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Lima FA, Otte F, Vakili M, Ardana-Lamas F, Biednov M, Dall’Antonia F, Frankenberger P, Gawelda W, Gelisio L, Han H, Huang X, Jiang Y, Kloos M, Kluyver T, Knoll M, Kubicek K, Bermudez Macias IJ, Schulz J, Turkot O, Uemura Y, Valerio J, Wang H, Yousef H, Zalden P, Khakhulin D, Bressler C, Milne C. Experimental capabilities for liquid jet samples at sub-MHz rates at the FXE Instrument at European XFEL. J Synchrotron Radiat 2023; 30:1168-1182. [PMID: 37860937 PMCID: PMC10624029 DOI: 10.1107/s1600577523008159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
The Femtosecond X-ray Experiments (FXE) instrument at the European X-ray Free-Electron Laser (EuXFEL) provides an optimized platform for investigations of ultrafast physical, chemical and biological processes. It operates in the energy range 4.7-20 keV accommodating flexible and versatile environments for a wide range of samples using diverse ultrafast X-ray spectroscopic, scattering and diffraction techniques. FXE is particularly suitable for experiments taking advantage of the sub-MHz repetition rates provided by the EuXFEL. In this paper a dedicated setup for studies on ultrafast biological and chemical dynamics in solution phase at sub-MHz rates at FXE is presented. Particular emphasis on the different liquid jet sample delivery options and their performance is given. Our portfolio of high-speed jets compatible with sub-MHz experiments includes cylindrical jets, gas dynamic virtual nozzles and flat jets. The capability to perform multi-color X-ray emission spectroscopy (XES) experiments is illustrated by a set of measurements using the dispersive X-ray spectrometer in von Hamos geometry. Static XES data collected using a multi-crystal scanning Johann-type spectrometer are also presented. A few examples of experimental results on ultrafast time-resolved X-ray emission spectroscopy and wide-angle X-ray scattering at sub-MHz pulse repetition rates are given.
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Affiliation(s)
- F. A. Lima
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - F. Otte
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Fakultät für Physik, Technical University Dortmund, Dortmund, Germany
| | - M. Vakili
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - M. Biednov
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - W. Gawelda
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - L. Gelisio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - X. Huang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Jiang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - T. Kluyver
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - M. Knoll
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - K. Kubicek
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
- Institut für Experimentalphysik, Universität Hamburg, 22607 Hamburg, Germany
| | | | - J. Schulz
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - O. Turkot
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Y. Uemura
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - J. Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Wang
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - H. Yousef
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - P. Zalden
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - D. Khakhulin
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - C. Bressler
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- The Hamburg Centre for Ultrafast Imaging, 22761 Hamburg, Germany
- Institut für Experimentalphysik, Universität Hamburg, 22607 Hamburg, Germany
| | - C. Milne
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
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2
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Roder AE, Johnson KEE, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Chung M, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lässig M, Luksza M, Das S, Gresham D, Ghedin E. Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data. mBio 2023; 14:e0104623. [PMID: 37389439 PMCID: PMC10470513 DOI: 10.1128/mbio.01046-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 07/01/2023] Open
Abstract
High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant-calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller and use of replicate sequencing have the most significant impact on single-nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false-negative rates. When replicates are not available, using a combination of multiple callers with more stringent cutoffs is recommended. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intra-host viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intra-host variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host cell, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus nor strongly beneficial can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in the inclusion of false-positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant-calling tools. We used simulated and synthetic data to test their performance against a true set of variants and then used these studies to inform variant identification in data from SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.
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Affiliation(s)
- A. E. Roder
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - K. E. E. Johnson
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - M. Knoll
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - M. Khalfan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - B. Wang
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - S. Schultz-Cherry
- Department of Infectious Diseases, St Jude Children Research Hospital, Memphis, Tennessee, USA
| | - S. Banakis
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - A. Kreitman
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - C. Mederos
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - J.-H. Youn
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - R. Mercado
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - W. Wang
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - M. Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
| | - D. Ruchnewitz
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - M. I. Samanovic
- Department of Medicine, New York University Langone Vaccine Center, New York, New York, USA
| | - M. J. Mulligan
- Department of Medicine, New York University Langone Vaccine Center, New York, New York, USA
| | - M. Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - M. Luksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - S. Das
- Department of Laboratory Medicine, NIH, Bethesda, Maryland, USA
| | - D. Gresham
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - E. Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, DIR, NIAID, NIH, Bethesda, Maryland, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
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Davis M, Voss K, Turnbull JB, Gustin AT, Knoll M, Muruato A, Hsiang TY, Dinnon KH, Leist SR, Nickel K, Baric RS, Ladiges W, Akilesh S, Smith KD, Gale M. A C57BL/6 Mouse model of SARS-CoV-2 infection recapitulates age- and sex-based differences in human COVID-19 disease and recovery. Res Sq 2022:rs.3.rs-2194450. [PMID: 36415465 PMCID: PMC9681052 DOI: 10.21203/rs.3.rs-2194450/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We present a comprehensive analysis of SARS-CoV-2 infection and recovery in wild type C57BL/6 mice, demonstrating that this is an ideal model of infection and recovery that accurately phenocopies acute human disease arising from the ancestral SARS-CoV-2. Disease severity and infection kinetics are age- and sex-dependent, as has been reported for humans, with older mice and males in particular exhibiting decreased viral clearance and increased mortality. We identified key parallels with human pathology, including intense virus positivity in bronchial epithelial cells, wide-spread alveolar involvement, recruitment of immune cells to the infected lungs, and acute bronchial epithelial cell death. Moreover, older animals experienced increased virus persistence, delayed dispersal of immune cells into lung parenchyma, and morphologic evidence of tissue damage and inflammation. Parallel analysis of SCID mice revealed that the adaptive immune response was not required for recovery from COVID disease symptoms nor early phase clearance of virus but was required for efficient clearance of virus at later stages of infection. Finally, transcriptional analyses indicated that induction and duration of key innate immune gene programs may explain differences in age-dependent disease severity. Importantly, these data demonstrate that SARS-CoV-2-mediated disease in C57BL/6 mice accurately phenocopies human disease across ages and establishes a platform for future therapeutic and genetic screens for not just SARS-CoV-2 but also novel coronaviruses that have yet to emerge.
