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Giczewska A, Pastuszak K, Houweling M, Abdul KU, Faaij N, Wedekind L, Noske D, Wurdinger T, Supernat A, Westerman BA. Longitudinal drug synergy assessment using convolutional neural network image-decoding of glioblastoma single-spheroid cultures. Neurooncol Adv 2023; 5:vdad134. [PMID: 38047207 PMCID: PMC10691443 DOI: 10.1093/noajnl/vdad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
Background In recent years, drug combinations have become increasingly popular to improve therapeutic outcomes in various diseases, including difficult to cure cancers such as the brain cancer glioblastoma. Assessing the interaction between drugs over time is critical for predicting drug combination effectiveness and minimizing the risk of therapy resistance. However, as viability readouts of drug combination experiments are commonly performed as an endpoint where cells are lysed, longitudinal drug-interaction monitoring is currently only possible through combined endpoint assays. Methods We provide a method for massive parallel monitoring of drug interactions for 16 drug combinations in 3 glioblastoma models over a time frame of 18 days. In our assay, viabilities of single neurospheres are to be estimated based on image information taken at different time points. Neurosphere images taken on the final day (day 18) were matched to the respective viability measured by CellTiter-Glo 3D on the same day. This allowed to use of machine learning to decode image information to viability values on day 18 as well as for the earlier time points (on days 8, 11, and 15). Results Our study shows that neurosphere images allow us to predict cell viability from extrapolated viabilities. This enables to assess of the drug interactions in a time window of 18 days. Our results show a clear and persistent synergistic interaction for several drug combinations over time. Conclusions Our method facilitates longitudinal drug-interaction assessment, providing new insights into the temporal-dynamic effects of drug combinations in 3D neurospheres which can help to identify more effective therapies against glioblastoma.
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Affiliation(s)
- Anna Giczewska
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Krzysztof Pastuszak
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
- Center of Biostatistics and Bioinformatics, Medical University of Gdańsk, Gdańsk, Poland
- Department of Algorithms and System Modeling, Gdansk University of Technology, Gdańsk, Poland
| | - Megan Houweling
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- The WINDOW Consortium (www.window-consortium.org)
| | - Kulsoom U Abdul
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- The WINDOW Consortium (www.window-consortium.org)
| | - Noa Faaij
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Laurine Wedekind
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - David Noske
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Thomas Wurdinger
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- The WINDOW Consortium (www.window-consortium.org)
| | - Anna Supernat
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
- Center of Biostatistics and Bioinformatics, Medical University of Gdańsk, Gdańsk, Poland
| | - Bart A Westerman
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- The WINDOW Consortium (www.window-consortium.org)
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Houweling M, Giczewska A, Abdul K, Nieuwenhuis N, Küçükosmanoglu A, Pastuszak K, Buijsman RC, Wesseling P, Wedekind L, Noske D, Supernat A, Bailey D, Watts C, Wurdinger T, Westerman BA. Screening of predicted synergistic multi-target therapies in glioblastoma identifies new treatment strategies. Neurooncol Adv 2023; 5:vdad073. [PMID: 37455945 PMCID: PMC10347974 DOI: 10.1093/noajnl/vdad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
Background IDH-wildtype glioblastoma (GBM) is a highly malignant primary brain tumor with a median survival of 15 months after standard of care, which highlights the need for improved therapy. Personalized combination therapy has shown to be successful in many other tumor types and could be beneficial for GBM patients. Methods We performed the largest drug combination screen to date in GBM, using a high-throughput effort where we selected 90 drug combinations for their activity onto 25 patient-derived GBM cultures. 43 drug combinations were selected for interaction analysis based on their monotherapy efficacy and were tested in a short-term (3 days) as well as long-term (18 days) assay. Synergy was assessed using dose-equivalence and multiplicative survival metrics. Results We observed a consistent synergistic interaction for 15 out of 43 drug combinations on patient-derived GBM cultures. From these combinations, 11 out of 15 drug combinations showed a longitudinal synergistic effect on GBM cultures. The highest synergies were observed in the drug combinations Lapatinib with Thapsigargin and Lapatinib with Obatoclax Mesylate, both targeting epidermal growth factor receptor and affecting the apoptosis pathway. To further elaborate on the apoptosis cascade, we investigated other, more clinically relevant, apoptosis inducers and observed a strong synergistic effect while combining Venetoclax (BCL targeting) and AZD5991 (MCL1 targeting). Conclusions Overall, we have identified via a high-throughput drug screening several new treatment strategies for GBM. Moreover, an exceptionally strong synergistic interaction was discovered between kinase targeting and apoptosis induction which is suitable for further clinical evaluation as multi-targeted combination therapy.
