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Chen Z, Gustavsson EK, Macpherson H, Anderson C, Clarkson C, Rocca C, Self E, Alvarez Jerez P, Scardamaglia A, Pellerin D, Montgomery K, Lee J, Gagliardi D, Luo H, Hardy J, Polke J, Singleton AB, Blauwendraat C, Mathews KD, Tucci A, Fu YH, Houlden H, Ryten M, Ptáček LJ. Adaptive Long-Read Sequencing Reveals GGC Repeat Expansion in ZFHX3 Associated with Spinocerebellar Ataxia Type 4. Mov Disord 2024; 39:486-497. [PMID: 38197134 DOI: 10.1002/mds.29704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/29/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Spinocerebellar ataxia type 4 (SCA4) is an autosomal dominant ataxia with invariable sensory neuropathy originally described in a family with Swedish ancestry residing in Utah more than 25 years ago. Despite tight linkage to the 16q22 region, the molecular diagnosis has since remained elusive. OBJECTIVES Inspired by pathogenic structural variation implicated in other 16q-ataxias with linkage to the same locus, we revisited the index SCA4 cases from the Utah family using novel technologies to investigate structural variation within the candidate region. METHODS We adopted a targeted long-read sequencing approach with adaptive sampling on the Oxford Nanopore Technologies (ONT) platform that enables the detection of segregating structural variants within a genomic region without a priori assumptions about any variant features. RESULTS Using this approach, we found a heterozygous (GGC)n repeat expansion in the last coding exon of the zinc finger homeobox 3 (ZFHX3) gene that segregates with disease, ranging between 48 and 57 GGC repeats in affected probands. This finding was replicated in a separate family with SCA4. Furthermore, the estimation of this GGC repeat size in short-read whole genome sequencing (WGS) data of 21,836 individuals recruited to the 100,000 Genomes Project in the UK and our in-house dataset of 11,258 exomes did not reveal any pathogenic repeats, indicating that the variant is ultrarare. CONCLUSIONS These findings support the utility of adaptive long-read sequencing as a powerful tool to decipher causative structural variation in unsolved cases of inherited neurological disease. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Zhongbo Chen
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
| | - Emil K Gustavsson
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
| | - Hannah Macpherson
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Claire Anderson
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
| | - Chris Clarkson
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Clarissa Rocca
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Eleanor Self
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Pilar Alvarez Jerez
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Annarita Scardamaglia
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - David Pellerin
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Kylie Montgomery
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
| | - Jasmaine Lee
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Delia Gagliardi
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Huihui Luo
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - John Hardy
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
- Reta Lila Weston Institute, Queen Square Institute of Neurology, University College London, London, United Kingdom
- UK Dementia Research Institute, University College London, London, United Kingdom
- NIHR University College London Hospitals Biomedical Research Centre, London, United Kingdom
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, China
| | - James Polke
- The Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Andrew B Singleton
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Katherine D Mathews
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
- Department of Neurology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Arianna Tucci
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Ying-Hui Fu
- Department of Neurology, University of California San Francisco, San Francisco, California, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
- Weill Institute for Neuroscience, University of California San Francisco, San Francisco, California, USA
- Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, California, USA
| | - Henry Houlden
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
- The Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
| | - Louis J Ptáček
- Department of Neurology, University of California San Francisco, San Francisco, California, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
- Weill Institute for Neuroscience, University of California San Francisco, San Francisco, California, USA
- Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, California, USA
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2
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Adams S, Norman K, Kemp J, Jacobs Z, Costelloe M, Fairbairn A, Robins R, Stock E, Moss P, Smith T, Love S, Manne T, Lowe KM, Logan I, Manoel M, McFadden K, Burns D, Falkiner Z, Clarkson C. Early human occupation of Australia's eastern seaboard. Sci Rep 2024; 14:2579. [PMID: 38296988 PMCID: PMC10830458 DOI: 10.1038/s41598-024-52000-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/12/2024] [Indexed: 02/02/2024] Open
Abstract
Secure archaeological evidence for human occupation on the eastern seaboard of Australia before ~ 25,000 years ago has proven elusive. This has prompted some researchers to argue that the coastal margins remained uninhabited prior to 25 ka. Here we show evidence for human occupation beginning between 30 ± 6 and 49 ± 8 ka at Wallen Wallen Creek (WWC), and at Middle Canalpin Creek (MCA20) between 38 ± 8 and 41 ± 8 ka. Both sites are located on the western side of Minjerribah (North Stradbroke Island), the second largest sand island in the world, isolated by rising sea levels in the early Holocene. The earliest occupation phase at both sites consists of charcoal and heavily retouched stone artefacts made from exotic raw materials. Heat-treatment of imported silcrete artefacts first appeared in sediment dated to ~ 30,000 years ago, making these amongst Australia's oldest dated heat-treated artefacts. An early human presence on Minjerribah is further suggested by palaeoenvironmental records of anthropogenic burning beginning by 45,000 years ago. These new chronologies from sites on a remnant portion of the continental margin confirm early human occupation along Sahul's now-drowned eastern continental shelf.
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Affiliation(s)
- Shaun Adams
- Australian Research Centre of Human Evolution, Griffith University, Nathan, QLD, 4111, Australia.
- Everick Foundation, 9/110 Mary St, Brisbane, QLD, 4000, Australia.
| | - Kasih Norman
- Australian Research Centre of Human Evolution, Griffith University, Nathan, QLD, 4111, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Canberra, Australia
| | - Justine Kemp
- Australian Research Centre of Human Evolution, Griffith University, Nathan, QLD, 4111, Australia
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Canberra, Australia
| | - Michael Costelloe
- Quandamooka Yoolooburrabee Aboriginal Corporation, 100 East Coast Rd, Dunwich, QLD, 4183, Australia
| | - Andrew Fairbairn
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Canberra, Australia
- School of Social Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Richard Robins
- Everick Foundation, 9/110 Mary St, Brisbane, QLD, 4000, Australia
| | - Errol Stock
- Triple-E Consultants, Tarragindi, QLD, 4121, Australia
| | - Patrick Moss
- School of the Environment, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Tam Smith
- School of Social Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Serena Love
- Everick Foundation, 9/110 Mary St, Brisbane, QLD, 4000, Australia
| | - Tiina Manne
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Canberra, Australia
- School of Social Science, The University of Queensland, St Lucia, QLD, 4072, Australia
- Max Planck Institute of Geoanthropology, Kahlaische Strasse 10, 07745, Jena, Germany
| | - Kelsey M Lowe
- School of Social Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - India Logan
- School of Social Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Michael Manoel
- School of Social Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Karen McFadden
- Quandamooka Yoolooburrabee Aboriginal Corporation, 100 East Coast Rd, Dunwich, QLD, 4183, Australia
| | - Darren Burns
- Quandamooka Yoolooburrabee Aboriginal Corporation, 100 East Coast Rd, Dunwich, QLD, 4183, Australia
| | - Zac Falkiner
- Everick Foundation, 9/110 Mary St, Brisbane, QLD, 4000, Australia
- School of Social Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Chris Clarkson
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia.
