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1. Interpretability analysis on a pathology foundation model reveals biologically relevant embeddings across modalities

Author

Le, Nhat, Shen, Ciyue, Shah, Chintan, Martin, Blake, Shenker, Daniel, Padigela, Harshith, Hipp, Jennifer, Grullon, Sean, Abel, John, Pokkalla, Harsha Vardhan, and Juyal, Dinkar

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Mechanistic interpretability has been explored in detail for large language models (LLMs). For the first time, we provide a preliminary investigation with similar interpretability methods for medical imaging. Specifically, we analyze the features from a ViT-Small encoder obtained from a pathology Foundation Model via application to two datasets: one dataset of pathology images, and one dataset of pathology images paired with spatial transcriptomics. We discover an interpretable representation of cell and tissue morphology, along with gene expression within the model embedding space. Our work paves the way for further exploration around interpretable feature dimensions and their utility for medical and clinical applications.

Published
2024

2. PLUTO: Pathology-Universal Transformer

Author

Juyal, Dinkar, Padigela, Harshith, Shah, Chintan, Shenker, Daniel, Harguindeguy, Natalia, Liu, Yi, Martin, Blake, Zhang, Yibo, Nercessian, Michael, Markey, Miles, Finberg, Isaac, Luu, Kelsey, Borders, Daniel, Javed, Syed Ashar, Krause, Emma, Biju, Raymond, Sood, Aashish, Ma, Allen, Nyman, Jackson, Shamshoian, John, Chhor, Guillaume, Sanghavi, Darpan, Thibault, Marc, Yu, Limin, Najdawi, Fedaa, Hipp, Jennifer A., Fahy, Darren, Glass, Benjamin, Walk, Eric, Abel, John, Pokkalla, Harsha, Beck, Andrew H., and Grullon, Sean

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

Published
2024

3. Using Whole Slide Image Representations from Self-Supervised Contrastive Learning for Melanoma Concordance Regression

Author

Grullon, Sean, Spurrier, Vaughn, Zhao, Jiayi, Chivers, Corey, Jiang, Yang, Motaparthi, Kiran, Bonham, Michael, and Ianni, Julianna

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Although melanoma occurs more rarely than several other skin cancers, patients' long term survival rate is extremely low if the diagnosis is missed. Diagnosis is complicated by a high discordance rate among pathologists when distinguishing between melanoma and benign melanocytic lesions. A tool that provides potential concordance information to healthcare providers could help inform diagnostic, prognostic, and therapeutic decision-making for challenging melanoma cases. We present a melanoma concordance regression deep learning model capable of predicting the concordance rate of invasive melanoma or melanoma in-situ from digitized Whole Slide Images (WSIs). The salient features corresponding to melanoma concordance were learned in a self-supervised manner with the contrastive learning method, SimCLR. We trained a SimCLR feature extractor with 83,356 WSI tiles randomly sampled from 10,895 specimens originating from four distinct pathology labs. We trained a separate melanoma concordance regression model on 990 specimens with available concordance ground truth annotations from three pathology labs and tested the model on 211 specimens. We achieved a Root Mean Squared Error (RMSE) of 0.28 +/- 0.01 on the test set. We also investigated the performance of using the predicted concordance rate as a malignancy classifier, and achieved a precision and recall of 0.85 +/- 0.05 and 0.61 +/- 0.06, respectively, on the test set. These results are an important first step for building an artificial intelligence (AI) system capable of predicting the results of consulting a panel of experts and delivering a score based on the degree to which the experts would agree on a particular diagnosis. Such a system could be used to suggest additional testing or other action such as ordering additional stains or genetic tests., Comment: Accepted at ECCV 2022 AIMIA Workshop. arXiv admin note: text overlap with arXiv:2109.07554

Published
2022

4. A Pathology Deep Learning System Capable of Triage of Melanoma Specimens Utilizing Dermatopathologist Consensus as Ground Truth

Author

Sankarapandian, Sivaramakrishnan, Kohn, Saul, Spurrier, Vaughn, Grullon, Sean, Soans, Rajath E., Ayyagari, Kameswari D., Chamarthi, Ramachandra V., Motaparthi, Kiran, Lee, Jason B., Shon, Wonwoo, Bonham, Michael, and Ianni, Julianna D.

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Although melanoma occurs more rarely than several other skin cancers, patients' long term survival rate is extremely low if the diagnosis is missed. Diagnosis is complicated by a high discordance rate among pathologists when distinguishing between melanoma and benign melanocytic lesions. A tool that allows pathology labs to sort and prioritize melanoma cases in their workflow could improve turnaround time by prioritizing challenging cases and routing them directly to the appropriate subspecialist. We present a pathology deep learning system (PDLS) that performs hierarchical classification of digitized whole slide image (WSI) specimens into six classes defined by their morphological characteristics, including classification of "Melanocytic Suspect" specimens likely representing melanoma or severe dysplastic nevi. We trained the system on 7,685 images from a single lab (the reference lab), including the the largest set of triple-concordant melanocytic specimens compiled to date, and tested the system on 5,099 images from two distinct validation labs. We achieved Area Underneath the ROC Curve (AUC) values of 0.93 classifying Melanocytic Suspect specimens on the reference lab, 0.95 on the first validation lab, and 0.82 on the second validation lab. We demonstrate that the PDLS is capable of automatically sorting and triaging skin specimens with high sensitivity to Melanocytic Suspect cases and that a pathologist would only need between 30% and 60% of the caseload to address all melanoma specimens., Comment: Accepted at ICCV 2021 CDpath workshop

Published
2021

5. Using Whole Slide Image Representations from Self-supervised Contrastive Learning for Melanoma Concordance Regression

Author

Grullon, Sean, Spurrier, Vaughn, Zhao, Jiayi, Chivers, Corey, Jiang, Yang, Motaparthi, Kiran, Lee, Jason, Bonham, Michael, Ianni, Julianna, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Karlinsky, Leonid, editor, Michaeli, Tomer, editor, and Nishino, Ko, editor

Published
2023
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6. The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

