12 results
py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis
- Benjamin H. Savitzky, Steven E. Zeltmann, Lauren A. Hughes, Hamish G. Brown, Shiteng Zhao, Philipp M. Pelz, Thomas C. Pekin, Edward S. Barnard, Jennifer Donohue, Luis Rangel DaCosta, Ellis Kennedy, Yujun Xie, Matthew T. Janish, Matthew M. Schneider, Patrick Herring, Chirranjeevi Gopal, Abraham Anapolsky, Rohan Dhall, Karen C. Bustillo, Peter Ercius, Mary C. Scott, Jim Ciston, Andrew M. Minor, Colin Ophus
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- Journal:
- Microscopy and Microanalysis / Volume 27 / Issue 4 / August 2021
- Published online by Cambridge University Press:
- 21 May 2021, pp. 712-743
- Print publication:
- August 2021
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Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.
The National Project on Achievement in Twins
- Sara A. Hart, Kim Martinez, Patrick C. Kennedy, Colleen M. Ganley, Jeanette Taylor
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- Journal:
- Twin Research and Human Genetics / Volume 22 / Issue 6 / December 2019
- Published online by Cambridge University Press:
- 04 October 2019, pp. 761-764
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The National Project on Achievement in Twins (NatPAT) began in 2017 as part of the third funding cycle of the Florida Learning Disabilities Research Center, a program project grant funded by the Eunice Kennedy Shriver National Institute of Child Health and Development. NatPAT will have a nationally representative sample of elementary school-aged twins in the United States. The overall goal of the project is to uncover salient factors, including genetic and environmental influences, which contribute to the co-development of reading and math performance during the critical developmental period of elementary school. Here we present the specific aims, methods and materials, and future directions of the project.
Chemical, Biological, Radiological, Nuclear, and Explosive (CBRNE) Science and the CBRNE Science Medical Operations Science Support Expert (CMOSSE)
- C. Norman Coleman, Judith L. Bader, John F. Koerner, Chad Hrdina, Kenneth D. Cliffer, John L. Hick, James J. James, Monique K. Mansoura, Alicia A. Livinski, Scott V. Nystrom, Andrea DiCarlo-Cohen, Maria Julia Marinissen, Lynne Wathen, Jessica M. Appler, Brooke Buddemeier, Rocco Casagrande, Derek Estes, Patrick Byrne, Edward M. Kennedy, Ann A. Jakubowski, Cullen Case, Jr, David M. Weinstock, Nicholas Dainiak, Dan Hanfling, Andrew L. Garrett, Natalie N. Grant, Daniel Dodgen, Irwin Redlener, Thomas F. MacKAY, Meghan Treber, Mary J. Homer, Tammy P. Taylor, Aubrey Miller, George Korch, Richard Hatchett
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- Journal:
- Disaster Medicine and Public Health Preparedness / Volume 13 / Issue 5-6 / December 2019
- Published online by Cambridge University Press:
- 17 June 2019, pp. 995-1010
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A national need is to prepare for and respond to accidental or intentional disasters categorized as chemical, biological, radiological, nuclear, or explosive (CBRNE). These incidents require specific subject-matter expertise, yet have commonalities. We identify 7 core elements comprising CBRNE science that require integration for effective preparedness planning and public health and medical response and recovery. These core elements are (1) basic and clinical sciences, (2) modeling and systems management, (3) planning, (4) response and incident management, (5) recovery and resilience, (6) lessons learned, and (7) continuous improvement. A key feature is the ability of relevant subject matter experts to integrate information into response operations. We propose the CBRNE medical operations science support expert as a professional who (1) understands that CBRNE incidents require an integrated systems approach, (2) understands the key functions and contributions of CBRNE science practitioners, (3) helps direct strategic and tactical CBRNE planning and responses through first-hand experience, and (4) provides advice to senior decision-makers managing response activities. Recognition of both CBRNE science as a distinct competency and the establishment of the CBRNE medical operations science support expert informs the public of the enormous progress made, broadcasts opportunities for new talent, and enhances the sophistication and analytic expertise of senior managers planning for and responding to CBRNE incidents.
