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152. Childhood cerebellar tumours mirror conserved fetal transcriptional programs

Author

Vladoiu, Maria C., primary, El-Hamamy, Ibrahim, additional, Donovan, Laura K., additional, Farooq, Hamza, additional, Holgado, Borja L., additional, Sundaravadanam, Yogi, additional, Ramaswamy, Vijay, additional, Hendrikse, Liam D., additional, Kumar, Sachin, additional, Mack, Stephen C., additional, Lee, John J. Y., additional, Fong, Vernon, additional, Juraschka, Kyle, additional, Przelicki, David, additional, Michealraj, Antony, additional, Skowron, Patryk, additional, Luu, Betty, additional, Suzuki, Hiromichi, additional, Morrissy, A. Sorana, additional, Cavalli, Florence M. G., additional, Garzia, Livia, additional, Daniels, Craig, additional, Wu, Xiaochong, additional, Qazi, Maleeha A., additional, Singh, Sheila K., additional, Chan, Jennifer A., additional, Marra, Marco A., additional, Malkin, David, additional, Dirks, Peter, additional, Heisler, Lawrence, additional, Pugh, Trevor, additional, Ng, Karen, additional, Notta, Faiyaz, additional, Thompson, Eric M., additional, Kleinman, Claudia L., additional, Joyner, Alexandra L., additional, Jabado, Nada, additional, Stein, Lincoln, additional, and Taylor, Michael D., additional

Published
2019
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153. Histone variant innovation in a rapidly evolving chordate lineage

Author

Jansen Pascal WTC, Campsteijn Coen, Moosmann Alexandra, Nasrallah Carole, Raasholm Martina, Stunnenberg Henk G, and Thompson Eric M

Subjects
histone complement, DNA repair, urochordate, posttranslational modification, endocycle, gametogenesis, testes, H2A.Z, alternative splicing, Evolution, QH359-425
Abstract

Abstract Background Histone variants alter the composition of nucleosomes and play crucial roles in transcription, chromosome segregation, DNA repair, and sperm compaction. Modification of metazoan histone variant lineages occurs on a background of genome architecture that shows global similarities from sponges to vertebrates, but the urochordate, Oikopleura dioica, a member of the sister group to vertebrates, exhibits profound modification of this ancestral architecture. Results We show that a histone complement of 47 gene loci encodes 31 histone variants, grouped in distinct sets of developmental expression profiles throughout the life cycle. A particularly diverse array of 15 male-specific histone variants was uncovered, including a testes-specific H4t, the first metazoan H4 sequence variant reported. Universal histone variants H3.3, CenH3, and H2A.Z are present but O. dioica lacks homologs of macroH2A and H2AX. The genome encodes many H2A and H2B variants and the repertoire of H2A.Z isoforms is expanded through alternative splicing, incrementally regulating the number of acetylatable lysine residues in the functionally important N-terminal "charge patch". Mass spectrometry identified 40 acetylation, methylation and ubiquitylation posttranslational modifications (PTMs) and showed that hallmark PTMs of "active" and "repressive" chromatin were present in O. dioica. No obvious reduction in silent heterochromatic marks was observed despite high gene density in this extraordinarily compacted chordate genome. Conclusions These results show that histone gene complements and their organization differ considerably even over modest phylogenetic distances. Substantial innovation among all core and linker histone variants has evolved in concert with adaptation of specific life history traits in this rapidly evolving chordate lineage.

Published
2011
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156. Increased fitness of a key appendicularian zooplankton species under warmer, acidified seawater conditions

Author

Bouquet, Jean-Marie, Troedsson, Christofer, Novac, Aliona, Reeve, Magnus, Lechtenbörger, Anna K., Massart, Wendy, Skaar, Katrine S., Aasjord, Anne, Dupont, Sam, Thompson, Eric M., Bouquet, Jean-Marie, Troedsson, Christofer, Novac, Aliona, Reeve, Magnus, Lechtenbörger, Anna K., Massart, Wendy, Skaar, Katrine S., Aasjord, Anne, Dupont, Sam, and Thompson, Eric M.

