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1. Evaluating Parametric Integrals in the Minkowski Regime without Contour Deformation

Author

Jones, Stephen, Olsson, Anton, and Stone, Thomas

Subjects
High Energy Physics - Phenomenology, High Energy Physics - Theory
Abstract

We present selected examples demonstrating an alternative approach to contour deformation for numerically computing loop integrals in the Minkowski regime. This method focuses on identifying singular hypersurfaces (varieties of the $\mathscr{F}$ polynomial) and mapping them to known points which can then be resolved by employing blow-ups/sector decomposition techniques, thereby avoiding the need for contour deformation. Using this technique, we achieve improved convergence properties without the need for contour deformation, which is known to significantly increase the complexity of the integrand by introducing, for example, derivatives of the $\mathscr{F}$ polynomial and complicated Jacobians. We highlight that while we have only tested the approach on selected one-, two- and three-loop massless and one-loop massive examples, it shows promise for practical applications, offering potential benefits over the traditional approach. Evaluation times are compared with existing contour deformation implementations to illustrate the performance of this alternative method., Comment: Contribution to proceedings of the Loops and Legs in Quantum Field Theory conference (LL2024)

Published
2024

2. Electroweak corrections to Higgs boson pair production: The top-Yukawa and self-coupling contributions

Author

Heinrich, Gudrun, Jones, Stephen, Kerner, Matthias, Stone, Thomas, and Vestner, Augustin

Subjects
High Energy Physics - Phenomenology
Abstract

We present results for the Yukawa-enhanced and Higgs self-coupling type electroweak corrections to di-Higgs production in gluon fusion. The calculation of the corresponding four-scale, two-loop amplitude is carried out retaining the exact symbolic dependence on all masses and scales during the reduction to master integrals. The resulting integrals are then evaluated at high precision using both the series expansion of the differential equations and sector decomposition. Differential cross sections for the di-Higgs invariant mass and the transverse momentum of a Higgs boson are shown, where we find that the corrections are most pronounced at low invariant mass and transverse momentum., Comment: 33 pages, 7 figures, 4 tables

Published
2024

8. Prediction for 2-Year Vision Outcomes Using Early Morphologic and Functional Responses in the Comparison of Age-related Macular Degeneration Treatments Trials

