states in the 16-dimensional ground manifold, reaching average fidelities FCS = 0.92 and FLS = 0.88 using similar amounts of incomplete data. Surprisingly, the main advantage of CS in our protocol is an increased robustness to experimental imperfections

P.O.S. coverage index: Measurement procedure of the relationship between ball and hand

Este trabajo diseña un novedoso procedimiento de medición que relaciona el tamaño de la mano y el tamaño del balón. Se detalla este procedimiento ideado para la determinación del “Índice de Cobertura de la Mano Porras, Oliver, Sosa” (I.C.M.P.O.S.) sobre el balón. A partir de tres medidas obtenidas de la mano dominante de los deportistas con la mano en máxima apertura tomadas sobre un plano, calcularemos sus coordenadas en el espacio, y las aplicaremos sobre la esfera del balón. Posteriormente, a través de una fórmula, y teniendo en cuenta el valor central de la medida de la circunferencia del balón del deporte y de la categoría deportiva correspondiente, podremos conocer el Índice de Cobertura de la mano del deportista sobre el balón, o cantidad del balón que un deportista es capaz de abarcar con su mano completamente abierta respecto a la media esfera del balón de su categoría deportivaThis paper designs a novel measurement procedure that relates the size of the hand and the size of the ball. This procedure was devised in order to determine the "Hand Coverage Index of Porras, Oliver, Sosa" (H.C.I.P.O.S.) on the ball. Using three measurements obtained from the dominant hand of athletes with the hand on its maximum aperture taken on a flat plane, we calculated their coordinates in space, and their applications on the sphere of the ball. Subsequently, through a formula, and taking into account the central value of the measurement of the circumference of the ball and the corresponding sport category, we will be able to know the Hand Coverage Index of the athlete over the ball, or the surface of the ball that an athlete is able to cover with his fully open hand with respect to the the sphere of the ball of his sport categor

A simplified implementation of the stationary liquid mass balance method for on-line OUR monitoring in animal cell cultures

This is the peer reviewed version of the following article: [Fontova, A. , Lecina, M. , López‐Repullo, J. , Martínez‐Monge, I. , Comas, P. , Bragós, R. and Cairó, J. J. (2018), A simplified implementation of the stationary liquid mass balance method for on‐line OUR monitoring in animal cell cultures. J. Chem. Technol. Biotechnol. doi:10.1002/jctb.5551], which has been published in final form at [doi:10.1002/jctb.5551]. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.BACKGROUND: Compared with other methods, the stationary liquid mass balance method for oxygen uptake rate (OUR) determination offers advantages in terms of estimation accuracy and reduction of stress. However, the need for sophisticated instrumentation, like mass flow controllers and gas analysers, has historically limited wider implementation of such a method. In this paper, a new simplified method based on inexpensive valves for the continuous estimation of OUR in animal cell cultures is evaluated. The determination of OUR values is based on accurate operation of the dissolved oxygen (DO) control loop and monitoring of its internal variables. RESULTS: The method developed was tested empirically in 2¿L bioreactor HEK293 batch cultures. OUR profiles obtained by a dynamic method, global mass balance method and the developed simplified method were monitored and compared. The results show how OUR profile obtained with the proposed method better follows the off-line cell density determination. The OUR estimation frequency was also increased, improving the method capabilities and applications. The theoretical rationale of the method was extended to the sensitivity analysis which was analytically and numerically approached. CONCLUSIONS: The results showed the proposed method to be not only cheap, but also a reliable alternative to monitor the metabolic activity in bioreactors in many biotechnological processes, being a useful tool for high cell density culture strategies implementation based on OUR monitoring.Peer ReviewedPostprint (published version