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Hallqvist A, Koyi H, de Petris L, Lindberg K, Farooqi S, Helland Å, Wikström A, Johansson M, Planck M, Lindberg L, Yksnøy Ø, Grønberg B, Helbekkmo N, Nyman J. 63MO Safety analysis of durvalumab following stereotactic body radiotherapy (SBRT) in early-stage non-small cell lung cancer (NSCLC) patients: A first report of a randomized phase II trial (ASTEROID). J Thorac Oncol 2021. [DOI: 10.1016/s1556-0864(21)01905-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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2
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Bhardwaj RM, McMahon JA, Nyman J, Price LS, Konar S, Oswald IDH, Pulham CR, Price SL, Reutzel-Edens SM. A Prolific Solvate Former, Galunisertib, under the Pressure of Crystal Structure Prediction, Produces Ten Diverse Polymorphs. J Am Chem Soc 2019; 141:13887-13897. [DOI: 10.1021/jacs.9b06634] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajni M. Bhardwaj
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jennifer A. McMahon
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jonas Nyman
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
- School of Pharmacy, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Louise S. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Sumit Konar
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Iain D. H. Oswald
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral St, Glasgow G4 0RE, U.K
| | - Colin R. Pulham
- School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Sarah L. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Susan M. Reutzel-Edens
- Small Molecule Design & Development, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
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3
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Abstract
A novel pumpkin-orange polymorph of ROY was matched to a predicted structure and refined to PXRD data.
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Affiliation(s)
| | - Jonas Nyman
- Small Molecule Design & Development
- Eli Lilly and Company
- Indianapolis
- USA
- School of Pharmacy
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4
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Abstract
Because of excessive electron delocalization, the polymorphs of ROY constitute a surprisingly challenging system for crystal structure prediction.
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Affiliation(s)
- Jonas Nyman
- School of Pharmacy
- University of Wisconsin – Madison
- Madison
- USA
- Small Molecule Design & Development
| | - Lian Yu
- School of Pharmacy
- University of Wisconsin – Madison
- Madison
- USA
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5
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Nyman J, Bergström S, Björkestrand H, Svärd A, Ekman S, Lundin E, Holmberg E, Johansson M, Friesland S, Hallqvist A. MA05.07 Dose Escalated Chemo-RT to 84 Gy in Stage III NSCLC Appears Excessively Toxic: Results from a Randomized Phase II Trial. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Westman JO, Nyman J, Manara RMA, Mapelli V, Franzén CJ. A novel chimaeric flocculation protein enhances flocculation in Saccharomyces cerevisiae. Metab Eng Commun 2018; 6:49-55. [PMID: 29896447 PMCID: PMC5994806 DOI: 10.1016/j.meteno.2018.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 04/06/2018] [Accepted: 04/07/2018] [Indexed: 01/29/2023] Open
Abstract
Yeast flocculation is the reversible formation of multicellular complexes mediated by lectin-like cell wall proteins binding to neighbouring cells. Strong flocculation can improve the inhibitor tolerance and fermentation performance of yeast cells in second generation bioethanol production. The strength of flocculation increases with the size of the flocculation protein and is strain dependent. However, the large number of internal repeats in the sequence of FLO1 from Saccharomyces cerevisiae S288c makes it difficult to recombinantly express the gene to its full length. In the search for novel flocculation genes resulting in strong flocculation, we discovered a DNA sequence, FLONF, that gives NewFlo phenotype flocculation in S. cerevisiae CEN.PK 113-7D. The nucleotide sequence of the internal repeats of FLONF differed from those of FLO1. We hypothesized that a chimaeric flocculation gene made up of a FLO1 variant derived from S. cerevisiae S288c and additional repeats from FLONF from S. cerevisiae CCUG 53310 would be more stable and easier to amplify by PCR. The constructed gene, FLOw, had 22 internal repeats compared to 18 in FLO1. Expression of FLOw in otherwise non-flocculating strains led to strong flocculation. Despite the length of the gene, the cassette containing FLOw could be easily amplified and transformed into yeast strains of different genetic background, leading to strong flocculation in all cases tested. The developed gene can be used as a self-immobilization technique or to obtain rapidly sedimenting cells for application in e.g. sequential batches without need for centrifugation. A novel gene sequence conferring NewFlo phenotype flocculation was isolated. The chimaeric gene FLOw was constructed from parts of FLO1 and FLONF. Overexpression of FLOw gave strong flocculation in several S. cerevisiae strains.
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Affiliation(s)
- Johan O Westman
- Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Industrial Biotechnology, 412 96 Göteborg, Sweden
| | - Jonas Nyman
- University of Southampton, Chemistry, University Road, Southampton SO17 1BJ, UK
| | - Richard M A Manara
- University of Southampton, Chemistry, University Road, Southampton SO17 1BJ, UK
| | - Valeria Mapelli
- Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Industrial Biotechnology, 412 96 Göteborg, Sweden
| | - Carl Johan Franzén
- Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Industrial Biotechnology, 412 96 Göteborg, Sweden
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7
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Fernström E, Minta K, Andreasson U, Sandelius Å, Wasling P, Brinkmalm A, Höglund K, Blennow K, Nyman J, Zetterberg H, Kalm M. Cerebrospinal fluid markers of extracellular matrix remodelling, synaptic plasticity and neuroinflammation before and after cranial radiotherapy. J Intern Med 2018; 284:211-225. [PMID: 29664192 DOI: 10.1111/joim.12763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
BACKGROUND Advances in the treatment of brain tumours have increased the number of long-term survivors, but at the cost of side effects following cranial radiotherapy ranging from neurocognitive deficits to outright tissue necrosis. At present, there are no tools reflecting the molecular mechanisms underlying such side effects, and thus no means to evaluate interventional effects after cranial radiotherapy. Therefore, fluid biomarkers are of great clinical interest. OBJECTIVE Cerebrospinal fluid (CSF) levels of proteins involved in inflammatory signalling, synaptic plasticity and extracellular matrix (ECM) integrity were investigated following radiotherapy to the brain. METHODS Patients with small-cell lung cancer (SCLC) eligible for prophylactic cranial irradiation (PCI) were asked to participate in the study. PCI was prescribed either as 2 Gy/fraction to a total dose of 30 Gy (limited disease) or 4 Gy/fraction to 20 Gy (extensive disease). CSF was collected by lumbar puncture at baseline, 3 months and 1 year following PCI. Protein concentrations were measured using immunobased assays or mass spectrometry. RESULTS The inflammatory markers IL-15, IL-16 and MCP-1/CCL2 were elevated in CSF 3 months following PCI compared to baseline. The plasticity marker GAP-43 was elevated 3 months following PCI, and the same trend was seen for SNAP-25, but not for SYT1. The investigated ECM proteins, brevican and neurocan, showed a decline following PCI. There was a strong correlation between the progressive decline of soluble APPα and brevican levels. CONCLUSION To our knowledge, this is the first time ECM-related proteins have been shown to be affected by cranial radiotherapy in patients with cancer. These findings may help us to get a better understanding of the mechanisms behind side effects following radiotherapy.
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Affiliation(s)
- E Fernström
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - K Minta
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology at the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - U Andreasson
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology at the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Å Sandelius
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology at the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - P Wasling
- Department of Physiology, Institute of Neuroscience and Physiology at the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - A Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology at the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - K Höglund
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology at the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - K Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology at the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - J Nyman
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - H Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology at the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - M Kalm
- Department of Pharmacology, Institute of Neuroscience and Physiology at the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
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8
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Abstract
Prediction of true polymorphs as dynamic ensembles in contrast to hypothetical static crystal structures.
