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4. Targeted Next-Generation Sequencing Reveals Divergent Clonal Evolution in Components of Composite Pleomorphic Xanthoastrocytoma-Ganglioglioma

Author

Lucas, Calixto-Hope G, Davidson, Christian J, Alashari, Mouied, Putnam, Angelica R, Whipple, Nicholas S, Bruggers, Carol S, Mendez, Joe S, Cheshier, Samuel H, Walker, Jeffrey B, Ramani, Biswarathan, Cadwell, Cathryn R, Sullivan, Daniel V, Lu, Rufei, Mirchia, Kanish, Van Ziffle, Jessica, Devine, Patrick, Goldschmidt, Ezequiel, Hervey-Jumper, Shawn L, Gupta, Nalin, Bush, Nancy Ann Oberheim, Raleigh, David R, Bollen, Andrew, Tihan, Tarik, Pekmezci, Melike, Solomon, David A, Phillips, Joanna J, and Perry, Arie

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Biotechnology, Human Genome, Genetics, Rare Diseases, Cancer, Adolescent, Adult, Astrocytoma, Brain Neoplasms, Clonal Evolution, Cyclin-Dependent Kinase Inhibitor p16, DNA, Female, Ganglioglioma, High-Throughput Nucleotide Sequencing, Homozygote, Humans, Male, Mutation, Proto-Oncogene Proteins B-raf, Sequence Deletion, Young Adult, Collision tumor, Intratumoral heterogeneity, Molecular neuropathology, Neurooncology, Pleomorphic xanthoastrocytoma, Precision medicine, Clinical Sciences, Neurosciences, Neurology & Neurosurgery, Clinical sciences
Abstract

Composite pleomorphic xanthoastrocytoma-ganglioglioma (PXA-GG) is an extremely rare central nervous system neoplasm with 2 distinct but intermingled components. Whether this tumor represents a "collision tumor" of separate neoplasms or a monoclonal neoplasm with divergent evolution is poorly understood. Clinicopathologic studies and capture-based next generation sequencing were performed on extracted DNA from all available PXA-GG at 2 medical centers. Five PXA-GG were diagnosed in 1 male and 4 female patients ranging from 13 to 25 years in age. Four arose within the cerebral hemispheres; 1 presented in the cerebellar vermis. DNA was sufficient for analysis in 4 PXA components and 3 GG components. Four paired PXA and GG components harbored BRAF p.V600E hotspot mutations. The 4 sequenced PXA components demonstrated CDKN2A homozygous deletion by sequencing with loss of p16 (protein product of CDKN2A) expression by immunohistochemistry, which was intact in all assessed GG components. The PXA components also demonstrated more frequent copy number alterations relative to paired GG components. In one PXA-GG, shared chromosomal copy number alterations were identified in both components. Our findings support divergent evolution of the PXA and GG components from a common BRAF p.V600E-mutant precursor lesion, with additional acquisition of CDKN2A homozygous deletion in the PXA component as is typically seen in conventional PXA.

Published
2022

10. Comparison of downscaling techniques for high resolution soil moisture mapping

Author

Sabaghy, Sabah, Walker, Jeffrey, Renzullo, Luigi, Akbar, Ruzbeh, Chan, Steven, Chaubell, Julian, Das, Narendra, Dunbar, R. Scott, Entekhabi, Dara, Gevaert, Anouk, Jackson, Thomas, Merlin, Olivier, Moghaddam, Mahta, Peng, Jinzheng, Piepmeier, Jeffrey, Piles, Maria, Portal, Gerard, Rudiger, Christoph, Stefan, Vivien, Wu, Xiaoling, Ye, Nan, and Yueh, Simon

Subjects
Physics - Applied Physics
Abstract

Soil moisture impacts exchanges of water, energy and carbon fluxes between the land surface and the atmosphere. Passive microwave remote sensing at L-band can capture spatial and temporal patterns of soil moisture in the landscape. Both ESA and NASA have launched L-band radiometers, in the form of the SMOS and SMAP satellites respectively, to monitor soil moisture globally, every 3-day at about 40 km resolution. However, their coarse scale restricts the range of applications. While SMAP included an L-band radar to downscale the radiometer soil moisture to 9 km, the radar failed after 3 months and this initial approach is not applicable to developing a consistent long term soil moisture product across the two missions anymore. Existing optical-, radiometer-, and oversampling-based downscaling methods could be an alternative to the radar-based approach for delivering such data. Nevertheless, retrieval of a consistent high resolution soil moisture product remains a challenge, and there has been no comprehensive inter-comparison of the alternate approaches. This research undertakes an assessment of the different downscaling approaches using the SMAPEx-4 field campaign data

