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Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, Lee R, Mi H, Moxon S, Mungall CJ, Muruganugan A, Mushayahama T, Sternberg PW, Thomas PD, Van Auken K, Ramsey J, Siegele DA, Chisholm RL, Fey P, Aspromonte MC, Nugnes MV, Quaglia F, Tosatto S, Giglio M, Nadendla S, Antonazzo G, Attrill H, Dos Santos G, Marygold S, Strelets V, Tabone CJ, Thurmond J, Zhou P, Ahmed SH, Asanitthong P, Luna Buitrago D, Erdol MN, Gage MC, Ali Kadhum M, Li KYC, Long M, Michalak A, Pesala A, Pritazahra A, Saverimuttu SCC, Su R, Thurlow KE, Lovering RC, Logie C, Oliferenko S, Blake J, Christie K, Corbani L, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Smith C, Cuzick A, Seager J, Cooper L, Elser J, Jaiswal P, Gupta P, Jaiswal P, Naithani S, Lera-Ramirez M, Rutherford K, Wood V, De Pons JL, Dwinell MR, Hayman GT, Kaldunski ML, Kwitek AE, Laulederkind SJF, Tutaj MA, Vedi M, Wang SJ, D'Eustachio P, Aimo L, Axelsen K, Bridge A, Hyka-Nouspikel N, Morgat A, Aleksander SA, Cherry JM, Engel SR, Karra K, Miyasato SR, Nash RS, Skrzypek MS, Weng S, Wong ED, Bakker E, Berardini TZ, Reiser L, Auchincloss A, Axelsen K, Argoud-Puy G, Blatter MC, Boutet E, Breuza L, Bridge A, Casals-Casas C, Coudert E, Estreicher A, Livia Famiglietti M, Feuermann M, Gos A, Gruaz-Gumowski N, Hulo C, Hyka-Nouspikel N, Jungo F, Le Mercier P, Lieberherr D, Masson P, Morgat A, Pedruzzi I, Pourcel L, Poux S, Rivoire C, Sundaram S, Bateman A, Bowler-Barnett E, Bye-A-Jee H, Denny P, Ignatchenko A, Ishtiaq R, Lock A, Lussi Y, Magrane M, Martin MJ, Orchard S, Raposo P, Speretta E, Tyagi N, Warner K, Zaru R, Diehl AD, Lee R, Chan J, Diamantakis S, Raciti D, Zarowiecki M, Fisher M, James-Zorn C, Ponferrada V, Zorn A, Ramachandran S, Ruzicka L, Westerfield M. The Gene Ontology knowledgebase in 2023. Genetics 2023; 224:iyad031. [PMID: 36866529 PMCID: PMC10158837 DOI: 10.1093/genetics/iyad031] [Citation(s) in RCA: 232] [Impact Index Per Article: 232.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 03/04/2023] Open
Abstract
The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.
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Bateman A, Martin MJ, Orchard S, Magrane M, Agivetova R, Ahmad S, Alpi E, Bowler-Barnett EH, Britto R, Bursteinas B, Bye-A-Jee H, Coetzee R, Cukura A, Da Silva A, Denny P, Dogan T, Ebenezer T, Fan J, Castro LG, Garmiri P, Georghiou G, Gonzales L, Hatton-Ellis E, Hussein A, Ignatchenko A, Insana G, Ishtiaq R, Jokinen P, Joshi V, Jyothi D, Lock A, Lopez R, Luciani A, Luo J, Lussi Y, MacDougall A, Madeira F, Mahmoudy M, Menchi M, Mishra A, Moulang K, Nightingale A, Oliveira CS, Pundir S, Qi G, Raj S, Rice D, Lopez MR, Saidi R, Sampson J, Sawford T, Speretta E, Turner E, Tyagi N, Vasudev P, Volynkin V, Warner K, Watkins X, Zaru R, Zellner H, Bridge A, Poux S, Redaschi N, Aimo L, Argoud-Puy G, Auchincloss A, Axelsen K, Bansal P, Baratin D, Blatter MC, Bolleman J, Boutet E, Breuza L, Casals-Casas C, de Castro E, Echioukh KC, Coudert E, Cuche B, Doche M, Dornevil D, Estreicher A, Famiglietti ML, Feuermann M, Gasteiger E, Gehant S, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, Hyka-Nouspikel N, Jungo F, Keller G, Kerhornou A, Lara V, Le Mercier P, Lieberherr D, Lombardot T, Martin X, Masson P, Morgat A, Neto TB, Paesano S, Pedruzzi I, Pilbout S, Pourcel L, Pozzato M, Pruess M, Rivoire C, Sigrist C, Sonesson K, Stutz A, Sundaram S, Tognolli M, Verbregue L, Wu CH, Arighi CN, Arminski L, Chen C, Chen Y, Garavelli JS, Huang H, Laiho K, McGarvey P, Natale DA, Ross K, Vinayaka CR, Wang Q, Wang Y, Yeh LS, Zhang J, Ruch P, Teodoro D. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res 2021; 49:D480-D489. [PMID: 33237286 PMCID: PMC7778908 DOI: 10.1093/nar/gkaa1100] [Citation(s) in RCA: 3532] [Impact Index Per Article: 1177.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/21/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
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Oberbeck S, Schrader A, Warner K, Jungherz D, Crispatzu G, von Jan J, Chmielewski M, Ianevski A, Diebner HH, Mayer P, Kondo Ados A, Wahnschaffe L, Braun T, Müller TA, Wagle P, Bouska A, Neumann T, Pützer S, Varghese L, Pflug N, Thelen M, Makalowski J, Riet N, Göx HJM, Rappl G, Altmüller J, Kotrová M, Persigehl T, Hopfinger G, Hansmann ML, Schlößer H, Stilgenbauer S, Dürig J, Mougiakakos D, von Bergwelt-Baildon M, Roeder I, Hartmann S, Hallek M, Moriggl R, Brüggemann M, Aittokallio T, Iqbal J, Newrzela S, Abken H, Herling M. Noncanonical effector functions of the T-memory-like T-PLL cell are shaped by cooperative TCL1A and TCR signaling. Blood 2020; 136:2786-2802. [PMID: 33301031 PMCID: PMC7731789 DOI: 10.1182/blood.2019003348] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
T-cell prolymphocytic leukemia (T-PLL) is a poor-prognostic neoplasm. Differentiation stage and immune-effector functions of the underlying tumor cell are insufficiently characterized. Constitutive activation of the T-cell leukemia 1A (TCL1A) oncogene distinguishes the (pre)leukemic cell from regular postthymic T cells. We assessed activation-response patterns of the T-PLL lymphocyte and interrogated the modulatory impact by TCL1A. Immunophenotypic and gene expression profiles revealed a unique spectrum of memory-type differentiation of T-PLL with predominant central-memory stages and frequent noncanonical patterns. Virtually all T-PLL expressed a T-cell receptor (TCR) and/or CD28-coreceptor without overrepresentation of specific TCR clonotypes. The highly activated leukemic cells also revealed losses of negative-regulatory TCR coreceptors (eg, CTLA4). TCR stimulation of T-PLL cells evoked higher-than-normal cell-cycle transition and profiles of cytokine release that resembled those of normal memory T cells. More activated phenotypes and higher TCL1A correlated with inferior clinical outcomes. TCL1A was linked to the marked resistance of T-PLL to activation- and FAS-induced cell death. Enforced TCL1A enhanced phospho-activation of TCR kinases, second-messenger generation, and JAK/STAT or NFAT transcriptional responses. This reduced the input thresholds for IL-2 secretion in a sensitizer-like fashion. Mice of TCL1A-initiated protracted T-PLL development resembled such features. When equipped with epitope-defined TCRs or chimeric antigen receptors, these Lckpr-hTCL1Atg T cells gained a leukemogenic growth advantage in scenarios of receptor stimulation. Overall, we propose a model of T-PLL pathogenesis in which TCL1A enhances TCR signals and drives the accumulation of death-resistant memory-type cells that use amplified low-level stimulatory input, and whose loss of negative coregulators additionally maintains their activated state. Treatment rationales are provided by combined interception in TCR and survival signaling.
