Article
Biochemical Research Methods
Kazuhiro Maeda, Aoi Hatae, Yukie Sakai, Fred C. Boogerd, Hiroyuki Kurata
Summary: The Machine Learning-Aided Global Optimization (MLAGO) approach is proposed to solve the problems in parameter estimation for kinetic modeling. By combining machine learning-based K-m prediction and global optimization-based parameter estimation, MLAGO successfully estimates K-m values with reduced computational cost and achieves better understanding of complex cellular systems.
BMC BIOINFORMATICS
(2022)
Article
Engineering, Environmental
Thomas Krumpolc, D. W. Trahan, D. A. Hickman, L. T. Biegler
Summary: Applications of fixed-effects models for kinetic parameter estimation assume independence among batches, but biased residuals often exist in multiple longitudinal batch experiments with time series data. Nonlinear mixed-effects models provide an alternative approach to address the two types of random experimental variation resulting from longitudinal experiments: measurement error for each data point and random batch-to-batch variation. In our case study, implementing a mixed-effects model using nonlinear programming for a batch reactor system yields parameter estimates with less bias compared to a fixed-effects model. Additionally, the Bayesian notion of probability shares is applied to discriminate between several candidate mixed-effects models, demonstrating the ability to elucidate additional model information when fixed-effects models are inappropriate.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Hayley Boigenzahn, Leonardo D. Gonzalez, Jaron C. Thompson, Victor M. Zavala, John Yin
Summary: This study investigates the reactions between amino acids to form peptides using a computational network model. However, parameter estimation for peptide bond formation and hydrolysis reactions is challenging due to the network property called sloppiness. Nevertheless, reasonably accurate predictions of model behavior can still be made.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Verena Nold, Lisa Junghans, Lorenzo Bisgen, Raphael Drerup, Beate Presser, Ingo Gorr, Thomas Schwab, Bettina Knapp, Stefan Wieschalka
Summary: The analysis of data collected using design of experiments (DoE) is the gold standard for determining the influence of input parameters and their interactions on process performance and product quality. The intensified DoE (iDoE) approach has been successfully applied in mammalian cell culture, showing it to be a cost-efficient and promising tool for accelerating biopharmaceutical process development.
ENGINEERING IN LIFE SCIENCES
(2022)
Article
Computer Science, Interdisciplinary Applications
L. Dewasme, M. Makinen, V. Chotteau
Summary: This paper proposes a data-driven strategy for fast design of dynamic bioprocess models with minimal complexity, which can significantly improve bioprocess performances. The strategy involves the use of MLPCA to infer the minimal reaction scheme and a robust model predictive formulation to reduce the impact of model uncertainty.
COMPUTERS & CHEMICAL ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Julian Schmitz, Birgit Stute, Sarah Taeuber, Dietrich Kohlheyer, Eric von Lieres, Alexander Gruenberger
Summary: This paper presents an easy-to-implement cell retention concept to prevent cells from leaving microfluidic cultivation chambers, enabling reliable single-cell growth studies.
SCIENTIFIC REPORTS
(2023)
Article
Engineering, Chemical
Eduardo Sanchez-Ramirez, Brenda Huerta-Rosas, Juan Jose Quiroz-Ramirez, Victor Alejandro Suarez-Toriello, Gabriel Contreras-Zarazua, Juan Gabriel Segovia-Hernandez
Summary: This paper presents a generic optimization framework for solving parameter estimation and catalyst design problems. Kinetic data values were predicted using a stochastic optimization method in conjunction with Aspen Plus and experimental data. The validation results demonstrate the accuracy and good approximation of obtaining kinetic parameters, even in complex cases.
CHEMICAL ENGINEERING RESEARCH & DESIGN
(2022)
Review
Cell Biology
Shannon G. Klein, Alexandra Steckbauer, Samhan M. Alsolami, Silvia Arossa, Anieka J. Parry, Mo Li, Carlos M. Duarte
Summary: This article discusses the importance of characterizing, controlling, and reporting environmental conditions in mammalian cell cultures for biomedical research. The underreporting of critical parameters affecting cell culture environments is identified as a serious problem, and guidelines and recommendations for improvement are provided.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Giovanni Marco Nocera, Gaetano Viscido, Stefania Criscuolo, Simona Brillante, Fabrizia Carbone, Leopoldo Staiano, Sabrina Carrellal, Diego di Bernardo
Summary: Microfluidic-based cell culture allows for precise control of micro-environment, with broad potential applications. However, existing microfluidic systems are often designed for specific applications and require specialized equipment and expertise. In this study, we developed a versatile and user-friendly cell culture microfluidic platform called VersaLive, which can replace traditional cell culture formats, reducing costs and improving reproducibility across laboratories.
