1
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van Wyngaardt WM, Bowan AHH, Clark EL, Keevers CMB, Smith ML, Zarifi M, Stopic A. Cross-validation of standardisation techniques at ANSTO using cobalt-60 and learnings from the presence and identification of non-gamma-ray emitting impurities. Appl Radiat Isot 2023; 201:111027. [PMID: 37748217 DOI: 10.1016/j.apradiso.2023.111027] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/26/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
To fulfil the technical requirements for accreditation to ISO/IEC 17025, the end-to-end validation of all processes associated with standardising 60Co, including gravimetric source dispensing, primary standardisation by the 4π(LS)β-γ coincidence and live-timed anti-coincidence extrapolation techniques, and impurity determination were performed and documented. Pure-beta-emitting impurities in a 60Co stock solution were identified. The impact of such impurities on measurement by liquid scintillation counting and comparison in the ESIR are discussed. A fresh 60Co source was produced, standardised, and compared using the SIR.
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Affiliation(s)
- W M van Wyngaardt
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234 NSW, Australia.
| | - A H H Bowan
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234 NSW, Australia
| | - E L Clark
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234 NSW, Australia
| | - C M B Keevers
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234 NSW, Australia
| | - M L Smith
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234 NSW, Australia
| | - M Zarifi
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234 NSW, Australia
| | - A Stopic
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234 NSW, Australia
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2
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Smith ML, Sergi Z, Mignogna KM, Rodriguez NE, Tatom Z, MacLeod L, Choi KB, Philip V, Miles MF. Identification of Genetic and Genomic Influences on Progressive Ethanol Consumption in Diversity Outbred Mice. bioRxiv 2023:2023.09.15.554349. [PMID: 37745421 PMCID: PMC10515943 DOI: 10.1101/2023.09.15.554349] [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] [Indexed: 09/26/2023]
Abstract
Genetic factors play a significant role in the risk for development of alcohol use disorder (AUD). Using 3-bottle choice intermittent access ethanol (IEA), we have employed the Diversity Outbred (DO) mouse panel as a model of alcohol use disorder in a genetically diverse population. Through use of gene expression network analysis techniques, in combination with expression quantitative trait loci (eQTL) mapping, we have completed an extensive analysis of the influence of genetic background on gene expression changes in the prefrontal cortex (PFC). This approach revealed that, in DO mice, genes whose expression was significantly disrupted by intermittent ethanol in the PFC also tended to be those whose expression correlated to intake. This finding is in contrast to previous studies of both mice and nonhuman primates. Importantly, these analyses identified genes involved in myelination in the PFC as significantly disrupted by IEA, correlated to ethanol intake, and having significant eQTLs. Genes that code for canonical components of the myelin sheath, such as Mbp, also emerged as key drivers of the gene expression response to intermittent ethanol drinking. Several regulators of myelination were also key drivers of gene expression, and had significant QTLs, indicating that genetic background may play an important role in regulation of brain myelination. These findings underscore the importance of disruption of normal myelination in the PFC in response to prolonged ethanol exposure, that genetic variation plays an important role in this response, and that this interaction between genetics and myelin disruption in the presence of ethanol may underlie previously observed behavioral changes under intermittent access ethanol drinking such as escalation of consumption.
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Affiliation(s)
- M L Smith
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Z Sergi
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - K M Mignogna
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - N E Rodriguez
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Z Tatom
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - L MacLeod
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - K B Choi
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | - V Philip
- The Jackson Laboratory, Bar Harbor, Maine, USA
| | - M F Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, Virginia, USA
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3
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Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, Li H, Jerryd Meade M, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MR, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Laird Smith M, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Fai Au K, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. bioRxiv 2023:2023.07.25.550582. [PMID: 37546854 PMCID: PMC10402094 DOI: 10.1101/2023.07.25.550582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.
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Affiliation(s)
- Francisco J. Pardo-Palacios
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- These authors contributed equally to this work
| | - Dingjie Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Fairlie Reese
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Sílvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- These authors contributed equally to this work
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
- These authors contributed equally to this work
| | - Jane E. Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Maite De María
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Matthew S. Adams
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Gabriela Balderrama-Gutierrez
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Amit K. Behera
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Jose M. Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Flomics Biotech, Dr Aiguader 88, Barcelona 08003, Spain
- These authors contributed equally to this work
| | - Cindy E. Liang
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Haoran Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Marcus Jerryd Meade
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- These authors contributed equally to this work
| | - David A. Moraga Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Andrey D. Prjibelski
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- These authors contributed equally to this work
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Hamed Bostan
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Ashley M. Brooks
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Muhammed Hasan Çelik
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ying Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mei R,M. Du
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Jonathan Göke
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Saber Hafezqorani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Ralf Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Joseph Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jian Liang Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Matthias Lienhard
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Alla Mikheenko
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Dennis Mulligan
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Mihaela Pertea
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Matthew E. Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andre D. Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Alison D. Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Yuk Kei Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Changqing Wang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Brandon Y. Wong
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Chen Yang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Namrita Dhillon
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | | | - Luis Ferrández-Peral
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, USA
| | | | | | | | | | | | | | - Jorge Mestre-Tomás
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Jonathan M. Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nedka G. Panayotova
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
| | - Alejandro Paniagua
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | | | - Eric Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Brandon Saint-John
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Enrique Sapena
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK, UK
| | - Leon Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Melissa Laird Smith
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Hazuki Takahashi
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
| | | | - Piero Carninci
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
- Human Technopole, Milano, Italy
| | - Nancy D. Denslow
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, Department of Physiological Sciences,, University of Florida, Gainesville, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Margaret E. Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Hagen U. Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, USA
| | - Barbara J. Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Gloria M. Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- Center for Public Health Genomics
- UVA Cancer Center, University of Virginia, Charlottesville, USA
| | - Ali Mortazavi
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Angela N. Brooks
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
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4
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Jackson KJL, Kos JT, Lees W, Gibson WS, Smith ML, Peres A, Yaari G, Corcoran M, Busse CE, Ohlin M, Watson CT, Collins AM. A BALB/c IGHV Reference Set, Defined by Haplotype Analysis of Long-Read VDJ-C Sequences From F1 (BALB/c x C57BL/6) Mice. Front Immunol 2022; 13:888555. [PMID: 35720344 PMCID: PMC9205180 DOI: 10.3389/fimmu.2022.888555] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
The immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-read SMRT sequencing to amplify VDJ-C sequences from F1 (BALB/c x C57BL/6) hybrid animals. Strain variations were identified in the Ighm and Ighg2b genes, and analysis of VDJ rearrangements led to the inference of 278 germline IGHV alleles. 169 alleles are not present in the C57BL/6 genome reference sequence. To establish a set of expressed BALB/c IGHV germline gene sequences, we computationally retrieved IGHV haplotypes from the IgM dataset. Haplotyping led to the confirmation of 162 BALB/c IGHV gene sequences. A musIGHV398 pseudogene variant also appears to be present in the BALB/cByJ substrain, while a functional musIGHV398 gene is highly expressed in the BALB/cJ substrain. Only four of the BALB/c alleles were also observed in the C57BL/6 haplotype. The full set of inferred BALB/c sequences has been used to establish a BALB/c IGHV reference set, hosted at https://ogrdb.airr-community.org. We assessed whether assemblies from the Mouse Genome Project (MGP) are suitable for the determination of the genes of the IGH loci. Only 37 (43.5%) of the 85 confirmed IMGT-named BALB/c IGHV and 33 (42.9%) of the 77 confirmed non-IMGT IGHV were found in a search of the MGP BALB/cJ genome assembly. This suggests that current MGP assemblies are unsuitable for the comprehensive documentation of germline IGHVs and more efforts will be needed to establish strain-specific reference sets.
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Affiliation(s)
| | - Justin T. Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - William Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - William S. Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Melissa Laird Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Ayelet Peres
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christian E. Busse
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
- *Correspondence: Corey T. Watson, ; Andrew M. Collins,
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
- *Correspondence: Corey T. Watson, ; Andrew M. Collins,
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5
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Heranudin, Smith ML, van Wyngaardt WM, Guatelli S, Li E, Rosenfeld A. Characterisation of a well-type NaI(Tl) detector by means of a Monte Carlo simulation for radionuclide metrology application. Appl Radiat Isot 2021; 176:109889. [PMID: 34375816 DOI: 10.1016/j.apradiso.2021.109889] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/14/2021] [Accepted: 08/02/2021] [Indexed: 11/29/2022]
Abstract
A well-type NaI(Tl) detector was modelled and characterised by means of a Monte Carlo simulation, as part of a project to develop a 4πβ (Plastic Scintillator)-4πγ instrument to be used for the primary standardisation of radionuclides at ANSTO. The simulation based on GEANT4 was used to characterise the 4πγ detector in terms of potential dead layer/inactive materials, full energy peak efficiency, coincidence-summing correction, and energy resolution. An excellent agreement was obtained between the simulation results and the experimental measurements.
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Affiliation(s)
- Heranudin
- Centre for Medical Radiation Physics, University of Wollongong, NSW, Australia; Radionuclide Metrology, Australian Nuclear Science and Technology Organisation, NSW, Australia; National Nuclear Energy Agency of Indonesia, Tangerang, Indonesia.
| | - M L Smith
- Centre for Medical Radiation Physics, University of Wollongong, NSW, Australia; Radionuclide Metrology, Australian Nuclear Science and Technology Organisation, NSW, Australia
| | - W M van Wyngaardt
- Radionuclide Metrology, Australian Nuclear Science and Technology Organisation, NSW, Australia
| | - S Guatelli
- Centre for Medical Radiation Physics, University of Wollongong, NSW, Australia
| | - E Li
- Centre for Medical Radiation Physics, University of Wollongong, NSW, Australia
| | - A Rosenfeld
- Centre for Medical Radiation Physics, University of Wollongong, NSW, Australia
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6
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Kung L, Savage RM, da Silva EB, Polukis SA, Smith ML, Johnson ACB, Miller MA. The effects of air stress during storage and low packing density on the fermentation and aerobic stability of corn silage inoculated with Lactobacillus buchneri 40788. J Dairy Sci 2021; 104:4206-4222. [PMID: 33612226 DOI: 10.3168/jds.2020-19746] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 10/06/2020] [Accepted: 11/30/2020] [Indexed: 01/04/2023]
Abstract
We determined if a microbial inoculant could improve the fermentation and aerobic stability of corn silage subjected to various challenges during storage that included an air stress challenge and low packing density. In Experiment 1, whole-plant corn was untreated (CTR) or treated (INO, Lactobacillus buchneri 40788 and Pediococcus pentosaceus 12455. Five individually replicated 7.5-L silos, at a density of 240 kg of dry matter (DM)/m3, for each treatment were kept sealed (NAS) for 19 wk, air stressed early (ES, 3 h/wk for wk 1-9), or air stressed late during storage (LS, 3 h/wk for wk 10-19). Inoculation increased the number of agar-culturable lactic acid bacteria regardless of air stress status, but it did not affect the relative abundance of Lactobacillus. Early, but not late air stress, resulted in silages with a higher relative abundance of Acetobacter when compared with NAS. Silages treated with INO had greater concentrations of acetic acid than CTR. Numbers of yeasts were lowest for INO regardless of air stress and CTR-LS had the most yeasts among all treatments. Silages that were not air stressed had a higher relative abundance of Candida tropicalis than air stressed silages. Monascus purpureus was detected in ES and LS but not in NAS, and its relative abundance was numerically higher in CTR-ES than in INO-ES and statistically higher in CTR-LS compared with INO-LS. Early air stress numerically reduced aerobic stability compared with NAS, and there was a statistical tendency for lower stability in LS compared with NAS. Inoculation improved aerobic stability regardless of when the air stress occurred. In Experiment 2, corn silage was prepared with the same primary treatments of CTR and INO but was packed at a low (LD; 180 kg of DM/m3) or a normal (ND; 240 kg of DM/m3) density and sealed (NAS) or air stressed (AS; 24 h on d 28, 42, and 89) for 92 d of storage. The concentration of acetic acid was greater in INO compared with CTR and in AS compared with NAS. Numbers of yeasts were lower in NAS compared with AS regardless of inoculation and they were lower in INO-AS compared with CTR-AS. Treatment with INO improved aerobic stability but the improvement was better in NAS versus AS and better in ND versus LD. Overall, our experiments corroborate past findings showing that INO markedly improves the aerobic stability of corn silage but they are the first to show that improvement can be sustained even when the silage was exposed to regular air stresses and when packed at a low density.
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Affiliation(s)
- L Kung
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark 19716.
| | - R M Savage
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark 19716
| | - E B da Silva
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark 19716
| | - S A Polukis
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark 19716
| | - M L Smith
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark 19716
| | - A C B Johnson
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark 19716
| | - M A Miller
- Phaseolus Consulting, Wyndmoor, PA 19038
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7
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Bergeron CD, John JM, Sribhashyam M, Odonkor G, Oloruntoba O, Merianos AL, Horel S, Smith ML. County-Level Characteristics Driving Malnutrition Death Rates among Older Adults in Texas. J Nutr Health Aging 2021; 25:862-868. [PMID: 34409963 PMCID: PMC8013203 DOI: 10.1007/s12603-021-1626-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/09/2021] [Indexed: 11/26/2022]
Abstract
OBJECTIVES This study aims to identify older adult malnutrition in Texas, examine county-level characteristics associated with crude malnutrition death rates, and describe assets and opportunities available to address and improve malnutrition among the older population. DESIGN Secondary data analysis using the Centers for Disease Control and Prevention's WONDER online database, the U.S. Census 2014-2018 American Community Survey, and the U.S. Department of Agriculture's Food Access Research Atlas data. SETTING All 254 counties in the state of Texas. PARTICIPANTS Individuals aged 65 years and older. MEASUREMENT The dependent variable was the proportion of county-level malnutrition crude death rates. Independent variables included Health Provider Shortage Area designations, rurality, poverty status, food access, age, race, ethnicity, and education. RESULTS The overall malnutrition crude death rate in Texas was 65.6 deaths per 100,000 older Texans, ranging from 0 to 414.46 deaths per 100,000 depending on the county. Higher malnutrition crude death rates were associated with non-metropolitan counties (P=0.018), lower education (P=0.047), greater household poverty (P=0.010), and low food access (P<0.001). CONCLUSION Socioeconomic disadvantages at the county-level appear to be one of the root causes of malnutrition crude death rates in Texas.
