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3,100 results on '"Preston, J."'

2. Pareto Optimal Learning for Estimating Large Language Model Errors

Author

Zhao, Theodore, Wei, Mu, Preston, J. Samuel, and Poon, Hoifung

Subjects
Computer Science - Computation and Language, Statistics - Machine Learning
Abstract

Large Language Models (LLMs) have shown impressive abilities in many applications. When a concrete and precise answer is desired, it is important to have a quantitative estimation of the potential error rate. However, this can be challenging due to the text-in-text-out nature of generative models. We present a method based on Pareto optimization that generates a risk score to estimate the probability of error in an LLM response by integrating multiple sources of information. We prove theoretically that the error estimator optimized in our framework aligns with the LLM and the information sources in an Pareto optimal manner. Experimental results show that the risk scores estimated by our method are well correlated with the true LLM error rate, thus facilitating error correction. By dynamically combining with prompting strategies such as self-verification and information retrieval, we demonstrate the proposed method can be utilized to increase the performance of an LLM, surpassing state-of-the-art task specific models.

Published
2023

3. Coronal Heating as Determined by the Solar Flare Frequency Distribution Obtained by Aggregating Case Studies

Author

Mason, James Paul, Werth, Alexandra, West, Colin G., Youngblood, Allison A., Woodraska, Donald L., Peck, Courtney, Lacjak, Kevin, Frick, Florian G., Gabir, Moutamen, Alsinan, Reema A., Jacobsen, Thomas, Alrubaie, Mohammad, Chizmar, Kayla M., Lau, Benjamin P., Dominguez, Lizbeth Montoya, Price, David, Butler, Dylan R., Biron, Connor J., Feoktistov, Nikita, Dewey, Kai, Loomis, N. E., Bodzianowski, Michal, Kuybus, Connor, Dietrick, Henry, Wolfe, Aubrey M., Guerrero, Matt, Vinson, Jessica, Starbuck, Peter, Litton, Shelby D, Beck, M. G., Fisch, Jean-Paul, West, Ayana, Muniz, Alexis A., Chavez, Luis, Upthegrove, Zachary T., Runyon, Brenton M., Salazar, J., Kritzberg, Jake E., Murrel, Tyler, Ho, Ella, LaFemina, Quintin Y., Elbashir, Sara I., Chang, Ethan C., Hudson, Zachary A., Nussbaum, Rosemary O., Kennedy, Kellen, Kim, Kevin, Arango, Camila Villamil, Albakr, Mohammed A., Rotter, Michael, Garscadden, A. J., Salcido-Alcontar JR, Antonio, Pearl, Harrison M., Stepaniak, Tyler, Marquez, Josie A., Marsh, Lauren, Andringa, Jesse C, Osogwin, Austin, Shields, Amanda M., Brookins, Sarah, Hach, Grace K., Clausi, Alexis R., Millican, Emily B., Jaimes, Alan A, Graham, Alaina S., Burritt, John J., Perez, J. S., Ramirez, Nathaniel, Suri, Rohan, Myer, Michael S., Kresek, Zoe M., Goldsberry, C. A., Payne, Genevieve K., Jourabchi, Tara, Hu, J., Lucca, Jeffrey, Feng, Zitian, Gilpatrick, Connor B., Khan, Ibraheem A., Warble, Keenan, Sweeney, Joshua D., Dorricott, Philip, Meyer, Ethan, Kothamdi, Yash S., Sohail, Arman S., Grell, Kristyn, Floyd, Aidan, Bard, Titus, Mathieson, Randi M., Reed, Joseph, Cisneros, Alexis, Payne, Matthew P., Jarriel, J. R., Mora, Jacqueline Rodriguez, Sundell, M. E., Patel, Kajal, Alesmail, Mohammad, Alnasrallah, Yousef A, Abdullah, Jumana T., Molina-Saenz, Luis, Tayman, K. E., Brown, Gabriel T., Kerr-Layton, Liana, Berriman-Rozen, Zachary D., Hiatt, Quinn, Kalra, Etash, Ong, Jason, Vadayar, Shreenija, Shannahan, Callie D., Benke, Evan, zhang, Jinhua, Geisman, Jane, Martyr, Cara, Ameijenda, Federico, Akruwala, Ushmi H., Nehring, Molly, Kissner, Natalie, Rule, Ian C., Learned, Tyler, Smith, Alexandra N., Mazzotta, Liam, Rounsefell, Tyndall, Eyeson, Elizabeth A., Shelby, Arlee K., Moll, Tyler S, Menke, Riley, Shahba, Hannan, House Jr., Tony A., Clark, David B., Burns, Annemarie C., de La Beaujardiere, Tristan, Trautwein, Emily D., Plantz, Will, Reeves, Justin, Faber, Ian, Buxton, B. W., Highhouse, Nigel, Landrey, Kalin, Hansen, Connor M, Chen, Kevin, Hales, Ryder Buchanan, Borgerding, Luke R., Guo, Mutian, Crow, Christian J., Whittall, Lloyd C., Simmons, Conor, Folarin, Adeduni, Parkinson, Evan J., Rahn, Anna L., Blevins, Olivia, Morelock, Annalise M., Kelly, Nicholas, Parker, Nathan L., Smith, Kelly, Plzak, Audrey E., Saeb, David, Hares, Cameron T., Parker, Sasha R., McCoy, Andrew, Pham, Alexander V., Lauzon, Megan, Kennedy, Cayla J., Reyna, Andrea B., Acosta, Daniela M. Meza, Cool, Destiny J., Steinbarth, Sheen L., Mendoza-Anselmi, Patricia, Plutt, Kaitlyn E., Kipp, Isabel M, Rakhmonova, M., Brown, Cameron L., Van Anne, Gabreece, Moss, Alexander P., Golden, Olivia, Kirkpatrick, Hunter B., Colleran, Jake R., Sullivan, Brandon J, Tran, Kevin, Carpender, Michael Andrew, Mundy, Aria T., Koenig, Greta, Oudakker, Jessica, Engelhardt, Rasce, Ales, Nolan, Wexler, Ethan Benjamin, Beato, Quinn I, Chen, Lily, Cochran, Brooke, Hill, Paula, Hamilton, Sean R., Hashiro, Kyle, Khan, Usman, Martinez, Alexa M., Brockman, Jennifer L., Mallory, Macguire, Reed, Charlie, Terrile, Richard, Singh, Savi, Watson, James Adam, Creany, Joshua B., Price, Nicholas K., Miften, Aya M., Tran, Bryn, Kamenetskiy, Margaret, Martinez, Jose R., Opp, Elena N., Huang, Jianyang, Fails, Avery M., Belei, Brennan J., Slocum, Ryan, Astalos, Justin, East, Andrew, Nguyen, Lena P., Pherigo, Callie C, East, Andrew N., Li, David Y., Nelson, Maya LI, Taylor, Nicole, Odbayar, Anand, Rives, Anna Linnea, Mathur, Kabir P., Billingsley, Jacob, Polikoff, Hyden, Driscoll, Michael, Wilson, Orion K., Lahmers, Kyle, Toon, Nathaniel J., Lippincott, Sam, Musgrave, Andrew J., Gregory, Alannah H., Pitsuean-Meier, Sedique, Jesse, Trevor, Smith, Corey, Miles, Ethan J., Kainz, Sabrina J. H. T., Ji, Soo Yeun, Nguyen, Lena, Aryan, Maryam, Dinser, Alexis M., Shortman, Jadon, Bastias, Catalina S, Umbricht, Thomas D, Cage, Breonna, Randolph, Parker, Pollard, Matthew, Simone, Dylan M., Aramians, Andrew, Brecl, Ariana E., Robert, Amanda M., Zenner, Thomas, Saldi, Maxwell, Morales, Gavin, Mendez, Citlali, Syed, Konner, Vogel, Connor Maklain, Cone, Rebecca A., Berhanu, Naomi, Carpenter, Emily, Leoni, Cecilia, Bryan, Samuel, Ramachandra, Nidhi, Shaw, Timothy, Lee, E. C., Monyek, Eli, Wegner, Aidan B., Sharma, Shajesh, Lister, Barrett, White, Jamison R., Willard, John S., Sulaiman, S. A, Blandon, Guillermo, Narayan, Anoothi, Ruger, Ryan, Kelley, Morgan A., Moreno, Angel J., Balcer, Leo M, Ward-Chene, N. R. D., Shelby, Emma, Reagan, Brian D., Marsh, Toni, Sarkar, Sucheta, Kelley, Michael P., Fell, Kevin, Balaji, Sahana, Hildebrand, Annalise K., Shoha, Dominick, Nandu, Kshmya, Tucker, Julia, Cancio, Alejandro R., Wang, Jiawei, Rapaport, Sarah Grace, Maravi, Aimee S., Mayer, Victoria A., Miller, Andrew, Bence, Caden, Koke, Emily, Fauntleroy, John T, Doermer, Timothy, Al-Ghazwi, Adel, Morgan, Remy, Alahmed, Mohammed S., Mathavan, Adam Izz Khan Mohd Reduan, Silvester, H. K., Weiner, Amanda M., Liu, Nianzi, Iovan, Taro, Jensen, Alexander V., AlHarbi, Yazeed A., Jiang, Yufan, Zhang, Jiaqi, Jones, Olivia M., Huang, Chenqi, Reh, Eileen N., Alhamli, Dania, Pettine, Joshua, Zhou, Chongrui, Kriegman, Dylan, Yang, Jianing, Ash, Kevin, Savage, Carl, Kaiser, Emily, Augenstein, Dakota N., Padilla, Jacqueline, Stark, Ethan K., Hansen, Joshua A., Kokes, Thomas, Huynh, Leslie, Sanchez-Sanchez, Gustavo, Jeseritz, Luke A., Carillion, Emma L., Vepa, Aditya V., Khanal, Sapriya, Behr, Braden, Martin, Logan S., McMullan, Jesse J., Zhao, Tianwei, Williams, Abigail K., Alqabani, Emeen, Prinster, Gale H., Horne, Linda, Ruggles-Delgado, Kendall, Otto, Grant, Gomez, Angel R., Nguyen, Leonardo, Brumley, Preston J., Venegas, Nancy Ortiz, Varela, Ilian, Brownlow, Jordi, Cruz, Avril, Leiker, Linzhi, Batra, Jasleen, Hutabarat, Abigail P., Nunes-Valdes, Dario, Jameson, Connor, Naqi, Abdulaziz, Adams, Dante Q., Biediger, Blaine B., Borelli, William T, Cisne, Nicholas A., Collins, Nathaniel A., Curnow, Tyler L., Gopalakrishnan, Sean, Griffin, Nicholas F., Herrera, Emanuel, McGarvey, Meaghan V., Mellett, Sarah, Overchuk, Igor, Shaver, Nathan, Stratmeyer, Cooper N., Vess, Marcus T., Juels, Parker, Alyami, Saleh A., Gale, Skylar, Wallace, Steven P., Hunter, Samuel C, Lonergan, Mia C., Stewart, Trey, Maksimuk, Tiffany E., Lam, Antonia, Tressler, Judah, Napoletano, Elena R., Miller, Joshua B., Roy, Marc G., Chanders, Jasey, Fischer, Emmalee, Croteau, A. J., Kuiper, Nicolas A., Hoffman, Alex, DeBarros, Elyse, Curry, Riley T., Brzostowicz, A., Courtney, Jonas, Zhao, Tiannie, Szabo, Emi, Ghaith, Bandar Abu, Slyne, Colin, Beck, Lily, Quinonez, Oliver, Collins, Sarah, Madonna, Claire A., Morency, Cora, Palizzi, Mallory, Herwig, Tim, Beauprez, Jacob N., Ghiassi, Dorsa, Doran, Caroline R., Yang, Zhanchao, Padgette, Hannah M., Dicken, Cyrus A., Austin, Bryce W., Phalen, Ethan J., Xiao, Catherine, Palos, Adler, Gerhardstein, Phillip, Altenbern, Ava L., Orbidan, Dan, Dorr, Jackson A., Rivas, Guillermo A., Ewing, Calvin A, Giebner, B. C., McEntee, Kelleen, Kite, Emily R., Crocker, K. A., Haley, Mark S., Lezak, Adrienne R., McQuaid, Ella, Jeong, Jacob, Albaum, Jonathan, Hrudka, E. M., Mulcahy, Owen T., Tanguma, Nolan C., Oishi-Holder, Sean, White, Zachary, Coe, Ryan W., Boyer, Christine, Chapman, Mitchell G., Fortino, Elise, Salgado, Jose A., Hellweg, Tim, Martinez, Hazelia K., Mitchell, Alexander J., Schubert, Stephanie H., Schumacher, Grace K, Tesdahl, Corey D, Uphoff, C. H., Vassilyev, Alexandr, Witkoff, Briahn, Wolle, Jackson R., Dice, Kenzie A., Behrer, Timothy A., Bowen, Troy, Campbell, Andrew J, Clarkson, Peter C, Duong, Tien Q., Hawat, Elijah, Lopez, Christian, Olson, Nathaniel P., Osborn, Matthew, Peou, Munisettha E., Vaver, Nicholas J., Husted, Troy, Kallemeyn, Nicolas Ian, Spangler, Ava