Inhibition of Downy Brome (Bromus tectorum) Root Growth by a Phytotoxin from Pseudomonas fluorescens Strain D7
- Patrick J. Tranel, David R. Gealy, Ann C. Kennedy
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- Journal:
- Weed Technology / Volume 7 / Issue 1 / March 1993
- Published online by Cambridge University Press:
- 12 June 2017, pp. 134-139
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Field applications of the rhizobacterium, Pseudomonas fluorescens strain D7 (D7), have selectively suppressed downy brome in winter wheat test plots. A phytotoxin produced by D7 inhibits downy brome root growth. An assay system was developed for future investigations of the mechanism of action of this and other phytotoxins that inhibit root growth. A crude preparation of the phytotoxin, cell-free supernatant (CFS), had little activity on downy brome root elongation in a sand-petri plate system. CFS was very active in a hydroponic system, in which a 6% (v/v) concentration inhibited root elongation within 1.5 h. Inhibition of root elongation was reversible in this system. Root elongation of downy brome seedlings resumed within 3 h after removal from a 9-h incubation in 8% CFS. CFS from genetic variants of D7 did not substantially inhibit root growth and a semi-crystallized precipitation product from D7 CFS inhibited root growth similarly to D7 CFS, indicating that the phytotoxin present in the CFS was responsible for growth inhibition.
Induction of Polyphenol Oxidase Activity in Dormant Wild Oat (Avena fatua) Seeds and Caryopses: A Defense Response to Seed Decay Fungi
- E. Patrick Fuerst, James V. Anderson, Ann C. Kennedy, Robert S. Gallagher
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- Journal:
- Weed Science / Volume 59 / Issue 2 / June 2011
- Published online by Cambridge University Press:
- 20 January 2017, pp. 137-144
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Persistence of the soil seed bank requires both dormancy and resistance to seed decay organisms. However, there is little or no information evaluating biochemical responses of dormant weed seeds to pathogens. Wild oat caryopses were incubated with four pathogenic fungal isolates to evaluate the response of the pathogen defense enzyme, polyphenol oxidase (PPO). Caryopsis PPO activity was induced by three Fusarium spp. isolates previously obtained from whole seeds incubated in the field whereas caryopsis PPO activity was decreased by a Pythium isolate. Fusarium avenaceum isolate F.a.1 caused the greatest PPO induction and was studied in more detail. When whole wild oat seeds were incubated on F.a.1, PPO activity was induced in seeds, hulls (lemma and palea), and caryopses. Incubation of whole seeds on F.a.1 gradually induced caryopsis PPO activity over an 8-d period, whereas incubation of caryopses on F.a.1 over a 4-d period caused a greater and more rapid induction of PPO activity. Very little PPO activity could be leached from untreated caryopses, but nearly all of the induced PPO activity in F.a.1-treated caryopses was readily leached when incubated in buffer. In Western blots, both untreated and F.a.1-treated leachates contained a ∼57-kilodalton (kD) protein, putatively the mature and relatively inactive form of PPO. However, lower molecular weight antigenic proteins between ∼52 and ∼25 kD were strongly induced in F.a.1-treated caryopses, with this induction being correlated with the increase in PPO activity. We hypothesize that dormant weed seeds possess biochemical defenses against pathogens and, more specifically, that proteolysis in the presence of fungal pathogens may release an activated form of PPO from the surface of wild oat caryopses and hulls.
Effect of tillage, fungicide seed treatment, and soil fumigation on seed bank dynamics of wild oat (Avena fatua)
- Eric R. Gallandt, E. Patrick Fuerst, Ann C. Kennedy
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- Journal:
- Weed Science / Volume 52 / Issue 4 / August 2004
- Published online by Cambridge University Press:
- 20 January 2017, pp. 597-604
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No-tillage offers potential for improved soil quality, reduced erosion, and equal or increased crop yields. We hypothesized that, compared with conservation tillage (CT), no-tillage (NT) offers conditions more conducive to microbial decay of weed seed. In NT systems seed remain at or near the soil surface where crop residues, moisture, and lack of disturbance create an environment with greater soil microbial diversity. In late fall of 1998 and 1999, dormant seed of wild oat, either individually glued to plastic toothpicks or mixed with soil and placed in mesh bags, were buried (mean seed depth of 2.5 cm) in replicated field plots managed by NT or CT since 1982. Treatments including fungicide seed treatment (thiram + metalaxyl + captan) and soil fumigation (propylene oxide) provided estimates of the contribution of microorganisms to observed mortality. Seed were retrieved in May and August, 1999 and 2000. Contrary to our original hypothesis, the proportion of dead seed was generally similar in NT and CT systems. Lack of tillage system by seed or soil treatments affecting the proportion of dead or decayed seed suggests that the contribution of microorganisms to seed fate is similar in these tillage environments. However, the proportion of dormant seed was consistently lower in the NT compared with CT treatments; there was a corresponding increase in the proportion of germinated seed. Overall, more than half of the wild oat seed bank losses could be directly attributed to germination whereas losses due to decay were relatively minor by comparison. Despite favorable distribution of seed and improved quality of the surface-strata of soil in NT systems, this study fails to provide evidence that enhanced microbial decay will contribute to a “weed-suppressive” capacity in such cropping systems.