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Affiliation(s)
- Jonas Nyman
- School of Pharmacy
- University of Wisconsin – Madison
- Madison
- USA
- Small Molecule Design & Development
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9
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Addicoat M, Adjiman CS, Arhangelskis M, Beran GJO, Bowskill D, Brandenburg JG, Braun DE, Burger V, Cole J, Cruz-Cabeza AJ, Day GM, Deringer VL, Guo R, Hare A, Helfferich J, Hoja J, Iuzzolino L, Jobbins S, Marom N, McKay D, Mitchell JBO, Mohamed S, Neumann M, Nilsson Lill S, Nyman J, Oganov AR, Piaggi P, Price SL, Reutzel-Edens S, Rietveld I, Ruggiero M, Ryder MR, Sastre G, Schön JC, Taylor C, Tkatchenko A, Tsuzuki S, van den Ende J, Woodley SM, Woollam G, Zhu Q. Crystal structure evaluation: calculating relative stabilities and other criteria: general discussion. Faraday Discuss 2018; 211:325-381. [DOI: 10.1039/c8fd90031k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Adjiman CS, Brandenburg JG, Braun DE, Cole J, Collins C, Cooper AI, Cruz-Cabeza AJ, Day GM, Dudek M, Hare A, Iuzzolino L, McKay D, Mitchell JBO, Mohamed S, Neelamraju S, Neumann M, Nilsson Lill S, Nyman J, Oganov AR, Price SL, Pulido A, Reutzel-Edens S, Rietveld I, Ruggiero MT, Schön JC, Tsuzuki S, van den Ende J, Woollam G, Zhu Q. Applications of crystal structure prediction – organic molecular structures: general discussion. Faraday Discuss 2018; 211:493-539. [DOI: 10.1039/c8fd90032a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Addicoat M, Adjiman CS, Arhangelskis M, Beran GJO, Brandenburg JG, Braun DE, Burger V, Burow A, Collins C, Cooper A, Day GM, Deringer VL, Dyer MS, Hare A, Jelfs KE, Keupp J, Konstantinopoulos S, Li Y, Ma Y, Marom N, McKay D, Mellot-Draznieks C, Mohamed S, Neumann M, Nilsson Lill S, Nyman J, Oganov AR, Price SL, Reutzel-Edens S, Ruggiero M, Sastre G, Schmid R, Schmidt J, Schön JC, Spackman P, Tsuzuki S, Woodley SM, Yang S, Zhu Q. Structure searching methods: general discussion. Faraday Discuss 2018; 211:133-180. [DOI: 10.1039/c8fd90030b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Selent M, Nyman J, Roukala J, Ilczyszyn M, Oilunkaniemi R, Bygrave PJ, Laitinen R, Jokisaari J, Day GM, Lantto P. Inside Back Cover: Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129
Xe NMR Spectroscopy (Chem. Eur. J. 22/2017). Chemistry 2017. [DOI: 10.1002/chem.201700348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marcin Selent
- NMR Research Unit; Faculty of Science; University of Oulu; 90014 Oulu Finland
- Faculty of Chemistry; Wrocław University; Joliot Curie 14 50-383 Wrocław Poland
| | - Jonas Nyman
- Computational Systems Chemistry, School of Chemistry; University of Southampton; Southampton UK
| | - Juho Roukala
- NMR Research Unit; Faculty of Science; University of Oulu; 90014 Oulu Finland
| | - Marek Ilczyszyn
- Faculty of Chemistry; Wrocław University; Joliot Curie 14 50-383 Wrocław Poland
| | - Raija Oilunkaniemi
- Laboratory of Inorganic Chemistry; University of Oulu; 90014 Oulu Finland
| | - Peter J. Bygrave
- Computational Systems Chemistry, School of Chemistry; University of Southampton; Southampton UK
| | - Risto Laitinen
- Laboratory of Inorganic Chemistry; University of Oulu; 90014 Oulu Finland
| | - Jukka Jokisaari
- NMR Research Unit; Faculty of Science; University of Oulu; 90014 Oulu Finland
| | - Graeme M. Day
- Computational Systems Chemistry, School of Chemistry; University of Southampton; Southampton UK
| | - Perttu Lantto
- NMR Research Unit; Faculty of Science; University of Oulu; 90014 Oulu Finland
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13
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Selent M, Nyman J, Roukala J, Ilczyszyn M, Oilunkaniemi R, Bygrave PJ, Laitinen R, Jokisaari J, Day GM, Lantto P. Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129 Xe NMR Spectroscopy. Chemistry 2017; 23:5258-5269. [PMID: 28111848 PMCID: PMC5763392 DOI: 10.1002/chem.201604797] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 11/09/2022]
Abstract
An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by 129 Xe NMR spectroscopy. The high sensitivity of the 129 Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.
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Affiliation(s)
- Marcin Selent
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland.,Faculty of Chemistry, Wrocław University, Joliot Curie 14, 50-383, Wrocław, Poland
| | - Jonas Nyman
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
| | - Juho Roukala
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland
| | - Marek Ilczyszyn
- Faculty of Chemistry, Wrocław University, Joliot Curie 14, 50-383, Wrocław, Poland
| | - Raija Oilunkaniemi
- Laboratory of Inorganic Chemistry, University of Oulu, 90014, Oulu, Finland
| | - Peter J Bygrave
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
| | - Risto Laitinen
- Laboratory of Inorganic Chemistry, University of Oulu, 90014, Oulu, Finland
| | - Jukka Jokisaari
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland
| | - Graeme M Day
- Computational Systems Chemistry, School of Chemistry, University of Southampton, Southampton, UK
| | - Perttu Lantto
- NMR Research Unit, Faculty of Science, University of Oulu, 90014, Oulu, Finland
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14
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Holgersson G, Bergstrom S, Hallqvist A, Liv P, Nilsson J, Willen L, Nyman J, Ekman S, Henriksson R, Bergqvist M. The prognostic value of pre-treatment thrombocytosis in two cohorts of patients with non-small cell lung cancer treated with curatively intended chemoradiotherapy. Neoplasma 2017; 64:909-915. [DOI: 10.4149/neo_2017_614] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Nyman J, Day GM. Modelling temperature-dependent properties of polymorphic organic molecular crystals. Phys Chem Chem Phys 2016; 18:31132-31143. [PMID: 27812563 PMCID: PMC5299590 DOI: 10.1039/c6cp05447a] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/31/2016] [Indexed: 12/17/2022]
Abstract
We present a large-scale study of the temperature-dependence of structures, free energy differences and properties of polymorphic molecular organic crystals. Lattice-vibrational Gibbs free energy differences between 475 pairs of polymorphs of organic molecular crystals have been calculated at 0 K and at their respective melting points, using a highly accurate anisotropic multipole-based force field and including thermal expansion through the use of a (negative) thermal pressure. Re-ranking of the relative thermodynamic stability of the polymorphs in each pair indicates the possibility of an enantiotropic phase transition between the crystal structures, which occurs in 21% of the studied systems. While vibrational contributions to free energies can have a significant effect on thermodynamic stability, the impact of thermal expansion on polymorph free energy differences is generally very small. We also calculate thermal expansion coefficients for the 864 crystal structures and investigate the temperature-dependence of mechanical properties, and pairwise differences in these properties between polymorphs.
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Affiliation(s)
- Jonas Nyman
- School of Chemistry, University of Southampton, Southampton, UK.
| | - Graeme M Day
- School of Chemistry, University of Southampton, Southampton, UK.
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16
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Nyman J, Day GM. Lattice vibrations in molecular crystals: polymorphism and phase transitions. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316098119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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17
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Lindberg L, Ek A, Nyman J, Marcus C, Ulijaszek S, Nowicka P. Low grandparental social support combined with low parental socioeconomic status is closely associated with obesity in preschool-aged children: a pilot study. Pediatr Obes 2016; 11:313-6. [PMID: 26097148 DOI: 10.1111/ijpo.12049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 04/14/2015] [Accepted: 05/20/2015] [Indexed: 11/30/2022]
Abstract
While the influence of parental socioeconomic status (SES) on children's weight status is well known, the impact of other family-related aspects such as parental and grandparental social support is less understood. This study investigates the importance of parents' SES and social support (functional and structural) for weight status in a clinical sample of preschoolers 4-6 years old with obesity (n = 39, 56% girls; 73% of parents were overweight/obese, 50% were of non-Swedish origin). Linear regression analyses, simple and multiple, were performed on SES and social support with child BMI SDS (body mass index standard deviation score) as the dependent variable. The results show that parents' income and low emotional support from paternal grandparents were significantly associated with more severe obesity. The association between parental income and the child's BMI SDS was stronger among parents who had low emotional support from their own parents. In conclusion, grandparental social support may be protective against childhood obesity.
