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2. Author Correction: COSMOS: a platform for real-time morphology-based, label-free cell sorting using deep learning

Author

Salek, Mahyar, Li, Nianzhen, Chou, Hou-Pu, Saini, Kiran, Jovic, Andreja, Jacobs, Kevin B., Johnson, Chassidy, Lu, Vivian, Lee, Esther J., Chang, Christina, Nguyen, Phuc, Mei, Jeanette, Pant, Krishna P., Wong-Thai, Amy Y., Smith, Quillan F., Huang, Stephanie, Chow, Ryan, Cruz, Janifer, Walker, Jeff, Chan, Bryan, Musci, Thomas J., Ashley, Euan A., and Masaeli, Maddison (Mahdokht)

Published
2023
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3. COSMOS: a platform for real-time morphology-based, label-free cell sorting using deep learning

Author

Salek, Mahyar, Li, Nianzhen, Chou, Hou-Pu, Saini, Kiran, Jovic, Andreja, Jacobs, Kevin B., Johnson, Chassidy, Lu, Vivian, Lee, Esther J., Chang, Christina, Nguyen, Phuc, Mei, Jeanette, Pant, Krishna P., Wong-Thai, Amy Y., Smith, Quillan F., Huang, Stephanie, Chow, Ryan, Cruz, Janifer, Walker, Jeff, Chan, Bryan, Musci, Thomas J., Ashley, Euan A., and Masaeli, Maddison (Mahdokht)

Published
2023
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4. A stochastic and dynamical view of pluripotency in mouse embryonic stem cells

Author

Lin, Yen Ting, Hufton, Peter G., Lee, Esther J., and Potoyan, Davit A.

Subjects
Quantitative Biology - Molecular Networks, Condensed Matter - Statistical Mechanics, Physics - Biological Physics
Abstract

Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent state is regulated by complex genetic regulatory network. Latest advances in transcriptomics have made it possible to infer basic topologies of pluripotency governing networks. The inferred network topologies, however, only encode boolean information while remaining silent about the roles of dynamics and molecular noise in gene expression. These features are widely considered essential for functional decision making. Herein we developed a framework for extending the boolean level networks into models accounting for individual genetic switches and promoter architecture which allows mechanistic interrogation of the roles of molecular noise, external signaling, and network topology. We demonstrate the pluripotent state of the network to be a broad attractor which is robust to variations of gene expression. Dynamics of exiting the pluripotent state, on the other hand, is significantly influenced by the molecular noise originating from genetic switching events which makes cells more responsive to extracellular signals. Lastly we show that steady state probability landscape can be significantly remodeled by global gene switching rates alone which can be taken as a proxy for how global epigenetic modifications exert control over stability of pluripotent states., Comment: 11 pages, 7 figures

Published
2017
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15. Realtime morphological characterization and sorting of unlabeled viable cells using deep learning

Author

Salek, Mahyar, primary, Li, Nianzhen, additional, Chou, Hou-Pu, additional, Saini, Kiran, additional, Jovic, Andreja, additional, Jacobs, Kevin B., additional, Johnson, Chassidy, additional, Lee, Esther J., additional, Chang, Christina, additional, Nguyen, Phuc, additional, Mei, Jeanette, additional, Pant, Krishna P., additional, Wong-Thai, Amy Y., additional, Smith, Quillan F., additional, Huang, Stephanie, additional, Chow, Ryan, additional, Cruz, Janifer, additional, Walker, Jeff, additional, Chan, Bryan, additional, Musci, Thomas J., additional, Ashley, Euan A., additional, and Masaeli, Maddison (Mahdokht), additional

Published
2022
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16. Hospitalized Patients with 2009 Pandemic Influenza A (H1N1) Virus Infection in the United States—September—October 2009

Author

the 2009 Pandemic Influenza A (H1N1) Virus Fall Hospitalizations Investigation Team, Skarbinski, Jacek, Jain, Seema, Bramley, Anna, Lee, Esther J., Huang, Jean, Kirschke, David, Stone, Allison, Wedlake, Tiffany, Richards, Shawn M., Page, Shannon, Ragan, Patti, Bullion, Lesley, Neises, Daniel, Williams, Robin M., Petruccelli, Bruno P., Vandermeer, Meredith, Lofy, Kathryn H., Gindler, Jacqueline, and Finelli, Lyn

