1
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Lavoie JG, Clark W, McDonnell L, Nickel N, Dutton R, Kanayok J, Fowler-Woods M, Anawak J, Brown N, Voisey Clark G, Evaluardjuk-Palmer T, Wong ST, Sanguins J, Mudryj A, Mullins N, Ford M, Clark J. Mitigating the impact of the COVID-19 pandemic on Inuit living in Manitoba: community responses. Int J Circumpolar Health 2023; 82:2259135. [PMID: 37752773 PMCID: PMC10538448 DOI: 10.1080/22423982.2023.2259135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
We document community responses to the COVID-19 pandemic among Inuit living in the province of Manitoba, Canada. This study was conducted by the Manitoba Inuit Association and a Council of Inuit Elders, in partnership with researchers from the University of Manitoba. We present findings from 12 health services providers and decision-makers, collected in 2021.Although Public Health orders led to the closure of the Manitoba Inuit Association's doors to community events and drop-in activities, it also created opportunities for the creation of programming and events delivered virtually and through outreach. The pandemic exacerbated pre-existing health and social system's shortcomings (limited access to safe housing, food insecurity) and trauma-related tensions within the community. The Manitoba Inuit Association achieved unprecedented visibility with the provincial government, receiving bi-weekly reports of COVID-19 testing, results and vaccination rates for Inuit. We conclude that after over a decade of advocacy received with at best tepid enthusiasm by federal and provincial governments, the Manitoba Inuit Association was able effectively advocate for Inuit-centric programming, and respond to Inuit community's needs, bringing visibility to a community that had until then been largely invisible. Still, many programs have been fueled with COVID-19 funding, raising the issue of sustainability.
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Affiliation(s)
- Josée G. Lavoie
- Department of Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Ongomiizwin Indigenous Institute for Health and Healing, University of Manitoba, Winnipeg, Manitoba, Canada
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Wayne Clark
- Manitoba Centre for Health Policy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Leah McDonnell
- Ongomiizwin Indigenous Institute for Health and Healing, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nathan Nickel
- Department of Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Centre for Health Policy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Rachel Dutton
- Manitoba Inuit Association, Winnipeg, Manitoba, Canada
| | - Janet Kanayok
- Manitoba Inuit Association, Winnipeg, Manitoba, Canada
| | - Melinda Fowler-Woods
- Department of Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Family Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jack Anawak
- Isumataq Sivuliuqti, Qanuinngitsiarutiksait Study, Canada
| | - Nuqaalaq Brown
- Isumataq Sivuliuqti, Qanuinngitsiarutiksait Study, Canada
| | | | | | - sabrina T. Wong
- National Institute of Nursing Research, Division of Intramural Research, Bethesda, Manitoba, Canada
| | | | - Adriana Mudryj
- Ongomiizwin Indigenous Institute for Health and Healing, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Marti Ford
- Manitoba Inuit Association, Winnipeg, Manitoba, Canada
| | - Judy Clark
- Manitoba Inuit Association, Winnipeg, Manitoba, Canada
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2
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Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy AE, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett KD, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. Cell Rep 2023; 42:112432. [PMID: 37120812 PMCID: PMC10299810 DOI: 10.1016/j.celrep.2023.112432] [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: 12/14/2022] [Revised: 02/28/2023] [Accepted: 04/08/2023] [Indexed: 05/01/2023] Open
Abstract
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were still to be determined. Here, we show that phages encoding the major phage nucleus protein chimallin share 72 conserved genes encoded within seven gene blocks. Of these, 21 core genes are unique to nucleus-forming phage, and all but one of these genes encode proteins of unknown function. We propose that these phages comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryoelectron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication are conserved among diverse chimalliviruses and reveal variations on this replication mechanism. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
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Affiliation(s)
- Amy Prichard
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas G Laughlin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Amber Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kyle P Thomas
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika E Sy
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tara Spencer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aileen Asavavimol
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Allison Cafferata
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Mia Cameron
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Chiu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Demyan Davydov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Isha Desai
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gabriel Diaz
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Melissa Guereca
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kiley Hearst
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Leyi Huang
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Emily Jacobs
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika Johnson
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Samuel Kahn
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ryan Koch
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Adamari Martinez
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Meliné Norquist
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tyler Pau
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gino Prasad
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Katrina Saam
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Milan Sandhu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Angel Jose Sarabia
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Siena Schumaker
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aaron Sonin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ariya Uyeno
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Alison Zhao
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kit Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin Meyer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Rachel Dutton
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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3
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Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy A, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett K, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. bioRxiv 2023:2023.02.24.529968. [PMID: 36865095 PMCID: PMC9980170 DOI: 10.1101/2023.02.24.529968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown. By studying phages that encode the major phage nucleus protein chimallin, including previously sequenced yet uncharacterized phages, we discovered that chimallin-encoding phages share a set of 72 highly conserved genes encoded within seven distinct gene blocks. Of these, 21 core genes are unique to this group, and all but one of these unique genes encode proteins of unknown function. We propose that phages with this core genome comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryo-electron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication encoded in the core genome are conserved among diverse chimalliviruses, and reveal that non-core components can confer intriguing variations on this replication mechanism. For instance, unlike previously studied nucleus-forming phages, RAY doesn't degrade the host genome, and its PhuZ homolog appears to form a five-stranded filament with a lumen. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
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Lavoie JG, Clark W, McDonnell L, Nickel N, Dutton R, Kanayok J, Anawak J, Anawak C, Brown L, Clark GV, Evaluardjuk-Palmer M, Ford F, Fowler-Woods M, Wong S, Sanguins J, Katz A. Kivalliq Inuit women travelling to Manitoba for birthing: findings from the Qanuinngitsiarutiksait study. BMC Pregnancy Childbirth 2022; 22:870. [PMID: 36434515 PMCID: PMC9694830 DOI: 10.1186/s12884-022-05214-9] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The Qanuinngitsiarutiksait study aimed to develop detailed profiles of Inuit health service utilization in Manitoba, by Inuit living in Manitoba (approximately 1,500) and by Inuit from the Kivalliq region of Nunavut who travel to Manitoba to access care not available in Nunavut (approximately 16,000 per year). METHODS We used health administrative data routinely collected in Manitoba for all services provided and developed an algorithm to identify Inuit in the dataset. This paper focused on health services used by Inuit from the Kivalliq for prenatal care and birthing. RESULTS Our study found that approximately 80 percent of births to women from the Kivalliq region occur in Manitoba, primarily in Winnipeg. When perinatal care and birthing are combined, they constitute one third of all consults happening by Kivalliq residents in Manitoba. For scale, hospitalizations for childbirths to Kivalliq women about to only 5 percent of all childbirth-related hospitalizations in Manitoba. CONCLUSIONS The practice of evacuating women from the Kivalliq for perinatal care and birthing is rooted in colonialism, rationalized as ensuring that women whose pregnancy is at high risk have access to specialized care not available in Nunavut. While defendable, this practice is costly, and does not provide Inuit women a choice as to where to birth. Attempts at relocating birthing to the north have proven complex to operationalize. Given this, there is an urgent need to develop Inuit-centric and culturally appropriate perinatal and birthing care in Manitoba.