Genome-Wide Meta-Analysis of Longitudinal Alcohol Consumption Across Youth and Early Adulthood
- Daniel E. Adkins, Shaunna L. Clark, William E. Copeland, Martin Kennedy, Kevin Conway, Adrian Angold, Hermine Maes, Youfang Liu, Gaurav Kumar, Alaattin Erkanli, Ashwin A. Patkar, Judy Silberg, Tyson H. Brown, David M. Fergusson, L. John Horwood, Lindon Eaves, Edwin J. C. G. van den Oord, Patrick F. Sullivan, E. J. Costello
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- Journal:
- Twin Research and Human Genetics / Volume 18 / Issue 4 / August 2015
- Published online by Cambridge University Press:
- 17 June 2015, pp. 335-347
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The public health burden of alcohol is unevenly distributed across the life course, with levels of use, abuse, and dependence increasing across adolescence and peaking in early adulthood. Here, we leverage this temporal patterning to search for common genetic variants predicting developmental trajectories of alcohol consumption. Comparable psychiatric evaluations measuring alcohol consumption were collected in three longitudinal community samples (N = 2,126, obs = 12,166). Consumption-repeated measurements spanning adolescence and early adulthood were analyzed using linear mixed models, estimating individual consumption trajectories, which were then tested for association with Illumina 660W-Quad genotype data (866,099 SNPs after imputation and QC). Association results were combined across samples using standard meta-analysis methods. Four meta-analysis associations satisfied our pre-determined genome-wide significance criterion (FDR < 0.1) and six others met our ‘suggestive’ criterion (FDR <0.2). Genome-wide significant associations were highly biological plausible, including associations within GABA transporter 1, SLC6A1 (solute carrier family 6, member 1), and exonic hits in LOC100129340 (mitofusin-1-like). Pathway analyses elaborated single marker results, indicating significant enriched associations to intuitive biological mechanisms, including neurotransmission, xenobiotic pharmacodynamics, and nuclear hormone receptors (NHR). These findings underscore the value of combining longitudinal behavioral data and genome-wide genotype information in order to study developmental patterns and improve statistical power in genomic studies.
Contributors
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- By Mitchell Aboulafia, Frederick Adams, Marilyn McCord Adams, Robert M. Adams, Laird Addis, James W. Allard, David Allison, William P. Alston, Karl Ameriks, C. Anthony Anderson, David Leech Anderson, Lanier Anderson, Roger Ariew, David Armstrong, Denis G. Arnold, E. J. Ashworth, Margaret Atherton, Robin Attfield, Bruce Aune, Edward Wilson Averill, Jody Azzouni, Kent Bach, Andrew Bailey, Lynne Rudder Baker, Thomas R. Baldwin, Jon Barwise, George Bealer, William Bechtel, Lawrence C. Becker, Mark A. Bedau, Ernst Behler, José A. Benardete, Ermanno Bencivenga, Jan Berg, Michael Bergmann, Robert L. Bernasconi, Sven Bernecker, Bernard Berofsky, Rod Bertolet, Charles J. Beyer, Christian Beyer, Joseph Bien, Joseph Bien, Peg Birmingham, Ivan Boh, James Bohman, Daniel Bonevac, Laurence BonJour, William J. Bouwsma, Raymond D. Bradley, Myles Brand, Richard B. Brandt, Michael E. Bratman, Stephen E. Braude, Daniel Breazeale, Angela Breitenbach, Jason Bridges, David O. Brink, Gordon