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Affiliation(s)
- C D Bergeron
- Matthew Lee Smith, Department of Environmental and Occupational Health, School of Public Health, Texas A and M University, College Station, TX, USA,
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8
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da Silva EB, Smith ML, Savage RM, Polukis SA, Drouin P, Kung L. Effects of Lactobacillus hilgardii 4785 and Lactobacillus buchneri 40788 on the bacterial community, fermentation and aerobic stability of high-moisture corn silage. J Appl Microbiol 2020; 130:1481-1493. [PMID: 33040472 DOI: 10.1111/jam.14892] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 08/04/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 11/30/2022]
Abstract
AIMS To evaluate the capacity of Lactobacillus hilgardii and Lactobacillus buchneri on modifying the bacterial community and improving fermentation and aerobic stability of high-moisture corn (HMC). METHODS AND RESULTS High-moisture corn was untreated (CTR), treated with L. hilgardii (LH) or L. buchneri (LB) at 600 000 CFU per gram fresh weight, or with L. hilgardii and L. buchneri at 300 000 CFU per gram fresh weight each (LHLB), and stored for 10, 30 or 92 days. Compared to CTR, inoculated silages had higher Lactobacillaceae relative abundance, lower yeasts numbers and higher aerobic stability. Treatment with LHLB resulted in a higher acetic acid concentration than LH and higher 1,2 propanediol concentration than LB, such differences were numerically greater at 10 and 30 days but statistically greater at 92 days. At 10 days, all inoculated silages were more stable than CTR, but LHLB was even more stable than LB or LH. CONCLUSIONS The combination of L. hilgardii and L. buchneri had a synergistic effect on yeast inhibition, leading to greater improvements in aerobic stability as early as 10 days after ensiling. SIGNIFICANCE AND IMPACT OF THE STUDY Lactobacillus hilgardii, especially in combination with L. buchneri, can improve the aerobic stability of HMC after a very short period of ensiling.
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Affiliation(s)
- E B da Silva
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, USA
| | - M L Smith
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, USA
| | - R M Savage
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, USA
| | - S A Polukis
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, USA
| | - P Drouin
- Lallemand Specialties Inc, Milwaukee, WI, USA
| | - L Kung
- Department of Animal and Food Sciences, College of Agriculture and Natural Resources, University of Delaware, Newark, DE, USA
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9
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van Wyngaardt WM, Tobin SM, Lee S, Smith ML, Jackson TW, Ilter J, Howe B, Sarbutt A. Primary standardisation of technetium-99m by liquid scintillation coincidence counting. Appl Radiat Isot 2020; 156:108935. [PMID: 31675614 DOI: 10.1016/j.apradiso.2019.108935] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 09/26/2019] [Accepted: 10/09/2019] [Indexed: 11/18/2022]
Abstract
Technetium-99m was standardised by the 4π(LS)ce-γ coincidence extrapolation method. Sensitivity of the 4π(LS) channel to two types of radiation, namely conversion electrons and γ-rays, resulted in incorrect activity values being obtained when this was not adequately accounted for. Measurements were more robust when the LS detection efficiency was optimised, and when a γ-window setting was used that monitored the combined LS efficiency for conversion electrons and γ-rays. The primary standard was internationally compared through participation in the BIPM.RI(II)-K4.Tc99m key comparison.
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Affiliation(s)
- W M van Wyngaardt
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234, NSW, Australia.
| | - S M Tobin
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234, NSW, Australia
| | - S Lee
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234, NSW, Australia
| | - M L Smith
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234, NSW, Australia
| | - T W Jackson
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234, NSW, Australia
| | - J Ilter
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234, NSW, Australia
| | - B Howe
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234, NSW, Australia
| | - A Sarbutt
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, 2234, NSW, Australia
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10
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Nawani H, Smith ML, Wheeler AL, Widjaja E. Functional Connectivity Associated with Health-Related Quality of Life in Children with Focal Epilepsy. AJNR Am J Neuroradiol 2019; 40:1213-1220. [PMID: 31221633 DOI: 10.3174/ajnr.a6106] [Citation(s) in RCA: 1] [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] [Received: 02/26/2019] [Accepted: 05/16/2019] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Although functional connectivity has been linked to cognitive function in epilepsy, its relationship with physical, psychological, or social dysfunction is unknown. This study aimed to assess the relationship between network architecture from resting-state fMRI and health-related quality of life in children with medically intractable focal epilepsy. MATERIALS AND METHODS Forty-seven children with nonlesional focal epilepsy were included; 22 had frontal lobe epilepsy and 15 had temporal lobe epilepsy. We computed graph metrics of functional connectivity, including network segregation (clustering coefficient and modularity) and integration (characteristic path length and participation coefficient). Health-related quality of life was measured using the Quality of Life in Childhood Epilepsy questionnaire. We examined the associations between graph metrics and the Quality of Life in Childhood Epilepsy total and domains scores, with age, sex, age at seizure onset, fMRI motion, and network density as covariates. RESULTS There was a negative relationship between the clustering coefficient and total Quality of Life in Childhood Epilepsy score [t(40) = -2.0; P = .04] and social function [t(40) = -2.9; P = .005]. There was a positive association between the mean participation coefficient and total Quality of Life in Childhood Epilepsy score [t(40) = 2.2; P = .03] and cognition [t(40) = 3.8; P = .0004]. In temporal lobe epilepsy, there was a negative relationship between the clustering coefficient and total Quality of Life in Childhood Epilepsy score [t(8) = -2.8; P = .02] and social function [t(8) = -3.6; P = .0075] and between modularity and total Quality of Life in Childhood Epilepsy score [t(8) = -2.5; P = .04] and social function [t(8) = -4.4; P = .0021]. In frontal lobe epilepsy, there was no association between network segregation and integration and Quality of Life in Childhood Epilepsy total or domain scores. CONCLUSIONS Our findings indicate that there are other higher order brain functions beyond cognition, which may be linked with functional connectivity of the brain.
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Affiliation(s)
- H Nawani
- From Neurosciences and Mental Health (H.N., M.L.S., A.L.W., E.W.)
| | - M L Smith
- From Neurosciences and Mental Health (H.N., M.L.S., A.L.W., E.W.).,Departments of Psychology (M.L.S.)
| | - A L Wheeler
- From Neurosciences and Mental Health (H.N., M.L.S., A.L.W., E.W.) .,Physiology (A.L.W.), University of Toronto, Toronto, Ontario, Canada
| | - E Widjaja
- From Neurosciences and Mental Health (H.N., M.L.S., A.L.W., E.W.).,Diagnostic Imaging (E.W.).,Division of Neurology (E.W.), Hospital for Sick Children, Toronto, Ontario, Canada
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11
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Vollmer Dahlke DJ, Smith ML, Han G, Ory MG, Cohen E. Abstract P6-14-03: Metastatic breast cancer alliance's patient education and access to trials: Perceptions and actions. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p6-14-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Those living with metastatic breast cancer (MBC) have distinct and shifting concerns in regard to education and decision making in considering clinical trials as a treatment option. Clinical trials designs, are becoming increasingly complex, and many patients have concerns for biomarker requirements Aims/Research Questions
· What is the status of MBCA advocacy members' and partners' digital information, education and access to metastatic breast cancer trials?
· What plans do MBCA members/partners have for the next 6-18 months to educate and inform their constituents for the 2018 rollout of BreastCancerTrials.org's (BCT)Metastatic Trial Search (MTS) and Metastatic Trial Talk (MTT) and other trial matching systems?
· What are the top 5 barriers regarding trial enrollment?
· What are best practices for MBC trial education?
Research Methodology and Design
A comprehensive analysis was conducted comprising both secondary and primary research to inform these specific aims. Secondary research was conducted using previous capture of MBCA online digital resources and strengthened to include additional research on MBCA members and partners online resources including pages specifically devoted to clinical trials and metastatic clinical trials.
Mixed methods approaches include:
1) An assessment of MBCA members' and partners' digital media presence regarding MBC trials using a standardized form and rating system, and an analysis of MBCA members 2017 use of MTS using BCT secondary data;
2) Structured, recorded interviews with selected MBCA members/ partners, sharing the results of the assessments and querying them regarding their future plans and perceived barriers; and
3) Mixed methods analyses of the interview recordings using DeDoose to assess and articulate key trends and perceptions.
Statistical Methods
Simple frequency percentages and means were used in the assessment rankings of the MBCA members. DeDoose was used to provide mixed method analyses of the MBCA member and partner interviews. Results
Analysis of the MBCA members and partners websites and digital media showed that, increasingly, both groups use the full variety of digital media to educate their constituents regarding MBC clinical trials. The 13 MBCA advocacy members providing online access to BreastCancerTrials' MTS in 2017 provided 97% of the traffic to the MTS trial matching service. System types accessing the MTS widget were 57.3% desktops, 28.6% mobile devices and 14% tablets. Table 1 shows assessment totals of 5 categories of the 13 MBCA advocacy group members' websites using MTS as compared to the 19 MBCA members not using the widget. Table 2 shows the 2017 usage of BCT's MTS with 97% of the page views coming from MBCA members.
Table 1.Assessment Ratings of MBCA Advocacy Partners on Metastatic Trial Education/AccessAwareness of Trials (e.g. explains trial Phases)Knowledge SharingInterest in Metastatic Breast CancerAction Potential for clinical trial access or enrollmentTotal (0-100)13 MBCA Advocate Members with MTS widget22.1523.0024.3124.1593.6219 MBCA Members without MTS widget13.2113.9513.5311.9552.16
Table 2.2017 Use Of Metastatic Trial SearchBCT's Metastatic Trial Search (MTS) Results2017Annual Page views33,360Unique Sessions14,295Show Trials8,100Show Trials by month675Average Time on Site (minutes)3:34Total Engagement Events5,006
Citation Format: Vollmer Dahlke DJ, Smith ML, Han G, Ory MG, Cohen E. Metastatic breast cancer alliance's patient education and access to trials: Perceptions and actions [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-14-03.
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Affiliation(s)
- DJ Vollmer Dahlke
- TX A&M University's Center for Population Health and Aging, College Station, TX; University of California at San Francisco, San Francisco, CA
| | - ML Smith
- TX A&M University's Center for Population Health and Aging, College Station, TX; University of California at San Francisco, San Francisco, CA
| | - G Han
- TX A&M University's Center for Population Health and Aging, College Station, TX; University of California at San Francisco, San Francisco, CA
| | - MG Ory
- TX A&M University's Center for Population Health and Aging, College Station, TX; University of California at San Francisco, San Francisco, CA
| | - E Cohen
- TX A&M University's Center for Population Health and Aging, College Station, TX; University of California at San Francisco, San Francisco, CA
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12
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Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašić G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature 2018; 563:501-507. [PMID: 30429615 PMCID: PMC6421076 DOI: 10.1038/s41586-018-0692-z] [Citation(s) in RCA: 306] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 10/05/2018] [Indexed: 11/10/2022]
Abstract
Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector. An improved, fully re-annotated Aedes aegypti genome assembly (AaegL5) provides insights into the sex-determining M locus, chemosensory systems that help mosquitoes to hunt humans and loci involved in insecticide resistance and will help to generate intervention strategies to fight this deadly disease vector.
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Affiliation(s)
- Benjamin J Matthews
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, New York, NY, USA. .,Kavli Neural Systems Institute, New York, NY, USA.