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Canberra, Australia.
- School of Social Science, The University of Queensland, St Lucia, QLD, 4072, Australia.
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany.
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Schmidt AF, Bourfiss M, Alasiri A, Puyol-Anton E, Chopade S, van Vugt M, van der Laan SW, Gross C, Clarkson C, Henry A, Lumbers TR, van der Harst P, Franceschini N, Bis JC, Velthuis BK, te Riele AS, Hingorani AD, Ruijsink B, Asselbergs FW, van Setten J, Finan C. Druggable proteins influencing cardiac structure and function: Implications for heart failure therapies and cancer cardiotoxicity. Sci Adv 2023; 9:eadd4984. [PMID: 37126556 PMCID: PMC10132758 DOI: 10.1126/sciadv.add4984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Dysfunction of either the right or left ventricle can lead to heart failure (HF) and subsequent morbidity and mortality. We performed a genome-wide association study (GWAS) of 16 cardiac magnetic resonance (CMR) imaging measurements of biventricular function and structure. Cis-Mendelian randomization (MR) was used to identify plasma proteins associating with CMR traits as well as with any of the following cardiac outcomes: HF, non-ischemic cardiomyopathy, dilated cardiomyopathy (DCM), atrial fibrillation, or coronary heart disease. In total, 33 plasma proteins were prioritized, including repurposing candidates for DCM and/or HF: IL18R (providing indirect evidence for IL18), I17RA, GPC5, LAMC2, PA2GA, CD33, and SLAF7. In addition, 13 of the 25 druggable proteins (52%; 95% confidence interval, 0.31 to 0.72) could be mapped to compounds with known oncological indications or side effects. These findings provide leads to facilitate drug development for cardiac disease and suggest that cardiotoxicities of several cancer treatments might represent mechanism-based adverse effects.
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Affiliation(s)
- Amand F. Schmidt
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- UCL BHF Research Accelerator Centre, London, UK
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Mimount Bourfiss
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Abdulrahman Alasiri
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Esther Puyol-Anton
- Department of Biomedical Engineering, School of Biomedical Engineering and Imaging Sciences, King's College London, King's Health Partners, London, UK
| | - Sandesh Chopade
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- UCL BHF Research Accelerator Centre, London, UK
| | - Marion van Vugt
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- UCL BHF Research Accelerator Centre, London, UK
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Sander W. van der Laan
- Central Diagnostics Laboratory, Division Laboratory, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Christian Gross
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Chris Clarkson
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- UCL BHF Research Accelerator Centre, London, UK
| | - Albert Henry
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- UCL BHF Research Accelerator Centre, London, UK
- Institute of Health Informatics, Faculty of Population Health, University College London, London, UK
| | - Tom R. Lumbers
- UCL BHF Research Accelerator Centre, London, UK
- Institute of Health Informatics, Faculty of Population Health, University College London, London, UK
| | - Pim van der Harst
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Birgitta K. Velthuis
- Department of Radiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Anneline S. J. M. te Riele
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Netherlands Heart Institute, Utrecht, Netherlands
- Member of the European Reference Network for rare, low prevalence, and complex diseases of the heart (ERN GUARD HEART; http://guardheart.ern-net.eu)
| | - Aroon D. Hingorani
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- UCL BHF Research Accelerator Centre, London, UK
| | - Bram Ruijsink
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Biomedical Engineering, School of Biomedical Engineering and Imaging Sciences, King's College London, King's Health Partners, London, UK
| | - Folkert W. Asselbergs
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, Netherlands
- Institute of Health Informatics, Faculty of Population Health, University College London, London, UK
- Member of the European Reference Network for rare, low prevalence, and complex diseases of the heart (ERN GUARD HEART; http://guardheart.ern-net.eu)
| | - Jessica van Setten
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Chris Finan
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- UCL BHF Research Accelerator Centre, London, UK
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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4
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Gregory BRB, Kissinger JA, Clarkson C, Kimpe LE, Eickmeyer DC, Kurek J, Smol JP, Blais JM. Are fur farms a potential source of persistent organic pollutants or mercury to nearby freshwater ecosystems? Sci Total Environ 2022; 833:155100. [PMID: 35398138 DOI: 10.1016/j.scitotenv.2022.155100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
Farming of carnivorous animals for pelts potentially contaminates nearby ecosystems because animal feed and waste may contain persistent organic pollutants (POPs) and metals. Mink farms in Nova Scotia (NS), Canada, provide mink with feed partially composed of marine fish meal. To test whether mink farms potentially contribute contaminants to nearby lakes, we quantified organochlorine pesticides (OCP), polychlorinated biphenyls (PCB), and total mercury (THg) in mink/aquaculture feed, waste, and sediment collected from 14 lakes within rural southwest NS where mink farms are abundant and have operated for decades. Mercury, PCBs, dichlorodiphenyltrichloroethane (DDT), hexachlorocyclohexane (HCH), and dieldrin were present in mink/aquaculture feed and mink waste, indicating they are potential contaminant sources. Lakes with mink farms in their catchment exhibited significantly higher THgflux than lakes downstream of mink farming activity and reference lakes (p < 0.0001) after the intensification of mink farming in 1980, indicating mink farming activity is likely associated with increased lacustrine THgflux. Sedimentary ƩPCBflux was elevated in lakes with mink farms in their catchments, suggesting possible PCB contributions from mink farming, local agriculture, and atmospheric deposition. Elevated ƩDDT in lakes near mink farms relative to reference lakes suggests a possible enrichment related to mink farming, although mixed land use and historical DDT usage related to forestry in the region complicates DDT source attribution. Maximum dieldrinflux and HCHflux in lake sediment occurred coeval with peak worldwide usage in the 1970s and are unlikely to be associated with local mink farming. Lakes with mink farming activities in their catchments were associated with increased THgflux, ƩPCBflux, and possibly ƩDDTflux, suggesting a possible connection between marine fish meal, fur farms, and aquatic ecosystems in NS.