Author

Williams, David F., Beardsley, Sara, Bennett, Steven, Cantrill, Herbert, Chan-Tram, Carmen, Cheshier, Holly, Damato, Kathyrn, Davies, John, Dev, Sundeep, Enloe, Julianne, Follano, Gennaro, Gilbert, Peggy, Johnson, Jill, Jones, Tori, Mayleben, Lisa, Mittra, Robert, Moos, Martha, Neist, Ryan, Oestreich, Neal, Quiram, Polly, Ramsay, Robert, Ryan, Edwin, Schindeldecker, Stephanie, Snater, John, Steele, Trenise, Selders, Dwight, Tonsfeldt, Jessica, Valardi, Shelly, Fish, Gary Edd, Aguado, Hank A., Arceneaux, Sally, Arnwine, Jean, Bell, Kim, Bell, Tina, Boleman, Bob, Bradley, Patricia, Callanan, David, Coors, Lori, Creighton, Jodi, Crew, Timothy, Cummings, Kimberly, Dock, Christopher, Duignan, Karen, Fuller, Dwain, Gray, Keith, Hendrix, Betsy, Hesse, Nicholas, Jaramillo, Diana, Jost, Bradley, Lash, Sandy, Lonsdale, Laura, Mackens, Michael, Mutz, Karin, Potts, Michael, Sanchez, Brenda, Snyder, William, Solley, Wayne, Tarter, Carrie, Wang, Robert, Williams, Patrick, Perkins, Stephen L., Anderson, Nicholas, Arnold, Ann, Blais, Paul, Googe, Joseph, Higdon, Tina T., Hunt, Cecile, Johnson, Mary, Miller, James, Moore, Misty, Morris, Charity K., Morris, Christopher, Oelrich, Sarah, Oliver, Kristina, Seitz, Vicky, Whetstone, Jerry, Doft, Bernard H., Bedel, Jay, Bergren, Robert, Borthwick, Ann, Conrad, Paul, Fec, Amanda, Fulwylie, Christina, Ingram, Willia, Latham, Shawnique, Lester, Gina, Liu, Judy, Lobes, Louis, Lucko, Nicole M., Mechling, Holly, Merlotti, Lori, McBroom, Keith, Olsen, Karl, Puskas, Danielle, Rath, Pamela, Schmucker, Maria, Schueckler, Lynn, Schultz, Christina, Shultz, Heather, Steinberg, David, Vyas, Avni, Whale, Kim, Yeckel, Kimberly, Orth, David H., Arredondo, Linda S., Brown, Susan, Ciscato, Barbara J., Civantos, Joseph M., Figliulo, Celeste, Hasan, Sohail, Kosinski, Belinda, Muir, Dan, Nelson, Kiersten, Packo, Kirk, Pollack, John S., Rezaei, Kourous, Shelton, Gina, Townsend-Patrick, Shannya, Walsh, Marian, McDonald, H. Richard, Ansari, Nina, Bye, Amanda, Fu, Arthur D., Grout, Sean, Indermill, Chad, Johnson, Robert N., Jumper, J. Michael, Linares, Silvia, Lujan, Brandon J., Munden, Ames, Persons, Meredith, Rodriguez, Rosa, Rose, Jennifer M., Teske, Brandi, Urias, Yesmin, Young, Stephen, Dreyer, Richard F., Daniel, Howard, Connaughton, Michele, Handelman, Irvin, Hobbs, Stephen, Hoerner, Christine, Hudson, Dawn, Kopfer, Marcia, Lee, Michael, Lemley, Craig, Logan, Joe, Ma, Colin, Mallet, Christophe, Milliron, Amanda, Peters, Mark, Wohlsein, Harry, Pearlman, Joel A., Andrews, Margo, Bartlett, Melissa, Carlson, Nanette, Cox, Emily, Equi, Robert, Gonzalez, Marta, Griffin, Sophia, Hogue, Fran, Kennedy, Lance, Kryuchkov, Lana, Lopez, Carmen, Lopez, Danny, Luevano, Bertha, McKenna, Erin, Patel, Arun, Reed, Brian, Secor, Nyla, Sison, Iris R., Tsai, Tony, Varghis, Nina, Waller, Brooke, Wendel, Robert, Yebra, Reina, Roth, Daniel B., Deinzer, Jane, Fine, Howard, Green, Flory, Green, Stuart, Keyser, Bruce, Leff, Steven, Leviton, Amy, Martir, Amy, Mosenthine, Kristin, Muscle, Starr, Okoren, Linda, Parker, Sandy, Prenner, Jonathan, Price, Nancy, Rogers, Deana, Rosas, Linda, Schlosser, Alex, Studenko, Loretta, Tantum, Thea, Wheatley, Harold, Trese, Michael T., Aaberg, Thomas, Bezaire, Denis, Bridges, Craig, Bryant, Doug, Capone, Antonio, Coleman, Michelle, Consolo, Christina, Cook, Cindy, DuLong, Candice, Garretson, Bruce, Grooten, Tracy, Hammersley, Julie, Hassan, Tarek, Jessick, Heather, Jones, Nanette, Kinsman, Crystal, Krumlauf, Jennifer, Lewis, Sandy, Locke, Heather, Margherio, Alan, Markus, Debra, Marsh, Tanya, Neal, Serena, Noffke, Amy, Oh, Kean, Pence, Clarence, Preston, Lisa, Raphaelian, Paul, Regan, Virginia R., Roberts, Peter, Ruby, Alan, Sarrafizadeh, Ramin, Scherf, Marissa, Scott, Sarita, Sneed, Scott, Staples, Lisa, Terry, Brad, Trese, Matthew T., Videtich, Joan, Williams, George, Zajechowski, Mary, Joseph, Daniel P., Blinder, Kevin, Boyd, Lynda, Buckley, Sarah, Crow, Meaghan, Dinatale, Amanda, Engelbrecht, Nicholas, Forke, Bridget, Gabel, Dana, Grand, Gilbert, Grillion-Cerone, Jennifer, Holekamp, Nancy, Kelly, Charlotte, Nobel, Ginny, Pepple, Kelly, Raeber, Matt, Rao, P. Kumar, Ressel, Tammy, Schremp, Steven, Sgorlon, Merrilee, Shears, Shantia, Thomas, Matthew, Timma, Cathy, Vaughn, Annette, Walters, Carolyn, Weeks, Rhonda, Wehmeier, Jarrod, Wright, Tim, Berinstein, Daniel