Abstract

Ocean warming and acidification (OA) may alter the fitness of species in marine pelagic ecosystems through community effects or direct physiological impacts. We used the zooplanktonic appendicularian, Oikopleura dioica, to assess temperature and pH effects at mesocosm and microcosm scales. In mesocosms, both OA and warming positively impacted O. dioica abundance over successive generations. In microcosms, the positive impact of OA, was observed to result from increased fecundity. In contrast, increased pH, observed for example during phytoplankton blooms, reduced fecundity. Oocyte fertility and juvenile development were equivalent under all pH conditions, indicating that the positive effect of lower pH on O. dioica abundance was principally due to increased egg number. This effect was influenced by food quantity and quality, supporting possible improved digestion and assimilation at lowered pH. Higher temperature resulted in more rapid growth, faster maturation and earlier reproduction. Thus, increased temperature and reduced pH had significant positive impacts on O. dioica fitness through increased fecundity and shortened generation time, suggesting that predicted future ocean conditions may favour this zooplankton species. © 2018 Bouquet et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Published
2018
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159. 330 Socioeconomic Factors, Perioperative Complications, and 30-Day Readmission Rates Associated With Delayed Referral for Cranial Vault Reconstruction for Craniosynostosis

Author

Sergesketter, Amanda, primary, Elsamadicy, Aladine A, additional, Kemeny, Hanna, additional, Harward, Stephen C, additional, Krucoff, Kate B, additional, Krucoff, Max O, additional, Fuchs, Herbert E, additional, Thompson, Eric M, additional, Allori, Alexander, additional, Marcus, Jeffrey, additional, and Muh, Carrie R, additional

Published
2018
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165. HGG-22. PHASE 1b STUDY POLIO VACCINE SABIN-RHINOVIRUS POLIOVIRUS (PVSRIPO) FOR RECURRENT MALIGNANT GLIOMA IN CHILDREN

Author

Ashley, David M, primary, Thompson, Eric M, additional, Landi, Daniel, additional, Desjardins, Annick, additional, Friedman, Allan H, additional, Threatt, Stevie, additional, Herndon, II, James E, additional, Boulton, Susan, additional, McSherry, Frances, additional, Lipp, Eric S, additional, Sampson, John H, additional, Friedman, Henry S, additional, Bigner, Darell D, additional, and Gromeier, Matthias, additional

Published
2018
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174. Prognostic value of medulloblastoma extent of resection after accounting for molecular subgroup: a retrospective integrated clinical and molecular analysis

Author

McLendon, Roger E, Grant, Gerald, Rao, Amulya A Nageswara, Seow, Wan Tew, Bigner, Darell D, Leary, Sarah, Hielscher, Thomas, Perek-Polnik, Marta, Et Al, Bouffet, Eric, Perreault, Sebastien, Yao, Yu, Low, David C Y, Grajkowska, Wieslawa A, Hamilton, Ronald L, Li, Kay Ka Wai, Tominaga, Teiji, Kumabe, Toshihiro, Cho, Yoon-Jae, Luu, Betty, Thompson, Eric M, Mora, Jaume, Remke, Marc, Kim, Seung-Ki, Pollack, Ian F, Giannini, Caterina, Ng, Ho-Keung, Lee, Ji Yeoun, Lipp, Eric S, Chang, Kenneth T E, and Gururangan, Sridharan

Published
2016
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178. The role of angiogenesis in Group 3 medulloblastoma pathogenesis and survival

Author

Thompson, Eric M, primary, Keir, Stephen T, additional, Venkatraman, Talaignair, additional, Lascola, Christopher, additional, Yeom, Kristen W, additional, Nixon, Andrew B, additional, Liu, Yingmiao, additional, Picard, Daniel, additional, Remke, Marc, additional, Bigner, Darell D, additional, Ramaswamy, Vijay, additional, and Taylor, Michael D, additional

Published
2017
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180. An open repository of earthquake-triggered ground-failure inventories

Author

Schmitt, Robert G., primary, Tanyas, Hakan, additional, Nowicki Jessee, M. Anna, additional, Zhu, Jing, additional, Biegel, Katherine M., additional, Allstadt, Kate E., additional, Jibson, Randall W., additional, Thompson, Eric M., additional, van Westen, Cees J., additional, Sato, Hiroshi P., additional, Wald, David J., additional, Godt, Jonathan W., additional, Gorum, Tolga, additional, Xu, Chong, additional, Rathje, Ellen M., additional, and Knudsen, Keith L., additional

Published
2017
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182. The 2018 update of the US National Seismic Hazard Model: Overview of model and implications

Author

Petersen, Mark D., Shumway, Allison M., Powers, Peter M., Mueller, Charles S., Moschetti, Morgan P., Frankel, Arthur D., Rezaeian, Sanaz, McNamara, Daniel E., Luco, Nico, Boyd, Oliver S., Rukstales, Kenneth S., Jaiswal, Kishor S., Thompson, Eric M., Hoover, Susan M., Clayton, Brandon S., Field, Edward H., and Zeng, Yuehua

