30 results
Whole-genome sequencing for methicillin-resistant Staphylococcus aureus (MRSA) outbreak investigation in a neonatal intensive care unit
- Theresa Madigan, Scott A. Cunningham, Robin Patel, Kerryl E. Greenwood-Quaintance, Jean E. Barth, Priya Sampathkumar, Nicolynn C. Cole, Peggy C. Kohner, Christopher E. Colby, Garth F. Asay, Jennifer L. Fang, Christine A. Baker, Angela L. Heinrich, Kelly A. Fjerstad, Maria J. Lujero, Nicholas Chia, Patricio R. Jeraldo, Heidi Nelson, W. Charles Huskins
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 39 / Issue 12 / December 2018
- Published online by Cambridge University Press:
- 04 October 2018, pp. 1412-1418
- Print publication:
- December 2018
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Objective
To evaluate whole-genome sequencing (WGS) as a molecular typing tool for MRSA outbreak investigation.
DesignInvestigation of MRSA colonization/infection in a neonatal intensive care unit (NICU) over 3 years (2014–2017).
SettingSingle-center level IV NICU.
PatientsNICU infants and healthcare workers (HCWs).
MethodsInfants were screened for MRSA using a swab of the anterior nares, axilla, and groin, initially by targeted (ring) screening, and later by universal weekly screening. Clinical cultures were collected as indicated. HCWs were screened once using swabs of the anterior nares. MRSA isolates were typed using WGS with core-genome multilocus sequence typing (cgMLST) analysis and by pulsed-field gel electrophoresis (PFGE). Colonized and infected infants and HCWs were decolonized. Control strategies included reinforcement of hand hygiene, use of contact precautions, cohorting, enhanced environmental cleaning, and remodeling of the NICU.
ResultsWe identified 64 MRSA-positive infants: 53 (83%) by screening and 11 (17%) by clinical cultures. Of 85 screened HCWs, 5 (6%) were MRSA positive. WGS of MRSA isolates identified 2 large clusters (WGS groups 1 and 2), 1 small cluster (WGS group 3), and 8 unrelated isolates. PFGE failed to distinguish WGS group 2 and 3 isolates. WGS groups 1 and 2 were codistributed over time. HCW MRSA isolates were primarily in WGS group 1. New infant MRSA cases declined after implementation of the control interventions.
ConclusionWe identified 2 contemporaneous MRSA outbreaks alongside sporadic cases in a NICU. WGS was used to determine strain relatedness at a higher resolution than PFGE and was useful in guiding efforts to control MRSA transmission.
A study of a long-spacing mica-like mineral
- W. F. Cole
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- Journal:
- Clay Minerals / Volume 6 / Issue 4 / December 1966
- Published online by Cambridge University Press:
- 09 July 2018, pp. 261-281
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An interstratified clay mineral from Surges Bay, Tasmania, described by Cole & Carthew (1953) as containing a random stacking of illite and montmorillonite in the ratio of 3:2 and a regular stacking of illite and montmorillonite in the ratio of 1 : 1 is re-examined, after purification, and a new interpretation is made of the X-ray diffraction effects in terms of a single complex stacking model. The Fourier transform method of analysis used with an appropriate layer structure factor shows that the interstratification is produced by a three component stacking of 18% single mica layers (A), 10% double mica layers (ĀĀ) and 72% allevardite-like layers (ĀB̄) in which the A and ĀĀ layers are never together. This leads to the conclusion that the near regular interstratification of the mineral is due to structural and/or compositional variation from layer to layer within the parent crystals as suggested by Sudo, Hayashi & Shimoda (1962) to explain similar mineral types occurring in Japan.
On the characterization of ceramic clays
- W. F. Cole, C. J. Lancucki, D. A. Powell
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- Journal:
- Clay Minerals / Volume 9 / Issue 1 / July 1971
- Published online by Cambridge University Press:
- 09 July 2018, pp. 35-46
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Ceramic clays are characterized by a method that stems from the IL/MA procedure proposed by Keeling (1958a, b) but which is more rapid to perform and more basic in concept. By thermogravimetric methods an estimate is made of both OH water and interlayer plus physically adsorbed water. These are plotted against each other in a manner similar to the IL/MA plot. The composition of the clay can be characterized uniquely on such a diagram by estimating either the quartz or the free silica contents of a sample, its silt, and < 2μ fraction, and plotting for each on a 100% clay basis their OH water, and interlayer and physically adsorbed water. Simple methods are given for assessing these factors. The determination of interlayer water content could form the basis of a method of plant control of clay composition in a way similar to that proposed by Keeling using moisture adsorption determinations.
Family environments and leukocyte transcriptome indicators of a proinflammatory phenotype in children and parents
- Theodore F. Robles, Rena L. Repetti, Bridget M. Reynolds, Paul J. Chung, Jesusa M. G. Arevalo, Steven W. Cole
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- Journal:
- Development and Psychopathology / Volume 30 / Issue 1 / February 2018
- Published online by Cambridge University Press:
- 30 May 2017, pp. 235-253
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High conflict and low warmth in families may contribute to immune cells developing a tendency to respond to threats with exaggerated inflammation that is insensitive to inhibitory signaling. We tested associations between family environments and expression of genes bearing response elements for transcription factors that regulate inflammation: nuclear factor kappa B (NF-κB) and glucocorticoid receptor. The overall sample (47 families) completed interviews, questionnaires, and 8-week daily diary assessments of conflict and warmth, which were used to create composite family conflict and warmth scores. The diaries assessed upper respiratory infection (URI) symptoms, and URI episodes were clinically verified. Leukocyte RNA was extracted from whole blood samples provided by a subsample of 42 children (8–13 years of age) and 73 parents. In children, higher conflict and lower warmth were related to greater expression of genes bearing response elements for the proinflammatory transcription factor NF-κB, and more severe URI symptoms. In parents, higher conflict and lower warmth were also related to greater NF-κB–associated gene expression. Monocytes and dendritic cells were implicated as primary cellular sources of differential gene expression in the sample. Consistent with existing conceptual frameworks, stressful family environments were related to a proinflammatory phenotype at the level of the circulating leukocyte transcriptome.