M., Ayyad, Aida, Barazi, Mohammed K., Bickhart, Erica, Brady, Tracey, Byank, Lisa, Cronise, Alysia, Denny, Vanessa, Dunn, Courtney, Flory, Michael, Frantz, Robert, Garfinkel, Richard A., Gilbert, William, Lai, Michael M., Melamud, Alexander, Newgen, Janine, Newton, Shamekia, Oliver, Debbie, Osman, Michael, Sanders, Reginald, von Fricken, Manfred, Dugel, Pravin, Arenas, Sandra, Balea, Gabe, Bartoli, Dayna, Bucci, John, Cornelius, Jennifer A., Dickens, Scheleen, Doherty, Don, Dunlap, Heather, Goldenberg, David, Jamal, Karim, Jimenez, Norma, Kavanagh, Nicole, Kunimoto, Derek, Martin, John, Miner, Jessica, Mobley, Sarah, Park, Donald, Quinlan, Edward, Sipperley, Jack, Slagle, Carol, Smith, Danielle, Yafchak, Miguelina, Yager, Rohana, Flaxel, Christina J., Bailey, Steven, Francis, Peter, Howell, Chris, Hwang, Thomas, Ira, Shirley, Klein, Michael, Lauer, Andreas, Liesegang, Teresa, Lundquist, Ann, Nolte, Sarah, Nolte, Susan K., Pickell, Scott, Pope, Susan, Rossi, Joseph, Schain, Mitchell, Steinkamp, Peter, Toomey, Maureen D., Vahrenwald, Debora, West, Kelly, Hubbard, Baker, Andelman, Stacey, Bergstrom, Chris, Brower, Judy, Cribbs, Blaine, Curtis, Linda, Dobbs, Jannah, DuBois, Lindreth, Gaultney, Jessica, Gibbs, Deborah, Jordan, Debora, Leef, Donna, Martin, Daniel F., Myles, Robert, Olsen, Timothy, Schwent, Bryan, Srivastava, Sunil, Waldron, Rhonda, Antoszyk, Andrew N., Balasubramaniam, Uma, Brooks, Danielle, Brown, Justin, Browning, David, Clark, Loraine, Ennis, Sarah, Held, Susannah, Helms, Jennifer V., Herby, Jenna, Karow, Angie, Leotaud, Pearl, Massimino, Caterina, McClain, Donna, McOwen, Michael, Mindel, Jennifer, Pereira, Candace, Pierce, Rachel, Powers, Michele, Price, Angela, Rohrer, Jason, Sanders, Jason, Avery, Robert L., Avery, Kelly, Basefsky, Jessica, Beckner, Liz, Castellarin, Alessandro, Couvillion, Stephen, Giust, Jack, Giust, Matthew, Nasir, Maan, Pieramici, Dante, Rabena, Melvin, Risard, Sarah, See, Robert, Smith, Jerry, Wan, Lisha, Bakri, Sophie J., Abu-Yaghi, Nakhleh, Barkmeier, Andrew, Berg, Karin, Burrington, Jean, Edwards, Albert, Goddard, Shannon, Howard, Shannon, Iezzi, Raymond, Lewison, Denise, Link, Thomas, McCannel, Colin A., Overend, Joan, Pach, John, Ruszczyk, Margaret, Shultz, Ryan, Stephan, Cindy, Vogen, Diane, Bradford, Reagan H., Jr., Bergman, Vanessa, Burris, Russ, Butt, Amanda, Daniels, Beth, Dwiggins, Connie, Fransen, Stephen, Guerrero, Tiffany, Haivala, Darin, Harris, Amy, Icks, Sonny, Kingsley, Ronald, Redden, Lena, Richmond, Rob, Ross, Brittany, White, Kammerin, Youngberg, Misty, Topping, Trexler M., Bennett, Steve, Chong, Sandy, Ciotti, Mary, Cleary, Tina, Corey, Emily, Donovan, Dennis, Frederick, Albert, Freese, Lesley, Graham, Margaret, Gud, Natalya, Howard, Taneika, Jones, Mike, Morley, Michael, Moses, Katie, Stone, Jen, Ty, Robin, Wiegand, Torsten, Williams, Lindsey, Winder, Beth, Awh, Carl C., Amonette, Michelle, Arrindell, Everton, Beck, Dena, Busbee, Brandon, Dilback, Amy, Downs, Sara, Guidry, Allison, Gutow, Gary, Hardin, Jackey, Hines, Sarah, Hutchins, Emily, LaCivita, Kim, Lester, Ashley, Malott, Larry, McCain, MaryAnn, Miracle, Jayme, Moffat, Kenneth, Palazzotta, Lacy, Robinson, Kelly, Sonkin, Peter, Travis, Alecia, Wallace, Roy Trent, Winters, Kelly J., Wray, Julia, Harris, April E., Bunnell, Mari, Crooks, Katrina, Fitzgerald, Rebecca, Javid, Cameron, Kew, Corin, Kill, Erica, Kline, Patricia, Kreienkamp, Janet, Martinez, Maricruz, Moore, Roy Ann, Saavedra, Egbert, Taylor, LuAnne, Walsh, Mark, Wilson, Larry, Ciulla, Thomas A., Coyle, Ellen, Harrington, Tonya, Harris, Charlotte, Hood, Cindi, Kerr, Ingrid, Maturi, Raj, Moore, Dawn, Morrow, Stephanie, Savage, Jennifer, Sink, Bethany, Steele, Tom, Thukral, Neelam, Wilburn, Janet, Walker, Joseph P., Banks, Jennifer, Ciampaglia, Debbie, Dyshanowitz, Danielle, Frederick, Jennifer, Ghuman, A. Tom, Grodin, Richard, Kiesel, Cheryl, Knips, Eileen, McCue, Jonathan, Ortiz, Maria, Peters, Crystal, Raskauskas, Paul, Schoeman, Etienne, Sharma, Ashish, Wing, Glenn, Youngblood, Rebecca, Chandra, Suresh R., Altaweel, Michael, Blodi, Barbara, Burke, Kathryn, Dietzman, Kristine A., Gottlieb, Justin, Knutson, Gene, Krolnik, Denise, Nork, T. Michael, Olson, Shelly, Peterson, John, Reed, Sandra, Soderling, Barbara, Somers, Guy, Stevens, Thomas, Wealti, Angela, Bearelly, Srilaxmi, Branchaud, Brenda, Bryant, Joyce