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4
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Salome P, Walz D, Sforazzini F, Kudak A, Dostal M, Regnery S, Schlamp K, Thomas M, Herth F, Jäkel O, Heußel C, Hoerner-Rieber J, Debus J, Knoll M, Abdollahi A. Multi-Omics Classifier of Tumor Recurrence vs. Radiation-Induced Lung Fibrosis in NSCLC Patients Treated with SBRT. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1542] [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: 11/30/2022]
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5
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Vinci D, Jiang Y, Schubert R, Zalden P, Khakhulin D, Frankenberger P, Alves Lima F, Ardana-Lamas F, Deiter C, Biednov M, Huang X, Knoll M, Jimenez D, Otte F, Paul Dutta S, Wang H, Yousef H, Milne C. Ultrafast X-ray diffraction and scattering on the femtosecond X-ray experiment (FXE) instrument at the European XFEL: present status and future perspectives. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322090039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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6
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Roder AE, Johnson KEE, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lassig M, Łuksza M, Das S, Gresham D, Ghedin E. Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data. bioRxiv 2022:2021.05.05.442873. [PMID: 36656775 PMCID: PMC9836620 DOI: 10.1101/2021.05.05.442873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller, and use of replicate sequencing have the most significant impact on single nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false negative rates. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intrahost viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intrahost variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus, nor strongly beneficial, can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in inclusion of false positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant calling tools. We used simulated and synthetic data to test their performance against a true set of variants, and then used these studies to inform variant identification in data from clinical SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.
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7
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Knoll M, Gerhardter H, Tomazic P, Hochenauer C. Investigations of lateral particle distribution for spherical and highly non-spherical particles by means of steady-state/transient RANS and LES simulations. POWDER TECHNOL 2021. [DOI: 10.1016/j.powtec.2020.10.029] [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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8
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Knoll M, Balermpas P, von der Grün J, Tawk B, Adeberg S, Tinhofer I, Budach V, Linge A, Krause M, Stuschke M, Grosu A, Zips D, Combs S, Belka C, Kriegsmann M, Weichert W, Baumann M, Roedel C, Debus J, Abdollahi A. Superior Prognostic Performance of an Immunohistochemistry Trained DNA-Methylation Based PD-L1 Score in Patients with HNSCC Treated with Radiochemotherapy: A Multicenter Study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG). Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.925] [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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9
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Klein C, Schlegel J, Knoll M, Dokic I, Moustafa M, Mairani A, Brons S, Zimmermann A, Zenke F, Blaukat A, Debus J, Abdollahi A. Trimodal Therapy Consisting of DNA-PK Inhibition, PD-L1 Immune Checkpoint Blockade and Radiotherapy with Carbon Ions. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.916] [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: 11/17/2022]
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10
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Furkel J, Hasheminasab S, Moustafa M, Kriegsmann K, Schlegel J, Zhou C, Kriegsmann M, Debus J, Knoll M, Abdollahi A. Single Cell Transcriptomics Based Deconvolution Of Radiation Induced Lung Fibrosis (RILF) Model. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1713] [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: 11/29/2022]
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11
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Sforazzini F, Salome P, Kudak A, Ulrich M, Bougatf N, Debus J, Knoll M, Abdollahi A. pyCuRT: An Automated Data Curation Workflow for Radiotherapy Big Data Analysis using Pythons’ NyPipe. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.221] [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: 11/26/2022]
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12
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13
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Breitegger P, Schweighofer B, Wegleiter H, Knoll M, Lang B, Bergmann A. Towards low-cost QEPAS sensors for nitrogen dioxide detection. Photoacoustics 2020; 18:100169. [PMID: 32309133 PMCID: PMC7155225 DOI: 10.1016/j.pacs.2020.100169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 01/07/2020] [Accepted: 01/14/2020] [Indexed: 05/09/2023]
Abstract
Increasing awareness of the adverse health effects of air pollution leads to a demand of low-cost sensors for the measurement of pollutants such as NO2. However, commercially available low-cost sensors lack accuracy and long-term stability, and suffer from cross-sensitivity to other gases. These drawbacks can be overcome by the method of quartz-enhanced photoacoustic spectroscopy (QEPAS). In QEPAS modulated light is absorbed by the NO2 molecules, which results in the production of a sound wave. The sound wave is detected by resonance of a quartz tuning fork, which results in a measurable electric signal. Due to the small size of the tuning forks, the gas sensing element can be smaller than 1 cm3. We present the first bare fork QEPAS setup for the ppb-level detection of NO2, which is ideally suited for environmental trace gas detection without the need of using micro-resonators. Micro-resonators are commonly used to amplify photoacoustic signals. However, micro-resonators have different dependencies on environmental conditions than tuning forks, which makes them difficult to operate in changing conditions. In contrast, our bare fork QEPAS setup is more robust and easily adopted by the use of a low-cost temperature and humidity sensor. By using acoustic filters the integration time could be increased to offer higher sensitivity at a continuous flow rate of 200 std cm3 min-1. The 1σ noise equivalent concentration is determined to 21 ppb NO2 in synthetic air for 120 s measurement time, allowing detection which satisfies international health and safety standards thresholds.