COMMUNICATIONS BIOLOGY
(2022)
Article
Engineering, Electrical & Electronic
Mohamed Ershadh, M. Meenakshi
Summary: The article proposes a new methodology for modeling the parameters of the multipath structure in an indoor UWB propagation channel, aiming to simplify the estimation process and compare the performance of different UWB propagation models in realistic environments.
IEEE TRANSACTIONS ON ANTENNAS AND PROPAGATION
(2021)
Review
Biochemical Research Methods
Karen A. Esmonde-White, Maryann Cuellar, Ian R. Lewis
Summary: Biopharmaceuticals have revolutionized medicine through active ingredient molecules and improved indications. Utilizing Quality by Design and Process Analytical Technology frameworks has led to consistent product quality and real-time control in bioprocessing, with Raman spectroscopy playing a key role in monitoring and controlling upstream processes.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Thermodynamics
Shang-Hao Liu, Yan-Ru Wang, Chung Hwei Su, Chen-Rui Cao
Summary: Organic peroxides have a long history in the industry, particularly in the polymer sector, but their self-reactive and hazardous properties continue to pose safety challenges. Despite extensive research and new safety technologies, thermal hazards from emerging organic peroxides remain a concern, highlighting the need for attention and solutions in the safety area. Evaluating the thermal hazard mode of a substance is crucial for establishing safety parameters in the actual operation process.
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY
(2021)
Article
Engineering, Biomedical
Yi Zhang, Si-yang Li, Hang-ju Zhu, Jun-Wei Lai, Shuo-shuo Sune, Yue Line, Xing-ling Li, Zhao-bin Guo, Ziheng Lv, Hongxu Meng, Ke Hu, Ming Xu, Ting-ting Yu
Summary: A novel technique that promotes protein production in mammalian cells by forming multicellular spheroids has been proposed. This finding provides a new approach for improving large-scale mammalian protein expression cell systems.
MATERIALS TODAY BIO
(2023)
Article
Biochemistry & Molecular Biology
Martin H. Dominguez, Alexis Leigh Krup, Jonathon M. Muncie, Benoit G. Bruneau
Summary: Using improved and accessible computational tools, we reconstructed early murine cardiac development at single-cell resolution through four-dimensional whole-embryo light sheet imaging. The formation of opposing density and motility gradients by nascent mesoderm progenitors converts the temporal birth sequence of gastrulation into a spatial anterolateral-to-posteromedial arrangement. The cardiac crescent emerges to solidify spatial patterns, and progenitors undergo a mesenchymal-to-epithelial transition.
Article
Engineering, Electrical & Electronic
Bin Wang, Ramon Costa-Castello, Jing Na, Oscar de la Torre, Xavier Escaler
Summary: This paper proposes a new adaptive estimation approach for online parameter estimation of a piezoelectric cantilever beam. By introducing the Galerkin method and separating the time and space variables of the PDE, the unknown parameters of the derived ODE model can be estimated in real time.
IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS I-REGULAR PAPERS
(2023)
Article
Engineering, Chemical
S. C. Galbraith, S. Park, Z. Huang, H. Liu, R. F. Meyer, M. Metzger, M. H. Flamm, S. Hurley, S. Yoon
CHEMICAL ENGINEERING RESEARCH & DESIGN
(2020)
Article
Biotechnology & Applied Microbiology
Jong Kwang Hong, Hock Chuan Yeo, Meiyappan Lakshmanan, Sung-Hyuk Han, Hyun Myoung Cha, Muri Han, Dong-Yup Lee
JOURNAL OF BIOTECHNOLOGY
(2020)
Review
Engineering, Environmental
Dingnan Lu, Sha Sha, Jiayue Luo, Zhuangrong Huang, Xiaoqi Zhang Jackie
JOURNAL OF HAZARDOUS MATERIALS
(2020)
Article
Plant Sciences
Lokanand Koduru, Hyang Yeon Kim, Meiyappan Lakshmanan, Bijayalaxmi Mohanty, Yi Qing Lee, Choong Hwan Lee, Dong-Yup Lee
MOLECULAR PLANT PATHOLOGY
(2020)
Letter
Biotechnology & Applied Microbiology
Christian Lieven, Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Meric Ataman, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Draeger, Birgitta E. Ebert, Janaka N. Edirisinghe, Jose P. Faria, Adam M. Feist, Georgios Fengos, Ronan M. T. Fleming, Beatriz Garcia-Jimenez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S. Henry, Henning Hermjakob, Markus J. Herrgard, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J. Koehorst, Matthias Koenig, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E. Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L. Medlock, Jonathan M. Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O. Palsson, Jason A. Papin, Kiran R. Patil, Mark Poolman, Nathan D. Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamin J. Sanchez, Peter J. Schaap, Rahuman S. Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaca, Jon Olav Vik, Judith A. H. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang
