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An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges
- Karamarie Fecho, Chris Bizon, Tursynay Issabekova, Sierra Moxon, Anne E. Thessen, Shervin Abdollahi, Sergio E. Baranzini, Basazin Belhu, William E. Byrd, Lawrence Chung, Andrew Crouse, Marc P. Duby, Stephen Ferguson, Aleksandra Foksinska, Laura Forero, Jennifer Friedman, Vicki Gardner, Gwênlyn Glusman, Jennifer Hadlock, Kristina Hanspers, Eugene Hinderer, Charlotte Hobbs, Gregory Hyde, Sui Huang, David Koslicki, Philip Mease, Sandrine Muller, Christopher J. Mungall, Stephen A. Ramsey, Jared Roach, Irit Rubin, Shepherd H. Schurman, Anath Shalev, Brett Smith, Karthik Soman, Sarah Stemann, Andrew I. Su, Casey Ta, Paul B. Watkins, Mark D. Williams, Chunlei Wu, Colleen H. Xu, The Biomedical Data Translator Consortium
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- Journal:
- Journal of Clinical and Translational Science / Volume 7 / Issue 1 / 2023
- Published online by Cambridge University Press:
- 14 September 2023, e214
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Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder efforts to harmonize and integrate across these diverse sources. As part of The Biomedical Translator Consortium, we have developed a knowledge graph–based question-answering system designed to augment human reasoning and accelerate translational scientific discovery: the Translator system. We have applied the Translator system to answer biomedical questions in the context of a broad array of diseases and syndromes, including Fanconi anemia, primary ciliary dyskinesia, multiple sclerosis, and others. A variety of collaborative approaches have been used to research and develop the Translator system. One recent approach involved the establishment of a monthly “Question-of-the-Month (QotM) Challenge” series. Herein, we describe the structure of the QotM Challenge; the six challenges that have been conducted to date on drug-induced liver injury, cannabidiol toxicity, coronavirus infection, diabetes, psoriatic arthritis, and ATP1A3-related phenotypes; the scientific insights that have been gleaned during the challenges; and the technical issues that were identified over the course of the challenges and that can now be addressed to foster further development of the prototype Translator system. We close with a discussion on Large Language Models such as ChatGPT and highlight differences between those models and the Translator system.
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- By Victoria M. Allen, Frederic Amant, Sarah Armstrong, Thomas F. Baskett, Michael A. Belfort, Meredith Birsner, Renee D. Boss, Leanne Bricker, Josaphat K. Byamugisha, Giorgio Capogna, Michael P. Casaer, Frank A. Chervenak, Vicki Clark, Filip Claus, Malachy O. Columb, Charles Cox, Jean T. Cox, Vegard Dahl, John Davison, Jan Deprest, Clifford S. Deutschman, Roland Devlieger, Karim Djekidel, Steven Dymarkowski, Roshan Fernando, Clare Fitzpatrick, Sreedhar Gaddipati, Thierry Girard, Emily Gordon, Ian A. Greer, David Grooms, Sina Haeri, Katy Harrison, Edward J. Hayes, Michelle Hladunewich, Andra H. James, Tracey Johnston, Bellal Joseph, Erin Keely, Ruth Landau, Stephen E. Lapinsky, Susanna I. Lee, Larry Leeman, Hennie Lombaard, Stephen Lu, Alison MacArthur, Laura A. Magee, Paul E. Marik, Laurence B. McCullough, Alexandre Mignon, Carlo Missant, Jack Moodley, Lisa E. Moore, Kate Morse, Warwick D. Ngan Kee, Catherine Nelson-Piercy, Clemens M. Ortner, Geraldine O’Sullivan, Luis