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MESH Headings
- Animals
- Humans
- Immunologic Memory
- Leukemia, Prolymphocytic, T-Cell/genetics
- Leukemia, Prolymphocytic, T-Cell/immunology
- Leukemia, Prolymphocytic, T-Cell/pathology
- Mice
- Mice, Knockout
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Signal Transduction/genetics
- Signal Transduction/immunology
- T-Lymphocytes/immunology
- T-Lymphocytes/pathology
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Affiliation(s)
- S Oberbeck
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - A Schrader
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - K Warner
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- Senckenberg Institute of Pathology, Goethe University, Frankfurt am Main, Germany
| | - D Jungherz
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - G Crispatzu
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - J von Jan
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - M Chmielewski
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - A Ianevski
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - H H Diebner
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry Dresden, Technische Universität Dresden, Dresden, Germany
| | - P Mayer
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - A Kondo Ados
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - L Wahnschaffe
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - T Braun
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - T A Müller
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - P Wagle
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
| | - A Bouska
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - T Neumann
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - S Pützer
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - L Varghese
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - N Pflug
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
| | - M Thelen
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - J Makalowski
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - N Riet
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - H J M Göx
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
| | - G Rappl
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - J Altmüller
- Cologne Center for Genomics, Institute of Human Genetics, UoC, Cologne, Germany
| | - M Kotrová
- Medical Department II of Hematology and Oncology, University Hospital of Schleswig Holstein, Campus Kiel, Kiel, Germany
| | - T Persigehl
- Department of Radiology, UoC, Cologne, Germany
| | - G Hopfinger
- Center for Oncology and Hematology, Kaiser-Franz-Josef-Spital, Vienna, Austria
| | - M L Hansmann
- Senckenberg Institute of Pathology, Goethe University, Frankfurt am Main, Germany
| | - H Schlößer
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - S Stilgenbauer
- Department III of Internal Medicine, University Hospital Ulm, Ulm, Germany
| | - J Dürig
- Clinic for Hematology, University Hospital Essen, Essen, Germany
| | - D Mougiakakos
- Department of Medicine 5, Hematology, and Oncology, University Hospital Erlangen, Erlangen, Germany
| | | | - I Roeder
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Informatics and Biometry Dresden, Technische Universität Dresden, Dresden, Germany
| | - S Hartmann
- Senckenberg Institute of Pathology, Goethe University, Frankfurt am Main, Germany
| | - M Hallek
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
| | - R Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
- Ludwig Boltzmann Institute for Cancer Research, Medical University of Vienna, Vienna, Austria; and
| | - M Brüggemann
- Medical Department II of Hematology and Oncology, University Hospital of Schleswig Holstein, Campus Kiel, Kiel, Germany
| | - T Aittokallio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - J Iqbal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - S Newrzela
- Senckenberg Institute of Pathology, Goethe University, Frankfurt am Main, Germany
| | - H Abken
- RCI Regensburg Center for Interventional Immunology, Regensburg, Germany
| | - M Herling
- Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, and
- Center for Molecular Medicine Cologne, University of Cologne (UoC), Cologne, Germany
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Nicol D, Joly Y, Kaye J, Knoppers B, Meslin EM, Nielsen J, Otlowski M, Warner K. Don Chalmers: His Contributions to Legal Research and Education, Health Law, and Research Ethics, Locally and Globally. J Law Med 2020; 28:289-297. [PMID: 33415906] [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] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Distinguished Professor Don Chalmers retired from the Law Faculty at the University of Tasmania on Friday 10 July 2020. This article is dedicated to Don, providing a brief account and acknowledgment of his fine contributions to legal research and education and law reform, particularly in the field of health and medical law, research ethics and policy reform. He has been an excellent colleague, mentor, leader, teacher, and researcher. He deserves to enjoy a long and rewarding retirement, though we, and many others, will not allow him to slip entirely out of the limelight. Don is still much needed, and still has so much to give in our ongoing quest to ensure that legal, research ethics and policy responses are adequate in reaping the benefits and responding to the challenges of biomedical advances.
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Affiliation(s)
- Dianne Nicol
- Professor of Law and Director of the Centre for Law and Genetics, Law Faculty, University of Tasmania
| | - Yann Joly
- Professor of Law and member of the Centre of Genomics and Policy, McGill University, Canada
| | - Jane Kaye
- Professor of Law and Director, Centre for Health, Law and Emerging Technologies University of Oxford and Centre for Health, Law and Emerging Technologies, Melbourne Law School, University of Melbourne
| | - Bartha Knoppers
- Professor of Law and Director of the Centre of Genomics and Policy, McGill University, Canada
| | - Eric M Meslin
- President and CEO, Council of Canadian Academies; former Executive Director, US National Bioethics Advisory Commission; Adjunct Professor, Dalla Lana School of Public Health, University of Toronto, Canada
| | - Jane Nielsen
- Associate Professor of Law and member of the Centre for Law and Genetics, Law Faculty, University of Tasmania
| | - Margaret Otlowski
- Professor of Law and Deputy Director of the Centre for Law and Genetics, Law Faculty and Pro Vice Chancellor (Culture, Wellbeing and Sustainability) University of Tasmania
| | - Kate Warner
- Emeritus Professor of Law, University of Tasmania and Governor, State of Tasmania
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Bartels L, Gelb K, Spiranovic C, Warner K, Roberts L, Davis J. What does the public think about sex offender registers? Findings from a national Australian study. Psychiatr Psychol Law 2020; 28:560-575. [PMID: 35558146 PMCID: PMC9090429 DOI: 10.1080/13218719.2020.1805813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article presents data from questions about sex offender registration orders in a large national survey on Australian public opinion about adult sex offenders. It outlines the legislative frameworks that govern these registers in Australia and discusses the use of public registers, the research on the effectiveness of sex offender registers, and Australian attitudes to such registers. Our surveys of three cohorts of members of the Australian public reveal strong public support for sex offender registers, especially for cases involving child victims. However, there was also support for judicial discretion in the imposition of orders and reduced support for automatic registration where a non-custodial sentence is imposed. The Australian Government has recently announced the establishment of a national public sex offender register, but our findings show limited support for this approach. The implications for policy and practice are considered.