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Affiliation(s)
- Josée G. Lavoie
- grid.21613.370000 0004 1936 9609University of Manitoba, Winnipeg, MB Canada
| | - Wayne Clark
- grid.17089.370000 0001 2190 316XUniversity of Alberta, Edmonton, AB Canada
| | - Leah McDonnell
- grid.21613.370000 0004 1936 9609University of Manitoba, Winnipeg, MB Canada
| | - Nathan Nickel
- grid.21613.370000 0004 1936 9609University of Manitoba, Winnipeg, MB Canada
| | | | | | | | | | | | | | | | | | | | - Sabrina Wong
- grid.17091.3e0000 0001 2288 9830University of British Columbia, Vancouver, BC Canada
| | | | - Alan Katz
- grid.21613.370000 0004 1936 9609University of Manitoba, Winnipeg, MB Canada
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5
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Clark W, Lavoie JG, Mcdonnell L, Nickel N, Anawak J, Brown L, Clark G, Evaluardjuk-Palmer M, Ford F, Dutton R, Wong S, Sanguins J, Katz A. Trends in Inuit health services utilisation in Manitoba: findings from the Qanuinngitsiarutiksait study. Int J Circumpolar Health 2022; 81:2073069. [PMID: 35543481 PMCID: PMC9103522 DOI: 10.1080/22423982.2022.2073069] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
There is a notable lack of research related to trends in Inuit accessing health services throughout the land known as Canada. Given Nunavut’s reliance on specialised services provided in the Northwest Territories, Alberta, Manitoba, and Ontario, this gap is particularly problematic, making it more difficult for Nunangat to proactively plan new programs for emerging needs, and for provinces to respond to those needs. The Qanuinngitsiarutiksait study aimed to address this gap by developing detailed profiles of Inuit accessing health services in Manitoba. We used administrative data routinely collected by Manitoba agencies, to support the development of Inuit-centric services. It was conducted in partnership with the Manitoba Inuit Association, and Inuit Elders from Nunavut Canada and Manitoba. We focused on two interrelated cohorts: Kivallirmiut (Inuit from the Kivalliq region of Nunavut) who come to Winnipeg to access specialised services; and Manitobamiut (Inuit already living in Manitoba). Findings show that health services are primarily accessed in Winnipeg. Half of health services accessed by Kivallirmiut are for in-patient care at facilities with the Winnipeg Regional Health Authority. The other half are for advanced out-patient care including specialist consults. For Kivallirmiut, hospitalisation for pregnancy and birth are the most prevalent reasons for hospitalisation, followed by diseases of the respiratory system. Noteworthy, rates of hospitalisation for conditions treatable in primary healthcare for Kivallirmiut are considerably lower than those for Manitobans living in the northern part of the province (where comparable constraints exist). For Inuit adults, rates of hospitalisation for these conditions are comparable to those of Manitobans living in small communities. Inuit living in Manitoba are most often hospitalised for mental health reasons, although other reasons are nearly as prevalent. Our results support the need for more Inuit-centric health programming in Winnipeg.
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Affiliation(s)
- Wayne Clark
- Indigenous Health Initiatives, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Canada
| | - Josée G Lavoie
- Director of Ongomiizwin Research, Professor, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Leah Mcdonnell
- Ongomiizwin Research, University of Manitoba, Winnipeg, Canada
| | - Nathan Nickel
- Director of Ongomiizwin Research, Professor, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | | | | | | | | | | | | | - Sabrina Wong
- School of Nursing, University of British Columbia, Vancouver, Canada
| | - Julianne Sanguins
- Health & Wellness Department, Manitoba Métis Federation, Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Alan Katz
- Department of Family Medicine, University of Manitoba, Winnipeg, Canada
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6
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Mcdonnell L, Lavoie JG, Clark W, Dutton R, Anawak C, Anawak J, Brown L, Clark G, Evaluardjuk-Palmer M, Ford F. Unforeseen benefits: outcomes of the Qanuinngitsiarutiksait study. Int J Circumpolar Health 2022; 81:2008614. [PMID: 35100941 PMCID: PMC8812791 DOI: 10.1080/22423982.2021.2008614] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Scientific publications predominantly focus on research outcomes. Increasingly, community partnerships and relationships are mentioned, especially in research conducted with Indigenous communities. In partnership-based research, Indigenous communities expect researchers to contribute in a multitude of ways that go beyond doing research. This article reports on a series of unforeseen, yet positive contributions realised in the Qanuinngitsiarutiksait study, undertaken between 2015 and 2021. These contributions are different from the main outcomes of the study. Salient unforeseen benefits included the strengthening of the Manitoba Inuit community through hosting community feasts, games, and virtual events; creating opportunities to increase the visibility of Inuit Elders at University public events; supporting the growth of the Manitoba Inuit Association in terms of staff, programmes, and presence at provincial policy tables; leveraging relationships towards the development of Inuit-centric primary healthcare services in Winnipeg; creating a method to identify Inuit in provincial administrative datasets which were used to track COVID-19 infection rates and ensure equity in access to testing and vaccines. As a result, the Manitoba Inuit Association's visibility has increased, and Inuit Elders have become essential contributors of Indigenous knowledge at Manitoba-based events, as First Nations and Metis have been for decades. This transformation appears to be sustainable.
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Affiliation(s)
- Leah Mcdonnell
- Ongomiizwin Research, University of Manitoba, Winnipeg, Canada
| | - Josée G Lavoie
- Ongomiizwin Research, University of Manitoba, Winnipeg, Canada.,Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Wayne Clark
- Indigenous Health Initiatives, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Canada
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7
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Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K. Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. Nat Biotechnol 2021; 39:169-173. [PMID: 33169034 PMCID: PMC7971188 DOI: 10.1038/s41587-020-0700-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [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: 01/13/2020] [Revised: 08/26/2020] [Accepted: 09/09/2020] [Indexed: 12/23/2022]
Abstract
We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.
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Affiliation(s)
- Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Ivan Laponogov
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Zheng Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Sophie L F Doran
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Ilaria Belluomo
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Dennis Veselkov
- Intelligify Limited, London, UK
- Department of Computing, Imperial College, South Kensington Campus, London, UK
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Louis Felix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Katherine N Maloney
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry, Point Loma Nazarene University, San Diego, CA, USA
| | - Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Alexey V Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Aleksandr Smirnov
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Xiuxia Du
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kenneth L Jones
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Madeleine Ernst
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Section for Clinical Mass Spectrometry, Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Justin J J van der Hooft
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Mabel Gonzalez
- Department of Chemistry, Universidad de los Andes, Bogotá, Colombia
| | - Chiara Carazzone
- Department of Chemistry, Universidad de los Andes, Bogotá, Colombia
| | - Adolfo Amézquita
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Chris Callewaert
- Center for Microbial Ecology and Technology, Ghent, Belgium
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - James T Morton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Andrea Albarracín Orio
- IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Andrea M Smania
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Sneha P Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Erika Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Rachel Gregor
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael M Meijler
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stav Eyal
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Brooke Anderson
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rachel Dutton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Raphaël Lugan
- UMR Qualisud, Université d'Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France
| | - Pauline Le Boulch
- UMR Qualisud, Université d'Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France
| | - Yann Guitton
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Stephanie Prevost
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Audrey Poirier
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Gaud Dervilly
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Bruno Le Bizec
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Aaron Fait
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Noga Sikron Persi
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Chao Song
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Kelem Gashu
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Roxana Coras
- Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Monica Guma
- Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Julia Manasson
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose U Scher
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Dinesh Kumar Barupal
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Reza Mirnezami
- Department of Colorectal Surgery, Royal Free Hospital NHS Foundation Trust, Hampstead, London, UK
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis RAS, Moscow, Russian Federation
| | - Larisa N Kulikova
- Рeoples' Friendship University of Russia (RUDN University), Moscow, Russian Federation
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - George B Hanna
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
| | - Kirill Veselkov
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK.