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Affiliation(s)
- B R B Gregory
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - J A Kissinger
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - C Clarkson
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - L E Kimpe
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - D C Eickmeyer
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - J Kurek
- Department of Geography and Environment, Mount Allison University, Sackville, NB E4L 1E2, Canada
| | - J P Smol
- Paleoecolgical Environmental Assessment and Research Lab (PEARL), Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - J M Blais
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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5
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Clarkson C, Gibbons Y, Roe A, Whitby E, Carter H, Williamson A, Yerburgh R, Smith R, Smith B. An evaluation of the safety of telephone first consultations in physiotherapy MSK practice. Physiotherapy 2022. [DOI: 10.1016/j.physio.2021.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Mohr A, Tianyuan C, Clarkson C, Brooke G, Teif V, Zwacka R. Fas-threshold signalling in MSCs causes tumour progression and metastasis. Cytotherapy 2021. [DOI: 10.1016/s1465324921002735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Bradshaw CJA, Norman K, Ulm S, Williams AN, Clarkson C, Chadœuf J, Lin SC, Jacobs Z, Roberts RG, Bird MI, Weyrich LS, Haberle SG, O'Connor S, Llamas B, Cohen TJ, Friedrich T, Veth P, Leavesley M, Saltré F. Stochastic models support rapid peopling of Late Pleistocene Sahul. Nat Commun 2021; 12:2440. [PMID: 33927195 PMCID: PMC8085232 DOI: 10.1038/s41467-021-21551-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 02/02/2021] [Indexed: 02/02/2023] Open
Abstract
The peopling of Sahul (the combined continent of Australia and New Guinea) represents the earliest continental migration and settlement event of solely anatomically modern humans, but its patterns and ecological drivers remain largely conceptual in the current literature. We present an advanced stochastic-ecological model to test the relative support for scenarios describing where and when the first humans entered Sahul, and their most probable routes of early settlement. The model supports a dominant entry via the northwest Sahul Shelf first, potentially followed by a second entry through New Guinea, with initial entry most consistent with 50,000 or 75,000 years ago based on comparison with bias-corrected archaeological map layers. The model's emergent properties predict that peopling of the entire continent occurred rapidly across all ecological environments within 156-208 human generations (4368-5599 years) and at a plausible rate of 0.71-0.92 km year-1. More broadly, our methods and approaches can readily inform other global migration debates, with results supporting an exit of anatomically modern humans from Africa 63,000-90,000 years ago, and the peopling of Eurasia in as little as 12,000-15,000 years via inland routes.
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Affiliation(s)
- Corey J A Bradshaw
- Global Ecology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia.
| | - Kasih Norman
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Sean Ulm
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- College of Arts, Society and Education, James Cook University, Cairns, QLD, Australia
| | - Alan N Williams
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Climate Change Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- EMM Consulting, St Leonards, NSW, Australia
| | - Chris Clarkson
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- School of Social Science, University of Queensland, Brisbane, QLD, Australia
- Max Planck Institute for the Science of Human History, Jena, Germany
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Joël Chadœuf
- UR 1052, French National Institute for Agricultural Research (INRA), Montfavet, France
| | - Sam C Lin
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Zenobia Jacobs
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Richard G Roberts
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Michael I Bird
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | - Laura S Weyrich
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Simon G Haberle
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Department of Archaeology and Natural History, School of Culture, History and Language, Australian National University, Canberra, ACT, Australia
| | - Sue O'Connor
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Department of Archaeology and Natural History, School of Culture, History and Language, Australian National University, Canberra, ACT, Australia
| | - Bastien Llamas
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, Australia
| | - Tim J Cohen
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Tobias Friedrich
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa, Honolulu, Hawai'i, USA
| | - Peter Veth
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- Archaeology and the Centre for Rock Art Research and Management M257, School of Social Sciences, University of Western Australia, Crawley, WA, Australia
| | - Matthew Leavesley
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
- College of Arts, Society and Education, James Cook University, Cairns, QLD, Australia
- Department of Anthropology and Sociology, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Frédérik Saltré
- Global Ecology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW, Australia
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Florin SA, Roberts P, Marwick B, Patton NR, Shulmeister J, Lovelock CE, Barry LA, Hua Q, Nango M, Djandjomerr D, Fullagar R, Wallis LA, Fairbairn AS, Clarkson C. Pandanus nutshell generates a palaeoprecipitation record for human occupation at Madjedbebe, northern Australia. Nat Ecol Evol 2021; 5:295-303. [PMID: 33495592 PMCID: PMC7929916 DOI: 10.1038/s41559-020-01379-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/28/2020] [Accepted: 12/03/2020] [Indexed: 11/11/2022]
Abstract
Little is known about the Pleistocene climatic context of northern Australia at the time of early human settlement. Here we generate a palaeoprecipitation proxy using stable carbon isotope analysis of modern and archaeological pandanus nutshell from Madjedbebe, Australia's oldest known archaeological site. We document fluctuations in precipitation over the last 65,000 years and identify periods of lower precipitation during the penultimate and last glacial stages, Marine Isotope Stages 4 and 2. However, the lowest effective annual precipitation is recorded at the present time. Periods of lower precipitation, including the earliest phase of occupation, correspond with peaks in exotic stone raw materials and artefact discard at the site. This pattern is interpreted as suggesting increased group mobility and intensified use of the region during drier periods.
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Affiliation(s)
- S Anna Florin
- School of Social Science, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Patrick Roberts
- School of Social Science, The University of Queensland, Brisbane, Queensland, Australia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ben Marwick
- Department of Anthropology, University of Washington, Seattle, WA, USA
| | - Nicholas R Patton
- School of Earth and Environment, University of Canterbury, Christchurch, New Zealand
| | - James Shulmeister
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
- School of Earth and Environment, University of Canterbury, Christchurch, New Zealand
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Catherine E Lovelock
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Linda A Barry
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales, Australia
| | - Quan Hua
- Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales, Australia
| | - May Nango
- Gundjeihmi Aboriginal Corporation, Jabiru, Northern Territory, Australia
| | | | - Richard Fullagar
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Lynley A Wallis
- Griffith Centre for Social and Cultural Research, Griffith University, Nathan, Queensland, Australia
| | - Andrew S Fairbairn
- School of Social Science, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Chris Clarkson
- School of Social Science, The University of Queensland, Brisbane, Queensland, Australia.