Published
2020
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11. Using a Novel Instrumented Roller to Estimate Soil Dry Density During Compaction

Author

Tophel, Amir, Walker, Jeffrey P., Dutta, Troyee Tanu, Kodikara, Jayantha, di Prisco, Marco, Series Editor, Chen, Sheng-Hong, Series Editor, Vayas, Ioannis, Series Editor, Kumar Shukla, Sanjay, Series Editor, Sharma, Anuj, Series Editor, Kumar, Nagesh, Series Editor, Wang, Chien Ming, Series Editor, Gomes Correia, António, editor, Azenha, Miguel, editor, Cruz, Paulo J. S., editor, Novais, Paulo, editor, and Pereira, Paulo, editor

Published
2023
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13. The immunohistochemical, DNA methylation, and chromosomal copy number profile of cauda equina paraganglioma is distinct from extra-spinal paraganglioma

Author

Ramani, Biswarathan, Gupta, Rohit, Wu, Jasper, Barreto, Jairo, Bollen, Andrew W, Tihan, Tarik, Mummaneni, Praveen V, Ames, Christopher, Clark, Aaron, Oberheim Bush, Nancy Ann, Butowski, Nicholas, Phillips, Daniel, King, Bruce E, Bator, Susan M, Treynor, Elizabeth C, Zherebitskiy, Viktor, Quinn, Paula S, Walker, Jeffrey B, Pekmezci, Melike, Sullivan, Daniel V, Hofmann, Jeffrey W, Sloan, Emily A, M. Chang, Susan, Berger, Mitchel S, Solomon, David A, and Perry, Arie

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Neurosciences, Clinical Research, Human Genome, Adult, Aged, Aged, 80 and over, Cauda Equina, Central Nervous System Neoplasms, DNA Copy Number Variations, DNA Methylation, Female, Germ-Line Mutation, Humans, Immunohistochemistry, Male, Middle Aged, Paraganglioma, Young Adult, Cauda equina paraganglioma, Filum terminale, Neuroendocrine tumor, Molecular neuropathology, Succinate dehydrogenase, DNA methylation profiling, Clinical Sciences, Neurology & Neurosurgery
Abstract

Paragangliomas are neuroendocrine tumors of the autonomic nervous system that are variably clinically functional and have a potential for metastasis. Up to 40% occur in the setting of a hereditary syndrome, most commonly due to germline mutations in succinate dehydrogenase (SDHx) genes. Immunohistochemically, paragangliomas are characteristically GATA3-positive and cytokeratin-negative, with loss of SDHB expression in most hereditary cases. In contrast, the rare paragangliomas arising in the cauda equina (CEP) or filum terminale region have been shown to be hormonally silent, clinically indolent, and have variable keratin expression, suggesting these tumors may represent a separate pathologic entity. We retrospectively evaluated 17 CEPs from 11 male and 6 female patients with a median age of 38 years (range 21-82), none with a family history of neuroendocrine neoplasia. Six of the 17 tumors demonstrated prominent gangliocytic or ganglioneuromatous differentiation. By immunohistochemistry, none of the CEPs showed GATA3 positivity or loss of SDHB staining; all 17 CEPs were cytokeratin positive. Genome-wide DNA methylation profiling was performed on 12 of the tumors and compared with publicly available genome-wide DNA methylation data. Clustering analysis showed that CEPs form a distinct epigenetic group, separate from paragangliomas of extraspinal sites, pheochromocytomas, and other neuroendocrine neoplasms. Copy number analysis revealed diploid genomes in the vast majority of CEPs, whereas extraspinal paragangliomas were mostly aneuploid with recurrent trisomy 1q and monosomies of 1p, 3, and 11, none of which were present in the cohort of CEP. Together, these findings indicate that CEPs likely represent a distinct entity. Future genomic studies are needed to further elucidate the molecular pathogenesis of these tumors.