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Affiliation(s)
- Lorana Bartels
- Centre for Social Research Methods, Australian National University, Canberra, ACT, Australia
- Canberra Law School, University of Canberra, Canberra, ACT, Australia
- Faculty of Law, University of Tasmania, Hobart, TAS, Australia
| | - Karen Gelb
- Department of Criminology, University of Melbourne, Melbourne, VIC, Australia
| | | | - Kate Warner
- Faculty of Law, University of Tasmania, Hobart, TAS, Australia
| | - Lynne Roberts
- School of Psychology, Curtin University, Perth, WA, Australia
| | - Julia Davis
- School of Law, University of South Australia, Adelaide, SA, Australia
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Brown O, Dave B, Geynisman J, Warner K, Gillingham A, Kenton K, Mueller M, Collins S, Lewicky-Gaupp C. 12: Vaginal electrical stimulation for postpartum neuromuscular recovery: The VESPR study. Am J Obstet Gynecol 2020. [DOI: 10.1016/j.ajog.2019.12.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Marygold SJ, Attrill H, Speretta E, Warner K, Magrane M, Berloco M, Cotterill S, McVey M, Rong Y, Yamaguchi M. The DNA polymerases of Drosophila melanogaster. Fly (Austin) 2020; 14:49-61. [PMID: 31933406 PMCID: PMC7714529 DOI: 10.1080/19336934.2019.1710076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
DNA synthesis during replication or repair is a fundamental cellular process that is catalyzed by a set of evolutionary conserved polymerases. Despite a large body of research, the DNA polymerases of Drosophila melanogaster have not yet been systematically reviewed, leading to inconsistencies in their nomenclature, shortcomings in their functional (Gene Ontology, GO) annotations and an under-appreciation of the extent of their characterization. Here, we describe the complete set of DNA polymerases in D. melanogaster, applying nomenclature already in widespread use in other species, and improving their functional annotation. A total of 19 genes encode the proteins comprising three replicative polymerases (alpha-primase, delta, epsilon), five translesion/repair polymerases (zeta, eta, iota, Rev1, theta) and the mitochondrial polymerase (gamma). We also provide an overview of the biochemical and genetic characterization of these factors in D. melanogaster. This work, together with the incorporation of the improved nomenclature and GO annotation into key biological databases, including FlyBase and UniProtKB, will greatly facilitate access to information about these important proteins.
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Affiliation(s)
- Steven J Marygold
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge, UK
| | - Helen Attrill
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge, UK
| | - Elena Speretta
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Kate Warner
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Michele Magrane
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Maria Berloco
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro" , Bari, Italy
| | - Sue Cotterill
- Department Basic Medical Sciences, St Georges University London , London, UK
| | - Mitch McVey
- Department of Biology, Tufts University , Medford, MA, USA
| | - Yikang Rong
- School of Life Sciences, Sun Yat-sen University , Guangzhou, China
| | - Masamitsu Yamaguchi
- Department of Applied Biology and Advanced Insect Research Promotion Center, Kyoto Institute of Technology , Kyoto, Japan
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van Hengel AJ, Capelletti C, Brohee M, Anklam E, Baumgartner MCS, Abbott M, Baumgartner S, Bremer M, Clarke D, Cleroux C, Demeulemester C, Eckhart F, Gelencser E, Hefle S, Herrnegger H, Hörtner H, Kyriakidis S, Lowe R, Marx G, Mayer W, Paschke A, Robert MC, Schneede K, Sherlock R, Suter D, Warner K, Werner M. Validation of Two Commercial Lateral Flow Devices for the Detection of Peanut Proteins in Cookies: Interlaboratory Study. J AOAC Int 2019. [DOI: 10.1093/jaoac/89.2.462] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Results are reported for an interlaboratory validation study of 2 commercially available lateral flow devices (dipstick tests) designed to detect peanut residues in food matrixes. The test samples used in this study were cookies containing peanuts at 7 different concentrations in the range of 030 mg peanuts/kg food matrix. The test samples with sufficient and proven homogeneity were prepared in our laboratory. The analyses of the samples (5 times per level by each laboratory) were performed by 18 laboratories worldwide, which submitted a total of 1260 analytical results. One laboratory was found to be an outlier for one of the test kits. In general, both test kits performed well. However, some false-negative results were reported for all matrixes containing <21 mg peanuts/kg cookie. It must be stressed that the test kits were challenged beyond their cut-off limits (5 mg/kg, depending on the food matrix). One test kit showed fewer false-negative results, but it led to some false-positive results for the blank materials. The sensitivity of the dipstick tests approaches that achieved with enzyme-linked immunosorbent assays.
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Affiliation(s)
- Arjon J van Hengel
- European Commission, Directorate General Joint Research Centre, Institute for Reference Materials and Measurements, Retieseweg 111, B-2440, Geel, Belgium
| | - Claudia Capelletti
- European Commission, Directorate General Joint Research Centre, Institute for Reference Materials and Measurements, Retieseweg 111, B-2440, Geel, Belgium
| | - Marcel Brohee
- European Commission, Directorate General Joint Research Centre, Institute for Reference Materials and Measurements, Retieseweg 111, B-2440, Geel, Belgium
| | - Elke Anklam
- European Commission, Directorate General Joint Research Centre, Institute for Reference Materials and Measurements, Retieseweg 111, B-2440, Geel, Belgium
| | - M-C S Baumgartner
- European Commission, Directorate General Joint Research Centre, Institute for Reference Materials and Measurements, Retieseweg 111, B-2440, Geel, Belgium
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Abstract
Public availability of biological sequences is essential for their widespread access and use by the research community. The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and functional data. While most protein sequences entering UniProt are imported from other source databases containing nucleotide or 3-D structure data, protein sequences determined at the protein level can be submitted directly to UniProt. To this end, UniProt provides a Web interface called SPIN. This service enables researchers to make their de novo-sequenced proteins available to the scientific community and acquire UniProt accession numbers for use in publications. This unit explains the process of submitting a protein sequence to UniProt using SPIN. The basic protocol describes all the necessary steps for a single sequence. A support protocol gives guidance on how best to deal with exceptionally large datasets. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Klemens Pichler
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Kate Warner
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Michele Magrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.,SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.,Protein Information Resource, Georgetown University Medical Center, Washington, D.C.,Protein Information Resource, University of Delaware, Newark, Delaware
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Abstract
In 2001 and 2002, print, radio and television gave extensive coverage to a series of gang rapes in Bankstown and other suburbs of south-west Sydney. The coverage attacked the laxity and inefficiency of the criminal justice system and immigration policy. It fuelled public fears about increases in crime in particular areas and fear of “ethnic gangs” and racially-motivated crime. The sentences imposed on three youths of Lebanese background in the first of these cases to be dealt with attracted widespread criticism from politicians, the media and the public because of their leniency. These events occurred at a time when issues of race were in the news as a result of the arrival of “boat people”, followed by a heightened fear of terrorism because of the events of September 11, 2001. The issue of gang rape by ethnic-minority youth resurfaced in August 2002 when a second group of offenders, again Lebanese-Australian youth, were sentenced, this time with gaol terms which for the most part were applauded for their severity. In parliament, legislation was introduced to increase penalties and political parties engaged in a pre-election law-and-order auction. These events are portrayed as an example of how a localised story about crime can become “racialised” and linked with debates about asylum-seekers and terrorism. This article attempts to draw out some of the criminal-justice issues from this story. In particular it explores some of the flaws in the sentencing process that assisted in inflaming the debate. A pedagogical role for judges is suggested in relation to the public understanding of crime and guideline judgements are recommended.