Depression and the risk of autoimmune disease: a nationally representative, prospective longitudinal study
- N. W. Andersson, L. N. Gustafsson, N. Okkels, F. Taha, S. W. Cole, P. Munk-Jørgensen, R. D. Goodwin
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- Journal:
- Psychological Medicine / Volume 45 / Issue 16 / December 2015
- Published online by Cambridge University Press:
- 14 August 2015, pp. 3559-3569
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Background.
Autoimmune diseases are associated with substantial morbidity and mortality, yet the etiology remains unclear. Depression has been implicated as a risk factor for various immune-related disorders but little is known about the risk of autoimmune disease. This study examined the association between depression and the risk of autoimmune disease, and investigated the temporal and dose-response nature of these relationships.
Method.A prospective population-based study including approximately 1.1 million people was conducted using linked Danish registries. Depression and autoimmune diseases were diagnosed by physicians and documented in medical records. In total, 145 217 individuals with depression were identified between 1995 and 2012. Survival analyses were used to estimate the relative risk of autoimmune disease among those with, compared to without, depression. Analyses were adjusted for gender, age, and co-morbid mental disorders.
Results.Depression was associated with a significantly increased risk of autoimmune disease [incidence rate ratio (IRR) 1.25, 95% CI 1.19–1.31], compared to those without a history of depression. Results suggest a general increased risk of autoimmune diseases following the onset of depression during first year (IRR 1.29, 95% CI 1.05–1.58), which remained elevated for the ensuing 11 years and beyond (IRR 1.53, 95% CI 1.34–1.76). Findings did not support a dose-response relationship.
Conclusions.Depression appears to be associated with an increased risk of a range of autoimmune diseases. Depression may play a role in the etiology of certain autoimmune conditions. If replicated, findings could highlight additional clinical implications in the treatment and management of depression. Future studies are needed to investigate the possible social, genetic, and neurobiological underpinnings of these relationships.
Gravitational-Wave Detection Using Pulsars: Status of the Parkes Pulsar Timing Array Project
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- G. B. Hobbs, M. Bailes, N. D. R. Bhat, S. Burke-Spolaor, D. J. Champion, W. Coles, A. Hotan, F. Jenet, L. Kedziora-Chudczer, J. Khoo, K. J. Lee, A. Lommen, R. N. Manchester, J. Reynolds, J. Sarkissian, W. van Straten, S. To, J. P. W. Verbiest, D. Yardley, X. P. You
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- Journal:
- Publications of the Astronomical Society of Australia / Volume 26 / Issue 2 / 2009
- Published online by Cambridge University Press:
- 05 March 2013, pp. 103-109
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The first direct detection of gravitational waves may be made through observations of pulsars. The principal aim of pulsar timing-array projects being carried out worldwide is to detect ultra-low frequency gravitational waves (f ∼ 10−9–10−8 Hz). Such waves are expected to be caused by coalescing supermassive binary black holes in the cores of merged galaxies. It is also possible that a detectable signal could have been produced in the inflationary era or by cosmic strings. In this paper, we review the current status of the Parkes Pulsar Timing Array project (the only such project in the Southern hemisphere) and compare the pulsar timing technique with other forms of gravitational-wave detection such as ground- and space-based interferometer systems.
The Parkes Pulsar Timing Array Project
- R. N. Manchester, G. Hobbs, M. Bailes, W. A. Coles, W. van Straten, M. J. Keith, R. M. Shannon, N. D. R. Bhat, A. Brown, S. G. Burke-Spolaor, D. J. Champion, A. Chaudhary, R. T. Edwards, G. Hampson, A. W. Hotan, A. Jameson, F. A. Jenet, M. J. Kesteven, J. Khoo, J. Kocz, K. Maciesiak, S. Oslowski, V. Ravi, J. R. Reynolds, J. M. Sarkissian, J. P. W. Verbiest, Z. L. Wen, W. E. Wilson, D. Yardley, W. M. Yan, X. P. You
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- Journal:
- Publications of the Astronomical Society of Australia / Volume 30 / 2013
- Published online by Cambridge University Press:
- 24 January 2013, e017
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A ‘pulsar timing array’ (PTA), in which observations of a large sample of pulsars spread across the celestial sphere are combined, allows investigation of ‘global’ phenomena such as a background of gravitational waves or instabilities in atomic timescales that produce correlated timing residuals in the pulsars of the array. The Parkes Pulsar Timing Array (PPTA) is an implementation of the PTA concept based on observations with the Parkes 64-m radio telescope. A sample of 20 ms pulsars is being observed at three radio-frequency bands, 50 cm (~700 MHz), 20 cm (~1400 MHz), and 10 cm (~3100 MHz), with observations at intervals of two to three weeks. Regular observations commenced in early 2005. This paper describes the systems used for the PPTA observations and data processing, including calibration and timing analysis. The strategy behind the choice of pulsars, observing parameters, and analysis methods is discussed. Results are presented for PPTA data in the three bands taken between 2005 March and 2011 March. For 10 of the 20 pulsars, rms timing residuals are less than 1 μs for the best band after fitting for pulse frequency and its first time derivative. Significant ‘red’ timing noise is detected in about half of the sample. We discuss the implications of these results on future projects including the International Pulsar Timing Array and a PTA based on the Square Kilometre Array. We also present an ‘extended PPTA’ data set that combines PPTA data with earlier Parkes timing data for these pulsars.