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Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K. Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. Nat Biotechnol 2021. [PMID: 33169034 DOI: 10.1038/s41587-41020-40700-41583] [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] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.
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Affiliation(s)
- Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Ivan Laponogov
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Zheng Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Sophie L F Doran
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Ilaria Belluomo
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Dennis Veselkov
- Intelligify Limited, London, UK
- Department of Computing, Imperial College, South Kensington Campus, London, UK
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Louis Felix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Katherine N Maloney
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry, Point Loma Nazarene University, San Diego, CA, USA
| | - Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Alexey V Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Aleksandr Smirnov
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Xiuxia Du
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kenneth L Jones
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Madeleine Ernst
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Section for Clinical Mass Spectrometry, Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Justin J J van der Hooft
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Mabel Gonzalez
- Department of Chemistry, Universidad de los Andes, Bogotá, Colombia
| | - Chiara Carazzone
- Department of Chemistry, Universidad de los Andes, Bogotá, Colombia
| | - Adolfo Amézquita
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Chris Callewaert
- Center for Microbial Ecology and Technology, Ghent, Belgium
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - James T Morton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Andrea Albarracín Orio
- IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - Andrea M Smania
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
| | - Sneha P Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Erika Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Rachel Gregor
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael M Meijler
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stav Eyal
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Brooke Anderson
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rachel Dutton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Raphaël Lugan
- UMR Qualisud, Université d'Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France
| | - Pauline Le Boulch
- UMR Qualisud, Université d'Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France
| | - Yann Guitton
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Stephanie Prevost
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Audrey Poirier
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Gaud Dervilly
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Bruno Le Bizec
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
| | - Aaron Fait
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Noga Sikron Persi
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Chao Song
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Kelem Gashu
- The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
| | - Roxana Coras
- Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Monica Guma
- Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Julia Manasson
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose U Scher
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Dinesh Kumar Barupal
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Reza Mirnezami
- Department of Colorectal Surgery, Royal Free Hospital NHS Foundation Trust, Hampstead, London, UK
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis RAS, Moscow, Russian Federation
| | - Larisa N Kulikova
- Рeoples' Friendship University of Russia (RUDN University), Moscow, Russian Federation
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
| | - George B Hanna
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
| | - Kirill Veselkov
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK.
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Hayward A, Cidro J, Dutton R, Passey K. A review of health and wellness studies involving Inuit of Manitoba and Nunavut. Int J Circumpolar Health 2020; 79:1779524. [PMID: 32543995 PMCID: PMC7480607 DOI: 10.1080/22423982.2020.1779524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 04/16/2020] [Accepted: 06/01/2020] [Indexed: 01/22/2023] Open
Abstract
The purpose of this review is to summarise past Inuit health and wellness studies in Manitoba and the Kivalliq region of Nunavut to provide a snapshot of the types of studies available and identify the gaps in knowledge. Research to date has largely been disease-based and often provides comparisons between Indigenous and non-Indigenous people. Distinct Inuit experiences are rarely written about from an Inuit perspective. However, Inuit Tapiriit Kanatami, the national organisation of Inuit in Canada, and Pauktuutit Inuit Women of Canada have been leaders in strengths-based community research and publications that address priorities determined by the Inuit, including the 2018 Inuit Tapiriit Kanatami document National Inuit Strategy on Research (132).
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Affiliation(s)
- Ashley Hayward
- Student Peace and Conflict Studies, University of Winnipeg, Winnipeg, Canada
| | - Jaime Cidro
- Anthropology, University of Winnipeg, Canada Research Chair, Health and Culture, Winnipeg, Canada
| | | | - Kara Passey
- Development Practice: Indigenous Development (MDP) Student, University of Winnipeg, Winnipeg, Canada
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Sellors V, Akers A, Bostock E, Dutton R, Apoola A. P151 How effective is targeted outreach? Br J Vener Dis 2012. [DOI: 10.1136/sextrans-2012-050601c.151] [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: 11/04/2022]
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12
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Sen A, Hu P, Mackenzie C, Xiao Y, Dutton R. 306: Video Technologies in Emergency Health Research in Assessing Quality of Care: A Study of Trauma Resuscitation Milestones. Ann Emerg Med 2009. [DOI: 10.1016/j.annemergmed.2009.06.337] [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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13
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Sen A, Hu P, Mackenzie C, Dutton R, Jordan S, Xiao Y, Scalea T. 452: Continuous Out-of-Hospital Vital Signs Acquisition Improves Trauma Triage. Ann Emerg Med 2009. [DOI: 10.1016/j.annemergmed.2009.06.493] [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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14
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15
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Bartlett PF, Richards LR, Kilpatrick TJ, Talman PT, Bailey KA, Brooker GJ, Dutton R, Koblar SA, Nurcombe V, Ford MO. Factors regulating the differentiation of neural precursors in the forebrain. Ciba Found Symp 2007; 193:85-99; discussion 117-26. [PMID: 8727488 DOI: 10.1002/9780470514795.ch5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Precursors from the neuroepithelium of the developing cortex and the adult subventricular zone can be cloned in vitro after stimulation with fibroblast growth factor 2 (FGF-2), and they have the potential to give rise to both neurons and glia. The generation of neurons from these clones can be stimulated by either a factor derived from an astrocyte precursor line, Ast-1, or FGF-1. We have shown that neuronal differentiation stimulated by FGF-1 can be inhibited by diacylglycerol lipase inhibitor and mimicked by arachidonic acid, suggesting that the neuronal differentiation is signalled through the phospholipase C gamma pathway. The sequential expression of FGF-2, followed by FGF within the developing forebrain neuroepithelium, fits with the different functions that the two FGFs play in precursor regulation. We have shown that the precursor response to FGF-1 is regulated by a heparan sulphate proteoglycan expressed within the developing neuroepithelium. Precursors restricted to the astrocyte cell lineage can be stimulated by epidermal growth factor or FGF-2F however, the differentiation into glial fibrillary acidic protein-positive astrocytes appears to require a cytokine acting through the leukaemia inhibitory factor-beta receptor.
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Affiliation(s)
- P F Bartlett
- Walter and Eliza Hall Institute of Medical Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
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16
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Guymer I, Dutton R. Application of transient storage modelling to solute transport across a surcharged manhole. Water Sci Technol 2007; 55:65-73. [PMID: 17425073 DOI: 10.2166/wst.2007.096] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Results from previous solute tracer laboratory experiments across circular surcharged manhole structures by Guymer et al. have been used to optimise parameters within Hart's transient storage model (TSM). A surcharge threshold level for the model parameters is evident and this is explained in relation to jet theory. The ability to decompose the TSM is demonstrated with reference to frequency of exchange with the storage zone allowing the proportions of solute entering these regions to be inferred, together with an indication of storage volume retention times.