Author

LBNE Collaboration, Adams, Corey, Adams, David, Akiri, Tarek, Alion, Tyler, Anderson, Kris, Andreopoulos, Costas, Andrews, Mike, Anghel, Ioana, Anjos, João Carlos Costa dos, Antonello, Maddalena, Arrieta-Diaz, Enrique, Artuso, Marina, Asaadi, Jonathan, Bai, Xinhua, Baibussinov, Bagdat, Baird, Michael, Balantekin, Baha, Baller, Bruce, Baptista, Brian, Barker, D'Ann, Barker, Gary, Barletta, William A., Barr, Giles, Bartoszek, Larry, Bashyal, Amit, Bass, Matt, Bellini, Vincenzo, Benetti, Pietro Angelo, Berger, Bruce E., Bergevin, Marc, Berman, Eileen, Berns, Hans-Gerd, Bernstein, Adam, Bernstein, Robert, Bhandari, Babu, Bhatnagar, Vipin, Bhuyan, Bipul, Bian, Jianming, Bishai, Mary, Blake, Andrew, Blaszczyk, Flor, Blaufuss, Erik, Bleakley, Bruce, Blucher, Edward, Blusk, Steve, Bocean, Virgil, Boffelli, F., Boissevain, Jan, Bolton, Timothy, Bonesini, Maurizio, Boyd, Steve, Brandt, Andrew, Breedon, Richard, Bromberg, Carl, Brown, Ralph, Brunetti, Giullia, Buchanan, Norman, Bugg, Bill, Busenitz, Jerome, Calligarich, E., Camilleri, Leslie, Carminati, Giada, Carr, Rachel, Castromonte, Cesar, Cavanna, Flavio, Centro, Sandro, Chen, Alex, Chen, Hucheng, Chen, Kai, Cherdack, Daniel, Chi, Cheng-Yi, Childress, Sam, Choudhary, Brajesh Chandra, Christodoulou, Georgios, Christofferson, Cabot-Ann, Church, Eric, Cline, David, Coan, Thomas, Cocco, Alfredo, Coelho, Joao, Coleman, Stephen, Conrad, Janet M., Convery, Mark, Corey, Robert, Corwin, Luke, Cranshaw, Jack, Cronin-Hennessy, Daniel, Curioni, A., da Motta, Helio, Davenne, Tristan, Davies, Gavin S., Dazeley, Steven, De, Kaushik, de Gouvea, Andre, de Jong, Jeffrey K., Demuth, David, Densham, Chris, Diwan, Milind, Djurcic, Zelimir, Dolfini, R., Dolph, Jeffrey, Drake, Gary, Dye, Stephen, Dyuang, Hongue, Edmunds, Daniel, Elliott, Steven, Elnimr, Muhammad, Eno, Sarah, Enomoto, Sanshiro, Escobar, Carlos O., Evans, Justin, Falcone, A., Falk, Lisa, Farbin, Amir, Farnese, Christian, Fava, Angela, Felde, John, Fernandes, S., Ferroni, Fernando, Feyzi, Farshid, Fields, Laura, Finch, Alex, Fitton, Mike, Fleming, Bonnie, Fowler, Jack, Fox, Walt, Friedland, Alex, Fuess, Stu, Fujikawa, Brian, Gallagher, Hugh, Gandhi, Raj, Garvey, Gerald, Gehman, Victor M., de Geronimo, Gianluigi, Gibin, Daniele, Gill, Ronald, Gomes, Ricardo A., Goodman, Maury C., Goon, Jason, Graf, Nicholas, Graham, Mathew, Gran, Rik, Grant, Christopher, Grant, Nick, Greenlee, Herbert, Greenler, Leland, Grullon, Sean, Guardincerri, Elena, Guarino, Victor, Guarnaccia, Evan, Guedes, Germano, Guenette, Roxanne, Guglielmi, Alberto, Guzzo, Marcelo M., Habig, Alec T., Hackenburg, Robert W., Hadavand, Haleh, Hahn, Alan, Haigh, Martin, Haines, Todd, Handler, Thomas, Hans, Sunej, Hartnell, Jeff, Harton, John, Hatcher, Robert, Hatzikoutelis, Athans, Hays, Steven, Hazen, Eric, Headley, Mike, Heavey, Anne, Heeger, Karsten, Heise, Jaret, Hellauer, Robert, Hewes, V, Himmel, Alexander, Hogan, Matthew, Holanda, Pedro, Holin, Anna, Horton-Smith, Glenn, Howell, Joe, Hurh, Patrick, Huston, Joey, Hylen, James, Imlay, Richard, Insler, Jonathan, Introzzi, G., Isvan, Zeynep, Jackson, Chris, Jacobsen, John, Jaffe, David E., James, Cat, Jen, Chun-Min, Johnson, Marvin, Johnson, Randy, Johnson, Robert, Johnson, Scott, Johnston, William, Johnstone, John, Jones, Ben J. P., Jostlein, H., Junk, Thomas, Kadel, Richard, Kaess, Karl, Karagiorgi, Georgia, Kaspar, Jarek, Katori, Teppei, Kayser, Boris, Kearns, Edward, Keener, Paul, Kemp, Ernesto, Kettell, Steve H., Kirby, Mike, Klein, Joshua, Koizumi, Gordon, Kopp, Sacha, Kormos, Laura, Kropp, William, Kudryavtsev, Vitaly A., Kumar, Ashok, Kumar, Jason, Kutter, Thomas, La Zia, Franco, Lande, Kenneth, Lane, Charles, Lang, Karol, Lanni, Francesco, Lanza, Richard, Latorre, Tony, Learned, John, Lee, David, Lee, Kevin, Li, Qizhong, Li, Shaorui, Li, Yichen, Li, Zepeng, Libo, Jiang, Linden, Steve, Ling, Jiajie, Link, Jonathan, Littenberg, Laurence, Liu, Hu, Liu, Qiuguang, Liu, Tiankuan, Losecco, John, Louis, William, Lundberg, Byron, Lundin, Tracy, Lundy, Jay, Machado, Ana Amelia, Maesano, Cara, Magill, Steve, Mahler, George, Malon, David, Malys, Stephen, Mammoliti, Francesco, Mandal, Samit Kumar, Mann, Anthony, Mantsch, Paul, Marchionni, Alberto, Marciano, William, Mariani, Camillo, Maricic, Jelena, Marino, Alysia, Marshak, Marvin, Marshall, John, Matsuno, Shiegenobu, Mauger, Christopher, Mavrokoridis, Konstantinos, Mayer, Nate, McCauley, Neil, McCluskey, Elaine, McDonald, Kirk, McFarland, Kevin, McKee, David, McKeown, Robert, McTaggart, Robert, Mehdiyev, Rashid, Mei, Dongming, Menegolli, A., Meng, Guang, Meng, Yixiong, Mertins, David, Messier, Mark, Metcalf, William, Milincic, Radovan, Miller, William, Mills, Geoff, Mishra, Sanjib R., Mokhov, Nikolai, Montanari, Claudio, Montanari, David, Moore, Craig, Morfin, Jorge, Morgan, Ben, Morse, William, Moss, Zander, Moura, Célio A., Mufson, Stuart, Muller, David, Musser, Jim, Naples, Donna, Napolitano, Jim, Newcomer, Mitch, Nichol, Ryan, Nicholls, Tim, Niner, Evan, Norris, Barry, Nowak, Jaroslaw, O'Keeffe, Helen, Oliveira, Roberto, Olson, Travis, Page, Brian, Pakvasa, Sandip, Palamara, Ornella, Paley, Jon, Paolone, Vittorio, Papadimitriou, Vaia, Park, Seongtae, Parsa, Zohreh, Partyka, Kinga, Paulos, Bob, Pavlovic, Zarko, Peeters, Simon, Perch, Andy, Perkin, Jon D., Petti, Roberto, Petukhov, Andre, Pietropaolo, Francesco, Plunkett, Robert, Polly, Chris, Pordes, Stephen, Potekhin, Maxim, Potenza, Renato, Prakash, Arati, Prokofiev, Oleg, Qian, Xin, Raaf, Jennifer L., Radeka, Veljko, Rakhno, Igor, Ramachers, Yorck, Rameika, Regina, Ramsey, John, Rappoldi, A., Raselli, G. L., Ratoff, Peter, Ravindra, Shreyas, Rebel, Brian, Reichenbacher, Juergen, Reitzner, Dianne, Rescia, Sergio, Richardson, Martin, Rielage, Kieth, Riesselmann, Kurt, Robinson, Matt, Rochester, Leon, Ronquest, Michael, Rosen, Marc, Rossella, M., Rubbia, Carlo, Rucinski, Russ, Sahijpal, Sandeep, Sahoo, Himansu, Sala, Paola, Salmiera, Delia, Samios, Nicholas, Sanchez, Mayly, Scaramelli, Alberto, Schellman, Heidi, Schmitt, Richard, Schmitz, David, Schneps, Jack, Scholberg, Kate, Segreto, Ettore, Seibert, Stanley, Sexton-Kennedy, Liz, Shaevitz, Mike, Shanahan, Peter, Sharma, Rahul, Shaw, Terri, Simos, Nikolaos, Singh, Venktesh, Sinnis, Gus, Sippach, William, Skwarnicki, Tomasz, Smy, Michael, Sobel, Henry, Soderberg, Mitch, Sondericker, John, Sondheim, Walter, Sousa, Alexandre, Spooner, Neil J. C., Stancari, Michelle, Stancu, Ion, Stefan, Dorota, Stefanik, Andy, Stewart, James, Stone, Sheldon, Strait, James, Strait, Matthew, Striganov, Sergei, Sullivan, Gregory, Sun, Yujing, Suter, Louise, Svenson, Andrew, Svoboda, Robert, Szczerbinska, Barbara, Szelc, Andrzej, Szydagis, Matthew, Söldner-Rembold, Stefan, Talaga, Richard, Tamsett, Matthew, Tariq, Salman, Tayloe, Rex, Taylor, Charles, Taylor, David, Teymourian, Artin, Themann, Harry, Thiesse, Matthew, Thomas, Jenny, Thompson, Lee F., Thomson, Mark, Thorn, Craig, Thorpe, Matt, Tian, Xinchun, Tiedt, Doug, Toki, Walter, Tolich, Nikolai, Torti, M., Toups, Matt, Touramanis, Christos, Tripathi, Mani, Tropin, Igor, Tsai, Yun-Tse, Tull, Craig, Tzanov, Martin, Urheim, Jon, Usman, Shawn, Vagins, Mark, Valdiviesso, Gustavo, Van Berg, Rick, Van de Water, Richard, Van Gemmeren, Peter, Varanini, Filippo, Varner, Gary, Vaziri, Kamran, Velev, Gueorgui, Ventura, Sandro, Vignoli, Chiara, Viren, Brett, Wahl, Dan, Waldron, Abby, Walter, Christopher W., Wang, Hanguo, Wang, Wei, Warburton, Karl, Warner, David, Wasserman, Ryan, Watson, Blake, Weber, Alfons, Wei, Wenzhao, Wells, Douglas, Wetstein, Matthew, White, Andy, White, Hywel, Whitehead, Lisa, Whittington, Denver, Willhite, Joshua, Wilson, Robert J., Winslow, Lindley, Wood, Kevin, Worcester, Elizabeth, Worcester, Matthew, Xin, Tian, Yarritu, Kevin, Ye, Jingbo, Yeh, Minfang, Yu, Bo, Yu, Jae, Yuan, Tianlu, Zani, A., Zeller, Geralyn P., Zhang, Chao, Zimmerman, Eric D., and Zwaska, Robert