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.
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9
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Florin SA, Fairbairn AS, Nango M, Djandjomerr D, Marwick B, Fullagar R, Smith M, Wallis LA, Clarkson C. The first Australian plant foods at Madjedbebe, 65,000-53,000 years ago. Nat Commun 2020; 11:924. [PMID: 32066741 PMCID: PMC7026095 DOI: 10.1038/s41467-020-14723-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 03/05/2019] [Accepted: 01/29/2020] [Indexed: 11/08/2022] Open
Abstract
There is little evidence for the role of plant foods in the dispersal of early modern humans into new habitats globally. Researchers have hypothesised that early movements of human populations through Island Southeast Asia and into Sahul were driven by the lure of high-calorie, low-handling-cost foods, and that the use of plant foods requiring processing was not common in Sahul until the Holocene. Here we present the analysis of charred plant food remains from Madjedbebe rockshelter in northern Australia, dated to between 65 kya and 53 kya. We demonstrate that Australia's earliest known human population exploited a range of plant foods, including those requiring processing. Our finds predate existing evidence for such subsistence practices in Sahul by at least 23ky. These results suggest that dietary breadth underpinned the success of early modern human populations in this region, with the expenditure of labour on the processing of plants guaranteeing reliable access to nutrients in new environments.
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Affiliation(s)
- S Anna Florin
- School of Social Science, University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Andrew S Fairbairn
- School of Social Science, University of Queensland, Brisbane, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW, 2522, Australia
- Depatrment of Archaeology, Max Planck Institute for the Science of Human History, Kahlaiche Strasse 10, 07745, Jena, Germany
| | - May Nango
- Gundjeihmi Aboriginal Corporation, 5 Gregory Place, Jabiru, NT, 0886, Australia
| | - Djaykuk Djandjomerr
- Gundjeihmi Aboriginal Corporation, 5 Gregory Place, Jabiru, NT, 0886, Australia
| | - Ben Marwick
- Department of Anthropology, University of Washington, Seattle, WA, 98195, USA
| | - Richard Fullagar
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Mike Smith
- College of Humanities, Arts and Social Sciences, Flinders University, Adelaide, SA, 5042, Australia
- Centre for Historical Research, National Museum of Australia, Canberra, ACT, 2601, Australia
| | - Lynley A Wallis
- Nulungu Research Institute, University of Notre Dame Australia, Broome, WA, 6725, Australia
- Griffith Centre for Social and Cultural Research, Griffith University, Brisbane, QLD, 4111, Australia
| | - Chris Clarkson
- School of Social Science, University of Queensland, Brisbane, QLD, 4072, Australia.
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW, 2522, Australia.
- Depatrment of Archaeology, Max Planck Institute for the Science of Human History, Kahlaiche Strasse 10, 07745, Jena, Germany.
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Adamek J, Clarkson C, Coates L, Durrer R, Kunz M. Bias and scatter in the Hubble diagram from cosmological large-scale structure. Int J Clin Exp Med 2019. [DOI: 10.1103/physrevd.100.021301] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Gasaway C, Mastalerz M, Krause F, Clarkson C, Debuhr C. Application of micro-FTIR mapping and SEM to study compositional heterogeneity of siltstones: Example from the Late Devonian-Early Mississippian Middle Bakken Member. J Microsc 2017; 269:195-211. [PMID: 28795400 DOI: 10.1111/jmi.12615] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 02/01/2017] [Revised: 06/13/2017] [Accepted: 07/15/2017] [Indexed: 11/29/2022]
Abstract
This paper explores the applicability of micro-FTIR mapping to study heterogeneity of organic matter-lean siltstones. Closely spaced samples of Late Devonian dolomitic siltstones of the Middle Bakken Member were analysed with micro-FTIR, powder X-ray diffraction, and scanning electron microscopy (SEM) to explore the distribution and chemical properties of organic matter (OM), muscovite/feldspar/clay group, carbonates, and quartz, and their influence on porosity and permeability of these rocks. Our results show that quartz is the dominant component of the samples, and the main mineralogical differences between the samples are reflected in the abundance of carbonate minerals. Organic matter content is usually far below 1 wt. % and dominantly represented by terrestrially derived vitrinite and inertinite. Micro-FTIR mapping demonstrates that the more spatially connected quartz and muscovite/feldspar/clays become, the larger permeability in the rock develops, and these correlations are especially strong for planes parallel to bedding. In contrast, carbonate connectivity shows a strong negative correlation with permeability. No correlations between connectivity of components and porosity have been detected. These observations suggest that micro-FTIR not only can document compositional heterogeneity of siltstones, but also has potential to help understanding their permeability systems.
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Affiliation(s)
- C Gasaway
- Department of Geological Sciences, Indiana University, Bloomington, Indiana, U.S.A
| | - M Mastalerz
- Indiana Geological Survey, Indiana University, Bloomington, Indiana, U.S.A
| | - F Krause
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
| | - C Clarkson
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
| | - C Debuhr
- Department of Geoscience, University of Calgary, Calgary, Alberta, Canada
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12
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Clarkson C, Jacobs Z, Marwick B, Fullagar R, Wallis L, Smith M, Roberts RG, Hayes E, Lowe K, Carah X, Florin SA, McNeil J, Cox D, Arnold LJ, Hua Q, Huntley J, Brand HEA, Manne T, Fairbairn A, Shulmeister J, Lyle L, Salinas M, Page M, Connell K, Park G, Norman K, Murphy T, Pardoe C. Human occupation of northern Australia by 65,000 years ago. Nature 2017; 547:306-310. [DOI: 10.1038/nature22968] [Citation(s) in RCA: 518] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/19/2017] [Indexed: 12/21/2022]
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Abstract
The notion that the evolution of core reduction strategies involved increasing efficiency in cutting edge production is prevalent in narratives of hominin technological evolution. Yet a number of studies comparing two different knapping technologies have found no significant differences in edge production. Using digital analysis methods we present an investigation of raw material efficiency in eight core technologies broadly representative of the long-term evolution of lithic technology. These are bipolar, multiplatform, discoidal, biface, Levallois, prismatic blade, punch blade and pressure blade production. Raw material efficiency is assessed by the ratio of cutting edge length to original core mass. We also examine which flake attributes contribute to maximising raw material efficiency, as well as compare the difference between expert and intermediate knappers in terms of cutting edge produced per gram of core. We identify a gradual increase in raw material efficiency over the broad sweep of lithic technological evolution. The results indicate that the most significant transition in efficiency likely took place with the introduction of small foliate biface, Levallois and prismatic blade knapping, all introduced in the Middle Stone Age / Middle Palaeolithic among early Homo sapiens and Neanderthals. This suggests that no difference in raw material efficiency existed between these species. With prismatic blade technology securely dated to the Middle Palaeolithic, by including the more recent punch and pressure blade technology our results dispel the notion that the transition to the Upper Palaeolithic was accompanied by an increase in efficiency. However, further increases in cutting edge efficiency are evident, with pressure blades possessing the highest efficiency in this study, indicating that late/epi-Palaeolithic and Neolithic blade technologies further increased efficiency.