W., Crowell, Sara, Fekrat, Sharon, Gammage, Merritt, Harrison, Cheala, Jones, Sarah, McClain, Noreen, McCuen, Brooks, Mruthyunjaya, Prithvi, Queen, Jeanne, Sarin, Neeru, Skalak, Cindy, Skelly, Marriner, Suner, Ivan, Tomany, Ronnie, Welch, Lauren, Park, Susanna S., Cassidy, Allison, Chandra, Karishma, Good, Idalew, Imson, Katrina, Sashi, Kaur, Metzler, Helen, Morse, Lawrence, Redenbo, Ellen, Salvador, Marisa, Telander, David, Thomas, Mark, Wallace, Cindy, Barr, Charles C., Battcher, Amanda, Bottorff, Michelle, Chasteen, Mary, Clark, Kelly, Denning, Diane, Schoen, Debra, Schultz, Amy, Tempel, Evie, Wheeler, Lisa, Whittington, Greg K., Stone, Thomas W., Blevins, Todd, Buck, Michelle, Cruz, Lynn, Heath, Wanda, Holcomb, Diana, Isernhagen, Rick, Kidd, Terri, Kitchens, John, Sears, Cathy, Slade, Ed, Van Arsdall, Jeanne, VanHoose, Brenda, Wolfe, Jenny, Wood, William, Zilis, John, Crooks, Carol, Disney, Larry, Liu, Mimi, Petty, Stephen, Sall, Sandra, Folk, James C., Aly, Tracy, Brotherton, Abby, Critser, Douglas, Hinz, Connie J., Karakas, Stefani, Kirschner, Valerie, Lester, Cheyanne, Montague, Cindy, Russell, Stephen, Stockman, Heather, Taylor, Barbara, Verdick, Randy, Walshire, Jean, Thompson, John T., Connell, Barbara, Constantine, Maryanth, Davis, John L., Jr., Gwen Holsapple, Hunter, Lisa, Lenane, C. Nicki, Mitchell, Robin, Russel, Leslie, Sjaarda, Raymond, Brown, David M., Benz, Matthew, Burns, Llewellyn, Carranza, JoLene G., Fish, Richard, Goates, Debra, Hay, Shayla, Jeffers, Theresa, Kegley, Eric, Kubecka, Dallas, McGilvra, Stacy, Richter, Beau, Sneed, Veronica, Stoever, Cary, Tellez, Isabell, Wong, Tien, Kim, Ivana, Andreoli, Christopher, Barresi, Leslie, Brett, Sarah, Callahan, Charlene, Capaccioli, Karen, Carli, William, Coppola, Matthew, Emmanuel, Nicholas, Evans, Claudia, Fagan, Anna, Grillo, Marcia, Head, John, Kieser, Troy, Lee, Elaine, Lord, Ursula, Miretsky, Edward, Palitsch, Kate, Petrin, Todd, Reader, Liz, Reznichenko, Svetlana, Robertson, Mary, Smith, Justin, Vavvas, Demetrios, Wells, John, Cahill, Cassie, Clark, W. Lloyd, Henry, Kayla, Johnson, David, Miller, Peggy, Oliver, LaDetrick, Spivey, Robbin, Swinford, Tiffany, Taylor, Mallie, Lambert, Michael, Chase, Kris, Fredrickson, Debbie, Khawly, Joseph, Lazarte, Valerie, Lowd, Donald, Miller, Pam, Willis, Arthur, Ferrone, Philip J., Almonte, Miguel, Arnott, Rachel, Aviles, Ingrid, Carbon, Sheri, Chitjian, Michael, DAmore, Kristen, Elliott, Christin, Fastenberg, David, Golub, Barry, Graham, Kenneth, Lavorna, AnnMarie, Murphy, Laura, Palomo, Amanda, Puglisi, Christina, Rhee, David, Romero, Juan, Rosenblatt, Brett, Salcedo, Glenda, Schlameuss, Marianne, Shakin, Eric, Sookhai, Vasanti, Kaiser, Richard, Affel, Elizabeth, Brown, Gary, Centinaro, Christina, Fine, Deborah, Fineman, Mitchell, Formoso, Michele, Garg, Sunir, Grande, Lisa, Herbert, Carolyn, Ho, Allen, Hsu, Jason, Jay, Maryann, Lavetsky, Lisa, Liebenbaum, Elaine, Maguire, Joseph, Monsonego, Julia, O’Connor, Lucia, Pierce, Lisa, Regillo, Carl, Rosario, Maria, Spirn, Marc, Vander, James, Walsh, Jennifer, Davidorf, Frederick H., Barnett, Amanda, Chang, Susie, Christoforidis, John, Elliott, Joy, Justice, Heather, Letson, Alan, McKinney, Kathryne, Perry, Jeri, Salerno, Jill A., Savage, Scott, Shelley, Stephen, Singerman, Lawrence J., Coney, Joseph, DuBois, John, DuBois, Kimberly, Greanoff, Gregg, Himmelman, Dianne, Ilc, Mary, McNamara, Elizabeth, Novak, Michael, Pendergast, Scott, Rath, Susan, Smith-Brewer, Sheila, Tanner, Vivian, Weiss, Diane E., Zegarra, Hernando, Halperin, Lawrence, Aramayo, Patricia, Dhalla, Mandeep, Fernandez, Brian, Fernandez, Cindy, Lopez, Jaclyn, Lopez, Monica, Mariano, Jamie, Murphy, Kellie, Sherley, Clifford, Veksler, Rita, Rahhal, Firas, Babikian, Razmig, Boyer, David, Hami, Sepideh, Kessinger, Jeff, Kurokouchi, Janet, Mukarram, Saba, Pachman, Sarah, Protacio, Eric, Sierra, Julio, Tabandeh, Homayoun, Zamboni, Adam, Elman, Michael, Belz, Jennifer, Butcher, Tammy, Cain, Theresa, Coffey, Teresa, Firestone, Dena, Gore, Nancy, Singletary, Pamela, Sotirakos, Peter, Starr, JoAnn, Meredith, Travis A., Barnhart, Cassandra J., Cantrell, Debra, Esquejo-Leon, RonaLyn, Houghton, Odette, Kaur, Harpreet, NDure, Fatoumatta, Glatzer, Ronald, Joffe, Leonard, Schindler, Reid, Xue, Katie, Hua, Peiying, Maguire, Maureen G., Daniel, Ebenezer, Jaffe, Glenn J., Grunwald, Juan E., and Ying, Gui-shuang