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Affiliation(s)
- P Breitegger
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
| | - B Schweighofer
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
| | - H Wegleiter
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
| | - M Knoll
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
| | - B Lang
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
| | - A Bergmann
- Institute of Electrical Measurement and Sensor Systems, Graz University of Technology, 8010 Graz, Austria
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Rathe JA, Gale Jr. M, Knoll M. 2608. Restriction of Rhinovirus Infection Depends on Virus Sensing and Early IFN Induction. Open Forum Infect Dis 2019. [PMCID: PMC6810392 DOI: 10.1093/ofid/ofz360.2286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Methods Results Conclusion Disclosures
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Affiliation(s)
- Jennifer A Rathe
- University of Washington, Seattle Children’s Hospital, Seattle, Washington
| | | | - Megan Knoll
- University of Washington, Seattle, Washington
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15
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Tasca GA, Angus L, Bonli R, Drapeau M, Fitzpatrick M, Hunsley J, Knoll M. Outcome and progress monitoring in psychotherapy: Report of a Canadian Psychological Association Task Force. ACTA ACUST UNITED AC 2019. [DOI: 10.1037/cap0000181] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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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16
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Knoll M, Gerhardter H, Prieler R, Mühlböck M, Tomazic P, Hochenauer C. Particle classification and drag coefficients of irregularly-shaped combustion residues with various size and shape. POWDER TECHNOL 2019. [DOI: 10.1016/j.powtec.2019.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Gerhardter H, Prieler R, Schluckner C, Knoll M, Hochenauer C, Mühlböck M, Tomazic P, Schroettner H. Modelling convective heat transfer to non-spherical particles. POWDER TECHNOL 2019. [DOI: 10.1016/j.powtec.2018.11.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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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18
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Chow KT, Driscoll C, Loo YM, Knoll M, Gale M. IRF5 regulates unique subset of genes in dendritic cells during West Nile virus infection. J Leukoc Biol 2018; 105:411-425. [PMID: 30457675 DOI: 10.1002/jlb.ma0318-136rrr] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/14/2018] [Accepted: 10/17/2018] [Indexed: 01/08/2023] Open
Abstract
Pathogen recognition receptor (PRR) signaling is critical for triggering innate immune activation and the expression of immune response genes, including genes that impart restriction against virus replication. RIG-I-like receptors and TLRs are PRRs that signal immune activation and drive the expression of antiviral genes and the production of type I IFN leading to induction of IFN-stimulated genes, in part through the interferon regulatory factor (IRF) family of transcription factors. Previous studies with West Nile virus (WNV) showed that IRF3 and IRF7 regulate IFN expression in fibroblasts and neurons, whereas macrophages and dendritic cells (DCs) retained the ability to induce IFN-β in the absence of IRF3 and IRF7 in a manner implicating IRF5 in PRR signaling actions. Here we assessed the contribution of IRF5 to immune gene induction in response to WNV infection in DCs. We examined IRF5-dependent gene expression and found that loss of IRF5 in mice resulted in modest and subtle changes in the expression of WNV-regulated genes. Anti-IRF5 chromatin immunoprecipitation with next-generation sequencing of genomic DNA coupled with mRNA analysis revealed unique IRF5 binding motifs within the mouse genome that are distinct from the canonical IRF binding motif and that link with IRF5-target gene expression. Using integrative bioinformatics analyses, we identified new IRF5 primary target genes in DCs in response to virus infection. This study provides novel insights into the distinct and unique innate immune and immune gene regulatory program directed by IRF5.
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Affiliation(s)
- Kwan T Chow
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA.,Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Connor Driscoll
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
| | - Yueh-Ming Loo
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
| | - Megan Knoll
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
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19
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Chow KT, Wilkins C, Narita M, Green R, Knoll M, Loo YM, Gale M. Differential and Overlapping Immune Programs Regulated by IRF3 and IRF5 in Plasmacytoid Dendritic Cells. J Immunol 2018; 201:3036-3050. [PMID: 30297339 DOI: 10.4049/jimmunol.1800221] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/13/2018] [Indexed: 01/20/2023]
Abstract
We examined the signaling pathways and cell type-specific responses of IFN regulatory factor (IRF) 5, an immune-regulatory transcription factor. We show that the protein kinases IKKα, IKKβ, IKKε, and TANK-binding kinase 1 each confer IRF5 phosphorylation/dimerization, thus extending the family of IRF5 activator kinases. Among primary human immune cell subsets, we found that IRF5 is most abundant in plasmacytoid dendritic cells (pDCs). Flow cytometric cell imaging revealed that IRF5 is specifically activated by endosomal TLR signaling. Comparative analyses revealed that IRF3 is activated in pDCs uniquely through RIG-I-like receptor (RLR) signaling. Transcriptomic analyses of pDCs show that the partitioning of TLR7/IRF5 and RLR/IRF3 pathways confers differential gene expression and immune cytokine production in pDCs, linking IRF5 with immune regulatory and proinflammatory gene expression. Thus, TLR7/IRF5 and RLR-IRF3 partitioning serves to polarize pDC response outcome. Strategies to differentially engage IRF signaling pathways should be considered in the design of immunotherapeutic approaches to modulate or polarize the immune response for specific outcome.
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Affiliation(s)
- Kwan T Chow
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109.,Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region; and
| | - Courtney Wilkins
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109
| | - Miwako Narita
- Laboratory of Hematology and Oncology, Graduate School of Health Sciences, Niigata University, Niigata, Niigata Prefecture 950-2181, Japan
| | - Richard Green
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109
| | - Megan Knoll
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109
| | - Yueh-Ming Loo
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109;
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109;
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Gerhardter H, Prieler R, Mayr B, Knoll M, Mühlböck M, Tomazic P, Hochenauer C. Evaluation of drag models for particles and powders with non-uniform size and shape. POWDER TECHNOL 2018. [DOI: 10.1016/j.powtec.2018.02.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nowrouzi A, Sertorio M, Akbarpour M, Kuhar M, Golestaneh AF, Schwager C, Perentesis J, Zheng Y, Debus J, Wells S, Wells J, Abdollahi A, Knoll M. Radiobiological Effects of Photon, Proton and Carbon Ion Irradiation on Human Pluripotent-Stem-Cell-Derived Gastrointestinal Organoids. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.2075] [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: 11/30/2022]
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Hemann EA, Grigg JB, Wilkins CR, Knoll M, Iadonato SP, Bedard K, Probst P, Loo YM, Gale M. A small-molecule RIG-I agonist functions to enhance vaccine protection against influenza A virus infection. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.76.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Viral sensing by RIG-I and downstream activation of antiviral defenses along with the induction of innate immune cytokines is essential from protection against influenza A virus (IAV) infection. We have identified a novel, small-molecule RIG-I agonist, KIN1148, which binds and activates RIG-I to signal the activation of IRF3 and the innate immune response. We are developing this molecule as an adjuvant to enhance vaccination against pandemic H1N1 (pH1N1) IAV. Ex vivo treatment of dendritic cells with KIN1148 leads to their activation and maturation. We determined the ability of KIN1148 to enhance suboptimal IAV vaccine responses in vivo. Administration of KIN1148 leads enhanced protection during high dose pH1N1 infection following a single, intramuscular administration of KIN1148 with IAV vaccine. This increase in protection is accompanied by a significant reduction in virus titers, as well as lung pathology. Analysis of the immune response induced following vaccination with KIN1148 as well as challenge demonstrates an increase in chemoattractant cytokines, germinal center B cells, IAV-specific antibodies, and IAV-specific CD4 and CD8 T cells compared to vaccination alone, indicating the induction of a broad anti-IAV immune response. Together these results demonstrate that prophylactic drug targeting of the RIG-I pathway with a small molecule enhances vaccine protection and highlight the potential of KIN1148 to enhancing vaccines against RNA virus infection.