NATURE BIOTECHNOLOGY
(2020)
Review
Microbiology
Chaminda Jayampath Seneviratne, Preethi Balan, Tanujaa Suriyanarayanan, Meiyappan Lakshmanan, Dong-Yup Lee, Mina Rho, Nicholas Jakubovics, Bernd Brandt, Wim Crielaard, Egija Zaura
CRITICAL REVIEWS IN MICROBIOLOGY
(2020)
Correction
Biotechnology & Applied Microbiology
Christian Lieven, Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Meric Ataman, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Draeger, Birgitta E. Ebert, Janaka N. Edirisinghe, Jose P. Faria, Adam M. Feist, Georgios Fengos, Ronan M. T. Fleming, Beatriz Garcia-Jimenez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S. Henry, Henning Hermjakob, Markus J. Herrgard, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J. Koehorst, Matthias Koenig, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E. Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L. Medlock, Jonathan M. Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O. Palsson, Jason A. Papin, Kiran R. Patil, Mark Poolman, Nathan D. Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamin J. Sanchez, Peter J. Schaap, Rahuman S. Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaca, Jon Olav Vik, Judith A. H. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang
NATURE BIOTECHNOLOGY
(2020)
Article
Engineering, Chemical
Zhuangrong Huang, Seongkyu Yoon
Article
Biotechnology & Applied Microbiology
Zhuangrong Huang, Jianlin Xu, Andrew Yongky, Caitlin S. Morris, Ashli L. Polanco, Michael Reily, Michael C. Borys, Zheng Jian Li, Seongkyu Yoon
BIOCHEMICAL ENGINEERING JOURNAL
(2020)
Article
Biotechnology & Applied Microbiology
Zhuangrong Huang, Seongkyu Yoon
BIOCHEMICAL ENGINEERING JOURNAL
(2020)
Article
Biotechnology & Applied Microbiology
Hock Chuan Yeo, Jongkwang Hong, Meiyappan Lakshmanan, Dong-Yup Lee
METABOLIC ENGINEERING
(2020)
Article
Engineering, Chemical
Zhuangrong Huang, Jianlin Xu, Jun Tian, Kathryn L. Aron, Yueming Qian, Michael C. Borys, Zhengjian Li, Girish Pendse
Summary: This study investigated the effects of the antioxidant rosmarinic acid (RA) on CHO cell cultures using transcriptomics analysis. The results showed that RA treatment modified gene expression and strongly affected the signaling pathways involved in cell survival and cell death. Furthermore, these signaling pathways continued to be up-regulated over time, indicating their importance in the cell culture process.
Article
Cell Biology
Lokanand Koduru, Meiyappan Lakshmanan, Yi Qing Lee, Pooi-Leng Ho, Pei-Yu Lim, Wei Xuan Ler, Say Kong Ng, Dongseok Kim, Doo-Sang Park, Mazlina Banu, Dave Siak Wei Ow, Dong-Yup Lee
Summary: This study investigates the differences in growth, intestinal persistence, and postbiotic biosynthesis of six representative lactic acid bacteria (LAB) and their interactions with gut bacteria under different dietary regimes. The findings suggest that the attributes of probiotics are specific to both diet and species, and cannot be solely explained by genomics. Additionally, high-fat/low-carb diets may have detrimental effects on most LAB. The results highlight the importance of personalized probiotic design.
Article
Biochemistry & Molecular Biology
Yoon-Mi Choi, Dong-Hyuk Choi, Yi Qing Lee, Lokanand Koduru, Nathan E. Lewis, Meiyappan Lakshmanan, Dong-Yup Lee
Summary: The biomass equation in genome-scale metabolic models is used as the de facto objective function in flux balance analysis. However, the macromolecular composition of cells can change across different environmental conditions, raising concerns about the use of the same biomass equation in multiple conditions. Through qualitative and quantitative investigations, it was found that while macromolecular building blocks vary notably, the fundamental biomass monomer units are not appreciably different. Based on these findings, ensemble representations of the biomass equation were proposed to account for the natural variation of cellular constituents, leading to more accurate flux predictions.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Caitlin Morris, Ashli Polanco, Andrew Yongky, Jianlin Xu, Zhuangrong Huang, Jia Zhao, Kevin S. McFarland, Seoyoung Park, Bethanne Warrack, Michael Reily, Michael C. Borys, Zhengjian Li, Seongkyu Yoon
BIORESOURCES AND BIOPROCESSING
(2020)