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151. LiCROM: Linear-Subspace Continuous Reduced Order Modeling with Neural Fields

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Chang, Yue, Chen, Peter Yichen, Wang, Zhecheng, Chiaramonte, Maurizio M., Carlberg, Kevin, Grinspun, Eitan, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Chang, Yue, Chen, Peter Yichen, Wang, Zhecheng, Chiaramonte, Maurizio M., Carlberg, Kevin, and Grinspun, Eitan

Abstract

Linear reduced-order modeling (ROM) simplifies complex simulations by approximating the behavior of a system using a simplified kinematic representation. Typically, ROM is trained on input simulations created with a specific spatial discretization, and then serves to accelerate simulations with the same discretization. This discretization-dependence is restrictive. Becoming independent of a specific discretization would provide flexibility to mix and match mesh resolutions, connectivity, and type (tetrahedral, hexahedral) in training data; to accelerate simulations with novel discretizations unseen during training; and to accelerate adaptive simulations that temporally or parametrically change the discretization. We present a flexible, discretization-independent approach to reduced-order modeling. Like traditional ROM, we represent the configuration as a linear combination of displacement fields. Unlike traditional ROM, our displacement fields are continuous maps from every point on the reference domain to a corresponding displacement vector; these maps are represented as implicit neural fields. With linear continuous ROM (LiCROM), our training set can include multiple geometries undergoing multiple loading conditions, independent of their discretization. This opens the door to novel applications of reduced order modeling. We can now accelerate simulations that modify the geometry at runtime, for instance via cutting, hole punching, and even swapping the entire mesh. We can also accelerate simulations of geometries unseen during training. We demonstrate one-shot generalization, training on a single geometry and subsequently simulating various unseen geometries.

Published
2024

152. Neural Stress Fields for Reduced-order Elastoplasticity and Fracture

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Zong, Zeshun, Li, Xuan, Li, Minchen, Chiaramonte, Maurizio M., Matusik, Wojciech, Grinspun, Eitan, Carlberg, Kevin, Jiang, Chenfanfu, Chen, Peter Yichen, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Zong, Zeshun, Li, Xuan, Li, Minchen, Chiaramonte, Maurizio M., Matusik, Wojciech, Grinspun, Eitan, Carlberg, Kevin, Jiang, Chenfanfu, and Chen, Peter Yichen

Abstract

We propose a hybrid neural network and physics framework for reduced-order modeling of elastoplasticity and fracture. State-of-the-art scientific computing models like the Material Point Method (MPM) faithfully simulate large-deformation elastoplasticity and fracture mechanics. However, their long runtime and large memory consumption render them unsuitable for applications constrained by computation time and memory usage, e.g., virtual reality. To overcome these barriers, we propose a reduced-order framework. Our key innovation is training a low-dimensional manifold for the Kirchhoff stress field via an implicit neural representation. This low-dimensional neural stress field (NSF) enables efficient evaluations of stress values and, correspondingly, internal forces at arbitrary spatial locations. In addition, we also train neural deformation and affine fields to build low-dimensional manifolds for the deformation and affine momentum fields. These neural stress, deformation, and affine fields share the same low-dimensional latent space, which uniquely embeds the high-dimensional simulation state. After training, we run new simulations by evolving in this single latent space, which drastically reduces the computation time and memory consumption. Our general continuum-mechanics-based reduced-order framework is applicable to any phenomena governed by the elastodynamics equation. To showcase the versatility of our framework, we simulate a wide range of material behaviors, including elastica, sand, metal, non-Newtonian fluids, fracture, contact, and collision. We demonstrate dimension reduction by up to 100,000 × and time savings by up to 10 ×.

Published
2024

153. E-engagement: A guide for Public Sector Managers

Author

Chen, Peter

Subjects
websites, information resources management, communiciation technologies, Decision-making, E-democracy, Policy, Public sector, Software, bic Book Industry Communication::G Reference, information & interdisciplinary subjects::GT Interdisciplinary studies::GTC Communication studies
Abstract

Over the last twenty years, advanced communication technologies have become pervasive throughout Western society. These technologies have not only revolutionised the delivery of public and private services, they have shaped consumers’ expectations about service quality. This guide (written for managers who have an interest in expanding their approach to public engagement, rather than IT professionals) assesses the value that new communications and computing technology can bring to interactions with a range of potential stakeholders. An engaging, provocative and thorough survey of available technologies and potential applications, this is a ‘must read’ for policy and program practitioners who are considering options for electronic engagement.

Published
2007
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154. Rethinking Academic Support: Improving the Academic Outcomes of Students in High-Risk STEM Courses with Synchronous Videoconferencing

Author

Rennar-Potacco, Donna, Orellana, Anymir, Chen, Peter, and Salazar, Andres

Abstract

This article presents findings of a study conducted to determine the impact of academic support provided through videoconferencing on the academic outcomes of Science, Technology, Engineering, and Mathematics students enrolled in high-risk science courses in higher education. A quasi-experimental nonequivalent posttest only design was employed to determine if grade and retention outcomes of students receiving online academic support through videoconferencing were equivalent to outcomes received by students receiving face-to-face academic support and students not receiving academic support. Data from 1,276 students were analyzed and significant differences were found in rate of retention and final grades of "Cs or above" among the three groups. The untutored group had the lowest rate. There was no significant difference in retention or final grade proportions for online and face-to-face groups, providing evidence that synchronous academic support through videoconferencing is as effective as face-to-face academic support.