Subjects
High Energy Physics - Experiment, High Energy Physics - Phenomenology, Physics - Accelerator Physics, Physics - Instrumentation and Detectors
Abstract

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess., Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figures

Published
2013

7. Searching for High Energy Diffuse Astrophysical Muon Neutrinos with IceCube

Author

Grullon, Sean

Subjects
Astrophysics - High Energy Astrophysical Phenomena, High Energy Physics - Experiment
Abstract

The IceCube Neutrino Observatory is a 1 $km^{3}$ detector currently under construction at the South Pole. Searching for high energy neutrinos from unresolved astrophysical sources is one of the main analysis strategies used in the search for astrophysical neutrinos with the IceCube Neutrino Observatory. A hard energy spectrum of neutrinos from isotropically distributed astrophysical sources could contribute to form a detectable signal above the atmospheric neutrino background. A reliable method of estimating the energy of the neutrino-induced lepton is crucial for identifying astrophysical neutrinos. An analysis is underway using data from the half completed detector taken during its 2008-2009 science run., Comment: Proceedings from the 2010 Lake Louise Winter Institute. 4 pages, 3 figures

Published
2010

8. A Pathology Deep Learning System Capable of Triage of Melanoma Specimens Utilizing Dermatopathologist Consensus as Ground Truth

Author

Sankarapandian, Sivaramakrishnan, primary, Kohn, Saul, additional, Spurrier, Vaughn, additional, Grullon, Sean, additional, Soans, Rajath E., additional, Ayyagari, Kameswari D., additional, Chamarthi, Ramachandra V., additional, Motaparthi, Kiran, additional, Lee, Jason B., additional, Shon, Wonwoo, additional, Bonham, Michael, additional, and Ianni, Julianna D., additional

Published
2021
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12. Limits on a muon flux from neutralino annihilations in the sun with the IceCube 22-string detector