A, Mccurry, Kyle, Schultze, Courtney, Troisi, Thomas, Thomas, Daniel, Ort, Althea E., Singh, Maya A., Soon, Caitlin, Patton, Catherine, Billman, Jayce A., Jarvis, Sam, Hitt, Travis, Masri, Mirna, Albalushi, Yusef J., Schofer, Matthew J, Linnane, Katherine B., Knott, Philip Whiting, Valencia, Whitney, Arias-Robles, Brian A., Ryder, Diana, Simone, Anna, Abrams, Jonathan M., Belknap, Annelene L., Rouse, Charlotte, Reynolds, Alexander, Petric, Romeo S. L., Gomez, Angel A., Meiselman-Ashen, Jonah B., Carey, Luke, Dias, John S., Fischer-White, Jules, Forbes, Aidan E., Galarraga, Gabriela, Kennedy, Forrest, Lawlor, Rian, Murphy, Maxwell J., Norris, Cooper, Quarderer, Josh, Waller, Caroline, Weber, Robert J., Gunderson, Nicole, Boyne, Tom, Gregory, Joshua A., Propper, Henry Austin, von Peccoz, Charles B. Beck, Branch, Donovan, Clarke, Evelyn, Cutler, Libby, Dabberdt, Frederick M., Das, Swagatam, Figueirinhas, John Alfred D., Fougere, Benjamin L., Roy, Zoe A., Zhao, Noah Y., Cox, Corben L., Barnhart, Logan D. W., Craig, Wilmsen B., Moll, Hayden, Pohle, Kyle, Mueller, Alexander, Smith, Elena K., Spicer, Benjamin C., Aycock, Matthew C., Bat-Ulzii, Batchimeg, Murphy, Madalyn C., Altokhais, Abdullah, Thornally, Noah R., Kleinhaus, Olivia R., Sarfaraz, Darian, Barnes, Grant M., Beard, Sara, Banda, David J, Davis, Emma A. B., Huebsch, Tyler J., Wagoner, Michaela, Griego, Justus, Hale, Jack J. Mc, Porter, Trevor J., Abrashoff, Riley, Phan, Denise M., Smith, Samantha M., Srivastava, Ashish, Schlenker, Jared A. W., Madsen, Kasey O., Hirschmann, Anna E., Rankin, Frederick C, Akbar, Zainab A., Blouin, Ethan, Coleman-Plante, Aislinn, Hintsa, Evan, Lookhoff, Emily, Amer, Hamzi, Deng, Tianyue, Dvorak, Peter, Minimo, Josh, Plummer, William C., Ton, Kelly, Solt, Lincoln, AlAbbas, Batool H., AlAwadhi, Areej A., Cooper, Nicholas M., Corbitt, Jessica S, Dunlap, Christian, Johnson, Owen, Malone, Ryan A., Tellez, Yesica, Wallace, Logan, Ta, Michael-Tan D., Wheeler, Nicola H., Ramirez, Ariana C., Huang, Shancheng, Mehidic, Amar, Christiansen, Katherine E, Desai, Om, Domke, Emerson N., Howell, Noah H., Allsbrook, Martin, Alnaji, Teeb, England, Colin, Siles, Nathan, Burton, Nicholas David, Cruse, Zoe, Gilmartin, Dalton, Kim, Brian T., Hattendorf, Elsie, Buhamad, Maryam, Gayou, Lily, Seglem, Kasper, Alkhezzi, Tameem, Hicks, Imari R., Fife, Ryann, Pelster, Lily M., Fix, Alexander, Sur, Sohan N., Truong, Joshua K., Kubiak, Bartlomiej, Bondar, Matthew, Shi, Kyle Z., Johnston, Julia, Acevedo, Andres B., Lee, Junwon, Solorio, William J., Johnston, Braedon Y., McCormick, Tyler, Olguin, Nicholas, Pastor, Paige J., Wilson, Evan M., Trunko, Benjamin L., Sjoroos, Chris, Adams, Kalvyn N, Bell, Aislyn, Brumage-Heller, Grant, Canales, Braden P., Chiles, Bradyn, Driscoll, Kailer H., Hill, Hallie, Isert, Samuel A., Ketterer, Marilyn, Kim, Matthew M., Mewhirter, William J., Phillips, Lance, Phommatha, Krista, Quinn, Megan S., Reddy, Brooklyn J., Rippel, Matthew, Russell, Bowman, Williams, Sajan, Pixley, Andrew M., Gapin, Keala C., Peterson, B., Ruprecht, Collin, Hardie, Isabelle, Li, Isaac, Erickson, Abbey, Gersabeck, Clint, Gopalani, Mariam, Allanqawi, Nasser, Burton, Taylor, Cahn, Jackson R., Conti, Reese, White, Oliver S., Rojec, Stewart, Hogen, Blake A., Swartz, Jason R., Dick, R., Battist, Lexi, Dunn, Gabrielle M., Gasser, Rachel, Logan, Timothy W., Sinkovic, Madeline, Schaller, Marcus T., Heintz, Danielle A., Enrich, Andrew, Sanchez, Ethan S., Perez, Freddy, Flores, Fernando, Kapla, Shaun D., Shockley, Michael C., Phillips, Justin, Rumley, Madigan, Daboub, Johnston, Karsh, Brennan J., Linders, Bridget, Chen, Sam, Do, Helen C., Avula, Abhinav, French, James M., Bertuccio, Chrisanna, Hand, Tyler, Lee, Adrianna J., Neeland, Brenna K, Salazar, Violeta, Andrew, Carter, Barmore, Abby, Beatty, Thomas, Alonzi, Nicholas, Brown, Ryan, Chandler, Olivia M., Collier, Curran, Current, Hayden, Delasantos, Megan E., Bonilla, Alberto Espinosa de los Monteros, Fowler, Alexandra A., Geneser, Julianne R., Gentry, Eleanor, Gustavsson, E. R., Hansson, Jonathan, Hao, Tony Yunfei, Herrington, Robert N., Kelly, James, Kelly, Teagan, Kennedy, Abigail, Marquez, Mathew J., Meillon, Stella, Palmgren, Madeleine L., Pesce, Anneliese, Ranjan, Anurag, Robertson, Samuel M., Smith, Percy, Smith, Trevor J, Soby, Daniel A., Stratton, Grant L., Thielmann, Quinn N., Toups, Malena C., Veta, Jenna S., Young, Trenton J., Maly, Blake, Manzanares, Xander R., Beijer, Joshua, George, Jacob D., Mills, Dylan P., Ziebold, Josh J, Chambers, Paige, Montoya, Michael, Cheang, Nathan M., Anderson, Hunter J., Duncan, Sheridan J., Ehrlich, Lauren, Hudson, Nathan C., Kiechlin, Jack L., Koch, Will, Lee, Justin, Menassa, Dominic, Oakes, S. H., Petersen, Audrey J., Bunsow, J. R. Ramirez, Bay, Joshua, Ramirez, Sacha, Fenwick, Logan D., Boyle, Aidan P., Hibbard, Lea Pearl, Haubrich, Calder, Sherry, Daniel P., Jenkins, Josh, Furney, Sebastian, Velamala, Anjali A., Krueger, Davis J., Thompson, William N., Chhetri, Jenisha, Lee, Alexis Ying-Shan, Ray, Mia G. V., Recchia, John C., Lengerich, Dylan, Taulman, Kyle, Romero, Andres C., Steward, Ellie N., Russell, Sloan, Hardwick, Dillon F., Wootten, Katelynn, Nguyen, Valerie A., Quispe, Devon, Ragsdale, Cameron, Young, Isabel, Atchley-Rivers, N. S., Stribling, Jordin L., Gentile, Julia G, Boeyink, Taylor A., Kwiatkowski, Daniel, Dupeyron, Tomi Oshima, Crews, Anastasia, Shuttleworth, Mitchell, Dresdner, Danielle C., Flackett, Lydia, Haratsaris, Nicholas, Linger, Morgan I, Misener, Jay H., Patti, Samuel, Pine, Tawanchai P., Marikar, Nasreen, Matessi, Giorgio, Routledge, Allie C., Alkaabi, Suhail, Bartman, Jessica L., Bisacca, Gabrielle E., Busch, Celeste, Edwards, Bree, Staudenmier, Caitlyn, Starling, Travis, McVey, Caden, Montano, Maximus, Contizano, Charles J., Taylor, Eleanor, McIntyre, James K., Victory, Andrew, McCammon, Glen S., Kimlicko, Aspen, Sheldrake, Tucker, Shelchuk, Grace, Von Reich, Ferin J., Hicks, Andrew J., O'neill, Ian, Rossman, Beth, Taylor, Liam C., MacDonald, William, Becker, Simone E., Han, Soonhee, O'Sullivan, Cian, Wilcove, Isaac, Brennan, David J., Hanley, Luke C., Hull, Owen, Wilson, Timothy R., Kalmus, Madison H., Berv, Owen A., Harris, Logan Swous, Doan, Chris H, Londres, Nathan, Parulekar, Anish, Adam, Megan M., Angwin, Abigail, Cabbage, Carter C., Colleran, Zachary, Pietras, Alex, Seux, Octave, Oros, Ryan, Wilkinson, Blake C., Nguyen, Khoa D, Trank-Greene, Maedee, Barone, Kevin M., Snyder, G. L., Biehle, Samuel J, Billig, Brennen, Almquist, Justin Thomas, Dixon, Alyssa M., Erickson, Benjamin, Evans, Nathan, Genne, SL, Kelly, Christopher M, Marcus, Serafima M., Ogle, Caleb, Patel, Akhil, Vendetti, Evan, Courtney, Olivia, Deel, Sean, Del Foco, Leonardo, Gjini, Michael, Haines, Jessica, Hoff, Isabelle J., Jones, M. R., Killian, Dominic, Kuehl, Kirsten, Kuester, Chrisanne, Lantz, Maxwell B., Lee, Christian J, Mauer, Graham, McKemey, Finbar K., Millican, Sarah J., Rosasco, Ryan, Stewart, T. C., VanEtten, Eleanor, Derwin, Zachary, Serio, Lauren, Sickler, Molly G., Blake, Cassidy A., Patel, Neil S., Fox, Margaret, Gray, Michael J, Ziegler, Lucas J., Kumar, Aman Priyadarshi, Polly, Madelyn, Mesgina, Sarah, McMorris, Zane, Griffin, Kyle J., Haile, L. N., Bassel, Claire, Dixon, Thomas J., Beattie, Ryan, Houck, Timothy J, Rodgers, Maeve, Trofino, Tyson R., Lukianow, Dax, Smart, Korben, Hall, Jacqueline L., Bone, Lauren, Baldwin, James O., Doane, Connor, Almohsen, Yousef A., Stamos, Emily, Acha, Iker, Kim, Jake, Samour II, Antonio E., Chavali, S., Kanokthippayakun, Jeerakit, Gotlib, Nicholas, Murphy, Ryan C., Archibald, Jack. W., Brimhall, Alexander J, Boyer, Aidan, Chapman, Logan T., Chadda, Shivank, Sibrell, Lisa, Vallery, Mia M., Conroy, Thomas C., Pan, Luke J., Balajonda, Brian, Fuhrman, Bethany E. S., Alkubaisi, Mohamed, Engelstad, Jacob, Dodrill, Joshua, Fuchs, Calvin R., Bullard-Connor, Gigi, Alhuseini, Isehaq, Zygmunt, James C., Sipowicz, Leo, Hayrynen, Griffin A., McGill, Riley M., Keating, Caden J., Hart, Omer, Cyr, Aidan St., Steinsberger, Christopher H., Thoman, Gerig, Wood, Travis M., Ingram, Julia A., Dominguez, J., Georgiades, Nathaniel James, Johnson, Matthew, Johnson, Sawyer, Pedersen, Alexander J., Ralapanawe, Anoush K, Thomas, Jeffrey J., Sato, Ginn A., Reynolds, Hope, Nasser, Liebe, Mizzi, Alexander Z., Damgaard, Olivia, Baflah, Abdulrahman A., Liu, Steven Y., Salindeho, Adam D., Norden, Kelso, Gearhart, Emily E., Krajnak, Zack, Szeremeta, Philip, Amos, Meggan, Shin, Kyungeun, Muckenthaler, Brandon A., Medialdea, Melissa, Beach, Simone, Wilson, Connor B., Adams, Elena R, Aldhamen, Ahmed, Harris, Coyle M., Hesse, Troy M., Golding, Nathan T., Larter, Zachary, Hernandez, Angel, Morales, Genaro, Traxler, Robert B., Alosaimi, Meshal, Fitton, Aidan F., Aaron, James Holland, Lee, Nathaniel F., Liao, Ryan Z., Chen, Judy, French, Katherine V., Loring, Justin, Colter, Aurora, McConvey, Rowan, Colozzi, Michael, Vann, John D., Scheck, Benjamin T., Weigand, Anthony A, Alhabeeb, Abdulelah, Idoine, Yolande, Woodard, Aiden L., Medellin, Mateo M., Ratajczyk, Nicholas O, Tobin, Darien P., Collins, Jack C., Horning, Thomas M., Pellatz, Nick, Pitten, John, Lordi, Noah, Patterson, Alyx, Hoang, Thi D, Zimmermann, Ingrid H, Wang, Hongda, Steckhahn, Daniel, Aradhya, Arvind J., Oliver, Kristin A., Cai, Yijian, Wang, Chaoran, Yegovtsev, Nikolay, Wu, Mengyu, Ganesan, Koushik, Osborne, Andrew, Wickenden, Evan, Meyer, Josephine C., Chaparro, David, Visal, Aseem, Liu, Haixin, Menon, Thanmay S., Jin, Yan, Wilson, John, Erikson, James W., Luo, Zheng, Shitara, Nanako, Nelson, Emma E, Geerdts, T. R., Ortiz, Jorge L Ramirez, and Lewandowski, H. J.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