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Affiliation(s)
- I Guymer
- School of Engineering, University of Warwick, Coventry, CV4 7AL, UK.
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Edwards-Lee T, Ringman JM, Chung J, Werner J, Morgan A, St George Hyslop P, Thompson P, Dutton R, Mlikotic A, Rogaeva E, Hardy J. An African American family with early-onset Alzheimer disease and an APP (T714I) mutation. Neurology 2005; 64:377-9. [PMID: 15668448 DOI: 10.1212/01.wnl.0000149761.70566.3e] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [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] [Indexed: 11/15/2022] Open
Abstract
The occurrence of an APP T174I mutation is described in a large American family of African descent with Alzheimer disease. The clinical characteristics were an unusually early onset of disease (early 30s), similar to a previously reported age at onset of this mutation in an Austrian family. Distinct from that family, seizures and myoclonus were prominent features of the disease in this kindred.
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Affiliation(s)
- T Edwards-Lee
- Department of Neurology,Harbor-UCLA Medical Center, Torrance, USA
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19
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Miles M, Mayes M, Dutton R. The effects of spinosad, a naturally derived insect control agent, to the honeybee (Apis melifera). Meded Rijksuniv Gent Fak Landbouwkd Toegep Biol Wet 2003; 67:611-6. [PMID: 12696428] [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: 03/01/2023]
Abstract
Spinosad is a novel insect control agent derived by fermentation of the Actinomycete bacterium, Saccharopolyspora spinosa. Spinosad controls many caterpillar pests in vines, pome fruit and vegetables (including tomatoes and peppers), thrips in tomatoes, peppers and ornamental cultivation and dipterous leafminers in vegetables and ornamentals. Application rates vary between 25 to 100 g of active substance per hectare (g as/ha) and 4.8 to 36 g of active substance per hectolitre (g as/hL) depending on the crop and target pest. It is important that plant protection products are authorized for use only in ways that do not pose an unacceptable risk of harm to honeybees. For this purpose testing was performed to enable the safety of spinosad to be evaluated. The effects of spinosad to honeybees have been extensively researched. Testing has been performed under a variety of conditions in a range of countries globally. Studies to determine the acute toxicity of spinosad under laboratory conditions were conducted to generate LD50 or LC50 values for oral and contact routes of administration. These demonstrated that spinosad was highly toxic to worker honeybees under worst case laboratory conditions and that the oral route of exposure provided the greater risk. Residue tests conducted under laboratory, semi-field and field conditions on worker honeybees foraging on treated foliage indicated that dry product residues were harmless. Therefore the effects seen in the laboratory acute toxicity tests did not translate to a more realistic exposure scenario indicating that safe use patterns for the product can be developed. Semi-field cage studies have also demonstrated that spinosad was safe to bees when applied to flowering crops during periods of bee activity. The majority of studies conducted have indicated that spinosad does not adversely affect honeybee behaviour, brood or queen. It can be concluded that spinosad when used according to the approved product label recommendations, would be safe to foraging worker bees, queen and brood. Additional levels of safety could be achieved by avoiding situations where bees would forage primarily on aphid honey dew.
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Affiliation(s)
- M Miles
- Dow AgroSciences, Abingdon, OX14 4RN, U.K
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Zhang Y, Stabernack CR, Dutton R, Sonner J, Trudell JR, Mihic SJ, Yamakura T, Harris RA, Gong D, Eger EI. Luciferase as a model for the site of inhaled anesthetic action. Anesth Analg 2001; 93:1246-52. [PMID: 11682406 DOI: 10.1097/00000539-200111000-00041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
UNLABELLED The in vivo potencies of anesthetics correlate with their capacity to suppress the reaction of luciferin with luciferase. In addition, luciferin has structural resemblances to etomidate. These observations raise the issues of whether luciferin, itself, might affect anesthetic requirement, and whether luciferase resembles the site of anesthetic action. Because the polar luciferin is unlikely to cross the blood-brain barrier (we found that the olive oil/water partition coefficient was 100 +/- 36 x 10(-7)), we studied these issues in rats by measuring the effect of infusion of luciferin in artificial cerebrospinal fluid into the lumbar subarachnoidal space and into the cerebral intraventricular space on the MAC (the minimum alveolar anesthetic concentration required to eliminate movement in response to a noxious stimulus in 50% of tested subjects) of isoflurane. MAC in rats given lumbar intrathecal doses of luciferin estimated to greatly exceed anesthetizing doses of etomidate, did not differ significantly from MAC in rats receiving only artificial cerebrospinal fluid into the lumbar intrathecal space. MAC slightly decreased when doses of luciferin estimated to greatly exceed anesthetizing doses of etomidate were infused intraventricularly (P < 0.05). In contrast to the absent or minimal effects of luciferin, intrathecal or intraventricular infusion of etomidate at similar or smaller doses significantly decreased isoflurane MAC. Luciferin did not affect +-aminobutyric acid type A or acetylcholine receptors expressed in Xenopus oocytes. These results suggest that luciferin has minimal or no anesthetic effects. It also suggests that luciferin/luciferase may not provide a good surrogate for the site at which anesthetics act, if this site is on the surface of neuronal cells. IMPLICATIONS In proportion to their potencies, anesthetics inhibit luciferin's action on luciferase, and luciferin structurally resembles the anesthetic etomidate. However, in contrast to etomidate, luciferin given intrathecally or into the third cerebral ventricle does not have anesthetic actions, and it does not affect +-aminobutyric acid or acetylcholine receptors in vitro. Luciferase may not provide a good surrogate for the site at which anesthetics act.
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Affiliation(s)
- Y Zhang
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94143-0464, USA
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Zhang Y, Stabernack C, Sonner J, Dutton R, Eger EI. Both Cerebral GABAA Receptors and Spinal GABAA Receptors Modulate the Capacity of Isoflurane to Produce Immobility. Anesth Analg 2001; 92:1585-9. [PMID: 11375851 DOI: 10.1097/00000539-200106000-00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We previously demonstrated that intrathecal administration of the noncompetitive gamma-aminobutyric acid type A (GABA(A)) receptor antagonist picrotoxin increased isoflurane MAC (the minimum alveolar concentration of anesthetic producing immobility in 50% of animals) by a maximum (ceiling effect) of approximately 40%. We also found that IV administration of picrotoxin increased MAC by more than 60%, without evidence of a ceiling effect. The larger increase with IV administration suggested a role of cerebral GABA(A) receptors. Accordingly, in this study we examined the effect of intracerebroventricular administration of picrotoxin in rats, finding that picrotoxin infusion into the third ventricle increased isoflurane MAC by a maximum of approximately 40%, without finding a ceiling effect. In addition, we concurrently infused picrotoxin into the intrathecal and intracerebroventricular spaces, producing an increase in MAC in excess of 70%, also with no evidence of a ceiling effect. The dose-response relationship for the intrathecal-intraventricular infusion paralleled that of the IV infusion but was shifted to the left by an order of magnitude. We conclude that both cerebral and spinal GABA(A) receptors modulate the capacity of inhaled anesthetics to produce immobility. Because other studies have shown that the spinal cord, and not the brain, mediates the capacity of inhaled anesthetics to produce immobility, these results call into question the relevance of GABA(A) receptors to the immobilizing action of isoflurane.