Abstract

During 2017–2018, the National Seismic Hazard Model for the conterminous United States was updated as follows: (1) an updated seismicity catalog was incorporated, which includes new earthquakes that occurred from 2013 to 2017; (2) in the central and eastern United States (CEUS), new ground motion models were updated that incorporate updated median estimates, modified assessments of the associated epistemic uncertainties and aleatory variabilities, and new soil amplification factors; (3) in the western United States (WUS), amplified shaking estimates of long-period ground motions at sites overlying deep sedimentary basins in the Los Angeles, San Francisco, Seattle, and Salt Lake City areas were incorporated; and (4) in the conterminous United States, seismic hazard is calculated for 22 periods (from 0.01 to 10 s) and 8 uniform VS30maps (ranging from 1500 to 150 m/s). We also include a description of updated computer codes and modeling details. Results show increased ground shaking in many (but not all) locations across the CEUS (up to ~30%), as well as near the four urban areas overlying deep sedimentary basins in the WUS (up to ~50%). Due to population growth and these increased hazard estimates, more people live or work in areas of high or moderate seismic hazard than ever before, leading to higher risk of undesirable consequences from forecasted future ground shaking.

Published
2020
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183. Sharing data and code facilitates reproducible and impactful research

Author

Baker, Jack W, Crowley, Helen, Wald, David, Rathje, Ellen, Au, Siu-Kui, Bradley, Brendon A, Burton, Henry, Cabas, Ashly, Cattari, Serena, Cauzzi, Carlo, Cavalieri, Francesco, Contreras, Santina, Costa, Rodrigo, Eguchi, Ronald T, Lallemant, David, Lignos, Dimitrios G, Maurer, Brett W, Molina Hutt, Carlos, Sextos, Anastasios, Seyhan, Emel, Silva, Vitor, Sucuoğlu, Haluk, Taciroglu, Ertugrul, and Thompson, Eric M

Abstract

Modern research often involves the collection or analysis of data and the use of specialized computer algorithms. Traditional text articles thus provide only partial documentation of a research study. Readers have limited ability to reproduce or utilize work if the source data are not available or if it relies on an algorithm that is described, but code is not provided. Fortunately, a wide variety of tools are now available to support the publication of research data and code. The effort required to publish data is now relatively small, and the benefits can be immense. This opinion article discusses trends toward increased sharing in academic publishing. It describes opportunities and resources to support data and code sharing and describes the benefits for both authors and readers. Finally, it discusses how Earthquake Spectrais providing resources and enhancing its policies to establish the sharing of data as the default procedure when publishing in the journal, and encourage the sharing of code and other resources.

Published
2024
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184. Data-driven adjustments for combined use of NGA-East hard-rock ground motion and site amplification models

Author

Ramos-Sepúlveda, María E, Stewart, Jonathan P, Parker, Grace A, Moschetti, Morgan P, Thompson, Eric M, Brandenberg, Scott J, Hashash, Youssef MA, and Rathje, Ellen M

Abstract

Model development in the Next Generation Attenuation-East (NGA-East) project included two components developed concurrently and independently: (1) earthquake ground-motion models (GMMs) that predict the median and aleatory variability of various intensity measures conditioned on magnitude and distance, derived for a reference hard-rock site condition with an average shear-wave velocity in the upper 30 m (VS30) = 3000 m/s; and (2) a site amplification model that modifies intensity measures for softer site conditions. We investigate whether these models, when used in tandem, are compatible with ground-motion recordings in central and eastern North America (CENA) using an expanded version of the NGA-East database that includes new events from November 2011 (end date of NGA-East data curation) to April 2022. Following this expansion, the data set has 187 events, 2096 sites, and 16,272 three-component recordings, although the magnitude range remains limited (∼4 to 5.8). We compute residuals using 17 NGA-East GMMs and three data selection criteria that reflect within-CENA regional variations in ground-motion attributes. Mixed-effects regression of the residuals reveals a persistent pattern in which ground motions are overpredicted at short periods (0.01–0.6 s, including peak ground acceleration (PGA)) and underpredicted at longer periods. These misfits are regionally variable, with the Texas–Oklahoma–Kansas region having larger absolute misfits than other parts of CENA. Two factors potentially influencing these misfits are (1) differences in the site amplification models used to adjust the data to the reference condition during NGA-East GMM development relative to CENA amplification models applied since the 2018 National Seismic Hazard Model (NSHM), and (2) potential bias in simulation-based factors used to adjust ground motions from the hard-rock reference condition to a VS30= 760 m/s condition. We provide adjustment factors and their epistemic uncertainties and discuss implications for applications.