Evaluation of Potential Environmental Contamination Sources for the Presence of Multidrug-Resistant Bacteria Linked to Wound Infections in Combat Casualties
- Edward F. Keen III, Katrin Mende, Heather C. Yun, Wade K. Aldous, Timothy E. Wallum, Charles H. Guymon, David W. Cole, Helen K. Crouch, Matthew E. Griffith, Bernadette L. Thompson, Joel T. Rose, Clinton K. Murray
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 33 / Issue 9 / September 2012
- Published online by Cambridge University Press:
- 02 January 2015, pp. 905-911
- Print publication:
- September 2012
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Objective.
To determine whether multidrug-resistant (MDR) gram-negative organisms are present in Afghanistan or Iraq soil samples, contaminate standard deployed hospital or modular operating rooms (ORs), or aerosolize during surgical procedures.
Design.Active surveillance.
Setting.US military hospitals in the United States, Afghanistan, and Iraq.
Methods.Soil samples were collected from sites throughout Afghanistan and Iraq and analyzed for presence of MDR bacteria. Environmental sampling of selected newly established modular and deployed OR high-touch surfaces and equipment was performed to determine the presence of bacterial contamination. Gram-negative bacteria aerosolization during OR surgical procedures was determined by microbiological analysis of settle plate growth.
Results.Subsurface soil sample isolates recovered in Afghanistan and Iraq included various pansusceptible members of Enterobacteriaceae, Vibrio species, Pseudomonas species, Acinetobacter Iwojfii, and coagulase-negative Staphylococcus (CNS). OR contamination studies in Afghanistan revealed 1 surface with a Micrococcus luteus. Newly established US-based modular ORs and the colocated fixed-facility ORs revealed no gram-negative bacterial contamination prior to the opening of the modular OR and 5 weeks later. Bacterial aerosolization during surgery in a deployed fixed hospital revealed a mean gram-negative bacteria colony count of 12.8 colony-forming units (CFU)/dm2/h (standard deviation [SD], 17.0) during surgeries and 6.5 CFU/dm2/h (SD, 7.5; P = .14) when the OR was not in use.
Conclusion.This study demonstrates no significant gram-negative bacilli colonization of modular and fixed-facility ORs or dirt and no significant aerosolization of these bacilli during surgical procedures. These results lend additional support to the role of nosocomial transmission of MDR pathogens or the colonization of the patient themselves prior to injury.
Molecular signatures of peripheral blood mononuclear cells during chronic interferon-α treatment: relationship with depression and fatigue
- J. C. Felger, S. W. Cole, T. W. W. Pace, F. Hu, B. J. Woolwine, G. H. Doho, C. L. Raison, A. H. Miller
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- Journal:
- Psychological Medicine / Volume 42 / Issue 8 / August 2012
- Published online by Cambridge University Press:
- 09 December 2011, pp. 1591-1603
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Background
Interferon-alpha (IFN-α) treatment for infectious disease and cancer causes high rates of depression and fatigue, and has been used to investigate the impact of inflammatory cytokines on brain and behavior. However, little is known about the transcriptional impact of chronic IFN-α on immune cells in vivo and its relationship to IFN-α-induced behavioral changes.
MethodGenome-wide transcriptional profiling was performed on peripheral blood mononuclear cells (PBMCs) from 21 patients with chronic hepatitis C virus (HCV) either awaiting IFN-α therapy (n=10) or at 12 weeks of IFN-α treatment (n=11).
ResultsSignificance analysis of microarray data identified 252 up-regulated and 116 down-regulated gene transcripts. Of the up-regulated genes, 2′-5′-oligoadenylate synthetase 2 (OAS2), a gene linked to chronic fatigue syndrome (CFS), was the only gene that was differentially expressed in patients with IFN-α-induced depression/fatigue, and correlated with depression and fatigue scores at 12 weeks (r=0.80, p=0.003 and r=0.70, p=0.017 respectively). Promoter-based bioinformatic analyses linked IFN-α-related transcriptional alterations to transcription factors involved in myeloid differentiation, IFN-α signaling, activator protein-1 (AP1) and cAMP responsive element binding protein/activation transcription factor (CREB/ATF) pathways, which were derived primarily from monocytes and plasmacytoid dendritic cells. IFN-α-treated patients with high depression/fatigue scores demonstrated up-regulation of genes bearing promoter motifs for transcription factors involved in myeloid differentiation, IFN-α and AP1 signaling, and reduced prevalence of motifs for CREB/ATF, which has been implicated in major depression.
ConclusionsDepression and fatigue during chronic IFN-α administration were associated with alterations in the expression (OAS2) and transcriptional control (CREB/ATF) of genes linked to behavioral disorders including CFS and major depression, further supporting an immune contribution to these diseases.