Author

Aguilar Sanchez, Juan Antonio, Abdou, Yasser, Ackermann, Markus, Adams, John, Ahlers, Markus, Andeen, K., Auffenberg, Jan, Bai, Xinhua, Baker, Michael, Barwick, S.W., Bay, Ryan, Bazo Alba, J.L., Beattie, K., Beatty, J.J., Bechet, Sabrina, Becker, Julia, Becker, K.-H., Benabderrahmane, M.L., Berdermann, Jens, Berghaus, Patrick, Berley, D., Bernardini, Elisa, Bertrand, Daniel, Besson, David, Bissok, Martin, Blaufuss, E., Boersma, David, Bohm, C., Bolmont, Julien, Böser, Sybille, Botner, O., Bradley, Louise, Braun, James, Breder, D., Burgess, T., Castermans, Thierry, Chirkin, Dmitry, Christy, Brian, Clem, J., Cohen, S, Cowen, D.F., D'Agostino, M.V., Danninger, Matthias, Day, Christopher, De Clercq, Catherine, Demirörs, L., Depaepe, O., Descamps, Freija, Desiati, Paolo, De Vries-Uiterweerd, G., Deyoung, Tyce, Diaz-Velez, J.C., Dreyer, Jens, Dumm, Jon, Duvoort, Martijn, Edwards, W.R., Ehrlich, R., Eisch, J., Ellsworth, R.W., Engdegård, Olle, Euler, Sebastian, Evenson, Paul, Fadiran, Oladipo, Fazely, Ali, Feusels, T., Filimonov, Kirill, Finley, Chad, Foerster, M.M., Fox, Bronwyn, Franckowiak, Anna, Franke, Robert, Gaisser, Thomas, Gallagher, Joseph, Ganugapati, R., Gerhardt, Lisa, Gladstone, Laura, Goldschmidt, Azriel, Goodman, J.A., Gozzini, R., Grant, D., Griesel, T., Gross, Andreas, Grullon, Sean, Gunasingha, Rathnayaka, Gurtner, Michael, Ha, Changhyon, Hallgren, Anita, Halzen, Francis, Han, Kahae, Hanson, Kael, Hasegawa, Y., Heise, J., Helbing, Klaus, Herquet, P., Hickford, Stephanie, Hill, Gary, Hoffman, Kara, Hoshina, Kotoyo, Hubert, Dominicus, Huelsnitz, W., Hülß, Jan Patrick, Hulth, P.O., Hultqvist, K., Hussain, Syed A., Imlay, Richard, Inaba, M., Ishihara, Aya, Jacobsen, Janet, Japaridze, George Sh, Johansson, Henrik, Joseph, Joe, Kampert, K.-H., Kappes, A., Karg, Timo, Karle, Albrecht, Kelley, John, Kenny, Patrick, Kiryluk, Joanna, Kislat, F., Klein, Spencer, Klepser, S., Knops, S., Kohnen, G., Kolanoski, Hermann, Köpke, L., Kowalski, Marek, Kowarik, T., Krasberg, Mark, Kuehn, Kyler, Kuwabara, T., Labare, Mathieu, Lafebre, Sven, Laihem, Karim, Landsman, H., Lauer, Tod, Leich, Holger, Lennarz, Dirk, Lucke, Andreas, Lundberg, J., Lünemann, Jan, Madsen, Jes, Majumdar, P., Maruyama, Reina, Mase, K., Matis, Hope, McParland, Chuck, Meagher, Kevin, Merck, Martin, Mészáros, P., Middell, Eike, Milke, Natalie, Miyamoto, Hiroko, Mohr, Anna, Montaruli, T., Morse, Robert, Movit, Steven, Münich, Kirsten, Nahnhauer, Rolf, Nam, Jiwoo, Nießen, Peter, Nygren, David, Odrowski, Sirin, Olivas, Alex, Olivo, Martino, Ono, Masaaki, Panknin, Sebastian, Patton, S., Pérez De Los Heros, Carlos, Petrovic, Jéléna, Piegsa, Anne, Pieloth, Damian, Pohl, Annika, Porrata, R., Potthoff, N., Price, Buford, Prikockis, Michael, Przybylski, G.T., Rawlins, Katherine, Redl, Peter, Resconi, Elisa, Rhode, Wolfgang, Ribordy, Mathieu, Rizzo, Alessandro, Rodrigues, Jorge, Roth, Peter, Rothmaier, Florian, Rott, C., Roucelle, Cécile, Rutledge, D., Ryckbosch, D., Sander, H.-G., Sarkar, Subir, Satalecka, Konstancja, Schlenstedt, Stefan, Schmidt, Thomas H., Schneider, Dominique, Schukraft, Anne, Schulz, Olaf, Schunck, M., Seckel, David, Semburg, Benjamin, Seo, Hye-Sook, Sestayo, Yolanda, Seunarine, Suruj, Silvestri, Anna, Slipak, A., Spiczak, Glenn, Spiering, Ch, Stamatikos, Michael, Stanev, Todor, Stephens, G. S F, Stezelberger, Thorsten, Stokstad, Robert, Stoufer, M.C., Stoyanov, Stoyan, Strahler, E.A., Straszheim, T., Sulanke, Karl Heinz, Sullivan, G.W., Swillens, Quentin, Taboada, Ignacio, Tarasova, Oksana, Tepe, Andreas, Ter-Antonyan, Samvel, Terranova, Carlo, Tilav, Serap, Tluczykont, M., Toale, P.A., Tosi, Delia, Turčan, Doru, Van Eijndhoven, N. A M, Vandenbroucke, Justin, Van Overloop, Arne, Voigt, B., Walck, Ch, Waldenmaier, Tilo, Walter, Markus, Wendt, Christopher, Westerhoff, Stefan, Whitehorn, Nathan, Wiebusch, Christopher, Wiedemann, A., Wikström, Gustav, Williams, Dyfri, Wischnewski, R., Wissing, Henrike, Woschnagg, Kurt, Xu, Xianwu, Yodh, G., Yoshida, Sho, Aguilar Sanchez, Juan Antonio, Abdou, Yasser, Ackermann, Markus, Adams, John, Ahlers, Markus, Andeen, K., Auffenberg, Jan, Bai, Xinhua, Baker, Michael, Barwick, S.W., Bay, Ryan, Bazo Alba, J.L., Beattie, K., Beatty, J.J., Bechet, Sabrina, Becker, Julia, Becker, K.-H., Benabderrahmane, M.L., Berdermann, Jens, Berghaus, Patrick, Berley, D., Bernardini, Elisa, Bertrand, Daniel, Besson, David, Bissok, Martin, Blaufuss, E., Boersma, David, Bohm, C., Bolmont, Julien, Böser, Sybille, Botner, O., Bradley, Louise, Braun, James, Breder, D., Burgess, T., Castermans, Thierry, Chirkin, Dmitry, Christy, Brian, Clem, J., Cohen, S, Cowen, D.F., D'Agostino, M.V., Danninger, Matthias, Day, Christopher, De Clercq, Catherine, Demirörs, L., Depaepe, O., Descamps, Freija, Desiati, Paolo, De Vries-Uiterweerd, G., Deyoung, Tyce, Diaz-Velez, J.C., Dreyer, Jens, Dumm, Jon, Duvoort, Martijn, Edwards, W.R., Ehrlich, R., Eisch, J., Ellsworth, R.W., Engdegård, Olle, Euler, Sebastian, Evenson, Paul, Fadiran, Oladipo, Fazely, Ali, Feusels, T., Filimonov, Kirill, Finley, Chad, Foerster, M.M., Fox, Bronwyn, Franckowiak, Anna, Franke, Robert, Gaisser, Thomas, Gallagher, Joseph, Ganugapati, R., Gerhardt, Lisa, Gladstone, Laura, Goldschmidt, Azriel, Goodman, J.A., Gozzini, R., Grant, D., Griesel, T., Gross, Andreas, Grullon, Sean, Gunasingha, Rathnayaka, Gurtner, Michael, Ha, Changhyon, Hallgren, Anita, Halzen, Francis, Han, Kahae, Hanson, Kael, Hasegawa, Y., Heise, J., Helbing, Klaus, Herquet, P., Hickford, Stephanie, Hill, Gary, Hoffman, Kara, Hoshina, Kotoyo, Hubert, Dominicus, Huelsnitz, W., Hülß, Jan Patrick, Hulth, P.O., Hultqvist, K., Hussain, Syed A., Imlay, Richard, Inaba, M., Ishihara, Aya, Jacobsen, Janet, Japaridze, George Sh, Johansson, Henrik, Joseph, Joe, Kampert, K.-H., Kappes, A., Karg, Timo, Karle, Albrecht, Kelley, John, Kenny, Patrick, Kiryluk, Joanna, Kislat, F., Klein, Spencer, Klepser, S., Knops, S., Kohnen, G., Kolanoski, Hermann, Köpke, L., Kowalski, Marek, Kowarik, T., Krasberg, Mark, Kuehn, Kyler, Kuwabara, T., Labare, Mathieu, Lafebre, Sven, Laihem, Karim, Landsman, H., Lauer, Tod, Leich, Holger, Lennarz, Dirk, Lucke, Andreas, Lundberg, J., Lünemann, Jan, Madsen, Jes, Majumdar, P., Maruyama, Reina, Mase, K., Matis, Hope, McParland, Chuck, Meagher, Kevin, Merck, Martin, Mészáros, P., Middell, Eike, Milke, Natalie, Miyamoto, Hiroko, Mohr, Anna, Montaruli, T., Morse, Robert, Movit, Steven, Münich, Kirsten, Nahnhauer, Rolf, Nam, Jiwoo, Nießen, Peter, Nygren, David, Odrowski, Sirin, Olivas, Alex, Olivo, Martino, Ono, Masaaki, Panknin, Sebastian, Patton, S., Pérez De Los Heros, Carlos, Petrovic, Jéléna, Piegsa, Anne, Pieloth, Damian, Pohl, Annika, Porrata, R., Potthoff, N., Price, Buford, Prikockis, Michael, Przybylski, G.T., Rawlins, Katherine, Redl, Peter, Resconi, Elisa, Rhode, Wolfgang, Ribordy, Mathieu, Rizzo, Alessandro, Rodrigues, Jorge, Roth, Peter, Rothmaier, Florian, Rott, C., Roucelle, Cécile, Rutledge, D., Ryckbosch, D., Sander, H.-G., Sarkar, Subir, Satalecka, Konstancja, Schlenstedt, Stefan, Schmidt, Thomas H., Schneider, Dominique, Schukraft, Anne, Schulz, Olaf, Schunck, M., Seckel, David, Semburg, Benjamin, Seo, Hye-Sook, Sestayo, Yolanda, Seunarine, Suruj, Silvestri, Anna, Slipak, A., Spiczak, Glenn, Spiering, Ch, Stamatikos, Michael, Stanev, Todor, Stephens, G. S F, Stezelberger, Thorsten, Stokstad, Robert, Stoufer, M.C., Stoyanov, Stoyan, Strahler, E.A., Straszheim, T., Sulanke, Karl Heinz, Sullivan, G.W., Swillens, Quentin, Taboada, Ignacio, Tarasova, Oksana, Tepe, Andreas, Ter-Antonyan, Samvel, Terranova, Carlo, Tilav, Serap, Tluczykont, M., Toale, P.A., Tosi, Delia, Turčan, Doru, Van Eijndhoven, N. A M, Vandenbroucke, Justin, Van Overloop, Arne, Voigt, B., Walck, Ch, Waldenmaier, Tilo, Walter, Markus, Wendt, Christopher, Westerhoff, Stefan, Whitehorn, Nathan, Wiebusch, Christopher, Wiedemann, A., Wikström, Gustav, Williams, Dyfri, Wischnewski, R., Wissing, Henrike, Woschnagg, Kurt, Xu, Xianwu, Yodh, G., and Yoshida, Sho