D. Pacheco, Fathima Paruk, Melina Pectasides, Nigel Pereira, Patricia Peticca, Sharon T. Phelan, Felicity Plaat, Lauren A. Plante, Michael P. Plevyak, Dianne Plews, Wendy Pollock, Laura C. Price, Peter Rhee, Leiv Arne Rosseland, Kathryn M. Rowan, Helen Ryan, Helen Scholefield, Neil S. Seligman, Nadir Sharawi, Alex Sia, Bob Silver, Mieke Soens, Ulrich J. Spreng, Silvia Stirparo, Nova Szoka, Andrew Tang, Kha M. Tran, Els Troost, Lawrence C. Tsen, Derek Tuffnell, Kristel Van Calsteren, Marc Van de Velde, Marcel Vercauteren, Chris Verslype, Peter von Dadelszen, Carl Waldman, Michelle Walters, Linda Watkins, Paul Westhead, Cynthia A. Wong, Gerda G. Zeeman, Joost J. Zwart
- Edited by Marc van de Velde, Helen Scholefield, Lauren A. Plante
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- Book:
- Maternal Critical Care
- Published online:
- 05 July 2013
- Print publication:
- 04 July 2013, pp ix-xiv
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- By Jennifer L. Allen, Inés Baños, Isabel Boege, Susan M. Bögels, Sam Cartwright-Hatton, Sarah Clark, Judith A. Cohen, Cathy Creswell, Esther I. de Bruin, Jessica Deighton, Helen F. Dodd, Caroline L. Donovan, Nicola Dummett, Sandra Dunsmuir, Melinda Edwards, Lara J. Farrell, Iyabo A. Fatimilehin, Andrew Fugard, Peter Fuggle, Philip Graham, Alice M. Gregory, Amira Hassan, Kevin Hilbert, Jennifer L. Hudson, Georgina C. Krebs, Jennifer Y. F. Lau, Anthony P. Mannarino, Sonja March, Ella L. Milliner, Laura K. Murray, Lynne Murray, Carol Newall, Thomas H. Ollendick, Dennis Ougrin, Ronald M. Rapee, Shirley Reynolds, Natalie Rodriguez, Benjamin C. Schwartzman, Stephen Scott, Susan H. Spence, Paul Stallard, Ellen Trautmann, David Trickey, Cynthia M. Turner, Saskia van der Oord, Beth Watkins, Miranda Wolpert, Jeffrey J. Wood
- Edited by Philip Graham, Shirley Reynolds, University of Reading
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- Book:
- Cognitive Behaviour Therapy for Children and Families
- Published online:
- 05 March 2013
- Print publication:
- 14 March 2013, pp viii-x
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- By Aakash Agarwala, Linda S. Aglio, Rae M. Allain, Paul D. Allen, Houman Amirfarzan, Yasodananda Kumar Areti, Amit Asopa, Edwin G. Avery, Patricia R. Bachiller, Angela M. Bader, Rana Badr, Sibinka Bajic, David J. Baker, Sheila R. Barnett, Rena Beckerly, Lorenzo Berra, Walter Bethune, Sascha S. Beutler, Tarun Bhalla, Edward A. Bittner, Jonathan D. Bloom, Alina V. Bodas, Lina M. Bolanos-Diaz, Ruma R. Bose, Jan Boublik, John P. Broadnax, Jason C. Brookman, Meredith R. Brooks, Roland Brusseau, Ethan O. Bryson, Linda A. Bulich, Kenji Butterfield, William R. Camann, Denise M. Chan, Theresa S. Chang, Jonathan E. Charnin, Mark Chrostowski, Fred Cobey, Adam B. Collins, Mercedes A. Concepcion, Christopher W. Connor, Bronwyn Cooper, Jeffrey B. Cooper, Martha Cordoba-Amorocho, Stephen B. Corn, Darin J. Correll, Gregory J. Crosby, Lisa J. Crossley, Deborah J. Culley, Tomas Cvrk, Michael N. D'Ambra, Michael Decker, Daniel F. Dedrick, Mark Dershwitz, Francis X. Dillon, Pradeep Dinakar, Alimorad G. Djalali, D. John Doyle, Lambertus Drop, Ian F. Dunn, Theodore E. Dushane, Sunil Eappen, Thomas Edrich, Jesse M. Ehrenfeld, Jason M. Erlich, Lucinda L. Everett, Elliott S. Farber, Khaldoun Faris, Eddy M. Feliz, Massimo Ferrigno, Richard S. Field, Michael G. Fitzsimons, Hugh L. Flanagan Jr., Vladimir Formanek, Amanda A. Fox, John A. Fox, Gyorgy Frendl, Tanja S. Frey, Samuel M. Galvagno Jr., Edward R. Garcia, Jonathan D. Gates, Cosmin