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Nath SC, Menendez L, Friedrich Ben-Nun I. Overcoming the Variability of iPSCs in the Manufacturing of Cell-Based Therapies. Int J Mol Sci 2023; 24:16929. [PMID: 38069252 PMCID: PMC10706975 DOI: 10.3390/ijms242316929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Various factors are known to contribute to the diversity of human induced pluripotent stem cells (hiPSCs). Among these are the donor's genetic background and family history, the somatic cell source, the iPSC reprogramming method, and the culture system of choice. Moreover, variability is seen even in iPSC clones, generated in a single reprogramming event, where the donor, somatic cell type, and reprogramming platform are the same. The diversity seen in iPSC lines often translates to epigenetic differences, as well as to differences in the expansion rate, iPSC line culture robustness, and their ability to differentiate into specific cell types. As such, the diversity of iPSCs presents a hurdle to standardizing iPSC-based cell therapy manufacturing. In this review, we will expand on the various factors that impact iPSC diversity and the strategies and tools that could be taken by the industry to overcome the differences amongst various iPSC lines, therefore enabling robust and reproducible iPSC-based cell therapy manufacturing processes.
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Affiliation(s)
- Suman C. Nath
- Cell Therapy Process Department, Lonza Inc., Houston, TX 77047, USA; (S.C.N.); (L.M.)
| | - Laura Menendez
- Cell Therapy Process Department, Lonza Inc., Houston, TX 77047, USA; (S.C.N.); (L.M.)
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2
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Mohamad Zamani NS, Wan Zaki WMD, Abd Hamid Z, Baseri Huddin A. Future stem cell analysis: progress and challenges towards state-of-the art approaches in automated cells analysis. PeerJ 2022; 10:e14513. [PMID: 36573241 PMCID: PMC9789697 DOI: 10.7717/peerj.14513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Background and Aims A microscopic image has been used in cell analysis for cell type identification and classification, cell counting and cell size measurement. Most previous research works are tedious, including detailed understanding and time-consuming. The scientists and researchers are seeking modern and automatic cell analysis approaches in line with the current in-demand technology. Objectives This article provides a brief overview of a general cell and specific stem cell analysis approaches from the history of cell discovery up to the state-of-the-art approaches. Methodology A content description of the literature study has been surveyed from specific manuscript databases using three review methods: manuscript identification, screening, and inclusion. This review methodology is based on Prism guidelines in searching for originality and novelty in studies concerning cell analysis. Results By analysing generic cell and specific stem cell analysis approaches, current technology offers tremendous potential in assisting medical experts in performing cell analysis using a method that is less laborious, cost-effective, and reduces error rates. Conclusion This review uncovers potential research gaps concerning generic cell and specific stem cell analysis. Thus, it could be a reference for developing automated cells analysis approaches using current technology such as artificial intelligence and deep learning.
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Affiliation(s)
- Nurul Syahira Mohamad Zamani
- Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Department of Electrical, Electronic and Systems Engineering, UKM Bangi, Selangor, Malaysia
| | - Wan Mimi Diyana Wan Zaki
- Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Department of Electrical, Electronic and Systems Engineering, UKM Bangi, Selangor, Malaysia
| | - Zariyantey Abd Hamid
- Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Biomedical Science Programme and Centre for Diagnostic, Therapeutic and Investigative Science, Kuala Lumpur, W. P. Kuala Lumpur, Malaysia
| | - Aqilah Baseri Huddin
- Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Department of Electrical, Electronic and Systems Engineering, UKM Bangi, Selangor, Malaysia
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3
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Fakunle ES, Pratola VG, Peterson SE, Loring JF, Madanat H. The Promoting Equity in Stem Cell Genomics Survey. Regen Med 2022; 17:203-218. [PMID: 35255713 DOI: 10.2217/rme-2021-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study aimed to determine knowledge and attitudes toward induced pluripotent stem cell technology and biobanking. Methods: A survey instrument was developed to determine individuals' knowledge of and attitudes toward these technologies. Results: Results from 276 ethnically diverse participants who took the online survey demonstrated significant associations (p ≤ 0. 05) in knowledge by ethnicity and race regarding properties of stem cells, different types of stem cells and previous sample donation behavior. Significantly more Whites 39% (n = 53) compared with Blacks or African-Americans 19.2% (n = 14) had previous knowledge of induced pluripotent stem cells (χ2 = 8.544; p = 0.003) Conclusion: Overall, White race was associated with greater knowledge about stem cells and biobanks and greater willingness to donate samples for future research.
