1
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Destro F, Wu W, Srinivasan P, Joseph J, Bal V, Neufeld C, Wolfrum JM, Manalis SR, Sinskey AJ, Springs SL, Barone PW, Braatz RD. The state of technological advancement to address challenges in the manufacture of rAAV gene therapies. Biotechnol Adv 2024; 76:108433. [PMID: 39168354 DOI: 10.1016/j.biotechadv.2024.108433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/04/2024] [Accepted: 08/17/2024] [Indexed: 08/23/2024]
Abstract
Current processes for the production of recombinant adeno-associated virus (rAAV) are inadequate to meet the surging demand for rAAV-based gene therapies. This article reviews recent advances that hold the potential to address current limitations in rAAV manufacturing. A multidisciplinary perspective on technological progress in rAAV production is presented, underscoring the necessity to move beyond incremental refinements and adopt a holistic strategy to address existing challenges. Since several recent reviews have thoroughly covered advancements in upstream technology, this article provides only a concise overview of these developments before moving to pivotal areas of rAAV manufacturing not well covered in other reviews, including analytical technologies for rapid and high-throughput measurement of rAAV quality attributes, mathematical modeling for platform and process optimization, and downstream approaches to maximize efficiency and rAAV yield. Novel technologies that have the potential to address the current gaps in rAAV manufacturing are highlighted. Implementation challenges and future research directions are critically discussed.
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Affiliation(s)
- Francesco Destro
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Weida Wu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Prasanna Srinivasan
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John Joseph
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vivekananda Bal
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caleb Neufeld
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacqueline M Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anthony J Sinskey
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Paul W Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Richard D Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Geremia M, Bezzo F, Ierapetritou MG. Design space determination of pharmaceutical processes: Effects of control strategies and uncertainty. Eur J Pharm Biopharm 2024; 194:159-169. [PMID: 38110160 DOI: 10.1016/j.ejpb.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
The identification of process Design Space (DS) is of high interest in highly regulated industrial sectors, such as pharmaceutical industry, where assurance of manufacturability and product quality is key for process development and decision-making. If the process can be controlled by a set of manipulated variables, the DS can be expanded in comparison to an open-loop scenario, where there are no controls in place. Determining the benefits of control strategies may be challenging, particularly when the available model is complex and computationally expensive - which is typically the case of pharmaceutical manufacturing. In this study, we exploit surrogate-based feasibility analysis to determine whether the process satisfies all process constraints by manipulating the process inputs and reduce the effect of uncertainty. The proposed approach is successfully tested on two simulated pharmaceutical case studies of increasing complexity, i.e., considering (i) a single pharmaceutical unit operation, and (ii) a pharmaceutical manufacturing line comprised of a sequence of connected unit operations. Results demonstrate that different control actions can be effectively exploited to operate the process in a wider range of inputs and mitigate uncertainty.
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Affiliation(s)
- Margherita Geremia
- CAPE-Lab - Computer-Aided Process Engineering Laboratory, Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, PD, Italy
| | - Fabrizio Bezzo
- CAPE-Lab - Computer-Aided Process Engineering Laboratory, Department of Industrial Engineering, University of Padova, Via Marzolo 9, 35131 Padova, PD, Italy
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3
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Zhao H, Deng HD, Cohen AE, Lim J, Li Y, Fraggedakis D, Jiang B, Storey BD, Chueh WC, Braatz RD, Bazant MZ. Learning heterogeneous reaction kinetics from X-ray videos pixel by pixel. Nature 2023; 621:289-294. [PMID: 37704764 PMCID: PMC10499602 DOI: 10.1038/s41586-023-06393-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/30/2023] [Indexed: 09/15/2023]
Abstract
Reaction rates at spatially heterogeneous, unstable interfaces are notoriously difficult to quantify, yet are essential in engineering many chemical systems, such as batteries1 and electrocatalysts2. Experimental characterizations of such materials by operando microscopy produce rich image datasets3-6, but data-driven methods to learn physics from these images are still lacking because of the complex coupling of reaction kinetics, surface chemistry and phase separation7. Here we show that heterogeneous reaction kinetics can be learned from in situ scanning transmission X-ray microscopy (STXM) images of carbon-coated lithium iron phosphate (LFP) nanoparticles. Combining a large dataset of STXM images with a thermodynamically consistent electrochemical phase-field model, partial differential equation (PDE)-constrained optimization and uncertainty quantification, we extract the free-energy landscape and reaction kinetics and verify their consistency with theoretical models. We also simultaneously learn the spatial heterogeneity of the reaction rate, which closely matches the carbon-coating thickness profiles obtained through Auger electron microscopy (AEM). Across 180,000 image pixels, the mean discrepancy with the learned model is remarkably small (<7%) and comparable with experimental noise. Our results open the possibility of learning nonequilibrium material properties beyond the reach of traditional experimental methods and offer a new non-destructive technique for characterizing and optimizing heterogeneous reactive surfaces.