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA
| | | | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - William J Glassford
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Margaret Herre
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.,Kavli Neural Systems Institute, New York, NY, USA
| | - Seth N Redmond
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Gareth D Weedall
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK.,Liverpool John Moores University, Liverpool, UK
| | - Yang Wu
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China.,Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - Sanjit S Batra
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA
| | - Carlos A Brito-Sierra
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Steven D Buckingham
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | - Corey L Campbell
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Saki Chan
- Bionano Genomics, San Diego, CA, USA
| | - Eric Cox
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin R Evans
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Thanyalak Fansiri
- Vector Biology and Control Section, Department of Entomology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Igor Filipović
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Albin Fontaine
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Unité de Parasitologie et Entomologie, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 2000, Paris, France.,Aix Marseille Université, IRD, AP-HM, SSA, UMR Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), IHU - Méditerranée Infection, Marseille, France
| | - Andrea Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | | | - Vinita S Joardar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Andrew K Jones
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Raissa G G Kay
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Vamsi K Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | - Gareth J Lycett
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | | | - Michael R Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Arina D Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA
| | - Frederick A Partridge
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | | | - Aviva Presser Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Bioengineering, Rice University, Houston, TX, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA
| | - Vidya Ramasamy
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sourav Roy
- Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Karla Saavedra-Rodriguez
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Shruti Sharan
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Atashi Sharma
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA
| | | | - Joe Turner
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | | | - Zhilei Zhao
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Omar S Akbari
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - William C Black
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Han Cao
- Bionano Genomics, San Diego, CA, USA
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Catherine A Hill
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Alexander S Raikhel
- Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - David B Sattelle
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | - Igor V Sharakhov
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA.,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | | | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard S Mann
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 2000, Paris, France
| | - Jeffrey R Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Maria V Sharakhova
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA.,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Zhijian Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Carolyn S McBride
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | | | | | - Daniel E Neafsey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Adam M Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Leslie B Vosshall
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA.,Kavli Neural Systems Institute, New York, NY, USA
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13
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Washington TR, Hilliard TS, Mingo CA, Hall RK, Smith ML, Lea JI. ORGANIZATIONAL READINESS TO IMPLEMENT HEALTH PROMOTION PROGRAMS IN HEALTHCARE. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.1493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - T S Hilliard
- American Institutes for Research, Chapel Hill, North Carolina
| | - C A Mingo
- Georgia State University, Atlanta, Georgia
| | - R K Hall
- Duke University School of Medicine, Durham, North Carolina
| | - M L Smith
- Texas A&M School of Public Health, College Station, Texas
| | - J I Lea
- Emory University School of Medicine, Atlanta, Georgia
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14
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Zhao N, Sebastiano V, Moshkina N, Mena N, Hultquist J, Jimenez-Morales D, Ma Y, Rialdi A, Albrecht R, Fenouil R, Sánchez-Aparicio MT, Ayllon J, Ravisankar S, Haddad B, Ho JSY, Low D, Jin J, Yurchenko V, Prinjha RK, Tarakhovsky A, Squatrito M, Pinto D, Allette K, Byun M, Smith ML, Sebra R, Guccione E, Tumpey T, Krogan N, Greenbaum B, van Bakel H, García-Sastre A, Marazzi I. Influenza virus infection causes global RNAPII termination defects. Nat Struct Mol Biol 2018; 25:885-893. [PMID: 30177761 PMCID: PMC10754036 DOI: 10.1038/s41594-018-0124-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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] [Received: 11/02/2017] [Accepted: 08/09/2018] [Indexed: 12/23/2022]
Abstract
Viral infection perturbs host cells and can be used to uncover regulatory mechanisms controlling cellular responses and susceptibility to infections. Using cell biological, biochemical, and genetic tools, we reveal that influenza A virus (IAV) infection induces global transcriptional defects at the 3' ends of active host genes and RNA polymerase II (RNAPII) run-through into extragenic regions. Deregulated RNAPII leads to expression of aberrant RNAs (3' extensions and host-gene fusions) that ultimately cause global transcriptional downregulation of physiological transcripts, an effect influencing antiviral response and virulence. This phenomenon occurs with multiple strains of IAV, is dependent on influenza NS1 protein, and can be modulated by SUMOylation of an intrinsically disordered region (IDR) of NS1 expressed by the 1918 pandemic IAV strain. Our data identify a strategy used by IAV to suppress host gene expression and indicate that polymorphisms in IDRs of viral proteins can affect the outcome of an infection.
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Affiliation(s)
- Nan Zhao
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vittorio Sebastiano
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Natasha Moshkina
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nacho Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judd Hultquist
- Department of Medicine (Infectious Diseases), Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David Jimenez-Morales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Yixuan Ma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alex Rialdi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Randy Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Romain Fenouil
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maria Teresa Sánchez-Aparicio
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan Ayllon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sweta Ravisankar
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Bahareh Haddad
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Jessica Sook Yuin Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Diana Low
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Rab K Prinjha
- Epinova Epigenetics Discovery Performance Unit, Immuno-Inflammation Therapy Area, GlaxoSmithKline, Medicines Research Centre, Stevenage, UK
| | - Alexander Tarakhovsky
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY, USA
| | - Massimo Squatrito
- Cancer Cell Biology Programme, Centro Nacional de Investigaciones Oncológicas, CNIO, Madrid, Spain
| | - Dalila Pinto
- Department of Psychiatry, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimaada Allette
- Department of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minji Byun
- Department of Medicine, Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa Laird Smith
- Department of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Terrence Tumpey
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin Greenbaum
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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15
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Law N, Smith ML, Widjaja E. Thalamocortical Connections and Executive Function in Pediatric Temporal and Frontal Lobe Epilepsy. AJNR Am J Neuroradiol 2018; 39:1523-1529. [PMID: 29880477 DOI: 10.3174/ajnr.a5691] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 04/11/2018] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Largely accepted in the literature is the role the interconnections between the thalamus and cortex play in generalized epilepsy. However, thalamocortical involvement is less understood in focal epilepsy in terms of the effect of seizures on thalamocortical circuitry in the developing brain and subsequent cognitive outcome. We investigated thalamocortical pathway microstructure in pediatric frontal lobe epilepsy and temporal lobe epilepsy and examined the associations between pathway microstructure and measures of executive function. MATERIALS AND METHODS We examined thalamocortical connections in 24 children with frontal lobe epilepsy, 17 patients with temporal lobe epilepsy, and 25 healthy children using DTI. We investigated several executive function measures in patients and controls, which were distilled into latent executive function components to compare among groups, and the associations between measures of thalamocortical microstructure and executive function. RESULTS We found no differences in thalamocortical pathway microstructure between the groups, but aspects of executive function (mental flexibility/inhibition/shifting) were impaired in the frontal lobe epilepsy group compared with controls. In patients with frontal lobe epilepsy, younger age at seizure onset and a greater number of antiepileptic drugs were associated with DTI indices indicative of damaged/less developed thalamocortical pathways. In patients with temporal lobe epilepsy, poorer performance on all measures of executive function was associated with DTI indices reflective of damaged/less developed pathways. CONCLUSIONS Our results give insight into vulnerable neural networks in pediatric focal epilepsy and suggest thalamocortical pathway damage as a potential mechanism of executive function impairment in temporal lobe epilepsy but not frontal lobe epilepsy. Identifying structure-function relations can help inform how we measure functional and cognitive/behavioral outcomes in these populations.
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Affiliation(s)
- N Law
- From the Department of Psychology (N.L., M.L.S.), University of Toronto, Toronto, Ontario, Canada.,Department of Psychology (N.L., M.L.S.).,Program in Neurosciences and Mental Health (N.L., M.L.S.)
| | - M L Smith
- From the Department of Psychology (N.L., M.L.S.), University of Toronto, Toronto, Ontario, Canada.,Department of Psychology (N.L., M.L.S.).,Program in Neurosciences and Mental Health (N.L., M.L.S.)
| | - E Widjaja
- Diagnostic Imaging (E.W.) .,Division of Neurology (E.W.), Hospital for Sick Children, Toronto, Ontario, Canada
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16
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Hansen MF, Smith ML, Smith LN, Abdul Jabbar K, Forbes D. Automated monitoring of dairy cow body condition, mobility and weight using a single 3D video capture device. COMPUT IND 2018; 98:14-22. [PMID: 29997403 PMCID: PMC6034442 DOI: 10.1016/j.compind.2018.02.011] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we propose a low-cost automated system for the unobtrusive and continuous welfare monitoring of dairy cattle on the farm. We argue that effective and regular monitoring of multiple condition traits is not currently practicable and go on to propose 3D imaging technology able to acquire differing forms of related animal condition data (body condition, lameness and weight), concurrently using a single device. Results obtained under farm conditions in continuous operation are shown to be comparable or better than manual scoring of the herd. We also consider inherent limitations of using scoring and argue that sensitivity to relative change over successive observations offers greater benefit than the use of what may be considered abstract and arbitrary scoring systems.
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Affiliation(s)
- M F Hansen
- Centre for Machine Vision, BRL, UWE, Bristol, UK
| | - M L Smith
- Centre for Machine Vision, BRL, UWE, Bristol, UK
| | - L N Smith
- Centre for Machine Vision, BRL, UWE, Bristol, UK
| | | | - D Forbes
- Kingshay Farming & Conservation Ltd, Glastonbury, Somerset, UK
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17
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van Wyngaardt WM, Smith ML, Jackson TW, Howe B, Tobin SM, Reinhard MI. Development of the Australian Standard for Germanium-68 by two Liquid Scintillation Counting methods. Appl Radiat Isot 2018; 134:79-84. [PMID: 29102160 DOI: 10.1016/j.apradiso.2017.10.005] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 09/04/2017] [Accepted: 10/02/2017] [Indexed: 10/18/2022]
Abstract
In response to the increasing application of 68Ge/68Ga and 68Ga in nuclear medicine, an international comparison of activity measurement of 68Ge in equilibrium with 68Ga was organised. ANSTO standardised the comparison solution by the 4π(LS)β+-γ coincidence extrapolation and TDCR efficiency calculation methods, with excellent agreement between the two results. The primary standard was transferred to the ANSTO Secondary Standard Ionisation Chamber. Internationally traceable Australian Certified Reference Materials (ACRMs) of 68Ge/68Ga can now be prepared in various measurement geometries applied in nuclear medicine.
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Affiliation(s)
- W M van Wyngaardt
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights 2234, NSW, Australia.
| | - M L Smith
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights 2234, NSW, Australia
| | - T W Jackson
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights 2234, NSW, Australia
| | - B Howe
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights 2234, NSW, Australia
| | - S M Tobin
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights 2234, NSW, Australia
| | - M I Reinhard
- Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights 2234, NSW, Australia
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18
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Frank ES, Basila D, Collyar D, Pinto D, Smith ML, Geirisch J, Lynch T, Hwang S. Abstract P5-17-04: Changing the DCIS conversation: Development of an alternative discourse by patient stakeholders in the COMET study. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p5-17-04] [Citation(s) in RCA: 1] [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: 11/16/2022]
Abstract
Abstract
The conversation about ductal carcinoma in situ (DCIS) is structured and influenced by traditional oncology values and beliefs, resulting in current standards of guideline concordant care (GCC). It is now widely known that DCIS is a heterogeneous condition requiring a tailored treatment approach based on characteristics of the specific lesion. Further, “low-risk” DCIS—defined as low grade, hormone-receptor positive condition—may be a subset with lower likelihood of progression to invasive breast cancer. Yet, most women diagnosed with any type of DCIS are encouraged to undergo the same immediate, aggressive treatments that women diagnosed with invasive breast cancer receive. Emerging evidence suggests that surgery may not increase overall survival compared to no surgery in many women diagnosed with low-risk DCIS.
The COMET (Comparison of Operative to Monitoring and Endocrine Therapy) study is a new randomized, prospective clinical trial funded by the Patient-Centered Outcomes Research Institute that aims to determine whether active surveillance is a safe and reasonable alternative to GCC for patients with low-risk DCIS. COMET also seeks to change the way patients, providers, and other key stakeholders view DCIS management options. Thus, COMET governance integrates patient collaborators into every aspect of planning and development via a Patient Leadership Team (PLT) and an independent external multi-stakeholder advisory board (SAB). The PLT is a fully integrated, yet autonomous part of the COMET study governance and is comprised of 4 patient advocates who meet independently and with COMET Principal Investigators (PIs). The SAB is a fully external and independent body of clinicians, content experts, payers, patients and patient advocates, and policymaker advisors.
To facilitate the cultural shift, the PLT developed communication materials with language and terminology that aims to communicate a diagnosis of DCIS without increasing unnecessary fear and anxiety that often accompanies a diagnosis of invasive cancer. In collaboration with study team PI's and the SAB, PLT also has developed content for a newly established website (www.DCISoptions.org), which includes patient-centered materials that aim to help newly diagnosed patients understand that a majority of DCIS is low-risk and that they have time to make informed decisions about their care.
The PLT contends that managing DCIS is as much a cultural phenomenon as a scientific one. As such, changing the conversation about DCIS between medical providers and patients is essential for generating a cultural shift in understanding the condition, correcting risk perception, and enabling improvement in patient experience. The novel approach of a stand-alone PLT that is also integrated throughout the trial's stakeholder structure ensures patient-centered involvement across all aspects of the study. The unique talents of each stakeholder group are leveraged in a unified effort to educate the DCIS community about low-risk DCIS, with the overarching goal of enabling a patient to choose the treatment approach that best reflects her risk profile and personal preferences, thus minimizing potential physical, emotional, and financial harms.
Citation Format: Frank ES, Basila D, Collyar D, Pinto D, Smith ML, Geirisch J, Lynch T, Hwang S. Changing the DCIS conversation: Development of an alternative discourse by patient stakeholders in the COMET study [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-17-04.