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Warner K, Schulze T, Lischer C. Treatment of Osteoarthritis with ACS (IRAP®) on 26 horses – retrospective study. PFERDEHEILKUNDE 2016. [DOI: 10.21836/pem20160307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Gregory JA, Smith AM, Pearce EC, Lambour RL, Shah RY, Clark HR, Warner K, Osgood RM, Woods DF, DeCew AE, Forman SE, Mendenhall L, DeFranzo CM, Dolat VS, Loomis AH. Development and application of spherically curved charge-coupled device imagers. Appl Opt 2015; 54:3072-3082. [PMID: 25967223 DOI: 10.1364/ao.54.003072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/27/2015] [Indexed: 06/04/2023]
Abstract
Operation of a CCD imager on a curved focal surface offers advantages to flat focal planes, especially for lightweight, relatively simple optical systems. The first advantage is that the modulation transfer function can approach diffraction-limited performance for a spherical focal surface employed in large field-of-view or large-format imagers. The second advantage is that a curved focal surface maintains more uniform illumination as a function of radius from the field center. Examples of applications of curved imagers, described here, include a small compact imager and the large curved array used in the Space Surveillance Telescope. The operational characteristics and mechanical limits of an imager deformed to a 15 mm radius are also described.
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Rengstl B, Newrzela S, Heinrich T, Weiser C, Thalheimer FB, Schmid F, Warner K, Hartmann S, Schroeder T, Küppers R, Rieger MA, Hansmann ML. Re-fusion of Small Mononucleated Hodgkin Cells Leads to Multinucleated Reed-Sternberg Cells. Klin Padiatr 2014. [DOI: 10.1055/s-0034-1371097] [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: 10/25/2022]
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Abstract
AbstractPolyimides are of great interest as insulators for microelectronic fabrication due to their low dielectric constant and planarizing properties. However, they are thermally sensitive films. Nonetheless, preliminary results clearly demonstrate that nickel lines readily can be laser-pyrolytically drawn over polyimide films.While elevated laser power will damage underlying polyimide films, microelectronic quality nickel lines can be drawn using nickel carbonyl at relatively low laser intensities over polyimides with little or no change in the electrical characteristics. Polyimide's lower thermal conductivity relative to silicon dioxide facilitates increased nickel deposition rates. Self-limiting effects have been observed during the deposition that can lead to near microelectronically ideal line cross sections.
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Cummings M, Warner K, Pierce J, Chapman S. Remembering Ron Davis. Tob Control 2009. [DOI: 10.1136/tc.2008.028613] [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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Bolton S, Borthwick D, Bell N, Wibberley G, Henderson K, Warner K, Horne N, Borgen P. Developing a guideline to enable lung cancer nurse specialists to consistently communicate key MDT decisions to patients. Lung Cancer 2009. [DOI: 10.1016/s0169-5002(09)70096-0] [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: 10/21/2022]
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18
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Warner K, Miller J, Demurin Y. Oxidative Stability of Crude Mid-Oleic Sunflower Oils from Seeds with High γ- and δ-Tocopherol Levels. J AM OIL CHEM SOC 2008. [DOI: 10.1007/s11746-008-1212-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Winkler JK, Warner K, Glynn MT. Effect of Deep-Fat Frying on Phytosterol Content in Oils with Differing Fatty Acid Composition. J AM OIL CHEM SOC 2007. [DOI: 10.1007/s11746-007-1138-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Jordan N, Boody G, Broussard W, Glover JD, Keeney D, McCown BH, McIsaac G, Muller M, Murray H, Neal J, Pansing C, Turner RE, Warner K, Wyse D. Environment. Sustainable development of the agricultural bio-economy. Science 2007; 316:1570-1. [PMID: 17569847 DOI: 10.1126/science.1141700] [Citation(s) in RCA: 213] [Impact Index Per Article: 12.5] [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: 11/02/2022]
Abstract
A U.S. farm policy shift to joint production of commodities and ecological services will advance sustainable agriculture.
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Affiliation(s)
- N Jordan
- Agronomy and Plant Genetics Department, University of Minnesota, St. Paul, MN 55018, USA.
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Abstract
Tumors of the oral cavity are highly vascularized malignancies. Disruption of neovascular networks was shown to limit the access of nutrients and oxygen to tumor cells and inhibit tumor progression. Here, we evaluated the effect of the activation of an artificial death switch (iCaspase-9) expressed in neovascular endothelial cells on the progression of oral tumors. We used biodegradable scaffolds to co-implant human dermal microvascular endothelial cells stably expressing iCaspase-9 (HDMEC-iCasp9) with oral cancer cells expressing luciferase (OSCC3-luc or UM-SCC-17B-luc) in immunodeficient mice. Alternatively, untransduced HDMEC were co-implanted with oral cancer cells, and a transcriptionaly targeted adenovirus (Ad-VEGFR2-iCasp-9) was injected locally to deliver iCaspase-9 to neovascular endothelial cells. In vivo bioluminescence demonstrated that tumor progression was inhibited, and immunohistochemistry showed that microvessel density was decreased, when iCaspase-9 was activated in tumor-associated microvessels. We conclude that activation of iCaspase-9 in neovascular endothelial cells is sufficient to inhibit the progression of xenografted oral tumors.