Gauran, Brian J. Gelfand, Simon Gelman, Alexander C. Gerhart, Peter Gerner, Omid Ghalambor, Christopher J. Gilligan, Christian D. Gonzalez, Noah E. Gordon, William B. Gormley, Thomas J. Graetz, Wendy L. Gross, Amit Gupta, James P. Hardy, Seetharaman Hariharan, Miriam Harnett, Philip M. Hartigan, Joaquim M. Havens, Bishr Haydar, Stephen O. Heard, James L. Helstrom, David L. Hepner, McCallum R. Hoyt, Robert N. Jamison, Karinne Jervis, Stephanie B. Jones, Swaminathan Karthik, Richard M. Kaufman, Shubjeet Kaur, Lee A. Kearse Jr., John C. Keel, Scott D. Kelley, Albert H. Kim, Amy L. Kim, Grace Y. Kim, Robert J. Klickovich, Robert M. Knapp, Bhavani S. Kodali, Rahul Koka, Alina Lazar, Laura H. Leduc, Stanley Leeson, Lisa R. Leffert, Scott A. LeGrand, Patricio Leyton, J. Lance Lichtor, John Lin, Alvaro A. Macias, Karan Madan, Sohail K. Mahboobi, Devi Mahendran, Christine Mai, Sayeed Malek, S. Rao Mallampati, Thomas J. Mancuso, Ramon Martin, Matthew C. Martinez, J. A. Jeevendra Martyn, Kai Matthes, Tommaso Mauri, Mary Ellen McCann, Shannon S. McKenna, Dennis J. McNicholl, Abdel-Kader Mehio, Thor C. Milland, Tonya L. K. Miller, John D. Mitchell, K. Annette Mizuguchi, Naila Moghul, David R. Moss, Ross J. Musumeci, Naveen Nathan, Ju-Mei Ng, Liem C. Nguyen, Ervant Nishanian, Martina Nowak, Ala Nozari, Michael Nurok, Arti Ori, Rafael A. Ortega, Amy J. Ortman, David Oxman, Arvind Palanisamy, Carlo Pancaro, Lisbeth Lopez Pappas, Benjamin Parish, Samuel Park, Deborah S. Pederson, Beverly K. Philip, James H. Philip, Silvia Pivi, Stephen D. Pratt, Douglas E. Raines, Stephen L. Ratcliff, James P. Rathmell, J. Taylor Reed, Elizabeth M. Rickerson, Selwyn O. Rogers Jr., Thomas M. Romanelli, William H. Rosenblatt, Carl E. Rosow, Edgar L. Ross, J. Victor Ryckman, Mônica M. Sá Rêgo, Nicholas Sadovnikoff, Warren S. Sandberg, Annette Y. Schure, B. Scott Segal, Navil F. Sethna, Swapneel K. Shah, Shaheen F. Shaikh, Fred E. Shapiro, Torin D. Shear, Prem S. Shekar, Stanton K. Shernan, Naomi Shimizu, Douglas C. Shook, Kamal K. Sikka, Pankaj K. Sikka, David A. Silver, Jeffrey H. Silverstein, Emily A. Singer, Ken Solt, Spiro G. Spanakis, Wolfgang Steudel, Matthias Stopfkuchen-Evans, Michael P. Storey, Gary R. Strichartz, Balachundhar Subramaniam, Wariya Sukhupragarn, John Summers, Shine Sun, Eswar Sundar, Sugantha Sundar, Neelakantan Sunder, Faraz Syed, Usha B. Tedrow, Nelson L. Thaemert, George P. Topulos, Lawrence C. Tsen, Richard D. Urman, Charles A. Vacanti, Francis X. Vacanti, Joshua C. Vacanti, Assia Valovska, Ivan T. Valovski, Mary Ann Vann, Susan Vassallo, Anasuya Vasudevan, Kamen V. Vlassakov, Gian Paolo Volpato, Essi M. Vulli, J. Matthias Walz, Jingping Wang, James F. Watkins, Maxwell Weinmann, Sharon L. Wetherall, Mallory Williams, Sarah H. Wiser, Zhiling Xiong, Warren M. Zapol, Jie Zhou
- Edited by Charles Vacanti, Scott Segal, Pankaj Sikka, Richard Urman
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- Book:
- Essential Clinical Anesthesia
- Published online:
- 05 January 2012
- Print publication:
- 11 July 2011, pp xv-xxviii
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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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- Book:
- The Causes of Epilepsy
- Published online:
- 05 March 2012
- Print publication:
- 14 April 2011, pp ix-xvi