Published
2024
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185. Basin effects from 3D simulated ground motions in the Greater Los Angeles region for use in seismic hazard analyses

Author

Moschetti, Morgan P, Thompson, Eric M, and Withers, Kyle

Abstract

We develop basin-depth-scaling models (i.e. “basin terms”) from the long-period (T≥2s) simulated ground motions of the Southern California Earthquake Center (SCEC) CyberShake project for use in seismic hazard analyses at sites within the sedimentary basins of southern California. Basin terms use the Next Generation Attenuation (NGA)-West-2 ground-motion models (GMMs) as reference models and use their functional forms with slight modifications. We investigate the use of two approaches to incorporate the time-averaged shear-wave velocity in the upper 30 m (VS30) in these calculations and find that the use of site-specific and uniform VS30has minor effects on the resulting basin terms for this data set. By centering the simulated ground motions on the basin terms, we separate the information from the simulations about absolute ground-motion level from information relating to the relative amplifications, such as the differences between shallow- and deep-basin sites. Recent observations from sedimentary basins of southern California indicate that additional amplification effect may persist at relatively shallow basin depths (i.e. the GMM basin terms should have positive values when differential depths, δZ1, are near zero), and we present models for “centered” and “adjusted” basin-depth scaling models that reflect this potential. The simulation-modified GMMs are appropriate for crustal sources and for deep-basin sites (δZ1>0) within basins of the Greater Los Angeles region, for the magnitudes and distances defined by each of the reference NGA-West-2 GMMs.

Published
2024
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186. The 2023 US National Seismic Hazard Model: Ground-motion characterization for the conterminous United States

Author

Moschetti, Morgan P, Aagaard, Brad T, Ahdi, Sean K, Altekruse, Jason, Boyd, Oliver S, Frankel, Arthur D, Herrick, Julie, Petersen, Mark D, Powers, Peter M, Rezaeian, Sanaz, Shumway, Allison M, Smith, James A, Stephenson, William J, Thompson, Eric M, and Withers, Kyle B

Abstract

We update the ground-motion characterization for the 2023 National Seismic Hazard Model (NSHM) for the conterminous United States. The update includes the use of new ground-motion models (GMMs) in the Cascadia subduction zone; an adjustment to the central and eastern United States (CEUS) GMMs to reduce misfits with observed data; an updated boundary for the application of GMMs for shallow, crustal earthquakes in active tectonic regions (i.e. western United States (WUS)) and stable continental regions (i.e. CEUS); and the use of improved models for the site response of deep sedimentary basins in the WUS and CEUS. Site response updates include basin models for the California Great Valley and for the Portland and Tualatin basins, Oregon, as well as long-period basin effects from three-dimensional simulations in the Greater Los Angeles region and in the Seattle basin; in the CEUS, we introduce a broadband (0.01- to 10-s period) amplification model for the effects of the passive-margin basins of the Atlantic and Gulf Coastal Plains. In addition, we summarize progress on implementing rupture directivity models into seismic hazard models, although they are not incorporated in the 2023 NSHM. We implement the ground-motion characterization for the 2023 NSHM in the US Geological Survey’s code for probabilistic seismic hazard analysis, nshmp-haz-v2, and present the sensitivity of hazard to these changes. Hazard calculations indicate widespread effects from adjustments to the CEUS GMMs, from the incorporation of Coastal Plain amplification effects, and from the treatment of shallow-basin and out-of-basin sites in the San Francisco Bay Area and Los Angeles region, as well as locally important changes from subduction-zone GMMs, and from updated and new WUS basins.

Published
2024
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187. Prognostic value of medulloblastoma extent of resection after accounting for molecular subgroup: a retrospective integrated clinical and molecular analysis