Abstract

SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2009

13. Search for point sources of high energy neutrinos with final data from AMANDA-II

Author

Aguilar Sanchez, Juan Antonio, Ackermann, Markus, Adams, John, Ahlers, Markus, Ahrens, J., Andeen, K., Auffenberg, Jan, Bai, Xinhua, Baker, Michael, Baret, B., Barwick, S.W., Bay, Ryan, Bazo Alba, J.L., Beattie, K., Becka, T., Becker, Julia, Becker, K.-H., Berdermann, Jens, Berghaus, Patrick, Berley, D., Bernardini, Elisa, Bertrand, Daniel, Besson, David, Blaufuss, E., Boersma, David, Bohm, C., Bolmont, Julien, Böser, Sybille, Botner, O., Braun, James, Breder, D., Burgess, T., Castermans, Thierry, Chirkin, Dmitry, Christy, Brian, Clem, J., Cowen, D.F., D'Agostino, M.V., Danninger, Matthias, Davour, A., Day, Christopher, Depaepe, O., De Clercq, Catherine, Demirörs, L., Descamps, Freija, Desiati, Paolo, De Vries-Uiterweerd, G., Deyoung, Tyce, Diaz-Velez, J.C., Dreyer, Jens, Dumm, Jon, Duvoort, Martijn, Edwards, W.R., Ehrlich, R., Eisch, J., Ellsworth, R.W., Engdegård, Olle, Euler, Sebastian, Evenson, Paul, Fadiran, Oladipo, Fazely, Ali, Filimonov, Kirill, Finley, Chad, Foerster, M.M., Fox, Bronwyn, Franckowiak, Anna, Franke, Robert, Gaisser, Thomas, Gallagher, Joseph, Ganugapati, R., Gerhardt, Lisa, Gladstone, Laura, Goldschmidt, Azriel, Goodman, J.A., Gozzini, R., Grant, D., Griesel, T., Gross, Andreas, Grullon, Sean, Gunasingha, Rathnayaka, Gurtner, Michael, Ha, Changhyon, Hallgren, Anita, Halzen, Francis, Han, Kahae, Hanson, Kael, Hardtke, R., Hasegawa, Y., Heise, J., Helbing, Klaus, Hellwig, Martin, Herquet, P., Hickford, Stephanie, Hill, Gary, Hodges, Jessica, Hoffman, Kara, Hoshina, Kotoyo, Hubert, Dominicus, Huelsnitz, W., Hughey, B., Hülß, Jan Patrick, Hulth, P.O., Hultqvist, K., Hundertmark, Stephan, Hussain, Syed A., Imlay, Richard, Inaba, M., Ishihara, Aya, Jacobsen, Janet, Japaridze, George Sh, Johansson, Henrik, Joseph, Joe, Kampert, K.-H., Kappes, A., Karg, Timo, Karle, Albrecht, Kawai, Hideyuki, Kelley, John, Kiryluk, Joanna, Kislat, F., Klein, Spencer, Klepser, S., Kohnen, G., Kolanoski, Hermann, Köpke, L., Kowalski, Marek, Kowarik, T., Krasberg, Mark, Kuehn, Kyler, Kuwabara, T., Labare, Mathieu, Laihem, Karim, Landsman, H., Lauer, Tod, Leich, Holger, Leier, D., Lewis, Carol, Lucke, Andreas, Lundberg, J., Lünemann, Jan, Madsen, Jes, Maruyama, Reina, Mase, K., Matis, Hope, McParland, Chuck, Meagher, Kevin, Meli, A., Merck, Martin, Messarius, T., Mészáros, P., Miyamoto, Hiroko, Mohr, Anna, Montaruli, T., Morse, Robert, Movit, Steven, Münich, Kirsten, Nahnhauer, Rolf, Nam, Jiwoo, Nießen, Peter, Nygren, David, Odrowski, Sirin, Olivas, Alex, Olivo, Martino, Ono, Masaaki, Panknin, Sebastian, Patton, S., Pérez De Los Heros, Carlos, Petrovic, Jéléna, Piegsa, Anne, Pieloth, Damian, Pohl, Annika, Porrata, R., Potthoff, N., Pretz, J., Price, Buford, Przybylski, G.T., Rawlins, Katherine, Razzaque, S., Redl, Peter, Resconi, Elisa, Rhode, Wolfgang, Ribordy, Mathieu, Rizzo, Alessandro, Robbins, W.J., Rodriguez, J., Roth, Peter, Rothmaier, Florian, Rott, C., Roucelle, Cécile, Rutledge, D., Ryckbosch, D., Sander, H.-G., Sarkar, Subir, Satalecka, Konstancja, Schlenstedt, Stefan, Schmidt, Thomas H., Schneider, Dominique, Schultz, O., Seckel, David, Semburg, Benjamin, Seo, Hye-Sook, Sestayo, Yolanda, Seunarine, Suruj, Silvestri, Anna, Smith, Alexandre, Song, C., Spiczak, Glenn, Spiering, Ch, Stamatikos, Michael, Stanev, Todor, Stezelberger, Thorsten, Stokstad, Robert, Stoufer, M.C., Stoyanov, Stoyan, Strahler, E.A., Straszheim, T., Sulanke, Karl Heinz, Sullivan, G.W., Swillens, Quentin, Taboada, Ignacio, Tarasova, Oksana, Tepe, Andreas, Ter-Antonyan, Samvel, Tilav, Serap, Tluczykont, M., Toale, P.A., Tosi, Delia, Turčan, Doru, Van Eijndhoven, N. A M, Vandenbroucke, Justin, Van Overloop, Arne, Viscomi, Vincent, Vogt, Christian, Voigt, B., Walck, Ch, Waldenmaier, Tilo, Walter, Markus, Wendt, Christopher, Westerhoff, Stefan, Whitehorn, Nathan, Wiebusch, Christopher, Wiedemann, Ch, Wikström, Gustav, Williams, Dyfri, Wischnewski, R., Wissing, Henrike, Woschnagg, Kurt, Xu, Xianwu, Yodh, G., Yoshida, Sho, Aguilar Sanchez, Juan Antonio, Ackermann, Markus, Adams, John, Ahlers, Markus, Ahrens, J., Andeen, K., Auffenberg, Jan, Bai, Xinhua, Baker, Michael, Baret, B., Barwick, S.W., Bay, Ryan, Bazo Alba, J.L., Beattie, K., Becka, T., Becker, Julia, Becker, K.-H., Berdermann, Jens, Berghaus, Patrick, Berley, D., Bernardini, Elisa, Bertrand, Daniel, Besson, David, Blaufuss, E., Boersma, David, Bohm, C., Bolmont, Julien, Böser, Sybille, Botner, O., Braun, James, Breder, D., Burgess, T., Castermans, Thierry, Chirkin, Dmitry, Christy, Brian, Clem, J., Cowen, D.F., D'Agostino, M.V., Danninger, Matthias, Davour, A., Day, Christopher, Depaepe, O., De Clercq, Catherine, Demirörs, L., Descamps, Freija, Desiati, Paolo, De Vries-Uiterweerd, G., Deyoung, Tyce, Diaz-Velez, J.C., Dreyer, Jens, Dumm, Jon, Duvoort, Martijn, Edwards, W.R., Ehrlich, R., Eisch, J., Ellsworth, R.W., Engdegård, Olle, Euler, Sebastian, Evenson, Paul, Fadiran, Oladipo, Fazely, Ali, Filimonov, Kirill, Finley, Chad, Foerster, M.M., Fox, Bronwyn, Franckowiak, Anna, Franke, Robert, Gaisser, Thomas, Gallagher, Joseph, Ganugapati, R., Gerhardt, Lisa, Gladstone, Laura, Goldschmidt, Azriel, Goodman, J.A., Gozzini, R., Grant, D., Griesel, T., Gross, Andreas, Grullon, Sean, Gunasingha, Rathnayaka, Gurtner, Michael, Ha, Changhyon, Hallgren, Anita, Halzen, Francis, Han, Kahae, Hanson, Kael, Hardtke, R., Hasegawa, Y., Heise, J., Helbing, Klaus, Hellwig, Martin, Herquet, P., Hickford, Stephanie, Hill, Gary, Hodges, Jessica, Hoffman, Kara, Hoshina, Kotoyo, Hubert, Dominicus, Huelsnitz, W., Hughey, B., Hülß, Jan Patrick, Hulth, P.O., Hultqvist, K., Hundertmark, Stephan, Hussain, Syed A., Imlay, Richard, Inaba, M., Ishihara, Aya, Jacobsen, Janet, Japaridze, George Sh, Johansson, Henrik, Joseph, Joe, Kampert, K.-H., Kappes, A., Karg, Timo, Karle, Albrecht, Kawai, Hideyuki, Kelley, John, Kiryluk, Joanna, Kislat, F., Klein, Spencer, Klepser, S., Kohnen, G., Kolanoski, Hermann, Köpke, L., Kowalski, Marek, Kowarik, T., Krasberg, Mark, Kuehn, Kyler, Kuwabara, T., Labare, Mathieu, Laihem, Karim, Landsman, H., Lauer, Tod, Leich, Holger, Leier, D., Lewis, Carol, Lucke, Andreas, Lundberg, J., Lünemann, Jan, Madsen, Jes, Maruyama, Reina, Mase, K., Matis, Hope, McParland, Chuck, Meagher, Kevin, Meli, A., Merck, Martin, Messarius, T., Mészáros, P., Miyamoto, Hiroko, Mohr, Anna, Montaruli, T., Morse, Robert, Movit, Steven, Münich, Kirsten, Nahnhauer, Rolf, Nam, Jiwoo, Nießen, Peter, Nygren, David, Odrowski, Sirin, Olivas, Alex, Olivo, Martino, Ono, Masaaki, Panknin, Sebastian, Patton, S., Pérez De Los Heros, Carlos, Petrovic, Jéléna, Piegsa, Anne, Pieloth, Damian, Pohl, Annika, Porrata, R., Potthoff, N., Pretz, J., Price, Buford, Przybylski, G.T., Rawlins, Katherine, Razzaque, S., Redl, Peter, Resconi, Elisa, Rhode, Wolfgang, Ribordy, Mathieu, Rizzo, Alessandro, Robbins, W.J., Rodriguez, J., Roth, Peter, Rothmaier, Florian, Rott, C., Roucelle, Cécile, Rutledge, D., Ryckbosch, D., Sander, H.-G., Sarkar, Subir, Satalecka, Konstancja, Schlenstedt, Stefan, Schmidt, Thomas H., Schneider, Dominique, Schultz, O., Seckel, David, Semburg, Benjamin, Seo, Hye-Sook, Sestayo, Yolanda, Seunarine, Suruj, Silvestri, Anna, Smith, Alexandre, Song, C., Spiczak, Glenn, Spiering, Ch, Stamatikos, Michael, Stanev, Todor, Stezelberger, Thorsten, Stokstad, Robert, Stoufer, M.C., Stoyanov, Stoyan, Strahler, E.A., Straszheim, T., Sulanke, Karl Heinz, Sullivan, G.W., Swillens, Quentin, Taboada, Ignacio, Tarasova, Oksana, Tepe, Andreas, Ter-Antonyan, Samvel, Tilav, Serap, Tluczykont, M., Toale, P.A., Tosi, Delia, Turčan, Doru, Van Eijndhoven, N. A M, Vandenbroucke, Justin, Van Overloop, Arne, Viscomi, Vincent, Vogt, Christian, Voigt, B., Walck, Ch, Waldenmaier, Tilo, Walter, Markus, Wendt, Christopher, Westerhoff, Stefan, Whitehorn, Nathan, Wiebusch, Christopher, Wiedemann, Ch, Wikström, Gustav, Williams, Dyfri, Wischnewski, R., Wissing, Henrike, Woschnagg, Kurt, Xu, Xianwu, Yodh, G., and Yoshida, Sho