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Li Y, Abeghyan S, Berndgen K, Baha-Shanjani M, Deron G, Englisch U, Karabekyan S, Ketenoglu B, Knoll M, Wolff-Fabris F, Viehweger M, Yakopov M, Pflueger J. Magnetic Measurement Techniques for the Large-Scale Production of Undulator Segments for the European XFEL. ACTA ACUST UNITED AC 2015. [DOI: 10.1080/08940886.2015.1037679] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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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Ben-Shoshan M, Soller L, Harrington DW, Knoll M, La Vieille S, Fragapane J, Joseph L, St Pierre Y, Wilson K, Elliott SJ, Clarke AE. Eczema in early childhood, sociodemographic factors and lifestyle habits are associated with food allergy: a nested case-control study. Int Arch Allergy Immunol 2015; 166:199-207. [PMID: 25926095 DOI: 10.1159/000381829] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 03/23/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Studies suggest an increase in food allergy prevalence over the last decade, but the contributing factors remain unknown. The aim of this study was to evaluate the association between the most common food allergies and atopic history, sociodemographic characteristics and lifestyle habits. METHODS We conducted a case-control study nested within the SPAACE study (Surveying Prevalence of Food Allergy in All Canadian Environments) – a cross-Canada, random telephone survey. Cases consisted of individuals with probable food allergy (self-report of convincing symptoms and/or physician diagnosis) to milk, egg, peanut, tree nut, shellfish, fish, wheat, soy, or sesame. Controls consisted of nonallergic individuals, matched for age. Cases and controls were queried on personal and family history of atopy, sociodemographic characteristics and lifestyle habits. Multivariate logistic regression was used to evaluate the association between atopy, sociodemographic characteristics and lifestyle habits with probable food allergy. RESULTS Between September 2010 and September 2011, 480 cases and 4,950 controls completed the questionnaire. For all 9 allergens, factors associated with a higher risk of probable allergy were as follows: (1) personal history of eczema (in the first 2 years of life), asthma or hay fever (odds ratio, OR 2.3, 95% CI 1.6-3.5; OR 2.8, 95% CI 2.2-3.6, and OR 2.3, 95% CI 1.8-3.0, respectively), (2) maternal, paternal or sibling's food allergy (OR 3.7, 95% CI 2.5-5.6; OR 3.0, 95% CI 1.8-5.1, and OR 3.1, 95% CI 2.2-4.2), (3) high household income (top 20%; OR 1.5, 95% CI 1.2-2.0). Males and older individuals were less likely to have food allergy (OR 0.7, 95% CI 0.6-0.9, and OR 0.99, 95% CI 0.99-1.00). Eczema in the first 2 years of life was the strongest risk factor for egg, peanut, tree nut and fish allergy. CONCLUSIONS This is the largest population-based nested case-control study exploring factors associated with food allergies. Our results reveal that, in addition to previously reported factors, eczema in the first 2 years of life is consistently associated with food allergies.
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Affiliation(s)
- Moshe Ben-Shoshan
- Division of Pediatric Allergy and Clinical Immunology, Department of Pediatrics, McGill University Health Center, Montreal, Que., Canada
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Soller L, Ben-Shoshan M, Harrington DW, Knoll M, Fragapane J, Joseph L, St. Pierre Y, La Vieille S, Wilson K, Elliott SJ, Clarke AE. Adjusting for nonresponse bias corrects overestimates of food allergy prevalence. The Journal of Allergy and Clinical Immunology: In Practice 2015; 3:291-293.e2. [DOI: 10.1016/j.jaip.2014.11.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 10/24/2022]
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Potter B, Lob M, Mercaldo R, Hetzler A, Kaistha V, Khan H, Kingston N, Knoll M, Maloy‐Franklin B, Melvin K, Ruiz‐Pelet P, Ozsoy N, Schmitt E, Wheeler L, Potter M, Rutter M, Yahn G, Parente D. A long‐term study examining the antibacterial effectiveness of Agion silver zeolite technology on door handles within a college campus. Lett Appl Microbiol 2014; 60:120-127. [DOI: 10.1111/lam.12356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/02/2014] [Accepted: 10/24/2014] [Indexed: 01/07/2023]
Affiliation(s)
- B.A. Potter
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - M. Lob
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - R. Mercaldo
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - A. Hetzler
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - V. Kaistha
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - H. Khan
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - N. Kingston
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - M. Knoll
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - B. Maloy‐Franklin
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - K. Melvin
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - P. Ruiz‐Pelet
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - N. Ozsoy
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - E. Schmitt
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | - L. Wheeler
- Department of Biology Penn State Erie The Behrend College Erie PA USA
| | | | - M.A. Rutter
- Department of Mathematics Penn State Erie The Behrend College Erie PA USA
| | - G. Yahn
- Advanced Finishing USA Fairview PA USA
| | - D.H. Parente
- Sam and Irene Black School of Business Penn State Erie The Behrend College Erie PA USA
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Knoll M, Pei X, Zelefsky M. Long-Term Urinary and Rectal Tolerance in Prostate Cancer Survivors Treated With Definitive Conformal Radiation Therapy. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.2092] [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: 10/24/2022]
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Soller L, Ben-Shoshan M, Harrington DW, Knoll M, Fragapane J, Joseph L, St Pierre Y, La Vieille S, Wilson K, Elliott SJ, Clarke AE. Prevalence and predictors of food allergy in Canada: a focus on vulnerable populations. J Allergy Clin Immunol Pract 2014; 3:42-9. [PMID: 25577617 DOI: 10.1016/j.jaip.2014.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/10/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Studies suggest that individuals of low education and/or income, new Canadians (immigrated <10 years ago), and individuals of Aboriginal identity may have fewer food allergies than the general population. However, given the difficulty in recruiting such populations (hereafter referred to as vulnerable populations), by using conventional survey methodologies, the prevalence of food allergy among these populations in Canada has not been estimated. OBJECTIVES To estimate the prevalence of food allergy among vulnerable populations in Canada, to compare with the nonvulnerable populations and to identify demographic characteristics predictive of food allergy. METHODS By using 2006 Canadian Census data, postal codes with high proportions of vulnerable populations were identified and households were randomly selected to participate in a telephone survey. Information on food allergies and demographics was collected. Prevalence estimates were weighted by using Census data to account for the targeted sampling. Multivariable logistic regression was used to identify predictors of food allergy. RESULTS Of 12,762 eligible households contacted, 5734 households completed the questionnaire (45% response rate). Food allergy was less common among adults without postsecondary education versus those with postsecondary education (6.4% [95% CI, 5.5%-7.3%] vs 8.9% [95% CI, 7.7%-10%]) and new Canadians versus those born in Canada (3.2% [95% CI, 2.2%-4.3%] vs 8.2% [95% CI, 7.4%-9.1%]). There was no difference in prevalence between those of low and of high income or those with and without Aboriginal identity. CONCLUSION Analysis of our data suggests that individuals of low education and new Canadians self-report fewer allergies, which may be due to genetics, environment, lack of appropriate health care, or lack of awareness of allergies, which reduces self-report.