Author

Thompson, Eric M, Hielscher, Thoma, Bouffet, Eric, Remke, Marc, Luu, Betty, Gururangan, Sridharan, Mclendon, Roger E, Bigner, Darell D, Lipp, Eric S, Perreault, Sebastien, Cho, Yoon-Jae, Grant, Gerald, Kim, Seung-Ki, Lee, Ji Yeoun, Rao, Amulya A Nageswara, Giannini, Caterina, Li, Kay Ka Wai, Ng, Ho-Keung, Yao, Yu, Kumabe, Toshihiro, Tominaga, Teiji, Grajkowska, Wieslawa A, Perek-Polnik, Marta, Low, David C Y, Seow, Wan Tew, Chang, Kenneth T E, Mora, Jaume, Pollack, Ian F, Hamilton, Ronald L, Leary, Sarah, Moore, Andrew S, Ingram, Wendy J, Hallahan, Andrew R, Jouvet, Anne, Fèvre-Montange, Michelle, Vasiljevic, Alexandre, Faure-Conter, Cecile, Shofuda, Tomoko, Kagawa, Naoki, Hashimoto, Naoya, Jabado, Nada, Weil, Alexander G, Gayden, Tenzin, Wataya, Takafumi, Shalaby, Tarek, Grotzer, Michael, Zitterbart, Karel, Sterba, Jaroslav, Kren, Leo, Hortobágyi, Tibor, Klekner, Almo, László, Bognár, Pócza, Tímea, Hauser, Peter, Schüller, Ulrich, Jung, Shin, Jang, Woo-Youl, French, Pim J, Kros, Johan M, van Veelen, Marie-Lise C, Massimi, Luca, Leonard, Jeffrey R, Rubin, Joshua B, Vibhakar, Rajeev, Chambless, Lola B, Cooper, Michael K, Thompson, Reid C, Faria, Claudia C, Carvalho, Alice, Nunes, Sofia, Pimentel, José, Fan, Xing, Muraszko, Karin M, López-Aguilar, Enrique, Lyden, David, Garzia, Livia, Shih, David J H, Kijima, Noriyuki, Schneider, Christian, Adamski, Jennifer, Northcott, Paul A, Kool, Marcel, Jones, David T W, Chan, Jennifer A, Nikolic, Ana, Garre, Maria Luisa, Van Meir, Erwin G, Osuka, Satoru, Olson, Jeffrey J, Jahangiri, Arman, Castro, Brandyn A, Gupta, Nalin, Weiss, William A, Moxon-Emre, Iska, Mabbott, Donald J, Lassaletta, Alvaro, Hawkins, Cynthia E, Tabori, Uri, Drake, Jame, Kulkarni, Abhaya, Dirks, Peter, Rutka, James T, Korshunov, Andrey, Pfister, Stefan M, Packer, Roger J, Ramaswamy, Vijay, Taylor, Michael D, Thompson, Eric M, Hielscher, Thoma, Bouffet, Eric, Remke, Marc, Luu, Betty, Gururangan, Sridharan, Mclendon, Roger E, Bigner, Darell D, Lipp, Eric S, Perreault, Sebastien, Cho, Yoon-Jae, Grant, Gerald, Kim, Seung-Ki, Lee, Ji Yeoun, Rao, Amulya A Nageswara, Giannini, Caterina, Li, Kay Ka Wai, Ng, Ho-Keung, Yao, Yu, Kumabe, Toshihiro, Tominaga, Teiji, Grajkowska, Wieslawa A, Perek-Polnik, Marta, Low, David C Y, Seow, Wan Tew, Chang, Kenneth T E, Mora, Jaume, Pollack, Ian F, Hamilton, Ronald L, Leary, Sarah, Moore, Andrew S, Ingram, Wendy J, Hallahan, Andrew R, Jouvet, Anne, Fèvre-Montange, Michelle, Vasiljevic, Alexandre, Faure-Conter, Cecile, Shofuda, Tomoko, Kagawa, Naoki, Hashimoto, Naoya, Jabado, Nada, Weil, Alexander G, Gayden, Tenzin, Wataya, Takafumi, Shalaby, Tarek, Grotzer, Michael, Zitterbart, Karel, Sterba, Jaroslav, Kren, Leo, Hortobágyi, Tibor, Klekner, Almo, László, Bognár, Pócza, Tímea, Hauser, Peter, Schüller, Ulrich, Jung, Shin, Jang, Woo-Youl, French, Pim J, Kros, Johan M, van Veelen, Marie-Lise C, Massimi, Luca, Leonard, Jeffrey R, Rubin, Joshua B, Vibhakar, Rajeev, Chambless, Lola B, Cooper, Michael K, Thompson, Reid C, Faria, Claudia C, Carvalho, Alice, Nunes, Sofia, Pimentel, José, Fan, Xing, Muraszko, Karin M, López-Aguilar, Enrique, Lyden, David, Garzia, Livia, Shih, David J H, Kijima, Noriyuki, Schneider, Christian, Adamski, Jennifer, Northcott, Paul A, Kool, Marcel, Jones, David T W, Chan, Jennifer A, Nikolic, Ana, Garre, Maria Luisa, Van Meir, Erwin G, Osuka, Satoru, Olson, Jeffrey J, Jahangiri, Arman, Castro, Brandyn A, Gupta, Nalin, Weiss, William A, Moxon-Emre, Iska, Mabbott, Donald J, Lassaletta, Alvaro, Hawkins, Cynthia E, Tabori, Uri, Drake, Jame, Kulkarni, Abhaya, Dirks, Peter, Rutka, James T, Korshunov, Andrey, Pfister, Stefan M, Packer, Roger J, Ramaswamy, Vijay, and Taylor, Michael D