Published
2023
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10. Recurrent adamantinomatous craniopharyngiomas show MAPK pathway activation, clonal evolution and rare TP53-loss-mediated malignant progression.

Author

Apps, John R., Gonzalez-Meljem, Jose Mario, Guiho, Romain, Pickles, Jessica C., Prince, Eric, Schwalbe, Edward, Joshi, Nikhil, Stone, Thomas J., Ogunbiyi, Olumide, Chalker, Jane, Bassey, Akang, Otto, Georg, Davies, Rosalind, Hughes, Debbie, Brandner, Sebastian, Tan, Enrica, Lee, Victoria, Hayhurst, Caroline, Kline, Cassie, and Castellano, Sergi

Subjects
BRAIN tumors, WHOLE genome sequencing, CRANIOPHARYNGIOMA, RNA sequencing, MITOGEN-activated protein kinases
Abstract

The two types of craniopharyngioma, adamantinomatous (ACP) and papillary (PCP), are clinically relevant tumours in children and adults. Although the biology of primary craniopharyngioma is starting to be unravelled, little is known about the biology of recurrence. To fill this gap in knowledge, we have analysed through methylation array, RNA sequencing and pERK1/2 immunohistochemistry a cohort of paired primary and recurrent samples (32 samples from 14 cases of ACP and 4 cases of PCP). We show the presence of copy number alterations and clonal evolution across recurrence in 6 cases of ACP, and analysis of additional whole genome sequencing data from the Children's Brain Tumour Network confirms chromosomal arm copy number changes in at least 7/67 ACP cases. The activation of the MAPK/ERK pathway, a feature previously shown in primary ACP, is observed in all but one recurrent cases of ACP. The only ACP without MAPK activation is an aggressive case of recurrent malignant human craniopharyngioma harbouring a CTNNB1 mutation and loss of TP53. Providing support for a functional role of this TP53 mutation, we show that Trp53 loss in a murine model of ACP results in aggressive tumours and reduced mouse survival. Finally, we characterise the tumour immune infiltrate showing differences in the cellular composition and spatial distribution between ACP and PCP. Together, these analyses have revealed novel insights into recurrent craniopharyngioma and provided preclinical evidence supporting the evaluation of MAPK pathway inhibitors and immunomodulatory approaches in clinical trials in against recurrent ACP. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Mechanisms of place recognition and path integration based on the insect visual system

Author

Stone, Thomas Jonathan, Webb, Barbara, and Heinze, Stanley

Subjects
navigation, place recognition, localisation, localization, ultraviolet, path integration, central complex, UV, spherical harmonics, insect, biorobotics
Abstract

Animals are often able to solve complex navigational tasks in very challenging terrain, despite using low resolution sensors and minimal computational power, providing inspiration for robots. In particular, many species of insect are known to solve complex navigation problems, often combining an array of different behaviours (Wehner et al., 1996; Collett, 1996). Their nervous system is also comparatively simple, relative to that of mammals and other vertebrates. In the first part of this thesis, the visual input of a navigating desert ant, Cataglyphis velox, was mimicked by capturing images in ultraviolet (UV) at similar wavelengths to the ant’s compound eye. The natural segmentation of ground and sky lead to the hypothesis that skyline contours could be used by ants as features for navigation. As proof of concept, sky-segmented binary images were used as input for an established localisation algorithm SeqSLAM (Milford and Wyeth, 2012), validating the plausibility of this claim (Stone et al., 2014). A follow-up investigation sought to determine whether using the sky as a feature would help overcome image matching problems that the ant often faced, such as variance in tilt and yaw rotation. A robotic localisation study showed that using spherical harmonics (SH), a representation in the frequency domain, combined with extracted sky can greatly help robots localise on uneven terrain. Results showed improved performance to state of the art point feature localisation methods on fast bumpy tracks (Stone et al., 2016a). In the second part, an approach to understand how insects perform a navigational task called path integration was attempted by modelling part of the brain of the sweat bee Megalopta genalis. A recent discovery that two populations of cells act as a celestial compass and visual odometer, respectively, led to the hypothesis that circuitry at their point of convergence in the central complex (CX) could give rise to path integration. A firing rate-based model was developed with connectivity derived from the overlap of observed neural arborisations of individual cells and successfully used to build up a home vector and steer an agent back to the nest (Stone et al., 2016b). This approach has the appeal that neural circuitry is highly conserved across insects, so findings here could have wide implications for insect navigation in general. The developed model is the first functioning path integrator that is based on individual cellular connections.

Published
2017

13. Genomic classification and analysis of epilepsy-associated glioneuronal tumours

Author

Stone, Thomas John, Jacques, T. S., and Ham, J.