Published
2019
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155. Summary of Expansions and Updates in GREET® 2022

Author

Wang, Michael, primary, Elgowainy, Amgad, additional, Lee, Uisung, additional, Baek, Kwang, additional, Bafana, Adarsh, additional, Benavides, Pahola, additional, Burnham, Andrew, additional, Cai, Hao, additional, Cappello, Vincenzo, additional, Chen, Peter, additional, Gan, Yu, additional, Gracida-Alvarez, Ulises, additional, Hawkins, Troy, additional, Iyer, Rakesh, additional, Kelly, Jarod, additional, Kim, Taemin, additional, Kumar, Shishir, additional, Kwon, Hoyoung, additional, Lee, Kyuha, additional, Liu, Xinyu, additional, Lu, Zifeng, additional, Masum, Farhad, additional, Ng, Clarence, additional, Ou, Longwen, additional, Reddi, Krishna, additional, Siddique, Nazib, additional, Sun, Pingping, additional, Vyawahare, Pradeep, additional, Xu, Hui, additional, and Zaimes, George, additional

Published
2022
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156. An automatic variable laser power attenuator for continuous-wave quantum cascade lasers in cryogenic ion vibrational predissociation spectroscopy.

Author

Gorbachev, Vladimir, Miloglyadova, Larisa, and Chen, Peter

Subjects
TUNABLE lasers, MULTIPHOTON absorption, MID-infrared lasers, LASERS, SPECTROMETRY, QUANTUM cascade lasers
Abstract

Cryogenic ion vibrational predissociation (CIVP) spectroscopy is an established and valuable technique for molecular elucidation in the gas phase. CIVP relies on tunable lasers, wherein among typical laser schemes, the application of mid-infrared continuous-wave quantum cascade laser (cw-QCL) is the most robust and elegant solution, as we have recently demonstrated. However, potential challenges arise from an inhomogeneous character across laser power tuning curves. A large laser power output could have undesired consequences, such as multiphoton absorption or saturation effects. Significant variations in laser power tuning curves could potentially alter the shape of the investigated band, particularly for diffuse bands. In this study, we have developed and introduced an automatic variable laser power attenuator designed to keep the laser power output uniform at a user-defined value across the entire available spectral range. We demonstrated the application of this attenuator in obtaining CIVP spectra of a model compound with a diffuse N–H–N band. This approach enhances the reliability of measuring diffuse bands and overall applicability of cw-QCL. [ABSTRACT FROM AUTHOR]

Published
2024
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157. Differentiation of Prior SARS-CoV-2 Infection and Postacute Sequelae by Standard Clinical Laboratory Measurements in the RECOVER Cohort.

Author

Erlandson, Kristine M., Geng, Linda N., Selvaggi, Caitlin A., Thaweethai, Tanayott, Chen, Peter, Erdmann, Nathan B., Goldman, Jason D., Henrich, Timothy J., Hornig, Mady, Karlson, Elizabeth W., Katz, Stuart D., Kim, C., Cribbs, Sushma K., Laiyemo, Adeyinka O., Letts, Rebecca, Lin, Janet Y., Marathe, Jai, Parthasarathy, Sairam, Patterson, Thomas F., and Taylor, Brittany D.

Subjects
BIOMARKERS, PLATELET count, PATHOLOGICAL laboratories, SARS-CoV-2, REGRESSION analysis
Abstract

This study evaluated whether SARS-CoV-2 infection led to persistent changes in common clinical laboratory tests in people with prior infection compared with those without prior infection and whether people with postacute sequelae of SARS-CoV-2 infection (PASC) have persistent laboratory changes compared with those who are unlikely to have PASC. Visual Abstract. Differentiation of Prior SARS-CoV-2 Infection and Postacute Sequelae by Standard Clinical Laboratory Measurements in the RECOVER Cohort: This study evaluated whether SARS-CoV-2 infection led to persistent changes in common clinical laboratory tests in people with prior infection compared with those without prior infection and whether people with postacute sequelae of SARS-CoV-2 infection (PASC) have persistent laboratory changes compared with those who are unlikely to have PASC. Background: There are currently no validated clinical biomarkers of postacute sequelae of SARS-CoV-2 infection (PASC). Objective: To investigate clinical laboratory markers of SARS-CoV-2 and PASC. Design: Propensity score–weighted linear regression models were fitted to evaluate differences in mean laboratory measures by prior infection and PASC index (≥12 vs. 0). (ClinicalTrials.gov: NCT05172024) Setting: 83 enrolling sites. Participants: RECOVER-Adult cohort participants with or without SARS-CoV-2 infection with a study visit and laboratory measures 6 months after the index date (or at enrollment if >6 months after the index date). Participants were excluded if the 6-month visit occurred within 30 days of reinfection. Measurements: Participants completed questionnaires and standard clinical laboratory tests. Results: Among 10 094 participants, 8746 had prior SARS-CoV-2 infection, 1348 were uninfected, 1880 had a PASC index of 12 or higher, and 3351 had a PASC index of zero. After propensity score adjustment, participants with prior infection had a lower mean platelet count (265.9 × 10 9 cells/L [95% CI, 264.5 to 267.4 × 10 9 cells/L]) than participants without known prior infection (275.2 × 10 9 cells/L [CI, 268.5 to 282.0 × 10 9 cells/L]), as well as higher mean hemoglobin A 1c (HbA 1c) level (5.58% [CI, 5.56% to 5.60%] vs. 5.46% [CI, 5.40% to 5.51%]) and urinary albumin–creatinine ratio (81.9 mg/g [CI, 67.5 to 96.2 mg/g] vs. 43.0 mg/g [CI, 25.4 to 60.6 mg/g]), although differences were of modest clinical significance. The difference in HbA 1c levels was attenuated after participants with preexisting diabetes were excluded. Among participants with prior infection, no meaningful differences in mean laboratory values were found between those with a PASC index of 12 or higher and those with a PASC index of zero. Limitation: Whether differences in laboratory markers represent consequences of or risk factors for SARS-CoV-2 infection could not be determined. Conclusion: Overall, no evidence was found that any of the 25 routine clinical laboratory values assessed in this study could serve as a clinically useful biomarker of PASC. Primary Funding Source: National Institutes of Health. [ABSTRACT FROM AUTHOR]

