Depósito Académico
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Results
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.(2019) Heirendt, L. (Laurent); Arreckx, S. (Sylvain); Pfau, Thomas; Mendoza, S.N. (Sebastián N.); Richelle, A. (Anne); Heinken, Almut; Haraldsdóttir, H.S. (Hulda S.); Wachowiak, J. (Jacek); Keating, S.M. (Sarah M.); Vlasov, V. (Vanja); Magnusdóttir, S. (Stefania); Ng, C. Y. (Chiam Yu); Preciat, G. (German); Zagare, A. (Alise); Chan, S.H.J. (Siu H.J.); Aurich, M.K. (Maike K.); Clancy, C.M. (Catherine M.); Modamio, J. (Jennifer); Sauls, J.T. (John T.); Noronha, A. (Alberto); Bordbar, A. (Aarash); Cousins, B. (Benjamin); El Assal, D.C. (Diana C.); Valcárcel-García, L.V. (Luis Vitores); Apaolaza-Emparanza, I.(Iñigo); Ghaderi, S. (Susan); Ahookhosh, M. (Masoud); Ben Guebila, M. (Marouen); Kostromins, A. (Andrejs); Sompairac, N. (Nicolas); Le, H.M. (Hoai M.); Ma, D. (Ding); Sun, Y. (Yuekai); Wang, L. (Lin); Yurkovich, J.T. (James T.); Oliveira, M.A.P. (Miguel A.P.); Vuong, P.T. (Phan T.); El Assal, L.P. (Lemmer P.); Kuperstein, I. (Inna); Zinovyev, A. (Andrei); Hinton, H.S. (H.Scott); Bryant, W.A. (William A.); Aragón-Artacho, F.J. (Francisco J.); Planes-Pedreño, F.J. (Francisco Javier); Stalidzans, E. (Egils); Maass, A. (Alejandro); Vempala, S. (Santosh); Hucka, M. (Michael); Saunders, M.A. (Michael A.); Maranas, C.D. (Costas D.); Lewis, N.E. (Nathan E.); Sauter, T. (Thomas); Palsson, B. O. (Bernhard O.); Thiele, I. (Inés); Fleming, R.M.T. (Ronan M.T.)Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods.
- Inhibition of a G9a/DNMT network triggers immune-mediated bladder cancer regression(2019) Segovia, C. (Cristina); San-Jose-Eneriz, E. (Edurne); Munera-Maravilla, E. (Ester); Martínez-Fernández, M. (Mónica); Garate, L. (Leire); Miranda, E. (Estibaliz); Vilas-Zornoza, A. (Amaia); Lodewijk, I. (Iris); Rubio, C. (Carolina); Segrelles, C. (Carmen); Valcárcel-García, L.V. (Luis Vitores); Rabal, O. (Obdulia); Casares, N. (Noelia); Bernardini, A. (Alejandra); Suárez-Cabrera, C. (Cristian); Lopez-Calderón, F. (Fernando); Fortes, P. (Puri)Bladder cancer is lethal in its advanced, muscle-invasive phase with very limited therapeutic advances(1,2). Recent molecular characterization has defined new (epi) genetic drivers and potential targets for bladder cancer(3,4). The immune checkpoint inhibitors have shown remarkable efficacy but only in a limited fraction of bladder cancer patients(5-8). Here, we show that high G9a (EHMT2) expression is associated with poor clinical outcome in bladder cancer and that targeting G9a/DNMT methyltransferase activity with a novel inhibitor (CM-272) induces apoptosis and immunogenic cell death. Using an immunocompetent quadruple-knockout (Pten(loxP/loxP); Trp53(loxP/loxP); Rb1(loxP/loxP); Rbl1(-/-)) transgenic mouse model of aggressive metastatic, muscle-invasive bladder cancer, we demonstrate that CM-272 + cisplatin treatment results in statistically significant regression of established tumors and metastases. The antitumor effect is significantly improved when CM-272 is combined with anti-programmed cell death ligand 1, even in the absence of cisplatin. These effects are associated with an endogenous antitumor immune response and immunogenic cell death with the conversion of a cold immune tumor into a hot tumor. Finally, increased G9a expression was associated with resistance to programmed cell death protein 1 inhibition in a cohort of patients with bladder cancer. In summary, these findings support new and promising opportunities for the treatment of bladder cancer using a combination of epigenetic inhibitors and immune checkpoint blockade.
- rMTA: robust metabolic transformation analysis.(2019) Valcárcel-García, L.V. (Luis Vitores); Torrano, V. (Verónica); Tobalina-Segura, L. (Luis); Carracedo, A. (Arkaitz); Planes-Pedreño, F.J. (Francisco Javier)
- Is design of experiments really used? A survey of Basque industries.(2008) Tanco-Rainusso, M. (Martín); Viles-Díez, E. (Elisabeth); Ilzarbe, L. (Laura); Álvarez-Sánchez-Arjona, M.J. (María Jesús)A new survey is presented concerning the knowledge and use of the design of experiments technique (DoE) within industry in the Basque Country, a region recognised throughout Europe for its quality management. The survey was carried out within manufacturing companies, yielding a response rate of 18%. Results show that 94% of companies undertake experimentation; most of them use one-factor-at-a-time strategies, and only 20% of those follow a pre-established statistical methodology. Survey results show that research and development and manufacturing make up 85% of DoE use. Furthermore, results show that lack of knowledge about general statistics is commonplace and only 31% of companies claim to be knowledgeable about DoE. In addition, although Taguchi methods are well known among companies, only 7% apply this method. Despite every effort by specialists in quality and statistics, DoE has yet to be applied as widely as it could and should be.