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Affiliation(s)
- M.S. Pinsky
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan School of Dentistry, 1011 N. University, Rm. 2309, Ann Arbor, MI 48109-1078, USA
- Department of Oral and Maxillofacial Surgery, University of Michigan School of Dentistry, 1011 N. University, Rm. 2309, Ann Arbor, MI 48109-1078, USA
| | - W. Song
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan School of Dentistry, 1011 N. University, Rm. 2309, Ann Arbor, MI 48109-1078, USA
| | - Z. Dong
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan School of Dentistry, 1011 N. University, Rm. 2309, Ann Arbor, MI 48109-1078, USA
| | - K. Warner
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan School of Dentistry, 1011 N. University, Rm. 2309, Ann Arbor, MI 48109-1078, USA
| | - B. Zeitlin
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan School of Dentistry, 1011 N. University, Rm. 2309, Ann Arbor, MI 48109-1078, USA
| | - E. Karl
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan School of Dentistry, 1011 N. University, Rm. 2309, Ann Arbor, MI 48109-1078, USA
| | - D.E. Hall
- Center for Molecular Imaging, Department of Radiology, University of Michigan School of Medicine, Ann Arbor
| | - J.E. Nör
- Angiogenesis Research Laboratory, Department of Cariology, Restorative Sciences, and Endodontics, University of Michigan School of Dentistry, 1011 N. University, Rm. 2309, Ann Arbor, MI 48109-1078, USA
- *corresponding author,
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Warner K, Laszlo JA. Addition of ferulic acid, ethyl ferulate, and feruloylated monoacyl- and diacylglycerols to salad oils and frying oils. J AM OIL CHEM SOC 2005. [DOI: 10.1007/s11746-005-1123-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- K. Warner
- ; USDA/ARS/NCAUR; 1815 N. University St. Peoria 61604 IL
| | - J. A. Laszlo
- ; USDA/ARS/NCAUR; 1815 N. University St. Peoria 61604 IL
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Affiliation(s)
- P. N. Pintauro
- Department of Chemical Engineering, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemical Engineering, Tulane University, New Orleans, Louisiana 70118, and U.S. Department of Agriculture, Food Quality and Safety Research, NCAUR, ARS, USDA, Peoria, Illinois 61604
| | - Maria Paula Gil
- Department of Chemical Engineering, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemical Engineering, Tulane University, New Orleans, Louisiana 70118, and U.S. Department of Agriculture, Food Quality and Safety Research, NCAUR, ARS, USDA, Peoria, Illinois 61604
| | - K. Warner
- Department of Chemical Engineering, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemical Engineering, Tulane University, New Orleans, Louisiana 70118, and U.S. Department of Agriculture, Food Quality and Safety Research, NCAUR, ARS, USDA, Peoria, Illinois 61604
| | - G. List
- Department of Chemical Engineering, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemical Engineering, Tulane University, New Orleans, Louisiana 70118, and U.S. Department of Agriculture, Food Quality and Safety Research, NCAUR, ARS, USDA, Peoria, Illinois 61604
| | - W. Neff
- Department of Chemical Engineering, Case Western Reserve University, Cleveland, Ohio 44106, Department of Chemical Engineering, Tulane University, New Orleans, Louisiana 70118, and U.S. Department of Agriculture, Food Quality and Safety Research, NCAUR, ARS, USDA, Peoria, Illinois 61604
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Affiliation(s)
- G. A. Garzón
- Cereal Products and Food Science; NCAUR, ARS, USDA; 61604 Peoria Illinois
| | - K. Warner
- Food and Industrial Oil; NCAUR, ARS, USDA; 61604 Peoria Illinois
| | - F. C. Felker
- Cereal Products and Food Science; NCAUR, ARS, USDA; 61604 Peoria Illinois
- 6011 N. Rosemead Dr. 61614 Peoria IL
| | | | - F. Eller
- New Crops and Processing Research; NCAUR, ARS, USDA; 61604 Peoria Illinois
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Abstract
Sarcocystis neurona merozoites were examined for their ability to invade and divide in bovine turbinate (BT) cell cultures after treatment with cysteine (iodoacetamide), aspartic (pepstatin A), metallo-(1,10-phenanthroline and ethylene glycol-bis(aminoethylether)-tetraacetic acid [EGTA]), or serine (4-[2-aminoethyl]-benzenesulfonyl fluoride hydrochloride [AEBSF], phenylmethane sulphonyl fluoride [PMSF], and tosyl lysyl chloramethyl ketone [TLCK]) protease inhibitors. Significant (P < 0.01) inhibition of serine protease activity by PMSF and TLCK led to a reduction of 86 and 78% in merozoites produced in BT cell cultures, respectively, whereas AEBSF (1 mM) led to a 68% reduction in merozoites produced in BT cell cultures and a reduction of 84 and 92% at higher AEBSF concentrations (2 and 3 mM, respectively). Pepstatin A and iodoacetamide failed to cause any inhibition in merozoite production, whereas 1,10-phenanthroline and EGTA caused slight, but not significant, inhibition at 6 and 17%, respectively. In zymograms, 2 bands of protease activity between 65- and 70-kDa molecular weight were seen. The protease activity was inhibited by AEBSF but not by E-64 (cysteine protease inhibitor), EGTA, iodoacetamide, or pepstatin A. In native zymograms, the protease activity was highest between a pH range of 8 and 10. These data suggest that merozoites of S. neurona have serine protease activity with a relative molecular weight range between 65 and 70 kDa and optimal pH range between 8 and 10, which is essential for host cell entry at least in vitro. The protease activity described here could be a potential target for chemotherapy development.
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Affiliation(s)
- S C Barr
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA.
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Warner K. Major career decisions: pursuing postgraduate training. J Am Pharm Assoc (Wash) 2001; 41:798-9. [PMID: 11765104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- K Warner
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, USA
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Pejchar L, Warner K. A river might run through it again: criteria for consideration of dam removal and interim lessons from California. Environ Manage 2001; 28:561-575. [PMID: 11568839 DOI: 10.1007/s002670010244] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Resource managers are increasingly being challenged by stakeholder groups to consider dam removal as a policy option and as a tool for watershed management. As more dam owners face high maintenance costs, and rivers as spawning grounds for anadromous fish become increasingly valuable, dam removal may provide the greatest net benefit to society. This article reviews the impact of Endangered Species Act listings for anadromous fish and recent shifts in the Federal Energy Regulatory Commission's hydropower benefit-costs analysis and discusses their implications for dam removal in California. We propose evaluative criteria for consideration of dam removal and apply them to two case studies: the Daguerre and Englebright Dams on the Yuba River and the Scott and Van Horne Dams on the South Eel River, California.
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Affiliation(s)
- L Pejchar
- Department of Environmental Studies, UC Santa Cruz, California 95064, USA
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Abstract
Spaghetti was prepared by replacing either 5 or 10% semolina or farina with corn gluten meal, a high-protein fraction from the wet milling of corn, to increase the protein content of pasta. Spaghetti fortified with corn gluten meal had a similar cooked weight and cooking loss but was less firm compared with the control. The overall flavor quality score of the spaghetti decreased with the increasing additions of either water-washed, water/ethanol-washed or regular corn gluten meal because of the higher intensity of the fermented flavor. Spaghetti with acceptable quality can be prepared with 5% water/ethanol-washed corn gluten meal, thereby improving its nutritional value while providing an additional market for corn gluten meal.