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Affiliation(s)
- Lianne Soller
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Center, Montreal, Quebec, Canada.
| | - Moshe Ben-Shoshan
- Division of Pediatric Allergy and Clinical Immunology, Department of Pediatrics, McGill University Health Center, Montreal, Quebec, Canada
| | | | - Megan Knoll
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Center, Montreal, Quebec, Canada
| | - Joseph Fragapane
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Center, Montreal, Quebec, Canada
| | - Lawrence Joseph
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Center, Montreal, Quebec, Canada; Department of Epidemiology and Biostatistics, McGill University, Montreal, Quebec, Canada
| | - Yvan St Pierre
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Center, Montreal, Quebec, Canada
| | | | - Kathi Wilson
- Department of Geography, University of Toronto, Toronto, Ontario, Canada
| | - Susan J Elliott
- Faculty of Applied Health Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - Ann E Clarke
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Center, Montreal, Quebec, Canada; Division of Rheumatology, University of Calgary, Calgary, Alberta, Canada
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Soller L, Cherkaoui S, Ben-Shoshan M, Harrington DW, Knoll M, Fragapane J, Joseph L, St Pierre Y, La Vieille S, Wilson K, Elliott SJ, Clarke AE. Likelihood of being prescribed an epinephrine autoinjector in allergic Canadians with lower educational levels. Ann Allergy Asthma Immunol 2014; 113:326-9. [PMID: 25087187 DOI: 10.1016/j.anai.2014.06.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/06/2014] [Accepted: 06/17/2014] [Indexed: 11/25/2022]
Affiliation(s)
- Lianne Soller
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada.
| | - Sabrine Cherkaoui
- Division of Internal Medicine, Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Moshe Ben-Shoshan
- Division of Pediatric Allergy and Clinical Immunology, Department of Pediatrics, McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Megan Knoll
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Joseph Fragapane
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Lawrence Joseph
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada; Department of Epidemiology and Biostatistics, McGill University, Montreal, Quebec, Canada
| | - Yvan St Pierre
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Kathi Wilson
- Department of Geography, University of Toronto, Toronto, Ontario, Canada
| | - Susan J Elliott
- Faculty of Applied Health Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - Ann E Clarke
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada; Division of Rheumatology, University of Calgary, Calgary, Alberta, Canada
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Dumane V, Hunt M, Steinberger E, Knoll M, Green S, Bakst R. SU-E-T-342: Use of Patient Geometry Measurements to Predict Dosimetric Gain with VMAT Over 3D for Chestwall and Regional Nodal Radiation. Med Phys 2014. [DOI: 10.1118/1.4888675] [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: 11/07/2022] Open
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Soller L, Ben‐Shoshan M, Knoll M, Harrington D, Fragapane J, Joseph L, St Pierre Y, La Vieille S, Wilson K, Elliott S, Clarke A. PD16 ‐ Prevalence of childhood food allergy in Canada: a focus on under‐represented populations. Clin Transl Allergy 2014. [PMCID: PMC4082123 DOI: 10.1186/2045-7022-4-s1-p16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Ben-Shoshan M, Soller L, Harrington D, Knoll M, Vieille SL, Fragapane J, Joseph L, Pierre YS, Wilson K, Elliott S, Clarke AE. Environmental and Sociodemographic Factors Associated With Food Allergy: A Nested Case-Control Study. J Allergy Clin Immunol 2014. [DOI: 10.1016/j.jaci.2013.12.733] [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: 10/25/2022]
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Dumane V, Knoll M, Green S, Bakst R. Comparison of VMAT, Partially Wide Tangents, and Photon/Electrons for Treatment of Reconstructed Chest Wall, Supraclavicular, Axillary, and Internal Mammary Nodes. Int J Radiat Oncol Biol Phys 2013. [DOI: 10.1016/j.ijrobp.2013.06.2017] [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: 11/15/2022]
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Philippi M, Altenhöner T, Köhler M, Schmidt J, Roth S, Knoll M. Wahrgenommene soziale Unterstützung und subjektive Gesundheit von Krankenhauspatienten. Gesundheitswesen 2013. [DOI: 10.1055/s-0033-1354045] [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: 10/26/2022]
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Soller L, Knoll M, Ben-Shoshan M, Harrington DW, Fragapane J, Joseph L, St Pierre Y, St Pierre Y, La Vieille S, Wilson K, Elliott SJ, Clarke AE. The prevalence of food allergy among Aboriginal people in Canada. Clin Transl Allergy 2013. [PMCID: PMC3723655 DOI: 10.1186/2045-7022-3-s3-p77] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Knoll M, Soller L, Ben-Shoshan M, Harrington D, Fragapane J, Joseph L, La Vieille S, St-Pierre Y, Wilson K, Elliott S, Clarke A. The use of incentives in vulnerable populations for a telephone survey: a randomized controlled trial. BMC Res Notes 2012; 5:572. [PMID: 23083313 PMCID: PMC3503563 DOI: 10.1186/1756-0500-5-572] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 10/17/2012] [Indexed: 11/16/2022] Open
Abstract
Background Poor response rates in prevalence surveys can lead to nonresponse bias thereby compromising the validity of prevalence estimates. We conducted a telephone survey of randomly selected households to estimate the prevalence of food allergy in the 10 Canadian provinces between May 2008 and March 2009 (the SCAAALAR study: Surveying Canadians to Assess the Prevalence of Common Food Allergies and Attitudes towards Food LAbeling and Risk). A household response rate of only 34.6% was attained, and those of lower socioeconomic status, lower education and new Canadians were underrepresented. We are now attempting to target these vulnerable populations in the SPAACE study (Surveying the Prevalence of Food Allergy in All Canadian Environments) and are evaluating strategies to increase the response rate. Although the success of incentives to increase response rates has been demonstrated previously, no studies have specifically examined the use of unconditional incentives in these vulnerable populations in a telephone survey. The pilot study will compare response rates between vulnerable Canadian populations receiving and not receiving an incentive. Findings Randomly selected households were randomly assigned to receive either a $5 incentive or no incentive. The between group differences in response rates and 95% confidence intervals (CIs) were calculated. The response rates for the incentive and non-incentive groups were 36.1% and 28.7% respectively, yielding a between group difference of 7.4% (−0.7%, 15.6%). Conclusion Although the wide CI precludes definitive conclusions, our results suggest that unconditional incentives are effective in vulnerable populations for telephone surveys.