Subjects
618.92
Abstract

INTRODUCTION: Glioneuronal tumours are a group of low-grade epilepsy-associated tumours with marked variability in their histological features, resulting in a lack of diagnostic consensus between institutions. This is confounded by a dearth of knowledge regarding their underlying biology, and subsequent lack of robust biologically informed diagnostic tools. This lack of understanding also impedes the development of novel and targeted treatment strategies. METHODS: I have undertaken a comprehensive molecular analysis of the most prevalent glioneuronal tumours: ganglioglioma and dysembryoplastic neuroepithelial tumours. I have used RNA sequencing and Illumina 450K methylation arrays to classify tumours in an unsupervised manner according to their genomic profiles. I then carried out in silico analyses on these datasets to identify genes, gene networks, and pathways that are differentially regulated between groups. Additionally, I have undertaken molecular assays to identify mutations that are specific to each group. Finally, I have used immunohistochemistry to assess a number of potential diagnostic markers revealed by expression profiling. RESULTS: Unsupervised clustering revealed glioneuronal tumours classify into two molecular groups (termed Group 1 and Group 2), which are only partially consistent with histological classification. Group 1 is defined by an astrocytic expression phenotype and an enrichment for BRAF-V600E mutations. Group 2 is defined by an oligodendrocyte precursor phenotype and an enrichment for FGFR1 mutations. A number of disease relevant networks and pathways are differentially regulated between these groups. Additionally, immunohistochemistry against Cyclin-D1 and PDGFRα can be used to distinguish tumour groups from one another. CONCLUSION: This is the first comprehensive genomic investigation of a large cohort of glioneuronal tumours without prior histological bias. I present data suggesting the current histological classification of these lesions is insufficient, and recommend a novel biologically informed strategy. My results also provide insight into the pathways underlying the development of these tumours. This information may assist in the development of novel treatment strategies.

Published
2017

16. ARCSTONE: calibration of lunar spectral reflectance from space. Prototype instrument concept, analysis, and results

Author

Courrier, Hans, primary, Swanson, Rand, additional, Lukashin, Constantine, additional, Buleri, Christine, additional, Carvo, John, additional, Cooney, Michael, additional, Davis, Warren, additional, Halterman, Alexander, additional, Hoskins, Alan, additional, Jackson, Trevor, additional, Kehoe, Mike, additional, Kopp, Greg, additional, Nguyen, Thuan, additional, Ryan, Noah, additional, Roithmayr, Carlos, additional, Smith, Paul, additional, Stebbins, Mike, additional, Stone, Thomas, additional, and Young, Cindy, additional

Published
2023
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22. Do Birds of a Feather Cheat Together? How Personality and Relationships Affect Student Cheating

Author

Scrimpshire, Alex J., Stone, Thomas H., Kisamore, Jennifer L., and Jawahar, I. M.

Abstract

Academic misconduct is widespread in schools, colleges, and universities and it appears to be an international phenomenon that also spills over into the workplace (Nonis and Swift 2001; Sims 1993; Stone et al. 2011). To this end, while a great deal of research has investigated various individual components such as, demographic, personality and situational factors that contribute to cheating, research has yet to examine "why" students help others cheat and "which" students are being asked to help others cheat. In this study, we investigated if the closeness of the relationship to the individual requesting help in cheating to the individual being asked to help cheat, influenced the decision to help cheat. We also investigated if past cheating behavior predicted how an individual would respond to requests to cheat. Additionally, we sought to answer the following questions; "whether" minor cheating is more prevalent than serious cheating, "what" personality factors predict helping others cheat, "who" is helped, and "how" people rationalize helping others cheat. Results indicate minor cheating to be more prevalent, prudent personalities are less likely to have cheated or to help others cheat, individuals are more likely to help friends cheat than to help strangers, and past cheating behaviors is indicative of helping others to cheat. Implications for research and practice are discussed.

Published
2017
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25. Tumour compartment transcriptomics demonstrates the activation of inflammatory and odontogenic programmes in human adamantinomatous craniopharyngioma and identifies the MAPK/ERK pathway as a novel therapeutic target

Author

Apps, John R., Carreno, Gabriela, Gonzalez-Meljem, Jose Mario, Haston, Scott, Guiho, Romain, Cooper, Julie E., Manshaei, Saba, Jani, Nital, Hölsken, Annett, Pettorini, Benedetta, Beynon, Robert J., Simpson, Deborah M., Fraser, Helen C., Hong, Ying, Hallang, Shirleen, Stone, Thomas J., Virasami, Alex, Donson, Andrew M., Jones, David, Aquilina, Kristian, Spoudeas, Helen, Joshi, Abhijit R., Grundy, Richard, Storer, Lisa C. D., Korbonits, Márta, Hilton, David A., Tossell, Kyoko, Thavaraj, Selvam, Ungless, Mark A., Gil, Jesus, Buslei, Rolf, Hankinson, Todd, Hargrave, Darren, Goding, Colin, Andoniadou, Cynthia L., Brogan, Paul, Jacques, Thomas S., Williams, Hywel J., and Martinez-Barbera, Juan Pedro

Published
2018
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26. DNA methylation‐based classification of glioneuronal tumours synergises with histology and radiology to refine accurate molecular stratification

Author

Stone, Thomas J., primary, Mankad, Kshitij, additional, Tan, Ai Peng, additional, Jan, Wajanat, additional, Pickles, Jessica C., additional, Gogou, Maria, additional, Chalker, Jane, additional, Slodkowska, Iwona, additional, Pang, Emily, additional, Kristiansen, Mark, additional, Madhan, Gaganjit K., additional, Forrest, Leysa, additional, Hughes, Deborah, additional, Koutroumanidou, Eleni, additional, Mistry, Talisa, additional, Ogunbiyi, Olumide, additional, Ahmed, Saira W., additional, Cross, J. Helen, additional, Hubank, Mike, additional, Hargrave, Darren, additional, and Jacques, Thomas S., additional