- Practical applications of design of experiments in the field of engineering: A bibliographical review.(2008) Ilzarbe, L. (Laura); Álvarez-Sánchez-Arjona, M.J. (María Jesús); Viles-Díez, E. (Elisabeth); Tanco-Rainusso, M. (Martín)The design of experiments (DoE) methodology is a technique that has been applied for many years in industry to improve quality. In this study, a summary of 77 cases of practical DoE application in the field of engineering is presented. All of the cases were published in important scientific journals between 2001 and 2005. The type of design that is applied, the size of the experiment, the number of factors that influence the response variable, and the sector of application of the design are analyzed. In addition, the increasing use of these designs over time is demonstrated.
- How is Experimentation Carried Out by Companies? A Survey of Three European Regions.(2008) Tanco-Rainusso, M. (Martín); Viles-Díez, E. (Elisabeth); Ilzarbe, L. (Laura); Álvarez-Sánchez-Arjona, M.J. (María Jesús)A survey was carried out to characterize experimentation in three different European regions: the Baden-Wurttemberg region, The Basque Country and the rest of Spain. Results of the survey show that even though experimentation is a frequent activity, almost 95% of companies conduct experiments; the strategies used to carry them out are primitive. The one-factor-at-a-time strategy is used by 75% of companies far more than the 23%, which apply design of experiments (DoE). Results show that this may be due to the current lack of knowledge of DoE in these regions, where only 33% are familiar with the technique. Finally, the rate of applications of DoE among Six Sigma users is 40%, twice that of non-users, which stands at 19%.
- Applying Design of Experiments to a Lift Test Rig(2010) Viles-Díez, E. (Elisabeth); Tanco-Rainusso, M. (Martín); Isasa, I. (Inge); Arteche, U. (Unai); Sagartzazu, X. (Xabier)As comfort has become an important factor in the lift industry, validated lift models are currently a significant research area. In this article, we present an analysis of a lift guiding system, which transmits vibrations to the cabin and affects passengers' comfort. The project consisted of determining the most important lift guiding system factors that affect a lift's comfort. The Design of Experiments technique was chosen as the best technique available to maximize the information gathered from the experiments. in order to carry out the experiments, a lift test rig was specially constructed in order to simulate a real installation. We screened and analyzed the influence of many factors on the response with an adapted factorial fractional design. This article shows the steps carried out in planning and analyzing the experiments, putting special emphasis on the planning during every phase of the DoE application. This research project was co-developed by a research center, a university and a well-known Spanish lift company.
- Improving intranet knowledge transfer through resident engineers.(2011) Mateo, R. (Ricardo); Tanco-Rainusso, M. (Martín); Santos-García, J. (Javier)Purpose - This research paper aims to explore how intranet mechanisms for knowledge transfer in a multinational automotive company can he improved with the inclusion Of a human interface. specifically a resident engineer. A resident engineer is an assembly line employee who spends the majority of their lime in the Advanced Engineering Center, which aims to improve knowledge transfer through face-to-face interaction. Design/methodology/approach - A multinational automotive company was selected for the study Six years of data containing all product modifications were analyzed. Findings The paper concludes that electronic knowledge transfer can be significantly improved when resident engineers physically interact with the Advanced Engineering Center Intranet knowledge transfer alone cannot overcome the considerable handicap involved in knowledge assimilation. Practical implications - For companies with Advanced Engineering Centers located far from assembly-line plants. the creation of specific human mechanisms to explain the knowledge generated and to reduce approval time is indispensable. Originality/value - This research paper features a complete case study from a multinational automotive company with more than EGO analyzed modifications.
- A factorial design study to determine the significant parameters of fresh concrete lateral pressure and initial rate of pressure decay.(2011) Santilli-Almaraz, A. (Adrián); Puente-Urruzmendi, I.(Iñigo); Tanco-Rainusso, M. (Martín)
- Simulation-Based Process Design and Integration for the Sustainable Retrofit of Chemical Processes.(2011) Hernández-Enríquez, A. (Aurora); Tanco-Rainusso, M. (Martín); Kim, J.K. (Jin Kuk)This research proposes a novel Retrofit Design Approach based on process simulation and the Response Surface Methodology (RSM). The approach comprises a diagnosis stage to select the, promising variables through a sensitivity analysis, an evaluation stage to assess the impact of the promising variables, and to identify the most important factors through RSM. A reduced model from the process response behavior is built, and an optimization is carried out with the reduced model to identify optimal conditions and performance of the system, subject to objective function and model constraints. All these procedures are simulation-supported. The main advantage of the proposed approach is to handle a large industrial-scale design problem within a reasonable computational effort and to obtain a reduced model based on the most important factors Limitations for the developed method include that the global optimality of the solutions found is not fully guaranteed, while large computational time for simulation may be required when the large number of factors and levels need to be considered, although this is Offset by the reduced optimization time. The proposed Retrofit Design Approach has been applied to the NGL (natural gas liquids) recovery process, in which steady-state process simulation using Aspen Plus TM has been carried out, and complex design interactions existed for retrofit scenarios have been systematically evaluated, leading to optimal strategies for retrofitting through the proposed design method. Both the continuous and discrete design options are considered in the retrofit design, and the results showed that the approach is effective to provide reliable, cost-effective solutions which yield to economic and environmental improvements in the studied processes. The promising sets of retrofit design options were presented as a portfolio of investment opportunities for supporting further decision-making procedures.