Abstract

Background Patients with incomplete surgical resection of medulloblastoma are controversially regarded as having a marker of high-risk disease, which leads to patients undergoing aggressive surgical resections, so-called second-look surgeries, and intensified chemoradiotherapy. All previous studies assessing the clinical importance of extent of resection have not accounted for molecular subgroup. We analysed the prognostic value of extent of resection in a subgroup-specific manner. Methods We retrospectively identified patients who had a histological diagnosis of medulloblastoma and complete data about extent of resection and survival from centres participating in the Medulloblastoma Advanced Genomics International Consortium. We collected from resections done between April, 1997, and February, 2013, at 35 international institutions. We established medulloblastoma subgroup affiliation by gene expression profiling on frozen or formalin-fixed paraffin-embedded tissues. We classified extent of resection on the basis of postoperative imaging as gross total resection (no residual tumour), near-total resection (<1·5 cm2tumour remaining), or sub-total resection (≥1·5 cm2tumour remaining). We did multivariable analyses of overall survival and progression-free survival using the variables molecular subgroup (WNT, SHH, group 4, and group 3), age (<3 vs ≥3 years old), metastatic status (metastases vs no metastases), geographical location of therapy (North America/Australia vs rest of the world), receipt of chemotherapy (yes vs no) and receipt of craniospinal irradiation (<30 Gy or >30 Gy vs no craniospinal irradiation). The primary analysis outcome was the effect of extent of resection by molecular subgroup and the effects of other clinical variables on overall and progression-free survival. Findings We included 787 patients with medulloblastoma (86 with WNT tumours, 242 with SHH tumours, 163 with group 3 tumours, and 296 with group 4 tumours) in our multivariable Cox models o

Published
2016

189. Utility of diffusion tensor imaging studies linked to neuronavigation and other modalities in repeat hemispherotomy for intractable epilepsy

Author

Kiehna, Erin N., primary, Widjaja, Elysa, additional, Holowka, Stephanie, additional, Carter Snead, O., additional, Drake, James, additional, Weiss, Shelly K., additional, Ochi, Ayako, additional, Thompson, Eric M., additional, Go, Cristina, additional, Otsubo, Hiroshi, additional, Donner, Elizabeth J., additional, and Rutka, James T., additional

Published
2016
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190. Prognostic value of medulloblastoma extent of resection after accounting for molecular subgroup: a retrospective integrated clinical and molecular analysis

Author

Thompson, Eric M, primary, Hielscher, Thomas, additional, Bouffet, Eric, additional, Remke, Marc, additional, Luu, Betty, additional, Gururangan, Sridharan, additional, McLendon, Roger E, additional, Bigner, Darell D, additional, Lipp, Eric S, additional, Perreault, Sebastien, additional, Cho, Yoon-Jae, additional, Grant, Gerald, additional, Kim, Seung-Ki, additional, Lee, Ji Yeoun, additional, Rao, Amulya A Nageswara, additional, Giannini, Caterina, additional, Li, Kay Ka Wai, additional, Ng, Ho-Keung, additional, Yao, Yu, additional, Kumabe, Toshihiro, additional, Tominaga, Teiji, additional, Grajkowska, Wieslawa A, additional, Perek-Polnik, Marta, additional, Low, David C Y, additional, Seow, Wan Tew, additional, Chang, Kenneth T E, additional, Mora, Jaume, additional, Pollack, Ian F, additional, Hamilton, Ronald L, additional, Leary, Sarah, additional, Moore, Andrew S, additional, Ingram, Wendy J, additional, Hallahan, Andrew R, additional, Jouvet, Anne, additional, Fèvre-Montange, Michelle, additional, Vasiljevic, Alexandre, additional, Faure-Conter, Cecile, additional, Shofuda, Tomoko, additional, Kagawa, Naoki, additional, Hashimoto, Naoya, additional, Jabado, Nada, additional, Weil, Alexander G, additional, Gayden, Tenzin, additional, Wataya, Takafumi, additional, Shalaby, Tarek, additional, Grotzer, Michael, additional, Zitterbart, Karel, additional, Sterba, Jaroslav, additional, Kren, Leos, additional, Hortobágyi, Tibor, additional, Klekner, Almos, additional, László, Bognár, additional, Pócza, Tímea, additional, Hauser, Peter, additional, Schüller, Ulrich, additional, Jung, Shin, additional, Jang, Woo-Youl, additional, French, Pim J, additional, Kros, Johan M, additional, van Veelen, Marie-Lise C, additional, Massimi, Luca, additional, Leonard, Jeffrey R, additional, Rubin, Joshua B, additional, Vibhakar, Rajeev, additional, Chambless, Lola B, additional, Cooper, Michael K, additional, Thompson, Reid C, additional, Faria, Claudia C, additional, Carvalho, Alice, additional, Nunes, Sofia, additional, Pimentel, José, additional, Fan, Xing, additional, Muraszko, Karin M, additional, López-Aguilar, Enrique, additional, Lyden, David, additional, Garzia, Livia, additional, Shih, David J H, additional, Kijima, Noriyuki, additional, Schneider, Christian, additional, Adamski, Jennifer, additional, Northcott, Paul A, additional, Kool, Marcel, additional, Jones, David T W, additional, Chan, Jennifer A, additional, Nikolic, Ana, additional, Garre, Maria Luisa, additional, Van Meir, Erwin G, additional, Osuka, Satoru, additional, Olson, Jeffrey J, additional, Jahangiri, Arman, additional, Castro, Brandyn A, additional, Gupta, Nalin, additional, Weiss, William A, additional, Moxon-Emre, Iska, additional, Mabbott, Donald J, additional, Lassaletta, Alvaro, additional, Hawkins, Cynthia E, additional, Tabori, Uri, additional, Drake, James, additional, Kulkarni, Abhaya, additional, Dirks, Peter, additional, Rutka, James T, additional, Korshunov, Andrey, additional, Pfister, Stefan M, additional, Packer, Roger J, additional, Ramaswamy, Vijay, additional, and Taylor, Michael D, additional