Contributors
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- By Douglas L. Arnold, Laura J. Balcer, Amit Bar-Or, Sergio E. Baranzini, Frederik Barkhof, Robert A. Bermel, Francois A. Bethoux, Dennis N. Bourdette, Richard K. Burt, Peter A. Calabresi, Zografos Caramanos, Tanuja Chitnis, Stacey S. Cofield, Jeffrey A. Cohen, Nadine Cohen, Alasdair J. Coles, Devon Conway, Stuart D. Cook, Gary R. Cutter, Peter J. Darlington, Ann Dodds-Frerichs, Ranjan Dutta, Gilles Edan, Michelle Fabian, Franz Fazekas, Massimo Filippi, Elizabeth Fisher, Paulo Fontoura, Corey C. Ford, Robert J. Fox, Natasha Frost, Alex Z. Fu, Siegrid Fuchs, Kazuo Fujihara, Kristin M. Galetta, Jeroen J.G. Geurts, Gavin Giovannoni, Nada Gligorov, Ralf Gold, Andrew D. Goodman, Myla D. Goldman, Jenny Guerre, Stephen L. Hauser, Peter B. Imrey, Douglas R. Jeffery, Stephen E. Jones, Adam I. Kaplin, Michael W. Kattan, B. Mark Keegan, Kyle C. Kern, Zhaleh Khaleeli, Samia J. Khoury, Joep Killestein, Soo Hyun Kim, R. Philip Kinkel, Stephen C. Krieger, Lauren B. Krupp, Emmanuelle Le Page, David Leppert, Scott Litwiller, Fred D. Lublin, Henry F. McFarland, Joseph C. McGowan, Don Mahad, Jahangir Maleki, Ruth Ann Marrie, Paul M. Matthews, Francesca Milanetti, Aaron E. Miller, Deborah M. Miller, Xavier Montalban, Charity J. Morgan, Ichiro Nakashima, Sridar Narayanan, Avindra Nath, Paul W. O’Connor, Jorge R. Oksenberg, A. John Petkau, Michael D. Phillips, J. Theodore Phillips, Tammy Phinney, Sean J. Pittock, Sarah M. Planchon, Chris H. Polman, Alexander Rae-Grant, Stephen M. Rao, Stephen C. Reingold, Maria A. Rocca, Richard A. Rudick, Amber R. Salter, Paula Sandler, Jaume Sastre-Garriga, John R. Scagnelli, Dana J. Serafin, Lynne Shinto, Nancy L. Sicotte, Jack H. Simon, Per Soelberg Sørensen, Ryan E. Stagg, James M. Stankiewicz, Lael A. Stone, Amy Sullivan, Matthew Sutliff, Jessica Szpak, Alan J. Thompson, Bruce D. Trapp, Helen Tremlett, Maria Trojano, Orla Tuohy, Rhonda R. Voskuhl, Marc K. Walton, Mike P. Wattjes, Emmanuelle Waubant, Martin S. Weber, Howard L Weiner, Brian G. Weinshenker, Bianca Weinstock-Guttman, Jeffrey L. Winters, Jerry S. Wolinsky, Vijayshree Yadav, E. Ann Yeh, Scott S. Zamvil
- Edited by Jeffrey A. Cohen, Richard A. Rudick
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- Book:
- Multiple Sclerosis Therapeutics
- Published online:
- 05 December 2011
- Print publication:
- 20 October 2011, pp viii-xii
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- By Antony R. Absalom, Lorenz Breuer, Christoph S. Burkhart, Rowan M. Burnstein, Ian Calder, Jonathan P. Coles, Amanda Cox, Marek Czosnyka, Armagan Dagal, Judith Dinsmore, Derek Duane, Kristin Engelhard, Ari Ercole, Rik Fox, Sabrina G. Galloway, Arnab Ghosh, Arun K. Gupta, Nicholas Hirsch, Robin Howard, Peter Hutchinson, Nicole C. Keong, Martin Köhrmann, Arthur M. Lam, Andrea Lavinio, Brian P. Lemkuil, Luca Longhi, Craig D. McClain, Robert Macfarlane, Basil F. Matta, Stephan A. Mayer, David K. Menon, Andrew W. Michell, Dick Moberg, Paul G. Murphy, Clara Poon, Amit Prakash, Frank Rasulo, Fred Rincon, Stefan Schwab, Martin Smith, Sulpicio G. Soriano, Luzius A. Steiner, Nino Stocchetti, Stephan P. Strebel, Jane Sturgess, Magnus Teig, Tonny Veenith, Christian Werner, Christian Zweifel
- Edited by Basil F. Matta, David K. Menon, Martin Smith
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- Book:
- Core Topics in Neuroanaesthesia and Neurointensive Care
- Published online:
- 05 December 2011
- Print publication:
- 13 October 2011, pp vii-x
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- By Jane E. Adcock, Yahya Aghakhani, A. Anand, Eva Andermann, Frederick Andermann, Alexis Arzimanoglou, Sandrine Aubert, Nadia Bahi-Buisson, Carman Barba, Agatino Battaglia, Geneviève Bernard, Nadir E. Bharucha, Laurence A. Bindoff, William Bingaman, Francesca Bisulli, Thomas P. Bleck, Stewart G. Boyd, Andreas Brunklaus, Harry Bulstrode, Jorge G. Burneo, Laura Canafoglia, Laura Cantonetti, Roberto H. Caraballo, Fernando Cendes, Kevin E. Chapman, Patrick Chauvel, Richard F. M. Chin, H. T. Chong, Fahmida A. Chowdhury, Catherine J. Chu-Shore, Rolando Cimaz, Andrew J. Cole, Bernard Dan, Geoffrey Dean, Alessio De Ciantis, Fernando De Paolis, Rolando F. Del Maestro, Irissa M. Devine, Carlo Di Bonaventura, Concezio Di Rocco, Henry B. Dinsdale, Maria Alice Donati, François Dubeau, Michael Duchowny, Olivier