Flare frequency distributions represent a key approach to addressing one of the largest problems in solar and stellar physics: determining the mechanism that counter-intuitively heats coronae to temperatures that are orders of magnitude hotter than the corresponding photospheres. It is widely accepted that the magnetic field is responsible for the heating, but there are two competing mechanisms that could explain it: nanoflares or Alfv\'en waves. To date, neither can be directly observed. Nanoflares are, by definition, extremely small, but their aggregate energy release could represent a substantial heating mechanism, presuming they are sufficiently abundant. One way to test this presumption is via the flare frequency distribution, which describes how often flares of various energies occur. If the slope of the power law fitting the flare frequency distribution is above a critical threshold, $\alpha=2$ as established in prior literature, then there should be a sufficient abundance of nanoflares to explain coronal heating. We performed $>$600 case studies of solar flares, made possible by an unprecedented number of data analysts via three semesters of an undergraduate physics laboratory course. This allowed us to include two crucial, but nontrivial, analysis methods: pre-flare baseline subtraction and computation of the flare energy, which requires determining flare start and stop times. We aggregated the results of these analyses into a statistical study to determine that $\alpha = 1.63 \pm 0.03$. This is below the critical threshold, suggesting that Alfv\'en waves are an important driver of coronal heating., Comment: 1,002 authors, 14 pages, 4 figures, 3 tables, published by The Astrophysical Journal on 2023-05-09, volume 948, page 71