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Affiliation(s)
- Y V Wu
- Fermentation Biotechnology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604, USA.
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Affiliation(s)
- S. L. Abidi
- ; Oil Chemical Research; NCAUR, USDA, ARS; 1815 N. University St. 61604 Peoria IL
| | - K. Warner
- ; Oil Chemical Research; NCAUR, USDA, ARS; 1815 N. University St. 61604 Peoria IL
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Warner K, Neff WE, Byrdwell WC, Gardner HW. Effect of oleic and linoleic acids on the production of deep-fried odor in heated triolein and trilinolein. J Agric Food Chem 2001; 49:899-905. [PMID: 11262047 DOI: 10.1021/jf000822f] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
To determine sources of desirable deep-fried flavor in frying oils, degradation products from heated triolein and trilinolein with 5-31% polar compounds representing low to high deterioration were evaluated by purge-trap gas chromatography-mass spectrometry-olfactometry. (E,E)-2,4-Decadienal, 2-heptenal, 2-octenal, 2,4-nonadienal, and 2,4-octadienal produced deep-fried odor at moderate-strong intensities in heated trilinolein. However, unexpected aldehydes-2,4-decadienal, 2,4-undecadienal, 2,4-nonadienal, and 2-octenal (all <15 ppm)-were produced in triolein heated for 6 h. These dienals possibly were produced by hydroperoxidation and/or hydroxylation followed by dehydration of 2-alkenals. The 2-alkenals were produced from thermal decomposition of hydroperoxides, epoxides, and keto and dimeric compounds produced during the heating of triolein. These aldehydes produced low intensities of deep-fried odor in triolein. This information helps to explain sources of the deep-fried flavor that is characteristic of high linoleic frying oils but which is only at low intensity levels in high oleic frying oils.
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Affiliation(s)
- K Warner
- Food Quality and Safety Research and Bioactive Active Constituents Research, ARS/NCAUR, U.S. Department of Agriculture, Peoria, Illinois 61604, USA.
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Warner K, Neff WE, List GR, Pintauro P. Electrochemical hydrogenation of edible oils in a solid polymer electrolyte reactor. Sensory and compositional characteristics of low Trans soybean oils. J AM OIL CHEM SOC 2000. [DOI: 10.1007/s11746-000-0175-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
The clinical utility of the Thrombotest, a method for determining the prothrombin time that is uniquely sensitive to the presence of proteins invoked by vitamin K absence (PIVKA), was prospectively evaluated and compared to routine coagulation tests in cats with clinically suspected bleeding tendencies. Abnormal PIVKA clotting values were determined by comparison to results of a concurrently evaluated pooled feline plasma sample and by use of an absolute cutoff value of 25.2 seconds. To be recognized as abnormal, PIVKA clotting values had to be >20% of the pooled feline plasma PIVKA clotting time (the "20% rule") or > or =25.2 seconds (mean + 2 standard deviations of 150 different pooled feline plasma samples). Among the disorders in the population examined were 74 cats with liver disease and 19 cats with severe inflammatory bowel disease. Overall, a prolonged PIVKA clotting time based on the 25.2-second cutoff was found in 39.3% of cats, and based on the 20% rule in 40.7% of cats. An abnormal prothrombin time (PT) developed in 5.8% of cats, an abnormal APTT in 14% of cats, subnormal fibrinogen in 8.8% of cats, and thrombocytopenia in 3.3% of cats. Bleeding tendencies were confirmed in 22 cats, of which abnormal PIVKA clotting times were recognized in 95.5%, abnormal PT in 21%, abnormal activated partial thromboplastin time in 25%, hypofibrinogenemia in 16.7%, and thrombocytopenia in 4.5%. Response to treatment with vitamin K was demonstrated in 21 of 24 cats with an abnormal PIVKA clotting time. In these cats, an abnormal PIVKA clotting time normalized within 3 to 5 days of parenteral vitamin K administration. Cats responding to vitamin K administration had hepatic lipidosis (n = 7), severe inflammatory bowel disease (n = 4), severe inflammatory bowel disease associated with cholangiohepatitis (n = 5), and miscellaneous disorders (n = 5). Using either endpoint, the PIVKA clotting time is more sensitive for the detection of cats with coagulopathies than routinely used coagulation assessments in our hospital. Our findings confirm that cats with hepatic lipidosis, severe cholangiohepatitis, and severe inflammatory bowel disease develop coagulopathies responsive to vitamin K administration.
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Affiliation(s)
- S A Center
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853-6401, USA.
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Thibonnier M, Kilani A, Rahman M, DiBlasi TP, Warner K, Smith MC, Leenhardt AF, Brouard R. Effects of the nonpeptide V(1) vasopressin receptor antagonist SR49059 in hypertensive patients. Hypertension 1999; 34:1293-300. [PMID: 10601133 DOI: 10.1161/01.hyp.34.6.1293] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We assessed the clinical and pharmacological profile of the orally active V(1) vascular vasopressin (AVP) receptor nonpeptide antagonist SR49059 (SR) during the osmotic stimulation of AVP release in hypertensive patients. In a double-blind crossover-versus-placebo study, 24 untreated stage I or II essential hypertensive patients (12 whites and 12 blacks) received a single 300 mg oral dose of SR 2 hours before the stimulation of AVP secretion with a 5% hypertonic saline infusion. Hemodynamic, humoral, and hormonal parameters were monitored for up to 28 hours after drug administration. SR did not alter blood pressure or heart rate before the saline infusion and did not reduce the blood pressure increment induced by the hypertonic saline infusion. However, the blood pressure peak at the end of the hypertonic saline infusion was slightly lower in the presence of SR (P=0.04). Heart rate was significantly faster between 4 and 6 hours after SR administration (P=0.02). The rise in plasma sodium and osmolality triggered by the saline infusion was not modified by SR, but AVP release was slightly greater in the presence of SR (P<0.0003). AVP-induced aggregation of blood platelets in vitro was significantly reduced by SR, with a peak effect 2 hours after drug administration that coincided with the SR peak plasma concentration. Plasma renin activity and aldosterone before and after the saline infusion were not modified by SR. Urine volume and osmolality were not altered by SR administration. SR effects were similar in the 2 ethnic groups as well as in salt-sensitive versus salt-resistant patients. In a situation of AVP osmotic release and volume expansion in hypertensive patients, a single oral dose of the V(1) vascular AVP receptor nonpeptide antagonist SR49059, which is able to block AVP-induced platelet aggregation, exerts a transient vasodilation effect that is not associated with a sustained blood pressure reduction. SR49059 is a pure V(1) vascular receptor antagonist that is devoid of V(2) renal receptor actions.