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Affiliation(s)
- ES Frank
- Dana-Farber Cancer Institute, Boston, MA; Patient Advocates in Research, Danville, CA; Research Advocacy Network, Plano, TX; Duke University, Durham, NC
| | - D Basila
- Dana-Farber Cancer Institute, Boston, MA; Patient Advocates in Research, Danville, CA; Research Advocacy Network, Plano, TX; Duke University, Durham, NC
| | - D Collyar
- Dana-Farber Cancer Institute, Boston, MA; Patient Advocates in Research, Danville, CA; Research Advocacy Network, Plano, TX; Duke University, Durham, NC
| | - D Pinto
- Dana-Farber Cancer Institute, Boston, MA; Patient Advocates in Research, Danville, CA; Research Advocacy Network, Plano, TX; Duke University, Durham, NC
| | - ML Smith
- Dana-Farber Cancer Institute, Boston, MA; Patient Advocates in Research, Danville, CA; Research Advocacy Network, Plano, TX; Duke University, Durham, NC
| | - J Geirisch
- Dana-Farber Cancer Institute, Boston, MA; Patient Advocates in Research, Danville, CA; Research Advocacy Network, Plano, TX; Duke University, Durham, NC
| | - T Lynch
- Dana-Farber Cancer Institute, Boston, MA; Patient Advocates in Research, Danville, CA; Research Advocacy Network, Plano, TX; Duke University, Durham, NC
| | - S Hwang
- Dana-Farber Cancer Institute, Boston, MA; Patient Advocates in Research, Danville, CA; Research Advocacy Network, Plano, TX; Duke University, Durham, NC
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19
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Hemadou A, Giudicelli V, Smith ML, Lefranc MP, Duroux P, Kossida S, Heiner C, Hepler NL, Kuijpers J, Groppi A, Korlach J, Mondon P, Ottones F, Jacobin-Valat MJ, Laroche-Traineau J, Clofent-Sanchez G. Pacific Biosciences Sequencing and IMGT/HighV-QUEST Analysis of Full-Length Single Chain Fragment Variable from an In Vivo Selected Phage-Display Combinatorial Library. Front Immunol 2017; 8:1796. [PMID: 29326697 PMCID: PMC5742356 DOI: 10.3389/fimmu.2017.01796] [Citation(s) in RCA: 20] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 11/30/2017] [Indexed: 12/14/2022] Open
Abstract
Phage-display selection of immunoglobulin (IG) or antibody single chain Fragment variable (scFv) from combinatorial libraries is widely used for identifying new antibodies for novel targets. Next-generation sequencing (NGS) has recently emerged as a new method for the high throughput characterization of IG and T cell receptor (TR) immune repertoires both in vivo and in vitro. However, challenges remain for the NGS sequencing of scFv from combinatorial libraries owing to the scFv length (>800 bp) and the presence of two variable domains [variable heavy (VH) and variable light (VL) for IG] associated by a peptide linker in a single chain. Here, we show that single-molecule real-time (SMRT) sequencing with the Pacific Biosciences RS II platform allows for the generation of full-length scFv reads obtained from an in vivo selection of scFv-phages in an animal model of atherosclerosis. We first amplified the DNA of the phagemid inserts from scFv-phages eluted from an aortic section at the third round of the in vivo selection. From this amplified DNA, 450,558 reads were obtained from 15 SMRT cells. Highly accurate circular consensus sequences from these reads were generated, filtered by quality and then analyzed by IMGT/HighV-QUEST with the functionality for scFv. Full-length scFv were identified and characterized in 348,659 reads. Full-length scFv sequencing is an absolute requirement for analyzing the associated VH and VL domains enriched during the in vivo panning rounds. In order to further validate the ability of SMRT sequencing to provide high quality, full-length scFv sequences, we tracked the reads of an scFv-phage clone P3 previously identified by biological assays and Sanger sequencing. Sixty P3 reads showed 100% identity with the full-length scFv of 767 bp, 53 of them covering the whole insert of 977 bp, which encompassed the primer sequences. The remaining seven reads were identical over a shortened length of 939 bp that excludes the vicinity of primers at both ends. Interestingly these reads were obtained from each of the 15 SMRT cells. Thus, the SMRT sequencing method and the IMGT/HighV-QUEST functionality for scFv provides a straightforward protocol for characterization of full-length scFv from combinatorial phage libraries.
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Affiliation(s)
| | - Véronique Giudicelli
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Institut de Génétique Humaine, IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France
| | | | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Institut de Génétique Humaine, IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France
| | - Patrice Duroux
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Institut de Génétique Humaine, IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France
| | - Sofia Kossida
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Institut de Génétique Humaine, IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France
| | | | | | | | - Alexis Groppi
- Université de Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB), Bordeaux, France
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20
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Landais E, Murrell B, Briney B, Murrell S, Rantalainen K, Berndsen ZT, Ramos A, Wickramasinghe L, Smith ML, Eren K, de Val N, Wu M, Cappelletti A, Umotoy J, Lie Y, Wrin T, Algate P, Chan-Hui PY, Karita E, Ward AB, Wilson IA, Burton DR, Smith D, Pond SLK, Poignard P. HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage. Immunity 2017; 47:990-1003.e9. [PMID: 29166592 PMCID: PMC5736302 DOI: 10.1016/j.immuni.2017.11.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 08/08/2017] [Accepted: 10/31/2017] [Indexed: 01/16/2023]
Abstract
Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb lineage targeting the Env V2 apex and the Ab-Env co-evolution that led to development of neutralization breadth. The lineage Abs bore an anionic heavy chain complementarity-determining region 3 (CDRH3) of 25 amino acids, among the shortest known for this class of Abs, and achieved breadth with only 10% nucleotide somatic hypermutation and no insertions or deletions. The data suggested a role for Env glycoform heterogeneity in the activation of the lineage germline B cell. Finally, we showed that localized diversity at key V2 epitope residues drove bnAb maturation toward breadth, mirroring the Env evolution pattern described for another donor who developed V2-apex targeting bnAbs. Overall, these findings suggest potential strategies for vaccine approaches based on germline-targeting and serial immunogen design.
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Affiliation(s)
- Elise Landais
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA.
| | - Ben Murrell
- Department of Medicine, University of California San Diego, San Diego, CA 92103, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sasha Murrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Zachary T Berndsen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alejandra Ramos
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Lalinda Wickramasinghe
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Melissa Laird Smith
- Icahn School of Medicine and Icahn Institute for Genomics and Multiscale Biology at Mount Sinai, New York, NY 10029, USA
| | - Kemal Eren
- Biomedical Informatics, University of California San Diego, San Diego, CA 92103, USA; Bioinformatics and Systems Biology, University of California San Diego, San Diego, CA 92103, USA
| | - Natalia de Val
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Audrey Cappelletti
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Institut de Biologie Structurale, Université Grenoble Alpes, Commissariat a l'Energie Atomique, Centre National de Recherche Scientifique and Centre Hospitalier Universitaire Grenoble Alpes, 38044 Grenoble, France
| | - Jeffrey Umotoy
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Yolanda Lie
- Monogram Biosciences Inc., Laboratory Corporation of America Holdings, San Francisco CA 94080, USA
| | - Terri Wrin
- Monogram Biosciences Inc., Laboratory Corporation of America Holdings, San Francisco CA 94080, USA
| | - Paul Algate
- Theraclone Sciences, Inc., Seattle, WA 98104, USA
| | | | - Etienne Karita
- Rwanda-Zambia HIV Research Group, Project San Francisco, Kigali, Rwanda
| | | | | | - Andrew B Ward
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02114, USA
| | - Davey Smith
- Department of Medicine, University of California San Diego, San Diego, CA 92103, USA; Veterans Affairs Healthcare System, San Diego, CA 92161, USA
| | | | - Pascal Poignard
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA; Institut de Biologie Structurale, Université Grenoble Alpes, Commissariat a l'Energie Atomique, Centre National de Recherche Scientifique and Centre Hospitalier Universitaire Grenoble Alpes, 38044 Grenoble, France.
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21
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Patel AB, Mangold AR, Costello CM, Nagel TH, Smith ML, Hayden RE, Sekulic A. Frequent loss of inositol polyphosphate-5-phosphatase in oropharyngeal squamous cell carcinoma. J Eur Acad Dermatol Venereol 2017; 32:e36-e37. [PMID: 28696004 DOI: 10.1111/jdv.14462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- A B Patel
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Phoenix, AZ, USA
| | - A R Mangold
- Department of Dermatology, Mayo Clinic, Scottsdale, AZ, USA
| | - C M Costello
- Department of Dermatology, Mayo Clinic, Scottsdale, AZ, USA.,University of Arizona College of Medicine - Tucson, Tucson, AZ, USA
| | - T H Nagel
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Phoenix, AZ, USA
| | - M L Smith
- Department of Pathology, Mayo Clinic, Phoenix, AZ, USA
| | - R E Hayden
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Phoenix, AZ, USA
| | - A Sekulic
- Department of Dermatology, Mayo Clinic, Scottsdale, AZ, USA
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22
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Abstract
Background The growing prevalence of chronic conditions in the ageing workforce has been shown to have a negative impact in terms of optimal work performance and quality of life. It is therefore important to understand the factors associated with sickness absence due to health problems. Aims To examine the socio-demographics, health status indicators, barriers to self-care and social support associated with working adults missing work because of chronic conditions. Methods We analysed data from working adults in the USA with one or more chronic conditions who completed the National Council on Aging (NCOA) Chronic Care Survey. Analyses were performed using SPSS version 22; independent sample t-tests and chi-squared tests were used to compare sample characteristics and logistic regression was used to assess factors associated with missed work as a dichotomous outcome variable. Results Among the 250 study subjects, employees who reported poorer general health status [odd ratio (OR) = 1.62, P < 0.05], more physician visits (OR = 1.45, P < 0.01), not having enough money for their health (OR = 3.69, P < 0.01) and a higher reliance on their co-workers (OR = 1.71, P < 0.05) were significantly more likely to report sickness absence due to their chronic conditions. Conclusions To reduce absences among employees with chronic conditions, employers need to understand the importance of factors such as employee income, resources and knowledge of disease self-care. US employers should explore opportunities for employees to offset health care costs, apply appropriate time-flexible work policies and encourage employees' participation in health knowledge enhancing interventions.
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Affiliation(s)
- L Meng
- Workplace Health Group, Department of Health Promotion and Behavior, College of Public Health, The University of Georgia, 346 Wright Hall, Athens, GA 30602, USA
| | - K T Robinson
- Workplace Health Group, Department of Health Promotion and Behavior, College of Public Health, The University of Georgia, 346 Wright Hall, Athens, GA 30602, USA
| | - M L Smith
- Institute of Gerontology, Department of Health Promotion and Behavior, College of Public Health, The University of Georgia, #101 Hudson Hall, Athens, GA 30602, USA.,Center for Population Health and Aging, Department of Health Promotion and Community Health Sciences, School of Public Health, Texas A&M University, TAMU 1266, College Station, TX 77842, USA
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23
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Watson CT, Matsen FA, Jackson KJL, Bashir A, Smith ML, Glanville J, Breden F, Kleinstein SH, Collins AM, Busse CE. Comment on “A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data”. J I 2017; 198:3371-3373. [DOI: 10.4049/jimmunol.1700306] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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24
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Smith ML, McGuinness J, O'Reilly MK, Nolke L, Murray JG, Jones JFX. The role of 3D printing in preoperative planning for heart transplantation in complex congenital heart disease. Ir J Med Sci 2017; 186:753-756. [PMID: 28124282 DOI: 10.1007/s11845-017-1564-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 01/09/2017] [Accepted: 01/16/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The presence of a structural cardiac defect in the setting of dextrocardia is extremely rare. Graspable models allow enhanced appreciation of aberrant structures and vascular relations, particularly in rare and complex cases. This is the first case report of the use of a replica of a patients' anatomy to plan the surgical strategy in the setting of dextrocardia. AIMS We intend to demonstrate the benefit of three-dimensional printing to enhance preoperative planning in complex congenital heart disease undergoing heart transplantation. The anomalous structures encountered include situs inversus dextrocardia, transposition of the great vessels, a single atrium and a dilated double-outlet single right ventricle. METHODS Computed Tomography acquisition was performed with the use of ECG multiphase gating technology and contrast enhancement. The structures of interest were segmented and the generated 3D mesh was exported as a stereolithographic (STL) file. The model was printed on a Z-Corp 250 binder jetting printer. Post processing techniques were used to enhance model strength. RESULTS Pre-operative 3D visualisation of the patients' anatomy allowed for a more comprehensive surgical strategy to be planned, thus reducing the intra-operative duration and cross-clamp time which are recognised to correlate with reduced patient morbidity. CONCLUSION The ongoing advances in medical image procurement and 3D processing software and printing technology will continue to enhance preoperative planning and thereby improve patient care. We demonstrate the pivotal role played by such technologies in advancing spatial comprehension of complex aberrant anatomy.
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Affiliation(s)
- M L Smith
- Discipline of Anatomy, School of Medicine, University College Dublin, Dublin 4, Ireland.
| | - J McGuinness
- Department of Cardiothoracic Surgery, Mater Misericordiae University Hospital, Eccles Street, Dublin, Ireland
| | - M K O'Reilly
- Department of Radiology, Mater Misericordiae University Hospital, Eccles Street, Dublin, Ireland
| | - L Nolke
- Department of Cardiothoracic Surgery, Mater Misericordiae University Hospital, Eccles Street, Dublin, Ireland
| | - J G Murray
- Department of Radiology, Mater Misericordiae University Hospital, Eccles Street, Dublin, Ireland
| | - J F X Jones
- Discipline of Anatomy, School of Medicine, University College Dublin, Dublin 4, Ireland
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25
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Giardino WJ, Rodriguez ED, Smith ML, Ford MM, Galili D, Mitchell SH, Chen A, Ryabinin AE. Control of chronic excessive alcohol drinking by genetic manipulation of the Edinger-Westphal nucleus urocortin-1 neuropeptide system. Transl Psychiatry 2017; 7:e1021. [PMID: 28140406 PMCID: PMC5299395 DOI: 10.1038/tp.2016.293] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/25/2016] [Accepted: 12/15/2016] [Indexed: 11/23/2022] Open
Abstract
Midbrain neurons of the centrally projecting Edinger-Westphal nucleus (EWcp) are activated by alcohol, and enriched with stress-responsive neuropeptide modulators (including the paralog of corticotropin-releasing factor, urocortin-1). Evidence suggests that EWcp neurons promote behavioral processes for alcohol-seeking and consumption, but a definitive role for these cells remains elusive. Here we combined targeted viral manipulations and gene array profiling of EWcp neurons with mass behavioral phenotyping in C57BL/6 J mice to directly define the links between EWcp-specific urocortin-1 expression and voluntary binge alcohol intake, demonstrating a specific importance for EWcp urocortin-1 activity in escalation of alcohol intake.