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Affiliation(s)
- Megan Knoll
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada.
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Klenske J, Knoll M, Kornovski Y. [Global ablation of endometrium as a new uterus sparing operative method in uterine dysfunctional bleeding]. Akush Ginekol (Sofiia) 2012; 51:17-20. [PMID: 23610912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A new method of endometrial ablation has been presented. This is the method of bipolar tridimensional device "NOVA SURE". This innovative method enables to destruct the basal and functional layer of the uterus and thus leads to amenorrhea and hypomenorrhea.
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Zurawski V, Driscoll A, Deluca A, Knoll M, Murdoch D, O’Connor O, Dupont-Rouzeyrol M, Missotte I, Moïsi J, Besson-Leaud L, Chevalier C, Debarnot V, Levine O, Mermond S. Lower respiratory infections (LRIs) etiologies in hospitalized children in New Caledonia: a PERCH pilot study. BMC Proc 2011. [DOI: 10.1186/1753-6561-5-s1-p108] [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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Therre P, Riemer-Hommel P, Knoll M. [School meals at secondary schools: an analysis in the district of St. Wendel in the Province Saarland, Germany]. Gesundheitswesen 2011; 74:467-75. [PMID: 21796587 DOI: 10.1055/s-0031-1280848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
INTRODUCTION This study focuses on the nutrition of young people in schools. The Saarland state government mandates the implementation of the "quality standards for school meals", developed by the Germany Society of Nutrition (Deutschen Gesellschaft für Ernährung, DGE) in schools offering school meals. This research evaluates the state of implementation. METHODS 4-week menu plans were evaluated using a stratified random sample of selected schools (n25%-sample=5, ntotal=23). In addition, all catering services of the district (ncaterer=5) were interviewed by written survey focused on any information on the company, the type of food, the menu design as well as general information. RESULTS None of the analysed menu plans met the DGE standard. The analysis of the menu plans allows for an assessment of the nutritional quality of food. Interviews with caterers provide background information on menu design. DISCUSSION The analysis of a randomised 25%-sample shows that the target specifications of the DGE are only implemented by a small number of schools in the exemplary selected district of St. Wendel, Germany. As the German Child and Youth Health Survey (KiGGS), also this evaluation shows that the quality of school meals deviates significantly from the recommendations of the DGE. There is a clear need for action.
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Affiliation(s)
- P Therre
- HTW des Saarlandes, Fakultät für Sozialwissenschaften, Dept. Gesundheit und Pflege, Saarbrücken
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Zurawski V, Driscoll A, Deluca A, Knoll M, Murdoch D, O’Connor O, Dupont-Rouzeyrol M, Missotte I, Moïsi J, Besson-Leaud L, Chevalier C, Debarnot V, Levine O, Mermond S. Lower respiratory infections (LRIs) etiologies in hospitalized children in New Caledonia: a PERCH pilot study. BMC Proc 2011. [PMCID: PMC3019423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- V Zurawski
- Pasteur Institute of New Caledonia, Noumea, New Caledonia
| | - A Driscoll
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - A Deluca
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - M Knoll
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - D Murdoch
- Department of Microbiology, Canterbury Health Laboratories, Christchurch, New Zealand
| | - O O’Connor
- Pasteur Institute of New Caledonia, Noumea, New Caledonia
| | | | - I Missotte
- Paediatric Ward, Territorial Hospital Center of Magenta, Noumea, New Caledonia
| | - J Moïsi
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - L Besson-Leaud
- Paediatric Ward, Territorial Hospital Center of Magenta, Noumea, New Caledonia
| | - C Chevalier
- Paediatric Emergency Unit, Territorial Hospital Center of Magenta, Noumea, New Caledonia
| | - V Debarnot
- Paediatric Emergency Unit, Territorial Hospital Center of Magenta, Noumea, New Caledonia
| | - O Levine
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - S Mermond
- Pasteur Institute of New Caledonia, Noumea, New Caledonia
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Abstract
Oxidative stress during reperfusion of ischemia is associated with a phenotypic change in circulating monocytes from CD14++CD16- to a proinflammatory CD14+CD16+ subpopulation resulting in altered immunity and development of organ failure. However, the mechanism responsible remains unknown. We hypothesize that this phenotypic change, modeled by hydrogen peroxide exposure in vitro, is due to oxidative-induced intracellular calcium flux and distinct cytoskeletal and lipid raft changes. Peripheral blood monocytes obtained from healthy volunteers underwent 100 mM H2O2 exposure for 0 to 24 h. Selected cells were pretreated with 2 microM cytochalasin D, 1 microM lactrunculin A, or 30 microM 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid for 30 min. Cells underwent fluorescence-activated cell sorter for CD14, CD16, and cytokine expression. Cellular and lipid raft CD16 expression was determined by immunoblot and confocal microscopy. H2O2 exposed monocytes underwent a rapid time-dependent increase in the surface expression of CD16 from 12.81% +/- 3.53% to 37.12% +/- 7.61% at 24 h (P = 0.001). Total cellular CD16 was not changed by H2O2, but an increase in lipid raft and decrease in intracellular CD16 expression were seen after H2O2 exposure. This increase in CD16 expression was associated with a 27% increase in intracellular TNF-alpha, an alteration in actin polymerization, and the formation of raft macrodomains. These changes induced by H2O2 were inhibited by inhibition of actin polymerization (cytochalasin D and lactrunculin A) and intracellular calcium flux [1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid]. This study provides the first evidence that phenotypic alterations induced by oxidative stress during reperfusion may occur as a result of changes in cytoskeletal architecture due to calcium flux that result in lipid raft alterations rather than solely from demargination and/or production of bone marrow-derived CD16+ monocytes.