Published
2024
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159. How temperature impacts material properties and photovoltaic performance of mixed-halide perovskite via light-induced ion migration.

Author

Kung, Po-Kai, Li, Ming-Hsien, Lin, Chen-Fu, and Chen, Peter

Abstract

Lead halide perovskites applied in solar cells have gained significant attention due to their rapidly increasing power conversion efficiency. However, their intrinsic instability, stemming from their ionic nature, hampers the commercialization of perovskite solar cells. The scope of this paper is to extend the characterization of light-induced ion migration via temperature-dependent measurement based on the polaron-invoked ion migration model. The investigation reveals that light-induced phase segregation intensifies with rising temperature, as indicated by stoichiometry variation and crystal compression. This intensification facilitates the formation of iodide-rich domains within the perovskite film. The formation of such domains is correlated with promoted carrier recombination in perovskite solar cells, as observed through electrochemical impedance spectra. Consequently, the facilitated carrier recombination process leads to a notable decline in the power conversion efficiency of a perovskite solar cell, reducing to <20% of its original value as the temperature increases from 300 K to 500 K. Moreover, the intensified ion migration due to heat also impacts the stability of both the perovskite material and the whole device. Extended illumination duration and high temperature lead to the decomposition of perovskite, resulting in the formation of insulated PbI2 that deteriorates the performance of perovskite solar cells. This degradation is irreversible and results in rapid decomposition at high temperatures, as evidenced by the deterioration of photovoltaic performance of perovskite solar cells within 30 minutes of operation at 500 K. The temperature-dependent characterization reveals a cascading process originating from light-induced ion migration, followed by phase segregation and iodide-rich domain formation. These processes significantly impact the perovskite solar cells in terms of carrier transport/recombination behavior and operational stability. [ABSTRACT FROM AUTHOR]

Published
2024
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160. After the killing fields: Post-pandemic changes in journalism employment in Australia and Aotearoa New Zealand.

Author

COKLEY, JOHN, CHEN, PETER JOHN, BERESFORD, JOANNA, and BUNDY, ALEXIS

Subjects
JOURNALISM, ENTREPRENEURSHIP, ORGANIZATIONAL change, URBANIZATION, CREATIVE ability
Abstract

This article continues a longitudinal national study of journalism employment in Australia and contributes to new understandings of journalism employment in Australia and Aotearoa/New Zealand. Results suggest a shift in the organisational landscape of the media in Australia, with an expansion of large organisations at the 'top,' and a considerable loss of small micro-ventures (largely based online) at the 'bottom.' Implications include stronger centralised editorial control at the corporate level, urbanisation and homogenisation of media producers and product, and reduced opportunities for creative entry-level roles. [ABSTRACT FROM AUTHOR]

Published
2024
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167. Large Language Models for Design and Manufacturing

Author

Makatura, Liane, primary, Foshey, Michael, additional, Wang, Bohan, additional, Hähnlein, Felix, additional, Ma, Pingchuan, additional, Deng, Bolei, additional, Tjandrasuwita, Megan, additional, Spielberg, Andrew, additional, Owens, Crystal Elaine, additional, Chen, Peter Yichen, additional, Zhao, Allan, additional, Zhu, Amy, additional, Norton, Wil J., additional, Gu, Edward, additional, Jacob, Joshua, additional, Li, Yifei, additional, Schulz, Adriana, additional, and Matusik, Wojciech, additional

Published
2024
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168. Continuous evolution of compact protein degradation tags regulated by selective molecular glues

Author

Mercer, Jaron A. M., primary, DeCarlo, Stephan J., additional, Roy Burman, Shourya S., additional, Sreekanth, Vedagopuram, additional, Nelson, Andrew T., additional, Hunkeler, Moritz, additional, Chen, Peter J., additional, Donovan, Katherine A., additional, Kokkonda, Praveen, additional, Tiwari, Praveen K., additional, Shoba, Veronika M., additional, Deb, Arghya, additional, Choudhary, Amit, additional, Fischer, Eric S., additional, and Liu, David R., additional

Published
2024
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170. De novo variants in DENND5B cause a neurodevelopmental disorder