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Affiliation(s)
- Y Zhang
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, California
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Dutton R, Bartlett PF. Precursor cells in the subventricular zone of the adult mouse are actively inhibited from differentiating into neurons. Dev Neurosci 2000; 22:96-105. [PMID: 10657702 DOI: 10.1159/000017431] [Citation(s) in RCA: 11] [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: 11/19/2022] Open
Abstract
The adult mouse subventricular zone (SVZ) contains precursor cells capable of generating new neurons which populate the olfactory bulb. The SVZ precursors, however, appear to be restricted in their capacity to generate neurons in other regions of the brain indicating a tight regulation of their differentiation. We demonstrate in vitro that explants of SVZ are unable to generate neurons from dividing precursors, even though precursors are present and dividing within explant cultures. However, when plated as single cells in fibroblast growth factor-1 or with no growth factor, approximately 1% of harvested cells gave rise to clones containing neurons and astrocytes, indicating that bipotential precursors were present in the explants. Inhibitory effects of cell density were more directly shown by plating freshly isolated SVZ cells, or explant-derived SVZ cells, at increasing cell density. The frequency of neuron-containing wells was found to be greatly reduced at higher cell concentrations: >100 cells/well in the case of explant-derived cells and >500 cells in the case of freshly isolated cells. Thus, it appears that the precursor's ability to generate neurons is actively inhibited by paracrine mechanisms which may be mediated by either cell-cell contact or by short-range factors.
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Affiliation(s)
- R Dutton
- The Walter and Eliza Hall Institute of Medical Research, PO The Royal Melbourne Hospital, Parkville, Vic., Australia
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Abstract
Fluid resuscitation after traumatic hemorrhage has historically been instituted as soon after injury as possible. Patients suffering from hemorrhagic shock may receive several liters of crystalloid, in addition to colloid solutions, in an attempt to normalize blood pressure, heart rate, urine output, and mental status, which are the traditional end-points of resuscitation. Current theory and recent investigations have questioned this dogma. Resuscitation goals may be different between when the patient is actively hemorrhaging, and once bleeding has been controlled. Newer markers of tissue and organ system perfusion may allow a more precise determination of adequate resuscitation.
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Affiliation(s)
- M McCunn
- Department of Anesthesiology, R Adams Cowley Shock Trauma Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
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Dutton R, Yamada T, Turnley A, Bartlett PF, Murphy M. Regulation of spinal motoneuron differentiation by the combined action of Sonic hedgehog and neurotrophin 3. Clin Exp Pharmacol Physiol 1999; 26:746-8. [PMID: 10499166 DOI: 10.1046/j.1440-1681.1999.03108.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [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: 11/20/2022]
Abstract
1. The development of ventral cell types in the spinal cord, including motor neurons, requires the growth factor Sonic hedgehog (Shh). However, it is still unknown whether Shh acts directly on precursors to induce these cell types and whether additional factors are required for induction. 2. To further investigate the precise role of Shh in spinal motoneuron development, we used low-density cultures of murine spinal cord precursor cells. 3. Although purified Shh stimulated neuronal differentiation, it did not increase the proportion of neurons expressing the motoneuron marker Islet-1 (Isl-1). In contrast, purified Shh induced Isl-1 expression in neural tube explants, suggesting that additional neural tube-derived factors are required to induce motoneuron differentiation. 4. A factor implicated in motoneuron development, neurotrophin 3 (NT3), had no effect on Isl-1 expression; however, in combination with Shh, it induced Isl-1 expression in the majority of neurons in the low-density cultures. Furthermore, in explant cultures, Shh-induced Isl-1 expression was blocked by an anti-NT3 antibody. 5. In addition, previous studies have shown expression of NT3 in the region of motoneuron differentiation and the loss of spinal fusimotor neurons in NT3-knockout animals. 6. Taken together, these findings suggest that Shh can act directly on spinal cord precursors to promote neuronal differentiation, but induction of Isl-1 expression and motor differentiation requires additional factors, including NT3.
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Affiliation(s)
- R Dutton
- Department of Anatomy and Cell Biology, University of Melbourne, Parkville, Victoria, Australia
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Dutton R, Yamada T, Turnley A, Bartlett PF, Murphy M. Sonic hedgehog promotes neuronal differentiation of murine spinal cord precursors and collaborates with neurotrophin 3 to induce Islet-1. J Neurosci 1999; 19:2601-8. [PMID: 10087073 PMCID: PMC6786072] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Sonic hedgehog (Shh) is strongly implicated in the development of ventral structures in the nervous system. Addition of Sonic hedgehog protein to chick spinal cord explants induces floor plate and motoneuron development. Whether Shh acts directly to induce these cell types or whether their induction is mediated by additional factors is unknown. To further investigate the role of Shh in spinal neuron development, we have used low-density cultures of murine spinal cord precursor cells. Shh stimulated neuronal differentiation; however, it did not increase the proportion of neurons expressing the first postmitotic motoneuron marker Islet-1. Moreover, Shh did induce Islet-1 expression in neural tube explants, suggesting that it acts in combination with neural tube factors to induce motoneurons. Another factor implicated in motoneuron development is neurotrophin 3 (NT3), and when assayed in isolated precursor cultures, it had no effect on Islet-1 expression. However, the combination of N-terminal Shh and NT3 induced Islet-1 expression in the majority of neurons in low-density cultures of caudal intermediate neural plate. Furthermore, in explant cultures, Shh-mediated Islet-1 expression was blocked by an anti-NT3 antibody. Previous studies have shown expression of NT3 in the region of motoneuron differentiation and that spinal fusimotor neurons are lost in NT3 knock-out animals. Taken together, these findings suggest that Shh can act directly on spinal cord precursors to promote neuronal differentiation, but induction of Islet-1 expression is regulated by factors additional to Shh, including NT3.
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Affiliation(s)
- R Dutton
- Department of Anatomy and Cell Biology, The University of Melbourne, Parkville, Victoria, Australia 3052
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Abstract
In the developing forebrain, mounting evidence suggests that neural stem cell proliferation and differentiation is regulated by growth factors. In vitro in the presence of serum, stem cell proliferation is predominantly mediated by fibroblast growth factor-2 (FGF-2) whereas neuronal differentiation can be triggered by FGF-1 in association with a specific heparan sulphate proteoglycan. On the other hand, astrocyte differentiation in vivo and in vitro appears to be dependent on signalling through the leukaemia inhibitory factor receptor (LIFR). The evidence suggests that in the absence of LIFR signalling, the stem cell population is present at approximately the same frequency and can generate neurons but is blocked from producing astrocytes that express glial fibrillary acidic protein (GFAP) or have trophic functions. The block can be overcome by other growth factors such as BMP-2/4 or interferon-gamma, providing further evidence that the inhibition to astrocyte development does not result from loss of a precursor population. Signalling through the LIFR, in addition to stimulating astrocyte differentiation, may also inhibit neuronal differentiation, which may explain why this receptor is expressed at the earliest stages of neurogenesis. Another signalling system which also exerts its influence on neurogenesis through active inhibition is Delta-Notch. We show in vitro that at high cell densities which impede neuronal production by FGF-1, lowering the levels of expression of the receptor Notch by antisense oligonucleotide results in a significant increase in neuronal production. Thus, stem cell differentiation appears to be dependent on the outcome of interactions between a number of signalling pathways, some which promote specific lineages and some which inhibit.