Published
2016
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194. USGS approach to real-time estimation of earthquake-triggered ground failure - Results of 2015 workshop

Author

Allstadt, Kate E., primary, Thompson, Eric M., additional, Wald, David J., additional, Hamburger, Michael W., additional, Godt, Jonathan W., additional, Knudsen, Keith L., additional, Jibson, Randall W., additional, Jessee, M. Anna, additional, Zhu, Jing, additional, Hearne, Michael, additional, Baise, Laurie G., additional, Tanyas, Hakan, additional, and Marano, Kristin D., additional

Published
2016
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196. The clinical importance of medulloblastoma extent of resection: a systematic review.

Author

Thompson, Eric M., Bramall, Alexa, Herndon, James E., Taylor, Michael D., and Ramaswamy, Vijay

Abstract

Background: Although the majority of current medulloblastoma adjuvant therapy protocols treat patients with ≥ 1.5 cm2 residual tumor as high risk with increased craniospinal irradiation, the true prognostic significance of extent of resection (EOR) in medulloblastoma is unknown.Objectives: We sought to synthesize the body of literature on EOR and survival to determine if a definitive association exists.Data sources/eligibility criteria: A PubMed search was conducted for the terms “medulloblastoma” combined with “extent of resection,” “overall survival,” “progression free survival,” “gross total resection,” “near total resection,” “partial resection,” or “subtotal resection.” Studies that performed a statistical analysis of EOR and survival were included.Results: Sixteen articles including 1489 patients found a statistically significant association between EOR and survival, 20 articles including 2335 patients did not find a significant association between EOR and survival, and 14 articles including 2950 patients had mixed results. The three articles that accounted for molecular subgroup found varying associations between EOR and progression free survival, while no association was found between EOR and overall survival.Limitations: This review is limited by inconsistent definitions of EOR, the retrospective nature of the articles analyzed, and infrequent use of multivariate statistical analyses.Conclusions: The prognostic importance of EOR for medulloblastoma is unclear and warrants re-evaluation, particularly in the context of molecular subgrouping. [ABSTRACT FROM AUTHOR]

Published
2018
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198. A self‐cleaning biological filter: How appendicularians mechanically control particle adhesion and removal.

Author

Conley, Keats R., Gemmell, Brad J., Bouquet, Jean‐Marie, Thompson, Eric M., and Sutherland, Kelly R.