Published
2023
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5. Bayesian calibration of simulation models: A tutorial and an Australian smoking behaviour model

Author

Wade, Stephen, Weber, Marianne F, Sarich, Peter, Vaneckova, Pavla, Behar-Harpaz, Silvia, Ngo, Preston J, Cressman, Sonya, Gartner, Coral E, Murray, John M, Blakely, Tony A, Banks, Emily, Tammemagi, Martin C, Canfell, Karen, and Caruana, Michael

Subjects
Statistics - Applications, Statistics - Computation, 62P20 (Primary) 62M09 (Secondary), G.3
Abstract

Simulation models of epidemiological, biological, ecological, and environmental processes are increasingly being calibrated using Bayesian statistics. The Bayesian approach provides simple rules to synthesise multiple data sources and to calculate uncertainty in model output due to uncertainty in the calibration data. As the number of tutorials and studies published grow, the solutions to common difficulties in Bayesian calibration across these fields have become more apparent, and a step-by-step process for successful calibration across all these fields is emerging. We provide a statement of the key steps in a Bayesian calibration, and we outline analyses and approaches to each step that have emerged from one or more of these applied sciences. Thus we present a synthesis of Bayesian calibration methodologies that cut across a number of scientific disciplines. To demonstrate these steps and to provide further detail on the computations involved in Bayesian calibration, we calibrated a compartmental model of tobacco smoking behaviour in Australia. We found that the proportion of a birth cohort estimated to take up smoking before they reach age 20 years in 2016 was at its lowest value since the early 20th century, and that quit rates were at their highest. As a novel outcome, we quantified the rate that ex-smokers switched to reporting as a 'never smoker' when surveyed later in life; a phenomenon that, to our knowledge, has never been quantified using cross-sectional survey data., Comment: 49 pages, 5 figures, 17 tables

Published
2022

10. A case study to engage students in the research design and ethics of high-throughput metagenomics

Author

Courtney Carroll Alexander, Monica M. Gaudier-Diaz, Adam J. Kleinschmit, Preston J. Dihle, Scott A. Salger, Nic Vega, and Sabrina D. Robertson

Subjects
case study, research design, ethics, microbiome, metagenomics, next-generation sequencing, Special aspects of education, LC8-6691, Biology (General), QH301-705.5
Abstract

ABSTRACTCase studies present students with an opportunity to learn and apply course content through problem solving and critical thinking. Supported by the High-throughput Discovery Science & Inquiry-based Case Studies for Today’s Students (HITS) Research Coordination Network, our interdisciplinary team designed, implemented, and assessed two case study modules entitled “You Are What You Eat.” Collectively, the case study modules present students with an opportunity to engage in experimental research design and the ethical considerations regarding microbiome research and society. In this manuscript, we provide instructors with tools for adopting or adapting the research design and/or the ethics modules. To date, the case has been implemented using two modalities (remote and in-person) in three courses (Microbiology, Physiology, and Neuroscience), engaging over 200 undergraduate students. Our assessment data demonstrate gains in content knowledge and students’ perception of learning following case study implementation. Furthermore, when reflecting on our experiences and student feedback, we identified ways in which the case study could be modified for different settings. In this way, we hope that the “You Are What You Eat” case study modules can be implemented widely by instructors to promote problem solving and critical thinking in the traditional classroom or laboratory setting when discussing next-generation sequencing and/or metagenomics research.

Published
2024
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11. Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures

Author

Gavin Melaugh, Vincent A. Martinez, Perrin Baker, Preston J. Hill, P. Lynne Howell, Daniel J. Wozniak, and Rosalind J. Allen

Subjects
Microbial ecology, QR100-130
Abstract

Abstract Pseudomonas aeruginosa forms suspended multicellular aggregates when cultured in liquid media. These aggregates may be important in disease, and/or as a pathway to biofilm formation. The polysaccharide Psl and extracellular DNA (eDNA) have both been implicated in aggregation, but previous results depend strongly on the experimental conditions. Here we develop a quantitative microscopy-based method for assessing changes in the size distribution of suspended aggregates over time in growing cultures. For exponentially growing cultures of P. aeruginosa PAO1, we find that aggregation is mediated by cell-associated Psl, rather than by either eDNA or secreted Psl. These aggregates arise de novo within the culture via a growth process that involves both collisions and clonal growth, and Psl non-producing cells do not aggregate with producers. In contrast, we find that stationary phase (overnight) cultures contain a different type of multicellular aggregate, in which both eDNA and Psl mediate cohesion. Our findings suggest that the physical and biological properties of multicellular aggregates may be very different in early-stage vs late-stage bacterial cultures.