G. Brittan, Justin Broackes, Dan W. Brock, Aaron Bronfman, Jeffrey E. Brower, Bartosz Brozek, Anthony Brueckner, Jeffrey Bub, Lara Buchak, Otavio Bueno, Ann E. Bumpus, Robert W. Burch, John Burgess, Arthur W. Burks, Panayot Butchvarov, Robert E. Butts, Marina Bykova, Patrick Byrne, David Carr, Noël Carroll, Edward S. Casey, Victor Caston, Victor Caston, Albert Casullo, Robert L. Causey, Alan K. L. Chan, Ruth Chang, Deen K. Chatterjee, Andrew Chignell, Roderick M. Chisholm, Kelly J. Clark, E. J. Coffman, Robin Collins, Brian P. Copenhaver, John Corcoran, John Cottingham, Roger Crisp, Frederick J. Crosson, Antonio S. Cua, Phillip D. Cummins, Martin Curd, Adam Cureton, Andrew Cutrofello, Stephen Darwall, Paul Sheldon Davies, Wayne A. Davis, Timothy Joseph Day, Claudio de Almeida, Mario De Caro, Mario De Caro, John Deigh, C. F. Delaney, Daniel C. Dennett, Michael R. DePaul, Michael Detlefsen, Daniel Trent Devereux, Philip E. Devine, John M. Dillon, Martin C. Dillon, Robert DiSalle, Mary Domski, Alan Donagan, Paul Draper, Fred Dretske, Mircea Dumitru, Wilhelm Dupré, Gerald Dworkin, John Earman, Ellery Eells, Catherine Z. Elgin, Berent Enç, Ronald P. Endicott, Edward Erwin, John Etchemendy, C. Stephen Evans, Susan L. Feagin, Solomon Feferman, Richard Feldman, Arthur Fine, Maurice A. Finocchiaro, William FitzPatrick, Richard E. Flathman, Gvozden Flego, Richard Foley, Graeme Forbes, Rainer Forst, Malcolm R. Forster, Daniel Fouke, Patrick Francken, Samuel Freeman, Elizabeth Fricker, Miranda Fricker, Michael Friedman, Michael Fuerstein, Richard A. Fumerton, Alan Gabbey, Pieranna Garavaso, Daniel Garber, Jorge L. A. Garcia, Robert K. Garcia, Don Garrett, Philip Gasper, Gerald Gaus, Berys Gaut, Bernard Gert, Roger F. Gibson, Cody Gilmore, Carl Ginet, Alan H. Goldman, Alvin I. Goldman, Alfonso Gömez-Lobo, Lenn E. Goodman, Robert M. Gordon, Stefan Gosepath, Jorge J. E. Gracia, Daniel W. Graham, George A. Graham, Peter J. Graham, Richard E. Grandy, I. Grattan-Guinness, John Greco, Philip T. Grier, Nicholas Griffin, Nicholas Griffin, David A. Griffiths, Paul J. Griffiths, Stephen R. Grimm, Charles L. Griswold, Charles B. Guignon, Pete A. Y. Gunter, Dimitri Gutas, Gary Gutting, Paul Guyer, Kwame Gyekye, Oscar A. Haac, Raul Hakli, Raul Hakli, Michael Hallett, Edward C. Halper, Jean Hampton, R. James Hankinson, K. R. Hanley, Russell Hardin, Robert M. Harnish, William Harper, David Harrah, Kevin Hart, Ali Hasan, William Hasker, John Haugeland, Roger Hausheer, William Heald, Peter Heath, Richard Heck, John F. Heil, Vincent F. Hendricks, Stephen Hetherington, Francis Heylighen, Kathleen Marie Higgins, Risto Hilpinen, Harold T. Hodes, Joshua Hoffman, Alan Holland, Robert L. Holmes, Richard Holton, Brad W. Hooker, Terence E. Horgan, Tamara Horowitz, Paul Horwich, Vittorio Hösle, Paul Hoβfeld, Daniel Howard-Snyder, Frances Howard-Snyder, Anne Hudson, Deal W. Hudson, Carl A. Huffman, David L. Hull, Patricia Huntington, Thomas Hurka, Paul Hurley, Rosalind Hursthouse, Guillermo Hurtado, Ronald E. Hustwit, Sarah Hutton, Jonathan Jenkins Ichikawa, Harry A. Ide, David Ingram, Philip J. Ivanhoe, Alfred L. Ivry, Frank Jackson, Dale Jacquette, Joseph Jedwab, Richard Jeffrey, David Alan Johnson, Edward Johnson, Mark D. Jordan, Richard Joyce, Hwa Yol Jung, Robert Hillary Kane, Tomis Kapitan, Jacquelyn Ann K. Kegley, James A. Keller, Ralph Kennedy, Sergei Khoruzhii, Jaegwon