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Affiliation(s)
- M Thibonnier
- Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals, Cleveland, Ohio 44106-4951, USA.
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Abstract
Fats and oils are heated at high temperatures during baking, grilling and pan frying; however, deep fat frying is the most common method of high temperature treatment. Deep fat frying is a popular food preparation method because it produces desirable fried food flavor, golden brown color and crisp texture. For example, in the U.S. in 1994, approximately 12 billion pounds of fats and oils were used with 5.5 billion pounds used for frying and baking (USDA, 1995). Fried snack foods accounted for 2.9 billion pounds of oil, whereas 2 billion pounds were used for frying in restaurants (USDA, 1995). Because of such large consumption of frying oils and fats, the effects of high temperatures on these oils and fats is of major concern both for product quality and nutrition. This chapter will discuss the process of frying and the chemical and physical reactions that occur. The products formed from these reactions will be reviewed as well as information on the effects of the products and the control of these deteriorative reactions.
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Affiliation(s)
- K Warner
- National Center for Agricultural Utilization Research, U.S. Dept. of Agriculture, Peoria, Illinois 61604, USA
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Acar P, Laskari C, Rhodes J, Pandian N, Warner K, Marx G. Three-dimensional echocardiographic analysis of valve anatomy as a determinant of mitral regurgitation after surgery for atrioventricular septal defects. Am J Cardiol 1999; 83:745-9. [PMID: 10080430 DOI: 10.1016/s0002-9149(98)00982-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mitral regurgitation (MR) is a significant complication after atrioventricular septal defect (AVSD) surgery. The relation of the valve leaflet morphology and the MR mechanism remains a conundrum. Two-dimensional echocardiography depicts leaflet edges, whereas volume-rendered 3-dimensional echocardiography provides direct visualization of the surface areas of the mitral valve leaflets. This study examines the relation of mitral valve anatomy as determined by 3-dimensional echocardiography with MR origins in patients after AVSD repair. Twenty-seven patients with AVSD surgery and Doppler color MR were prospectively enrolled (median age was 5 years and 16 patients had Down syndrome). Doppler color flow imaging of the MR jet and 3-dimensional echocardiography of the mitral valve were performed with a probe in the transthoracic or transesophageal position. Enface 3-dimensional views of the mitral valve from the left atrium were reconstructed. Analysis of the 3-dimensional data was possible in 21 of the 27 patients. Mean area ratios of the 3 mitral leaflets were calculated (superior 40 +/- 7%, inferior 35 +/- 5%, mural 25 +/- 6%). Both intra and interobserver variability on the area measurements were <5%. In 12 patients (group 1) the jet appeared to emanate medially from the region of coaptation of the superior and inferior components of the anterior leaflet. In 9 patients (group 2) the jet emanated more laterally from the region toward the mural leaflet. The area ratios of the inferior leaflet were 32 +/- 4% in group 1 and 38 +/- 6% in group 2 (p = 0.02). The area ratios of the mural leaflet were 28 +/- 5% in group 1 and 21 +/- 5% in group 2 (p = 0.007). The superior leaflet area ratio was not different in groups 1 and 2, 40 +/- 9% and 41 +/- 6%, respectively. Three-dimensional echocardiography provides new insight into the anatomic determinants of MR following AVSD surgery.
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Affiliation(s)
- P Acar
- Pediatric Cardiology, Tuft-New England Medical Center, Boston, Massachusetts, USA
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Abstract
Cervical traction is administered by various techniques ranging from supine mechanical motorized cervical traction to seated cervical traction using an over-the-door pulley support with attached weights. Duration of cervical traction can range from a few minutes to 20 to 30 min, once or twice weekly to several times per day. Anecdotal evidence suggests efficacy and safety, but there is no documentation of efficacy of cervical traction beyond short-term pain reduction. Because of a clinical impression that a simplified, inexpensive, over-the-door home cervical traction method of treatment requiring 5 min of cervical traction twice daily was efficacious for both cervical pain and radiculopathic syndromes, we undertook a retrospective study of 58 outpatients treated between 1994 and 1996. Age range was 29 to 84 (mean, 56) yr. Twenty-three males and 35 females were classified as Grade 1 to Grade 3 according to the Quebec Task Force of Whiplash-Associated Disorders Cohort Study. Outcomes were as follows: Grade 1 (mild)--4 of 4 (100%) patients improved; Grade 2 (moderate)--34 of 44 (77%) patients improved (P < 0.01), 5 were unchanged, and 5 felt their symptoms were aggravated by cervical traction; Grade 3 (patients with radiculopathy)--9 of 10 (90%) patients improved (P < 0.01). In a retrospective study, a brief (3-5 min), over-the-door home cervical traction modality provided symptomatic relief in 81% of the patients with mild to moderately severe (Grade 3) cervical spondylosis syndromes. Prospective, randomized assessment of cervical traction for this and other methods is needed.
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Affiliation(s)
- R L Swezey
- Swezey Institute, Arthritis and Back Pain Center, Santa Monica, California 90403, USA
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Geller B, Cooper TB, Zimerman B, Frazier J, Williams M, Heath J, Warner K. Lithium for prepubertal depressed children with family history predictors of future bipolarity: a double-blind, placebo-controlled study. J Affect Disord 1998; 51:165-75. [PMID: 10743849 DOI: 10.1016/s0165-0327(98)00178-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Because of negative studies of TCAs for prepubertal major depressive disorder (PMDD) and because of the potentially high switch rate of PMDD to prepubertal bipolarity (BP), it was hypothesized that lithium would be efficacious treatment for PMDD in children who also had family history (FH) predictors of future BP. METHODS A double-blind, placebo-controlled, and pharmacokinetically dosed study of lithium for PMDD with FH predictors of future BP was performed. Random assignment was stratified by FH of BP-I or mania versus loaded/multigenerational (L/M) FH of MDD without BP-I or mania. Comprehensive assessments were done during a six week outpatient protocol that included weekly serum lithium levels. RESULTS Mean age was 10.7+/-1.2 years; 17 subjects were randomized to active and 13 to placebo; 80% had FH of BP-I or mania (40% of parents had BP-I or mania); and 20% had FH of L/M MDD. Using both intent to treat with last observation carried forward (n = 30) and completer (n = 24) analyses, there were no significant differences on continuous or categorical measures between active and placebo groups. Mean serum lithium level was 0.99+/-0.16 mEq/l. There were no significant differences between mean total daily dose or mean serum lithium levels between responders and non-responders. LIMITATIONS Four subjects on active drug were discontinued because of dose-limiting side effects (three were cognitive impairment). Future studies of treatment for PMDD should consider alternative drugs. CLINICAL RELEVANCE Lithium was not significantly more efficacious than placebo for PMDD with FH predictors of future BP.
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Affiliation(s)
- B Geller
- Washington University School of Medicine, St. Louis, MO 63110, USA.