Published
2023
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29. The role of deep roots in the hydrological and carbon cycles of Amazonian forests and pastures

Author

Nepstad, Daniel C, de Carvalho, Claudio R, Davidson, Eric A, Jipp, Peter H, Lefebvre, Paul A, Negreiros, Gustavo H, da Silva, Elson D, Stone, Thomas A, Trumbore, Susan E, and Vieira, Simone

Subjects
Life on Land, General Science & Technology
Abstract

DEFORESTATION and logging transform more forest in eastern and southern Amazonia than in any other region of the world1-3. This forest alteration affects regional hydrology4-11 and the global carbon cycle12-14, but current analyses of these effects neglect an important deep-soil link between the water and carbon cycles. Using rainfall data, satellite imagery and field studies, we estimate here that half of the closed forests of Brazilian Amazonia depend on deep root systems to maintain green canopies during the dry season. Evergreen forests in northeastern Pará state maintain evapotranspiration during five-month dry periods by absorbing water from the soil to depths of more than 8m. In contrast, although the degraded pastures of this region also contain deep-rooted woody plants, most pasture plants substantially reduce their leaf canopy in response to seasonal drought, thus reducing dry-season evapotranspiration and increasing potential subsurface runoff relative to the forests they replace. Deep roots that extract water also provide carbon to the soil. The forest soil below 1 m depth contains more carbon than does above-ground biomass, and as much as 15% of this deep-soil carbon turns over on annual or decadal timescales. Thus, forest alteration that affects depth distributions of carbon inputs from roots may also affect net carbon storage in the soil. © 2002 Nature Publishing Group.

Published
1994

31. Extending the Spectral Range of the RObotic Lunar Observatory (ROLO) Model to Climate Science-relevant Wavelengths

Author

Young, Cindy L., Stone, Thomas, Daniels, Janet, Snow, Martin, Clark, Roger, and Williams, Jean-Pierre

Abstract

A critical aspect of monitoring and understanding climate change is maintaining a continuous Earth Radiation Budget (ERB) record. The radiation budget is the balance between absorbed solar radiation and emitted thermal IR radiation by the Earth-atmosphere system, and ERB sensors require shortwave (SW) broadband measurements from 0.2 – 5 μm. Calibration accuracy, stability, and inter-consistency among different instruments are key to developing reliable composite long-term data records, but achieving sufficiently low uncertainties for these performance metrics poses a significant challenge. For this purpose, space-borne instruments commonly carry on-board references for calibration at various wavelengths, but these increase mass and mission complexity, and therefore cost, and are subject to degradation in the space environment. We present a new path towards accurate on-orbit calibration for SW broadband sensors. The Moon can be considered a natural solar diffuser that can be used as a calibration target by reflected-solar radiometer instruments and can be viewed by most Earth orbiting sensors. Using the Moon as a high accuracy on-orbit reference for ERB sensors will help reduce the time it takes to detect trends in climate variables to better inform public policy and societal actions, and may allow for more robust gap-tolerant observing systems in the future. The Moon has an exceptionally stable visible to SWIR reflectance, but its brightness is continually changing. Predicting this changing brightness requires an analytical model, the most reliable of which is the RObotic Lunar Observatory (ROLO) model, which has been established at the 0.35 – 2.45 μm spectral range. The lunar reflected UV radiation from 0.2 – 0.3 μm and reflected/emitted NIR radiation beyond 2.45 μm not accounted for by the ROLO model are small, but this additional uncertainty (on the order of a few percent) is enough to prevent using the Moon as an absolute calibration reference over the SW broadband range. We present a method for expanding the spectral range of the ROLO lunar calibration reference from the current 0.35 μm UV limit to 0.2 μm, and from the current 2.45 μm IR limit to 5.0 μm to fit the specific needs of the climate science community for absolute calibration. This expanded lunar reference will support past, present, and future ERB measurements in the SW broadband.

Published
2022

32. Addressing Needs to Achieve High-accuracy Lunar Calibration

Author

Stone, Thomas C.

Abstract

Established techniques that use the reflected light from the Moon for sensor radiometric calibration typically utilize the spatially integrated quantity of lunar spectral irradiance. The USGS ROLO model (and its replicated variants) has seen widespread use as the reference for lunar calibration since its development in the early 2000s. Although absolute scale uncertainties persist in the current ROLO model version, a predictive model for lunar spectral irradiance potentially can achieve tenths-percent uncertainty or better, with SI traceability. This would enable a number of important capabilities for on-orbit calibration of Earth observing sensors. To advance development toward a high-accuracy lunar calibration reference requires obtaining new characterization measurements of the Moon that have verified uncertainties and traceability to primary radiometric standards. But to reach the levels of accuracy potentially achievable for lunar calibration also requires increased attention to and improvement in techniques for deriving irradiance measurements from Moon observations acquired by imaging sensors. For example, properly evaluating the oversampling of the Moon disk can present a considerable challenge for line-scanning imagers. The Operational Land Imager (OLI) on Landsats 8 and 9 provides a superb test bed for developing techniques for high-precision measurements of lunar irradiance from line-scanned Moon images. Both OLI instruments observe the Moon monthly at about 7 degrees phase angle, scanning the disk with all 14 Focal Plane Modules over two orbits. The 30-meter ground resolution produces Moon images with disk diameters of about 250 pixels, and the scans oversample the Moon by factors of about 8. The lunar disk can be framed using line-of-sight analysis derived from the Landsat ancillary data feed. This paper will discuss how newly available, high-accuracy lunar irradiance measurements can inform the absolute scale for redeveloping the lunar calibration reference, and will overview the advanced techniques being developed for processing the line-scanned images of the Moon acquired by OLI.