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Affiliation(s)
- W J Giardino
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - E D Rodriguez
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - M L Smith
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - M M Ford
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - D Galili
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - S H Mitchell
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - A Chen
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel,Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - A E Ryabinin
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA,Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. E-mail:
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26
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Heilman RL, Mathur A, Smith ML, Kaplan B, Reddy KS. Increasing the Use of Kidneys From Unconventional and High-Risk Deceased Donors. Am J Transplant 2016; 16:3086-3092. [PMID: 27172238 DOI: 10.1111/ajt.13867] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [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: 03/21/2016] [Revised: 04/19/2016] [Accepted: 05/03/2016] [Indexed: 01/25/2023]
Abstract
In this paper, we have reviewed the literature and report on kidney donors that are currently used at relatively low rates. Kidneys from donors with acute kidney injury (AKI) seem to have outcomes equivalent to those from donors without AKI, provided one can rule out significant cortical necrosis. Kidneys from donors with preexisting diabetes or hypertension may have marginally lower aggregate survival but still provide patients with a significant benefit over remaining on the wait list. The Kidney Donor Profile Index derives only an aggregate association with survival with a very modest C statistic; therefore, the data indicated that this index should not be the sole reason to discard a kidney, except perhaps in patients with extremely low estimated posttransplant survival scores. It is important to note that the Scientific Registry of Transplant Recipients models of risk adjustment should allay concerns regarding regulatory issues for observed outcomes falling below expectations. The successful utilization of kidneys from donation after cardiac death over the past decade shows how expanding our thinking can translate into more patients benefiting from transplantation. Given the growing number of patients on the wait list, broadening our approach to kidney acceptance could have an important impact on the population with end-stage renal disease. Many lives could be prolonged by carefully considering use of kidneys that are often discarded.
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Affiliation(s)
- R L Heilman
- Department of Medicine, Mayo Clinic, Phoenix, AZ.
| | - A Mathur
- Department of Surgery, Mayo Clinic, Phoenix, AZ
| | - M L Smith
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ
| | - B Kaplan
- Department of Medicine, Mayo Clinic, Phoenix, AZ
| | - K S Reddy
- Department of Surgery, Mayo Clinic, Phoenix, AZ
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27
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Demetris AJ, Bellamy C, Hübscher SG, O'Leary J, Randhawa PS, Feng S, Neil D, Colvin RB, McCaughan G, Fung JJ, Del Bello A, Reinholt FP, Haga H, Adeyi O, Czaja AJ, Schiano T, Fiel MI, Smith ML, Sebagh M, Tanigawa RY, Yilmaz F, Alexander G, Baiocchi L, Balasubramanian M, Batal I, Bhan AK, Bucuvalas J, Cerski CTS, Charlotte F, de Vera ME, ElMonayeri M, Fontes P, Furth EE, Gouw ASH, Hafezi-Bakhtiari S, Hart J, Honsova E, Ismail W, Itoh T, Jhala NC, Khettry U, Klintmalm GB, Knechtle S, Koshiba T, Kozlowski T, Lassman CR, Lerut J, Levitsky J, Licini L, Liotta R, Mazariegos G, Minervini MI, Misdraji J, Mohanakumar T, Mölne J, Nasser I, Neuberger J, O'Neil M, Pappo O, Petrovic L, Ruiz P, Sağol Ö, Sanchez Fueyo A, Sasatomi E, Shaked A, Shiller M, Shimizu T, Sis B, Sonzogni A, Stevenson HL, Thung SN, Tisone G, Tsamandas AC, Wernerson A, Wu T, Zeevi A, Zen Y. 2016 Comprehensive Update of the Banff Working Group on Liver Allograft Pathology: Introduction of Antibody-Mediated Rejection. Am J Transplant 2016; 16:2816-2835. [PMID: 27273869 DOI: 10.1111/ajt.13909] [Citation(s) in RCA: 361] [Impact Index Per Article: 45.1] [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: 05/06/2016] [Revised: 06/01/2016] [Accepted: 05/25/2016] [Indexed: 02/06/2023]
Abstract
The Banff Working Group on Liver Allograft Pathology reviewed and discussed literature evidence regarding antibody-mediated liver allograft rejection at the 11th (Paris, France, June 5-10, 2011), 12th (Comandatuba, Brazil, August 19-23, 2013), and 13th (Vancouver, British Columbia, Canada, October 5-10, 2015) meetings of the Banff Conference on Allograft Pathology. Discussion continued online. The primary goal was to introduce guidelines and consensus criteria for the diagnosis of liver allograft antibody-mediated rejection and provide a comprehensive update of all Banff Schema recommendations. Included are new recommendations for complement component 4d tissue staining and interpretation, staging liver allograft fibrosis, and findings related to immunosuppression minimization. In an effort to create a single reference document, previous unchanged criteria are also included.
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Affiliation(s)
- A J Demetris
- University of Pittsburgh Medical Center, Pittsburgh, PA
| | - C Bellamy
- The University of Edinburgh, Edinburgh, Scotland
| | | | - J O'Leary
- Baylor University Medical Center, Dallas, TX
| | - P S Randhawa
- University of Pittsburgh Medical Center, Pittsburgh, PA
| | - S Feng
- University of California San Francisco Medical Center, San Francisco, CA
| | - D Neil
- Queen Elizabeth Hospital Birmingham, Birmingham, UK
| | - R B Colvin
- Massachusetts General Hospital, Boston, MA
| | - G McCaughan
- Royal Prince Alfred Hospital, Sydney, Australia
| | | | | | - F P Reinholt
- Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - H Haga
- Kyoto University Hospital, Kyoto, Japan
| | - O Adeyi
- University Health Network and University of Toronto, Toronto, Canada
| | - A J Czaja
- Mayo Clinic College of Medicine, Rochester, MN
| | - T Schiano
- Mount Sinai Medical Center, New York, NY
| | - M I Fiel
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - M L Smith
- Mayo Clinic Health System, Scottsdale, AZ
| | - M Sebagh
- AP-HP Hôpital Paul-Brousse, Paris, France
| | - R Y Tanigawa
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - F Yilmaz
- University of Ege, Faculty of Medicine, Izmir, Turkey
| | | | - L Baiocchi
- Policlinico Universitario Tor Vergata, Rome, Italy
| | | | - I Batal
- Columbia University College of Physicians and Surgeons, New York, NY
| | - A K Bhan
- Massachusetts General Hospital, Boston, MA
| | - J Bucuvalas
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - C T S Cerski
- Universidade Federal do Rio Grande do Sul, Hospital de Clinicas de Porto Alegre, Porto Alegre, Brazil
| | | | | | - M ElMonayeri
- Ain Shams University, Wady El-Neel Hospital, Cairo, Egypt
| | - P Fontes
- University of Pittsburgh Medical Center, Pittsburgh, PA
| | - E E Furth
- Hospital of the University of Pennsylvania, Philadelphia, PA
| | - A S H Gouw
- University Medical Center Groningen, Groningen, the Netherlands
| | | | - J Hart
- University of Chicago Hospitals, Chicago, IL
| | - E Honsova
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - W Ismail
- Beni-Suef University, Beni-Suef, Egypt
| | - T Itoh
- Kobe University Hospital, Kobe, Japan
| | | | - U Khettry
- Lahey Hospital and Medical Center, Burlington, MA
| | | | - S Knechtle
- Duke University Health System, Durham, NC
| | - T Koshiba
- Soma Central Hospital, Soma, Fukushima, Japan
| | - T Kozlowski
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - C R Lassman
- David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - J Lerut
- Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - J Levitsky
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | - L Licini
- Pope John XXIII Hospital, Bergamo, Italy
| | - R Liotta
- Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione, University of Pittsburgh Medical Center, Palermo, Italy
| | - G Mazariegos
- Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, PA
| | - M I Minervini
- University of Pittsburgh Medical Center, Pittsburgh, PA
| | - J Misdraji
- Massachusetts General Hospital, Boston, MA
| | - T Mohanakumar
- St. Joseph's Hospital and Medical Center, Norton Thoracic Institute, Phoenix, AZ
| | - J Mölne
- University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - I Nasser
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA
| | - J Neuberger
- Queen Elizabeth Hospital Birmingham, Birmingham, UK
| | - M O'Neil
- University of Kansas Medical Center, Kansas City, KS
| | - O Pappo
- Hadassah Medical Center, Jerusalem, Israel
| | - L Petrovic
- University of Southern California, Los Angeles, CA
| | - P Ruiz
- University of Miami, Miami, FL
| | - Ö Sağol
- School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | | | - E Sasatomi
- University of North Carolina School of Medicine, Chapel Hill, NC
| | - A Shaked
- University of Pennsylvania Health System, Philadelphia, PA
| | - M Shiller
- Baylor University Medical Center, Dallas, TX
| | - T Shimizu
- Toda Chuo General Hospital, Saitama, Japan
| | - B Sis
- University of Alberta Hospital, Edmonton, Canada
| | - A Sonzogni
- Pope John XXIII Hospital, Bergamo, Italy
| | | | - S N Thung
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - G Tisone
- University of Rome-Tor Vergata, Rome, Italy
| | | | - A Wernerson
- Karolinska University Hospital, Stockholm, Sweden
| | - T Wu
- Tulane University School of Medicine, New Orleans, LA
| | - A Zeevi
- University of Pittsburgh, Pittsburgh, PA
| | - Y Zen
- Kobe University Hospital, Kobe, Japan
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28
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Sargazi M, Smith ML, Worth RC, Roberts NB. A rare ganglioneuroblastoma secreting dopamine and the value of its measurement in diagnosis and prognosis. Ann Clin Biochem 2016; 43:73-6. [PMID: 16390613 DOI: 10.1258/000456306775141704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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
A case is described of a patient with a ganglioneuroblastoma, initially located in the right adrenal, which produced an excess of dopamine (7646 and 7959 nmol/24 h), approximately two and a half times the upper limit of the normal daily urine output. The urinary excretion of noradrenaline, adrenaline and methylated derivatives was always within the normal reference ranges. The patient was generally well, with normal blood pressure and only mild flushes. Two years after surgical resection, recurrence was indicated by an increase in urinary dopamine (8507 nmol/24 h); it was located in the tumour bed and left side of the neck by CT and 123I MIBG scans. The patient was treated with a high dose of 131I MIBG, with subsequent reduction in dopamine production. This was repeated on four other occasions, the latest being in January 2005. The output of dopamine was thus used as a marker of tumour diagnosis and progression and it is recommended that the assay of dopamine be included in the screening of catecholamine-secreting tumours to avoid possible misdiagnosis.
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Affiliation(s)
- M Sargazi
- Department of Clinical Biochemistry & Metabolic Medicine, Royal Liverpool University Hospital, Prescot Street, Liverpool, UK
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29
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Smith LN, Farooq AR, Smith ML, Ivanov IE, Orlando A. Realistic and interactive high-resolution 4D environments for real-time surgeon and patient interaction. Int J Med Robot 2016; 13. [PMID: 27439562 DOI: 10.1002/rcs.1761] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 03/31/2016] [Revised: 05/24/2016] [Accepted: 06/10/2016] [Indexed: 01/13/2023]
Abstract
BACKGROUND Remote consultations that are realistic enough to be useful medically offer considerable clinical, logistical and cost benefits. Despite advances in virtual reality and vision hardware and software, these benefits are currently often unrealised. METHOD The proposed approach combines high spatial and temporal resolution 3D and 2D machine vision with virtual reality techniques, in order to develop new environments and instruments that will enable realistic remote consultations and the generation of new types of useful clinical data. RESULTS New types of clinical data have been generated for skin analysis and respiration measurement; and the combination of 3D with 2D data was found to offer potential for the generation of realistic virtual consultations. CONCLUSION An innovative combination of high resolution machine vision data and virtual reality online methods, promises to provide advanced functionality and significant medical benefits, particularly in regions where populations are dispersed or access to clinicians is limited. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- L N Smith
- Department of Engineering, Design and Mathematics, University of the West of England, Bristol, UK
| | - A R Farooq
- Department of Engineering, Design and Mathematics, University of the West of England, Bristol, UK
| | - M L Smith
- Department of Engineering, Design and Mathematics, University of the West of England, Bristol, UK
| | - I E Ivanov
- Department of Engineering, Design and Mathematics, University of the West of England, Bristol, UK
| | - A Orlando
- Department of Engineering, Design and Mathematics, University of the West of England, Bristol, UK
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30
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Laird Smith M, Murrell B, Eren K, Ignacio C, Landais E, Weaver S, Phung P, Ludka C, Hepler L, Caballero G, Pollner T, Guo Y, Richman D, Poignard P, Paxinos EE, Kosakovsky Pond SL, Smith DM. Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples. Virus Evol 2016; 2:vew018. [PMID: 29492273 DOI: 10.1093/ve/vew018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The ability to study rapidly evolving viral populations has been constrained by the read length of next-generation sequencing approaches and the sampling depth of single-genome amplification methods. Here, we develop and characterize a method using Pacific Biosciences' Single Molecule, Real-Time (SMRT®) sequencing technology to sequence multiple, intact full-length human immunodeficiency virus-1 env genes amplified from viral RNA populations circulating in blood, and provide computational tools for analyzing and visualizing these data.