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Abstract
BACKGROUND This addendum to 'Prepubertal and early adolescent bipolarity differentiate from ADHD by mania criteria; grandiose delusions; ultra-rapid or ultradian cycling' (in this volume) provides (1) a description of Washington University at St. Louis Kiddie Schedule for Affective Disorders and Schizophrenia (WASH-U-KSADS) with sample sections (hypersexuality, rapid cycling); (2) a comparison of WASH-U-KSADS to KSADS-P/L and KSADS-1986 and (3) a comparison of WASH-U-KSADS to Child Behavior Checklist (CBCL) and Teachers Report Form (TRF) data. METHODS Data were from the first 60 bipolar (BP) and first 60 ADHD subjects of 270 consecutively ascertained cases (90 BP, 90 ADHD and 90 community controls) in the NIMH funded 'Phenomenology and Course of Pediatric Bipolarity' study. Comprehensive assessments included the WASH-U-KSADS (administered blindly to mothers and separately to children), CBCL and TRF. RESULTS As reported elsewhere in this volume, WASH-U-KSADS data significantly differentiated BP and ADHD groups. Significant differences were also found with the parent-rated CBCL and the teacher-rated TRF, thereby providing cross-modality and cross-informant validation of the WASH-U-KSADS. Because of the close agreement with published CBCL data from another investigator, cross-site validation also occurred. LIMITATIONS Venues for consecutive ascertainment from the lowest socioeconomic status classes were unavailable due to current health care policies. CLINICAL RELEVANCE CBCL and TRF data separated BP from ADHD groups, largely by non-specific externalizing dimensions (e.g., hyperactivity, aggressivity). Clinically relevant differentiation by categorical mania-specific criteria (e.g., elated mood, grandiosity, racing thoughts) occurred with WASH-U-KSADS data. Both types of data are crucial for genetic and neurobiological studies.
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Affiliation(s)
- B Geller
- Washington University School of Medicine, St. Louis, MO, 63110, USA.
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Goodman MM, Clark MI, Warner K. Key-Gaskell syndrome in three cats. Vet Rec 1998; 143:428. [PMID: 9807798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Hijazi ZM, Patel H, Cao QL, Warner K. Transcatheter retrograde radio-frequency perforation of the pulmonic valve in pulmonary atresia with intact ventricular septum, using a 2 French catheter. Cathet Cardiovasc Diagn 1998; 45:151-4. [PMID: 9786393 DOI: 10.1002/(sici)1097-0304(199810)45:2<151::aid-ccd10>3.0.co;2-o] [Citation(s) in RCA: 13] [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] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A neonate with pulmonary atresia with intact ventricular septum (PA/IVS) underwent successful retrograde transcatheter perforation of the pulmonary valve, using a 2 Fr radio-frequency catheter with subsequent anterograde balloon dilation of the valve. Due to persistent hypoxemia, the neonate underwent placement of a 4-mm modified Blalock-Taussig shunt. Transcatheter retrograde transductal perforation of the pulmonic valve in PA/IVS is feasible and may be a potential alternative to anterograde perforation.
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Affiliation(s)
- Z M Hijazi
- Department of Pediatrics, Floating Hospital for Children at New England Medical Center, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.
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Warner K, Garcia J, Oldknow M, Provine K, Lucero J. The Doña Ana County experience: systems of care in a managed care environment. Behav Healthc Tomorrow 1997; 6:42-6. [PMID: 10177346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- K Warner
- Office of Managed Care Services, New Mexico Children, Youth and Families Department, USA
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Abstract
A previously healthy, 31-year-old man was evaluated in the emergency department after being violently assaulted. A harsh, continuous murmur was noted on physical examination. Transthoracic and transesophageal echocardiograms were interpreted as showing a ruptured sinus of Valsalva aneurysm with a shunt into the right atrium and a tricuspid valve vegetation. The patient was treated with antibiotics for presumed endocarditis. Subsequent echocardiographic and surgical evaluation showed no evidence of past or present endocarditis. Rather, the sinus of Valsalva aneurysm and rupture gave the appearance of a valvular mass. This report shows some of the potential pitfalls in the delineation of abnormalities related to sinus of Valsalva aneurysms and rupture.
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Affiliation(s)
- J Kuvin
- Cardiovascular Imaging and Hemodynamic Laboratory, New England Medical Center, Tufts University School of Medicine, Boston, MA 02111, USA
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Affiliation(s)
- K. Warner
- Food Quality and Safety Research; NCAUR, ARS, USDA; Peoria Illinois 61604
| | - P. Orr
- Red River Valley Potato Research Laboratory; ARS, USDA; East Grand Forks Minnesota 56721
| | - M. Glynn
- Red River Valley Potato Research Laboratory; ARS, USDA; East Grand Forks Minnesota 56721
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Warner K, Adlof R. . Trends Food Sci Technol 1996; 7:275-276. [DOI: 10.1016/0924-2244(96)81205-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Miller DS, Schwartz SL, Geggel RL, Smith JJ, Warner K, Pandian NG. Detection of partial anomalous right pulmonary venous return with an intact atrial septum by transesophageal echocardiography. J Am Soc Echocardiogr 1995; 8:924-7. [PMID: 8611293 DOI: 10.1016/s0894-7317(05)80017-3] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Partial anomalous pulmonary venous drainage with intact atrial septum is a rare congenital anomaly. We report a case of a 63-year-old woman who recently had dyspnea on minimal exertion and was found to have pulmonary hypertension, right atrial enlargement, and right ventricular enlargement by two-dimensional transthoracic echocardiography. Transesophageal echocardiography demonstrated anomalous venous drainage of the right lung into the superior vena cava with an intact interatrial septum. This diagnosis was confirmed by angiography and the patient underwent successful repair. This case illustrates the importance of locating all four pulmonary veins in patients with pulmonary hypertension or suspected intracardiac shunt in addition to scanning the atrial septum.
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Affiliation(s)
- D S Miller
- Division of Cardiology, Tufts University School of Medicine, New England Medical Center Hospitals, Boston, MA, USA
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Peck DL, Warner K. Accident or suicide? Single-vehicle car accidents and the intent hypothesis. Adolescence 1995; 30:463-472. [PMID: 7676880] [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: 05/21/2023]
Abstract
Brief case studies of single-vehicle crashes are used to explore the relationship between this method of death and the intent to suicide. The concept of parasuicide guides this investigation and the data reported suggest that the hypothesized relationship may be valid. The authors conclude with a discussion of implications involving this mode of behavior.
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Affiliation(s)
- D L Peck
- University of Alabama, Tuscaloosa 35487-0320, USA
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Warner K, Beamish JR. Frequency dependence of sound propagation in superfluid-filled porous media. Phys Rev B Condens Matter 1994; 50:15896-15908. [PMID: 9975959 DOI: 10.1103/physrevb.50.15896] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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