Author

Scala, Marcello, primary, Tomati, Valeria, additional, Ferla, Matteo, additional, Lena, Mariateresa, additional, Cohen, Julie S., additional, Fatemi, Ali, additional, Brokamp, Elly, additional, Bican, Anna, additional, Phillips, John A., additional, Koziura, Mary E., additional, Nicouleau, Michael, additional, Rio, Marlene, additional, Siquier, Karine, additional, Boddaert, Nathalie, additional, Musante, Ilaria, additional, Tamburro, Serena, additional, Baldassari, Simona, additional, Iacomino, Michele, additional, Scudieri, Paolo, additional, Rosenfeld, Jill A., additional, Bellus, Gary, additional, Reed, Sara, additional, Al Saif, Hind, additional, Russo, Rossana Sanchez, additional, Walsh, Matthew B., additional, Cantagrel, Vincent, additional, Crunk, Amy, additional, Gustincich, Stefano, additional, Ruggiero, Sarah M., additional, Fitzgerald, Mark P., additional, Helbig, Ingo, additional, Striano, Pasquale, additional, Severino, Mariasavina, additional, Salpietro, Vincenzo, additional, Pedemonte, Nicoletta, additional, Zara, Federico, additional, Acosta, Maria T., additional, Adams, David R., additional, Alvarez, Raquel L., additional, Alvey, Justin, additional, Allworth, Aimee, additional, Andrews, Ashley, additional, Ashley, Euan A., additional, Afzali, Ben, additional, Bacino, Carlos A., additional, Bademci, Guney, additional, Balasubramanyam, Ashok, additional, Baldridge, Dustin, additional, Bale, Jim, additional, Bamshad, Michael, additional, Barbouth, Deborah, additional, Bayrak-Toydemir, Pinar, additional, Beck, Anita, additional, Beggs, Alan H., additional, Behrens, Edward, additional, Bejerano, Gill, additional, Bellen, Hugo J., additional, Bennett, Jimmy, additional, Bernstein, Jonathan A., additional, Berry, Gerard T., additional, Bivona, Stephanie, additional, Blue, Elizabeth, additional, Bohnsack, John, additional, Bonner, Devon, additional, Botto, Lorenzo, additional, Briere, Lauren C., additional, Brown, Gabrielle, additional, Burke, Elizabeth A., additional, Burrage, Lindsay C., additional, Butte, Manish J., additional, Byers, Peter, additional, Byrd, William E., additional, Carey, John, additional, Carrasquillo, Olveen, additional, Cassini, Thomas, additional, Chang, Ta Chen Peter, additional, Chanprasert, Sirisak, additional, Chao, HsiaoTuan, additional, Chinn, Ivan, additional, Clark, Gary D., additional, Coakley, Terra R., additional, Cobban, Laurel A., additional, Cogan, Joy D., additional, Coggins, Matthew, additional, Cole, F. Sessions, additional, Colley, Heather A., additional, Cope, Heidi, additional, Corona, Rosario, additional, Craigen, William J., additional, Crouse, Andrew B., additional, Cunningham, Michael, additional, D’Souza, Precilla, additional, Dai, Hongzheng, additional, Dasari, Surendra, additional, Davis, Joie, additional, Dayal, Jyoti G., additional, Delgado, Margaret, additional, Dell'Angelica, Esteban C., additional, Dipple, Katrina, additional, Doherty, Daniel, additional, Dorrani, Naghmeh, additional, Doss, Argenia L., additional, Douine, Emilie D., additional, Earl, Dawn, additional, Eckstein, David J., additional, Emrick, Lisa T., additional, Eng, Christine M., additional, Falk, Marni, additional, Fieg, Elizabeth L., additional, Fisher, Paul G., additional, Fogel, Brent L., additional, Forghani, Irman, additional, Fu, Jiayu, additional, Gahl, William A., additional, Glass, Ian, additional, Goddard, Page C., additional, Godfrey, Rena A., additional, Grajewski, Alana, additional, Gropman, Andrea, additional, Halley, Meghan C., additional, Hamid, Rizwan, additional, Hanchard, Neal, additional, Hassey, Kelly, additional, Hayes, Nichole, additional, High, Frances, additional, Hing, Anne, additional, Hisama, Fuki M., additional, Holm, Ingrid A., additional, Hom, Jason, additional, Horike-Pyne, Martha, additional, Huang, Alden, additional, Huang, Yan, additional, Hutchison, Sarah, additional, Introne, Wendy, additional, Isasi, Rosario, additional, Izumi, Kosuke, additional, Jarvik, Gail P., additional, Jarvik, Jeffrey, additional, Jayadev, Suman, additional, Jean-Marie, Orpa, additional, Jobanputra, Vaidehi, additional, Kaitryn, Emerald, additional, Ketkar, Shamika, additional, Kiley, Dana, additional, Kilich, Gonench, additional, Kobren, Shilpa