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Affiliation(s)
- Joseph Cuschieri
- Department of Surgery, University of Washington, Seattle, Washington, USA.
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Vering T, Adam S, Berns T, Schäfer R, Schwartenbeck G, Steinkuhl R, Tombach B, Knoll M. Erprobung von VISY-1 im Realtest: Probenahme und Glucosebestimmung. BIOMED ENG-BIOMED TE 2009. [DOI: 10.1515/bmte.1998.43.s1.562] [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: 11/15/2022]
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Gocke D, Kolter G, Gauchenova E, Knoll M, Berthold Sjöberg C, Schneider G, Pleiss J, Müller M, Pohl M. Rationales Enzymdesign für die (S)-selektive Benzoinkondensation. CHEM-ING-TECH 2009. [DOI: 10.1002/cite.200950205] [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: 11/05/2022]
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Schaeffer V, Cuschieri J, Garcia I, Knoll M, Billgren J, Jelacic S, Bulger E, Maier R. The priming effect of C5a on monocytes is predominantly mediated by the p38 MAPK pathway. Shock 2007; 27:623-30. [PMID: 17505301 PMCID: PMC6014696 DOI: 10.1097/shk.0b013e31802fa0bd] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The dysregulation of the inflammatory response after trauma leads to significant morbidity and mortality. Monocytes and macrophages play a central role in the orchestration of the inflammatory response after injury. Serum interleukin-6 (IL-6) concentration correlates with poor outcomes after injury. Tumor necrosis factor-alpha (TNF-alpha) is a proinflammatory cytokine that plays a crucial role in the pathogenesis of multiple organ dysfunction syndrome. Furthermore, in the presence of C5a, monocytes and macrophages have potentiated responses, but the mechanisms underlying this response remain largely unknown. Peripheral blood mononuclear cells (PBMCs) were isolated from healthy volunteers and pretreated with C5a (100 ng/mL) for 1 h before adding lipopolysaccharide (LPS) (10 ng/mL) for up to 20 h. Inhibitors for the mitogen-activated protein kinases (MAPKs) were added 1 h before adding C5a. C5a primes monocytes for LPS-induced IL-6 and TNF-alpha production. Treatment of PBMCs with C5a leads to a rapid activation of the 3 MAPK pathways. SP600125 (inhibitor of c-Jun NH2-terminal kinase MAPK) and PD98059 (inhibitor of extracellular signal-regulated kinase MAPK) did not affect the C5a priming of the LPS-induced IL-6 and TNF-alpha production, whereas SB203580, a specific inhibitor of p38 MAPK, did suppress the C5a priming effect. These results demonstrate that C5a primes adherent PBMCs and modulates LPS-induced IL-6 and TNF-alpha production. Results from extracellular signal-regulated kinase and c-Jun NH2-terminal kinase MAPK blockade suggest that these signaling pathways have minimal or no role in reprogramming LPS-mediated IL-6 and TNF-alpha production. On the contrary, in PBMCs, C5a activates the p38 cascade, and this pathway plays a major role in the C5a enhancement of LPS-induced IL-6 and TNF-alpha production.
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Affiliation(s)
- Valérie Schaeffer
- Department of Surgery, Harborview Medical Center, Seattle, Washington 98104, USA.
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Okpara-Hofmann J, Knoll M, Dürr M, Schmitt B, Borneff-Lipp M. Comparison of low-temperature hydrogen peroxide gas plasma sterilization for endoscopes using various Sterrad models. J Hosp Infect 2005; 59:280-5. [PMID: 15749314 DOI: 10.1016/j.jhin.2004.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [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: 09/20/2002] [Accepted: 09/09/2004] [Indexed: 11/26/2022]
Abstract
This study compared the effectiveness of sterilizing four types of endoscope using different models of the Sterrad system (Sterrad 50, 100, 100S and 200). Sterilization levels meeting international requirements were attained in all cases with carriers inoculated with Geobacillus stearothermophilus spores. The endoscopes were tested in half cycles ('overkill'). This is the first study to compare the Sterrad models marketed to date in terms of effective sterilization of endoscopes with narrow lumens.
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Affiliation(s)
- J Okpara-Hofmann
- Institute of Hygiene, Medical Faculty, Martin-Luther-University Halle-Wittenberg, Johann-Andreas-Segner-Str. 12, D-06097 Halle/Saale, Germany.