Abstract

SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2009

14. The IceCube data acquisition system: Signal capture, digitization, and timestamping

Author

Aguilar Sanchez, Juan Antonio, Ackermann, Markus, Adams, John, Ahlers, Markus, Ahrens, J., Andeen, K., Auffenberg, Jan, Bai, Xinhua, Baker, Michael, Barwick, S.W., Bay, Ryan, Bazo Alba, J.L., Beattie, K., Becka, T., Becker, Julia, Becker, K.-H., Berghaus, Patrick, Berley, D., Bernardini, Elisa, Bertrand, Daniel, Besson, David, Bingham, B., Blaufuss, E., Boersma, David, Bohm, C., Bolmont, Julien, Böser, Sybille, Botner, O., Braun, James, Breeder, D., Burgess, T., Carithers, William, Castermans, Thierry, Chen, Hui, Chirkin, Dmitry, Christy, Brian, Clem, J., Cowen, D.F., D'Agostino, M.V., Danninger, Matthias, Davour, A., Day, Christopher, Depaepe, O., De Clercq, Catherine, Demirörs, L., Descamps, Freija, Desiati, Paolo, De Vries-Uiterweerd, G., Deyoung, Tyce, Diaz-Velez, J.C., Dreyer, Jens, Dumm, Jon, Duvoort, Martijn, Edwards, W.R., Ehrlich, R., Eisch, J., Ellsworth, R.W., Engdegård, Olle, Euler, Sebastian, Evenson, Paul, Fadiran, Oladipo, Fazely, Ali, Feusels, T., Filimonov, Kirill, Finley, Chad, Foerster, M.M., Fox, Bronwyn, Franckowiak, Anna, Franke, Robert, Gaisser, Thomas, Gallagher, Joseph, Ganugapati, R., Gerhardt, Lisa, Gladstone, Laura, Glowacki, D., Goldschmidt, Azriel, Goodman, J.A., Gozzini, R., Grant, D., Griesel, T., Gross, Andreas, Grullon, Sean, Gunasingha, Rathnayaka, Gurtner, Michael, Ha, Changhyon, Hallgren, Anita, Halzen, Francis, Han, Kahae, Hanson, Kael, Hardtke, R., Hasegawa, Y., Haugen, J., Hays, D., Heise, J., Helbing, Klaus, Hellwig, Martin, Herquet, P., Hickford, Stephanie, Hill, Gary, Hodges, Jessica, Hoffman, Kara, Hoshina, Kotoyo, Hubert, Dominicus, Huelsnitz, W., Hughey, B., Hülß, Jan Patrick, Hulth, P.O., Hultqvist, K., Hussain, Syed A., Imlay, Richard, Inaba, M., Ishihara, Aya, Jacobsen, Janet, Japaridze, George Sh, Johansson, Henrik, Jones, Andy, Joseph, Joe, Kampert, K.-H., Kappes, A., Karg, Timo, Karle, Albrecht, Kawai, Hideyuki, Kelley, John, Kiryluk, Joanna, Kislat, F., Klein, Spencer, Kleinfelder, Stuart, Klepser, S., Kohnen, G., Kolanoski, Hermann, Köpke, L., Aguilar Sanchez, Juan Antonio, Ackermann, Markus, Adams, John, Ahlers, Markus, Ahrens, J., Andeen, K., Auffenberg, Jan, Bai, Xinhua, Baker, Michael, Barwick, S.W., Bay, Ryan, Bazo Alba, J.L., Beattie, K., Becka, T., Becker, Julia, Becker, K.-H., Berghaus, Patrick, Berley, D., Bernardini, Elisa, Bertrand, Daniel, Besson, David, Bingham, B., Blaufuss, E., Boersma, David, Bohm, C., Bolmont, Julien, Böser, Sybille, Botner, O., Braun, James, Breeder, D., Burgess, T., Carithers, William, Castermans, Thierry, Chen, Hui, Chirkin, Dmitry, Christy, Brian, Clem, J., Cowen, D.F., D'Agostino, M.V., Danninger, Matthias, Davour, A., Day, Christopher, Depaepe, O., De Clercq, Catherine, Demirörs, L., Descamps, Freija, Desiati, Paolo, De Vries-Uiterweerd, G., Deyoung, Tyce, Diaz-Velez, J.C., Dreyer, Jens, Dumm, Jon, Duvoort, Martijn, Edwards, W.R., Ehrlich, R., Eisch, J., Ellsworth, R.W., Engdegård, Olle, Euler, Sebastian, Evenson, Paul, Fadiran, Oladipo, Fazely, Ali, Feusels, T., Filimonov, Kirill, Finley, Chad, Foerster, M.M., Fox, Bronwyn, Franckowiak, Anna, Franke, Robert, Gaisser, Thomas, Gallagher, Joseph, Ganugapati, R., Gerhardt, Lisa, Gladstone, Laura, Glowacki, D., Goldschmidt, Azriel, Goodman, J.A., Gozzini, R., Grant, D., Griesel, T., Gross, Andreas, Grullon, Sean, Gunasingha, Rathnayaka, Gurtner, Michael, Ha, Changhyon, Hallgren, Anita, Halzen, Francis, Han, Kahae, Hanson, Kael, Hardtke, R., Hasegawa, Y., Haugen, J., Hays, D., Heise, J., Helbing, Klaus, Hellwig, Martin, Herquet, P., Hickford, Stephanie, Hill, Gary, Hodges, Jessica, Hoffman, Kara, Hoshina, Kotoyo, Hubert, Dominicus, Huelsnitz, W., Hughey, B., Hülß, Jan Patrick, Hulth, P.O., Hultqvist, K., Hussain, Syed A., Imlay, Richard, Inaba, M., Ishihara, Aya, Jacobsen, Janet, Japaridze, George Sh, Johansson, Henrik, Jones, Andy, Joseph, Joe, Kampert, K.-H., Kappes, A., Karg, Timo, Karle, Albrecht, Kawai, Hideyuki, Kelley, John, Kiryluk, Joanna, Kislat, F., Klein, Spencer, Kleinfelder, Stuart, Klepser, S., Kohnen, G., Kolanoski, Hermann, and Köpke, L.

