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1. Contributors

Author

Herand Abcarian, Fizan Abdullah, Michael A. Abramson, Christopher J. Abularrage, Reid B. Adams, John. Adamski, Steven A. Ahrendt, Nita Ahuja, Hasan B. Alam, John C. Alverdy, David N. Armstrong, George J. Arnaoutakis, Alejandro Arnold, Zachary M. Arthurs, Horacio J. Asbun, Nancy L. Ascher, Theodor Asgeirsson, Stanley W. Ashley, Gildy V. Babiera, James H. Balcom, Zsolt J. Balogh, Farzaneh Banki, Adrian Barbul, Philip S. Barie, Todd W. Bauer, David E. Beck, Mazen I. Bedri, Manijeh Berenji, David L. Berger, Thomas A. Bergman, Stepheny D. Berry, Richard P. Billingham, Elisa H. Birnbaum, James H. Black, Kirby I. Bland, Grant V. Bochicchio, Philippe Bouchard, Judy C. Boughey, Steven P. Bowers, Colin M. Brady, Steven B. Brandes, Peter Brant-Zawadzki, Kenneth L. Brayman, Stacy A. Brethauer, Malcolm V. Brock, Benjamin S. Brooke, James T. Broome, Carl J. Brown, F. Charles Brunicardi, Thomas M. Brushart, Timothy G. Buchman, Eileen M. Bulger, J. Bracken Burns, Ronald W. Busuttil, John Byrne, Glenda G. Callender, Mark P. Callery, Richard P. Cambria, Andrew M. Cameron, John L. Cameron, Jeffrey Campsen, Joseph A. Caprini, Jonathan Carter, Abigail S. Caudle, Eugene P. Ceppa, Marisa Cevasco, Elliot L. Chaikof, Sricharan Chalikonda, Vinay Chandrasekhara, Vivek Chaudhry, Haiquan Chen, Herbert Chen, Aaron M. Cheng, Michael A. Choti, Kathleen K. Christians, A. Britton Christmas, Heidi Chua, Albert K. Chun, Alice Chung, Orlo H. Clark, Sean P. Cleary, Christine S. Cocanour, Panna A. Codner, Thomas H. Cogbill, Patrick S. Collier, Mark F. Conrad, Joel D. Cooper, Cybil Corning, Vicente Cortes, Joseph S. Coselli, Randall O. Craft, Martin A. Croce, Jessica Crow, Robert F. Cuff, Joseph J. Cullen, Steven C. Cunningham, Myriam J. Curet, Alan P.B. Dackiw, Nabil N. Dagher, R. Clement Darling, Nancy E. Davidson, John J. Degliuomini, Amy C. Degnim, Conor P. Delaney, Ronald P. DeMatteo, Steven R. DeMeester, Tom R. DeMeester, Daniel T. Dempsey, Ashwin L. deSouza, E. Gene Deune, Wayne C. DeVos, Justin B. Dimick, Timothy R. Donahue, Jonathan M. Dort, Eric J. Dozois, Elizabeth Dreesen, Quan-Yang Duh, Scott A. Dulchavsky, Mark D. Duncan, Umamaheshwar Duvvuri, Soumitra R. Eachempati, Jeffrey Eakin, Frederic E. Eckhauser, Barish H. Edil, Eric D. Edwards, Meghan Edwards, David T. Efron, Jonathan E. Efron, Philip A. Efron, E. Christopher Ellison, Trevor A. Ellison, Amgad El Sherif, Guillermo A. Escobar, Domenic P. Esposito, Douglas B. Evans, Heather L. Evans, Peter J. Fabri, Ronald M. Fairman, Houssam Farres, Richard H. Feins, David V. Feliciano, Charles M. Ferguson, Mark K. Ferguson, Cristina R. Ferrone, George S. Ferzli, Alessandro Fichera, Aaron S. Fink, David Fink, Rhonda Fishel, Kerry Fisher, William E. Fisher, Timothy C. Fitzgibbons, James W. Fleshman, Lewis M. Flint, Tanya R. Flohr, Jaime I. Flores, Sara P. Fogarty, Paul J. Foley, Yuman Fong, Charles M. Friel, Eric R. Frykberg, Joseph C. Fuller, Michele A. Gadd, Philippe Gailloud, Charles Galanis, James J. Gallagher, Scott F. Gallagher, Bryan