Dulac, Monika Eisermann, Brent Elliott, Bernt A. Engelsen, Kevin Farrell, Natalio Fejerman, Rosalie E. Ferner, Silvana Franceschetti, Robert Friedlander, Antonio Gambardella, Hector H. Garcia, Serena Gasperini, Lorenzo Genitori, Gioia Gioi, Flavio Giordano, Leif Gjerstad, Daniel G. Glaze, Howard P. Goodkin, Sidney M. Gospe, Andrea Grassi, William P. Gray, Renzo Guerrini, Marie-Christine Guiot, William Harkness, Andrew G. Herzog, Linda Huh, Margaret J. Jackson, Thomas S. Jacques, Anna C. Jansen, Sigmund Jenssen, Michael R. Johnson, Dorothy Jones-Davis, Reetta Kälviäinen, Peter W. Kaplan, John F. Kerrigan, Autumn Marie Klein, Matthias Koepp, Edwin H. Kolodny, Kandan Kulandaivel, Ruben I. Kuzniecky, Ahmed Lary, Yolanda Lau, Anna-Elina Lehesjoki, Maria K. Lehtinen, Holger Lerche, Michael P. T. Lunn, Snezana Maljevic, Mark R. Manford, Carla Marini, Bindu Menon, Giulia Milioli, Eli M. Mizrahi, Manish Modi, Márcia Elisabete Morita, Manuel Murie-Fernandez, Vivek Nambiar, Lina Nashef, Vincent Navarro, Aidan Neligan, Ruth E. Nemire, Charles R. J. C. Newton, John O'Donavan, Hirokazu Oguni, Teiichi Onuma, Andre Palmini, Eleni Panagiotakaki, Pasquale Parisi, Elena Parrini, Liborio Parrino, Ignacio Pascual-Castroviejo, M. Scott Perry, Perrine Plouin, Charles E. Polkey, Suresh S. Pujar, Karthik Rajasekaran, R. Eugene Ramsey, Rahul Rathakrishnan, Roberta H. Raven, Guy M. Rémillard, David Rosenblatt, M. Elizabeth Ross, Abdulrahman Sabbagh, P. Satishchandra, Swati Sathe, Ingrid E. Scheffer, Philip A. Schwartzkroin, Rod C. Scott, Frédéric Sedel, Michelle J. Shapiro, Elliott H. Sherr, Michael Shevell, Simon D. Shorvon, Adrian M. Siegel, Gagandeep Singh, S. Sinha, Barbara Spacca, Waney Squier, Carl E. Stafstrom, Bernhard J. Steinhoff, Andrea Taddio, Gianpiero Tamburrini, C. T. Tan, Raymond Y. L. Tan, Erik Taubøll, Robert W. Teasell, Mario Giovanni Terzano, Federica Teutonico, Suzanne A. Tharin, Elizabeth A. Thiele, Pierre Thomas, Paolo Tinuper, Dorothée Kasteleijn-Nolst Trenité, Sumeet Vadera, Pierangelo Veggiotti, Jean-Pierre Vignal, J. M. Walshe, Elizabeth J. Waterhouse, David Watkins, Ruth E. Williams, Yue-Hua Zhang, Benjamin Zifkin, Sameer M. Zuberi
- Edited by Simon D. Shorvon, Frederick Andermann, Renzo Guerrini
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- The Causes of Epilepsy
- Published online:
- 05 March 2012
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- 14 April 2011, pp ix-xvi
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Quality Assurance Testing for Modern Optical Imaging Systems
- Robert F. Stack, Carol J. Bayles, Anne-Marie Girard, Karen Martin, Cynthia Opansky, Katherine Schulz, Richard W. Cole
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- Journal:
- Microscopy and Microanalysis / Volume 17 / Issue 4 / August 2011
- Published online by Cambridge University Press:
- 11 April 2011, pp. 598-606
- Print publication:
- August 2011
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The days of being able to ascertain instrument performance by simply peering through the eye pieces at a specimen are gone. However, users and granting agencies need to be confident that data collected on these instruments is uniform and quantifiable both over time and between instruments. Ideally, a LASER should not fluctuate, illumination should be completely uniform, and colors should be perfectly aligned. To check the current performance of imaging equipment, we conducted a worldwide research study utilizing three image-based tests: long-/short-term illumination stability, co-registration of signals across various wavelengths, and field illumination uniformity. To differentiate between “acceptable” and “unacceptable” performance, the deviation in illumination power could not exceed 10% (long term) or 3% (short term), the difference in the center-of-mass of imaged multicolored beads could not exceed >1 pixel between different wavelengths, and field illumination values could not exceed 10% (horizontal) or 20% (diagonal) deviation. This study established the current state of microscope performance through simple, efficient, and robust tests, while defining relative standards to assist cores in maintaining their instruments in optimal operating conditions. We developed cross-platform performance standards that will improve the validity of quantitative measurements made using various light microscopes.