Published
2020

28. Sentinel-1 soil moisture at 1 km resolution: a validation study

Author

Balenzano, Anna, Mattia, Francesco, Satalino, Giuseppe, Lovergine, Francesco P., Palmisano, Davide, Peng, Jian, Marzahn, Philip, Wegmüller, Urs, Cartus, Oliver, Dąbrowska-Zielińska, Katarzyna, Musial, Jan P., Davidson, Malcolm W.J., Pauwels, Valentijn R.N., Cosh, Michael H., McNairn, Heather, Johnson, Joel T., Walker, Jeffrey P., Yueh, Simon H., Entekhabi, Dara, Kerr, Yann H., and Jackson, Thomas J.

Published
2021
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32. A roadmap for high-resolution satellite soil moisture applications – confronting product characteristics with user requirements

Author

Peng, Jian, Albergel, Clement, Balenzano, Anna, Brocca, Luca, Cartus, Oliver, Cosh, Michael H., Crow, Wade T., Dabrowska-Zielinska, Katarzyna, Dadson, Simon, Davidson, Malcolm W.J., de Rosnay, Patricia, Dorigo, Wouter, Gruber, Alexander, Hagemann, Stefan, Hirschi, Martin, Kerr, Yann H., Lovergine, Francesco, Mahecha, Miguel D., Marzahn, Philip, Mattia, Francesco, Musial, Jan Pawel, Preuschmann, Swantje, Reichle, Rolf H., Satalino, Giuseppe, Silgram, Martyn, van Bodegom, Peter M., Verhoest, Niko E.C., Wagner, Wolfgang, Walker, Jeffrey P., Wegmüller, Urs, and Loew, Alexander

Published
2021
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35. Carbon, water and energy fluxes in agricultural systems of Australia and New Zealand

Author

Cleverly, James, Vote, Camilla, Isaac, Peter, Ewenz, Cacilia, Harahap, Mahrita, Beringer, Jason, Campbell, David I., Daly, Edoardo, Eamus, Derek, He, Liang, Hunt, John, Grace, Peter, Hutley, Lindsay B., Laubach, Johannes, McCaskill, Malcolm, Rowlings, David, Rutledge Jonker, Susanna, Schipper, Louis A., Schroder, Ivan, Teodosio, Bertrand, Yu, Qiang, Ward, Phil R., Walker, Jeffrey P., Webb, John A., and Grover, Samantha P.P.

Published
2020
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36. Comprehensive analysis of alternative downscaled soil moisture products

Author

Sabaghy, Sabah, Walker, Jeffrey P., Renzullo, Luigi J., Akbar, Ruzbeh, Chan, Steven, Chaubell, Julian, Das, Narendra, Dunbar, R. Scott, Entekhabi, Dara, Gevaert, Anouk, Jackson, Thomas J., Loew, Alexander, Merlin, Olivier, Moghaddam, Mahta, Peng, Jian, Peng, Jinzheng, Piepmeier, Jeffrey, Rüdiger, Christoph, Stefan, Vivien, Wu, Xiaoling, Ye, Nan, and Yueh, Simon

Published
2020
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42. Author Correction: The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