A. Gaspard, Colleen B. Gaughan, Susan L. Gearhart, David A. Geller, Christos S. Georgiades, Jean-Francois H. Geschwind, Bashar Ghosheh, Samuel A. Giday, Armando E. Giuliano, Natalia Glebova, Nelson H. Goldberg, Jerry Goldstone, Suman Golla, Jessica E. Gosnell, Jeffrey R. Gourley, Jay A. Graham, Jayleen Grams, Michael P. Grant, Ana M. Grau, Axel Grothey, Marlon A. Guerrero, Jose G. Guillem, Adil H. Haider, Bruce Lee Hall, David C. Han, John W. Harmon, Kristi L. Harold, Amy P. Harper, Hobart W. Harris, Samad Hashimi, Heitham T. Hassoun, Elliott R. Haut, Marie-Noëlle Hébert-Blouin, Richard F. Heitmiller, J. Michael Henderson, B. Todd Heniford, Peter K. Henke, H. Franklin Herlong, Jonathan M. Hernandez, Philip J. Hess, Jonathan R. Hiatt, O. Joe Hines, Richard A. Hodin, John P. Hoffman, Johnny C. Hong, Toshitaka Hoppo, Jan K. Horn, Francis J. Hornicek, Rydhwana Hossain, Thomas J. Howard, David B. Hoyt, Jennifer E. Hrabe, Tjasa Hranjec, Tracy L. Hull, Mark D. Iannettoni, David A. Iannitti, Kamran Idrees, Elizabeth A. Ignacio, Tim A. Iseli, Hiromichi Ito, Heather Jacene, Lana L. Jackson, Lenworth M. Jacobs, Lisa K. Jacobs, Sanjay Jagannath, Nicholas Jaszczak, Vijay Jayaraman, Juan Carlos Jimenez, Judy Jin, Blair A. Jobe, Jennifer E. Joh, Eric K. Johnson, Jonas T. Johnson, Lynt B. Johnson, Michael Johnson, Sreenivasa Jonnalagadda, Gregory J. Jurkovich, Stefan S. Kachala, Anthony N. Kalloo, Giorgos C. Karakousis, Ryan D. Katz, Thomas Keane, Electron Kebebew, K. Craig Kent, Tara S. Kent, Mouen Khashab, Arman Kilic, Elizabeth Min Hui Kim, Yongsik Kim, Jonathan C. King, Tari A. King, Andrew W. Kirkpatrick, Allen Kong, Richard A. Kozarek, Mark J. Krasna, Helen Krontiras, David Kuwayama, Edward C.S. Lai, Alysandra Lal, Glenn M. LaMuraglia, Kwan N. Lau, Harish Lavu, Peter F. Lawrence, Karl A. LeBlanc, Anna M. Ledgerwood, Scott A. LeMaire, Barry C. Lembersky, William H. Leukhardt, Ryan Li, Keith D. Lillemoe, Pamela A. Lipsett, Evan C. Lipsitz, Alex G. Little, Charles E. Lucas, James D. Luketich, Ying Wei Lum, Sean P. Lyden, Bruce V. MacFadyen, Maria Lucia L. Madariaga, Thomas H. Magnuson, Ronald V. Maier, Martin A. Makary, Rohit Makhija, Mark A. Malangoni, Mahmoud B. Malas, Paul N. Manson, Peter W. Marcello, Jeffrey M. Marks, Michael R. Marohn, Terri R. Martin, Tomas D. Martin, Douglas J. Mathisen, Brent D. Matthews, Peter J. Mazzaglia, John E. McDermott, David W. McFadden, Christopher R. McHenry, Robert C. McIntyre, Elisabeth C. McLemore, Robin S. McLeod, John D. Mellinger, Nicholas Melo, Genevieve B. Melton, Andrew J. Meltzer, W. Scott Melvin, Maria Clara Mendoza, Ryan Messiner, Anthony A. Meyer, William C. Meyers, Fabrizio Michelassi, Keith W. Millikan, Thomas J. Miner, Jeffrey F. Moley, Frederick A. Moore, Ellen H. Morrow, Monica Morrow, Angela K. Moss, Fady Moustarah, Sami Mufeed, Roberta L. Muldoon, Ashok Muniappan, Erin H. Murphy, Peter Muscarella, Maurice Y. Nahabedian, Lena M. Napolitano, William H. Nealon, Todd Neideen, Leigh A. Neumayer, Naeem A. Newman, Hien T. Nguyen, Kevin Tri Nguyen, Mehrdad Nikfarjam, Jeffrey A. Norton, Charles