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Affiliation(s)
- L Lindberg
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - A Ek
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - J Nyman
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - C Marcus
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - S Ulijaszek
- Unit for Biocultural Variation and Obesity, Institute of Social and Cultural Anthropology, University of Oxford, Oxford, UK
| | - P Nowicka
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.,Unit for Biocultural Variation and Obesity, Institute of Social and Cultural Anthropology, University of Oxford, Oxford, UK
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18
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Reilly AM, Cooper RI, Adjiman CS, Bhattacharya S, Boese AD, Brandenburg JG, Bygrave PJ, Bylsma R, Campbell JE, Car R, Case DH, Chadha R, Cole JC, Cosburn K, Cuppen HM, Curtis F, Day GM, DiStasio Jr RA, Dzyabchenko A, van Eijck BP, Elking DM, van den Ende JA, Facelli JC, Ferraro MB, Fusti-Molnar L, Gatsiou CA, Gee TS, de Gelder R, Ghiringhelli LM, Goto H, Grimme S, Guo R, Hofmann DWM, Hoja J, Hylton RK, Iuzzolino L, Jankiewicz W, de Jong DT, Kendrick J, de Klerk NJJ, Ko HY, Kuleshova LN, Li X, Lohani S, Leusen FJJ, Lund AM, Lv J, Ma Y, Marom N, Masunov AE, McCabe P, McMahon DP, Meekes H, Metz MP, Misquitta AJ, Mohamed S, Monserrat B, Needs RJ, Neumann MA, Nyman J, Obata S, Oberhofer H, Oganov AR, Orendt AM, Pagola GI, Pantelides CC, Pickard CJ, Podeszwa R, Price LS, Price SL, Pulido A, Read MG, Reuter K, Schneider E, Schober C, Shields GP, Singh P, Sugden IJ, Szalewicz K, Taylor CR, Tkatchenko A, Tuckerman ME, Vacarro F, Vasileiadis M, Vazquez-Mayagoitia A, Vogt L, Wang Y, Watson RE, de Wijs GA, Yang J, Zhu Q, Groom CR. Report on the sixth blind test of organic crystal structure prediction methods. Acta Crystallogr B Struct Sci Cryst Eng Mater 2016; 72:439-59. [PMID: 27484368 PMCID: PMC4971545 DOI: 10.1107/s2052520616007447] [Citation(s) in RCA: 298] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/04/2016] [Indexed: 05/05/2023]
Abstract
The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.
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Affiliation(s)
- Anthony M. Reilly
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Richard I. Cooper
- Chemical Crystallography, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England
| | - Claire S. Adjiman
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Saswata Bhattacharya
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - A. Daniel Boese
- Department of Chemistry, Institute of Physical and Theoretical Chemistry, University of Graz, Heinrichstraße 28/IV, 8010 Graz, Austria
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Peter J. Bygrave
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Rita Bylsma
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Josh E. Campbell
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - David H. Case
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Renu Chadha
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Jason C. Cole
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Katherine Cosburn
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Physics, University of Toronto, Toronto, Canada M5S 1A7
| | - Herma M. Cuppen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Farren Curtis
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Graeme M. Day
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Robert A. DiStasio Jr
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Dennis M. Elking
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508, USA
| | - Joost A. van den Ende
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Julio C. Facelli
- Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
- Department of Biomedical Informatics, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
| | - Marta B. Ferraro
- Departamento de Física and Ifiba (CONICET) Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina
| | - Laszlo Fusti-Molnar
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508, USA
| | - Christina-Anna Gatsiou
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Thomas S. Gee
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - René de Gelder
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Luca M. Ghiringhelli
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Hitoshi Goto
- Educational Programs on Advanced Simulation Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
- Department of Computer Science and Engineering, Graduate School of Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Rui Guo
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Detlef W. M. Hofmann
- CRS4, Parco Scientifico e Tecnologico, POLARIS, Edificio 1, 09010 PULA, Italy
- FlexCryst, Schleifweg 23, 91080 Uttenreuth, Germany
| | - Johannes Hoja
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Rebecca K. Hylton
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Luca Iuzzolino
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Wojciech Jankiewicz
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Daniël T. de Jong
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - John Kendrick
- Faculty of Life Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, England
| | - Niek J. J. de Klerk
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hsin-Yu Ko
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | | | - Xiayue Li
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Sanjaya Lohani
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
| | - Frank J. J. Leusen
- Faculty of Life Sciences, University of Bradford, Richmond Road, Bradford BD7 1DP, England
| | - Albert M. Lund
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508, USA
- Department of Chemistry, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
| | - Jian Lv
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, People’s Republic of China
| | - Yanming Ma
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, People’s Republic of China
| | - Noa Marom
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Materials Science and Engineering and Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Artëm E. Masunov
- NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, PAV400, Orlando, FL 32826, USA
- Department of Chemistry, University of Central Florida, 4111 Libra Drive PSB225, Orlando, FL 32816, USA
- Department of Physics, University of Central Florida, 4111 Libra Drive PSB430, Orlando, FL 32816, USA
- Department of Condensed Matter Physics, National Research Nuclear University MEPhI, Kashirskoye shosse 31, Moscow 115409, Russia
| | - Patrick McCabe
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - David P. McMahon
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Hugo Meekes
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Michael P. Metz
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | - Alston J. Misquitta
- School of Physics and Astronomy, Queen Mary University of London, London E1 4NS, England
| | | | - Bartomeu Monserrat
- Cavendish Laboratory, 19, J. J. Thomson Avenue, Cambridge CB3 0HE, England
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854-8019, USA
| | - Richard J. Needs
- Cavendish Laboratory, 19, J. J. Thomson Avenue, Cambridge CB3 0HE, England
| | | | - Jonas Nyman
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Shigeaki Obata
- Educational Programs on Advanced Simulation Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Artem R. Oganov
- Department of Geosciences, Center for Materials by Design, and Institute for Advanced Computational Science, SUNY Stony Brook, NY 11794-2100, USA
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Centers, Bldg. 3, Moscow Region, 143026, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny City, Moscow Region 141700, Russia
- International Center for Materials Discovery, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi’an 710072, China
| | - Anita M. Orendt
- Center for High Performance Computing, University of Utah, 155 South 1452 East Room 405, Salt Lake City, UT 84112-0190, USA
| | - Gabriel I. Pagola
- Departamento de Física and Ifiba (CONICET) Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina
| | - Constantinos C. Pantelides
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Chris J. Pickard
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge CB3 0FS, England
- Department of Physics and Astronomy, University College London, Gower St., London WC1E 6BT, England
| | - Rafal Podeszwa
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Louise S. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Sarah L. Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Angeles Pulido
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Murray G. Read
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Elia Schneider
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Christoph Schober
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Gregory P. Shields
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
| | - Pawanpreet Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Isaac J. Sugden
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA
| | | | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg
| | - Mark E. Tuckerman
- Department of Chemistry, New York University, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
| | - Francesca Vacarro
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA
- Department of Chemistry, Loyola University, New Orleans, LA 70118, USA
| | - Manolis Vasileiadis
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, London SW7 2AZ, England
| | | | - Leslie Vogt
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Yanchao Wang
- State Key Laboratory of Superhard Materials, Jilin University, Changchun 130012, People’s Republic of China
| | - Rona E. Watson
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
| | - Gilles A. de Wijs
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jack Yang
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, England
| | - Qiang Zhu
- Department of Geosciences, Center for Materials by Design, and Institute for Advanced Computational Science, SUNY Stony Brook, NY 11794-2100, USA
| | - Colin R. Groom
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England
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Nyman J, Lindblad A, Fjellson A, Karlge-Nilsson E, Hjelte L. WS02.2 Gastrostomy tubes in patients with cystic fibrosis in Sweden. J Cyst Fibros 2016. [DOI: 10.1016/s1569-1993(16)30067-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Nyman J, Pundyke OS, Day GM. Accurate force fields and methods for modelling organic molecular crystals at finite temperatures. Phys Chem Chem Phys 2016; 18:15828-37. [PMID: 27230942 DOI: 10.1039/c6cp02261h] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present an assessment of the performance of several force fields for modelling intermolecular interactions in organic molecular crystals using the X23 benchmark set. The performance of the force fields is compared to several popular dispersion corrected density functional methods. In addition, we present our implementation of lattice vibrational free energy calculations in the quasi-harmonic approximation, using several methods to account for phonon dispersion. This allows us to also benchmark the force fields' reproduction of finite temperature crystal structures. The results demonstrate that anisotropic atom-atom multipole-based force fields can be as accurate as several popular DFT-D methods, but have errors 2-3 times larger than the current best DFT-D methods. The largest error in the examined force fields is a systematic underestimation of the (absolute) lattice energy.
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Affiliation(s)
- Jonas Nyman
- School of Chemistry, University of Southampton, Southampton, UK.
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Lindberg L, Ek A, Nyman J, Marcus C, Ulijaszek S, Nowicka P. Low parental economic capital and low grandparental social support are closely associated with obesity in preschool-aged children. Preliminary findings. Appetite 2015. [DOI: 10.1016/j.appet.2014.12.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Nyman J, Ek A, Marcus C, Nowicka P. Comparing different treatment approaches to childhood obesity in preschoolers. Preliminary results of the More and Less study, a randomized controlled trial. Appetite 2015. [DOI: 10.1016/j.appet.2014.12.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abstract
Lattice energy, entropy and free energy differences for over 500 pairs of known polymorphs are computed and discussed.