Author

Pastorello, Gilberto, Trotta, Carlo, Canfora, Eleonora, Chu, Housen, Christianson, Danielle, Cheah, You-Wei, Poindexter, Cristina, Chen, Jiquan, Elbashandy, Abdelrahman, Humphrey, Marty, Isaac, Peter, Polidori, Diego, Reichstein, Markus, Ribeca, Alessio, van Ingen, Catharine, Vuichard, Nicolas, Zhang, Leiming, Amiro, Brian, Ammann, Christof, Arain, M. Altaf, Ardö, Jonas, Arkebauer, Timothy, Arndt, Stefan K., Arriga, Nicola, Aubinet, Marc, Aurela, Mika, Baldocchi, Dennis, Barr, Alan, Beamesderfer, Eric, Marchesini, Luca Belelli, Bergeron, Onil, Beringer, Jason, Bernhofer, Christian, Berveiller, Daniel, Billesbach, Dave, Black, Thomas Andrew, Blanken, Peter D., Bohrer, Gil, Boike, Julia, Bolstad, Paul V., Bonal, Damien, Bonnefond, Jean-Marc, Bowling, David R., Bracho, Rosvel, Brodeur, Jason, Brümmer, Christian, Buchmann, Nina, Burban, Benoit, Burns, Sean P., Buysse, Pauline, Cale, Peter, Cavagna, Mauro, Cellier, Pierre, Chen, Shiping, Chini, Isaac, Christensen, Torben R., Cleverly, James, Collalti, Alessio, Consalvo, Claudia, Cook, Bruce D., Cook, David, Coursolle, Carole, Cremonese, Edoardo, Curtis, Peter S., D’Andrea, Ettore, da Rocha, Humberto, Dai, Xiaoqin, Davis, Kenneth J., De Cinti, Bruno, de Grandcourt, Agnes, De Ligne, Anne, De Oliveira, Raimundo C., Delpierre, Nicolas, Desai, Ankur R., Di Bella, Carlos Marcelo, di Tommasi, Paul, Dolman, Han, Domingo, Francisco, Dong, Gang, Dore, Sabina, Duce, Pierpaolo, Dufrêne, Eric, Dunn, Allison, Dušek, Jiří, Eamus, Derek, Eichelmann, Uwe, ElKhidir, Hatim Abdalla M., Eugster, Werner, Ewenz, Cacilia M., Ewers, Brent, Famulari, Daniela, Fares, Silvano, Feigenwinter, Iris, Feitz, Andrew, Fensholt, Rasmus, Filippa, Gianluca, Fischer, Marc, Frank, John, Galvagno, Marta, Gharun, Mana, Gianelle, Damiano, Gielen, Bert, Gioli, Beniamino, Gitelson, Anatoly, Goded, Ignacio, Goeckede, Mathias, Goldstein, Allen H., Gough, Christopher M., Goulden, Michael L., Graf, Alexander, Griebel, Anne, Gruening, Carsten, Grünwald, Thomas, Hammerle, Albin, Han, Shijie, Han, Xingguo, Hansen, Birger Ulf, Hanson, Chad, Hatakka, Juha, He, Yongtao, Hehn, Markus, Heinesch, Bernard, Hinko-Najera, Nina, Hörtnagl, Lukas, Hutley, Lindsay, Ibrom, Andreas, Ikawa, Hiroki, Jackowicz-Korczynski, Marcin, Janouš, Dalibor, Jans, Wilma, Jassal, Rachhpal, Jiang, Shicheng, Kato, Tomomichi, Khomik, Myroslava, Klatt, Janina, Knohl, Alexander, Knox, Sara, Kobayashi, Hideki, Koerber, Georgia, Kolle, Olaf, Kosugi, Yoshiko, Kotani, Ayumi, Kowalski, Andrew, Kruijt, Bart, Kurbatova, Julia, Kutsch, Werner L., Kwon, Hyojung, Launiainen, Samuli, Laurila, Tuomas, Law, Bev, Leuning, Ray, Li, Yingnian, Liddell, Michael, Limousin, Jean-Marc, Lion, Marryanna, Liska, Adam J., Lohila, Annalea, López-Ballesteros, Ana, López-Blanco, Efrén, Loubet, Benjamin, Loustau, Denis, Lucas-Moffat, Antje, Lüers, Johannes, Ma, Siyan, Macfarlane, Craig, Magliulo, Vincenzo, Maier, Regine, Mammarella, Ivan, Manca, Giovanni, Marcolla, Barbara, Margolis, Hank A., Marras, Serena, Massman, William, Mastepanov, Mikhail, Matamala, Roser, Matthes, Jaclyn Hatala, Mazzenga, Francesco, McCaughey, Harry, McHugh, Ian, McMillan, Andrew M. S., Merbold, Lutz, Meyer, Wayne, Meyers, Tilden, Miller, Scott D., Minerbi, Stefano, Moderow, Uta, Monson, Russell K., Montagnani, Leonardo, Moore, Caitlin E., Moors, Eddy, Moreaux, Virginie, Moureaux, Christine, Munger, J. William, Nakai, Taro, Neirynck, Johan, Nesic, Zoran, Nicolini, Giacomo, Noormets, Asko, Northwood, Matthew, Nosetto, Marcelo, Nouvellon, Yann, Novick, Kimberly, Oechel, Walter, Olesen, Jørgen Eivind, Ourcival, Jean-Marc, Papuga, Shirley A., Parmentier, Frans-Jan, Paul-Limoges, Eugenie, Pavelka, Marian, Peichl, Matthias, Pendall, Elise, Phillips, Richard P., Pilegaard, Kim, Pirk, Norbert, Posse, Gabriela, Powell, Thomas, Prasse, Heiko, Prober, Suzanne M., Rambal, Serge, Rannik, Üllar, Raz-Yaseef, Naama, Rebmann, Corinna, Reed, David, de Dios, Victor Resco, Restrepo-Coupe, Natalia, Reverter, Borja R., Roland, Marilyn, Sabbatini, Simone, Sachs, Torsten, Saleska, Scott R., Sánchez-Cañete, Enrique P., Sanchez-Mejia, Zulia M., Schmid, Hans Peter, Schmidt, Marius, Schneider, Karl, Schrader, Frederik, Schroder, Ivan, Scott, Russell L., Sedlák, Pavel, Serrano-Ortíz, Penélope, Shao, Changliang, Shi, Peili, Shironya, Ivan, Siebicke, Lukas, Šigut, Ladislav, Silberstein, Richard, Sirca, Costantino, Spano, Donatella, Steinbrecher, Rainer, Stevens, Robert M., Sturtevant, Cove, Suyker, Andy, Tagesson, Torbern, Takanashi, Satoru, Tang, Yanhong, Tapper, Nigel, Thom, Jonathan, Tomassucci, Michele, Tuovinen, Juha-Pekka, Urbanski, Shawn, Valentini, Riccardo, van der Molen, Michiel, van Gorsel, Eva, van Huissteden, Ko, Varlagin, Andrej, Verfaillie, Joseph, Vesala, Timo, Vincke, Caroline, Vitale, Domenico, Vygodskaya, Natalia, Walker, Jeffrey P., Walter-Shea, Elizabeth, Wang, Huimin, Weber, Robin, Westermann, Sebastian, Wille, Christian, Wofsy, Steven, Wohlfahrt, Georg, Wolf, Sebastian, Woodgate, William, Li, Yuelin, Zampedri, Roberto, Zhang, Junhui, Zhou, Guoyi, Zona, Donatella, Agarwal, Deb, Biraud, Sebastien, Torn, Margaret, and Papale, Dario