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Affiliation(s)
- Antoine Muller
- School of Social Science, The University of Queensland, St Lucia, Queensland, Australia
- * E-mail:
| | - Chris Clarkson
- School of Social Science, The University of Queensland, St Lucia, Queensland, Australia
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14
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Clarkson C, Adams N, Caplin N. Korean hand acupuncture for pregnancy related pelvic girdle pain: a feasibility study. Physiotherapy 2016. [DOI: 10.1016/j.physio.2016.10.247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Abstract
Eosinophilic esophagitis (EoE) has been reported to be more prevalent in patients with esophageal atresia/tracheoesophageal fistula (EA-TEF). To date, there is limited data on the management of EoE in this group of patients. The aim of this study is to evaluate the treatment outcomes of EoE in children with EA-TEF. A retrospective chart review was performed on all EA-TEF children who were diagnosed with and treated for EoE between January 2000 and September 2013 at the Sydney Children's Hospital. Data collected included details of the patient's treatment, post-treatment endoscopy, symptoms and nutrition. Twenty patients were included in the study. Median age at diagnosis was 26 months (8-103 months), and median time from diagnosis to last follow-up was 23 months (2-132 months). Patients were treated with budesonide slurry, swallowed fluticasone, elimination diet alone or in combination. All patients were on proton pump inhibitors at time of diagnosis of EoE which was continued. Six out of seven patients who had furrowing/exudate in endoscopy at diagnosis had complete resolution at a median follow-up period of 26 months (P = 0.031). Median peak intraepithelial eosinophil count reduced significantly from 30/high-powered field (HPF) (19-80/HPF) to 8/HPF (0-85/HPF) (median time for improvement = 24 months) (P = 0.015). There was a significant reduction in symptoms of dysphagia and reflux post-treatment (P < 0.001). Prevalence of strictures significantly decreased (P = 0.016), as did need for dilatations (P = 0.004). In four out of six patients with gastrostomies at baseline, the feeding improved on treatment of EoE and the gastrostomy could be closed. There was also a nonsignificant trend towards improvement in weight and height 'z scores' of the patients. Treatment of EoE in children with EA-TEF was found to significantly reduce intraepithelial eosinophil count, symptoms, strictures and need for dilatations.
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Affiliation(s)
- L J Chan
- Department of Paediatric Gastroenterology, Sydney Children's Hospital, University of New South Wales, Sydney, New South Wales, Australia
| | - L Tan
- Department of Paediatric Gastroenterology, Sydney Children's Hospital, University of New South Wales, Sydney, New South Wales, Australia
| | - J Dhaliwal
- Department of Paediatric Gastroenterology, Sydney Children's Hospital, University of New South Wales, Sydney, New South Wales, Australia
| | - F Briglia
- Department of Paediatric Gastroenterology, Sydney Children's Hospital, University of New South Wales, Sydney, New South Wales, Australia
| | - C Clarkson
- Department of Paediatric Gastroenterology, Sydney Children's Hospital, University of New South Wales, Sydney, New South Wales, Australia
| | - U Krishnan
- Department of Paediatric Gastroenterology, Sydney Children's Hospital, University of New South Wales, Sydney, New South Wales, Australia
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16
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Hatcher H, Tsung Y, Qin SL, Clarkson C, Zhao M. IL-36 expression plays a potential role in acute kidney injury through down-regulation of inflammatory response. ACTA ACUST UNITED AC 2016. [DOI: 10.18081/2378-5225-016-06/16-26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Clarkson C, Smith M, Marwick B, Fullagar R, Wallis LA, Faulkner P, Manne T, Hayes E, Roberts RG, Jacobs Z, Carah X, Lowe KM, Matthews J, Florin SA. The archaeology, chronology and stratigraphy of Madjedbebe (Malakunanja II): A site in northern Australia with early occupation. J Hum Evol 2015; 83:46-64. [DOI: 10.1016/j.jhevol.2015.03.014] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 11/28/2022]
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18
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Adamek J, Clarkson C, Durrer R, Kunz M. Does small scale structure significantly affect cosmological dynamics? Phys Rev Lett 2015; 114:051302. [PMID: 25699430 DOI: 10.1103/physrevlett.114.051302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Indexed: 06/04/2023]
Abstract
The large-scale homogeneity and isotropy of the Universe is generally thought to imply a well-defined background cosmological model. It may not. Smoothing over structure adds in an extra contribution, transferring power from small scales up to large. Second-order perturbation theory implies that the effect is small, but suggests that formally the perturbation series may not converge. The amplitude of the effect is actually determined by the ratio of the Hubble scales at matter-radiation equality and today-which are entirely unrelated. This implies that a universe with significantly lower temperature today could have significant backreaction from more power on small scales, and so provides the ideal testing ground for understanding backreaction. We investigate this using two different N-body numerical simulations-a 3D Newtonian and a 1D simulation which includes all relevant relativistic effects. We show that while perturbation theory predicts an increasing backreaction as more initial small-scale power is added, in fact the virialization of structure saturates the backreaction effect at the same level independently of the equality scale. This implies that backreaction is a small effect independently of initial conditions. Nevertheless, it may still contribute at the percent level to certain cosmological observables and therefore it cannot be neglected in precision cosmology.