Published
2022

35. Military command authority : a phenomenological study of how U.S. Army company-grade leaders experience insubordination

Author

Stone, Thomas Woods and Stone, Thomas Woods

Subjects
Insubordination Case studies. United States, Command of troops Case studies., Insubordination Études de cas. États-Unis, Commandement des troupes Études de cas., Command of troops, Insubordination, United States
Abstract

The purpose of this hermeneutic phenomenology is to explore the experiences of U.S. Army company commanders regarding insubordinate acts aimed at undermining their legitimate command authority. The theory guiding this dissertation is French and Raven’s (1959) theory of social power, which states that power is divided into five unique forms that leaders use in exercising their will to accomplish tasks. This study particularly considers the legitimate power base, a form of social power often asserted by virtue of holding an office or formal organizational position. The setting is an Army post in western United States; the study sample comprises three groups of Army leaders: company commanders, squad leaders, and senior noncommissioned officers (NCOs). Data collection methods include interviews and letter writing. Besides uniquely investigating Army company-level commands, I discovered many Army leaders display a penchant for identifying and mitigating potential insubordination rather than allowing it to fester in the ranks. Stated as themes, soldiers want commanders who offer clear vision-casting efforts directed at mission accomplishment; authentic first-line supervisors strive to bridge the gap between the commander and the soldiers; and senior NCOs care enough to develop their subordinates, promoting a command climate that, in turn, improves military culture long term. Future research opportunities exist in exploring insubordination in other military services and components. Additionally recommended research opportunities include case studies and narrative research about leadership traits, development, and styles exhibited in contemporary military leaders.

Published
2022

38. LGG-46. Survival Of The Fittest? A Prognostic Evaluation of Paediatric Low-Grade Glioma (PLGG) Survivor Functional Outcomes

Author

Green, Katherine, primary, Dahl, Christine, additional, Jorgensen, Mette, additional, O'Hare, Patricia, additional, Opocher, Enrico, additional, Slater, Olga, additional, Gains, Jenny, additional, Chang, Yen-Ching, additional, Aquilina, Kristian, additional, Bowman, Richard, additional, Oldridge, Bronwen, additional, Jacques, Thomas S, additional, Stone, Thomas, additional, Gan, Hoong-Wei, additional, Bluebond-Langner, Myra, additional, and Hargrave, Darren, additional

Published
2022
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39. RARE-08. Profiling of recurrent adamantinomatous cranionpharyngioma confirms the activation of the MAPK pathway and identifies copy number aberrations in relapsed tumours

Author

Apps, John, primary, Pickles, Jessica, additional, Stone, Thomas, additional, Chalker, Jane, additional, Ogunbiyi, Olumide, additional, Schwalbe, Edward, additional, Brandner, Sebastian, additional, Otto, Georg, additional, Castellano, Sergi, additional, Jacques, Thomas, additional, Deutschbein, Timo, additional, and Martinez-Barbera, Juan Pedro, additional

Published
2022
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41. Using the Theory of Planned Behavior and Cheating Justifications to Predict Academic Misconduct

Author

Stone, Thomas H., Jawahar, I. M., and Kisamore, Jennifer L.

Abstract

Purpose: The purpose of this paper is to show that academic misconduct appears to be on the rise; some research has linked academic misconduct to unethical workplace behaviors. Unlike previous empirically-driven research, this theory-based study seeks to examine the usefulness of a modification of Ajzen's theory of planned behavior to predict academic misconduct. Design/methodology/approach: A total of 271 students enrolled at a US university were surveyed. Structural equation modeling was used to test the model. Findings: The modified theory of a planned behavior model in which intentions and justifications both serve as antecedents to behavior fits the data well. The model accounted for 22 per cent of the variance in intentions to cheat and 47 per cent of the variance in self-reported cheating. Research limitations/implications: The primary limitations of this research are the cross-sectional research design, the self-selected sample, and the single source of survey data. Practical implications: The study extends the TPB model in the prediction of misconduct behavior. Attitudes, subjective norms, behavioral control, intentions and justifications were related to cheating behaviors. Academic misconduct may be reduced by shaping attitudes toward cheating, changing perceptions of subjective norms regarding the prevalence of cheating, and lowering students' perceptions of their control of cheating by, for example, emphasis on the consequences of getting caught. Understanding and reducing academic misconduct are important for promoting ethical behavior and values in future worker and organization leaders. Originality/value: Identification of factors that influence academic misconduct is an important aspect of professional development research, given its link to workplace misconduct. To date, academic misconduct research has been primarily empirically- rather than theory-driven. The current study identifies factors that contribute to academic misconduct by extending an established theoretical model of behavior. (Contains 3 tables and 2 figures.)

Published
2009
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