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Affiliation(s)
- P F Bartlett
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
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Abstract
Class I MHC protein is induced in glia but not mature neurons by IFN-gamma. We have compared IFN-gamma signal transduction in these populations. There were identical levels of STAT1 homodimers and IRF-1 by gel-shift and IRF-1 mRNA was induced equally. However class I MHC, beta2-microglobulin and interleukin 1-beta converting enzyme mRNA levels were greatly reduced in neurons. These experiments show that there is no defect in expression of IRF-1 in response to IFN-gamma in mature mouse neurons but that insufficient class I MHC gene expression is induced for detectable cell surface protein expression.
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Affiliation(s)
- H E Thomas
- Burnet Clinical Research Unit, The Walter and Eliza Hall Institute of Medical Research, PO Royal Melbourne Hospital, Parkville. Vic., Australia
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Abstract
This article is concerned with the idea that neural precursor cells in vertebrates can self-renew and give rise to all cell types within the nervous system. Supportive evidence for this notion of neural stem cells comes from clonal analyses undertaken both in vivo and in vitro. Neural stem cells also give rise to other cells in the body, including skin melanocytes and a range of mesenchymal cells in the head and neck. What determines the fate of these stem cells is their initial location within the developing neural tube and their final location post migration from the proliferative zone of the neural tube. A population of cells in the adult brain also have the characteristics of classical stem cells, a finding that opens the way for potential replacement therapy in nervous system-degenerative diseases. Much of the work in our laboratory has been concerned with the regulation of expansion and differentiation of these cells into their myriad progeny and the role of a series of various growth factors in this process. Different factors, such as members of the fibroblast growth factor family, act at different times to regulate stem cell proliferation and differentiation. Some factors, including members of the TGF beta superfamily, appear to be directly involved in the specification of cell fate. Finally, we are beginning to be able to determine the steps in the development of some lineages from multipotential stem cell to fully functional differentiated cell.
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Affiliation(s)
- M Murphy
- Walter and Eliza Hall Institute of Medical Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
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Abstract
A number of different cytokines, each initially characterized on the basis of very different biological activities, all have very similar signalling pathways and share a similar tertiary structure. These cytokines include leukaemia inhibitory factor, ciliary neuronotrophic factor, oncostatin M, growth-promoting activity and cardiotrophin 1. They all have been found to regulate a number of properties of cells of the developing and mature nervous system in vitro and thus are neuroregulatory cytokines. The actions of these cytokines include regulation of neurotransmitter phenotype, differentiation of neuronal precursor cells both in the peripheral nervous system and in the spinal cord, survival of differentiated neurons, and regulation of development of both astrocytes and oligodendrocytes. In addition, studies in animal models show that these factors can rescue sensory and motor neurons from axotomy-induced cell death, which suggests that they can act as trauma factors for injured neurons. Analysis of the expression patterns of the different neuroregulatory cytokines and their receptors reveals that the receptors are expressed throughout nervous system development and following trauma, whereas the cytokines show temporal and spatial specific expression patterns. This is consistent with the idea that specific cytokines have specific roles in neural development and repair, but that their signalling pathways are shared. The phenotypes of the receptor knockouts show clear deficits in nervous system development, indicating a crucial role for LIF receptor signalling. Knockouts of individual cytokines are less dramatic, but LIF and CNTF knockouts do reveal deficits in maintenance of motor neurons or following trauma. Thus, whereas LIF and CNTF have clear roles in maintenance and following trauma, it is unclear which of the cytokines is involved in nervous system development. In clinical terms, these findings add further support to the use of these cytokines in nervous system trauma and disease.
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Affiliation(s)
- M Murphy
- Walter and Eliza Hall Institute of Medical Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
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31
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Abstract
The interaction of structurally constrained competitive NMDA receptor antagonists, (+/-)-cis-4-phosphonomethyl-2-piperidine carboxylic acid (CGS 19755), (2-amino-4,5-(1,2-cyclohexyl))-7-phosphonoheptanoic acid (NPC 12626), (+/-)-6-phosphonomethyl-de-cahydroisoquinoline-3-carboxylic acid (LY 274614), (S)-alpha-amino-5-phosphonomethyl[1,1'-biphenyl]-3-propanoic acid (SDZ EAB-515) and (S)-alpha-amino-5-phosphonomethyl[1,1':4',1"-terphenyl]-3-propa noi c acid (SDZ 215-439), with their receptor was assessed using radioligand binding, protection against neurotoxicity in cortical neuronal cultures and computerised molecular modelling. All compounds inhibited the specific binding of [3H]CGS 19755 and/or [3H]CGP 39653 (inhibition constants 40-2000 nM), and protected neuronal cultures from NMDA-mediated injury (IC50 values 1.3-5.6 microM). Quantitative conformational analyses indicated that the molecules fitted well to a NMDA receptor model. Our results draw attention to a deep hydrophobic pocket, defined by the bi- and terphenyl containing antagonists (SDZ EAB-515, SDZ 215-439), which may influence potency and selectivity.
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Affiliation(s)
- N S Cheung
- Department of Pharmacology, Monash University, Clayton, Victoria, Australia
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Greenberg F, Lewis RA, Potocki L, Glaze D, Parke J, Killian J, Murphy MA, Williamson D, Brown F, Dutton R, McCluggage C, Friedman E, Sulek M, Lupski JR. Multi-disciplinary clinical study of Smith-Magenis syndrome (deletion 17p11.2). Am J Med Genet 1996; 62:247-54. [PMID: 8882782 DOI: 10.1002/(sici)1096-8628(19960329)62:3<247::aid-ajmg9>3.0.co;2-q] [Citation(s) in RCA: 203] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Smith-Magenis syndrome (SMS) is a multiple congenital anomaly, mental retardation (MCA/MR) syndrome associated with deletion of chromosome 17 band p11.2. As part of a multi-disciplinary clinical, cytogenetic, and molecular approach to SMS, detailed clinical studies including radiographic, neurologic, developmental, ophthalmologic, otolaryngologic, and audiologic evaluations were performed on 27 SMS patients. Significant findings include otolaryngologic abnormalities in 94%, eye abnormalities in 85%, sleep abnormalities (especially reduced REM sleep) in 75%, hearing impairment in 68% (approximately 65% conductive and 35% sensorineural), scoliosis in 65%, brain abnormalities (predominantly ventriculomegaly) in 52%, cardiac abnormalities in at least 37%, renal anomalies (especially duplication of the collecting system) in 35%, low thyroxine levels in 29%, low immunoglobulin levels in 23%, and forearm abnormalities in 16%. The measured IQ ranged between 20-78, most patients falling in the moderate range of mental retardation at 40-54, although several patients scored in the mild or borderline range. The frequency of these many abnormalities in SMS suggests that patients should be evaluated thoroughly for associated complications both at the time of diagnosis and at least annually thereafter.