N., additional, Kohane, Isaac S., additional, Kohler, Jennefer N., additional, Korrick, Susan, additional, Krakow, Deborah, additional, Krasnewich, Donna M., additional, Kravets, Elijah, additional, Lalani, Seema R., additional, Lam, Byron, additional, Lam, Christina, additional, Lanpher, Brendan C., additional, Lanza, Ian R., additional, LeBlanc, Kimberly, additional, Lee, Brendan H., additional, Levitt, Roy, additional, Lewis, Richard A., additional, Liu, Pengfei, additional, Liu, Xue Zhong, additional, Longo, Nicola, additional, Loo, Sandra K., additional, Loscalzo, Joseph, additional, Maas, Richard L., additional, Macnamara, Ellen F., additional, MacRae, Calum A., additional, Maduro, Valerie V., additional, Maghiro, AudreyStephannie, additional, Mahoney, Rachel, additional, Malicdan, May Christine V., additional, Mamounas, Laura A., additional, Manolio, Teri A., additional, Mao, Rong, additional, Marom, Ronit, additional, Marth, Gabor, additional, Martin, Beth A., additional, Martin, Martin G., additional, Martínez-Agosto, Julian A., additional, Marwaha, Shruti, additional, McCauley, Jacob, additional, McConkie-Rosell, Allyn, additional, McCray, Alexa T., additional, McGee, Elisabeth, additional, Might, Matthew, additional, Miller, Danny, additional, Mirzaa, Ghayda, additional, Morava, Eva, additional, Moretti, Paolo, additional, Morimoto, Marie, additional, Mulvihill, John J., additional, Nakano-Okuno, Mariko, additional, Nelson, Stanley F., additional, Nieves-Rodriguez, Shirley, additional, Novacic, Donna, additional, Oglesbee, Devin, additional, Orengo, James P., additional, Pace, Laura, additional, Pak, Stephen, additional, Pallais, J. Carl, additional, Papp, Jeanette C., additional, Parker, Neil H., additional, Petcharet, Leoyklang, additional, Posey, Jennifer E., additional, Potocki, Lorraine, additional, Swerdzewski, Barbara N. Pusey, additional, Quinlan, Aaron, additional, Rao, Deepak A., additional, Raper, Anna, additional, Raskind, Wendy, additional, Renteria, Genecee, additional, Reuter, Chloe M., additional, Rives, Lynette, additional, Robertson, Amy K., additional, Rodan, Lance H., additional, Rosenthal, Elizabeth, additional, Rossignol, Francis, additional, Ruzhnikov, Maura, additional, Sabaii, Marla, additional, Sacco, Ralph, additional, Sampson, Jacinda B., additional, Saporta, Mario, additional, Schaechter, Judy, additional, Schedl, Timothy, additional, Schoch, Kelly, additional, Scott, Daryl A., additional, Seto, Elaine, additional, Sharma, Prashant, additional, Shashi, Vandana, additional, Shelkowitz, Emily, additional, Sheppeard, Sam, additional, Shin, Jimann, additional, Silverman, Edwin K., additional, Sinsheimer, Janet S., additional, Sisco, Kathy, additional, Smith, Edward C., additional, Smith, Kevin S., additional, Solnica-Krezel, Lilianna, additional, Solomon, Ben, additional, Spillmann, Rebecca C., additional, Stergachis, Andrew, additional, Stoler, Joan M., additional, Sullivan, Kathleen, additional, Sullivan, Jennifer A., additional, Sutton, Shirley, additional, Sweetser, David A., additional, Sybert, Virginia, additional, Tabor, Holly K., additional, Tan, Queenie K.-G., additional, Tan, Amelia L.M., additional, Tarakad, Arjun, additional, Taylor, Herman, additional, Tekin, Mustafa, additional, Telischi, Fred, additional, Thorson, Willa, additional, Tifft, Cynthia J., additional, Toro, Camilo, additional, Tran, Alyssa A., additional, Ungar, Rachel A., additional, Urv, Tiina K., additional, Vanderver, Adeline, additional, Velinder, Matt, additional, Viskochil, Dave, additional, Vogel, Tiphanie P., additional, Wahl, Colleen E., additional, Walker, Melissa, additional, Walley, Nicole M., additional, Wambach, Jennifer, additional, Wan, Jijun, additional, Wang, Lee-kai, additional, Wangler, Michael F., additional, Ward, Patricia A., additional, Wegner, Daniel, additional, Weisz Hubshman, Monika, additional, Wener, Mark, additional, Wenger, Tara, additional, Westerfield, Monte, additional, Wheeler, Matthew T., additional, Whitlock, Jordan, additional, Wolfe, Lynne A., additional, Worley, Kim, additional, Yamamoto, Shinya, additional, Zhang, Zhe, additional, and Zuchner, Stephan, additional