Published
2011
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17. Residual CIS after neoadjuvant chemotherapy and radical cystectomy for muscle invasive bladder cancer: Implications for neoadjuvant trials

Author

Gabrielson, Andrew T., primary, Daniels, Marcus J., additional, Rowe, Julian, additional, Alam, Ridwan, additional, Lee, Esther J., additional, Matoso, Andres, additional, De Felice, Anthony, additional, Hahn, Noah, additional, Hoffman-Censits, Jean, additional, Bivalacqua, Trinity J., additional, and Kates, Max, additional

Published
2022
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23. Characterization of population structure from the mitochondrial DNA vis-a-vis language and geography in Papua New Guinea

Author

Lee, Esther J., Koki, George, and Merriwether, D. Andrew

Subjects
Genetic research -- Analysis, Genetic research -- Chemical properties, Mitochondrial DNA -- Analysis, Mitochondrial DNA -- Chemical properties, Anthropology/archeology/folklore
Abstract

Situated along a corridor linking the Asian continent with the outer islands of the Pacific, Papua New Guinea has long played a key role in understanding the initial peopling of Oceania. The vast diversity in languages and unique geographical environments in the region have been central to the debates on human migration and the degree of interaction between the Pleistocene settlers and newer migrants. To better understand the role of Papua New Guinea in shaping the region's prehistory, we sequenced the mitochondrial DNA (mtDNA) control region of three populations, a total of 94 individuals, located in the East Sepik Province of Papua New Guinea. We analyzed these samples with a large data set of Oceania populations to examine the role of geography and language in shaping population structure within New Guinea and between the region and Island Melanesia. Our results from median-joining networks, star-cluster age estimates, and population genetic analyses show that while highland New Guinea populations seem to be the oldest settlers, there has been significant gene flow within New Guinea with little influence from geography or language. The highest genetic division is between Papuan speakers of New Guinea versus East Papuan speakers located outside of mainland New Guinea. Our study supports the weak language barriers to genetic structuring among populations in close contact and highlights the complexity of understanding the genetic histories of Papua New Guinea in association with language and geography. Am J Phys Anthropol 142:613-624, 2010. KEY WORDS Papua New Guinea; mtDNA; language; geography DOI 10.1002/ajpa.21284