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Affiliation(s)
- F Greenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Richards LJ, Kilpatrick TJ, Dutton R, Tan SS, Gearing DP, Bartlett PF, Murphy M. Leukaemia inhibitory factor or related factors promote the differentiation of neuronal and astrocytic precursors within the developing murine spinal cord. Eur J Neurosci 1996; 8:291-9. [PMID: 8714700 DOI: 10.1111/j.1460-9568.1996.tb01213.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.3] [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: 02/01/2023]
Abstract
Previously we have shown that leukaemia inhibitory factor (LIF) potentiates the development of murine spinal cord neurons in vitro, suggesting that it, or related factors, may play an important regulatory role in neuronal development. We have further investigated this role and show here that the generation of neurons in cultures of embryonic day 10 spinal cord cells is inhibited by antibodies to the beta subunit of the LIF receptor. Since there are more undifferentiated precursors in antibody-treated cultures than in control and LIF-treated cultures, it is concluded that the primary action of LIF, or related molecules, is to promote neuronal differentiation, not precursor survival. In addition, the failure of LIF to support neuronal survival in the period immediately following differentiation suggests that the increased numbers of neurons generated with LIF are not attributable to its neurotrophic action. By selecting neuronal precursors on the basis of their inability to express class 1 major histocompatibility complex molecules, it was shown that LIF acted directly upon these cells and not via an intermediary cell. LIF also appears to be involved in regulating the differentiation of astrocytes, since it increases the number of glial fibrillary protein (GFAP)-positive cells present in the cultures and since the spontaneous production of GFAP-positive cells is blocked by antibodies to the LIF beta receptor. These findings suggest that LIF or related factors promote the differentiation of neural precursors in the spinal cord, but that they are not involved in preferentially promoting precursors down a specific differentiation pathway.
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MESH Headings
- Animals
- Antibodies, Monoclonal/pharmacology
- Astrocytes/cytology
- Astrocytes/drug effects
- Biological Factors/pharmacology
- CHO Cells
- Cell Differentiation/drug effects
- Cell Division/drug effects
- Cell Lineage
- Cells, Cultured
- Coculture Techniques
- Cricetinae
- Culture Media/pharmacology
- Dosage Compensation, Genetic
- Fibroblasts/physiology
- Fibronectins/pharmacology
- Genes, Reporter
- Growth Inhibitors/pharmacology
- Interleukin-6
- Laminin/pharmacology
- Leukemia Inhibitory Factor
- Leukemia Inhibitory Factor Receptor alpha Subunit
- Lymphokines/pharmacology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred CBA
- Mice, Transgenic
- Neurons/cytology
- Neurons/drug effects
- Ornithine/pharmacology
- Receptors, Cytokine/drug effects
- Receptors, Cytokine/immunology
- Receptors, OSM-LIF
- Spinal Cord/cytology
- Spinal Cord/embryology
- Stem Cells/cytology
- Stem Cells/drug effects
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Affiliation(s)
- L J Richards
- Walter and Eliza Hall Institute of Medical Research and Collaborative Research Centre for Cellular Growth Factors, Royal Melbourne Hospital, 3050 Victoria, Australia
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Richards LJ, Murphy M, Dutton R, Kilpatrick TJ, Puche AC, Key B, Tan SS, Talman PS, Bartlett PF. Lineage specification of neuronal precursors in the mouse spinal cord. Proc Natl Acad Sci U S A 1995; 92:10079-83. [PMID: 7479730 PMCID: PMC40739 DOI: 10.1073/pnas.92.22.10079] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [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: 01/25/2023] Open
Abstract
We have investigated the differentiation potential of precursor cells within the developing spinal cord of mice and have shown that spinal cord cells from embryonic day 10 specifically give rise to neurons when plated onto an astrocytic monolayer, Ast-1. These neurons had the morphology of motor neurons and > 83% expressed the motor neuron markers choline acetyltransferase, peripherin, calcitonin gene-related peptide, and L-14. By comparison, < 10% of the neurons arising on monolayers of other neural cell lines or 3T3 fibroblasts had motor neuron characteristics. Cells derived from dorsal, intermediate, and ventral regions of the spinal cord all behaved similarly and gave rise to motor neuron-like cells when plated onto Ast-1. By using cells that expressed the lacZ reporter gene, it was shown that > 93% of cells present on the Ast-1 monolayers were motor neuron-like. Time-lapse analysis revealed that the precursors on the Ast-1 monolayers gave rise to neurons either directly or following a single cell division. Together, these results indicate that precursors in the murine spinal cord can be induced to differentiate into the motor neuron phenotype by factors produced by Ast-1 cells, suggesting that a similar factor(s) produced by cells akin to Ast-1 may regulate motor neuron differentiation in vivo.
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Affiliation(s)
- L J Richards
- Walter and Eliza Hall Institute of Medical Research, Royal Melbourne Hospital, Victoria, Australia
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35
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Bartlett PF, Richards LR, Kilpatrick TJ, Talman PS, Bailey KA, Brooker GJ, Dutton R, Koblar S, Nurcombe V, Ford M. Regulation of neural precursor differentiation in the embryonic and adult forebrain. Clin Exp Pharmacol Physiol 1995; 22:559-62. [PMID: 7586713 DOI: 10.1111/j.1440-1681.1995.tb02066.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [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: 01/26/2023]
Abstract
1. Precursors form the neuroepithelium of the developing cortex and also from the adult sub-ventricular zone, can be cloned in vitro after stimulation with fibroblast growth factor (FGF)-2 and have the potential to give rise to both neurons and glia. The generation of neurons from these clones can be stimulated by either a factor derived from an astrocyteprecursor line, Ast-1, or FGF-1. 2. Neuronal differentiation stimulated by FGF-1 can be inhibited by diacylglycerol-lipase inhibitor and mimicked by arachidonic acid, suggesting that the neuronal differentiation is signalled through the PCL gamma pathway. 3. The sequential expression of FGF-2 and FGF-1 within the developing forebrain neuroepithelium fits with the different functions the two FGF play in precursor regulation. 4. We have shown that the precursor response to FGF-1 is regulated by a heparan sulphate proteoglycan (HSPG) expressed within the developing neuroepithelium. Precursors restricted to the astrocyte cell lineage can be stimulated by epidermal growth factor or FGF-2; however, the differentiation into GFAP positive astrocytes appears to require a cytokine acting through the leukaemia inhibitory factor beta receptor.
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Affiliation(s)
- P F Bartlett
- Walter and Eliza Hall Institute of Medical Research, University of Melbourne, Parkville, Victoria, Australia
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37
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Dutton R, Moeck E, Spinks N, Coleman C, Cheadle B, Lane A, Miller A, Judd R, Lupton L. Advanced technologies for CANDU reactors. Nuclear Engineering and Design 1993. [DOI: 10.1016/0029-5493(93)90143-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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McCracken DR, Paquette J, Boniface HA, Graham WRC, Johnson RE, Briden NA, Cross WG, Arneja A, Tennant DC, Lone MA, Buyers WJL, Chambers KW, McIlwain AK, Attas EM, Dutton R. In search of nuclear fusion in electrolytic cells and in metal/gas systems. J Fusion Energ 1990. [DOI: 10.1007/bf02627577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abstract
The use of activity versus exercise has been a divisive topic that has separated occupational therapists into opposing factions regarding our legitimate tools. One approach to the resolution of this conflict is to use exercise as preparation and purposeful activity as application in a treatment plan. Preparation and application are not philosophically opposed concepts--They are the two ends of a continuum. The purpose of this paper is to explore how specific continua from the biomechanical and sensorimotor frames of reference can be used to generate specific guidelines about when to use activity and when to use exercise.