Contributors
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- By Rose Teteki Abbey, K. C. Abraham, David Tuesday Adamo, LeRoy H. Aden, Efrain Agosto, Victor Aguilan, Gillian T. W. Ahlgren, Charanjit Kaur AjitSingh, Dorothy B E A Akoto, Giuseppe Alberigo, Daniel E. Albrecht, Ruth Albrecht, Daniel O. Aleshire, Urs Altermatt, Anand Amaladass, Michael Amaladoss, James N. Amanze, Lesley G. Anderson, Thomas C. Anderson, Victor Anderson, Hope S. Antone, María Pilar Aquino, Paula Arai, Victorio Araya Guillén, S. Wesley Ariarajah, Ellen T. Armour, Brett Gregory Armstrong, Atsuhiro Asano, Naim Stifan Ateek, Mahmoud Ayoub, John Alembillah Azumah, Mercedes L. García Bachmann, Irena Backus, J. Wayne Baker, Mieke Bal, Lewis V. Baldwin, William Barbieri, António Barbosa da Silva, David Basinger, Bolaji Olukemi Bateye, Oswald Bayer, Daniel H. Bays, Rosalie Beck, Nancy Elizabeth Bedford, Guy-Thomas Bedouelle, Chorbishop Seely Beggiani, Wolfgang Behringer, Christopher M. Bellitto, Byard Bennett, Harold V. Bennett, Teresa Berger, Miguel A. Bernad, Henley Bernard, Alan E. Bernstein, Jon L. Berquist, Johannes Beutler, Ana María Bidegain, Matthew P. Binkewicz, Jennifer Bird, Joseph Blenkinsopp, Dmytro Bondarenko, Paulo Bonfatti, Riet en Pim Bons-Storm, Jessica A. Boon, Marcus J. Borg, Mark Bosco, Peter C. Bouteneff, François Bovon, William D. Bowman, Paul S. Boyer, David Brakke, Richard E. Brantley, Marcus Braybrooke, Ian Breward, Ênio José da Costa Brito, Jewel Spears Brooker, Johannes Brosseder, Nicholas Canfield Read Brown, Robert F. Brown, Pamela K. Brubaker, Walter Brueggemann, Bishop Colin O. Buchanan, Stanley M. Burgess, Amy Nelson Burnett, J. Patout Burns, David B. Burrell, David Buttrick, James P. Byrd, Lavinia Byrne, Gerado Caetano, Marcos Caldas, Alkiviadis Calivas, William J. Callahan, Salvatore Calomino, Euan K. Cameron, William S. Campbell, Marcelo Ayres Camurça, Daniel F. Caner, Paul E. Capetz, Carlos F. Cardoza-Orlandi, Patrick W. Carey, Barbara Carvill, Hal Cauthron, Subhadra Mitra Channa, Mark D. Chapman, James H. Charlesworth, Kenneth R. Chase, Chen Zemin, Luciano Chianeque, Philip Chia Phin Yin, Francisca H. Chimhanda, Daniel Chiquete, John T. Chirban, Soobin Choi, Robert Choquette, Mita Choudhury, Gerald Christianson, John Chryssavgis, Sejong Chun, Esther Chung-Kim, Charles M. A. Clark, Elizabeth A. Clark, Sathianathan Clarke, Fred Cloud, John B. Cobb, W. Owen Cole, John A Coleman, John J. Collins, Sylvia Collins-Mayo, Paul K. Conkin, Beth A. Conklin, Sean Connolly, Demetrios J. Constantelos, Michael A. Conway, Paula M. Cooey, Austin Cooper, Michael L. Cooper-White, Pamela Cooper-White, L. William Countryman, Sérgio Coutinho, Pamela Couture, Shannon Craigo-Snell, James L. Crenshaw, David Crowner, Humberto Horacio Cucchetti, Lawrence S. Cunningham, Elizabeth Mason Currier, Emmanuel Cutrone, Mary L. Daniel, David D. Daniels, Robert Darden, Rolf Darge, Isaiah Dau, Jeffry C. Davis, Jane Dawson, Valentin Dedji, John W. de Gruchy, Paul DeHart, Wendy J. 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Lotz, Andrew Louth, Robin W. Lovin, William Luis, Frank D. Macchia, Diarmaid N. J. MacCulloch, Kirk R. MacGregor, Marjory A. MacLean, Donald MacLeod, Tomas S. Maddela, Inge Mager, Laurenti Magesa, David G. Maillu, Fortunato Mallimaci, Philip Mamalakis, Kä Mana, Ukachukwu Chris Manus, Herbert Robinson Marbury, Reuel Norman Marigza, Jacqueline Mariña, Antti Marjanen, Luiz C. L. Marques, Madipoane Masenya (ngwan'a Mphahlele), Caleb J. D. Maskell, Steve Mason, Thomas Massaro, Fernando Matamoros Ponce, András Máté-Tóth, Odair Pedroso Mateus, Dinis Matsolo, Fumitaka Matsuoka, John D'Arcy May, Yelena Mazour-Matusevich, Theodore Mbazumutima, John S. McClure, Christian McConnell, Lee Martin McDonald, Gary B. McGee, Thomas McGowan, Alister E. McGrath, Richard J. McGregor, John A. McGuckin, Maud Burnett McInerney, Elsie Anne McKee, Mary B. McKinley, James F. McMillan, Ernan McMullin, Kathleen E. McVey, M. 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Phan, Isabel Apawo Phiri, William S. F. Pickering, Derrick G. Pitard, William Elvis Plata, Zlatko Plese, John Plummer, James Newton Poling, Ronald Popivchak, Andrew Porter, Ute Possekel, James M. Powell, Enos Das Pradhan, Devadasan Premnath, Jaime Adrían Prieto Valladares, Anne Primavesi, Randall Prior, María Alicia Puente Lutteroth, Eduardo Guzmão Quadros, Albert Rabil, Laurent William Ramambason, Apolonio M. Ranche, Vololona Randriamanantena Andriamitandrina, Lawrence R. Rast, Paul L. Redditt, Adele Reinhartz, Rolf Rendtorff, Pål Repstad, James N. Rhodes, John K. Riches, Joerg Rieger, Sharon H. Ringe, Sandra Rios, Tyler Roberts, David M. Robinson, James M. Robinson, Joanne Maguire Robinson, Richard A. H. Robinson, Roy R. Robson, Jack B. Rogers, Maria Roginska, Sidney Rooy, Rev. Garnett Roper, Maria José Fontelas Rosado-Nunes, Andrew C. Ross, Stefan Rossbach, François Rossier, John D. Roth, John K. Roth, Phillip Rothwell, Richard E. 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Yee, Viktor Yelensky, Yeo Khiok-Khng, Gustav K. K. Yeung, Angela Yiu, Amos Yong, Yong Ting Jin, You Bin, Youhanna Nessim Youssef, Eliana Yunes, Robert Michael Zaller, Valarie H. Ziegler, Barbara Brown Zikmund, Joyce Ann Zimmerman, Aurora Zlotnik, Zhuo Xinping