Published
2024
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174. Efficient prime editing in two-cell mouse embryos using PEmbryo

Author

Kim-Yip, Rebecca P., primary, McNulty, Ryan, additional, Joyce, Bradley, additional, Mollica, Antonio, additional, Chen, Peter J., additional, Ravisankar, Purnima, additional, Law, Benjamin K., additional, Liu, David R., additional, Toettcher, Jared E., additional, Ivakine, Evgueni A., additional, Posfai, Eszter, additional, and Adamson, Britt, additional

Published
2024
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177. A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3

Author

Paul, Maimuna S., primary, Michener, Sydney L., additional, Pan, Hongling, additional, Chan, Hiuling, additional, Pfliger, Jessica M., additional, Rosenfeld, Jill A., additional, Lerma, Vanesa C., additional, Tran, Alyssa, additional, Longley, Megan A., additional, Lewis, Richard A., additional, Weisz-Hubshman, Monika, additional, Bekheirnia, Mir Reza, additional, Bekheirnia, Nasim, additional, Massingham, Lauren, additional, Zech, Michael, additional, Wagner, Matias, additional, Engels, Hartmut, additional, Cremer, Kirsten, additional, Mangold, Elisabeth, additional, Peters, Sophia, additional, Trautmann, Jessica, additional, Mester, Jessica L., additional, Guillen Sacoto, Maria J., additional, Person, Richard, additional, McDonnell, Pamela P., additional, Cohen, Stacey R., additional, Lusk, Laina, additional, Cohen, Ana S.A., additional, Le Pichon, Jean-Baptiste, additional, Pastinen, Tomi, additional, Zhou, Dihong, additional, Engleman, Kendra, additional, Racine, Caroline, additional, Faivre, Laurence, additional, Moutton, Sébastien, additional, Denommé-Pichon, Anne-Sophie, additional, Koh, Hyun Yong, additional, Poduri, Annapurna, additional, Bolton, Jeffrey, additional, Knopp, Cordula, additional, Julia Suh, Dong Sun, additional, Maier, Andrea, additional, Toosi, Mehran Beiraghi, additional, Karimiani, Ehsan Ghayoor, additional, Maroofian, Reza, additional, Schaefer, Gerald Bradley, additional, Ramakumaran, Vijayalakshmi, additional, Vasudevan, Pradeep, additional, Prasad, Chitra, additional, Osmond, Matthew, additional, Schuhmann, Sarah, additional, Vasileiou, Georgia, additional, Russ-Hall, Sophie, additional, Scheffer, Ingrid E., additional, Carvill, Gemma L., additional, Mefford, Heather, additional, Bacino, Carlos A., additional, Lee, Brendan H., additional, Chao, Hsiao-Tuan, additional, Acosta, Maria T., additional, Adam, Margaret, additional, Adams, David R., additional, Alvarez, Raquel L., additional, Alvey, Justin, additional, Amendola, Laura, additional, Andrews, Ashley, additional, Ashley, Euan A., additional, Bademci, Guney, additional, Balasubramanyam, Ashok, additional, Baldridge, Dustin, additional, Bale, Jim, additional, Bamshad, Michael, additional, Barbouth, Deborah, additional, Bayrak-Toydemir, Pinar, additional, Beck, Anita, additional, Beggs, Alan H., additional, Behrens, Edward, additional, Bejerano, Gill, additional, Bellen, Hugo J., additional, Bennett, Jimmy, additional, Berg-Rood, Beverly, additional, Bernstein, Jonathan A., additional, Berry, Gerard T., additional, Bican, Anna, additional, Bivona, Stephanie, additional, Blue, Elizabeth, additional, Bohnsack, John, additional, Bonner, Devon, additional, Botto, Lorenzo, additional, Boyd, Brenna, additional, Briere, Lauren C., additional, Brown, Gabrielle, additional, Burke, Elizabeth A., additional, Burrage, Lindsay C., additional, Butte, Manish J., additional, Byers, Peter, additional, Byrd, William E., additional, Carey, John, additional, Carrasquillo, Olveen, additional, Cassini, Thomas, additional, Chang, Ta Chen Peter, additional, Chanprasert, Sirisak, additional, Chinn, Ivan, additional, Clark, Gary D., additional, Coakley, Terra R., additional, Cobban, Laurel A., additional, Cogan, Joy D., additional, Coggins, Matthew, additional, Cole, F. Sessions, additional, Colley, Heather A., additional, Cope, Heidi, additional, Corona, Rosario, additional, Craigen, William J., additional, Crouse, Andrew B., additional, Cunningham, Michael, additional, D’Souza, Precilla, additional, Dai, Hongzheng, additional, Dasari, Surendra, additional, Davis, Joie, additional, Dayal, Jyoti G., additional, Dell'Angelica, Esteban C., additional, Dipple, Katrina, additional, Doherty, Daniel, additional, Dorrani, Naghmeh, additional, Doss, Argenia L., additional, Douine, Emilie D., additional, Earl, Dawn, additional, Eckstein, David J., additional, Emrick, Lisa T., additional, Eng, Christine M., additional, Falk, Marni, additional, Fieg, Elizabeth L., additional, Fisher, Paul G., additional, Fogel, Brent L., additional, Forghani, Irman, additional, Gahl, William A., additional, Glass, Ian, additional, Gochuico, Bernadette, additional, Goddard, Page C., additional, Godfrey, Rena A., additional, Golden-Grant, Katie, additional, Grajewski, Alana, additional, Hadley, Don, additional, Hahn, Sihoun, additional, Halley, Meghan