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Affiliation(s)
- Julian Adamek
- Département de Physique Théorique & Center for Astroparticle Physics, Université de Genève, Quai E. Ansermet 24, CH-1211 Genève 4, Switzerland
| | - Chris Clarkson
- Astrophysics, Cosmology and Gravity Centre & Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
| | - Ruth Durrer
- Département de Physique Théorique & Center for Astroparticle Physics, Université de Genève, Quai E. Ansermet 24, CH-1211 Genève 4, Switzerland
| | - Martin Kunz
- Département de Physique Théorique & Center for Astroparticle Physics, Université de Genève, Quai E. Ansermet 24, CH-1211 Genève 4, Switzerland and African Institute for Mathematical Sciences, 6 Melrose Road, Muizenberg 7945, South Africa
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19
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20
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Clarkson C. Trouble with physics: Time to ditch Copernicus? New Sci 2013. [DOI: 10.1016/s0262-4079(13)60569-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Bolejko K, Clarkson C, Maartens R, Bacon D, Meures N, Beynon E. Antilensing: the bright side of voids. Phys Rev Lett 2013; 110:021302. [PMID: 23383886 DOI: 10.1103/physrevlett.110.021302] [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: 10/01/2012] [Indexed: 06/01/2023]
Abstract
More than half of the volume of our Universe is occupied by cosmic voids. The lensing magnification effect from those underdense regions is generally thought to give a small dimming contribution: objects on the far side of a void are supposed to be observed as slightly smaller than if the void were not there, which together with conservation of surface brightness implies net reduction in photons received. This is predicted by the usual weak lensing integral of the density contrast along the line of sight. We show that this standard effect is swamped at low redshifts by a relativistic Doppler term that is typically neglected. Contrary to the usual expectation, objects on the far side of a void are brighter than they would be otherwise. Thus the local dynamics of matter in and near the void is crucial and is only captured by the full relativistic lensing convergence. There are also significant nonlinear corrections to the relativistic linear theory, which we show actually underpredicts the effect. We use exact solutions to estimate that these can be more than 20% for deep voids. This remains an important source of systematic errors for weak lensing density reconstruction in galaxy surveys and for supernovae observations, and may be the cause of the reported extra scatter of field supernovae located on the edge of voids compared to those in clusters.
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Affiliation(s)
- Krzysztof Bolejko
- Sydney Institute for Astronomy, The University of Sydney, Sydney, New South Wales 2006, Australia
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22
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Williams JB, Clarkson C, Mant C, Drinkwater A, May E. Fat, oil and grease deposits in sewers: characterisation of deposits and formation mechanisms. Water Res 2012; 46:6319-6328. [PMID: 23039918 DOI: 10.1016/j.watres.2012.09.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 06/28/2012] [Accepted: 09/02/2012] [Indexed: 06/01/2023]
Abstract
Fat, oil and grease deposits (FOG) in sewers are a major problem and can cause sewer overflows, resulting in environmental damage and health risks. Often simplistically portrayed as cooling of fats, recent research has suggested that saponification may be involved in FOG formation. However there are still questions about the mechanisms effecting transformations in sewers and the role and source of metal cations involved in saponification. This study characterises FOG deposits from pumping stations, sewers and sewage works from different water hardness zones across the UK. The sites all had previous problems with FOG and most catchments contained catering and food preparation establishments. The FOG deposits were highly variable with moisture content ranging from 15 to 95% and oil content from 0 to 548 mg/g. Generally the pumping stations had lower moisture content and higher fat content, followed by the sewers then the sewage works. The water in contact with the FOG had high levels of oil (mean of about 800 mg/L) and this may indicate poor kitchen FOG management practices. FOG fatty acid profiles showed a transformation from unsaturated to saturated forms compared to typical cooking oils. This seems to relate to ageing in the sewer network or the mechanism of formation, as samples from pumping stations had higher proportions of C18:1 compared to C16. This may be due to microbial transformations by bacteria such as Clostridium sp. in a similar process to adipocere formation. There was an association between water hardness and increased Ca levels in FOG along with harder deposits and higher melting points. A link between FOG properties and water hardness has not been previously reported for field samples. This may also be due to microbial processes, such as biocalcification. By developing the understanding of these mechanisms it may be possible to more effectively control FOG deposits, especially when combined with promotion of behavioural change.
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Affiliation(s)
- J B Williams
- University of Portsmouth, School of Civil Engineering and Surveying, Portsmouth, Hants, UK.
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23
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Petraglia MD, Alsharekh A, Breeze P, Clarkson C, Crassard R, Drake NA, Groucutt HS, Jennings R, Parker AG, Parton A, Roberts RG, Shipton C, Matheson C, Al-Omari A, Veall MA. Hominin dispersal into the Nefud Desert and Middle palaeolithic settlement along the Jubbah Palaeolake, Northern Arabia. PLoS One 2012. [PMID: 23185454 PMCID: PMC3501467 DOI: 10.1371/journal.pone.0049840] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [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] [Indexed: 12/20/2022] Open
Abstract
The Arabian Peninsula is a key region for understanding hominin dispersals and the effect of climate change on prehistoric demography, although little information on these topics is presently available owing to the poor preservation of archaeological sites in this desert environment. Here, we describe the discovery of three stratified and buried archaeological sites in the Nefud Desert, which includes the oldest dated occupation for the region. The stone tool assemblages are identified as a Middle Palaeolithic industry that includes Levallois manufacturing methods and the production of tools on flakes. Hominin occupations correspond with humid periods, particularly Marine Isotope Stages 7 and 5 of the Late Pleistocene. The Middle Palaeolithic occupations were situated along the Jubbah palaeolake-shores, in a grassland setting with some trees. Populations procured different raw materials across the lake region to manufacture stone tools, using the implements to process plants and animals. To reach the Jubbah palaeolake, Middle Palaeolithic populations travelled into the ameliorated Nefud Desert interior, possibly gaining access from multiple directions, either using routes from the north and west (the Levant and the Sinai), the north (the Mesopotamian plains and the Euphrates basin), or the east (the Persian Gulf). The Jubbah stone tool assemblages have their own suite of technological characters, but have types reminiscent of both African Middle Stone Age and Levantine Middle Palaeolithic industries. Comparative inter-regional analysis of core technology indicates morphological similarities with the Levantine Tabun C assemblage, associated with human fossils controversially identified as either Neanderthals or Homo sapiens.
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Affiliation(s)
- Michael D Petraglia
- School of Archaeology, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom.
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Clifton T, Clarkson C, Bull P. Isotropic blackbody cosmic microwave background radiation as evidence for a homogeneous universe. Phys Rev Lett 2012; 109:051303. [PMID: 23006164 DOI: 10.1103/physrevlett.109.051303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Indexed: 06/01/2023]
Abstract
The question of whether the Universe is spatially homogeneous and isotropic on the largest scales is of fundamental importance to cosmology but has not yet been answered decisively. Surprisingly, neither an isotropic primary cosmic microwave background (CMB) nor combined observations of luminosity distances and galaxy number counts are sufficient to establish such a result. The inclusion of the Sunyaev-Zel'dovich effect in CMB observations, however, dramatically improves this situation. We show that even a solitary observer who sees an isotropic blackbody CMB can conclude that the Universe is homogeneous and isotropic in their causal past when the Sunyaev-Zel'dovich effect is present. Critically, however, the CMB must either be viewed for an extended period of time, or CMB photons that have scattered more than once must be detected. This result provides a theoretical underpinning for testing the cosmological principle with observations of the CMB alone.