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Affiliation(s)
- Megan Houweling
- Department of Neurosurgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain tumor center Amsterdam, Amsterdam, The Netherlands
- WINDOW consortium, Amsterdam, The Netherlands (www.window-consortium.org)
| | | | | | - Ninke Nieuwenhuis
- Department of Neurosurgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain tumor center Amsterdam, Amsterdam, The Netherlands
| | - Asli Küçükosmanoglu
- Department of Neurosurgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain tumor center Amsterdam, Amsterdam, The Netherlands
- WINDOW consortium, Amsterdam, The Netherlands (www.window-consortium.org)
| | - Krzysztof Pastuszak
- Medical University of Gdańsk, Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, 80-211 Gdańsk, Poland
- Department of Algorithms and Systems Modelling, Faculty of Electronics, Telecommunication and Informatics, Gdańsk University of Technology, 80-233 Gdańsk, Poland
- Medical University of Gdańsk, Centre of Biostatistics and Bioinformatics Analysis, 80-211 Gdańsk, Poland
| | | | - Pieter Wesseling
- Department of Pathology, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Princess Maxima Center for Pediatric Oncology, Laboratory for Childhood Cancer Pathology, Utrecht, The Netherlands
| | - Laurine Wedekind
- Department of Neurosurgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain tumor center Amsterdam, Amsterdam, The Netherlands
- WINDOW consortium, Amsterdam, The Netherlands (www.window-consortium.org)
| | - David Noske
- Department of Neurosurgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain tumor center Amsterdam, Amsterdam, The Netherlands
| | - Anna Supernat
- Medical University of Gdańsk, Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, 80-211 Gdańsk, Poland
- Medical University of Gdańsk, Centre of Biostatistics and Bioinformatics Analysis, 80-211 Gdańsk, Poland
| | - David Bailey
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cowley Road, Cambridge, CB4 0WS, UK
- WINDOW consortium, Amsterdam, The Netherlands (www.window-consortium.org)
| | - Colin Watts
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- WINDOW consortium, Amsterdam, The Netherlands (www.window-consortium.org)
| | - Thomas Wurdinger
- Department of Neurosurgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain tumor center Amsterdam, Amsterdam, The Netherlands
- WINDOW consortium, Amsterdam, The Netherlands (www.window-consortium.org)
| | - Bart A Westerman
- Corresponding Author: Dr. Bart A. Westerman, Department of Neurosurgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands ()
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Scheepbouwer C, Borland K, Aparicio E, Verschueren H, Wedekind L, Ramaker J, Misovic B, CM Kouwenhoven M, Noske D, Vandertop P, Wesseling P, Wurdinger T, Hackenberg M, Kellner S, Koppers-Lalic D. GENE-60. THE EPITRANSCRIPTOMIC CODE IN LGG: METABOLICALLY REPROGRAMMED IDH-MUTANT GLIOMAS ALTER tRNA MODIFICATION LANDSCAPE. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
BACKGROUND
Diffuse lower grade gliomas (LGGs) are generally slow growing primary central nervous system tumors that occur in early adult life. The prevalence of isocitrate dehydrogenase (IDH) mutations is high in LGG, and induces excess production of the oncometabolite 2-hydroxyglutarate (2-HG). These gain-of-function mutations play a key role in promoting metabolic reprogramming of the cancer cell that affects activity of α-KG dependent demethylases. Inhibition of DNA demethylase activity leads to glioma with a CpG island methylator phenotype (G-CIMP). Whether the activity of RNA demethylases and methylation status of tRNAs in LGG are modulated by changes in IDH-status is unknown. AIM: To investigate whether IDH mutations play a role in reprogramming of tRNA modifications in adult glioma.