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Affiliation(s)
- Melissa Laird Smith
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Ben Murrell
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Kemal Eren
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Caroline Ignacio
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Elise Landais
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Steven Weaver
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Pham Phung
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Colleen Ludka
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Lance Hepler
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Gemma Caballero
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Tristan Pollner
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Yan Guo
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Douglas Richman
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | | | - Pascal Poignard
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Ellen E Paxinos
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Sergei L Kosakovsky Pond
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Davey M Smith
- Pacific Biosciences, Menlo Park, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Biomedical Informatics, University of California, San Diego, San Diego, CA, USA.,Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, USA.,The International Aids Vaccine Initiative, Neutralizing Antibody Center, La Jolla, CA, USA.,LabCorp, Monogram Biosciences, South San Francisco, CA, USA.,Canyon Crest Academy, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, San Diego, CA, USA.,Veterans Affairs Healthcare System, San Diego, CA, USA.,Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
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31
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Vembar SS, Seetin M, Lambert C, Nattestad M, Schatz MC, Baybayan P, Scherf A, Smith ML. Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing. DNA Res 2016; 23:339-51. [PMID: 27345719 PMCID: PMC4991835 DOI: 10.1093/dnares/dsw022] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 11/24/2015] [Accepted: 05/10/2016] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing to estimate genetic diversity of Plasmodium falciparum, the most lethal malaria parasite, has proved challenging due to the skewed AT-richness [∼80.6% (A + T)] of its genome and the lack of technology to assemble highly polymorphic subtelomeric regions that contain clonally variant, multigene virulence families (Ex: var and rifin). To address this, we performed amplification-free, single molecule, real-time sequencing of P. falciparum genomic DNA and generated reads of average length 12 kb, with 50% of the reads between 15.5 and 50 kb in length. Next, using the Hierarchical Genome Assembly Process, we assembled the P. falciparum genome de novo and successfully compiled all 14 nuclear chromosomes telomere-to-telomere. We also accurately resolved centromeres [∼90–99% (A + T)] and subtelomeric regions and identified large insertions and duplications that add extra var and rifin genes to the genome, along with smaller structural variants such as homopolymer tract expansions. Overall, we show that amplification-free, long-read sequencing combined with de novo assembly overcomes major challenges inherent to studying the P. falciparum genome. Indeed, this technology may not only identify the polymorphic and repetitive subtelomeric sequences of parasite populations from endemic areas but may also evaluate structural variation linked to virulence, drug resistance and disease transmission.
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Affiliation(s)
- Shruthi Sridhar Vembar
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris 75015, France CNRS, ERL 9195, Paris 75015, France INSERM, Unit U1201, Paris 75015, France
| | | | | | | | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris 75015, France CNRS, ERL 9195, Paris 75015, France INSERM, Unit U1201, Paris 75015, France
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32
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Batra RK, Heilman RL, Smith ML, Thomas LF, Khamash HA, Katariya NN, Hewitt WR, Singer AL, Mathur AK, Huskey J, Chakkera HA, Moss A, Reddy KS. Rapid Resolution of Donor-Derived Glomerular Fibrin Thrombi After Deceased Donor Kidney Transplantation. Am J Transplant 2016; 16:1015-20. [PMID: 26689853 DOI: 10.1111/ajt.13561] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 08/16/2015] [Revised: 09/11/2015] [Accepted: 09/29/2015] [Indexed: 01/25/2023]
Abstract
The aim of this study was to determine the clinical and histologic outcomes related to transplanting kidneys from deceased donors with glomerular fibrin thrombi (GFT). We included all cases transplanted between October 2003 and October 2014 that had either a preimplantation biopsy or an immediate postreperfusion biopsy showing GFT. The study cohort included 61 recipients (9.9%) with GFT and 557 in the control group without GFT. Delayed graft function occurred in 49% of the GFT group and 39% in the control group (p = 0.14). Serum creatinine at 1, 4, and 12 months and estimated GFR at 12 months were similar in the two groups. Estimated 1-year graft survival was 93.2% in the GFT group and 95.1% in the control group (p = 0.22 by log-rank). Fifty-two of the 61 patients in the GFT group (85%) had a 1-month protocol biopsy, and only two biopsies (4%) showed residual focal glomerular thrombi. At the 1-year protocol biopsy, the prevalence of moderate to severe interstitial fibrosis and tubular atrophy was 24% in the GFT group and 30% in the control group (p = 0.42). We concluded that GFT resolves rapidly after transplantation and that transplanting selected kidneys from deceased donors with GFT is a safe practice.
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Affiliation(s)
- R K Batra
- Department of Surgery, Mayo Clinic, Phoenix, AZ
| | - R L Heilman
- Department of Medicine, Mayo Clinic, Phoenix, AZ
| | - M L Smith
- Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ
| | - L F Thomas
- Department of Medicine, Mayo Clinic, Phoenix, AZ
| | - H A Khamash
- Department of Medicine, Mayo Clinic, Phoenix, AZ
| | | | - W R Hewitt
- Department of Surgery, Mayo Clinic, Phoenix, AZ
| | - A L Singer
- Department of Surgery, Mayo Clinic, Phoenix, AZ
| | - A K Mathur
- Department of Surgery, Mayo Clinic, Phoenix, AZ
| | - J Huskey
- Department of Medicine, Mayo Clinic, Phoenix, AZ
| | - H A Chakkera
- Department of Medicine, Mayo Clinic, Phoenix, AZ
| | - A Moss
- Department of Surgery, Mayo Clinic, Phoenix, AZ
| | - K S Reddy
- Department of Surgery, Mayo Clinic, Phoenix, AZ
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33
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Smith ML, Li J, Cote DM, Ryabinin AE. Effects of isoflurane and ethanol administration on c-Fos immunoreactivity in mice. Neuroscience 2015; 316:337-43. [PMID: 26742790 DOI: 10.1016/j.neuroscience.2015.12.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 10/08/2015] [Revised: 11/17/2015] [Accepted: 12/25/2015] [Indexed: 11/19/2022]
Abstract
Noninvasive functional imaging holds great promise for the future of translational research, due to the ability to directly compare between preclinical and clinical models of psychiatric disorders. Despite this potential, concerns have been raised regarding the necessity to anesthetize rodent and monkey subjects during these procedures, because anesthetics may alter neuronal activity. For example, in studies on drugs of abuse and alcohol, it is not clear to what extent anesthesia can interfere with drug-induced neural activity. Therefore, the current study investigated whole-brain c-Fos activation following isoflurane anesthesia as well as ethanol-induced activation of c-Fos in anesthetized mice. In the first experiment, we examined effects of one or three sessions of gaseous isoflurane on c-Fos activation across the brain in male C57BL/6J mice. Isoflurane administration led to c-Fos activation in several areas, including the piriform cortex and lateral septum. Lower or similar levels of activation in these areas were detected after three sessions of isoflurane, suggesting that multiple exposures may eliminate some of the enhanced neuronal activation caused by acute isoflurane. In the second experiment, we investigated the ability of ethanol injection (1.5 or 2.5g/kgi.p.) to induce c-Fos activation under anesthesia. Following three sessions of isoflurane, 1.5g/kg of ethanol induced c-Fos in the central nucleus of amygdala and the centrally-projecting Edinger-Westphal nucleus (EWcp). This induction was lower after 2.5g/kg of ethanol. These results demonstrate that ethanol-induced neural activation can be detected in the presence of isoflurane anesthesia. They also suggest, that while habituation to isoflurane helps reduce neuronal activation, interaction between effects of anesthesia and alcohol can occur. Studies using fMRI imaging could benefit from using habituated animals and dose-response analyses.
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Affiliation(s)
- M L Smith
- Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Mail Code L470, Portland, OR 97239, USA
| | - J Li
- Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Mail Code L470, Portland, OR 97239, USA
| | - D M Cote
- Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Mail Code L470, Portland, OR 97239, USA
| | - A E Ryabinin
- Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Mail Code L470, Portland, OR 97239, USA; Portland Alcohol Research Center, Portland, OR, USA.
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34
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Vogan VM, Morgan BR, Powell TL, Smith ML, Taylor MJ. The neurodevelopmental differences of increasing verbal working memory demand in children and adults. Dev Cogn Neurosci 2015; 17:19-27. [PMID: 26615571 PMCID: PMC6990091 DOI: 10.1016/j.dcn.2015.10.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [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: 04/22/2015] [Revised: 08/26/2015] [Accepted: 10/13/2015] [Indexed: 01/10/2023] Open
Abstract
Working memory (WM) – temporary storage and manipulation of information in the mind – is a key component of cognitive maturation, and structural brain changes throughout development are associated with refinements in WM. Recent functional neuroimaging studies have shown that there is greater activation in prefrontal and parietal brain regions with increasing age, with adults showing more refined, localized patterns of activations. However, few studies have investigated the neural basis of verbal WM development, as the majority of reports examine visuo-spatial WM. We used fMRI and a 1-back verbal WM task with six levels of difficulty to examine the neurodevelopmental changes in WM function in 40 participants, twenty-four children (ages 9–15 yr) and sixteen young adults (ages 20–25 yr). Children and adults both demonstrated an opposing system of cognitive processes with increasing cognitive demand, where areas related to WM (frontal and parietal regions) increased in activity, and areas associated with the default mode network decreased in activity. Although there were many similarities in the neural activation patterns associated with increasing verbal WM capacity in children and adults, significant changes in the fMRI responses were seen with age. Adults showed greater load-dependent changes than children in WM in the bilateral superior parietal gyri, inferior frontal and left middle frontal gyri and right cerebellum. Compared to children, adults also showed greater decreasing activation across WM load in the bilateral anterior cingulate, anterior medial prefrontal gyrus, right superior lateral temporal gyrus and left posterior cingulate. These results demonstrate that while children and adults activate similar neural networks in response to verbal WM tasks, the extent to which they rely on these areas in response to increasing cognitive load evolves between childhood and adulthood.
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Affiliation(s)
- V M Vogan
- Diagnostic Imaging, Hospital for Sick Children, Toronto, ON, Canada; Applied Psychology and Human Development, Ontario Institute for Studies in Education, University of Toronto, Toronto, ON, Canada.
| | - B R Morgan
- Diagnostic Imaging, Hospital for Sick Children, Toronto, ON, Canada
| | - T L Powell
- Diagnostic Imaging, Hospital for Sick Children, Toronto, ON, Canada
| | - M L Smith
- Diagnostic Imaging, Hospital for Sick Children, Toronto, ON, Canada; Department of Psychology, University of Toronto, Toronto, ON, Canada
| | - M J Taylor
- Diagnostic Imaging, Hospital for Sick Children, Toronto, ON, Canada; Applied Psychology and Human Development, Ontario Institute for Studies in Education, University of Toronto, Toronto, ON, Canada; Department of Psychology, University of Toronto, Toronto, ON, Canada
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35
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Dearden JC, Hewitt M, Roberts DW, Enoch SJ, Rowe PH, Przybylak KR, Vaughan-Williams GD, Smith ML, Pillai GG, Katritzky AR. Mechanism-Based QSAR Modeling of Skin Sensitization. Chem Res Toxicol 2015; 28:1975-86. [PMID: 26382665 DOI: 10.1021/acs.chemrestox.5b00197] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many chemicals can induce skin sensitization, and there is a pressing need for non-animal methods to give a quantitative indication of potency. Using two large published data sets of skin sensitizers, we have allocated each sensitizing chemical to one of 10 mechanistic categories and then developed good QSAR models for the seven categories that have a sufficient number of chemicals to allow modeling. Both internal and external validation checks showed that each model had good predictivity.
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Affiliation(s)
- J C Dearden
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - M Hewitt
- School of Pharmacy, University of Wolverhampton , Wulfruna Street, Wolverhampton WV1 1LY, United Kingdom
| | - D W Roberts
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - S J Enoch
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - P H Rowe
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - K R Przybylak
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - G D Vaughan-Williams
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - M L Smith
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - G G Pillai
- Department of Chemistry, University of Florida , Gainsville, Florida 32611-7200, United States.,Institute of Chemistry, University of Tartu , 50411 Tartu, Estonia
| | - A R Katritzky
- Department of Chemistry, University of Florida , Gainsville, Florida 32611-7200, United States
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36
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Heilman RL, Smith ML, Reddy KS. Utilization of Kidneys With Acute Kidney Injury in the Extended Criteria Donor Setting. Am J Transplant 2015; 15:2783. [PMID: 26211677 DOI: 10.1111/ajt.13392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/20/2015] [Indexed: 01/25/2023]
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37
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Pohlmann-Eden B, Aldenkamp A, Baker GA, Brandt C, Cendes F, Coras R, Crocker CE, Helmstaedter C, Jones-Gotman M, Kanner AM, Mazarati A, Mula M, Smith ML, Omisade A, Tellez-Zenteno J, Hermann BP. The relevance of neuropsychiatric symptoms and cognitive problems in new-onset epilepsy - Current knowledge and understanding. Epilepsy Behav 2015; 51:199-209. [PMID: 26291774 DOI: 10.1016/j.yebeh.2015.07.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [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: 06/24/2015] [Accepted: 07/03/2015] [Indexed: 01/11/2023]
Abstract
Neurobehavioral and cognition problems are highly prevalent in epilepsy, but most research studies to date have not adequately addressed the precise nature of the relationship between these comorbidities and seizures. To address this complex issue and to facilitate collaborative, innovative research in the rising field of neurobehavioral comorbidities and cognition disturbances in new-onset epilepsy, international epilepsy experts met at the 3rd Halifax International Epilepsy Conference & Retreat at White Point, South Shore, Nova Scotia, Canada from September 18 to 20, 2014. This Conference Proceedings provides a summary of the conference proceedings. Specifically, the following topics are discussed: (i) role of comorbidities in epilepsy diagnosis and management, (ii) role of antiepileptic medications in understanding the relationship between epilepsy and neurobehavioral and cognition problems, and (iii) animal data and diagnostic approaches. Evidence to date, though limited, strongly suggests a bidirectional relationship between epilepsy and cognitive and psychiatric comorbidities. In fact, it is likely that seizures and neurobehavioral problems represent different symptoms of a common etiology or network-wide disturbance. As a reflection of this shared network, psychiatric comorbidities and/or cognition problems may actually precede the seizure occurrence and likely get often missed if not screened.