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- By Shamsuddin Akhtar, Greg Albert, Sidney Allison, Muhammad Anwar, Haruo Arita, Amanda Barker, Mary Hanna Bekhit, Jeanna Blitz, Tyson Bolinske, David Burbulys, Asokumar Buvanendran, Gregory Cain, Keith A. Candiotti, Daniel B. Carr, Derek Chalmers, John Charney, Rex Cheng, Roger Chou, Keun Sam Chung, Anna Clebone, Frederick Conlin, Susan Dabu-Bondoc, Tiffany Denepitiya-Balicki, Jeanette Derdemezi, Anahat Kaur Dhillon, Ho Dzung, Juan Jose Egas, Stephen M. Eskaros, Zhuang T. Fang, Claudia R. Fernandez Robles, Victor A. Filadora, Ellen Flanagan, Dan Froicu, Allison Gandey, Nehal Gatha, Boris Gelman, Christopher Gharibo, Muhammad K. Ghori, Brian Ginsberg, Michael E. Goldberg, Jeff Gudin, Thomas Halaszynski, Martin Hale, Dorothea Hall, Craig T. Hartrick, Justin Hata, Lars E. Helgeson, Joe C. Hong, Richard W. Hong, Balazs Horvath, Eric S. Hsu, Gabriel Jacobs, Jonathan S. Jahr, Rongjie Jaing, Inderjeet Singh Julka, Zeev N. Kain, Clinton Kakazu, Kianusch Kiai, Mary Keyes, Michael M. Kim, Peter G. Lacouture, Ryan Lanier, Vivian K. Lee, Mark J. Lema, Oscar A. de Leon-Casasola, Imanuel Lerman, Philip Levin, Steven Levin, JinLei Li, Eric C. Lin, Sharon Lin, David A. Lindley, Ana M. Lobo, Marisa Lomanto, Mirjana Lovrincevic, Brenda C. McClain, Tariq Malik, Jure Marijic, Joseph Marino, Laura Mechtler, Alan Miller, Carly Miller, Amit Mirchandani, Sukanya Mitra, Fleurise Montecillo, James M. Moore, Debra E. Morrison, Philip F. Morway, Carsten Nadjat-Haiem, Hamid Nourmand, Dana Oprea, Sunil J. Panchal, Edward J. Park, Kathleen Ji Park, Kellie Park, Parisa Partownavid, Akta Patel, Bijal Patel, Komal D. Patel, Neesa Patel, Swati Patel, Paul M. Peloso, Danielle Perret, Anthony DePlato, Marjorie Podraza Stiegler, Despina Psillides, Mamatha Punjala, Johan Raeder, Siamak Rahman, Aziz M. Razzuk, Maggy G. Riad, Kristin L. Richards, R. Todd Rinnier, Ian W. Rodger, Joseph Rosa, Abraham Rosenbaum, Alireza Sadoughi, Veena Salgar, Leslie Schechter, Michael Seneca, Yasser F. Shaheen, James H. Shull, Elizabeth Sinatra, Raymond S. Sinatra, Neil Singla, Neil Sinha, Denis V. Snegovskikh, Dmitri Souzdalnitski, Julie Sramcik, Zoreh Steffens, Alexander Timchenko, Vadim Tokhner, Marc C. Torjman, Co T. Truong, Nalini Vadivelu, Ashley Vaughn, Anjali Vira, Eugene R. Viscusi, Dajie Wang, Shu-ming Wang, J. Michael Watkins-Pitchford, Steven J. Weisman, Ira Whitten, Bryan S. Williams, Jeremy M. Wong, Thomas Wong, Christopher Wray, Yaw Wu, Anthony T. Yarussi, Laurie Yonemoto, Bita H. Zadeh, Jill Zafar, Martha Zegarra, Keren Ziv
- Edited by Raymond S. Sinatra, Jonathan S. Jahr, University of California, Los Angeles, School of Medicine, J. Michael Watkins-Pitchford
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- Book:
- The Essence of Analgesia and Analgesics
- Published online:
- 06 December 2010
- Print publication:
- 14 October 2010, pp xi-xviii
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The glial modulatory drug AV411 attenuates mechanical allodynia in rat models of neuropathic pain
- Annemarie Ledeboer, Tongyao Liu, Jennifer A. Shumilla, John H. Mahoney, Sharmila Vijay, Matthew I. Gross, Joseph A. Vargas, Lance Sultzbaugh, Mark D. Claypool, Laura M. Sanftner, Linda R. Watkins, Kirk W. Johnson
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- Journal:
- Neuron Glia Biology / Volume 2 / Issue 4 / November 2006
- Published online by Cambridge University Press:
- 26 February 2007, pp. 279-291
- Print publication:
- November 2006