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Pool-Zobel BL, Dornacher I, Lambertz R, Knoll M, Seitz HK. Genetic damage and repair in human rectal cells for biomonitoring: sex differences, effects of alcohol exposure, and susceptibilities in comparison to peripheral blood lymphocytes. Mutat Res 2004; 551:127-34. [PMID: 15225587 DOI: 10.1016/j.mrfmmm.2004.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [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: 08/15/2003] [Revised: 03/16/2004] [Accepted: 03/23/2004] [Indexed: 10/26/2022]
Abstract
INTRODUCTION Cells other than lymphocytes may be preferable as surrogate biomarkers during exposure monitoring. In nutritional toxicology, cells from colorectal tissues are particularly relevant for studying associations between food and cancer. Thus, we have previously shown that colonic cells of males have higher levels of DNA damage than females, which (among other factors) could be due to a higher consumption of alcoholic beverages by males. To test this hypothesis, we have performed a first exploratory study to compare DNA damage in rectal cells from biopsies of male patients with alcohol abuse and of male and female controls. Peripheral blood lymphocytes were additionally monitored to assess systemic exposure loads. METHODS Cells were isolated and subjected to microgelelectrophoresis +/- endonuclease III to measure DNA breaks and oxidized pyrimidine bases ("comet-assay"). Cell aliquots were treated with H(2)O(2) for 5min in suspension culture and processed immediately or after 60min to determine induced damage and its persistence. RESULTS Pooled data from subjects of all groups revealed that oxidative DNA damage in rectal cells directly correlated to damage in lymphocytes. Female controls had lower levels of DNA damage than male controls, confirming the previous studies. An unexpected result was that male alcohol abusers had significantly less genetic damage than male controls. Also, repair was detected in lymphocytes of male alcohol abusers and female controls, but not in male controls. CONCLUSION This is the first time the comet-assay has been used to detect genotoxicity in human rectal cells as a biomonitoring tool. Our pilot study confirms earlier reports on sex differences and indicates a good correlation between damage in rectal cells and damage in lymphocytes and implies that alcohol exposure enhances endogenous defence.
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Affiliation(s)
- B L Pool-Zobel
- Department of Nutritional Toxicology, Director of the Institute for Nutrition, Friedrich-Schiller-University of Jena, Dornburger Str. 25, 07743 Jena, Germany.
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Gorschlüter A, Mak LH, Sundermeier C, Ross B, Knoll M. Electro-magnetic base technology for estremely sensitive immunosensors and DNA-chips. BIOMED ENG-BIOMED TE 2003; 47 Suppl 1 Pt 1:213-6. [PMID: 12451820 DOI: 10.1515/bmte.2002.47.s1a.213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 11/15/2022]
Abstract
We report on the development of an innovative electro-magnetic base technology for estremely sensitive sensors allowing the electrical detection of biological analytes like antigenes or DNA as well as a simple multiple detection of binding forces occurring at specific bonds between proteins. The technology is based on the strong impact of specifically captured magnetic microbeads on an electrical current generated in a fluid by a small sensor chip with an array of activated microelectrodes. The new technological principle with the on-chip detection of analytes will be suitable for large scale applications due to its mass production compatible technologies and allow an alternative way to monitor relevant substances without the consumption of critical additional solutions and reagents.
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Affiliation(s)
- A Gorschlüter
- Institut für Chemo- und Biosensorik (ICB) e.V., D-48149 Münster, Deutschland.
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Perdomo J, Hinkers H, Sundermeier C, Seifert W, Martínez Morell O, Knoll M. Miniaturized real-time monitoring system for L-lactate and glucose using microfabricated multi-enzyme sensors. Biosens Bioelectron 2001; 15:515-22. [PMID: 11419648 DOI: 10.1016/s0956-5663(00)00087-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A miniaturized on-line monitoring system for the detection of L-lactate and glucose is presented. The system is based on a microfabricated multi-enzyme silicon sensor chip with flow channels integrated on the chip. The sensors were fabricated in containment technology. They were characterized in test solutions. The cross-talking behaviour was investigated and was found to be practically negligible. The linear measurement ranges of both glucose and lactate sensors were large enough for most practical applications. As a result of the miniaturization the analyte consumption could be reduced to a few nmol min(-1). The system was equipped with a microdialysis probe whose recovery was 45% for lactate and 37% for glucose in test solutions using a flow rate of 3 microl min(-1). Lower flow rates of 0.5 microl min(-1) resulted in recoveries of over 90%. The long-term stability of the system was acceptable. Initial measurements have also been performed in vitro using human blood serum.
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Affiliation(s)
- J Perdomo
- Centro de Investigaciones en Microelectrónica, Instituto Superior Politécnico Jose A. Echererria, Havana, Cuba
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50
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Riedl CR, Stephen RL, Daha LK, Knoll M, Plas E, Pflüger H. Electromotive administration of intravesical bethanechol and the clinical impact on acontractile detrusor management: introduction of a new test. J Urol 2000; 164:2108-11. [PMID: 11061937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
PURPOSE It is often difficult to determine the functional status of the detrusor muscle in patients with detrusor areflexia. We performed a clinical study to establish a test defining residual detrusor capacity in such patients. MATERIALS AND METHODS In phase 1, 5 controls with detrusor areflexia were tested with an intravesical instillation of 20 mg. bethanechol in 150 cc of sodium chloride 0.3% with and without 20 mA. of pulsed current applied via an electrode catheter through the saline. Cystometry simultaneously recorded intravesical pressure changes. In phase 2, 45 patients with detrusor areflexia were tested with electromotive administration of intravesical bethanechol. In phase 3, 25 mg. bethanechol given orally once daily were prescribed for 15 patients and voiding control was assessed after 6 weeks of therapy. RESULTS Neither bethanechol without current nor current through saline only led to increased intravesical pressure. However, we noted a mean pressure increase of 34 cm. water during the electromotive administration of bethanechol in 24 of 26 patients with areflexia and neurological disease compared to only 3 cm. water in 3 of 11 with a history of chronic bladder dilatation. Oral bethanechol restored spontaneous voiding in 9 of 11 patients who had had a positive response to the electromotive administration of bethanechol, whereas all 4 without a pressure increase during the electromotive administration of bethanechol did not void spontaneously. CONCLUSIONS Electromotive administration of intravesical bethanechol identifies patients with an atonic bladder and adequate residual detrusor muscle function who are candidates for restorative measures, such as oral bethanechol and intravesical electrostimulation. Those who do not respond to the electromotive administration of bethanechol do not benefit from oral bethanechol and are candidates for catheterization.
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Affiliation(s)
- C R Riedl
- Department of Urology, Municipal Hospital Lainz, Vienna, Austria
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