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Affiliation(s)
- Hongbo Zhao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haitao Dean Deng
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Alexander E Cohen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jongwoo Lim
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Yiyang Li
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Dimitrios Fraggedakis
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benben Jiang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - William C Chueh
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Richard D Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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4
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Srinivas SV, Karimi IA. Zone-wise Surrogate Modelling (ZSM) of Univariate Systems. Comput Chem Eng 2023. [DOI: 10.1016/j.compchemeng.2023.108249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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5
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Negri V, Vázquez D, Sales-Pardo M, Guimerà R, Guillén-Gosálbez G. Bayesian Symbolic Learning to Build Analytical Correlations from Rigorous Process Simulations: Application to CO 2 Capture Technologies. ACS OMEGA 2022; 7:41147-41164. [PMID: 36406548 PMCID: PMC9670717 DOI: 10.1021/acsomega.2c04736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Process modeling has become a fundamental tool to guide experimental work. Unfortunately, process models based on first principles can be expensive to develop and evaluate, and hard to use, particularly when convergence issues arise. This work proves that Bayesian symbolic learning can be applied to derive simple closed-form expressions from rigorous process simulations, streamlining the process modeling task and making process models more accessible to experimental groups. Compared to conventional surrogate models, our approach provides analytical expressions that are easier to communicate and manipulate algebraically to get insights into the process. We apply this method to synthetic data obtained from two basic CO2 capture processes simulated in Aspen HYSYS, identifying accurate simplified interpretable equations for key variables dictating the process economic and environmental performance. We then use these expressions to analyze the process variables' elasticities and benchmark an emerging CO2 capture process against the business as usual technology.
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Affiliation(s)
- Valentina Negri
- Institute
for Chemical and Bioengineering, Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093Zürich, Switzerland
| | - Daniel Vázquez
- Institute
for Chemical and Bioengineering, Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093Zürich, Switzerland
| | - Marta Sales-Pardo
- Department
of Chemical Engineering, Universitat Rovira
i Virgili, Tarragona43007, Catalonia, Spain
| | - Roger Guimerà
- Department
of Chemical Engineering, Universitat Rovira
i Virgili, Tarragona43007, Catalonia, Spain
- ICREA, Barcelona08010, Catalonia, Spain
| | - Gonzalo Guillén-Gosálbez
- Institute
for Chemical and Bioengineering, Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093Zürich, Switzerland
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6
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Latent variable method demonstrator – software for understanding multivariate data analytics algorithms. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.108014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Ahmad M, Karimi IA. Families of similar surrogate forms based on predictive accuracy and model complexity. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.107845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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8
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Affiliation(s)
- Leo H. Chiang
- Core R&D The Dow Chemical Company Lake Jackson Texas 77566 USA
| | - Birgit Braun
- Core R&D The Dow Chemical Company Lake Jackson Texas 77566 USA
| | - Zhenyu Wang
- Chemometrics, AI & Statistics The Dow Chemical Company Lake Jackson Texas 77566 USA
| | - Ivan Castillo
- Chemometrics, AI & Statistics The Dow Chemical Company Lake Jackson Texas 77566 USA
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9
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Lejarza F, Baldea M. Discovering governing equations via moving horizon learning: the case of reacting systems. AIChE J 2022. [DOI: 10.1002/aic.17567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Fernando Lejarza
- McKetta Department of Chemical Engineering The University of Texas at Austin Austin Texas USA
| | - Michael Baldea
- McKetta Department of Chemical Engineering The University of Texas at Austin Austin Texas USA
- Oden Institute for Computational Engineering and Sciences The University of Texas at Austin Austin Texas USA
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10
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Data-Driven Process System Engineering: contributions to its consolidation following the path laid down by George Stephanopoulos. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.107675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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12
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13
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Mojto M, Ľubušký K, Fikar M, Paulen R. Data-based design of inferential sensors for petrochemical industry. Comput Chem Eng 2021. [DOI: 10.1016/j.compchemeng.2021.107437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Kuo TC, Peng CY, Kuo CJ. Smart support system of material procurement for waste reduction based on big data and predictive analytics. INTERNATIONAL JOURNAL OF LOGISTICS-RESEARCH AND APPLICATIONS 2021. [DOI: 10.1080/13675567.2021.1969348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Tsai-Chi Kuo
- Department of Industrial Management, National Taiwan University of Science and Technology, Taipei, Taiwan
- Artificial Intelligence for Operations Management Research Center, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Chien-Yun Peng
- Department of Industrial and Systems Engineering, Chung Yuan Christian University, Taoyuan, Taiwan
| | - Chien-Jou Kuo
- Department of Industrial and Systems Engineering, Chung Yuan Christian University, Taoyuan, Taiwan
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15
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de Souza DC, Cabrita L, Galinha CF, Rato TJ, Reis MS. A Spectral AutoML approach for industrial soft sensor development: Validation in an oil refinery plant. Comput Chem Eng 2021. [DOI: 10.1016/j.compchemeng.2021.107324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Soft-Sensor for Class Prediction of the Percentage of Pentanes in Butane at a Debutanizer Column. SENSORS 2021; 21:s21123991. [PMID: 34207807 PMCID: PMC8228335 DOI: 10.3390/s21123991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 11/17/2022]
Abstract
Refineries are complex industrial systems that transform crude oil into more valuable subproducts. Due to the advances in sensors, easily measurable variables are continuously monitored and several data-driven soft-sensors are proposed to control the distillation process and the quality of the resultant subproducts. However, data preprocessing and soft-sensor modelling are still complex and time-consuming tasks that are expected to be automatised in the context of Industry 4.0. Although recently several automated learning (autoML) approaches have been proposed, these rely on model configuration and hyper-parameters optimisation. This paper advances the state-of-the-art by proposing an autoML approach that selects, among different normalisation and feature weighting preprocessing techniques and various well-known Machine Learning (ML) algorithms, the best configuration to create a reliable soft-sensor for the problem at hand. As proven in this research, each normalisation method transforms a given dataset differently, which ultimately affects the ML algorithm performance. The presented autoML approach considers the features preprocessing importance, including it, and the algorithm selection and configuration, as a fundamental stage of the methodology. The proposed autoML approach is applied to real data from a refinery in the Basque Country to create a soft-sensor in order to complement the operators' decision-making that, based on the operational variables of a distillation process, detects 400 min in advance with 98.925% precision if the resultant product does not reach the quality standards.
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