S. O'Mara, Raymond P. Onders, H. Leon Pachter, Theodore N. Pappas, Manish Parikh, Jason Park, Jose L. Pascual, Virendra I. Patel, Russell K. Pearl, Andrew B. Peitzman, John H. Pemberton, Bruce A. Perler, Nancy D. Perrier, Catherine E. Pesce, Joseph B. Petelin, Jeffrey H. Peters, Henrik Petrowsky, Jason M. Pfluke, Scott R. Philipp, Bradley J. Phillips, Greta L. Piper, Henry A. Pitt, Louis R. Pizano, Jeffrey L. Ponsky, Jason D. Prescott, Peter J. Pronovost, Gerd D. Pust, Aliaksei Pustavoitau, Juan Carlos Puyana, Umair Qazi, Robert R. Quickel, Jin H. Ra, Ariel N. Rad, Martin G. Radvany, Janice F. Rafferty, Reza Rahbari, Margarita Ramos, Bruce J. Ramshaw, Arthur Rawlings, Patrick R. Reardon, Howard A. Reber, Jennifer G. Reeder, Tobi Reidy, Andrew Reifsnyder, Thomas F. Reifsnyder, Andrew S. Resnick, William O. Richards, Erwin Rieder, John P. Roberts, Raymond E. Robinson, Thomas N. Robinson, Aurelio Rodriguez, Jose M. Rodriguez-Paz, Selwyn O. Rogers, Mark Romig, Glen S. Roseborough, Alexander S. Rosemurgy, Eben L. Rosenthal, Daniel C. Rossi, Gedge D. Rosson, Bashar Safar, Barry A. Salky, Rachel J. Santora, Shawn N. Sarin, Robert G. Sawyer, Harry C. Sax, Thomas M. Scalea, Philip R. Schauer, A. Frederick Schild, C. Max Schmidt, John G. Schneider, Martin A. Schreiber, Douglas J.E. Schuerer, Richard D. Schulick, C. William Schwab, Michael A. Schweitzer, Christopher Scortino, Anthony J. Senagore, Stephen M. Sentovich, Boris Sepesi, Melanie W. Seybt, Amit Shah, Paul C. Shellito, Alexander D. Shepard, Kirti Shetty, Jason K. Sicklick, Eric J. Silberfein, Ronald P. Silverman, Rache M. Simmons, Ronald F. Sing, Barbara L. Smith, C. Daniel Smith, Maurice A. Smith, R. Stephen Smith, Michael J. Snyder, Helen Sohn, David I. Soybel, Michael P. Spencer, Robert J. Spinner, Nicholas J. Spoerke, Scott R. Steele, Sharon L. Stein, Kent A. Stevens, Robert P. Sticca, Gregory V. Stiegmann, Jerry Stonemetz, Steven M. Strasberg, Michael B. Streiff, Stacey Su, Joseph F. Sucher, Marc Sussman, David E.R. Sutherland, Lee L. Swanstrom, Maakan Taghizadeh, Mark A. Talamini, John L. Tarpley, Servet Tatli, Spence M. Taylor, David J. Terris, Geoffrey B. Thompson, L. William Traverso, Donald D. Trunkey, Peter I. Tsai, Susan Tsai, Theodore N. Tsangaris, Robert Udelsman, Konstantin Umanskiy, Gilbert R. Upchurch, Marshall M. Urist, Harold C. Urschel, Parsia A. Vagefi, Philbert Y. Van, Kyle J. Van Arendonk, Jean-Nicolas Vauthey, Nirmal K. Veeramachaneni, George C. Velmahos, Anthony C. Venbrux, Charles M. Vollmer, Frank K. Wacker, Marc K. Wallack, R. Matthew Walsh, Grace J. Wang, Jennifer Y. Wang, Thomas N. Wang, Joshua A. Waters, Michael T. Watkins, Christopher M. Watson, Alexandra L.B. Webb, John A. Weigelt, Eric G. Weiss, Edward E. Whang, Eric B. Whitacre, D. Brandon Williams, Bruce G. Wolff, Christopher Wolfgang, Patricia Wong, Douglas E. Wood, Bhupender Yadav, Stephen C. Yang, Charles J. Yeo, Sam S. Yoon, Christopher J. You, Y. Nancy You, Yassar Youssef, Stéphane Zalinski, Gideon A. Zamir, Christopher K. Zarins, Martha A. Zeiger, Michael E. Zenilman, and Michael A. Zimmerman