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Controlling neuropathic pain is an unmet medical need and we set out to identify new therapeutic candidates. AV411 (ibudilast) is a relatively nonselective phosphodiesterase inhibitor that also suppresses glial-cell activation and can partition into the CNS. Recent data strongly implicate activated glial cells in the spinal cord in the development and maintenance of neuropathic pain. We hypothesized that AV411 might be effective in the treatment of neuropathic pain and, hence, tested whether it attenuates the mechanical allodynia induced in rats by chronic constriction injury (CCI) of the sciatic nerve, spinal nerve ligation (SNL) and the chemotherapeutic paclitaxel (Taxol¯). Twice-daily systemic administration of AV411 for multiple days resulted in a sustained attenuation of CCI-induced allodynia. Reversal of allodynia was of similar magnitude to that observed with gabapentin and enhanced efficacy was observed in combination. We further show that multi-day AV411 reduces SNL-induced allodynia, and reverses and prevents paclitaxel-induced allodynia. Also, AV411 cotreatment attenuates tolerance to morphine in nerve-injured rats. Safety pharmacology, pharmacokinetic and initial mechanistic analyses were also performed. Overall, the results indicate that AV411 is effective in diverse models of neuropathic pain and support further exploration of its potential as a therapeutic agent for the treatment of neuropathic pain.
Executive function in Tourette's syndrome and obsessive–compulsive disorder
- LAURA H. WATKINS, BARBARA J. SAHAKIAN, MARY M. ROBERTSON, DAVID M. VEALE, ROBERT D. ROGERS, KATHRYN M. PICKARD, MICHAEL R. F. AITKEN, TREVOR W. ROBBINS
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- Journal:
- Psychological Medicine / Volume 35 / Issue 4 / April 2005
- Published online by Cambridge University Press:
- 08 November 2004, pp. 571-582
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Background. Cognitive performance was compared in the genetically and neurobiologically related disorders of Tourette's syndrome (TS) and obsessive–compulsive disorder (OCD), in three domains of executive function: planning, decision-making and inhibitory response control.
Method. Twenty TS patients, twenty OCD patients and a group of age- and IQ-matched normal controls completed psychometric and computerized cognitive tests and psychiatric rating scales. The cognitive tests were well-characterized in terms of their sensitivity to other fronto-striatal disorders, and included pattern and spatial recognition memory, attentional set-shifting, and a Go/No-go set-shifting task, planning, and decision-making.
Results. Compared to controls, OCD patients showed selective deficits in pattern recognition memory and slower responding in both pattern and spatial recognition, impaired extra-dimensional shifting on the set-shifting test and impaired reversal of response set on the Go/No-go test. In contrast, TS patients were impaired in spatial recognition memory, extra-dimensional set-shifting, and decision-making. Neither group was impaired in planning. Direct comparisons between the TS and OCD groups revealed significantly different greater deficits for recognition memory latency and Go/No-go reversal for the OCD group, and quality of decision-making for the TS group.
Conclusions. TS and OCD show both differences (recognition memory, decision-making) and similarities (set-shifting) in selective profiles of cognitive function. Specific set-shifting deficits in the OCD group contrasted with their intact performance on other tests of executive function, such as planning and decision-making, and suggested only limited involvement of frontal lobe dysfunction, possibly consistent with OCD symptomatology.