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Affiliation(s)
- Timothy Clifton
- School of Physics and Astronomy, Queen Mary University of London, United Kingdom
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25
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Petraglia MD, Haslam M, Fuller DQ, Boivin N, Clarkson C. Out of Africa: new hypotheses and evidence for the dispersal of Homo sapiens along the Indian Ocean rim. Ann Hum Biol 2010; 37:288-311. [PMID: 20334598 DOI: 10.3109/03014461003639249] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The dispersal of Homo sapiens out of Africa is a significant topic in human evolutionary studies. Most investigators agree that our species arose in Africa and subsequently spread out to occupy much of Eurasia. Researchers have argued that populations expanded along the Indian Ocean rim at ca 60,000 years ago during a single rapid dispersal event, probably employing a coastal route towards Australasia. Archaeologists have been relatively silent about the movement and expansion of human populations in terrestrial environments along the Indian Ocean rim, although it is clear that Homo sapiens reached Australia by ca 45,000 years ago. Here, we synthesize and document current genetic and archaeological evidence from two major landmasses, the Arabian peninsula and the Indian subcontinent, regions that have been underplayed in the story of out of Africa dispersals. We suggest that modern humans were present in Arabia and South Asia earlier than currently believed, and probably coincident with the presence of Homo sapiens in the Levant between ca 130 and 70,000 years ago. We show that climatic and environmental fluctuations during the Late Pleistocene would have had significant demographic effects on Arabian and South Asian populations, though indigenous populations would have responded in different ways. Based on a review of the current genetic, archaeological and environmental data, we indicate that demographic patterns in Arabia and South Asia are more interesting and complex than surmised to date.
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Affiliation(s)
- Michael D Petraglia
- School of Archaeology, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK.
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Abstract
An important issue in cosmology is reconstructing the effective dark energy equation of state directly from observations. With so few physically motivated models, future dark energy studies cannot only be based on constraining a dark energy parameter space. We present a new nonparametric method which can accurately reconstruct a wide variety of dark energy behavior with no prior assumptions about it. It is simple, quick and relatively accurate, and involves no expensive explorations of parameter space. The technique uses principal component analysis and a combination of information criteria to identify real features in the data, and tailors the fitting functions to pick up trends and smooth over noise. We find that we can constrain a large variety of w(z) models to within 10%-20% at redshifts z≲1 using just SNAP-quality data.
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Affiliation(s)
- Chris Clarkson
- Centre for Astrophysics, Cosmology & Gravitation, University of Cape Town, South Africa
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Abstract
We propose consistency tests for the cosmological constant which provide a direct observational signal if Lambda is wrong, regardless of the densities of matter and curvature. As an example of its utility, our flat case test can warn of a small transition of the equation of state w(z) from w(z)=-1 of 20% from SNAP (Supernova Acceleration Probe) quality data at 4-sigma, even when direct reconstruction techniques see virtually no evidence for deviation from Lambda. It is shown to successfully rule out a wide range of non-Lambda dark energy models with no reliance on knowledge of Omega_{m} using SNAP quality data and a large range for using 10;{5} supernovae as forecasted for the Large Synoptic Survey Telescope.
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Affiliation(s)
- Caroline Zunckel
- Oxford University, Astrophysics, Denys Wilkinson Building, Keble Road, OX1 3RH, United Kingdom
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Abstract
To date, there has been no general way of determining if the Copernican principle--that we live at a typical position in the Universe--is in fact a valid assumption, significantly weakening the foundations of cosmology as a scientific endeavor. Here we present an observational test for the Copernican assumption which can be automatically implemented while we search for dark energy in the coming decade. Our test is entirely independent of any model for dark energy or theory of gravity and thereby represents a model-independent test of the Copernican principle.
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Affiliation(s)
- Chris Clarkson
- Cosmology and Gravity Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa
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Uzan JP, Clarkson C, Ellis GFR. Time drift of cosmological redshifts as a test of the Copernican principle. Phys Rev Lett 2008; 100:191303. [PMID: 18518435 DOI: 10.1103/physrevlett.100.191303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Indexed: 05/26/2023]
Abstract
We present the time drift of the cosmological redshift in a general spherically symmetric spacetime. We demonstrate that its observation would allow us to test the Copernican principle and so determine if our Universe is radially inhomogeneous, an important issue in our understanding of dark energy. In particular, when combined with distance data, this extra observable allows one to fully reconstruct the geometry of a spacetime describing a spherically symmetric underdense region around us, purely from background observations.
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Affiliation(s)
- Jean-Philippe Uzan
- Institut d'Astrophysique de Paris, Université Pierre and Marie Curie-Paris VI, CNRS-UMR 7095, Paris, France.
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Pang G, Andrews W, Clarkson C, Dwyer J, Holyday M, Jackson H, Kepreotes H, Lambert K, Paton M, Robertson K, Scott B, Stradling E, Talbot P, Wagner S, Ward K. Home enteral nutrition patients in NSW: Results from a one month audit of new and existing HEN patients from NSW public healthcare facilities. Nutrition 2008. [DOI: 10.1016/j.nut.2008.01.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Pang G, Andrews W, Clarkson C, Dwyer J, Holyday M, Jackson H, Kepreotes H, Lambert K, Paton M, Robertson K, Scott B, Stradling E, Talbot P, Wagner S, Ward K. Establishing a NSW HEN registry. Nutrition 2008. [DOI: 10.1016/j.nut.2008.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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33
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Seahra SS, Clarkson C, Maartens R. Detecting extra dimensions with gravity-wave spectroscopy: the black-string brane world. Phys Rev Lett 2005; 94:121302. [PMID: 15903904 DOI: 10.1103/physrevlett.94.121302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Indexed: 05/02/2023]
Abstract
Using the black string between two branes as a model of a brane-world black hole, we compute the gravity-wave perturbations and identify the features arising from the additional polarizations of the graviton. The standard four-dimensional gravitational wave signal acquires late-time oscillations due to massive modes of the graviton. The Fourier transform of these oscillations shows a series of spikes associated with the masses of the Kaluza-Klein modes, providing in principle a spectroscopic signature of extra dimensions.