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Affiliation(s)
- Eyitayo S Fakunle
- Founder at IFASEMB & Ilera "I am Pluripotent", Chandler, AZ 85286, USA.,Currently employed at Covis Pharmaceuticals, Grafenauweg 12, 6300 Zug, Switzerland.,J. Orin Edson Entrepreneurship + Innovation Institute, Venture Devils Program for startups, Arizona State University, Tempe, AZ 85281, USA
| | - Victoria Glenn Pratola
- The Scripps Research Institute, Center for Regenerative Medicine, La Jolla, CA 92037 USA
| | - Suzanne E Peterson
- The Scripps Research Institute, Center for Regenerative Medicine, La Jolla, CA 92037 USA
| | - Jeanne F Loring
- The Scripps Research Institute, Center for Regenerative Medicine, La Jolla, CA 92037 USA.,Graduate School of Public Health, Division of Health Promotion and Behavioral Science San Diego State University, San Diego, CA 92182, USA
| | - Hala Madanat
- Interim Vice President for Research and Innovation, Distinguished Professor, School of Public Health, Core Investigator, Institute for Behavioral and Community Health San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-4162
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4
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Tegtmeyer M, Nehme R. Leveraging the Genetic Diversity of Human Stem Cells in Therapeutic Approaches. J Mol Biol 2021; 434:167221. [PMID: 34474087 DOI: 10.1016/j.jmb.2021.167221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 01/14/2023]
Abstract
Since their discovery 15 years ago, human pluripotent stem cell (hPSC) technologies have begun to revolutionize science and medicine, rapidly expanding beyond investigative research to drug discovery and development. Efforts to leverage hPSCs over the last decade have focused on increasing both the complexity and in vivo fidelity of human cellular models through enhanced differentiation methods. While these evolutions have fostered novel insights into disease mechanisms and influenced clinical drug discovery and development, there are still several considerations that limit the utility of hPSC models. In this review, we highlight important, yet underexplored avenues to broaden their reach. We focus on (i) the importance of diversifying existing hPSC collections, and their utilization to investigate therapeutic strategies in individuals from different genetic backgrounds, ancestry and sex; (ii) considerations for the selection of therapeutically relevant hPSC-based models; (iii) strategies to adequately increase the scale of cell-based studies; and (iv) the advances and constraints of clinical trials in a dish. Moreover, we advocate for harnessing the translational capabilities of hPSC models along with the use of innovative, scalable approaches for understanding genetic biases and the impact of sex and ancestry on disease mechanisms and drug efficacy and response. The next decade of hPSC innovation is poised to provide vast insights into the genetic basis of human disease and enable rapid advances to develop, repurpose, and ensure the safety of the next generation of disease therapies across diverse human populations.