Published
2023
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12. Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast

Author

Jingxuan Chen, Preston J. Basting, Shunhua Han, David J. Garfinkel, and Casey M. Bergman

Subjects
Bioinformatics, High-throughput sequencing, Saccharomyces cerevisiae, Transposable elements, Variant calling, Genetics, QH426-470
Abstract

Abstract Background Many computational methods have been developed to detect non-reference transposable element (TE) insertions using short-read whole genome sequencing data. The diversity and complexity of such methods often present challenges to new users seeking to reproducibly install, execute, or evaluate multiple TE insertion detectors. Results We previously developed the McClintock meta-pipeline to facilitate the installation, execution, and evaluation of six first-generation short-read TE detectors. Here, we report a completely re-implemented version of McClintock written in Python using Snakemake and Conda that improves its installation, error handling, speed, stability, and extensibility. McClintock 2 now includes 12 short-read TE detectors, auxiliary pre-processing and analysis modules, interactive HTML reports, and a simulation framework to reproducibly evaluate the accuracy of component TE detectors. When applied to the model microbial eukaryote Saccharomyces cerevisiae, we find substantial variation in the ability of McClintock 2 components to identify the precise locations of non-reference TE insertions, with RelocaTE2 showing the highest recall and precision in simulated data. We find that RelocaTE2, TEMP, TEMP2 and TEBreak provide consistent estimates of $$\sim$$ ∼ 50 non-reference TE insertions per strain and that Ty2 has the highest number of non-reference TE insertions in a species-wide panel of $$\sim$$ ∼ 1000 yeast genomes. Finally, we show that best-in-class predictors for yeast applied to resequencing data have sufficient resolution to reveal a dyad pattern of integration in nucleosome-bound regions upstream of yeast tRNA genes for Ty1, Ty2, and Ty4, allowing us to extend knowledge about fine-scale target preferences revealed previously for experimentally-induced Ty1 insertions to spontaneous insertions for other copia-superfamily retrotransposons in yeast. Conclusion McClintock ( https://github.com/bergmanlab/mcclintock/ ) provides a user-friendly pipeline for the identification of TEs in short-read WGS data using multiple TE detectors, which should benefit researchers studying TE insertion variation in a wide range of different organisms. Application of the improved McClintock system to simulated and empirical yeast genome data reveals best-in-class methods and novel biological insights for one of the most widely-studied model eukaryotes and provides a paradigm for evaluating and selecting non-reference TE detectors in other species.

Published
2023
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13. Disruption of nontuberculous mycobacteria biofilms induces a highly vulnerable to antibiotic killing phenotype

Author

Nikola Kurbatfinski, Preston J. Hill, Noah Tobin, Cameron N. Kramer, Joseph Wickham, Steven D. Goodman, Luanne Hall-Stoodley, and Lauren O. Bakaletz

Subjects
Humanized monoclonal antibody, M. abscessus, M. avium, DNABII proteins, HupB, Tip-chimer peptide, Biotechnology, TP248.13-248.65, Microbiology, QR1-502
Abstract

Objectives: Structural or mucus hypersecretory pulmonary diseases such as cystic fibrosis (CF), wherein viscous mucus accumulates and clearance functions are impaired, predispose people to lung infection by inhaled bacteria that form biofilm aggregates. Nontuberculous mycobacteria (NTM), primarily Mycobacterium abscessus and Mycobacterium avium, are the growing cause of these lung infections and are extremely challenging to treat due to antibiotic recalcitrance. Better therapeutic approaches are urgently needed. We developed a humanized monoclonal antibody (HuTipMab) directed against a biofilm structural linchpin, the bacterial DNABII proteins, that rapidly disrupts biofilms and generates highly vulnerable newly released bacteria (NRel). Methods: HuTipMab's ability to recognize HupB, NTM's DNABII homologue was determined by ELISA. Relative ability of HuTipMab to disrupt biofilms formed by lab-passaged and clinical isolates of NTM was assessed by CLSM. Relative sensitivity of NTM NRel to antibiotic killing compared to when grown planktonically was evaluated by plate count. Results: HuTipMab recognized HupB and significantly disrupted NTM biofilms in a time- and dose-dependent manner. Importantly, NTM NRel of lab-passaged and clinical isolates were now highly sensitive to killing by amikacin and azithromycin. Conclusions: If successful, this combinatorial treatment strategy would empower existing antibiotics to more effectively kill NTM newly released from a biofilm by HuTipMab and thereby both improve clinical outcomes and perhaps decrease length of antibiotic treatment for people that are NTM culture-positive.

Published
2023
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14. Cardiac changes in collegiate athletes following SARS-CoV-2 infection and quarantine: a prospective Case-Control study

Author

Vanessa-Rose G. Turpin, Shannon K. Parr, Stephen T. Hammond, Zachary J. White, Preston J. Tickner, Chloe E. Chisam, Kyle V. Goerl, Jonathan A. Drezner, and Carl J. Ade

Subjects
SARS-CoV-2, collegiate athlete, COVID, cardiovascular changes, Medicine
Abstract

AbstractObjective Athletes are susceptible to acute respiratory tract infections, including SARS-CoV-2, which can affect cardiovascular function. We aimed to evaluate the impact of COVID-19 infection and quarantine on cardiac function in male and female collegiate athletes.Methods We conducted a single-center, prospective, case-control study and performed transthoracic echocardiography in a diverse group of convalescent SARS-CoV-2-positive athletes following a 10–14–day quarantine, matched to non-SARS-CoV-2 athletes. Data collection occurred from August 1, 2020, to May 31, 2021.Results We evaluated 61 SARS-CoV-2-positive athletes (20 ± 1 years, 39% female) and 61 controls (age 20 ± 2 years, 39% female). Echocardiography in SARS-CoV-2-positive athletes was performed on average 40 ± 38 days after infection diagnosis. All SARS-CoV-2-positive athletes had clinically normal systolic left ventricular function (LVEF > 50%). However, SARS-CoV-2-positive athletes exhibited mildly lower LVEF compared to controls (65 ± 6% vs. 72 ± 8%, respectively, p

Published
2023
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18. Colon and rectal cancer treatment patterns and their associations with clinical, sociodemographic and lifestyle characteristics: analysis of the Australian 45 and Up Study cohort

Author

Sarsha Yap, Emily He, Sam Egger, David E Goldsbury, Jie-Bin Lew, Preston J Ngo, Joachim Worthington, Hannah Rillstone, John R Zalcberg, Jeff Cuff, Robyn L Ward, Karen Canfell, Eleonora Feletto, and Julia Steinberg

Subjects
Colon cancer, Rectal cancer, Cancer treatment, Radiotherapy, Chemotherapy, Cancer surgery, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Colorectal cancer is the third most diagnosed cancer globally and the second leading cause of cancer death. We examined colon and rectal cancer treatment patterns in Australia. Methods From cancer registry records, we identified 1,236 and 542 people with incident colon and rectal cancer, respectively, diagnosed during 2006-2013 in the 45 and Up Study cohort (267,357 participants). Cancer treatment and deaths were determined via linkage to routinely collected data, including hospital and medical services records. For colon cancer, we examined treatment categories of “surgery only”, “surgery plus chemotherapy”, “other treatment” (i.e. other combinations of surgery/chemotherapy/radiotherapy), “no record of cancer-related treatment, died”; and, for rectal cancer, “surgery only”, “surgery plus chemotherapy and/or radiotherapy”, “other treatment”, and “no record of cancer-related treatment, died”. We analysed survival, time to first treatment, and characteristics associated with treatment receipt using competing risks regression. Results 86.4% and 86.5% of people with colon and rectal cancer, respectively, had a record of receiving any treatment ≤2 years post-diagnosis. Of those treated, 93.2% and 90.8% started treatment ≤2 months post-diagnosis, respectively. Characteristics significantly associated with treatment receipt were similar for colon and rectal cancer, with strongest associations for spread of disease and age at diagnosis (p

Published
2023
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19. Economic impact of using risk models for eligibility selection to the International lung screening Trial

Author

Cressman, Sonya, Weber, Marianne F., Ngo, Preston J., Wade, Stephen, Behar Harpaz, Silvia, Caruana, Michael, Tremblay, Alain, Manser, Renee, Stone, Emily, Atkar-Khattra, Sukhinder, Karikios, Deme, Ho, Cheryl, Fernandes, Aleisha, Yi Weng, Jing, McWilliams, Annette, Myers, Renelle, Mayo, John, Yee, John, Yuan, Ren, Marshall, Henry M, Fong, Kwun M, Lam, Stephen, Canfell, Karen, and Tammemägi, Martin C

Published
2023
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20. Contributors