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Affiliation(s)
- Jonas Nyman
- School of Chemistry
- University of Southampton
- Southampton, UK
| | - Graeme M. Day
- School of Chemistry
- University of Southampton
- Southampton, UK
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Nyman J, Day G. Predicting Porous Molecular Crystals and Clathrates. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314083740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The last decade has seen dramatic improvements in the theories and computer algorithms underlying computational Crystal Structure Predictions [1]. It is now possible to reliably obtain the most likely crystal structures of at least simple molecules starting from nothing more than a drawing of the molecule. We can now go even further and look for rare and exotic kinds of crystals such as porous molecular crystals, clathrates and inclusion compounds among our predictions and calculate their physical properties [2], paving the way for the "science of hypothetical materials". In our poster, we present results on the prediction of fluorophenol xenon clathrates. We have performed crystal structure predictions by global lattice energy searches on o- and m-fluorophenol. The predicted structures have then been analyzed for porosity and their likelihood of being clathrates. From the several thousands of predicted structures, we select a few likely candidates according to an empirical rule based on the guest to host volume ratio [3]. Results from solid state xenon-129 NMR indicate that we have successfully determined the crystal structures of both o- and m-fluorophenol xenon clathrates and we suggest that Crystal Structure Prediction in combination with xenon-129 NMR is a powerful method for determining the structures of clathrates in general.
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Abstract
BACKGROUND A reduced sense of smell may be one explanation for why patients with cancer in the ear, nose and throat (ENT) region who are treated with radiation therapy lose weight. The purpose of this study was to investigate whether radiation therapy has a negative effect on olfactory function and, if so, whether this effect is dose-related. METHODOLOGY Seventy-one patients were tested using odour-detection sensitivity and olfactory identification tests before radiation therapy and 20 months after it. RESULTS Patients who received radiation close to the olfactory organ showed a reduced sense of smell, in both tests. A multiple regression analysis showed that the radiation dose was related to decline in the olfactory function, while age, sex, chemotherapy and interactions between these variables were not. CONCLUSION Radiation therapy can damage olfactory cells.
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Nyman J, Lacintra MG, Westman JO, Berglin M, Lundin M, Lennartsson PR, Taherzadeh MJ. Pellet formation of zygomycetes and immobilization of yeast. N Biotechnol 2013; 30:516-22. [DOI: 10.1016/j.nbt.2013.05.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 10/26/2022]
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Hammerlid E, Silander E, Nyman J. PO-058: An Exploration of Factors Predicting Malnutrition in Patients with Advanced Head and Neck Cancer. Radiother Oncol 2013. [DOI: 10.1016/s0167-8140(15)34677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Karlsson K, Nyman J, Baumann P, Wersäll P, Gagliardi G, Johansson K, Persson J, Rutkowska E, Tullgren O, Lax I. A Retrospective Study of Bronchial Doses and Radiation-induced Atelectasis After SBRT of Lung Tumors Located Close to the Bronchial Tree. Int J Radiat Oncol Biol Phys 2012. [DOI: 10.1016/j.ijrobp.2012.07.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Persson GF, Nygaard DE, Hollensen C, Munck af Rosenschöld P, Mouritsen LS, Due AK, Berthelsen AK, Nyman J, Markova E, Roed AP, Roed H, Korreman S, Specht L. Interobserver delineation variation in lung tumour stereotactic body radiotherapy. Br J Radiol 2012; 85:e654-60. [PMID: 22919015 PMCID: PMC3487081 DOI: 10.1259/bjr/76424694] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 08/22/2011] [Accepted: 09/12/2011] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES In radiotherapy, delineation uncertainties are important as they contribute to systematic errors and can lead to geographical miss of the target. For margin computation, standard deviations (SDs) of all uncertainties must be included as SDs. The aim of this study was to quantify the interobserver delineation variation for stereotactic body radiotherapy (SBRT) of peripheral lung tumours using a cross-sectional study design. METHODS 22 consecutive patients with 26 tumours were included. Positron emission tomography/CT scans were acquired for planning of SBRT. Three oncologists and three radiologists independently delineated the gross tumour volume. The interobserver variation was calculated as a mean of multiple SDs of distances to a reference contour, and calculated for the transversal plane (SD(trans)) and craniocaudal (CC) direction (SD(cc)) separately. Concordance indexes and volume deviations were also calculated. RESULTS Median tumour volume was 13.0 cm(3), ranging from 0.3 to 60.4 cm(3). The mean SD(trans) was 0.15 cm (SD 0.08 cm) and the overall mean SD(cc) was 0.26 cm (SD 0.15 cm). Tumours with pleural contact had a significantly larger SD(trans) than tumours surrounded by lung tissue. CONCLUSIONS The interobserver delineation variation was very small in this systematic cross-sectional analysis, although significantly larger in the CC direction than in the transversal plane, stressing that anisotropic margins should be applied. This study is the first to make a systematic cross-sectional analysis of delineation variation for peripheral lung tumours referred for SBRT, establishing the evidence that interobserver variation is very small for these tumours.
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Affiliation(s)
- G F Persson
- Department of Radiation Oncology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark.
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Bergquist H, Johnsson E, Nyman J, Rylander H, Hammerlid E, Friesland S, Ejnell H, Lundell L, Ruth M. Combined stent insertion and single high-dose brachytherapy in patients with advanced esophageal cancer--results of a prospective safety study. Dis Esophagus 2012; 25:410-5. [PMID: 21899654 DOI: 10.1111/j.1442-2050.2011.01248.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Previous randomized studies comparing the two commonly used palliative treatments for incurable esophageal cancer, i.e. stent insertion and intraluminal brachytherapy, have revealed the pros and cons of each therapy. While stent treatment offers a more prompt effect, brachytherapy results in more long-lasting relief of dysphagia and a better health-related quality of life (HRQL) in those living longer. This prospective pilot study aimed to explore the feasibility and safety of combining these two regimes and incorporating a single high dose of internal radiation. Patients with newly diagnosed, incurable cancer of the esophagus and dysphagia were eligible for inclusion, and stent insertion followed by a single dose (12 Gy) of brachytherapy was performed as a two-stage procedure. Clinical parameters including HRQL and adverse events were registered at inclusion, and 1, 2, 3, 6, and 12 months later. Twelve patients (nine males) with a median age of 73 years (range 54-85) were included. Stent insertion followed by a single dose of brachytherapy was successfully performed in all but one patient who was treated with stent only. Relief of dysphagia was achieved in the majority of cases (10/11, P < 0.05), but HRQL did not improve except for dysphagia-related items. Only minor adverse events, including chest pain, reflux, and restenosis, were reported. The median survival time after inclusion was 6.6 months. Our conclusion is that the combination of stent insertion and single high-dose brachytherapy seems to be a feasible and safe palliative regime in patients with advanced esophageal cancer. Randomized trials comparing the efficacy of this strategy to stent insertion or brachytherapy alone are warranted.
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Affiliation(s)
- H Bergquist
- Department of ENT/H&N Surgery Surgery Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden.