Published
2011
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2. [29] Functional analyses of aquaporin water channel proteins

Author

John C. Mathai, Barbara L. Smith, Gregory M. Preston, and Peter Agre

Subjects
chemistry.chemical_compound, Biochemistry, Chemistry, polycyclic compounds, technology, industry, and agriculture, Gramicidin, Biophysics, Aquaporin, lipids (amino acids, peptides, and proteins), Model system, Biological membrane, Water Channel Proteins, Ion channel
Abstract

This article summarizes methods for the chemical synthesis and biophysical characterization of gramicidins with varying sequences and labels. The family of gramicidin channels has developed into a powerful model system for understanding fundamental properties, interactions, and dynamics of proteins and lipids generally, and ion channels specifically, in biological membranes.

Published
1999
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3. Prediction of primary breast cancer size and T-stage using micro-computed tomography in lumpectomy specimens

Author

Wafa M Sarraj, Rong Tang, Anas L Najjar, Molly Griffin, Anthony H Bui, Alan Zambeli-Ljepovic, Mike Senter-Zapata, Maya Lewin-Berlin, Leopoldo Fernandez, Juliette Buckley, Amy Ly, Elena Brachtel, Owen Aftreth, John Gilbertson, Yukako Yagi, Michele Gadd, Kevin S Hughes, Barbara L Smith, and James S Michaelson

Subjects
Breast cancer, breast imaging, gross pathology, micro-computed tomography, tumor size, Computer applications to medicine. Medical informatics, R858-859.7, Pathology, RB1-214
Abstract

Background: Histopathology is the only accepted method to measure and stage the breast tumor size. However, there is a need to find another method to measure and stage the tumor size when the pathological assessment is not available. Micro-computed tomography. (micro-CT) has the ability to measure tumor in three dimensions in an intact lumpectomy specimen. In this study, we aimed to determine the accuracy of micro-CT to measure and stage the primary tumor size in breast lumpectomy specimens, as compared to the histopathology. Materials and Methods: Seventy-two women who underwent lumpectomy surgery at the Massachusetts General Hospital Department of Surgery from June 2011 to September 2011, and from August 2013 to December 2013 participated in this study. The lumpectomy specimens were scanned using micro-CT followed by routine pathological processing. The maximum dimension of the invasive breast tumor was obtained from the micro-CT image and was compared to the corresponding pathology report for each subject. Results: The invasive tumor size measurement by micro-CT was underestimated in 24. cases. (33%), overestimated in 37. cases. (51%), and matched it exactly in 11. cases. (15%) compared to the histopathology measurement for all the cases. However, micro-CT T.stage classification differed from histopathology in only 11. (15.2%) with 6. cases. (8.3%) classified as a higher stage by micro-CT, and 5. cases. (6.9%) classified as lower compared to histopathology. In addition, micro-CT demonstrated a statically significant strong agreement (κ =0.6, P < 0.05) with pathological tumor size and staging for invasive ductal carcinoma. (IDC) group. In contrast, there was no agreement. (κ = .2, P = 0.67) between micro-CT and pathology in estimating and staging tumor size for invasive lobular carcinoma. (ILC) group. This could be explained by a small sample size. (7) for ILC group. Conclusions: Micro-CT is a promising modality for measuring and staging the IDC.

Published
2015
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4. The feasibility of using natural language processing to extract clinical information from breast pathology reports

Author

Julliette M Buckley, Suzanne B Coopey, John Sharko, Fernanda Polubriaginof, Brian Drohan, Ahmet K Belli, Elizabeth M. H. Kim, Judy E Garber, Barbara L Smith, Michele A Gadd, Michelle C Specht, Constance A Roche, Thomas M Gudewicz, and Kevin S Hughes

Subjects
Breast pathology reports, clinical decision support, natural language processing, Computer applications to medicine. Medical informatics, R858-859.7, Pathology, RB1-214
Abstract

Objective: The opportunity to integrate clinical decision support systems into clinical practice is limited due to the lack of structured, machine readable data in the current format of the electronic health record. Natural language processing has been designed to convert free text into machine readable data. The aim of the current study was to ascertain the feasibility of using natural language processing to extract clinical information from >76,000 breast pathology reports. Approach and Procedure: Breast pathology reports from three institutions were analyzed using natural language processing software (Clearforest, Waltham, MA) to extract information on a variety of pathologic diagnoses of interest. Data tables were created from the extracted information according to date of surgery, side of surgery, and medical record number. The variety of ways in which each diagnosis could be represented was recorded, as a means of demonstrating the complexity of machine interpretation of free text. Results: There was widespread variation in how pathologists reported common pathologic diagnoses. We report, for example, 124 ways of saying invasive ductal carcinoma and 95 ways of saying invasive lobular carcinoma. There were >4000 ways of saying invasive ductal carcinoma was not present. Natural language processor sensitivity and specificity were 99.1% and 96.5% when compared to expert human coders. Conclusion: We have demonstrated how a large body of free text medical information such as seen in breast pathology reports, can be converted to a machine readable format using natural language processing, and described the inherent complexities of the task.

Published
2012
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