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4. Cover

Author

Garvey, Stephen P., Devins, Neal, Graber, Mark A., Gross, Samuel R., and Ellsworth, Phoebe C.

Published
2002

5. Title, Copyright, Dedication

Author

Garvey, Stephen P., Devins, Neal, Graber, Mark A., Gross, Samuel R., and Ellsworth, Phoebe C.

Published
2002

6. Index

Author

Garvey, Stephen P., Devins, Neal, Graber, Mark A., Gross, Samuel R., and Ellsworth, Phoebe C.

Published
2002

11. Acknowledgments

Author

Garvey, Stephen P., Devins, Neal, Graber, Mark A., Gross, Samuel R., and Ellsworth, Phoebe C.

Published
2002

12. COVER STORIES: An intervention at the MAH in Geneva by Ugo Rondinone has revealed tensions and surprises beneath the surface of Le Sommeil, Felix Vallotton's seemingly peaceful painting of a sleeping woman, as curator Samuel Gross explains

Author

Gross, Samuel

Subjects
Sleep, Arts, visual and performing
Abstract

Felix Vallotton's Le Sommeil ('Sleep', 1908; Fig. 1) is currently not hanging on the walls of the Musee d'Art et d'Histoire in Geneva, where it normally lives, but instead is [...]

Published
2023

13. Evaluation of cell-free DNA approaches for multi-cancer early detection

Author

Jamshidi, Arash, Liu, Minetta C., Klein, Eric A., Venn, Oliver, Hubbell, Earl, Beausang, John F., Gross, Samuel, Melton, Collin, Fields, Alexander P., Liu, Qinwen, Zhang, Nan, Fung, Eric T., Kurtzman, Kathryn N., Amini, Hamed, Betts, Craig, Civello, Daniel, Freese, Peter, Calef, Robert, Davydov, Konstantin, Fayzullina, Saniya, Hou, Chenlu, Jiang, Roger, Jung, Byoungsok, Tang, Susan, Demas, Vasiliki, Newman, Joshua, Sakarya, Onur, Scott, Eric, Shenoy, Archana, Shojaee, Seyedmehdi, Steffen, Kristan K., Nicula, Virgil, Chien, Tom C., Bagaria, Siddhartha, Hunkapiller, Nathan, Desai, Mohini, Dong, Zhao, Richards, Donald A., Yeatman, Timothy J., Cohn, Allen L., Thiel, David D., Berry, Donald A., Tummala, Mohan K., McIntyre, Kristi, Sekeres, Mikkael A., Bryce, Alan, Aravanis, Alexander M., Seiden, Michael V., and Swanton, Charles

Published
2022
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15. A Selective Approach to Internal Inference

Author

Gross, Samuel M., Taylor, Jonathan, and Tibshirani, Robert

Subjects
Mathematics - Statistics Theory, Statistics - Methodology
Abstract

A common goal in modern biostatistics is to form a biomarker signature from high dimensional gene expression data that is predictive of some outcome of interest. After learning this biomarker signature, an important question to answer is how well it predicts the response compared to classical predictors. This is challenging, because the biomarker signature is an internal predictor -- one that has been learned using the same dataset on which we want to evaluate it's significance. We propose a new method for approaching this problem based on the technique of selective inference. Simulations show that our method is able to properly control the level of the test, and that in certain settings we have more power than sample splitting.

Published
2015

16. Software for Distributed Computation on Medical Databases: A Demonstration Project

Author

Narasimhan, Balasubramanian, Rubin, Daniel L., Gross, Samuel M., Bendersky, Marina, and Lavori, Philip W.