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Turesson I, Qvarnström F, Simonsson M, Thunberg U, Hermansson I, Book M, Johansson K, Nyman J. 1125 POSTER DNA Damage Response of Epithelial and Mesenchymal Cell Lineages in the Clinical Setting of Radiotherapy. Eur J Cancer 2011. [DOI: 10.1016/s0959-8049(11)70768-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mercke C, Sjödin H, Haugen H, Adell G, Wickart-Johansson G, Munck-Wikland EM, von Dobeln G, Nyman J. Survival, tumor control, and toxicity with TPF before accelerated radiotherapy potentiated with cetuximab for stage III-IV unresectable head and neck cancer: A phase II study. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.5552] [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: 11/20/2022] Open
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Hallqvist A, Wagenius G, Rylander H, Brodin O, Holmberg E, Lödén B, Ewers SB, Bergström S, Wichardt-Johansson G, Nilsson K, Ekberg L, Sederholm C, Nyman J. Concurrent cetuximab and radiotherapy after docetaxel-cisplatin induction chemotherapy in stage III NSCLC: satellite--a phase II study from the Swedish Lung Cancer Study Group. Lung Cancer 2010; 71:166-72. [PMID: 20541833 DOI: 10.1016/j.lungcan.2010.05.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 04/15/2010] [Accepted: 05/09/2010] [Indexed: 11/12/2022]
Abstract
BACKGROUND Several attempts to increase the locoregional control in locally advanced lung cancer including concurrent chemotherapy, accelerated fractionation and dose escalation have been made during the last years. As the EGFR directed antibody cetuximab has shown activity concurrent with radiotherapy in squamous cell carcinoma of the head and neck, as well as in stage IV NSCLC combined with chemotherapy, we wanted to investigate radiotherapy with concurrent cetuximab in locally advanced NSCLC, a tumour type often over expressing the EGF-receptor. METHODS Between February 2006 and August 2007 75 patients in stage III NSCLC with good performance status (PS 0 or 1) and adequate lung function (FEV1>1.0) were enrolled in this phase II study at eight institutions. Treatment consisted of 2 cycles of induction chemotherapy, docetaxel 75 mg/m² and cisplatin 75 mg/m² with 3 weeks interval. An initial dose of cetuximab 400 mg/m² was given before start of 3D-CRT to 68 Gy with 2 Gy per fraction in 7 weeks concurrent with weekly cetuximab 250 mg/m². TOXICITY was scored weekly during radiotherapy (CTC 3.0), and after treatment the patients were followed every third month with CT-scans, toxicity scoring and QLQ. RESULTS Seventy-one patients were eligible for analysis as four were incorrectly enrolled. HISTOLOGY adenocarcinoma 49%, squamous cell carcinoma 39% and other NSCLC 12%. The majority had PS 0 (62.5%), median age 62.2 (42-81), 50% were women and 37% had a pre-treatment weight loss>5%. TOXICITY esophagitis grade 1-2: 72%; grade 3: 1.4%. Hypersensitivity reactions grade 3-4: 5.6%. Febrile neutropenia grade 3-4: 15.4%. Skin reactions grade 1-2: 74%; grade 3: 4.2%. Diarrhoea grade 1-2: 38%; grade 3: 11.3%. Pneumonitis grade 1-2: 26.8%; grade 3: 4.2%; grade 5: 1.4%. The median follow-up was 39 months for patients alive and the median survival was 17 months with a 1-, 2- and 3-year OS of 66%, 37% and 29% respectively. Until now local or regional failure has occurred in 20 patients and 22 patients have developed distant metastases. Weight loss, PS and stage were predictive for survival in univariate as well as in multivariate analysis. CONCLUSION Induction chemotherapy followed by concurrent cetuximab and RT to 68 Gy is clearly feasible with promising survival. TOXICITY, e.g. pneumonitis and esophagitis is low compared to most schedules with concurrent chemotherapy. This treatment strategy should be evaluated in a randomised manner vs. concurrent chemoradiotherapy to find out if it is a valid treatment option.
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Affiliation(s)
- A Hallqvist
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Sweden.
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Mercke C, Haugen H, Adell G, Costa-Svedman F, Nyman J, Wickart-Johansson G, Sjödin H. Toxicity and one-year tumor control with induction chemotherapy and bioradiotherapy for locally advanced unresectable head and neck cancer. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.5581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Nyman J, Rundby C, Svenarud P, van der Linden J. Does CO 2 flushing of the empty CPB circuit decrease the number of gaseous emboli in the prime? Perfusion 2009; 24:249-55. [DOI: 10.1177/0267659109350241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Twenty (20) CPB-circuits were randomized to a CO2 group or a control group. In the CO 2 group, each circuit was flushed with CO2 (10L/min) at the top of the venous reservoir for 5 minutes, after which priming fluid was added without interruption of the CO2 inflow. Control group circuits were not flushed and contained air. A perfusionist, blinded to the study, started the pump (5L/min), ventilated the oxygenator (3L O2/min), and knocked on the oxygenator 20 times during the first and 14th minutes. Arterial line microemboli counts were registered with a Doppler for 15 minutes. In both groups, the median number of microemboli was highest during the first minute, 380.5 (288.75/422.25, 25th/75th percentile) counts in the control group versus 264.5 (171.75/422.25) counts in the CO 2 group (p=0.01). Throughout the experiment, the median microembolic count minute by minute in the CO2 group remained lower (p≤ 0 .004) than in the control group. Knocking on the reservoir (14th minute) increased the microemboli counts in both groups (p<0.01). The median values during the 15th minute were 15.5 and 0.5 in the control and the CO2 groups, respectively, which were 9% (15.5/173) and 0.5% (0.5/87), respectively, of the values registered after 14 minutes. In conclusion, CO 2 flushing of the empty circuit decreases the number of gaseous emboli in the prime compared with a conventional circuit that contains air before being primed with fluid. Knocking of the oxygenator releases gaseous emboli and the duration of re-circulating the circuit with prime influences the number of microemboli.
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Affiliation(s)
- J. Nyman
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Department of Cardiothoracic Surgery and Anesthesiology, Karolinska University Hospital, Stockholm, Sweden,
| | - C. Rundby
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Department of Cardiothoracic Surgery and Anesthesiology, Karolinska University Hospital, Stockholm, Sweden
| | - P. Svenarud
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Department of Cardiothoracic Surgery and Anesthesiology, Karolinska University Hospital, Stockholm, Sweden
| | - J. van der Linden
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Department of Cardiothoracic Surgery and Anesthesiology, Karolinska University Hospital, Stockholm, Sweden
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Fesse P, Nyman J, Book M, Hermansson I, Johansson K, Ahlgren J, Turesson I. 2026 Response of melanocytes to low doses of fractionated radiotherapy. EJC Suppl 2009. [DOI: 10.1016/s1359-6349(09)70542-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Mercke C, Wickart-Johansson G, Sjödin H, Adell G, Nyman J, Haugen H. Upfront chemotherapy and accelerated radiotherapy with EGFR inhibition for locally advanced inoperable head and neck cancer. J Clin Oncol 2009. [DOI: 10.1200/jco.2009.27.15_suppl.6040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
6040 Background: Concomitant chemoradiotherapy (CT/RT) is the standard treatment for locally advanced head and neck squamous cell carcinoma. However, late toxicity is substantial.This phase II trial explores the feasibility and efficacy of combining neoadjuvant TPF and accelerated RT where the concomitant cytostatic component is replaced with cetuximab (E), a chimeric IgG1 mAb against EGFR. Methods: Patients (pts) had previously untreated stage III/IV M0,WHO 0–1, unresectable squamous cell carcinoma of the oral cavity, oropharynx, larynx, or hypopharynx and were scheduled for 2 cycles of TPF (docetaxel 75 mg/m2 and cisplatin 75 mg/m2 day 1 and 5-FU 1,000 mg/m2 96 hours CI) every 3 weeks followed by RT (68 Gy/4.5 weeks) with E given one week before (400 mg/m2) and weekly during RT (250 mg/m2). A brachytherapy boost of 8 Gy was given to pts with oral cavity or oropharyngeal tumours. Neck dissection was planned for pts with N2–3 and complete response (CR) at the primary tumour. Tumour response was evaluated according to RECIST with CT, MRI or PET/CT after CT and at 6 weeks follow up. Toxicity (CTC 3.0) and quality of life (EORTC QLQ 30) was registered during and after treatment. Results: From 070401 to 081115 68 pts were enrolled, 56 had stage IV disease (T4, n = 14, N3, n = 9). Median age 57, 60 males, 3 oral cavity, 44 oropharynx, 10 larynx, and 11 hypopharynx. 30 pts were followed beyond 6 weeks and evaluated for response and early toxicity: stage IV disease 24 (T4, n = 6, N3, n = 3), median age 60, 25 males, 18 oropharynx, 5 larynx, and 7 hypopharynx. Remissions after TPF/after RT: CR 1/10, PR 15/18, SD 14/1, and PD 1. TPF as prescribed: 28/30 (pat refusal 1, renal insuff 1, dose reduction 0/28); E as prescribed: 22/30 (dermatitis 4, hypersensitivity 3, liver tox 1). Vital tumour in resected specimen 0/13. Alive at follow-up 29/30 (1 local failure). Conclusions: TPF followed by RT concomitant with E is feasible with manageable toxicities. Dermatitis in the irradiated neck, at least with the present accelerated fractionation, is troublesome to some patients but does not interrupt treatment and heals rapidly. To dispose of feeding tubes after disappearance of acute mucosal reactions has not been a problem. Early survival results are promising. Toxicity and survival results will be updated. [Table: see text]
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Affiliation(s)
- C. Mercke
- Karolinska Institute, Stockholm, Sweden; Sahlgrenska University Hospital, Göteborg, Sweden
| | - G. Wickart-Johansson
- Karolinska Institute, Stockholm, Sweden; Sahlgrenska University Hospital, Göteborg, Sweden
| | - H. Sjödin
- Karolinska Institute, Stockholm, Sweden; Sahlgrenska University Hospital, Göteborg, Sweden
| | - G. Adell
- Karolinska Institute, Stockholm, Sweden; Sahlgrenska University Hospital, Göteborg, Sweden
| | - J. Nyman
- Karolinska Institute, Stockholm, Sweden; Sahlgrenska University Hospital, Göteborg, Sweden
| | - H. Haugen
- Karolinska Institute, Stockholm, Sweden; Sahlgrenska University Hospital, Göteborg, Sweden
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Abstract
Statins stimulate bone formation in vitro and in vivo and, when given in large doses or by prolonged infusions, stimulate biomechanical strength of murine long bones with healing fractures. However, administration of statins by large oral doses or prolonged infusions to a fracture site is not a feasible therapeutic approach to hasten healing of human fractures. We administered lovastatin in biodegradable polymer nanobeads of poly(lactic-co-glycolide acid) to determine if lovastatin delivered in low doses in nanoparticles of a therapeutically acceptable scaffold could increase rates of healing in a standard preclinical model of femoral fracture. We found that these nanobeads: (1) stimulated bone formation in vitro at 5 ng/mL, (2) increased rates of healing in femoral fractures when administered as a single injection into the fracture site, and (3) decreased cortical fracture gap at 4 weeks as assessed by microcomputed tomography. These preclinical results suggest that lovastatin administered in a nanobead preparation may be therapeutically useful in hastening repair of human fractures.