MATERIALS AND METHODS
We combined small RNAseq and LC-MS/MS analysis to identify distinct tRNA processing patterns and methylation signatures in LGG tissues. To address important experimental bottlenecks that limit RNAseq-based detection of tRNA and possibly other modified small noncoding RNAs, we employed a tailored small RNAseq method with validation of specific methylation sites by mass-spectrometry.
RESULTS
Our customized small RNAseq approach yielded >100 fold increase in sequencing reads per tRNA type, thereby dramatically improving tRNA detection when compared to currently used small RNAseq approaches. Moreover, LC-MS/MS analysis revealed a higher abundance of modified nucleosides in tRNA from IDH-mutant LGG compared to IDH-wildtype LGG. Analysis of tRNA from IDH-mutant and IDH-wildtype LGG using the combination of our tailored small RNAseq and LC-MS/MS methodology demonstrated strong differential tRNA expression, tRFs processing and tRNA methylation.
CONCLUSION
We described an approach that makes use of tailored small RNA sequencing combined with mass-spectrometry that enables insights into cancer driven alterations in tRNA methylation patterns and differential tRNA processing signatures. Our data implies that tumor metabolic reprogramming deregulates tRNA methylation, contributing to an altered epitranscriptomic code in IDH-mutant LGG.
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Affiliation(s)
- Chantal Scheepbouwer
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Kayla Borland
- Ludwig Maximilians University Munich, Department of Chemistry, Munich, Germany
| | | | - Heleen Verschueren
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Laurine Wedekind
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Jip Ramaker
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Branko Misovic
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Mathilde CM Kouwenhoven
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurology, Amsterdam, Netherlands
| | - David Noske
- Amsterdam UMC, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Peter Vandertop
- Amsterdam UMC/AMC, Neurosurgical Center Amsterdam, Amsterdam, Netherlands
| | | | - Tom Wurdinger
- Amsterdam UMC, Cancer Center Amsterdam, Amsterdam, Netherlands
| | | | - Stefanie Kellner
- Ludwig Maximilians University Munich, Department of Chemistry, Munich, Germany
| | - Danijela Koppers-Lalic
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
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Meel M, de Gooijer M, Zwaan K, Waranecki P, Breur M, Buil L, Lagerweij T, Wedekind L, Twisk J, Koster J, Hashizume R, Raabe E, Carcaboso ÁM, Bugiani M, van Tellingen O, van Vuurden D, Kaspers G, Hulleman E. DIPG-04. INHIBITION OF AXL SENSITIZES DIFFUSE INTRINSIC PONTINE GLIOMA TO CYTOTOXIC THERAPIES. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Michaël Meel
- VU University Medical Center, Amsterdam, The Netherlands
| | - Mark de Gooijer
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kenn Zwaan
- VU University Medical Center, Amsterdam, The Netherlands
| | | | | | - Levi Buil
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | - Jos Twisk
- VU University Medical Center, Amsterdam, The Netherlands
| | - Jan Koster
- University of Amsterdam Academic Medical Center, Amsterdam, The Netherlands
| | - Rintaro Hashizume
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Eric Raabe
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | - Dannis van Vuurden
- VU University Medical Center, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Gertjan Kaspers
- VU University Medical Center, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Esther Hulleman
- VU University Medical Center, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Meel M, de Gooijer M, Navarro MG, Waranecki P, Breur M, Buil L, Wedekind L, Twisk J, Koster J, Hashizume R, Raabe E, Carcaboso ÁM, Bugiani M, van Tellingen O, van Vuurden D, Kaspers G, Hulleman E. DIPG-05. PRECLINICAL EFFICACY OF MELK INHIBITION IN DIFFUSE INTRINSIC PONTINE GLIOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Michaël Meel
- VU University Medical Center, Amsterdam, The Netherlands
| | - Mark de Gooijer
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Levi Buil