- Edited by Daniel Patte, Vanderbilt University, Tennessee
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- The Cambridge Dictionary of Christianity
- Published online:
- 05 August 2012
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- 20 September 2010, pp xi-xliv
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Susceptibility to praziquantel of male and female cercariae of praziquantel-resistant and susceptible isolates of Schistosoma mansoni
- Y.-S. Liang, W. Wang, J.-R. Dai, H.-J. Li, Y.-H. Tao, J.-F. Zhang, W. Li, Y.-C. Zhu, G.C. Coles, M.J. Doenhoff
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- Journal:
- Journal of Helminthology / Volume 84 / Issue 2 / June 2010
- Published online by Cambridge University Press:
- 18 September 2009, pp. 202-207
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Praziquantel (PZQ) is now widely used for the treatment of human schistosomiasis. However, in recent years, there has been a growing concern about the resistance of Schistosoma to PZQ. The mechanisms of PZQ action against Schistosoma and resistance of Schistosoma to PZQ are poorly understood. Here, we report differential susceptibilities to PZQ between male and female cercariae in the PZQ-susceptible and PZQ-resistant isolates of Schistosoma mansoni, using tail loss as a measurement of PZQ action. The miracidia were collected by hatching eggs collected from faeces of infected mice. Single-sex cercaria lines were made by infecting a single Biomphalaria glabrata snail with a single miracidium. The sex of each single-sex cercaria line was identified by a direct W1-specific polymerase chain reaction (PCR) technique. Single-sex cercariae of two isolates were exposed to four different concentrations of PZQ, respectively. The tail shedding of cercariae was observed under a dissecting microscope for five time points up to 100 min after adding PZQ. The results showed that male cercariae have higher tail-shedding rates than that of female cercariae when PZQ-susceptible isolates of S. mansoni are exposed to the same concentration of PZQ. But this phenomenon was not observed in the PZQ-resistant isolates. This sexual differential resistance phenomenon of S. mansoni suggests that resistance to PZQ is induced by decreasing the PZQ susceptibility of male worms. The experiment described here may also be useful for developing tests to detect PZQ resistance in the field.
Pulmonary atresia with intact ventricular septum: management of, and outcomes for, a cohort of 210 consecutive patients
- Umesh Dyamenahalli, Brian W. McCrindle, Cathy McDonald, Kalyani R. Trivedi, Jeffrey F. Smallhorn, Lee N. Benson, John Coles, William G. Williams, Robert M. Freedom
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- Cardiology in the Young / Volume 14 / Issue 3 / June 2004
- Published online by Cambridge University Press:
- 21 January 2005, pp. 299-308
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Objectives: We sought to determine trends, and outcomes, for a cohort of patients with pulmonary atresia with intact ventricular septum born between 1965 and 1998. Background: Pulmonary atresia with intact ventricular septum is a complex lesion that remains a therapeutic challenge, particularly regarding the suitability for biventricular repair. Methods: We identified 210 consecutive patients, and reviewed their medical records, initial angiograms, and echocardiograms, along with the relevant surgical and pathology reports. Results: The mean initial Z-score for the diameter of the tricuspid valve was −0.99 ± 1.95, with Ebstein's malformation in 8%. A right ventricular dependent coronary arterial circulation was found in 23%. The proportion of patients who received treatment increased over time, although placement of an arterial shunt was the predominant initial procedure throughout the experience. At the last follow-up, 107 patients had not reached the planned final stage of their repair, and 79% of these had died. Of the 103 reaching the final stage of planned repair, 58 had undergone attempted biventricular repair, with 34% dying; 14 had undergone attempted one and a half ventricular repair, with 7% dying, and 31 had undergone attempted functionally univentricular repair, with 10% dying. Overall, survival was 57% at the age of 1 year, 48% at 5 years, and 43% at 10 years. Survival improved over time, with survival of 75% at 1 year, and 67% at 5 years, for patients born between 1992 and 1998. An earlier date of birth, the presence of Ebstein's malformation, and prematurity were all significant independent factors associated with decreased survival. A greater severity of coronary arterial abnormalities was significantly associated with a greater likelihood of left ventricular dysfunction during follow-up. Conclusions: The outcomes for patients born with pulmonary atresia with intact ventricular septum have improved over time, albeit that careful initial management, and better selection, is still indicated for those planned to undergo biventricular repair.