Published
2021
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49. Contributors

Author

Ali, Hani, primary, Anderson, Tyler, additional, Bauer, Jean-Martin, additional, Bazo, Juan, additional, Bell, Veronica, additional, Brakenridge, G. Robert, additional, Casado, Mónica Rivas, additional, Ceola, Serena, additional, Chini, Marco, additional, Collischonn, Walter, additional, Dasgupta, Antara, additional, Demuzere, Matthias, additional, de Moraes Frasson, Renato Prata, additional, Dias de Paiva, Rodrigo Cauduro, additional, Dinga, Jéan Bienvenu, additional, Domeneghetti, Alessio, additional, Doyle, Colin, additional, Fialho Brêda, João Paulo, additional, Fleischmann, Ayan Santos, additional, Galantowicz, John F., additional, Gascoigne, Jonathon, additional, Glinskis, Emmalina, additional, Grimaldi, Stefania, additional, Ho, Jeff C., additional, Horna, Natalia, additional, Hostache, Renaud, additional, Kettner, A.J., additional, Khouakhi, Abdou, additional, Kruczkiewicz, Andrew, additional, Kugler, Zsofia, additional, Leinster, Paul, additional, Martinis, Sandro, additional, Mason, Jesse, additional, Matgen, Patrick, additional, Mazzoglio, Paola, additional, McClain, Shanna, additional, Muthusamy, Manoranjan, additional, N’diaye, Patrick Impeti, additional, Nghiem, Son. V., additional, Papa, Fabrice, additional, Pauwels, Valentijn R.N., additional, Picton, Jeff, additional, Rättich, Michaela, additional, Ramsankaran, RAAJ, additional, Ravanello, Mariane Moreira, additional, Rudorff, Conrado, additional, Schumann, Guy J-P., additional, Schwarz, Bessie, additional, Senol Cabi, Nalan, additional, Shen, X., additional, Tellman, Beth, additional, Thomson, Tina, additional, Vergara, Humberto, additional, Vu, William, additional, Walker, Jeffrey P., additional, Wang, Ruo-Qian, additional, Warrick, Olivia, additional, Weber, Sam, additional, Wieland, Marc, additional, and Zare, Mohammad, additional

Published
2021
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