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Jos Twisk
- VU University Medical Center, Amsterdam, The Netherlands
| | - Jan Koster
- University of Amsterdam Academic Medical Center, Amsterdam, The Netherlands
| | - Rintaro Hashizume
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Eric Raabe
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | - Dannis van Vuurden
- VU University Medical Center, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Gertjan Kaspers
- VU University Medical Center, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Esther Hulleman
- VU University Medical Center, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Tannous BA, Kerami M, Van der Stoop PM, Kwiatkowski N, Wang J, Zhou W, Kessler AF, Lewandrowski G, Hiddingh L, Sol N, Lagerweij T, Wedekind L, Niers JM, Barazas M, Nilsson RJA, Geerts D, De Witt Hamer PC, Hagemann C, Vandertop WP, Van Tellingen O, Noske DP, Gray NS, Würdinger T. Effects of the selective MPS1 inhibitor MPS1-IN-3 on glioblastoma sensitivity to antimitotic drugs. J Natl Cancer Inst 2013; 105:1322-31. [PMID: 23940287 DOI: 10.1093/jnci/djt168] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Glioblastomas exhibit a high level of chemotherapeutic resistance, including to the antimitotic agents vincristine and taxol. During the mitotic agent-induced arrest, glioblastoma cells are able to perform damage-control and self-repair to continue proliferation. Monopolar spindle 1 (MPS1/TTK) is a checkpoint kinase and a gatekeeper of the mitotic arrest. METHODS We used glioblastoma cells to determine the expression of MPS1 and to determine the effects of MPS1 inhibition on mitotic errors and cell viability in combination with vincristine and taxol. The effect of MPS1 inhibition was assessed in different orthotopic glioblastoma mouse models (n = 3-7 mice/group). MPS1 expression levels were examined in relation to patient survival. RESULTS Using publicly available gene expression data, we determined that MPS1 overexpression corresponds positively with tumor grade and negatively with patient survival (two-sided t test, P < .001). Patients with high MPS1 expression (n = 203) had a median and mean survival of 487 and 913 days (95% confidence intervals [CI] = 751 to 1075), respectively, and a 2-year survival rate of 35%, whereas patients with intermediate MPS1 expression (n = 140) had a median and mean survival of 858 and 1183 days (95% CI = 1177 to 1189), respectively, and a 2-year survival rate of 56%. We demonstrate that MPS1 inhibition by RNAi results in sensitization to antimitotic agents. We developed a selective small-molecule inhibitor of MPS1, MPS1-IN-3, which caused mitotic aberrancies in glioblastoma cells and, in combination with vincristine, induced mitotic checkpoint override, increased aneuploidy, and augmented cell death. MPS1-IN-3 sensitizes glioblastoma cells to vincristine in orthotopic mouse models (two-sided log-rank test, P < .01), resulting in prolonged survival without toxicity. CONCLUSIONS Our results collectively demonstrate that MPS1, a putative therapeutic target in glioblastoma, can be selectively inhibited by MPS1-IN-3 sensitizing glioblastoma cells to antimitotic drugs.
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Affiliation(s)
- Bakhos A Tannous
- Neuroscience Center and Molecular Neurogenetics Unit, Departments of Neurology, Harvard Medical School, Boston, MA, USA
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Jorke D, Wedekind L. Das Verhalten verschiedener Lymphozytenformen und der Lymphoidzellen unter dem Einfluß ionisierender Strahlen. ROFO-FORTSCHR RONTG 2009. [DOI: 10.1055/s-0029-1228311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Freund E, Wedekind L. [Use of nitrous oxide analgesia in the ambulatory surgical treatment of radius fractures]. Dtsch Gesundheitsw 1971; 26:1662-3. [PMID: 5144561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Jorke D, Wedekind L. [The behavior of various types of lymphocyte and lymphoid cells under the influence of ianizing rays]. Fortschr Geb Rontgenstr Nuklearmed 1968; 108:104-15. [PMID: 4970141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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