Subjects
Statistics - Computation, Computer Science - Mathematical Software, Computer Science - Software Engineering
Abstract

Bringing together the information latent in distributed medical databases promises to personalize medical care by enabling reliable, stable modeling of outcomes with rich feature sets (including patient characteristics and treatments received). However, there are barriers to aggregation of medical data, due to lack of standardization of ontologies, privacy concerns, proprietary attitudes toward data, and a reluctance to give up control over end use. Aggregation of data is not always necessary for model fitting. In models based on maximizing a likelihood, the computations can be distributed, with aggregation limited to the intermediate results of calculations on local data, rather than raw data. Distributed fitting is also possible for singular value decomposition. There has been work on the technical aspects of shared computation for particular applications, but little has been published on the software needed to support the "social networking" aspect of shared computing, to reduce the barriers to collaboration. We describe a set of software tools that allow the rapid assembly of a collaborative computational project, based on the flexible and extensible R statistical software and other open source packages, that can work across a heterogeneous collection of database environments, with full transparency to allow local officials concerned with privacy protections to validate the safety of the method. We describe the principles, architecture, and successful test results for the site-stratified Cox model and rank-k Singular Value Decomposition (SVD).

Published
2014

17. Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA

Author

Liu, Minetta C., Oxnard, Geoffrey R., Klein, Eric A., Smith, David, Richards, Donald, Yeatman, Timothy J., Cohn, Allen L., Lapham, Rosanna, Clement, Jessica, Parker, Alexander S., Tummala, Mohan K., McIntyre, Kristi, Sekeres, Mikkael A., Bryce, Alan H., Siegel, Robert, Wang, Xuezhong, Cosgrove, David P., Abu-Rustum, Nadeem R., Trent, Jonathan, Thiel, David D., Becerra, Carlos, Agrawal, Manish, Garbo, Lawrence E., Giguere, Jeffrey K., Michels, Ross M., Harris, Ronald P., Richey, Stephen L., McCarthy, Timothy A., Waterhouse, David M., Couch, Fergus J., Wilks, Sharon T., Krie, Amy K., Balaraman, Rama, Restrepo, Alvaro, Meshad, Michael W., Rieger-Christ, Kimberly, Sullivan, Travis, Lee, Christine M., Greenwald, Daniel R., Oh, William, Tsao, Che-Kai, Fleshner, Neil, Kennecke, Hagen F., Khalil, Maged F., Spigel, David R., Manhas, Atisha P., Ulrich, Brian K., Kovoor, Philip A., Stokoe, Christopher, Courtright, Jay G., Yimer, Habte A., Larson, Timothy G., Swanton, Charles, Seiden, Michael V., Cummings, Steven R., Absalan, Farnaz, Alexander, Gregory, Allen, Brian, Amini, Hamed, Aravanis, Alexander M., Bagaria, Siddhartha, Bazargan, Leila, Beausang, John F., Berman, Jennifer, Betts, Craig, Blocker, Alexander, Bredno, Joerg, Calef, Robert, Cann, Gordon, Carter, Jeremy, Chang, Christopher, Chawla, Hemanshi, Chen, Xiaoji, Chien, Tom C., Civello, Daniel, Davydov, Konstantin, Demas, Vasiliki, Desai, Mohini, Dong, Zhao, Fayzullina, Saniya, Fields, Alexander P., Filippova, Darya, Freese, Peter, Fung, Eric T., Gnerre, Sante, Gross, Samuel, Halks-Miller, Meredith, Hall, Megan P., Hartman, Anne-Renee, Hou, Chenlu, Hubbell, Earl, Hunkapiller, Nathan, Jagadeesh, Karthik, Jamshidi, Arash, Jiang, Roger, Jung, Byoungsok, Kim, TaeHyung, Klausner, Richard D., Kurtzman, Kathryn N., Lee, Mark, Lin, Wendy, Lipson, Jafi, Liu, Hai, Liu, Qinwen, Lopatin, Margarita, Maddala, Tara, Maher, M. Cyrus, Melton, Collin, Mich, Andrea, Nautiyal, Shivani, Newman, Jonathan, Newman, Joshua, Nicula, Virgil, Nicolaou, Cosmos, Nikolic, Ongjen, Pan, Wenying, Patel, Shilpen, Prins, Sarah A., Rava, Richard, Ronaghi, Neda, Sakarya, Onur, Satya, Ravi Vijaya, Schellenberger, Jan, Scott, Eric, Sehnert, Amy J., Shaknovich, Rita, Shanmugam, Avinash, Shashidhar, K.C., Shen, Ling, Shenoy, Archana, Shojaee, Seyedmehdi, Singh, Pranav, Steffen, Kristan K., Tang, Susan, Toung, Jonathan M., Valouev, Anton, Venn, Oliver, Williams, Richard T., Wu, Tony, Xu, Hui H., Yakym, Christopher, Yang, Xiao, Yecies, Jessica, Yip, Alexander S., Youngren, Jack, Yue, Jeanne, Zhang, Jingyang, Zhang, Lily, Zhang, Lori (Quan), Zhang, Nan, Curtis, Christina, Berry, Donald A., Liu, M.C., Oxnard, G.R., Klein, E.A., Swanton, C., and Seiden, M.V.