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Affiliation(s)
- Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Centre for Stem Cells and Regenerative Medicine, King's College London, London, UK
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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Hamdi Y, Zass L, Othman H, Radouani F, Allali I, Hanachi M, Okeke CJ, Chaouch M, Tendwa MB, Samtal C, Mohamed Sallam R, Alsayed N, Turkson M, Ahmed S, Benkahla A, Romdhane L, Souiai O, Tastan Bishop Ö, Ghedira K, Mohamed Fadlelmola F, Mulder N, Kamal Kassim S. Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:213-233. [PMID: 33794662 DOI: 10.1089/omi.2021.0004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Following the publication of the first human genome, OMICs research, including genomics, transcriptomics, proteomics, and metagenomics, has been on the rise. OMICs studies revealed the complex genetic diversity among human populations and challenged our understandings of genotype-phenotype correlations. Africa, being the cradle of the first modern humans, is distinguished by a large genetic diversity within its populations and rich ethnolinguistic history. However, the available human OMICs tools and databases are not representative of this diversity, therefore creating significant gaps in biomedical research. African scientists, students, and publics are among the key contributors to OMICs systems science. This expert review examines the pressing issues in human OMICs research, education, and development in Africa, as seen through a lens of computational biology, public health relevant technology innovation, critically-informed science governance, and how best to harness OMICs data to benefit health and societies in Africa and beyond. We underscore the disparities between North and Sub-Saharan Africa at different levels. A harmonized African ethnolinguistic classification would help address annotation challenges associated with population diversity. Finally, building on the existing strategic research initiatives, such as the H3Africa and H3ABioNet Consortia, we highly recommend addressing large-scale multidisciplinary research challenges, strengthening research collaborations and knowledge transfer, and enhancing the ability of African researchers to influence and shape national and international research, policy, and funding agendas. This article and analysis contribute to a deeper understanding of past and current challenges in the African OMICs innovation ecosystem, while also offering foresight on future innovation trajectories.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Fouzia Radouani
- Chlamydiae and Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Faculty of Science of Bizerte, Zarzouna, University of Carthage, Tunis, Tunisia
| | - Chiamaka Jessica Okeke
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Maureen Bilinga Tendwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Chaimae Samtal
- Laboratory of Biotechnology, Environment, Agri-food and Health, Faculty of Sciences Dhar El Mahraz-Sidi Mohammed Ben Abdellah University, Fez, Morocco.,University of Mohamed Premier, Oujda, Morocco
| | - Reem Mohamed Sallam
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt.,Department of Basic Medical Sciences, Faculty of Medicine, Galala University, Suez, Egypt
| | - Nihad Alsayed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Michael Turkson
- The National Institute for Mathematical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samah Ahmed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Faculty of Science of Bizerte, Zarzouna, University of Carthage, Tunis, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Faisal Mohamed Fadlelmola
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Samar Kamal Kassim
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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Cao L, der Meer ADV, Verbeek FJ, Passier R. Automated image analysis system for studying cardiotoxicity in human pluripotent stem cell-Derived cardiomyocytes. BMC Bioinformatics 2020; 21:187. [PMID: 32408861 PMCID: PMC7222481 DOI: 10.1186/s12859-020-3466-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/23/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cardiotoxicity, characterized by severe cardiac dysfunction, is a major problem in patients treated with different classes of anticancer drugs. Development of predictable human-based models and assays for drug screening are crucial for preventing potential drug-induced adverse effects. Current animal in vivo models and cell lines are not always adequate to represent human biology. Alternatively, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) show great potential for disease modelling and drug-induced toxicity screenings. Fully automated high-throughput screening of drug toxicity on hiPSC-CMs by fluorescence image analysis is, however, very challenging, due to clustered cell growth patterns and strong intracellular and intercellular variation in the expression of fluorescent markers. RESULTS In this paper, we report on the development of a fully automated image analysis system for quantification of cardiotoxic phenotypes from hiPSC-CMs that are treated with various concentrations of anticancer drugs doxorubicin or crizotinib. This high-throughput system relies on single-cell segmentation by nuclear signal extraction, fuzzy C-mean clustering of cardiac α-actinin signal, and finally nuclear signal propagation. When compared to manual segmentation, it generates precision and recall scores of 0.81 and 0.93, respectively. CONCLUSIONS Our results show that our fully automated image analysis system can reliably segment cardiomyocytes even with heterogeneous α-actinin signals.