An empirical approach to subtype identification in individuals with social phobia
- W. ENG, R. G. HEIMBERG, M. E. COLES, F. R. SCHNEIER, M. R. LIEBOWITZ
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- Psychological Medicine / Volume 30 / Issue 6 / November 2000
- Published online by Cambridge University Press:
- 16 November 2000, pp. 1345-1357
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Background. The present study used cluster analysis procedures to identify empirically subgroups of patients with social phobia in a large clinical sample.
Method. The Liebowitz Social Anxiety Scale (LSAS) was administered to 382 patients from several studies of the treatment of social phobia. LSAS fear ratings were summed into four subscale scores (social interaction, public speaking, observation by others, eating and drinking in public) based on a previous factor analytical study of the LSAS. In order to produce a stable and robust solution, these factor scores were submitted to a two-stage clustering procedure consisting of an agglomerative-hierarchical clustering method followed by an iterative non-hierarchical clustering method.
Results. Three patient subgroups were identified based on their pattern of feared social situations on the LSAS. These groups were labelled: (1) pervasive social anxiety; (2) moderate social interaction anxiety; and (3) dominant public speaking anxiety. Clusters differed significantly on age and age of social phobia onset, as well as on measures of social anxiety, general anxiety and depressive symptomatology. Clusters also differed in the percentage of assigned patients who met criteria for the generalized subtype of social phobia and avoidant personality disorder.
Conclusions. The results provide empirical support for the existence of three subgroups in a clinical sample of individuals with social phobia and contribute to the growing evidence for the heterogeneity of social phobia. Further study of the conceptual, clinical and aetiological significance of these subgroups is needed.
On the Role of the Underlying Microstructure on the Mechanical Properties of Microelectromechanical Systems (MEMS) Materials
- G. F. Dirras, G. Coles, A. J. Wagner, S. Carlo, C. Newman, K. J. Hemker, W. N. Sharpe, Jr
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- Journal:
- MRS Online Proceedings Library Archive / Volume 657 / 2000
- Published online by Cambridge University Press:
- 17 March 2011, EE5.22
- Print publication:
- 2000
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The microstructure of Low Pressure Chemical Vapor Deposition (LPCVD) Polycrystalline silicon (Polysilicon) thin films was investigated by means of scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), atomic force microscopy (AFM) and Auger electron spectroscopy (AES). SEM characterization of tensile tested samples showed a brittle like-rupture, along with grooves located at the surface sides of the sample. TEM investigations of as-deposited samples showed equiaxed or fully columnar grains bridging from the bottom to the top of the films. A microstructural coarsening was observed with annealing. In the as-deposited state, the films exhibited a {110} texture as showed by the XRD analysis. The films' top and bottom surfaces were observed to be smooth with a roughness (standard deviation) of about 11nm and 20 nm respectively. A chemical analysis of the thin films showed the presence of carbon and oxygen impurities on the surface and oxygen through the sample as observed in the depth profile. The hypothetical influence of these findings is subsequently discussed in relation to the measured mechanical properties.
The Materials Properties of a Nickel Based Composite Contact to n-Sic for Pulsed Power Switching
- M. W. Cole, P. C. Joshi, F. Ren, C. W. Hubbard, M. C. Wood, M. H. Ervin
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- Journal:
- MRS Online Proceedings Library Archive / Volume 622 / 2000
- Published online by Cambridge University Press:
- 15 March 2011, T8.2.1
- Print publication:
- 2000
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Novel Ni/WSi/Ti/Pt composite Ohmic contacts to n-SiC were investigated as a function of annealing temperatures up to 1000°C. The onset of Ohmic behavior occurred at annealing temperatures of 900°C. Annealing at temperatures between 950°and 1000°C yielded excellent Ohmic behavior. At these temperatures the contact-SiC interface was smooth, defect free and characterized by a narrow Ni2Si reaction region. The annealed contacts possessed atomically smooth surface morphologies and exhibited minimal contact expansion. The residual carbon, resultant from SiC decomposition, was constrained by reaction with the WSi and Ti metallization layers forming carbide phases of W and Ti. The locations of the carbide phases were spatially distant from the metal semiconductor interface. Our results demonstrate that the Ni/WSi/Ti/Pt composite Ohmic contact maintains the desirable electrical properties associated with Ni contacts and possess excellent interfacial, compositional and surface properties which are required for reliable high power and high temperature device operation.
Behavior of W and WSix Contact Metallization on n- and p- Type GaN
- X. A. Cao, F. Ren, J. R. Lothian, S. J. Pearton, C. R. Abernathy, J. C. Zolper, M. W. Cole, A. Zeitouny, M. Eizenberg, R. J. Shul
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- Journal:
- Materials Research Society Internet Journal of Nitride Semiconductor Research / Volume 4 / Issue S1 / 1999
- Published online by Cambridge University Press:
- 13 June 2014, pp. 684-690
- Print publication:
- 1999
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Sputter-deposited W-based contacts on p-GaN (NA∼1018 cm−3) display non-ohmic behavior independent of annealing temperature when measured at 25°C. The transition to ohmic behavior occurs above ∼250°C as more of the acceptors become ionized. The optimum annealing temperature is ∼700°C under these conditions. These contacts are much more thermally stable than the conventional Ni/Au metallization, which shows a severely degraded morphology even at 700°C. W-based contacts may be ohmic as-deposited on very heavily doped n-GaN, and the specific contact resistance improves with annealing up to ∼900°C.