C., additional, Hamid, Rizwan, additional, Hassey, Kelly, additional, Hayes, Nichole, additional, High, Frances, additional, Hing, Anne, additional, Hisama, Fuki M., additional, Holm, Ingrid A., additional, Hom, Jason, additional, Horike-Pyne, Martha, additional, Huang, Alden, additional, Hutchison, Sarah, additional, Introne, Wendy, additional, Isasi, Rosario, additional, Izumi, Kosuke, additional, Jamal, Fariha, additional, Jarvik, Gail P., additional, Jarvik, Jeffrey, additional, Jayadev, Suman, additional, Jean-Marie, Orpa, additional, Jobanputra, Vaidehi, additional, Karaviti, Lefkothea, additional, Ketkar, Shamika, additional, Kiley, Dana, additional, Kilich, Gonench, additional, Kobren, Shilpa N., additional, Kohane, Isaac S., additional, Kohler, Jennefer N., additional, Korrick, Susan, additional, Kozuira, Mary, additional, Krakow, Deborah, additional, Krasnewich, Donna M., additional, Kravets, Elijah, additional, Lalani, Seema R., additional, Lam, Byron, additional, Lam, Christina, additional, Lanpher, Brendan C., additional, Lanza, Ian R., additional, LeBlanc, Kimberly, additional, Levitt, Roy, additional, Liu, Pengfei, additional, Liu, Xue Zhong, additional, Longo, Nicola, additional, Loo, Sandra K., additional, Loscalzo, Joseph, additional, Maas, Richard L., additional, Macnamara, Ellen F., additional, MacRae, Calum A., additional, Maduro, Valerie V., additional, Maghiro, Audrey Stephannie, additional, Mahoney, Rachel, additional, Malicdan, May Christine V., additional, Mamounas, Laura A., additional, Manolio, Teri A., additional, Mao, Rong, additional, Maravilla, Kenneth, additional, Marom, Ronit, additional, Marth, Gabor, additional, Martin, Beth A., additional, Martin, Martin G., additional, Martínez-Agosto, Julian A., additional, Marwaha, Shruti, additional, McCauley, Jacob, additional, McConkie-Rosell, Allyn, additional, McCray, Alexa T., additional, McGee, Elisabeth, additional, Merritt, J. Lawrence, additional, Might, Matthew, additional, Mirzaa, Ghayda, additional, Morava, Eva, additional, Moretti, Paolo, additional, Mulvihill, John, additional, Nakano-Okuno, Mariko, additional, Nelson, Stanley F., additional, Newman, John H., additional, Nicholas, Sarah K., additional, Nickerson, Deborah, additional, Nieves-Rodriguez, Shirley, additional, Novacic, Donna, additional, Oglesbee, Devin, additional, Orengo, James P., additional, Pace, Laura, additional, Pak, Stephen, additional, Pallais, J. Carl, additional, Palmer, Christina G.S., additional, Papp, Jeanette C., additional, Parker, Neil H., additional, Phillips III, John A., additional, Posey, Jennifer E., additional, Potocki, Lorraine, additional, Pusey Swerdzewski, Barbara N., additional, Quinlan, Aaron, additional, Rao, Deepak A., additional, Raper, Anna, additional, Raskind, Wendy, additional, Renteria, Genecee, additional, Reuter, Chloe M., additional, Rives, Lynette, additional, Robertson, Amy K., additional, Rodan, Lance H., additional, Rosenwasser, Natalie, additional, Rossignol, Francis, additional, Ruzhnikov, Maura, additional, Sacco, Ralph, additional, Sampson, Jacinda B., additional, Saporta, Mario, additional, Schaechter, Judy, additional, Schedl, Timothy, additional, Schoch, Kelly, additional, Scott, Daryl A., additional, Scott, C. Ron, additional, Seto, Elaine, additional, Shashi, Vandana, additional, Shin, Jimann, additional, Silverman, Edwin K., additional, Sinsheimer, Janet S., additional, Sisco, Kathy, additional, Smith, Edward C., additional, Smith, Kevin S., additional, Solnica-Krezel, Lilianna, additional, Solomon, Ben, additional, Spillmann, Rebecca C., additional, Stoler, Joan M., additional, Sullivan, Kathleen, additional, Sullivan, Jennifer A., additional, Sun, Angela, additional, Sutton, Shirley, additional, Sweetser, David A., additional, Sybert, Virginia, additional, Tabor, Holly K., additional, Tan, Queenie K.-G., additional, Tan, Amelia L.M., additional, Tarakad, Arjun, additional, Tekin, Mustafa, additional, Telischi, Fred, additional, Thorson, Willa, additional, Tifft, Cynthia J., additional, Toro, Camilo, additional, Tran, Alyssa A., additional, Ungar, Rachel A., additional, Urv, Tiina K., additional, Vanderver, Adeline, additional, Velinder, Matt, additional, Viskochil, Dave, additional, Vogel, Tiphanie P., additional, Wahl, Colleen E., additional, Walker, Melissa, additional, Wallace, Stephanie, additional, Walley, Nicole M., additional, Wambach, Jennifer, additional, Wan, Jijun, additional, Wang, Lee-kai, additional, Wangler, Michael F., additional, Ward, Patricia A., additional, Wegner, Daniel, additional, Weisz Hubshman, Monika, additional, Wener, Mark, additional, Wenger, Tara, additional, Westerfield, Monte, additional, Wheeler, Matthew T., additional, Whitlock, Jordan, additional, Wolfe, Lynne A., additional, Worley, Kim, additional, Xiao, Changrui, additional, Yamamoto, Shinya, additional, Yang, John, additional, Zhang, Zhe, additional, and Zuchner, Stephan, additional