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Affiliation(s)
- Sanjeev S Seahra
- Institute of Cosmology & Gravitation, University of Portsmouth, Portsmouth PO1 2EG, United Kingdom
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34
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Joly E, Stevens J, Le Rolle A, González A, Mehling B, Clarkson C, Howard J, Butcher G. Co-evolution of rat Tap transporters and MHC class I RT1.A molecules. Immunol Lett 1997. [DOI: 10.1016/s0165-2478(97)85019-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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35
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Joly E, Leong L, Coadwell WJ, Clarkson C, Butcher GW. The rat MHC haplotype RT1c expresses two classical class I molecules. The Journal of Immunology 1996. [DOI: 10.4049/jimmunol.157.4.1551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
Cloning and characterization of classical MHC class I coding sequences of the laboratory rat Rattus norvegicus has been reported so far for only four haplotypes, RT1a, RT1(1), RT1n, and RT1u. In all four cases, only one RT1.A classical class I molecule was found. Here we report that, in contrast, the RT1c haplotype expresses two different classical class I molecules. Using recombinant rat strains, we find that allotypic serologic determinants carried by the two molecules map to the RT1.A region, and so we have named them RT1.A1c and RT1.A2c. Multiple clones of functional cDNAs for each of these two molecules were isolated using a recently developed PCR-based expression-cloning method. Using a panel of 20 RT1.Ac-reactive mAb, we find that six recognize RT1.A1c, seven recognize RT1.A2c, and seven recognize both. We also show that both molecules are recognized and distinguished by primary alloreactive cytotoxic T lymphocytes, and that they correspond to identifiable and distinct molecular species in cells that express RT1c naturally. These data all concur to demonstrate that the RT1.Ac region carries two different loci, each of which encodes a functional classical class I molecule.
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Affiliation(s)
- E Joly
- Department of Immunology, Babraham Institute, Cambridge, United Kingdom
| | - L Leong
- Department of Immunology, Babraham Institute, Cambridge, United Kingdom
| | - W J Coadwell
- Department of Immunology, Babraham Institute, Cambridge, United Kingdom
| | - C Clarkson
- Department of Immunology, Babraham Institute, Cambridge, United Kingdom
| | - G W Butcher
- Department of Immunology, Babraham Institute, Cambridge, United Kingdom
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36
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Joly E, Leong L, Coadwell WJ, Clarkson C, Butcher GW. The rat MHC haplotype RT1c expresses two classical class I molecules. J Immunol 1996; 157:1551-8. [PMID: 8759738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cloning and characterization of classical MHC class I coding sequences of the laboratory rat Rattus norvegicus has been reported so far for only four haplotypes, RT1a, RT1(1), RT1n, and RT1u. In all four cases, only one RT1.A classical class I molecule was found. Here we report that, in contrast, the RT1c haplotype expresses two different classical class I molecules. Using recombinant rat strains, we find that allotypic serologic determinants carried by the two molecules map to the RT1.A region, and so we have named them RT1.A1c and RT1.A2c. Multiple clones of functional cDNAs for each of these two molecules were isolated using a recently developed PCR-based expression-cloning method. Using a panel of 20 RT1.Ac-reactive mAb, we find that six recognize RT1.A1c, seven recognize RT1.A2c, and seven recognize both. We also show that both molecules are recognized and distinguished by primary alloreactive cytotoxic T lymphocytes, and that they correspond to identifiable and distinct molecular species in cells that express RT1c naturally. These data all concur to demonstrate that the RT1.Ac region carries two different loci, each of which encodes a functional classical class I molecule.
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Affiliation(s)
- E Joly
- Department of Immunology, Babraham Institute, Cambridge, United Kingdom
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37
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Joly E, Clarkson C, Howard JC, Butcher GW. Isolation of a functional cDNA encoding the RT1.Au MHC class I heavy chain by a novel PCR-based method. Immunogenetics 1995; 41:326-8. [PMID: 7721356 DOI: 10.1007/bf00172159] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- E Joly
- Department of Immunology, Babraham Institute, Cambridge, UK
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38
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Affiliation(s)
- D Symons
- AFRC Institute of Animal Physiology and Genetics Research, Babraham, Cambridge, UK
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39
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Abstract
We studied the records of 101 patients with delusional disorder admitted to the Psychiatric Hospital between 1920 and 1980 and divided the sample into those with jealous (43) and those with nonjealous (58) delusions. Patients and relatives were located by telephone and follow-up information was collected. Compared with the nonjealous patients, the jealous ones were more likely to have had a single delusion, and to have experienced a more benign course as indicated by a lower rate of hospitalization and outpatient treatment. The original delusion tended to remain and the illness did not develop into another form of delusional disorder or other psychiatric illness.
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Affiliation(s)
- R R Crowe
- University of Iowa College of Medicine, Department of Psychiatry, Iowa City 52242
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40
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Abstract
The frequency of generalized anxiety disorder was higher among first-degree relatives of probands with generalized anxiety (N = 20) than among the relatives of control subjects (N = 20), but it was not higher among relatives of probands with panic disorder (N = 40) or agoraphobia (N = 40). Also, the frequency of panic disorder was higher among relatives of probands with panic disorder than among control relatives but was not higher among relatives of generalized anxiety probands. Relatives of probands with generalized anxiety who had the same disorder had a mild, stress-related illness. The results confirm the separation between generalized anxiety disorder and panic disorder but challenge the distinction between generalized anxiety and adjustment disorders.
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41
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Abstract
Guinea-pig papillary muscles were voltage-clamped using the single sucrose gap technique. The maximum upstroke velocity of the action potential (Vmax) was used as an indicator of the sodium conductance. Lidocaine (5 mumol/l to 40 mumol/l) reduced Vmax in a use-dependent fashion. Block of sodium channels developed during channel opening and while the channels were inactivated. Block of inactivated channels was not voltage-dependent over the -40 mV to +40 mV range. Recovery from block occurs upon repolarization, and for a given diastolic interval the recovery is more complete as the membrane potential is hyperpolarized over the -80 mV to -150 mV range. These results can be accounted for in terms of the modulated receptor hypothesis, where lidocaine has a low affinity for rested sodium channels, but a high affinity for open and inactivated channels.
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Affiliation(s)
- T Matsubara
- Department of Pharmacology, University of California, San Francisco 94143
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