Published
2020
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18. Collaborative Regression

Author

Gross, Samuel M. and Tibshirani, Robert

Subjects
Quantitative Biology - Quantitative Methods, Statistics - Machine Learning
Abstract

We consider the scenario where one observes an outcome variable and sets of features from multiple assays, all measured on the same set of samples. One approach that has been proposed for dealing with this type of data is ``sparse multiple canonical correlation analysis'' (sparse mCCA). All of the current sparse mCCA techniques are biconvex and thus have no guarantees about reaching a global optimum. We propose a method for performing sparse supervised canonical correlation analysis (sparse sCCA), a specific case of sparse mCCA when one of the datasets is a vector. Our proposal for sparse sCCA is convex and thus does not face the same difficulties as the other methods. We derive efficient algorithms for this problem, and illustrate their use on simulated and real data., Comment: 13 pages, 4 figures

Published
2014

31. CONTRAlign: Discriminative Training for Protein Sequence Alignment

Author

Do, Chuong B., Gross, Samuel S., Batzoglou, Serafim, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Apostolico, Alberto, editor, Guerra, Concettina, editor, and Pevzner, Pavel A., editor

Published
2006
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32. Using Multiple Alignments to Improve Gene Prediction

Author

Gross, Samuel S., Brent, Michael R., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Miyano, Satoru, editor, Mesirov, Jill, editor, Kasif, Simon, editor, and Pevzner, Pavel A., editor

Published
2005
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34. BLAIR THURMAN: poussière magique.

Author

Gross, Samuel

Abstract

An interview with the artist Blair Thurman has been presented, discussing his practice, the role of found art in his work, and the use of abstraction. He describes his studio as a "Fluxus pile of junk," and emphasizes the importance of found forms and artifacts in his work, which he takes through various filters to understand how they relate to his other work. He also discusses the use of neon and other media in his work, which he views as a way of putting the studio into the gallery.

Published
2023

37. COVER STORIES.

Author

Gross, Samuel and Behrens, Edward

Abstract

The article reviews art exhibition "Le Sommell" by artist Félix Vallotton at the Musée d'Art et d'Histoire in Genevam Switzerland as of April 1, 2023.

Published
2023

39. Clinical Realism: Simulated Hearings Based on Actual Events in Students' Lives.

Author

Gross, Samuel R.

Abstract

A clinical law simulation exercise based on students testimony about events in their own lives was designed to train students as effective trial lawyers through direct and cross-examination, sensitization to the roles of other courtroom players, and consideration of social and ethical consequences of our trial methods. (MSE)