Author

Accorsi–Mendonça, Daniela, primary, Adams, David J., additional, Allen, Andrew M., additional, Alvarenga, Marlies, additional, Ardell, Jeffrey L., additional, Arnold, Amy C., additional, Ashton, Jesse L., additional, Badrov, Mark B., additional, Ballantyne, Brennan A., additional, Bardsley, Emma N., additional, Barez-Lopez, Soledad, additional, Barman, Susan M., additional, Barrett, Carolyn J., additional, Bauer, Deborah, additional, Bell, Christopher, additional, Ben-Tal, Alona, additional, Benarroch, Eduardo E., additional, Biaggioni, Italo, additional, Brandl, Katharina, additional, Brooks, Virginia L., additional, Brown, Amy E., additional, Browning, Kirsteen N., additional, Bryarly, Meredith, additional, Camargo, Livia L., additional, Camilleri, Michael, additional, Campbell, Preston J., additional, Caron, Marc G., additional, Carter, Jason R., additional, Chapleau, Mark W., additional, Charkoudian, Nisha, additional, Chelimsky, Gisela, additional, Chelimsky, Thomas C., additional, Chompoopong, Pitcha, additional, Claydon, Victoria E., additional, Clément, Gilles, additional, Convertino, Victor A., additional, Coon, Elizabeth A., additional, Cortelli, Pietro, additional, Davis, Stephen N., additional, Diedrich, André, additional, DiPette, Donald J., additional, Diz, Debra I., additional, Drake, Marcus J., additional, Eisenhofer, Graeme, additional, Elefteriou, Florent, additional, Elijovich, Fernando, additional, Elmenhorst, Eva-Maria, additional, English, Brett A., additional, Esler, Murray, additional, Esler, Rosemary, additional, Fadel, Paul J., additional, Fahrenholz, John M., additional, Fanciulli, Alessandra, additional, Fang, John Y., additional, Fealey, Robert D., additional, Ferreira, Nathanne S., additional, Filogonio, Renato, additional, Fink, Gregory D., additional, Fisher, James P., additional, Floras, John S., additional, Fountain, Samuel J., additional, Fu, Qi, additional, Fudim, Marat, additional, Furlan, Raffaello, additional, Gamboa, Alfredo, additional, Garland, Emily M., additional, Gibbons, Christopher H., additional, Giritharan, Andrew, additional, Goldstein, David S., additional, Golombék, Diego A., additional, Gomez-Sanchez, Elise P., additional, Gomez-Sanchez, Celso E., additional, Graham, Robert M., additional, Grassi, Guido, additional, Greenlund, Ian M., additional, Grubb, Blair P., additional, Guekht, Alla, additional, Guild, Sarah-Jane, additional, Guo, Ling, additional, Gurevich, Vsevolod V., additional, Habermann, Ralf, additional, Hadaya, Joseph, additional, Hahn, Maureen K., additional, Hanna, Peter, additional, Henderson, Luke A., additional, Herring, Neil, additional, Hilz, Max J., additional, Hunter, Peter, additional, Hyland, Keith, additional, Hyland, Lauren A., additional, Jackson, Edwin Kerry, additional, Jacob, Giris, additional, Jänig, Wilfrid, additional, Japundžić-Žigon, Nina, additional, Jones, Carrie K., additional, Joos, Karen M., additional, Jordan, Jens, additional, Joyce, William, additional, Kaidonis, Xenia, additional, Kaufmann, Horacio, additional, Kaye, David, additional, Khan Minhas, Abdul Mannan, additional, Kim, Joyce S., additional, Kitta, Takeya, additional, Kline, David D., additional, Konecny, Thomas, additional, Koons, Natalie J., additional, Kumar, Ambrish, additional, Laffer, Cheryl L., additional, Lagrange, Andre H., additional, Laiken, Nora, additional, Lambert, Gavin, additional, Lambert, Elisabeth, additional, Lamotte, Guillaume, additional, Lenders, Jacques W.M., additional, Levine, Benjamin D., additional, Leys, Fabian, additional, Limper, Ulrich, additional, Lin, Mabelle, additional, Listik, Eduardo, additional, Longmuir, Reid, additional, Low, David A., additional, Low, Phillip A., additional, Luther, James M., additional, Macefield, Vaughan G., additional, Machado, Benedito H., additional, Madel, Maria-Bernadette, additional, Martelli, Davide, additional, Mathias, Christopher J., additional, Mauermann, Michelle L., additional, McAllen, Robin M., additional, McBryde, Fiona D., additional, McKeon, Andrew, additional, McKinley, Michael J., additional, Menuet, Clément, additional, Milam, Douglas F., additional, Mohl, Marion C., additional, Montgomery, Johanna M., additional, Moraes, Davi J.A., additional, Morrison, Shaun F., additional, Murphy, David, additional, Nichols, Charles D., additional, Niewiński, Piotr, additional, Norcliffe-Kaufmann, Lucy, additional, Okamoto, Luis E., additional, Osanlouy, Mahyar, additional, Osborn, John W., additional, Oubaid, Viktor, additional, Palma, Jose-Alberto, additional, Pamporaki, Christina, additional, Parsons, Brian A., additional, Paterson, David J., additional, Paton, Julian F.R., additional, Peltier, Amanda C., additional, Pensato, Umberto, additional, Peterson, Sean M., additional, Phibbs, Fenna T., additional, Pierangeli, Giulia, additional, Potts, Jay D., additional, Rabinstein, Alejandro A., additional, Raizada, Mohan K., additional, Raj, Satish R., additional, Rand, Casey M., additional, Reichmann, Heinz, additional, Robertson, Calum, additional, Robertson, Rose Marie, additional, Robinson, Michael B., additional, Ruzieh, Mohammed, additional, Sandroni, Paola, additional, Sato, Takayuki, additional, Schiffrin, Ernesto L., additional, Schlaich, Markus, additional, Schondorf, Ronald, additional, Schultz, Harold D., additional, Scott, Michael M., additional, Seravalle, Gino, additional, Shannon, John R., additional, Sheikh, Abu Baker, additional, Shibao, Cyndya A., additional, Shivkumar, Kalyanam, additional, Shouman, Kamal, additional, Siepmann, Timo, additional, Singer, Wolfgang, additional, Soltani, Elias, additional, Somers, Virend, additional, Sridharan, Aadhavi, additional, Stefanova, Nadia, additional, Stewart, Julian, additional, Stiles, Lauren E., additional, Sunagawa, Kenji, additional, Tank, Jens, additional, Thijs, Roland D., additional, Tomek, Jakub, additional, Touyz, Rhian M., additional, Tracy, Jennifer A., additional, Travagli, R. Alberto, additional, Undem, Bradley J., additional, Urs, Nikhil, additional, Vernino, Steven, additional, Vianna, Lauro C., additional, Vigo, Daniel E., additional, Vizzard, Margaret A., additional, Wahba, Amr, additional, Waheed, Waqar, additional, Wang, Han-Jun, additional, Wang, Tobias, additional, Wang, Qin, additional, Wang, Ruihao, additional, Weese-Mayer, Debra E., additional, Wenning, Gregor K., additional, Wieling, Wouter, additional, Williams, Kevin W., additional, Winzer-Serhan, Ursula H., additional, Wood, Scott, additional, Yap, Kai Lee, additional, Yoshimura, Naoki, additional, Zavalin, Kirill A., additional, Zhuravlev, Dmitry, additional, Zoccal, Daniel B., additional, and Zubcevic, Jasenka, additional

Published
2023
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25. Cross-Modal Health State Estimation

Author

Nag, Nitish, Pandey, Vaibhav, Putzel, Preston J., Bhimaraju, Hari, Krishnan, Srikanth, and Jain, Ramesh C.