Abstract

IceCube is a km-scale neutrino observatory under construction at the South Pole with sensors both in the deep ice (InIce) and on the surface (IceTop). The sensors, called Digital Optical Modules (DOMs), detect, digitize and timestamp the signals from optical Cherenkov-radiation photons. The DOM Main Board (MB) data acquisition subsystem is connected to the central DAQ in the IceCube Laboratory (ICL) by a single twisted copper wire-pair and transmits packetized data on demand. Time calibration is maintained throughout the array by regular transmission to the DOMs of precisely timed analog signals, synchronized to a central GPS-disciplined clock. The design goals and consequent features, functional capabilities, and initial performance of the DOM MB, and the operation of a combined array of DOMs as a system, are described here. Experience with the first InIce strings and the IceTop stations indicates that the system design and performance goals have been achieved. © 2009 Elsevier B.V., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2009

15. Disruption of Ttll5/Stamp Gene (Tubulin Tyrosine Ligase-like Protein 5/SRC-1 and TIF2-associated Modulatory Protein Gene) in Male Mice Causes Sperm Malformation and Infertility

Author

Lee, Geun-Shik, primary, He, Yuanzheng, additional, Dougherty, Edward J., additional, Jimenez-Movilla, Maria, additional, Avella, Matteo, additional, Grullon, Sean, additional, Sharlin, David S., additional, Guo, Chunhua, additional, Blackford, John A., additional, Awasthi, Smita, additional, Zhang, Zhenhuan, additional, Armstrong, Stephen P., additional, London, Edra C., additional, Chen, Weiping, additional, Dean, Jurrien, additional, and Simons, S. Stoney, additional

Published
2013
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17. The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

Author

Adams, Corey, Adams, David, Akiri, Tarek, Alion, Tyler, Anderson, Kris, Andreopoulos, Costas, Andrews, Mike, Anghel, Ioana, Costa Dos Anjos, João Carlos, Maddalena Antonello, Arrieta-Diaz, Enrique, Artuso, Marina, Asaadi, Jonathan, Bai, Xinhua, Baibussinov, Bagdat, Baird, Michael, Balantekin, Baha, Baller, Bruce, Baptista, Brian, Barker, D. Ann, Barker, Gary, Barletta, William A., Barr, Giles, Bartoszek, Larry, Bashyal, Amit, Bass, Matt, Bellini, Vincenzo, Benetti, Pietro Angelo, Berger, Bruce E., Bergevin, Marc, Berman, Eileen, Berns, Hans-Gerd, Bernstein, Adam, Bernstein, Robert, Bhandari, Babu, Bhatnagar, Vipin, Bhuyan, Bipul, Bian, Jianming, Bishai, Mary, Blake, Andrew, Blaszczyk, Flor, Blaufuss, Erik, Bleakley, Bruce, Blucher, Edward, Blusk, Steve, Bocean, Virgil, Boffelli, F., Boissevain, Jan, Bolton, Timothy, Bonesini, Maurizio, Boyd, Steve, Brandt, Andrew, Breedon, Richard, Bromberg, Carl, Brown, Ralph, Brunetti, Giullia, Buchanan, Norman, Bugg, Bill, Busenitz, Jerome, Calligarich, E., Camilleri, Leslie, Carminati, Giada, Carr, Rachel, Castromonte, Cesar, Cavanna, Flavio, Centro, Sandro, Chen, Alex, Chen, Hucheng, Chen, Kai, Cherdack, Daniel, Chi, Cheng-Yi, Childress, Sam, Choudhary, Brajesh Chandra, Duyang, H., Christodoulou, Georgios, Christofferson, Cabot-Ann, Church, Eric, Cline, David, Coan, Thomas, Cocco, Alfredo, Coelho, Joao, Coleman, Stephen, Conrad, Janet M., Convery, Mark, Corey, Robert, Corwin, Luke, Cranshaw, Jack, Cronin-Hennessy, Daniel, Curioni, A., Da Motta, Helio, Davenne, Tristan, Davies, Gavin S., Dazeley, Steven, De, Kaushik, Gouvea, Andre, Jong, Jeffrey K., Demuth, David, Densham, Chris, Diwan, Milind, Djurcic, Zelimir, Dolfini, R., Dolph, Jeffrey, Drake, Gary, Dye, Stephen, Dyuang, Hongue, Edmunds, Daniel, Elliott, Steven, Habib, S., Elnimr, Muhammad, Eno, Sarah, Enomoto, Sanshiro, Escobar, Carlos O., Evans, Justin, Falcone, A., Falk, Lisa, Farbin, Amir, Farnese, Christian, Fava, Angela, Felde, John, Fernandes, S., Ferroni, Fernando, Feyzi, Farshid, Fields, Laura, Finch, Alex, Fitton, Mike, Fleming, Bonnie, Fowler, Jack, Fox, Walt, Friedland, Alex, Fuess, Stu, Fujikawa, Brian, Gallagher, Hugh, Gandhi, Raj, Garvey, Gerald, Gehman, Victor M., Geronimo, Gianluigi, Gibin, Daniele, Gill, Ronald, Gomes, Ricardo A., Goodman, Maury C., Goon, Jason, Johnson, R., Graf, Nicholas, Graham, Mathew, Gran, Rik, Grant, Christopher, Grant, Nick, Greenlee, Herbert, Greenler, Leland, Grullon, Sean, Guardincerri, Elena, Guarino, Victor, Guarnaccia, Evan, Guedes, Germano, Guenette, Roxanne, Guglielmi, Alberto, Guzzo, Marcelo M., Habig, Alec T., Hackenburg, Robert W., Hadavand, Haleh, Hahn, Alan, Haigh, Martin, Haines, Todd, Handler, Thomas, Hans, Sunej, Hartnell, Jeff, Harton, John, Hatcher, Robert, Hatzikoutelis, Athans, Hays, Steven, Hazen, Eric, Headley, Mike, Heavey, Anne, Heeger, Karsten, Heise, Jaret, Hellauer, Robert, Hewes, V., Himmel, Alexander, Hogan, Matthew, Holanda, Pedro, Holin, Anna, Horton-Smith, Glenn, Howell, Joe, Hurh, Patrick, Huston, Joey, Hylen, James, Imlay, Richard, Insler, Jonathan, Introzzi, G., Isvan, Zeynep, Jackson, Chris, Jacobsen, John, Jaffe, David E., James, Cat, Mann, W. A., Jen, Chun-Min, Johnson, Marvin, Johnson, Scott, Johnston, William, Johnstone, John, Jones, Ben J. P., Jostlein, H., Junk, Thomas, Kadel, Richard, Kaess, Karl, Karagiorgi, Georgia, Kaspar, Jarek, Katori, Teppei, Kayser, Boris, Kearns, Edward, Keener, Paul, Kemp, Ernesto, Kettell, Steve H., Kirby, Mike, Klein, Joshua, Koizumi, Gordon, Kopp, Sacha, Kormos, Laura, Kropp, William, Kudryavtsev, Vitaly A., Kumar, Ashok, Kumar, Jason, Kutter, Thomas, La Zia, Franco, Lande, Kenneth, Lane, Charles, Lang, Karol, Lanni, Francesco, Lanza, Richard, Latorre, Tony, Learned, John, Lee, David, Lee, Kevin, Mercurio, B., Moed Sher, S., Li, Qizhong, Li, Shaorui, Li, Yichen, Li, Zepeng, Libo, Jiang, Linden, Steve, Ling, Jiajie, Link, Jonathan, Littenberg, Laurence, Liu, H., Liu, Qiuguang, Liu, Tiankuan, Losecco, John, Louis, William, Lundberg, Byron, Lundin, Tracy, Lundy, Jay, Machado, Ana Amelia, Maesano, Cara, Magill, Steve, Mahler, George, Malon, David, Malys, Stephen, Mammoliti, Francesco, Mandal, Samit Kumar, Mann, Anthony, Paul Mantsch, Marchionni, Alberto, Marciano, William, Mariani, Camillo, Maricic, Jelena, Marino, Alysia, Marshak, Marvin, Marshall, John, Matsuno, Shiegenobu, Mauger, Christopher, Perdue, G., Rajendran, R., Mavrokoridis, Konstantinos, Mayer, Nate, Mccauley, Neil, Mccluskey, Elaine, Mcdonald, Kirk, Mcfarland, Kevin, Mckee, David, Mckeown, Robert, Mctaggart, Robert, Mehdiyev, Rashid, Mei, Dongming, Rosenfeld, C., Menegolli, A., Meng, Guang, Meng, Yixiong, Mertins, David, Messier, M. D., Metcalf, William, Milincic, Radovan, Miller, William, Mills, Geoff, Mishra, Sanjib R., Mokhov, Nikolai, Montanari, Claudio, Montanari, David, Moore, Craig, Morfin, Jorge, Morgan, Ben, Morse, William, Moss, Zander, Moura, Célio A., Mufson, Stuart, Muller, David, Musser, Jim, Naples, Donna, Napolitano, Jim, Newcomer, Mitch, Nichol, Ryan, Nicholls, Tim, Niner, Evan, Norris, Barry, Nowak, Jaroslaw, O Keeffe, Helen, Oliveira, Roberto, Olson, Travis, Page, Brian, Pakvasa, Sandip, Palamara, Ornella, Paley, Jon, Paolone, Vittorio, Papadimitriou, Vaia, Park, Seongtae, Parsa, Zohreh, Partyka, Kinga, Paulos, Bob, Pavlovic, Zarko, Peeters, Simon, Perch, Andy, Perkin, Jon D., Petti, Roberto, Petukhov, Andre, Pietropaolo, Francesco, Plunkett, Robert, Polly, Chris, Pordes, Stephen, Potekhin, Maxim, Potenza, Renato, Prakash, Arati, Prokofiev, Oleg, Qian, Xin, Raaf, Jennifer L., Radeka, Veljko, Rakhno, Igor, Ramachers, Yorck, Rameika, Regina, Ramsey, John, Rappoldi, A., Raselli, G. L., Ratoff, Peter, Ravindra, Shreyas, Rebel, Brian, Wachala, T., Reichenbacher, Juergen, Reitzner, Dianne, Rescia, Sergio, Richardson, Martin, Wendell, R., Rielage, Kieth, Riesselmann, Kurt, Robinson, Matt, Rochester, Leon, Ronquest, Michael, Rosen, Marc, Meyhandan, R., Rubbia, Carlo, Rucinski, Russ, Sahijpal, Sandeep, Sahoo, Himansu, Willis, W., Sala, Paola, Salmiera, Delia, Samios, Nicholas, Sanchez, Mayly, Wyman, T., Scaramelli, Alberto, Schellman, Heidi, Schmitt, Richard, Schmitz, David, Schneps, Jack, Scholberg, Kate, Segreto, Ettore, Seibert, Stanley, Sexton-Kennedy, Liz, Shaevitz, Mike, Shanahan, Peter, Sharma, Rahul, Shaw, Terri, Simos, Nikolaos, Singh, Venktesh, Sinnis, Gus, Sippach, William, Skwarnicki, Tomasz, Smy, Michael, Sobel, Henry, Soderberg, Mitch, Sondericker, John, Sondheim, Walter, Sousa, Alexandre, Spooner, Neil J. C., Stancari, Michelle, Stancu, Ion, Stefan, Dorota, Stefanik, Andy, Stewart, James, Stone, Sheldon, Strait, James, Strait, Matthew, Striganov, Sergei, Sullivan, Gregory, Sun, Yujing, Suter, Louise, Svenson, Andrew, Svoboda, Robert, Szczerbinska, Barbara, Szelc, Andrzej, Szydagis, Matthew, Söldner-Rembold, Stefan, Talaga, Richard, Tamsett, Matthew, Tariq, Salman, Tayloe, Rex, Taylor, Charles, Taylor, David, Teymourian, Artin, Themann, Harry, Thiesse, Matthew, Thomas, Jenny, Thompson, Lee F., Thomson, Mark, Thorn, Craig, Thorpe, Matt, Tian, Xinchun, Tiedt, Doug, Toki, Walter, Tolich, Nikolai, Torti, M., Toups, Matt, Touramanis, Christos, Tripathi, Mani, Tropin, Igor, Tsai, Yun-Tse, Tull, Craig, Tzanov, Martin, Urheim, Jon, Usman, Shawn, Vagins, Mark, Valdiviesso, Gustavo, Berg, Rick, Water, Richard, Gemmeren, Peter, Varanini, Filippo, Varner, Gary, Vaziri, Kamran, Velev, Gueorgui, Ventura, Sandro, Vignoli, Chiara, Viren, Brett, Wahl, Dan, Waldron, Abby, Walter, Christopher W., Wang, Hanguo, Wang, Wei, Warburton, Karl, Warner, David, Wasserman, Ryan, Watson, Blake, Weber, Alfons, Wei, Wenzhao, Wells, Douglas, Wetstein, Matthew, White, Andy, White, Hywel, Whitehead, Lisa, Whittington, Denver, Willhite, Joshua, Wilson, Robert J., Winslow, Lindley, Wood, Kevin, Worcester, Elizabeth, Worcester, Matthew, Xin, Tian, Yarritu, Kevin, Ye, Jingbo, Yeh, Minfang, Yu, B., Yu, Jae, Yuan, Tianlu, Zani, A., Zeller, Geralyn P., Zhang, Chao, Zimmerman, Eric D., Zwaska, Robert, Center for Neutrino Physics, and Physics