Kim, Yersu Kim, Nathan L. King, Patricia Kitcher, Peter D. Klein, E. D. Klemke, Virginia Klenk, George L. Kline, Christian Klotz, Simo Knuuttila, Joseph J. Kockelmans, Konstantin Kolenda, Sebastian Tomasz Kołodziejczyk, Isaac Kramnick, Richard Kraut, Fred Kroon, Manfred Kuehn, Steven T. Kuhn, Henry E. Kyburg, John Lachs, Jennifer Lackey, Stephen E. Lahey, Andrea Lavazza, Thomas H. Leahey, Joo Heung Lee, Keith Lehrer, Dorothy Leland, Noah M. Lemos, Ernest LePore, Sarah-Jane Leslie, Isaac Levi, Andrew Levine, Alan E. Lewis, Daniel E. Little, Shu-hsien Liu, Shu-hsien Liu, Alan K. L. Chan, Brian Loar, Lawrence B. Lombard, John Longeway, Dominic McIver Lopes, Michael J. Loux, E. J. Lowe, Steven Luper, Eugene C. Luschei, William G. Lycan, David Lyons, David Macarthur, Danielle Macbeth, Scott MacDonald, Jacob L. Mackey, Louis H. Mackey, Penelope Mackie, Edward H. Madden, Penelope Maddy, G. B. Madison, Bernd Magnus, Pekka Mäkelä, Rudolf A. Makkreel, David Manley, William E. Mann (W.E.M.), Vladimir Marchenkov, Peter Markie, Jean-Pierre Marquis, Ausonio Marras, Mike W. Martin, A. P. Martinich, William L. McBride, David McCabe, Storrs McCall, Hugh J. McCann, Robert N. McCauley, John J. McDermott, Sarah McGrath, Ralph McInerny, Daniel J. McKaughan, Thomas McKay, Michael McKinsey, Brian P. McLaughlin, Ernan McMullin, Anthonie Meijers, Jack W. Meiland, William Jason Melanson, Alfred R. Mele, Joseph R. Mendola, Christopher Menzel, Michael J. Meyer, Christian B. Miller, David W. Miller, Peter Millican, Robert N. Minor, Phillip Mitsis, James A. Montmarquet, Michael S. Moore, Tim Moore, Benjamin Morison, Donald R. Morrison, Stephen J. Morse, Paul K. Moser, Alexander P. D. Mourelatos, Ian Mueller, James Bernard Murphy, Mark C. Murphy, Steven Nadler, Jan Narveson, Alan Nelson, Jerome Neu, Samuel Newlands, Kai Nielsen, Ilkka Niiniluoto, Carlos G. Noreña, Calvin G. Normore, David Fate Norton, Nikolaj Nottelmann, Donald Nute, David S. Oderberg, Steve Odin, Michael O’Rourke, Willard G. Oxtoby, Heinz Paetzold, George S. Pappas, Anthony J. Parel, Lydia Patton, R. P. Peerenboom, Francis Jeffry Pelletier, Adriaan T. Peperzak, Derk Pereboom, Jaroslav Peregrin, Glen Pettigrove, Philip Pettit, Edmund L. Pincoffs, Andrew Pinsent, Robert B. Pippin, Alvin Plantinga, Louis P. Pojman, Richard H. Popkin, John F. Post, Carl J. Posy, William J. Prior, Richard Purtill, Michael Quante, Philip L. Quinn, Philip L. Quinn, Elizabeth S. Radcliffe, Diana Raffman, Gerard Raulet, Stephen L. Read, Andrews Reath, Andrew Reisner, Nicholas Rescher, Henry S. Richardson, Robert C. Richardson, Thomas Ricketts, Wayne D. Riggs, Mark Roberts, Robert C. Roberts, Luke Robinson, Alexander Rosenberg, Gary Rosenkranz, Bernice Glatzer Rosenthal, Adina L. Roskies, William L. Rowe, T. M. Rudavsky, Michael Ruse, Bruce Russell, Lilly-Marlene Russow, Dan Ryder, R. M. Sainsbury, Joseph Salerno, Nathan Salmon, Wesley C. Salmon, Constantine Sandis, David H. Sanford, Marco Santambrogio, David Sapire, Ruth A. Saunders, Geoffrey Sayre-McCord, Charles Sayward, James P. Scanlan, Richard Schacht, Tamar Schapiro, Frederick F. Schmitt, Jerome B. Schneewind, Calvin O. Schrag, Alan D. Schrift, George F. Schumm, Jean-Loup Seban, David N. Sedley, Kenneth Seeskin, Krister Segerberg, Charlene Haddock Seigfried, Dennis M. Senchuk, James F. Sennett, William Lad Sessions, Stewart Shapiro, Tommie Shelby, Donald W. Sherburne, Christopher