Subjects
Computer Science - Computers and Society, Computer Science - Artificial Intelligence, Computer Science - Multimedia, Quantitative Biology - Quantitative Methods
Abstract

Individuals create and consume more diverse data about themselves today than any time in history. Sources of this data include wearable devices, images, social media, geospatial information and more. A tremendous opportunity rests within cross-modal data analysis that leverages existing domain knowledge methods to understand and guide human health. Especially in chronic diseases, current medical practice uses a combination of sparse hospital based biological metrics (blood tests, expensive imaging, etc.) to understand the evolving health status of an individual. Future health systems must integrate data created at the individual level to better understand health status perpetually, especially in a cybernetic framework. In this work we fuse multiple user created and open source data streams along with established biomedical domain knowledge to give two types of quantitative state estimates of cardiovascular health. First, we use wearable devices to calculate cardiorespiratory fitness (CRF), a known quantitative leading predictor of heart disease which is not routinely collected in clinical settings. Second, we estimate inherent genetic traits, living environmental risks, circadian rhythm, and biological metrics from a diverse dataset. Our experimental results on 24 subjects demonstrate how multi-modal data can provide personalized health insight. Understanding the dynamic nature of health status will pave the way for better health based recommendation engines, better clinical decision making and positive lifestyle changes., Comment: Accepted to ACM Multimedia 2018 Conference - Brave New Ideas, Seoul, Korea, ACM ISBN 978-1-4503-5665-7/18/10

Published
2018
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33. A smartphone-based approach for comprehensive soil microbiome profiling.

Author

Liang, Yan, Khanthaphixay, Bradley, Reynolds, Jocelyn, Leigh, Preston J., Lim, Melissa L., and Yoon, Jeong-Yeol

Subjects
MACHINE learning, SOIL testing, NUTRIENT cycles, SOIL profiles, SOIL sampling
Abstract

The soil microbiome is crucial for nutrient cycling, health, and plant growth. This study presents a smartphone-based approach as a low-cost and portable alternative to traditional methods for classifying bacterial species and characterizing microbial communities in soil samples. By harnessing bacterial autofluorescence detection and machine learning algorithms, the platform achieved an average accuracy of 88% in distinguishing common soil-related bacterial species despite the lack of biomarkers, nucleic acid amplification, or gene sequencing. Furthermore, it successfully identified dominant species within various bacterial mixtures with an accuracy of 76% and three-level soil health identification at an accuracy of 80%–82%, providing insights into microbial community dynamics. The influence of other soil conditions (pH and moisture) was relatively minor, showcasing the platform's robustness. Various field soil samples were also tested with this platform at 80% accuracy compared with the laboratory analyses, demonstrating the practicality and usability of this approach for on-site soil analysis. This study highlights the potential of the smartphone-based system as a valuable tool for soil assessment, microbial monitoring, and environmental management. [ABSTRACT FROM AUTHOR]

Published
2024
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34. Where the "ruber" Meets the Road: Using the Genome of the Red Diamond Rattlesnake to Unravel the Evolutionary Processes Driving Venom Evolution.

Author

Hirst, Samuel R, Rautsaw, Rhett M, VanHorn, Cameron M, Beer, Marc A, McDonald, Preston J, García, Ramsés Alejandro Rosales, Lopez, Bruno Rodriguez, Rincón, Alexandra Rubio, Chávez, Hector Franz, Vásquez-Cruz, Víctor, Hernández, Alfonso Kelly, Storfer, Andrew, Borja, Miguel, Castañeda-Gaytán, Gamaliel, Frandsen, Paul B, Parkinson, Christopher L, Strickland, Jason L, and Margres, Mark J

Subjects
PREY availability, POPULATION differentiation, PHENOTYPIC plasticity, TRANSCRIPTOMES, LIFE history theory, VENOM
Abstract

Understanding the proximate and ultimate causes of phenotypic variation is fundamental in evolutionary research, as such variation provides the substrate for selection to act upon. Although trait variation can arise due to selection, the importance of neutral processes is sometimes understudied. We presented the first reference-quality genome of the Red Diamond Rattlesnake (Crotalus ruber) and used range-wide 'omic data to estimate the degree to which neutral and adaptive evolutionary processes shaped venom evolution. We characterized population structure and found substantial genetic differentiation across two populations, each with distinct demographic histories. We identified significant differentiation in venom expression across age classes with substantially reduced but discernible differentiation across populations. We then used conditional redundancy analysis to test whether venom expression variation was best predicted by neutral divergence patterns or geographically variable (a)biotic factors. Snake size was the most significant predictor of venom variation, with environment, prey availability, and neutral sequence variation also identified as significant factors, though to a lesser degree. By directly including neutrality in the model, our results confidently highlight the predominant, yet not singular, role of life history in shaping venom evolution. [ABSTRACT FROM AUTHOR]

Published
2024
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35. Recent Uses of Paper Microfluidics in Isothermal Nucleic Acid Amplification Tests

Author

Jocelyn Reynolds, Reid S. Loeffler, Preston J. Leigh, Hannah A. Lopez, and Jeong-Yeol Yoon

Subjects
recombinase polymerase amplification, loop-mediated isothermal amplification, rolling circle amplification, lateral flow immunochromatographic assay, microfluidic paper-based analytic device, Biotechnology, TP248.13-248.65
Abstract

Isothermal nucleic acid amplification tests have recently gained popularity over polymerase chain reaction (PCR), as they only require a constant temperature and significantly simplify nucleic acid amplification. Recently, numerous attempts have been made to incorporate paper microfluidics into these isothermal amplification tests. Paper microfluidics (including lateral flow strips) have been used to extract nucleic acids, amplify the target gene, and detect amplified products, all toward automating the process. We investigated the literature from 2020 to the present, i.e., since the onset of the COVID-19 pandemic, during which a significant surge in isothermal amplification tests has been observed. Paper microfluidic detection has been used extensively for recombinase polymerase amplification (RPA) and its related methods, along with loop-mediated isothermal amplification (LAMP) and rolling circle amplification (RCA). Detection was conducted primarily with colorimetric and fluorometric methods, although a few publications demonstrated flow distance- and surface-enhanced Raman spectroscopic (SERS)-based detection. A good number of publications could be found that demonstrated both amplification and detection on paper microfluidic platforms. A small number of publications could be found that showed extraction or all three procedures (i.e., fully integrated systems) on paper microfluidic platforms, necessitating the need for future work.

Published
2023
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36. Experimental Evolution of Escherichia coli K-12 at High pH and with RpoS Induction

Author

Hamdallah, Issam, Torok, Nadia, Bischof, Katarina M, Majdalani, Nadim, Chadalavada, Sriya, Mdluli, Nonto, Creamer, Kaitlin E, Clark, Michelle, Holdener, Chase, Basting, Preston J, Gottesman, Susan, and Slonczewski, Joan L

Subjects
Microbiology, Biological Sciences, Genetics, Bacterial Proteins, Biological Evolution, Culture Media, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Hydrogen-Ion Concentration, Sigma Factor, Transcription Factors, evolution, high pH, PhoB, RpoS, Medical microbiology
Abstract

Experimental evolution of Escherichia coli K-12 W3110 by serial dilutions for 2,200 generations at high pH extended the range of sustained growth from pH 9.0 to pH 9.3. pH 9.3-adapted isolates showed mutations in DNA-binding regulators and envelope proteins. One population showed an IS1 knockout of phoB (encoding the positive regulator of the phosphate regulon). A phoB::kanR knockout increased growth at high pH. phoB mutants are known to increase production of fermentation acids, which could enhance fitness at high pH. Mutations in pcnB [poly(A) polymerase] also increased growth at high pH. Three out of four populations showed deletions of torI, an inhibitor of TorR, which activates expression of torCAD (trimethylamine N-oxide respiration) at high pH. All populations showed point mutations affecting the stationary-phase sigma factor RpoS, either in the coding gene or in genes for regulators of RpoS expression. RpoS is required for survival at extremely high pH. In our microplate assay, rpoS deletion slightly decreased growth at pH 9.1. RpoS protein accumulated faster at pH 9 than at pH 7. The RpoS accumulation at high pH required the presence of one or more antiadaptors that block degradation (IraM, IraD, and IraP). Other genes with mutations after high-pH evolution encode regulators, such as those encoded by yobG (mgrB) (PhoPQ regulator), rpoN (nitrogen starvation sigma factor), malI, and purR, as well as envelope proteins, such as those encoded by ompT and yahO Overall, E. coli evolution at high pH selects for mutations in key transcriptional regulators, including phoB and the stationary-phase sigma factor RpoS.IMPORTANCEEscherichia coli in its native habitat encounters high-pH stress such as that of pancreatic secretions. Experimental evolution over 2,000 generations showed selection for mutations in regulatory factors, such as deletion of the phosphate regulator PhoB and mutations that alter the function of the global stress regulator RpoS. RpoS is induced at high pH via multiple mechanisms.