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Affiliation(s)
- B Pohlmann-Eden
- Division of Neurology, Dalhousie University of Halifax, Canada; Brain Repair Center, Dalhousie University of Halifax, Canada.
| | - A Aldenkamp
- Epilepsiecentrum Kempenhaeghe, The Netherlands
| | - G A Baker
- Division of Neurosciences, University of Liverpool, United Kingdom
| | - C Brandt
- Bethel Epilepsy Center, Mara Hospital, Bielefeld, Germany
| | - F Cendes
- Department of Neurology, University of Campinas, São Paulo, Brazil
| | - R Coras
- Department of Neuropathology, University of Erlangen, Germany
| | - C E Crocker
- Division of Neurology, Dalhousie University of Halifax, Canada
| | | | - M Jones-Gotman
- McGill University, Montreal Neurological Institute, Montreal, Canada
| | - A M Kanner
- Epilepsy Center, University of Miami, Miller School of Medicine, USA
| | - A Mazarati
- Children's Discovery and Innovation Institute, D. Geffen School of Medicine at UCLA, Los Angeles, USA
| | - M Mula
- Epilepsy Group, Atkinson Morley Regional Neuroscience Centre, St. George's University Hospitals NHS Foundation Trust and Institute of Medical and Biomedical Sciences St. George's University of London, United Kingdom
| | - M L Smith
- Department of Psychology, University of Toronto, Canada
| | - A Omisade
- Division of Neurology, Dalhousie University of Halifax, Canada
| | | | - B P Hermann
- Department of Neurology, University of Wisconsin School of Medicine and Public Health, Madison, USA
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Heilman RL, Smith ML, Kurian SM, Huskey J, Batra RK, Chakkera HA, Katariya NN, Khamash H, Moss A, Salomon DR, Reddy KS. Transplanting Kidneys from Deceased Donors With Severe Acute Kidney Injury. Am J Transplant 2015; 15:2143-51. [PMID: 25808278 DOI: 10.1111/ajt.13260] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [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: 12/14/2014] [Revised: 01/21/2015] [Accepted: 02/05/2015] [Indexed: 01/25/2023]
Abstract
Our aim was to determine outcomes with transplanting kidneys from deceased donors with acute kidney injury, defined as a donor with terminal serum creatinine ≥2.0 mg/dL, or a donor requiring acute renal replacement therapy. We included all patients who received deceased donor kidney transplant from June 2004 to October 2013. There were 162 AKI donor transplant recipients (21% of deceased donor transplants): 139 in the standard criteria donor (SCD) and 23 in the expanded criteria donor (ECD) cohort. 71% of the AKI donors had stage 3 (severe AKI), based on acute kidney injury network (AKIN) staging. Protocol biopsies were done at 1, 4, and 12 months posttransplant. One and four month formalin-fixed paraffin embedded (FFPE) biopsies from 48 patients (24 AKI donors, 24 non-AKI) underwent global gene expression profiling using DNA microarrays (96 arrays). DGF was more common in the AKI group but eGFR, graft survival at 1 year and proportion with IF/TA>2 at 1 year were similar for the two groups. At 1 month, there were 898 differentially expressed genes in the AKI group (p-value <0.005; FDR <10%), but by 4 months there were no differences. Transplanting selected kidneys from deceased donors with AKI is safe and has excellent outcomes.
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Affiliation(s)
- R L Heilman
- Department of Medicine, Mayo Clinic, Phoenix, AZ
| | - M L Smith
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ
| | - S M Kurian
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - J Huskey
- Department of Medicine, Mayo Clinic, Phoenix, AZ
| | - R K Batra
- Department of Surgery, Mayo Clinic, Phoenix, AZ
| | - H A Chakkera
- Department of Medicine, Mayo Clinic, Phoenix, AZ
| | | | - H Khamash
- Department of Medicine, Mayo Clinic, Phoenix, AZ
| | - A Moss
- Department of Surgery, Mayo Clinic, Phoenix, AZ
| | - D R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - K S Reddy
- Department of Surgery, Mayo Clinic, Phoenix, AZ
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Widjaja E, Zamyadi M, Raybaud C, Snead OC, Doesburg SM, Smith ML. Disrupted Global and Regional Structural Networks and Subnetworks in Children with Localization-Related Epilepsy. AJNR Am J Neuroradiol 2015; 36:1362-8. [PMID: 25742984 DOI: 10.3174/ajnr.a4265] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [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] [Received: 09/21/2014] [Accepted: 01/02/2015] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Structural connectivity has been thought to be a less sensitive measure of network changes relative to functional connectivity in children with localization-related epilepsy. The aims of this study were to investigate the structural networks in children with localization-related epilepsy and to assess the relation among structural connectivity, intelligence quotient, and clinical parameters. MATERIALS AND METHODS Forty-five children with nonlesional localization-related epilepsy and 28 healthy controls underwent DTI. Global network (network strength, clustering coefficient, characteristic path length, global efficiency, and small-world parameters), regional network (nodal efficiency), and the network-based statistic were compared between patients and controls and correlated with intelligence quotient and clinical parameters. RESULTS Patients showed disrupted global network connectivity relative to controls, including reduced network strength, increased characteristic path length and reduced global efficiency, and reduced nodal efficiency in the frontal, temporal, and occipital lobes. Connectivity in multiple subnetworks was reduced in patients, including the frontal-temporal, insula-temporal, temporal-temporal, frontal-occipital, and temporal-occipital lobes. The frontal lobe epilepsy subgroup demonstrated more areas with reduced nodal efficiency and more impaired subnetworks than the temporal lobe epilepsy subgroup. Network parameters were not significantly associated with intelligence quotient, age at seizure onset, or duration of epilepsy. CONCLUSIONS We found disruption in global and regional networks and subnetworks in children with localization-related epilepsy. Regional efficiency and subnetworks were more impaired in frontal lobe epilepsy than in temporal lobe epilepsy. Future studies are needed to evaluate the implications of disrupted networks for surgical resection and outcomes for specific epileptogenic zones and the relation of disrupted networks to more complex cognitive function.
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Affiliation(s)
- E Widjaja
- From the Department of Diagnostic Imaging (E.W., M.Z., C.R., S.M.D.) Division of Neurology (E.W., O.C.S.)
| | - M Zamyadi
- From the Department of Diagnostic Imaging (E.W., M.Z., C.R., S.M.D.)
| | - C Raybaud
- From the Department of Diagnostic Imaging (E.W., M.Z., C.R., S.M.D.)
| | - O C Snead
- Division of Neurology (E.W., O.C.S.)
| | - S M Doesburg
- From the Department of Diagnostic Imaging (E.W., M.Z., C.R., S.M.D.) Neuroscience and Mental Health at Research Institute (S.M.D.), Hospital for Sick Children, Toronto, Ontario, Canada
| | - M L Smith
- Department of Psychology (M.L.S.), University of Toronto, Toronto, Ontario, Canada
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Smith LN, Smith ML, Fletcher ME, Henderson AJ. A 3D machine vision method for non-invasive assessment of respiratory function. Int J Med Robot 2015; 12:179-88. [PMID: 25968923 DOI: 10.1002/rcs.1669] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 11/12/2014] [Revised: 04/10/2015] [Accepted: 04/12/2015] [Indexed: 11/12/2022]
Abstract
BACKGROUND Respiratory function testing is important for detecting and monitoring illness, however, it is difficult for some patients, such as the young and severely ill, to perform conventional tests that require cooperation and/or patient contact. METHOD A new method was developed for non-contact breathing measurement, employing photometric stereo to capture the surface topography of the torso of an unconstrained subject. The surface is integrated to calculate time-dependent volume changes during respiration. RESULTS The method provides a useful means of continuously measuring volume changes during respiration with high spatial and temporal resolution. The system was tested by comparison with pneumotachometry equipment and a clear periodic signal, of a frequency corresponding to the reference data, was observed. CONCLUSION The approach is unique in performing breathing monitoring (with potential diagnostic capability) for unconstrained patients in virtually any lighting conditions (including darkness during sleep) and in a non-contact, unobtrusive (i.e. using imperceptible light) fashion. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- L N Smith
- Department of Engineering, Design and Mathematics, University of the West of England, Bristol, UK
| | - M L Smith
- Department of Engineering, Design and Mathematics, University of the West of England, Bristol, UK
| | - M E Fletcher
- Department of Engineering, Design and Mathematics, University of the West of England, Bristol, UK
| | - A J Henderson
- Department of Engineering, Design and Mathematics, University of the West of England, Bristol, UK
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Pecoits E, Smith ML, Catling DC, Philippot P, Kappler A, Konhauser KO. Atmospheric hydrogen peroxide and Eoarchean iron formations. Geobiology 2015; 13:1-14. [PMID: 25324177 DOI: 10.1111/gbi.12116] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/15/2014] [Indexed: 06/04/2023]
Abstract
It is widely accepted that photosynthetic bacteria played a crucial role in Fe(II) oxidation and the precipitation of iron formations (IF) during the Late Archean-Early Paleoproterozoic (2.7-2.4 Ga). It is less clear whether microbes similarly caused the deposition of the oldest IF at ca. 3.8 Ga, which would imply photosynthesis having already evolved by that time. Abiological alternatives, such as the direct oxidation of dissolved Fe(II) by ultraviolet radiation may have occurred, but its importance has been discounted in environments where the injection of high concentrations of dissolved iron directly into the photic zone led to chemical precipitation reactions that overwhelmed photooxidation rates. However, an outstanding possibility remains with respect to photochemical reactions occurring in the atmosphere that might generate hydrogen peroxide (H2 O2 ), a recognized strong oxidant for ferrous iron. Here, we modeled the amount of H2 O2 that could be produced in an Eoarchean atmosphere using updated solar fluxes and plausible CO2 , O2 , and CH4 mixing ratios. Irrespective of the atmospheric simulations, the upper limit of H2 O2 rainout was calculated to be <10(6) molecules cm(-2) s(-1) . Using conservative Fe(III) sedimentation rates predicted for submarine hydrothermal settings in the Eoarchean, we demonstrate that the flux of H2 O2 was insufficient by several orders of magnitude to account for IF deposition (requiring ~10(11) H2 O2 molecules cm(-2) s(-1) ). This finding further constrains the plausible Fe(II) oxidation mechanisms in Eoarchean seawater, leaving, in our opinion, anoxygenic phototrophic Fe(II)-oxidizing micro-organisms the most likely mechanism responsible for Earth's oldest IF.
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Affiliation(s)
- E Pecoits
- Equipe Géobiosphère, Institut de Physique du Globe-Sorbonne Paris Cité, Université Paris Diderot, CNRS, Paris, France; Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
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Schneider BP, Li L, Shen F, Miller KD, Radovich M, O'Neill A, Gray RJ, Lane D, Flockhart DA, Jiang G, Wang Z, Lai D, Koller D, Pratt JH, Dang CT, Northfelt D, Perez EA, Shenkier T, Cobleigh M, Smith ML, Railey E, Partridge A, Gralow J, Sparano J, Davidson NE, Foroud T, Sledge GW. Genetic variant predicts bevacizumab-induced hypertension in ECOG-5103 and ECOG-2100. Br J Cancer 2014; 111:1241-8. [PMID: 25117820 PMCID: PMC4453857 DOI: 10.1038/bjc.2014.430] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/26/2014] [Accepted: 07/08/2014] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Bevacizumab has broad anti-tumour activity, but substantial risk of hypertension. No reliable markers are available for predicting bevacizumab-induced hypertension. METHODS A genome-wide association study (GWAS) was performed in the phase III bevacizumab-based adjuvant breast cancer trial, ECOG-5103, to evaluate for an association between genotypes and hypertension. GWAS was conducted in those who had experienced systolic blood pressure (SBP) >160 mm Hg during therapy using binary analysis and a cumulative dose model for the total exposure of bevacizumab. Common toxicity criteria (CTC) grade 3-5 hypertension was also assessed. Candidate SNP validation was performed in the randomised phase III trial, ECOG-2100. RESULTS When using the phenotype of SBP>160 mm Hg, the most significant association in SV2C (rs6453204) approached and met genome-wide significance in the binary model (P=6.0 × 10(-8); OR=3.3) and in the cumulative dose model (P=4.7 × 10(-8); HR=2.2), respectively. Similar associations with rs6453204 were seen for CTC grade 3-5 hypertension but did not meet genome-wide significance. Validation study from ECOG-2100 demonstrated a statistically significant association between this SNP and grade 3/4 hypertension using the binary model (P-value=0.037; OR=2.4). CONCLUSIONS A genetic variant in SV2C predicted clinically relevant bevacizumab-induced hypertension in two independent, randomised phase III trials.
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Affiliation(s)
- B P Schneider
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - L Li
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - F Shen
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - K D Miller
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - M Radovich
- Department of General Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - A O'Neill
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - R J Gray
- Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - D Lane
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - D A Flockhart
- Indiana Institute for Personalized Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - G Jiang
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Z Wang
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - D Lai
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - D Koller
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - J H Pratt
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - C T Dang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - D Northfelt
- Department of Medicine, Mayo Clinic, Scottsdale, AZ 85054, USA
| | - E A Perez
- Mayo Clinic, Jacksonville, FL 32224, USA
| | - T Shenkier
- BCCA – Vancouver Cancer Center, Vancouver, BC, V5Z 4E6, USA
| | - M Cobleigh
- Department of Internal Medicine , Rush-Presbyterian-St. Luke's Medical Center, Chicago, IL 60612, USA
| | - M L Smith
- Research Advocacy Network, Plano, TX 75093, USA
| | - E Railey
- Research Advocacy Network, Plano, TX 75093, USA
| | - A Partridge
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - J Gralow
- University of Washington, Seattle, WA 98195, USA
| | - J Sparano
- Department of Oncology, Montefiore Hospital and Medical Center, Bronx, NY 10467, USA
| | - N E Davidson
- Cancer Institute and University of Pittsburgh Cancer Center, Pittsburgh, PA 15232, USA
| | - T Foroud
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - G W Sledge
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
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Bradshaw MJ, Smith ML. Multiscale relationships between fibronectin structure and functional properties. Acta Biomater 2014; 10:1524-31. [PMID: 23978411 DOI: 10.1016/j.actbio.2013.08.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 07/24/2013] [Accepted: 08/14/2013] [Indexed: 12/11/2022]
Abstract
Cell behavior is tightly coupled to the properties of the extracellular matrix (ECM) to which they attach. Fibronectin (Fn) forms a supermolecular, fibrillar component of the ECM that is prominent during development, wound healing and the progression of numerous diseases. This indicates that Fn has an important function in controlling cell behavior during dynamic events in vivo. The multiscale architecture of Fn molecules assembled into these fibers determines the ligand density of cell adhesion sites on the surface of the Fn fiber, Fn fiber porosity for cell signaling molecules such as growth factors, the mechanical stiffness of the Fn matrix and the adhesivity of Fn for its numerous soluble ligands. These parameters are altered by mechanical strain applied to the ECM. Recent efforts have attempted to link the molecular properties of Fn with bulk properties of Fn matrix fibers. Studies of isolated Fn fibers have helped to characterize the fiber's material properties and, in combination with models of Fn molecular behavior in the fibers, have begun to provide insights into the Fn molecular arrangement and intermolecular adhesions within the fibers. A review of these studies allows the development of an understanding of the mechanobiological functions of Fn.