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Affiliation(s)
- I R Garrett
- OsteoScreen Ltd., 2040 Babcock Road, San Antonio, Texas 78023, USA
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Dixon N, Páli T, Kee TP, Ball S, Harrison MA, Findlay JBC, Nyman J, Väänänen K, Finbow ME, Marsh D. Interaction of spin-labeled inhibitors of the vacuolar H+-ATPase with the transmembrane Vo-sector. Biophys J 2007; 94:506-14. [PMID: 17872954 PMCID: PMC2157245 DOI: 10.1529/biophysj.107.111781] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The osteoclast variant of the vacuolar H(+)-ATPase (V-ATPase) is a potential therapeutic target for combating the excessive bone resorption that is involved in osteoporosis. The most potent in a series of synthetic inhibitors based on 5-(5,6-dichloro-2-indolyl)-2-methoxy-2,4-pentadienamide (INDOL0) has demonstrated specificity for the osteoclast enzyme, over other V-ATPases. Interaction of two nitroxide spin-labeled derivatives (INDOL6 and INDOL5) with the V-ATPase is studied here by using the transport-active 16-kDa proteolipid analog of subunit c from the hepatopancreas of Nephrops norvegicus, in conjunction with electron paramagnetic resonance (EPR) spectroscopy. Analogous experiments are also performed with vacuolar membranes from Saccharomyces cerevisiae, in which subunit c of the V-ATPase is replaced functionally by the Nephrops 16-kDa proteolipid. The INDOL5 derivative is designed to optimize detection of interaction with the V-ATPase by EPR. In membranous preparations of the Nephrops 16-kDa proteolipid, the EPR spectra of INDOL5 contain a motionally restricted component that arises from direct association of the indolyl inhibitor with the transmembrane domain of the proteolipid subunit c. A similar, but considerably smaller, motionally restricted population is detected in the EPR spectra of the INDOL6 derivative in vacuolar membranes, in addition to the larger population from INDOL6 in the fluid bilayer regions of the membrane. The potent classical V-ATPase inhibitor concanamycin A at high concentrations induces motional restriction of INDOL5, which masks the spectral effects of displacement at lower concentrations of concanamycin A. The INDOL6 derivative, which is closest to the parent INDOL0 inhibitor, displays limited subtype specificity for the osteoclast V-ATPase, with an IC(50) in the 10-nanomolar range.
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Affiliation(s)
- Neil Dixon
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, Göttingen, Germany; University of Leeds, School of Chemistry and School of Biochemistry and Molecular Biology, Leeds, United Kingdom; University of Turku, Institute of Biomedicine, Department of Anatomy, Turku, Finland; and Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Tibor Páli
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, Göttingen, Germany; University of Leeds, School of Chemistry and School of Biochemistry and Molecular Biology, Leeds, United Kingdom; University of Turku, Institute of Biomedicine, Department of Anatomy, Turku, Finland; and Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Terence P. Kee
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, Göttingen, Germany; University of Leeds, School of Chemistry and School of Biochemistry and Molecular Biology, Leeds, United Kingdom; University of Turku, Institute of Biomedicine, Department of Anatomy, Turku, Finland; and Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Stephen Ball
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, Göttingen, Germany; University of Leeds, School of Chemistry and School of Biochemistry and Molecular Biology, Leeds, United Kingdom; University of Turku, Institute of Biomedicine, Department of Anatomy, Turku, Finland; and Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Michael A. Harrison
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, Göttingen, Germany; University of Leeds, School of Chemistry and School of Biochemistry and Molecular Biology, Leeds, United Kingdom; University of Turku, Institute of Biomedicine, Department of Anatomy, Turku, Finland; and Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - John B. C. Findlay
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, Göttingen, Germany; University of Leeds, School of Chemistry and School of Biochemistry and Molecular Biology, Leeds, United Kingdom; University of Turku, Institute of Biomedicine, Department of Anatomy, Turku, Finland; and Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Jonas Nyman
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, Göttingen, Germany; University of Leeds, School of Chemistry and School of Biochemistry and Molecular Biology, Leeds, United Kingdom; University of Turku, Institute of Biomedicine, Department of Anatomy, Turku, Finland; and Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Kalervo Väänänen
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, Göttingen, Germany; University of Leeds, School of Chemistry and School of Biochemistry and Molecular Biology, Leeds, United Kingdom; University of Turku, Institute of Biomedicine, Department of Anatomy, Turku, Finland; and Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Malcolm E. Finbow
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, Göttingen, Germany; University of Leeds, School of Chemistry and School of Biochemistry and Molecular Biology, Leeds, United Kingdom; University of Turku, Institute of Biomedicine, Department of Anatomy, Turku, Finland; and Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Derek Marsh
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, Göttingen, Germany; University of Leeds, School of Chemistry and School of Biochemistry and Molecular Biology, Leeds, United Kingdom; University of Turku, Institute of Biomedicine, Department of Anatomy, Turku, Finland; and Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
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Ellison LM, Nyman J, Caldwell D, McBean A. 13: Cryosurgery as a Primary Treatment for Prostate Cancer among Medicare Beneficiaries. J Urol 2007. [DOI: 10.1016/s0022-5347(18)30278-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Gentile M, Yan T, Tiquia SM, Fields MW, Nyman J, Zhou J, Criddle CS. Stability in a denitrifying fluidized bed reactor. Microb Ecol 2006; 52:311-21. [PMID: 16874554 DOI: 10.1007/s00248-006-9024-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Accepted: 03/09/2005] [Indexed: 05/11/2023]
Abstract
This study evaluates changes in the microbial community structure and function of a pilot-scale denitrifying fluidized bed reactor during periods of constant operating conditions and periods of perturbation. The perturbations consisted of a shutdown period without feed, two disturbances in which biofilms were mechanically sheared from carrier particles, and a twofold step increase in feed nitrate concentration. In the absence of perturbations, nitrate removal was stable and consistently greater than 99%. The structure and dynamics of the microbial community were studied using cloning and sequencing techniques and terminal restriction fragment length polymorphism (T-RFLP) of the SSU rRNA gene. Under unperturbed operating conditions, stable function was accompanied by high constancy and low variability of community structure with the majority of terminal restriction fragments (T-RFs) appearing throughout operation at consistent relative abundances. Several of the consistently present T-RFs correlated with clone sequences closely related to Acidovorax (98% similarity), Dechloromonas (99% similarity), and Zoogloea (98% similarity), genera recently identified by molecular analyses of similar systems. Significant changes in community structure and function were not observed after the shutdown period. In contrast, following the increase in loading rate and the mechanical disturbances, new T-RFs appeared. After both mechanical disturbances, function and community structure recovered. However, function was much more resilient than community structure. The similarity of response to the mechanical disturbances despite differences in community structure and operating conditions suggests that flexible community structure and potentially the activity of minor members under nonperturbation conditions promotes system recovery.