Published
2010

27. Contributors

Author

Ahmed, Syed M., primary, Alexandraki, Irene, additional, Amorosa, Louis F., additional, Anderson, Gregory J., additional, Andrade, Roberto A., additional, Bagley, Bruce, additional, Barrett, Bruce, additional, Basilan, Richard, additional, Beard, J. Mark, additional, Biggs, Wendy S., additional, Bland, Harold, additional, Bober, John F., additional, Brechtelsbauer, David A., additional, Buchanan, Jason N., additional, Buescher, Jennifer J., additional, Cadwallader, Kara, additional, Carroll, William E., additional, Carter, Charles, additional, Comeau, Douglas, additional, Crichlow, Renee, additional, Crouch, Earl R., additional, Crouch, Eric R., additional, David, Alan K., additional, DeGruy, Frank Verloin, additional, Dippel, Eric J., additional, Drezner, Jonathan A., additional, Dupras, Denise M., additional, Ewigman, Bernard, additional, Feero, W. Gregory, additional, Feinstein, Robert E., additional, Foreman, Blair, additional, Garrison, Gregory M., additional, Gingrich, Curtis, additional, Gordon, Andrea, additional, Grant, Thomas R., additional, Guerrera, Mary P., additional, Guirguis-Blake, Janelle, additional, Harmon, Kimberly G., additional, Heaton, Kevin, additional, Heidelbaugh, Joel J., additional, Hensrud, Donald D., additional, Hernandez-Trujillo, Vivian, additional, Herold, Arthur H., additional, Hershberger, Paul J., additional, Holleman, Robert, additional, Holten, Keith B., additional, Holtrop, Jodi Summers, additional, Houston, Thomas, additional, Hutchinson, Mark R., additional, Jonas, Wayne, additional, Kelly, Robert B., additional, Kimmel, Sanford R., additional, Koo, Hoonmo, additional, Kopes-Kerr, Colin P., additional, Kowalhuk, Alicia, additional, Krejci-Manwaring, Jennifer, additional, Lee, Esther J., additional, Lemkau, Jeanne P., additional, Lieberman, Phil, additional, Linares, Adriana C., additional, McBride, David R., additional, McCrary, David, additional, Merry, Stephen P., additional, Meyers, David, additional, Mitchell, Gregg, additional, Moeller, James L., additional, Mooradian, Arshag, additional, Moser, Scott E., additional, Noel, Mary Barth, additional, O'Handley, John G., additional, O'Kane, John W., additional, Osborn, Justin, additional, Paladine, Heather L., additional, Patel, Minal, additional, Pridjian, Gabriella, additional, Rakel, David P., additional, Rakel, Robert E., additional, Rascoe, Terry G., additional, Ratliff-Schaub, Karen, additional, Reed, Brian C., additional, Reis, Michael D., additional, Rindfleisch, J. Adam, additional, Ritter, R. Hal, additional, Roland, William E., additional, Rothberg, Brian, additional, Rust, George, additional, Samiuddin, Zishan, additional, Samraj, Gorge, additional, Schneck, Christopher D., additional, Schrager, Sarina B., additional, Schutt-Ainé, Ann I., additional, Seikel, Stacy, additional, Shah, Ashish R., additional, Shah, Krupa, additional, Shammas, Nicolas W., additional, Sherin, Kevin M., additional, Silverstein, Jeffrey A., additional, Smith, Alan J., additional, Smith, David A., additional, Smucker, Douglas R., additional, Snavely, Abby, additional, Stallworth, James, additional, Stevens, Nancy G., additional, Stiles, Melissa, additional, Strauch, Elizabeth M., additional, Susman, Jeff, additional, Swee, David, additional, Thompson, Margaret, additional, Tobin, Evan J., additional, Toth, Peter P., additional, Usatine, Richard P., additional, Wadland, William C., additional, Waldren, Steven, additional, Walsh, Kathleen, additional, Warner, Elizabeth A., additional, Westney, Gloria, additional, White, Russell D., additional, Williams, Dave E., additional, Wilson, George, additional, Wilson, Jane E., additional, Wolff, Tracy, additional, Zazove, Philip, additional, and Zeimet, Anthony, additional

Published
2011
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31. Breast-milk shedding of drug-resistant HIV-1 subtype C in women exposed to single-dose nevirapine

Author

Lee, Esther J., Kantor, Rami, Zijenah, Lynn, Sheldon, Wayne, Emel, Lynda, Mateta, Patrick, Johnston, Elizabeth, Wells, Jennifer, Shetty, Avinash K., Coovadia, Hoosen, Maldonado, Yvonne, Jones, Samuel Adeniyi, Mofenson, Lynne M., Contag, Christopher H., Bassett, Mary, and Katzenstein, David A.

Subjects
Nevirapine -- Dosage and administration, HIV infection -- Drug therapy, Disease transmission -- Drug therapy, Health
Published
2005

36. Effects of Local Antibiotic Delivery from Porous Space Maintainers on Infection Clearance and Induction of an Osteogenic Membrane in an Infected Bone Defect

Author

Shah, Sarita R., primary, Smith, Brandon T., additional, Tatara, Alexander M., additional, Molina, Eric R., additional, Lee, Esther J., additional, Piepergerdes, Trenton C., additional, Uhrig, Brent A., additional, Guldberg, Robert E., additional, Bennett, George N., additional, Wenke, Joseph C., additional, and Mikos, Antonios G., additional

Published
2017
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40. Technical Report: Correlation Between the Repair of Cartilage and Subchondral Bone in an Osteochondral Defect Using Bilayered, Biodegradable Hydrogel Composites

Author

Lu, Steven, primary, Lam, Johnny, additional, Trachtenberg, Jordan E., additional, Lee, Esther J., additional, Seyednejad, Hajar, additional, van den Beucken, Jeroen J.J.P., additional, Tabata, Yasuhiko, additional, Kasper, F. Kurtis, additional, Scott, David W., additional, Wong, Mark E., additional, Jansen, John A., additional, and Mikos, Antonios G., additional

Published
2015
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41. Improving travel models through peer review

Author

Culp, Michael and Lee, Esther J.