Shields, Roger A. Shiner, Sydney Shoemaker, Robert K. Shope, Kwong-loi Shun, Wilfried Sieg, A. John Simmons, Robert L. Simon, Marcus G. Singer, Georgette Sinkler, Walter Sinnott-Armstrong, Matti T. Sintonen, Lawrence Sklar, Brian Skyrms, Robert C. Sleigh, Michael Anthony Slote, Hans Sluga, Barry Smith, Michael Smith, Robin Smith, Robert Sokolowski, Robert C. Solomon, Marta Soniewicka, Philip Soper, Ernest Sosa, Nicholas Southwood, Paul Vincent Spade, T. L. S. Sprigge, Eric O. Springsted, George J. Stack, Rebecca Stangl, Jason Stanley, Florian Steinberger, Sören Stenlund, Christopher Stephens, James P. Sterba, Josef Stern, Matthias Steup, M. A. Stewart, Leopold Stubenberg, Edith Dudley Sulla, Frederick Suppe, Jere Paul Surber, David George Sussman, Sigrún Svavarsdóttir, Zeno G. Swijtink, Richard Swinburne, Charles C. Taliaferro, Robert B. Talisse, John Tasioulas, Paul Teller, Larry S. Temkin, Mark Textor, H. S. Thayer, Peter Thielke, Alan Thomas, Amie L. Thomasson, Katherine Thomson-Jones, Joshua C. Thurow, Vzalerie Tiberius, Terrence N. Tice, Paul Tidman, Mark C. Timmons, William Tolhurst, James E. Tomberlin, Rosemarie Tong, Lawrence Torcello, Kelly Trogdon, J. D. Trout, Robert E. Tully, Raimo Tuomela, John Turri, Martin M. Tweedale, Thomas Uebel, Jennifer Uleman, James Van Cleve, Harry van der Linden, Peter van Inwagen, Bryan W. Van Norden, René van Woudenberg, Donald Phillip Verene, Samantha Vice, Thomas Vinci, Donald Wayne Viney, Barbara Von Eckardt, Peter B. M. Vranas, Steven J. Wagner, William J. Wainwright, Paul E. Walker, Robert E. Wall, Craig Walton, Douglas Walton, Eric Watkins, Richard A. Watson, Michael V. Wedin, Rudolph H. Weingartner, Paul Weirich, Paul J. Weithman, Carl Wellman, Howard Wettstein, Samuel C. Wheeler, Stephen A. White, Jennifer Whiting, Edward R. Wierenga, Michael Williams, Fred Wilson, W. Kent Wilson, Kenneth P. Winkler, John F. Wippel, Jan Woleński, Allan B. Wolter, Nicholas P. Wolterstorff, Rega Wood, W. Jay Wood, Paul Woodruff, Alison Wylie, Gideon Yaffe, Takashi Yagisawa, Yutaka Yamamoto, Keith E. Yandell, Xiaomei Yang, Dean Zimmerman, Günter Zoller, Catherine Zuckert, Michael Zuckert, Jack A. Zupko (J.A.Z.)
- Edited by Robert Audi, University of Notre Dame, Indiana
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- Book:
- The Cambridge Dictionary of Philosophy
- Published online:
- 05 August 2015
- Print publication:
- 27 April 2015, pp ix-xxx
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Downregulation of Ccnd1 and Hes6 in rat hippocampus after chronic exposure to the antidepressant paroxetine
- Patrick C. McHugh, Geraldine R. Rogers, Dylan M. Glubb, Melanie D. Allington, Mark Hughes, Peter R. Joyce, Martin A. Kennedy
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- Journal:
- Acta Neuropsychiatrica / Volume 20 / Issue 6 / December 2008
- Published online by Cambridge University Press:
- 24 June 2014, pp. 307-313
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Objective:
The mechanism of action of antidepressant drugs is not fully understood. Application of genomic methods enables the identification of biochemical pathways that are regulated by antidepressants, and this may provide novel clues to the molecular and cellular actions of these drugs. The present study examined gene expression profiles in the hippocampus of rats exposed to chronic antidepressant treatment.