Published
1990

46. Evolution of genes and genomes on the Drosophila phylogeny

Author

Clark, Andrew G., Eisen, Michael B., Smith, Douglas R., Bergman, Casey M., Oliver, Brian, Markow, Therese A., Kaufman, Thomas C., Kellis, Manolis, Gelbart, William, Iyer, Venky N., Pollard, Daniel A., Sackton, Timothy B., Larracuente, Amanda M., Singh, Nadia D., Abad, Jose P., Abt, Dawn N., Adryan, Boris, Aguade, Montserrat, Akashi, Hiroshi, Anderson, Wyatt W., Aquadro, Charles F., Ardell, David H., Arguello, Roman, Artieri, Carlo G., Barbash, Daniel A., Barker, Daniel, Barsanti, Paolo, Batterham, Phil, Batzoglou, Serafim, Begun, Dave, Bhutkar, Arjun, Blanco, Enrico, Bosak, Stephanie A., Bradley, Robert K., Brand, Adrianne D., Brent, Michael R., Brooks, Angela N., Brown, Randall H., Butlin, Roger K., Caggese, Corrado, Calvi, Brian R., Bernardo de Carvalho, A., Caspi, Anat, Castrezana, Sergio, Celniker, Susan E., Chang, Jean L., Chapple, Charles, Chatterji, Sourav, Chinwalla, Asif, Civetta, Alberto, Clifton, Sandra W., Comeron, Josep M., Costello, James C., Coyne, Jerry A., Daub, Jennifer, David, Robert G., Delcher, Arthur L., Delehaunty, Kim, Do, Chuong B., Ebling, Heather, Edwards, Kevin, Eickbush, Thomas, Evans, Jay D., Filipski, Alan, Findeiß, Sven, Freyhult, Eva, Fulton, Lucinda, Fulton, Robert, Garcia, Ana C. L., Gardiner, Anastasia, Garfield, David A., Garvin, Barry E., Gibson, Greg, Gilbert, Don, Gnerre, Sante, Godfrey, Jennifer, Good, Robert, Gotea, Valer, Gravely, Brenton, Greenberg, Anthony J., Griffiths-Jones, Sam, Gross, Samuel, Guigo, Roderic, Gustafson, Erik A., Haerty, Wilfried, Hahn, Matthew W., Halligan, Daniel L., Halpern, Aaron L., Halter, Gillian M., Han, Mira V., Heger, Andreas, Hillier, LaDeana, Hinrichs, Angie S., Holmes, Ian, Hoskins, Roger A., Hubisz, Melissa J., Hultmark, Dan, Huntley, Melanie A., Jaffe, David B., Jagadeeshan, Santosh, Jeck, William R., Johnson, Justin, Jones, Corbin D., Jordan, William C., Karpen, Gary H., Kataoka, Eiko, Keightley, Peter D., Kheradpour, Pouya, Kirkness, Ewen F., Koerich, Leonardo B., Kristiansen, Karsten, Kudrna, Dave, Kulathinal, Rob J., Kumar, Sudhir, Kwok, Roberta, Lander, Eric, Langley, Charles H., Lapoint, Richard, Lazzaro, Brian P., Lee, So-Jeong, Levesque, Lisa, Li, Ruiqiang, Lin, Chiao-Feng, Lin, Michael F., Lindblad-Toh, Kerstin, Llopart, Ana, Long, Manyuan, Low, Lloyd, Lozovsky, Elena, Lu, Jian, Luo, Meizhong, Machado, Carlos A., Makalowski, Wojciech, Marzo, Mar, Matsuda, Muneo, Matzkin, Luciano, McAllister, Bryant, McBride, Carolyn S., McKernan, Brendan, McKernan, Kevin, Mendez-Lago, Maria, Minx, Patrick, Mollenhauer, Michael U., Montooth, Kristi, Mount, Stephen M., Mu, Xu, Myers, Eugene, Negre, Barbara, Newfeld, Stuart, Nielsen, Rasmus, Noor, Mohamed A. F., O'Grady, Patrick, Pachter, Lior, Papaceit, Montserrat, Parisi, Matthew J., Parisi, Michael, Parts, Leopold, Pedersen, Jakob S., Pesole, Graziano, Phillippy, Adam M., Ponting, Chris P., Pop, Mihai, Porcelli, Damiano, Powell, Jeffrey R., Prohaska, Sonja, Pruitt, Kim, Puig, Marta, Quesneville, Hadi, Ravi Ram, Kristipati, Rand, David, Rasmussen, Matthew D., Reed, Laura K., Reenan, Robert, Reily, Amy, Remington, Karin A., Rieger, Tania T., Ritchie, Michael G., Robin, Charles, Rogers, Yu-Hui, Rohde, Claudia, Rozas, Julio, Rubenfield, Marc J., Ruiz, Alfredo, Russo, Susan, Salzberg, Steven L., Sanchez-Gracia, Alejandro, Saranga, David J., Sato, Hajime, Schaeffer, Stephen W., Schatz, Michael C., Schlenke, Todd, Schwartz, Russell, Segarra, Carmen, Singh, Rama S., Sirot, Laura, Sirota, Marina, Sisneros, Nicholas B., Smith, Chris D., Smith, Temple F., Spieth, John, Stage, Deborah E., Stark, Alexander, Stephan, Wolfgang, Strausberg, Robert L., Strempel, Sebastian, Sturgill, David, Sutton, Granger, Sutton, Granger G., Tao, Wei, Teichmann, Sarah, Tobari, Yoshiko N., Tomimura, Yoshihiko, Tsolas, Jason M., Valente, Vera L. S., Venter, Eli, Craig Venter, J., Vicario, Saverio, Vieira, Filipe G., Vilella, Albert J., Villasante, Alfredo, Walenz, Brian, Wang, Jun, Wasserman, Marvin, Watts, Thomas, Wilson, Derek, Wilson, Richard K., Wing, Rod A., Wolfner, Mariana F., Wong, Alex, Ka-Shu Wong, Gane, Wu, Chung-I, Wu, Gabriel, Yamamoto, Daisuke, Yang, Hsiao-Pei, Yang, Shiaw-Pyng, Yorke, James A., Yoshida, Kiyohito, Zdobnov, Evgeny, Zhang, Peili, Zhang, Yu, Zimin, Aleksey V., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Christophe Acer, St, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Erii Husby, M, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Grabherr, Manfred, Kleber, Michael, Mauceli, Evan, and MacCallum, Iain