Subjects
APPENDICULARIA, HYDRODYNAMICS, FLUID dynamics, PHARYNGEAL diseases, PARTICLE size determination
Abstract

Abstract: Appendicularians are ubiquitous marine grazers that use tangential filtration to collect micron and submicron prey. The food‐concentrating filter (FCF) is the primary determinant of appendicularian prey selectivity, but the precise means by which it concentrates and conveys particles to the pharyngeal filter remain poorly understood. We used high‐speed videography to examine the mechanics of the FCF of Oikopleura dioica with high resolution to better understand how filter structure, hydrodynamics, and animal behavior affect feeding selectivity. We observed that filtration occurs through the process of serial adhesion and detachment of particles, and in this respect, differs from an industrial tangential filtration system. We demonstrate how filter elasticity and the hydrodynamics of pulsatile flow caused by the kinematics of the animal's tail contribute to the filter's self‐cleaning abilities. We present experimental observations showing that smaller particles (3 μm) adhere significantly more to the filter than larger ones (10 μm), but that, overall adhesion is quite low for an array of particle sizes (3–20 μm). This study provides a mechanistic basis for predicting the effects of appendicularian grazing on particle size spectra in the upper ocean. [ABSTRACT FROM AUTHOR]

Published
2018
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199. T2-weighted images are superior to other MR image types for the determination of diffuse intrinsic pontine glioma intratumoral heterogeneity.

Author

Harward, Stephen, Harrison Farber, S., Thompson, Eric M., Malinzak, Michael, and Becher, Oren

Subjects
BRAIN tumor treatment, MAGNETIC resonance imaging, HETEROGENEITY, CORPUS callosum, RADIOTHERAPY
Abstract

Purpose: Diffuse intrinsic pontine glioma (DIPG) remains the main cause of death in children with brain tumors. Given the inefficacy of numerous peripherally delivered agents to treat DIPG, convection enhanced delivery (CED) of therapeutic agents is a promising treatment modality. The purpose of this study was to determine which MR imaging type provides the best discrimination of intratumoral heterogeneity to guide future stereotactic implantation of CED catheters into the most cellular tumor regions.Methods: Patients ages 18 years or younger with a diagnosis of DIPG from 2000 to 2015 were included. Radiographic heterogeneity index (HI) of the tumor was calculated by measuring the standard deviation of signal intensity of the tumor (SDTumor) normalized to the genu of the corpus callosum (SDCorpus Callosum). Four MR image types (T2-weighted, contrast-enhanced T1-weighted, FLAIR, and ADC) were analyzed at several time points both before and after radiotherapy and chemotherapy. HI values across these MR image types were compared and correlated with patient survival.Results: MR images from 18 patients with DIPG were evaluated. The mean survival ± standard deviation was 13.8 ± 13.7 months. T2-weighted images had the highest HI (mean ± SD, 5.1 ± 2.5) followed by contrast-enhanced T1-weighted images (3.7 ± 1.5), FLAIR images (3.0 ± 1.1), and ADC maps (1.6 ± 0.4). ANOVA demonstrated that HI values were significantly higher for T2-weighted images than FLAIR (p < 0.01) and ADC (p < 0.0001). Following radiotherapy, T2-weighted and contrast-enhanced T1-weighted image HI values increased, while FLAIR and ADC HI values decreased. Univariate and multivariate analyses did not reveal a relationship between HI values and patient survival (p > 0.05).Conclusions: For children with DIPG, T2-weighted MRI demonstrates the greatest signal intensity variance suggesting tumor heterogeneity. Within this heterogeneity, T2-weighted signal hypointensity is known to correlate with increased cellularity and thus may represent a putative target for CED catheter placement in future clinical trials. [ABSTRACT FROM AUTHOR]

Published
2018
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200. Estimating Rupture Distances without a Rupture.

Author

Thompson, Eric M. and Worden, C. Bruce

Abstract

Most ground-motion prediction equations (GMPEs) require distances that are defined relative to a rupture model, such as the distance to the surface projection of the rupture (RJB) or the closest distance to the rupture plane (RRUP). There are a number of situations in which it is either necessary or advantageous to derive rupture distances from point-source distance metrics, such as hypocentral (RHYP) or epicentral (REPI) distance. For ShakeMap, it is necessary to provide an estimate of the shaking levels for events without rupture models, and before rupture models are available for events that eventually do have rupture models. In probabilistic seismic hazard analysis, it is often convenient to use point-source distances for gridded seismicity sources, particularly if a preferred rupture orientation is unknown. This avoids the computationally cumbersome task of computing rupture-based distances for virtual rupture planes across all strikes and dips for each source. We derive average rupture distances conditioned on REPI, magnitude, and (optionally) back azimuth, for a variety of assumed seismological constraints. Additionally, we derive adjustment factors for GMPE standard deviations that reflect the added uncertainty in the ground-motion estimation when point-source distances are used to estimate rupture distances. [ABSTRACT FROM AUTHOR]

Published
2018
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