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Affiliation(s)
- M J Bradshaw
- Department of Mechanical Engineering, Boston University, 44 Cummington St., ERB 502, Boston, MA 02215, USA
| | - M L Smith
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
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Cruz I, Cheetham JJ, Arnason JT, Yack JE, Smith ML. Alkamides from Echinacea disrupt the fungal cell wall-membrane complex. Phytomedicine 2014; 21:435-442. [PMID: 24252333 DOI: 10.1016/j.phymed.2013.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 08/15/2013] [Accepted: 10/17/2013] [Indexed: 06/02/2023]
Abstract
We tested the hypothesis that alkamides from Echinacea exert antifungal activity by disrupting the fungal cell wall/membrane complex. Saccharomyces cerevisiae cells were treated separately with each of seven synthetic alkamides found in Echinacea extracts. The resulting cell wall damage and cell viability were assessed by fluorescence microscopy after mild sonication. Membrane disrupting properties of test compounds were studied using liposomes encapsulating carboxyfluorescein. Negative controls included hygromycin and nourseothricin (aminoglycosides that inhibit protein synthesis), and the positive control used was caspofungin (an echinocandin that disrupts fungal cell walls). The results show that yeast cells exposed to sub-inhibitory concentrations of each of the seven alkamides and Echinacea extract exhibit increased frequencies of cell wall damage and death that were comparable to caspofungin and significantly greater than negative controls. Consistent with effects of cell wall damaging agents, the growth inhibition by three representative alkamides tested and caspofungin, but not hygromycin B, were partially reversed in sorbitol protection assays. Membrane disruption assays showed that the Echinacea extract and alkamides have pronounced membrane disruption activity, in contrast to caspofungin and other controls that all had little effect on membrane stability. A Quantitative Structure-Activity Relationship (QSAR) analysis was performed to study the effect of structural substituents on the antifungal activity of the alkamides. Among the set studied, diynoic alkamides showed the greatest antifungal and cell wall disruption activities while an opposite trend was observed in the membrane disruption assay where the dienoic group was more effective. We propose that alkamides found in Echinacea act synergistically to disrupt the fungal cell wall/membrane complex, an excellent target for specific inhibition of fungal pathogens. Structure-function relationships provide opportunities for synthesis of alkamide analogs with improved antifungal activities.
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Affiliation(s)
- I Cruz
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - J J Cheetham
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - J T Arnason
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - J E Yack
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - M L Smith
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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Kramb RC, Buskohl PR, Slone C, Smith ML, Vaia RA. Autonomic composite hydrogels by reactive printing: materials and oscillatory response. Soft Matter 2014; 10:1329-1336. [PMID: 24651297 DOI: 10.1039/c3sm51650d] [Citation(s) in RCA: 9] [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] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Autonomic materials are those that automatically respond to a change in environmental conditions, such as temperature or chemical composition. While such materials hold incredible potential for a wide range of uses, their implementation is limited by the small number of fully-developed material systems. To broaden the number of available systems, we have developed a post-functionalization technique where a reactive Ru catalyst ink is printed onto a non-responsive polymer substrate. Using a succinimide-amine coupling reaction, patterns are printed onto co-polymer or biomacromolecular films containing primary amine functionality, such as polyacrylamide (PAAm) or poly-N-isopropyl acrylamide (PNIPAAm) copolymerized with poly-N-(3-Aminopropyl)methacrylamide (PAPMAAm). When the films are placed in the Belousov-Zhabotinsky (BZ) solution medium, the reaction takes place only inside the printed nodes. In comparison to alternative BZ systems, where Ru-containing monomers are copolymerized with base monomers, reactive printing provides facile tuning of a range of hydrogel compositions, as well as enabling the formation of mechanically robust composite monoliths. The autonomic response of the printed nodes is similar for all matrices in the BZ solution concentrations examined, where the period of oscillation decreases in response to increasing sodium bromate or nitric acid concentration. A temperature increase reduces the period of oscillations and temperature gradients are shown to function as pace-makers, dictating the direction of the autonomic response (chemical waves).
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Affiliation(s)
- R C Kramb
- AFRL/RX Materials & Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH 45433, USA.
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Widjaja E, Zamyadi M, Raybaud C, Snead OC, Smith ML. Abnormal functional network connectivity among resting-state networks in children with frontal lobe epilepsy. AJNR Am J Neuroradiol 2013; 34:2386-92. [PMID: 23868148 DOI: 10.3174/ajnr.a3608] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND PURPOSE Epilepsy is considered a disorder of neural networks. The aims of this study were to assess functional connectivity within resting-state networks and functional network connectivity across resting-state networks by use of resting-state fMRI in children with frontal lobe epilepsy and to relate changes in resting-state networks with neuropsychological function. MATERIALS AND METHODS Fifteen patients with frontal lobe epilepsy and normal MR imaging and 14 healthy control subjects were recruited. Spatial independent component analysis was used to identify the resting-state networks, including frontal, attention, default mode network, sensorimotor, visual, and auditory networks. The Z-maps of resting-state networks were compared between patients and control subjects. The relation between abnormal connectivity and neuropsychological function was assessed. Correlations from all pair-wise combinations of independent components were performed for each group and compared between groups. RESULTS The frontal network was the only network that showed reduced connectivity in patients relative to control subjects. The remaining 5 networks demonstrated both reduced and increased functional connectivity within resting-state networks in patients. There was a weak association between connectivity in frontal network and executive function (P = .029) and a significant association between sensorimotor network and fine motor function (P = .004). Control subjects had 79 pair-wise independent components that showed significant temporal coherence across all resting-state networks except for default mode network-auditory network. Patients had 66 pairs of independent components that showed significant temporal coherence across all resting-state networks. Group comparison showed reduced functional network connectivity between default mode network-attention, frontal-sensorimotor, and frontal-visual networks and increased functional network connectivity between frontal-attention, default mode network-sensorimotor, and frontal-visual networks in patients relative to control subjects. CONCLUSIONS We found abnormal functional connectivity within and across resting-state networks in children with frontal lobe epilepsy. Impairment in functional connectivity was associated with impaired neuropsychological function.
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Harry BL, Smith ML, Burton JR, Dasari A, Eckhardt SG, Diamond JR. Medullary thyroid cancer and pseudocirrhosis: case report and literature review. ACTA ACUST UNITED AC 2013; 19:e36-41. [PMID: 22328846 DOI: 10.3747/co.19.840] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Pseudocirrhosis is a rare form of liver disease that can cause clinical symptoms and radiographic signs of cirrhosis; however, its histologic features suggest a distinct pathologic process. In the setting of cancer, hepatic metastases and systemic chemotherapy are suspected causes of pseudocirrhosis. Here, we present a patient with medullary thyroid carcinoma metastatic to the liver who developed pseudocirrhosis while on maintenance sunitinib after receiving 5-fluorouracil, leucovorin, and oxaliplatin (folfox) in combination with sunitinib. Cirrhotic change in liver morphology was accompanied by diffusely infiltrative carcinomatous disease resembling the primary tumor. We discuss the diagnosis of pseudocirrhosis in this case and review the literature regarding pseudocirrhosis in cancer.
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Affiliation(s)
- B L Harry
- Medical Scientist Training Program, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO, U.S.A
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Poumirol JM, Yu W, Chen X, Berger C, de Heer WA, Smith ML, Ohta T, Pan W, Goerbig MO, Smirnov D, Jiang Z. Magnetoplasmons in quasineutral epitaxial graphene nanoribbons. Phys Rev Lett 2013; 110:246803. [PMID: 25165953 DOI: 10.1103/physrevlett.110.246803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Indexed: 06/03/2023]
Abstract
We present an infrared transmission spectroscopy study of the inter-Landau-level excitations in quasineutral epitaxial graphene nanoribbon arrays. We observed a substantial deviation in energy of the L(0(-1)) → L(1(0)) transition from the characteristic square root magnetic-field dependence of two-dimensional graphene. This deviation arises from the formation of an upper-hybrid mode between the Landau-level transition and the plasmon resonance. In the quantum regime, the hybrid mode exhibits a distinct dispersion relation, markedly different from that expected for conventional two-dimensional systems and highly doped graphene.
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Affiliation(s)
- J M Poumirol
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, USA
| | - W Yu
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - X Chen
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - C Berger
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and CNRS/Institut Néel, BP166, 38042 Grenoble, France
| | - W A de Heer
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M L Smith
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - T Ohta
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - W Pan
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - M O Goerbig
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Sud, F-91405 Orsay cedex, France
| | - D Smirnov
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, USA
| | - Z Jiang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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White CB, Smith ML, Abidoye O, Lalla D. Abstract P6-09-11: Examining patient treatment choices involving efficacy, toxicity, and cost tradeoffs in the metastatic breast cancer setting. Cancer Res 2012. [DOI: 10.1158/0008-5472.sabcs12-p6-09-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Most patients with metastatic breast cancer are treated with chemotherapies and/or targeted therapies. These therapies have toxicity profiles that vary with agent(s) used. Patient attitudes towards different adverse events (AE's) may vary and factor into treatment decisions. Different patients may have specific feelings about tolerable and unacceptable AE's, especially when balanced against possible treatment benefit. As more agents/combinations become available, it becomes increasingly important to understand which adverse events impact treatment decisions. Previous research has shown that conjoint analysis (CA) is a valid methodology that allows patients to express preferences and is particularly useful when designed based on specific treatment profiles (Smith, ASCO 2011; Smith, ASCO 2012).
Methods: The objective of this study was to assess patient preferences using CA based on profiles of two MBC regimens (trastuzumab+docetaxel and T-DM1). Patients were presented pairs of hypothetical treatments (describing benefit, AE's, and cost) and asked what their preferred alternative was; a follow-up question asked if they would take the treatment if it were the only option available. Five AE's (alopecia, peripheral neuropathy, diarrhea, fatigue, and neutropenia) with differing likelihood, severity, and/or duration were included. There were 3 stages in preparing the CA survey: the first comprised two online focus groups conducted with patients with metastatic disease. Stage 2 included the development of the CA survey using patient language to describe the AE's and their impact, as well as images to represent likelihoods, progression-free survival (PFS), and costs. Stage 3 is initiating and will recruit patients with the assistance of several breast cancer organizations (target n= 600). Analysis of response patterns allows study of the influence of each variable and provides a basis for prediction of treatment choice for any combination of benefit, AE's, and cost. Final analysis will be complete in September 2012.
Results: Findings from the focus groups facilitated an understanding of PFS, of experience with and impact of the AE's on decision-making, and of attitudes. In Stage 2, the survey was pretested with seven patients and took approximately 20 minutes to complete. Feedback suggested the questions were relevant and realistic. Suggestions allowed for improvement of the CA explanatory material, as well as refinement of a few answer choices to questions outside the CA section of the survey. Final study results will present the proportion of patients who are predicted to prefer each of two treatment profiles, the impact of each attribute level on treatment preference and differing preferences seen in patient subgroups. This information will provide valuable insight into patient preferences and inform future development of new therapies. In addition, these results may generate discussion and consideration of patient preferences in conversations about patient care and treatment selection.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-09-11.
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Affiliation(s)
- CB White
- Carol B. White & Associates; Research Advocacy Network; Genentech, Inc
| | - ML Smith
- Carol B. White & Associates; Research Advocacy Network; Genentech, Inc
| | - O Abidoye
- Carol B. White & Associates; Research Advocacy Network; Genentech, Inc
| | - D Lalla
- Carol B. White & Associates; Research Advocacy Network; Genentech, Inc
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Abstract
The aim of this study was to use whole brain quantitative analysis to identify impaired white matter (WM) integrity using diffusion tensor imaging (DTI) in children with new-onset seizures. Thirty-five children with new-onset seizures and normal MRI were recruited. Twelve patients had generalized seizures, and 23 had partial seizures. Thirty-one healthy controls were also recruited. Whole brain fractional anisotropy (FA), apparent diffusion coefficient (ADC), radial diffusivity (RD) and axial diffusivity (AD) maps of patients were compared to controls, corrected for multiple comparisons. There was significantly reduced FA in left postcentral, elevated RD in left posterior cingulum and right external capsule, elevated AD in left middle temporal WM and left thalamus, and reduced AD in left anterior cingulum, left temporal, and right supramarginal WM in patients relative to controls. Patients with partial epilepsy showed elevated RD in bilateral posterior cingulum, increased AD in left middle frontal, reduced AD in left temporal, right parietal and right supramarginal WM. Patients with generalized epilepsy showed increased AD in right cerebellum, and reduced AD in left anterior cingulum and left middle temporal WM. The findings indicate that impaired WM integrity with abnormal myelin and axons is present in children with new-onset seizures.
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Affiliation(s)
- E Widjaja
- Diagnostic Imaging, Hospital for Sick Children, Toronto, Canada.
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