Subjects
Accelerator Physics (physics.acc-ph), Physics - Instrumentation and Detectors, Physics::Instrumentation and Detectors, hep-ex, FOS: Physical sciences, hep-ph, Instrumentation and Detectors (physics.ins-det), High Energy Physics - Experiment, High Energy Physics - Experiment (hep-ex), High Energy Physics - Phenomenology, High Energy Physics - Phenomenology (hep-ph), Physics - Accelerator Physics, High Energy Physics::Experiment, physics.ins-det, physics.acc-ph
Abstract

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess., Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figures

18. Disruption of Ttll5/Stamp Gene (Tubulin Tyrosine Ligase-like Protein 5/SRC-1 and TIF2-associated Modulatory Protein Gene) in Male Mice Causes Sperm Malformation and Infertility.

Author

Geun-Shik Lee, Yuanzheng He, Dougherty, Edward J., Jimenez-Movilla, Maria, Avella, Matteo, Grullon, Sean, Sharlin, David S., Chunhua Guo, Blackford Jr., John A., Awasthi, Smita, Zhang, Zhenhuan, Armstrong, Stephen P., London, Edra C., Weiping Chen, Dean, Jurrien, and Simons Jr., S. Stoney

Subjects
*TUBULINS, *TYROSINE, *GLUCOCORTICOIDS, *LABORATORY mice, *BIOCHEMISTRY
Abstract

TTLL5/STAMP (tubulin tyrosine ligase-like family member 5) has multiple activities in cells. TTLL5 is one of 13 TTLLs, has polyglutamylation activity, augments the activity of p160 coactivators (SRC-1 and TIF2) in glucocorticoid receptor-regulated gene induction and repression, and displays steroid-independent growth activity with several cell types. To examine TTLL5/ STAMPfunctions in whole animals, mice were prepared with an internal deletion that eliminated several activities of the Stamp gene. This mutation causes both reduced levels of STAMP mRNA and C-terminal truncation of STAMP protein. Homozygous targeted mutant (Stamptm/tm) mice appear normal except for marked decreases in male fertility associated with defects in progressive sperm motility. Abnormal axonemal structures with loss of tubulin doublets occur in most Stamptm/tm sperm tails in conjunction with substantial reduction in β-tubulin polyglutamylation, which closely correlates with the reduction in mutant STAMP mRNA. The axonemes in other structures appear unaffected. There is no obvious change in the organs for sperm development ofWTversus Stamptm/tm males despite the levels of WTSTAMP mRNA in testes being 20-fold higher than in any other organ examined. This defect in male fertility is unrelated to other Ttll genes or 24 genes previously identified as important for sperm function. Thus, STAMP appears to participate in a unique, tissue-selective TTLL-mediated pathway for β-tubulin polyglutamylation that is required for sperm maturation and motility and may be relevant for male fertility. [ABSTRACT FROM AUTHOR]

Published
2013
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19. Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells.

Author

Xu S, Grullon S, Ge K, and Peng W

Subjects
Cluster Analysis, Methylation, Algorithms, Biostatistics methods, Chromatin Immunoprecipitation methods, Computational Biology methods, Embryonic Stem Cells metabolism, Histones metabolism
Abstract

Chromatin states are the key to embryonic stem cell pluripotency and differentiation. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-Seq) is increasingly used to map chromatin states and to functionally annotate the genome. Many ChIP-Seq profiles, especially those of histone methylations, are noisy and diffuse. Here we describe SICER (Zang et al., Bioinformatics 25(15):1952-1958, 2009), an algorithm specifically designed to identify disperse ChIP-enriched regions with high sensitivity and specificity. This algorithm has found a lot of applications in epigenomic studies. In this Chapter, we will demonstrate in detail how to run SICER to delineate ChIP-enriched regions and assess their statistical significance, and to identify regions of differential enrichment when two chromatin states are compared.

Published
2014
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