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Drosophila 12 Genomes Consortium; Project Leaders; Andrew G. Clark (corresponding author) [1]; Michael B. Eisen (corresponding author) [2, 3]; Douglas R. Smith (corresponding author) [4]; Casey M. Bergman (corresponding [...]

Published
2007
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47. A manual of general anatomy, containing a concise description of the elementary tissues of the human body. From the French of A.L.J. Bayle and H. Hollard. By S.D. Gross, M.D.

Author

Bayle, Antoine Laurent Jessé, 1799-1858, Gross, Samuel D. (Samuel David), 1805-1884, Hollard, H. 1801-1866, Univ. of Mass Medical School, Lamar Soutter Library (archive.org), Bayle, Antoine Laurent Jessé, 1799-1858, Gross, Samuel D. (Samuel David), 1805-1884, and Hollard, H. 1801-1866

Subjects
Anatomy, Human anatomy, Rare books
Published
1828

48. Elements of pathological anatomy.

Author

Gross, Samuel D. (Samuel David), 1805-1884, Univ. of Mass Medical School, Lamar Soutter Library (archive.org), and Gross, Samuel D. (Samuel David), 1805-1884

Subjects
Anatomy, Rare books
Published
1843

50. Expert information and expert evidence: a preliminary taxonomy.

Author

Gross, Samuel R. and Mnookin, Jennifer L.

Subjects
Evidence, Expert -- Laws, regulations and rules, Evidence, Scientific -- Laws, regulations and rules, Daubert v. Merrell Dow Pharmaceuticals, Inc. (509 U.S. 579 (1993)), Kumho Tire Co. v. Carmichael (526 U.S. 137 (1999)), General Electric Co. v. Joiner (522 U.S. 136 (1997)), Government regulation, Federal Rules of Evidence (Fed. R. Evid. 702)
Published
2003

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