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Affiliation(s)
- M Gentile
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
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Wagenius G, Brodin O, Nyman J, Greim G, Hillerdal G, Riska H, Sundström S, Grönberg B, Wang M, Garmo H. Radiotherapy vs. temozolomide in the treatment of patients with lung cancer and brain metastases: A nordic randomized phase II study. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.7136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
7136 Background: Metastasis to the brain is the most common intracranial tumour and 20–40% of all cancer patients will develop brain metastases. Lung cancer is the most common primary tumour and compose of 40%-50% of all brain metasases. As the survival in many malignancies increases, brain metastases will be an increasing problem. It is therefore important to find new treatment options. The aim of this study was primary to study quality of life and to compare radiotherapy and Themozolomide in that context. Methods: Inclusion criterias were confirmed small cell or non-small cell lung cancer, multiple brain metastases, PS 0–2, no previous radiotherapy to the brain. Previous chemotherapy was allowed. Patients were randomized to arm A (radiotherapy 30 Gy over 10 fractions) or arm B (Temozolomide 200 mg/m2 day 1–5, new cycle on day 29). Quality of life (QoL) was measured with a general cancer module, EORTC QLQ-C30, and a brain cancer specific module, BCM20. The primary end-point was the proportion of patients in each treatment arm with maintained or better QoL score at 8 weeks compared to the base line evaluation. In this first analysis exclusion rate from the study at 8 weeks was used as a surrogate end-point. Results: 208 patients were included, 104 in arm A and 104 in arm B. 36 (17%) squamous cell, 97 (47%) adenocarcinomas, 10 (5%) large cell, 23 (11%) undifferentiated and 42 (20%) small-cell lung cancer were included. 93 (45%) patients were chemonaive. At 8 weeks, 79 patients were excluded from the study, 51 (49%) from the temozolomide arm and 28 (27%) from the radiotherapy arm. 53% of the patients with squamous cell carcinoma were excluded compared to 40% of small cell lung cancer, 33% of adenocarcinomas and 27% of large cell carcinomas. The exclusion rate at 8 weeks was higher among patients with symptoms at randomization compared to patients without symptoms. There were no difference in exclusion rate when comparing number or size of the metastases. Conclusion: The exclusion rate at 8 weeks was higher in the temozolomide arm compared to the radiotherapy arm. Histopathology and symptoms at randomization seems to be factors influencing the exclusion rate whereas number or size of metastases does not. Survival and quality of life data will be presented at the meeting. No significant financial relationships to disclose.
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Affiliation(s)
- G. Wagenius
- Department of Oncology, Uppsala, Sweden; Department of Oncology, Stockholm, Sweden; Department of Oncology, Gothenburg, Sweden; Department of Oncology, Borås, Sweden; Department of Lung Medicine, Stockholm, Sweden; Department of Lung Medicine, Helsinki, Finland; Department of Oncology, Trondheim, Norway; Department of Oncology, Oslo, Norway; Regional Oncologic Center, Uppsala, Sweden
| | - O. Brodin
- Department of Oncology, Uppsala, Sweden; Department of Oncology, Stockholm, Sweden; Department of Oncology, Gothenburg, Sweden; Department of Oncology, Borås, Sweden; Department of Lung Medicine, Stockholm, Sweden; Department of Lung Medicine, Helsinki, Finland; Department of Oncology, Trondheim, Norway; Department of Oncology, Oslo, Norway; Regional Oncologic Center, Uppsala, Sweden
| | - J. Nyman
- Department of Oncology, Uppsala, Sweden; Department of Oncology, Stockholm, Sweden; Department of Oncology, Gothenburg, Sweden; Department of Oncology, Borås, Sweden; Department of Lung Medicine, Stockholm, Sweden; Department of Lung Medicine, Helsinki, Finland; Department of Oncology, Trondheim, Norway; Department of Oncology, Oslo, Norway; Regional Oncologic Center, Uppsala, Sweden
| | - G. Greim
- Department of Oncology, Uppsala, Sweden; Department of Oncology, Stockholm, Sweden; Department of Oncology, Gothenburg, Sweden; Department of Oncology, Borås, Sweden; Department of Lung Medicine, Stockholm, Sweden; Department of Lung Medicine, Helsinki, Finland; Department of Oncology, Trondheim, Norway; Department of Oncology, Oslo, Norway; Regional Oncologic Center, Uppsala, Sweden
| | - G. Hillerdal
- Department of Oncology, Uppsala, Sweden; Department of Oncology, Stockholm, Sweden; Department of Oncology, Gothenburg, Sweden; Department of Oncology, Borås, Sweden; Department of Lung Medicine, Stockholm, Sweden; Department of Lung Medicine, Helsinki, Finland; Department of Oncology, Trondheim, Norway; Department of Oncology, Oslo, Norway; Regional Oncologic Center, Uppsala, Sweden
| | - H. Riska
- Department of Oncology, Uppsala, Sweden; Department of Oncology, Stockholm, Sweden; Department of Oncology, Gothenburg, Sweden; Department of Oncology, Borås, Sweden; Department of Lung Medicine, Stockholm, Sweden; Department of Lung Medicine, Helsinki, Finland; Department of Oncology, Trondheim, Norway; Department of Oncology, Oslo, Norway; Regional Oncologic Center, Uppsala, Sweden
| | - S. Sundström
- Department of Oncology, Uppsala, Sweden; Department of Oncology, Stockholm, Sweden; Department of Oncology, Gothenburg, Sweden; Department of Oncology, Borås, Sweden; Department of Lung Medicine, Stockholm, Sweden; Department of Lung Medicine, Helsinki, Finland; Department of Oncology, Trondheim, Norway; Department of Oncology, Oslo, Norway; Regional Oncologic Center, Uppsala, Sweden
| | - B. Grönberg
- Department of Oncology, Uppsala, Sweden; Department of Oncology, Stockholm, Sweden; Department of Oncology, Gothenburg, Sweden; Department of Oncology, Borås, Sweden; Department of Lung Medicine, Stockholm, Sweden; Department of Lung Medicine, Helsinki, Finland; Department of Oncology, Trondheim, Norway; Department of Oncology, Oslo, Norway; Regional Oncologic Center, Uppsala, Sweden
| | - M. Wang
- Department of Oncology, Uppsala, Sweden; Department of Oncology, Stockholm, Sweden; Department of Oncology, Gothenburg, Sweden; Department of Oncology, Borås, Sweden; Department of Lung Medicine, Stockholm, Sweden; Department of Lung Medicine, Helsinki, Finland; Department of Oncology, Trondheim, Norway; Department of Oncology, Oslo, Norway; Regional Oncologic Center, Uppsala, Sweden
| | - H. Garmo
- Department of Oncology, Uppsala, Sweden; Department of Oncology, Stockholm, Sweden; Department of Oncology, Gothenburg, Sweden; Department of Oncology, Borås, Sweden; Department of Lung Medicine, Stockholm, Sweden; Department of Lung Medicine, Helsinki, Finland; Department of Oncology, Trondheim, Norway; Department of Oncology, Oslo, Norway; Regional Oncologic Center, Uppsala, Sweden
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Hu Y, Nyman J, Muhonen P, Väänänen HK, Laitala-Leinonen T. Inhibition of the osteoclast V-ATPase by small interfering RNAs. FEBS Lett 2005; 579:4937-42. [PMID: 16115623 DOI: 10.1016/j.febslet.2005.07.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 07/19/2005] [Accepted: 07/25/2005] [Indexed: 10/25/2022]
Abstract
The multisubunit enzyme V-ATPase harbours isoforms of individual subunits. a3 is one of four 116 kDa subunit a isoforms, and it is crucial for bone resorption. We used small interfering RNA (siRNA) molecules to knock down a3 in rat osteoclast cultures. Labeled siRNA-molecules entered osteoclasts via endocytosis and knocked down the a3 mRNA. Bone resorption was decreased in siRNA-treated samples due to decreased acidification and osteoclast inactivation. Expression of a1 did not respond to decreased a3 levels, suggesting that a1 does not compensate for a3 in osteoclast cultures. Subunit a3 is thus an interesting target for novel nucleic acid therapy.
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Affiliation(s)
- Yingwei Hu
- Bone Biology Research Consortium, Department of Anatomy, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FIN-20520 Turku, Finland
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Bergquist H, Wenger U, Johnsson E, Nyman J, Ejnell H, Hammerlid E, Lundell L, Ruth M. Stent insertion or endoluminal brachytherapy as palliation of patients with advanced cancer of the esophagus and gastroesophageal junction. Results of a randomized, controlled clinical trial. Dis Esophagus 2005; 18:131-9. [PMID: 16045572 DOI: 10.1111/j.1442-2050.2005.00467.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Esophageal cancer often presents as advanced stage disease with a dismal prognosis, with only 10-15% of patients surviving 5 years. Therefore, in a large proportion of patients, palliative treatment is the only option available. The aim of this study was to prospectively compare the palliative effect of self-expandable stent placement with that of endoluminal brachytherapy regarding the effect on quality of life and on specific symptoms. Sixty-five patients with advanced cancer of the esophagus or gastroesophageal junction were randomized to treatment with either an Ultraflex expandable stent or high-dose-rate endoluminal brachytherapy with 7 Gy x 3 given in 2-4 weeks. Clinical assessment and health-related quality of life (HRQL) were measured at inclusion and 1, 3, 6, 9 and 12 months later. The HRQL was measured with standardized questionnaires (European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core 30, European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Oesophageal Module and Hospital Anxiety and Depression Scale). Twenty-eight patients completed the stent treatment and 24 patients the brachytherapy. The group of patients treated with stent reported significantly better HRQL scores for dysphagia (P < 0.05) at the 1-month follow-up, but most other HRQL scores, including functioning and symptom scales, deteriorated. Among brachytherapy-treated patients, improvement was found for the dysphagia-related scores at the 3-months follow-up, whereas other significant changes of scores were few. The median survival time was comparable in the two groups (around 120 days). In conclusion, insertion of self-expandable metal stents offered a more instant relief of dysphagia compared to endoluminal brachytherapy, but HRQL was more stable in the brachytherapy group.