Subjects
United States. Federal Highway Administration -- Management -- Evaluation, Transportation -- Models, Transportation planning -- Evaluation -- Models, Company business management, Business, Engineering and manufacturing industries, Government, Transportation industry
Abstract

These FHWA panels are helping States and metropolitan areas refine their travel demand models to enhance transportation decisionmaking. 'Travel models are key tools for making the decisions that shape our [...]

Published
2005

46. A genetic perspective of prehistoric hunter-gatherers in the Siberian Arctic: Mitochondrial DNA analysis of human remains from 8000years ago

Author

Lee, Esther J., Merriwether, D. Andrew, Kasparov, Alexei K., Khartanovich, Valery I., Nikolskiy, Pavel A., Shidlovskiy, Fedor K., Gromov, Andrei V., Chikisheva, Tatyana A., Chasnyk, Vyacheslav G., Timoshin, Valery B., Pavlova, Elena Y., and Pitulko, Vladimir V.

Abstract

Archaeological evidence of human occupation in Arctic Siberia dates to at least 27,000years before present (YBP) but the population history of these early inhabitants is not fully understood. Genetic research on contemporary indigenous Siberian populations has suggested a distinct pattern between populations from south/central Siberia and the extreme northeast Siberia. However, the picture is complicated by the fluctuations of movement by various cultural groups in the last millennium that has resulted in admixture as well as genetic drift. In order to better understand the genetic history of early humans in northern Siberia, we obtained ten human skeletal remains from four areas of the eastern Siberian Arctic, stretching from the low Yana River in the west to midstream of Bol'shaya Chukoch'ya River and Kolyma River in the east, and the Zhokhov site in the New Siberian Islands. We extracted DNA from the skeletal remains ranging from around 27,000YBP to as recent as the 18th century AD and analyzed the mitochondrial DNA (mtDNA) control region. We successfully identified five haplotypes that include haplogroups A2 and C4. The presence of haplogroup C4 in Arctic Siberia by 8000years ago illustrates the antiquity and widespread distribution of the maternal lineage in the region. On the other hand, haplogroup A2 is frequent among contemporary northeastern Siberian populations. Overall, the results from our ancient DNA analysis suggest maternal lineages among contemporary Siberians were present as far back as 8000years ago in the Siberian Arctic.

Published
2018
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48. Does training matter? : construction quality for a new start transit system : the case of Tren Urbano

Author

Ralph Gakenheimer., Massachusetts Institute of Technology. Dept. of Urban Studies and Planning., Lee, Esther J. (Esther Jung Mi), 1974, Ralph Gakenheimer., Massachusetts Institute of Technology. Dept. of Urban Studies and Planning., and Lee, Esther J. (Esther Jung Mi), 1974

Abstract

Thesis (M.C.P.)--Massachusetts Institute of Technology, Dept. of Urban Studies and Planning, 2002., Includes bibliographical references (p. 99-104)., As with many other large-scale infrastructure projects, the construction of a transit project is potentially vulnerable to quality failures, which can lead to completion delays and cost overruns. Especially with technologically advanced, new-start transit projects, a limitation or lack of skilled labor can exacerbate those risks. This thesis examines the case of Tren Urbano in San Juan, Puerto Rico, a rapid rail project currently being constructed in an area with limited on-island experience in the design, construction, operation or maintenance of such a technologically sophisticated transit system. The motivating question for this thesis is, does training matter for construction quality? The research findings of this thesis show that the multiple prime contractors operating under similar contractual arrangements and resource conditions in San Juan exhibit variations in the quality of construction. Research findings also reveal variations in the type of training programs established by the contractors. A limited conclusion is drawn that although training of inexperienced labor does not single-handedly insure high quality of construction, it nevertheless is important to the successful implementation of project design. Thus, this thesis argues that in order to maximize the quality of construction in a new transit system, the client-owners should create an appropriate strategy which carefully assesses and matches three factors: 1) procurement strategy, whether the conventional design-bid-build or innovative design-build arrangement, 2) contractor competence and experience, and 3) the existent local labor skill level or training capacity. A successful procurement strategy for the construction of future extensions to Tren Urbano should therefore consider: 1) choosing best-value bids over low bids, where the contractor has exhibited expertise and 2) training a broad range of skill sets, that includes explicit attention paid to the construction laborers and monitoring insp, by Esther J. Lee., M.C.P.

Published
2012

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