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Affiliation(s)
- R Dutton
- College of Allied Health Professions, Temple University, Philadelphia, Pennsylvania 19140
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Lozman J, Deno DC, Feustel PJ, Newell JC, Stratton HH, Sedransk N, Dutton R, Fortune JB, Shah DM. Pulmonary and cardiovascular consequences of immediate fixation or conservative management of long-bone fractures. Arch Surg 1986; 121:992-9. [PMID: 3741107 DOI: 10.1001/archsurg.1986.01400090018003] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We randomly assigned patients with multiple trauma who had tibial or femoral fractures to one of two groups--one group received immediate fixation of all fractures, and the second group received conservative orthopedic management, consisting of traction or plaster casts. Studies were conducted twice each day for four days following injury. Mean cardiac index was 1.3 L/min/m2 higher and mean shunt was 5.2% lower in the immediate fixation group compared with the group receiving conservative treatment. Other pulmonary and systemic hemodynamic variables did not differ between the groups. The incidence of fat macroglobules in blood aspirated from the pulmonary capillaries was higher when compared with that in pulmonary arterial blood but was not significantly different between the two treatment groups. Platelet count was significantly lower and fibrinogen concentration was significantly higher in the group receiving immediate fixation. We found no diagnostic significance of the incidence of fat macroglobules in samples of blood aspirated from the pulmonary circulation. We conclude that patients receiving immediate fixation had less pulmonary dysfunction following multiple trauma and long-bone fractures.
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Abstract
Occupational therapists have been asked with increasing frequency to function as consultants, yet most of the research on consultation has been published in other fields. Issues that have been investigated include negotiating consultation sponsorship, conducting needs assessments, and evaluating the consultant's effectiveness. For the purposes of our research the literature was used to generate a list of steps for designing a consultation package. The steps were then used in a six-month pilot contract to assess their usefulness for occupational therapy practice.
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Swain S, Wetzel M, Dutton R. Role of different T-cell replacing factors (TRFs) in the proliferation and differentiation of B-cell subsets. Cell Immunol 1982. [DOI: 10.1016/0008-8749(82)90357-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Annest SJ, Gottlieb M, Paloski WH, Stratton H, Newell JC, Dutton R, Powers SR. Detrimental effects of removing end-expiratory pressure prior to endotracheal extubation. Ann Surg 1980; 191:539-45. [PMID: 6989330 PMCID: PMC1344730 DOI: 10.1097/00000658-198005000-00004] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Patients recovering from acute respiratory insufficiency are usually not extubated until they can ventilate adequately while breathing spontaneously at ambient end-expiratory pressure (T-tube). It is hypothesized that this period of T-tube breathing might be detrimental to gas exchange since the endotracheal tube abolishes the expiratory retard produced by the glottis and thereby inhibits the patient's ability to maintain adequate functional residual capacity (FRC). To test this hypothesis, pulmonary function of 17 patients was compared during T-tube breathing and Continuous Positive Airway Pressure (CPAP) and after extubation. Intrapulmonary shunt was higher (p less than 0.05) and arterial PO2 and FRC were lower (p less than 0.05) during T-tube breathing than during CPAP or after extubation. In contrast, shunt, PaO2 and FRC were similar during CPAP and after extubation. Furthermore, after extubation there was an increase (p less than 0.05) in mean expiratory airway pressure as compared to T-tube breathing. A comparison of patients extubated from T-tube with patients extubated from CPAP showed no difference in postextubation shunt, PaO2 or FRC. These data suggest that endotracheal intubation should be accompanied by low levels of CPAP and that patients should be extubated directly from CPAP. The practice of placing patients in T-tube prior to extubation should be abandoned as unnecessary and potentially harmful.
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Dutton R, Feustel P, Berger A, Davies D. Chemoreceptor interaction during medullary perfusion. Chest 1978. [DOI: 10.1378/chest.73.2.258] [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: 11/01/2022] Open
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Dutton R, Nuttall K, Puls MP, Simpson LA. Mechanisms of hydrogen induced delayed cracking in hydride forming materials. ACTA ACUST UNITED AC 1977. [DOI: 10.1007/bf02644858] [Citation(s) in RCA: 185] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
Increased pulmonary artery pressure, an increase in pulmonary vascular resistance and an increase in physiologic dead space are consistent findings in patients with post-traumatic respiratory distress. Since mannitol has been shown to decrease renal vascular resistance following trauma, the effect of a bolus injection of 100 ml of 25% solution of this drug on pulmonary hemodynamics and physiologic dead space was investigated in 11 patients who had suffered multiple trauma. Five minutes after the injection, pulmonary vascular resistance fell (p less than .01), cardiac index increased (p less than .001) and physiologic dead space decreased (p less than .05). In contrast, the administration of 40 mg of furosemide produced no significant change in any of these parameters. Mannitol rapidly equilibrates in the extracellular space and exerts an osmotic effect across cell membranes. We postulate that the beneficial response to mannitol on the pulmonary vascular resistance and the improved perfusion of ventilated regions of the lung is due to a reduction in cell swelling and is not explainable by its diuretic effect. Improvement in the distribution of perfusion of pulmonary blood flow by mannitol may be a useful aid in the treatment of the post-traumatic form of the respiratory distress syndrome.
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Newell J, Levitsky M, Krasney J, Dutton R. Chemoreceptor effects on perfusion of hypoxic and atelectatic lung. Chest 1977. [DOI: 10.1378/chest.71.2.310] [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: 11/01/2022] Open
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Dutton R, Levitzky M, Berkman R. Carbon dioxide and liver blood flow. Bull Eur Physiopathol Respir 1976; 12:265-73. [PMID: 1016783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This study was designed to determine blood flow to the liver during hypercapnia and combined hypercapnia-hypoxia with the portal vein and hepatic artery intact except for placement of an electromagnetic flow probe around these vessels. Twenty mongrel dogs weighing 30-45 kg were anesthetized with pentobarbital and flow probes and occluders were surgically implanted. Ten of these dogs were subjected to hypercapnia alone. During inspiration of 6% CO2 in room air, portal vein flow increased from 588 +/- 73 ml/min to 731 +/- 113 ml/min (p less than .05), while hepatic artery flow did not change significantly from its control mean of 221 +/- 38 ml/min. In the remaining dogs, inhalation of 6% O2 resulted in a reduction of portal blood flow within 30 min from 527 +/- 55 ml/min to 381 +/- 41 ml/min (p less than .01). Again, mean hepatic artery flow did not increase significantly above its control of 273 +/- 43 ml/min. Subsequent inhalation of 6% CO2 plus 6% O2 (combined hypercapniahypoxia) for 30 min in these same animals resulted in a significant increase of portal vein blood flow from 514 +/- 46 ml/min to 716 +/- 116 ml/min (p less than .05). Thus, hypercapnia alone increases total liver blood flow, primarily by an increase in portal vein flow. Hypoxia results in a decrease in portal vein flow. The superimposition of hypercapnia on hypoxia restores blood flow to a level close to that found with hypercapnia alone. Hypercapnia in the range of 63 +/- 4 mmHg PCO2 overwhelms the tendency toward a reduction of portal vein blood flow induced by an arterial PO2 of 42 +/- 5 mmHg in the presence of mild hypocapnia (PCO2 : 30.2 +/- 1 mmHg).
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