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Affiliation(s)
- H Bergquist
- Department of Otorhinolaryngology, Sahlgrenska University Hospital, Göteborg, Sweden.
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Hallqvist A, Nyman J, Rylander H. P-767 Is the total dose of importance in thoracic radiotherapy ofsmall-cell lung cancer (SCLC) limited disease (LD)? Lung Cancer 2005. [DOI: 10.1016/s0169-5002(05)81260-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Hopewell JW, Nyman J, Turesson I. Time factor for acute tissue reactions following fractionated irradiation: a balance between repopulation and enhanced radiosensitivity. Int J Radiat Biol 2003; 79:513-24. [PMID: 14530160 DOI: 10.1080/09553000310001600907] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Experimental data for acute radiation-induced skin reactions are reviewed. These show that for dose fractionation schedules with gaps, repopulation is initiated after a lag period. After this lag period, the isoeffective dose for a given level of skin reaction first increases rapidly, but then slows. The timing of the lag period is related to the total turnover time of the tissue under investigation and, for example, is shorter in rodent skin than in pig or human skin. At the point when accelerated repopulation is initiated, there is a major shortening of the turnover time of the target cell population. At this time, there is evidence, for a short period, for an increase in radiosensitivity of the surviving stem cells in a number of acutely responding normal tissues. This effect is clearly illustrated by the results of experiments using sequential dose fractionation schedules. Prolongation of the schedule from 'short' to schedules that include irradiation over the period when the cell turnover is accelerated is associated with a marked increase in tissue radiosensitivity. Clinically, this is best illustrated by a comparison of the effects of accelerated fractionation schedules, involving multiple fractions/day, with daily fractionation schedules. The increase in radiosensitivity produced by the prolongation of the treatment from 2 to 4-5 weeks was equivalent to > or =1 Gy day(-1). Comparable findings were obtained from animal studies. In the oral mucosa of mice, the initiation of accelerated cell proliferation in surviving cells is associated with the loss of dose sparing by subsequent dose fractionation due to the loss of the capacity to repair sublethal damage. Studies in pig and human skin have indicated that increased radiosensitivity is associated with a loss of cells in the G1 phase of the cell cycle. A collation of these two sets of findings suggests that the repair of sublethal damage takes place over this phase of the cell cycle. One clinical implication of these findings is that the alpha/beta ratio for acute skin reaction changes with the length of the overall treatment time; it is approximately 4.0 Gy for 'short' fractionation schedules that avoid any shortening of the cell cycle time. This increases to 11.2-13.3 Gy for schedules given in 3-4 weeks and to approximately 35 Gy for schedules given in 5-6 weeks. Results for pig skin were in total agreement with those for human skin.
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Affiliation(s)
- J W Hopewell
- Department of Clinical Oncology, The Churchill Hospital, Oxford OX3 7LJ, UK.
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Turesson I, Bernefors R, Book M, Flogegård M, Hermansson I, Johansson KA, Lindh A, Sigurdardottir S, Thunberg U, Nyman J. Normal tissue response to low doses of radiotherapy assessed by molecular markers--a study of skin in patients treated for prostate cancer. Acta Oncol 2002; 40:941-51. [PMID: 11845959 DOI: 10.1080/02841860152708224] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The aim of this study was to evaluate normal tissue response by molecular markers to multifraction low doses of ionizing radiation, with the focus on changes in repopulation, estimated using Ki-67 as the proliferation marker, and on expressions of the p53 and p21 proteins, identified as key proteins in the DNA damage checkpoint. Repeated skin biopsies were taken from patients treated for prostate cancer with radiotherapy. The expressions of Ki-67, p53 and p21 of the keratinocytes in the basal cell layer of the epidermis were quantified immunohistochemically. The dose to the basal layer was 1.1 Gy per fraction, given five times per week for seven weeks. The indices of the three markers were determined over the whole period. A significant suppression of the Ki-67 index was observed during the first weeks, followed by a significant gradual increase in the Ki-67 index over the last weeks. The p53 and p21 protein levels were almost zero in the unirradiated skin. Upon irradiation, both the p53 and p21 index increased in a pattern very congruent to the Ki-67 index. In conclusion, daily fractions of about 1 Gy to the skin resulted in, for the keratinocytes in the basal layer, a cell growth arrest for a couple of weeks and a subsequent acceleration in repopulation during the following weeks of irradiation. The present findings also provided novel insights into the role of the p53/p21 pathway in the response of a normal epithelium to ionizing radiation as it is applied in radiotherapy.
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Affiliation(s)
- I Turesson
- Department of Oncology, Radiology and Clinical Immunology, Uppsala University Hospital, Sweden
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Stalfors J, Edström S, Björk-Eriksson T, Mercke C, Nyman J, Westin T. Accuracy of tele-oncology compared with face-to-face consultation in head and neck cancer case conferences. J Telemed Telecare 2002; 7:338-43. [PMID: 11747635 DOI: 10.1258/1357633011936976] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Telemedicine was introduced for weekly tumour case conferences between Sahlgrenska University Hospital and two district hospitals in Sweden. The accuracy of tele-oncology was determined using simulated telemedicine consultations, in which all the material relating to each case was presented but without the patient in person. The people attending the conference were asked to determine the tumour ('TNM') classification and treatment. The patient was then presented in person, to give the audience the opportunity to ask questions and perform a physical examination. Then a new discussion regarding the tumour classification and the treatment plan took place, and the consensus was recorded. Of the 98 consecutive patients studied in this way, 80 could be evaluated by both techniques. Of these 80, 73 (91%) had the same classification and treatment plan in the telemedicine simulation as in the subsequent face-to-face consultation. In four cases the TNM classification was changed and for three patients the treatment plan was altered. The specialists also had to state their degree of confidence in the tele-oncology decisions. When they recorded uncertainty about their decision, it was generally because they wanted to palpate the tumour. In five of the seven patients with a different outcome, the clinical evaluation was stated to be dubious or not possible. The results show that telemedicine can be used safely for the management of head and neck cancers.
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Affiliation(s)
- J Stalfors
- Department of Otolaryngology, Head and Neck Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden.
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Abstract
The purpose of this study is to describe the basic cardiac life-support (BLS) skills of nurses and nursing students in southern Finland and Hungary, and to assess the influence of resuscitation teaching and other group characteristics on performance. The data for the study were collected in the spring and autumn of 1997. The study group consisted of 75 nurses from Helsinki University Central Hospital's medical outcome unit, 188 final term students in four nursing institutes in Uusimaa county and 35 final term students in a Hungarian institute of nursing. A total of 298 people (34 men and 264 women) participated in the study. Background information was collected using a structured questionnaire devised specifically for this study. Resuscitation skills were measured using the Skillmeter Anne manikin. The manikin was placed supine during the test. After completing the questionnaire, every participant attempted resuscitation on the manikin - which was supplied with a printer - for 4 min. The results were printed out and attached to the questionnaires. The data were analysed using two-way frequency tables and logistic regression. Statistical differences were calculated using the chi(2)-test. The results showed that 53% of the participants had studied resuscitation during the last 6 months, but 7% had never participated in resuscitation teaching. Before testing, 55% of the participants estimated that their resuscitation skills were good. The results showed that 36% first assessed the patient's response, 67% opened the airway but only 3% determined pulselessness before starting to resuscitate. Twenty-one percent of the participants compressed correctly for at least half of the test and 33% ventilated correctly at least half of the time. Logistic regression showed that the best predictors for good response assessment skills went to those who were nursing students who had studied resuscitation skills sometime during the previous 6 months. The best predictor of the skill to open the airway was a positive attitude towards personal cardiopulmonary resuscitation (CPR) skills, i.e. self-confidence. The predictor for adequate skills in artificial ventilation was that they belonged in the group of nursing students who had benefited from recent resuscitation training (<6 months). In conclusion, the skills of the participants of the study can not be considered adequate in terms of an adequate and prompt assessment of the need for resuscitation, and a 50% success rate in artificial ventilation and chest compression.
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Affiliation(s)
- J Nyman
- Helsinki Polytechnic, Tukholmankatu 10, 00290, Helsinki, Finland.
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