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Affiliation(s)
- Lu Cao
- Imaging and Bioinformatics group, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, Leiden, 2333 CA, The Netherlands
| | - Andries D van der Meer
- Dept of Applied Stem Cell Technologies, MIRA Institute, University of Twente, Drienerlolaan 5, Enschede, 7522 NB, The Netherlands
| | - Fons J Verbeek
- Imaging and Bioinformatics group, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, Leiden, 2333 CA, The Netherlands.
| | - Robert Passier
- Dept of Applied Stem Cell Technologies, MIRA Institute, University of Twente, Drienerlolaan 5, Enschede, 7522 NB, The Netherlands. .,Dept of Anatomy and Embryology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands.
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7
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Hayashi Y, Ohnuma K, Furue MK. Pluripotent Stem Cell Heterogeneity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1123:71-94. [DOI: 10.1007/978-3-030-11096-3_6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Nagamura F. The Importance of Recruiting a Diverse Population for Stem Cell Clinical Trials. CURRENT STEM CELL REPORTS 2016. [DOI: 10.1007/s40778-016-0062-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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9
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Abstract
Integration of physiologically relevant in vitro assays at the earliest stages of drug discovery may improve the likelihood of successfully translating preclinical discoveries to the clinic. Assays based on in vitro-differentiated, human pluripotent stem cell (IVD hPSC)-derived cells, which may better model human physiology, are starting to impact the drug discovery process, but their implementation has been slower than originally anticipated. In this Perspective, we discuss imperatives for incorporating IVD hPSCs into drug discovery and the associated challenges.
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Affiliation(s)
- Sandra J Engle
- Pharmacokinetics, Dynamics and Metabolism, Pfizer, Eastern Point Road, Groton, CT 06340, USA.
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Esch MB, Smith AS, Prot JM, Oleaga C, Hickman JJ, Shuler ML. How multi-organ microdevices can help foster drug development. Adv Drug Deliv Rev 2014; 69-70:158-69. [PMID: 24412641 DOI: 10.1016/j.addr.2013.12.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 11/26/2013] [Accepted: 12/10/2013] [Indexed: 10/25/2022]
Abstract
Multi-organ microdevices can mimic tissue-tissue interactions that occur as a result of metabolite travel from one tissue to other tissues in vitro. These systems are capable of simulating human metabolism, including the conversion of a pro-drug to its effective metabolite as well as its subsequent therapeutic actions and toxic side effects. Since tissue-tissue interactions in the human body can play a significant role in determining the success of new pharmaceuticals, the development and use of multi-organ microdevices present an opportunity to improve the drug development process. The devices have the potential to predict potential toxic side effects with higher accuracy before a drug enters the expensive phase of clinical trials as well as to estimate efficacy and dose response. Multi-organ microdevices also have the potential to aid in the development of new therapeutic strategies by providing a platform for testing in the context of human metabolism (as opposed to animal models). Further, when operated with human biopsy samples, the devices could be a gateway for the development of individualized medicine. Here we review studies in which multi-organ microdevices have been developed and used in a ways that demonstrate how the devices' capabilities can present unique opportunities for the study of drug action. We will also discuss challenges that are inherent in the development of multi-organ microdevices. Among these are how to design the devices, and how to create devices that mimic the human metabolism with high authenticity. Since single organ devices are testing platforms for tissues that can later be combined with other tissues within multi-organ devices, we will also mention single organ devices where appropriate in the discussion.
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Krause KH, van Thriel C, De Sousa PA, Leist M, Hengstler JG. Monocrotophos in Gandaman village: India school lunch deaths and need for improved toxicity testing. Arch Toxicol 2013; 87:1877-81. [PMID: 23943209 DOI: 10.1007/s00204-013-1113-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 08/01/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Karl-Heinz Krause
- Department of Pathology and Immunology, Geneva Medical Faculty, Centre Medical Universitaire, University of Geneva (UNIGE), 1, rue Michel-Servet, 1211, Geneva 4, Switzerland,
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