Published
2024
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178. miR-323a-3p regulates lung fibrosis by targeting multiple profibrotic pathways

Author

Ge, Lingyin, Habiel, David M, Hansbro, Phil M, Kim, Richard Y, Gharib, Sina A, Edelman, Jeffery D, Königshoff, Melanie, Parimon, Tanyalak, Brauer, Rena, Huang, Ying, Allen, Jenieke, Jiang, Dianhua, Kurkciyan, Adrianne A, Mizuno, Takako, Stripp, Barry R, Noble, Paul W, Hogaboam, Cory M, and Chen, Peter

Subjects
Biomedical and Clinical Sciences, Lung, Genetics, Biotechnology, Rare Diseases, Clinical Research, 2.1 Biological and endogenous factors, Aetiology, Respiratory, Good Health and Well Being, Animals, Bleomycin, Bronchiolitis Obliterans, Cells, Cultured, Fibroblasts, Humans, Idiopathic Pulmonary Fibrosis, Lung Transplantation, Mice, Mice, Inbred C57BL, MicroRNAs, Respiratory Mucosa, Signal Transduction, Transforming Growth Factors, Biomedical and clinical sciences, Health sciences
Abstract

Maladaptive epithelial repair from chronic injury is a common feature in fibrotic diseases, which in turn activates a pathogenic fibroblast response that produces excessive matrix deposition. Dysregulated microRNAs (miRs) can regulate expression of multiple genes and fundamentally alter cellular phenotypes during fibrosis. Although several miRs have been shown to be associated with lung fibrosis, the mechanisms by which miRs modulate epithelial behavior in lung fibrosis are lacking. Here, we identified miR-323a-3p to be downregulated in the epithelium of lungs with bronchiolitis obliterans syndrome (BOS) after lung transplantation, idiopathic pulmonary fibrosis (IPF), and murine bleomycin-induced fibrosis. Antagomirs for miR-323a-3p augment, and mimics suppress, murine lung fibrosis after bleomycin injury, indicating that this miR may govern profibrotic signals. We demonstrate that miR-323a-3p attenuates TGF-α and TGF-β signaling by directly targeting key adaptors in these important fibrogenic pathways. Moreover, miR-323a-3p lowers caspase-3 expression, thereby limiting programmed cell death from inducers of apoptosis and ER stress. Finally, we find that epithelial expression of miR-323a-3p modulates inhibitory crosstalk with fibroblasts. These studies demonstrate that miR-323a-3p has a central role in lung fibrosis that spans across murine and human disease, and downregulated expression by the lung epithelium releases inhibition of various profibrotic pathways to promote fibroproliferation.

Published
2016

180. New Benchmark Set of Transition-Metal Coordination Reactions for the Assessment of Density Functionals

Author

Weymuth, Thomas, Couzijn, Erik P. A., Chen, Peter, and Reiher, Markus

Subjects
Physics - Chemical Physics, Condensed Matter - Materials Science, Condensed Matter - Strongly Correlated Electrons, Physics - Computational Physics
Abstract

We present the WCCR10 data set of ten ligand dissociation energies of large cationic transition metal complexes for the assessment of approximate exchange--correlation functionals. We analyze nine popular functionals, namely BP86, BP86-D3, B3LYP, B3LYP-D3, B97-D-D2, PBE, TPSS, PBE0, and TPSSh by mutual comparison and by comparison to experimental gas-phase data measured with well-known precision. The comparison of all calculated data reveals a large, system-dependent scattering of results with nonnegligible consequences for computational chemistry studies on transition metal compounds. Considering further the comparison with experiment, the non-empirical functionals PBE and TPSS turn out to be among the best functionals for our reference data set. The deviation can be lowered further by including Hartree--Fock exchange. Accordingly, PBE0 and TPSSh are the two most accurate functionals for our test set, but also these functionals exhibit deviations from experiment by up to 50 kJ/mol for individual reactions. As an important result we found no functional to be reliable for all reactions. Furthermore, for some of the ligand dissociation energies studied in this work, dispersion corrections yield results which increase the deviation from experiment. This deviation increases further if structure optimization including dispersion corrections is performed. Finally, we compare our results to other benchmark studies and highlight that the performance assessed for different density functionals depends significantly on the reference molecule set chosen., Comment: 36 pages, 7 figures, 3 tables

Published
2014
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188. Cyclodestruction

Author

Chang, Ta Chen Peter, Joos, Karen M., Grajewski, Alana L., editor, Bitrian, Elena, editor, Papadopoulos, Maria, editor, and Freedman, Sharon F., editor

Published
2018
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189. Trigeminal Neuralgia

Author

Chen, Peter Y., Chang, Eric L., editor, Brown, Paul D., editor, Lo, Simon S., editor, Sahgal, Arjun, editor, and Suh, John H., editor

Published
2018
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194. Concluding Remarks

Author

Thuy Tran, Ngoc Thanh, primary, Brahma, Sanjaya, additional, Hsu, Wen-Dung, additional, Lin, Shih-Yang, additional, Huang, Jow-Lay, additional, Yoshimura, Masahiro, additional, Jan, Jeng-Shiung, additional, Chen, Chia-Yun, additional, Chen, Peter, additional, Lin, Ming-Fa, additional, Kuo, Chin-Lung, additional, and Loan Le, Phung My, additional

Published
2021
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196. Introduction

Author

Brahma, Sanjaya, primary, Tran, Ngoc Thanh Thuy, additional, Hsu, Wen-Dung, additional, Kuo, Chin-Lung, additional, Lin, Shih-Yang, additional, Huang, Jow-Lay, additional, Yoshimura, Masahiro, additional, Le, Phung My Loan, additional, Jan, Jeng-Shiung, additional, Chen, Chia-Yun, additional, Chen, Peter, additional, and Lin, Ming-Fa, additional

Published
2021
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