Methods:Animals were treated for 12 days with the selective serotonin reuptake inhibitor paroxetine; then, hippocampal ribonucleic acid was recovered, and changes in gene expression were assessed by microarray analysis.
Results:A total of 160 genes that showed differential expression after paroxetine exposure were identified. Using functional relevance and observed fold change as selection criteria, the expression changes in a subset of these genes were confirmed by quantitative polymerase chain reaction.
Conclusion:Of this subset, only two genes, cyclin D1 (Ccnd1) and hairy and enhancer of split 6 (Hes6), showed robust and consistent changes in expression. Both genes were downregulated by paroxetine, and both have been previously implicated in neurogenesis. Further investigation of these two genes may provide new insight into the mechanism of action of antidepressants.
PINE ROOT COLLAR WEEVIL DAMAGE TO RED PINE PLANTATIONS IN MICHIGAN RELATED TO HOST AGE, TEMPERATURE, AND STAND LOCATION1
- Patrick C. Kennedy, Louis F. Wilson
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- Journal:
- The Canadian Entomologist / Volume 103 / Issue 12 / December 1971
- Published online by Cambridge University Press:
- 31 May 2012, pp. 1685-1690
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Pine root collar weevil damage is least on red pine plantations in cooler areas of northern Lower Michigan, and is inversely related to distance of the host from the nearest weevil infestation. Three hazard zones are suggested based on temperature. A high hazard zone occurs in the western part, a moderate zone in the central, and a low zone in the eastern part of the Lower Peninsula of Michigan.
UNDERSTORY VEGETATION ASSOCIATED WITH SARATOGA SPITTLEBUG DAMAGE IN MICHIGAN RED PINE PLANTATIONS 1
- Patrick C. Kennedy, Louis F. Wilson
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- Journal:
- The Canadian Entomologist / Volume 103 / Issue 10 / October 1971
- Published online by Cambridge University Press:
- 31 May 2012, pp. 1421-1426
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The amount of sweet-fern was significantly related to the degree of Saratoga spittlebug adult injury to red pine on study plots in Lower Michigan. Other host plants supporting spittlebugs must be extremely abundant before populations increase enough to cause heavy injury. A spittlebug risk-rating device is presented that specifies hazard in a red pine stand by plotting per cent sweet-fern against per cent other suitable hosts.
A dopamine transporter polymorphism is a risk factor for borderline personality disorder in depressed patients
- PETER R. JOYCE, PATRICK C. McHUGH, JANICE M. McKENZIE, PATRICK F. SULLIVAN, ROGER T. MULDER, SUZANNE E. LUTY, JANET D. CARTER, CHRISTOPHER M. A. FRAMPTON, C. ROBERT CLONINGER, ALLISON M. MILLER, MARTIN A. KENNEDY
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- Journal:
- Psychological Medicine / Volume 36 / Issue 6 / June 2006
- Published online by Cambridge University Press:
- 20 April 2006, pp. 807-813
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Background. Borderline personality disorder (BPD) is often co-morbid with major depression and may complicate its treatment. We were interested in differences in genetic and developmental risk factors between depressed patients with or without a co-morbid BPD.
Method. Out-patients with major depressive disorder were recruited for two treatment trials. Assessment of depressed patients included the assessment of personality disorders, developmental risk factors and DNA samples for genetic analyses.
Results. In each study there was a significant association between the 9-repeat allele of the dopamine transporter (DAT1) and BPD, with odds ratios (OR) >3 and p[les ]0·02. This association remained significant when developmental risk factors for BPD (childhood abuse and neglect and borderline temperament) were also included in the analyses. The OR was even larger in the depressed patients aged [ges ]35 years (OR 9·31, p=0·005).
Conclusion. This replicated association in depressed patients between the 9-repeat allele of DAT1 and BPD may provide clues to understanding the neurobiology of BPD. The finding that the association is larger in the older depressed patients, suggests that the 9-repeat allele may be associated with a poorer prognosis BPD, rather than a young adult limited variant of BPD.