Published
2018

37. Capacity of the 45 and Up Study to mobilise evidence-based improvements in cancer control: lung cancer case study

Author

Marianne F Weber, Preston J Ngo, Emily Banks, Julia Steinberg, David E Goldsbury, Paul Grogan, and Karen Canfell

Subjects
Public aspects of medicine, RA1-1270
Abstract

Objective: Over the 15 years since the 45 and Up Study (the Study) was established, researchers have harnessed its capacity for enabling rigorous, comprehensive investigation of cancer causes, care, and outcomes. For the first time in Australia, the entire cancer-control continuum could be investigated by linking questionnaire data with cancer registry notifications, hospital records, outpatient medical services and prescription medications at scale. Here, we use lung cancer as a case study to demonstrate the Study’s potential to improve cancer control. Method: Narrative description. Results: Between 2006–2013, approximately 1200 participants in the Study cohort who had no prior history of cancer were diagnosed with lung cancer, allowing the generation of novel, policy- and practice-relevant evidence for tobacco control, screening, and systems of care. The Study produced evidence on the continuing impact of smoking, including that ‘light smoking’ (1–5 cigarettes/day) is associated with nine times the risk of lung cancer compared to never-smoking; and that 54% of lung cancers could be avoided long-term if all Australians who smoked were to quit. The Study was used to validate a lung cancer screening risk prediction tool, correctly identifying 70% of the participants with a history of smoking who developed lung cancer within a 6-year period as ‘high-risk’. Potential inequities in lung cancer care were identified using the Study cohort, including suboptimal levels of radiotherapy utilisation, below benchmark levels of systemic therapy for patients with metastatic disease, and high numbers of emergency department presentations prior to diagnosis. Participants with lung cancer reported poorer quality of life than those with almost any other cancer type, and about 50% reported severe physical functioning limitations. The Study also provided the infrastructure for the first comprehensive report on lung cancer health system costs. Lessons learnt: As a statewide, population-based cohort, the Study provides reliable estimates of cancer risk, health services utilisation, and person-centred outcomes that can inform policy and practice decision making; and has provided the backbone for localising policy-relevant insights from international experience. We have found that the direct involvement of clinicians and policy makers in research design, and engagement with community networks, can yield tractable, policy-relevant, and ultimately impactful scientific insights.

Published
2022
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42. How Naive Is Contentful Moral Perception?

Author

Preston J. Werner

Subjects
moral perception, representationalism, naive realism, normative authority, Logic, BC1-199, Philosophy (General), B1-5802
Abstract

According to contentful moral perception (CMP), moral properties can be perceived in the same sense as tables, tigers, and tomatoes. Recently, Heather Logue (2012) has distinguished between two potential ways of perceiving a property. A Kantian Property (KP) in perception is one in which a perceiver’s access involves a detection of the property via a representational vehicle. A Berkeleyan Property (BP) in perception is one in which a perceiver’s access to the property involves that property as partly constitutive of the experience itself. In this paper, I set aside generalized arguments in favor of one view or another, and instead ask whether proponents of CMP have reasons to understand moral perception as Kantian or Berkeleyan. I explore three possible explanatory differences—(a) explaining the intrinsic motivating force of moral perceptions, (b) providing a metasemantics for moral properties, and (c) providing an epistemology of the normative authority of moral properties.

Published
2023
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44. Acid Evolution of Escherichia coli K-12 Eliminates Amino Acid Decarboxylases and Reregulates Catabolism

Author

He, Amanda, Penix, Stephanie R, Basting, Preston J, Griffith, Jessie M, Creamer, Kaitlin E, Camperchioli, Dominic, Clark, Michelle W, Gonzales, Alexandra S, Erazo, Jorge Sebastian Chávez, George, Nadja S, Bhagwat, Arvind A, and Slonczewski, Joan L

Subjects
Microbiology, Biological Sciences, Biomedical and Clinical Sciences, Genetics, 2.2 Factors relating to the physical environment, Aetiology, Acids, Aromatic-L-Amino-Acid Decarboxylases, Biological Evolution, Escherichia coli K12, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Hydrogen-Ion Concentration, acid, Escherichia coli, experimental evolution, GABA, low pH, RNA polymerase, decarboxylase, fnr, Medical microbiology
Abstract

Acid-adapted strains of Escherichia coli K-12 W3110 were obtained by serial culture in medium buffered at pH 4.6 (M. M. Harden, A. He, K. Creamer, M. W. Clark, I. Hamdallah, K. A. Martinez, R. L. Kresslein, S. P. Bush, and J. L. Slonczewski, Appl Environ Microbiol 81:1932-1941, 2015, https://doi.org/10.1128/AEM.03494-14). Revised genomic analysis of these strains revealed insertion sequence (IS)-driven insertions and deletions that knocked out regulators CadC (acid induction of lysine decarboxylase), GadX (acid induction of glutamate decarboxylase), and FNR (anaerobic regulator). Each acid-evolved strain showed loss of one or more amino acid decarboxylase systems, which normally help neutralize external acid (pH 5 to 6) and increase survival in extreme acid (pH 2). Strains from populations B11, H9, and F11 had an IS5 insertion or IS-mediated deletion in cadC, while population B11 had a point mutation affecting the arginine activator adiY The cadC and adiY mutants failed to neutralize acid in the presence of exogenous lysine or arginine. In strain B11-1, reversion of an rpoC (RNA polymerase) mutation partly restored arginine-dependent neutralization. All eight strains showed deletion or downregulation of the Gad acid fitness island. Strains with the Gad deletion lost the ability to produce GABA (gamma-aminobutyric acid) and failed to survive extreme acid. Transcriptome sequencing (RNA-seq) of strain B11-1 showed upregulated genes for catabolism of diverse substrates but downregulated acid stress genes (the biofilm regulator ariR, yhiM, and Gad). Other strains showed downregulation of H2 consumption mediated by hydrogenases (hya and hyb) which release acid. Strains F9-2 and F9-3 had a deletion of fnr and showed downregulation of FNR-dependent genes (dmsABC, frdABCD, hybABO, nikABCDE, and nrfAC). Overall, strains that had evolved in buffered acid showed loss or downregulation of systems that neutralize unbuffered acid and showed altered regulation of catabolism.IMPORTANCE Experimental evolution of an enteric bacterium under a narrow buffered range of acid pH leads to loss of genes that enhance fitness above or below the buffered pH range, including loss of enzymes that may raise external pH in the absence of buffer. Prominent modes of evolutionary change involve IS-mediated insertions and deletions that knock out key regulators. Over generations of acid stress, catabolism undergoes reregulation in ways that differ for each evolving strain.

Published
2017

45. Benzoate- and Salicylate-Tolerant Strains of Escherichia coli K-12 Lose Antibiotic Resistance during Laboratory Evolution

Author

Creamer, Kaitlin E, Ditmars, Frederick S, Basting, Preston J, Kunka, Karina S, Hamdallah, Issam N, Bush, Sean P, Scott, Zachary, He, Amanda, Penix, Stephanie R, Gonzales, Alexandra S, Eder, Elizabeth K, Camperchioli, Dominic W, Berndt, Adama, Clark, Michelle W, Rouhier, Kerry A, and Slonczewski, Joan L

Subjects
Microbiology, Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Biodefense, Antimicrobial Resistance, Human Genome, Vaccine Related, Genetics, Emerging Infectious Diseases, Prevention, Infection, Anti-Bacterial Agents, Anti-Inflammatory Agents, Non-Steroidal, Benzoates, Biological Evolution, Dose-Response Relationship, Drug, Drug Resistance, Microbial, Escherichia coli K12, Food Preservatives, Gene Expression Regulation, Bacterial, Salicylates, acid, aspirin, benzoate, chloramphenicol, Escherichia coli, experimental evolution, salicylate, antibiotic resistance, low pH, Medical microbiology
Abstract

Escherichia coli K-12 W3110 grows in the presence of membrane-permeant organic acids that can depress cytoplasmic pH and accumulate in the cytoplasm. We conducted experimental evolution by daily diluting cultures in increasing concentrations of benzoic acid (up to 20 mM) buffered at external pH 6.5, a pH at which permeant acids concentrate in the cytoplasm. By 2,000 generations, clones isolated from evolving populations showed increasing tolerance to benzoate but were sensitive to chloramphenicol and tetracycline. Sixteen clones grew to stationary phase in 20 mM benzoate, whereas the ancestral strain W3110 peaked and declined. Similar growth occurred in 10 mM salicylate. Benzoate-evolved strains grew like W3110 in the absence of benzoate, in media buffered at pH 4.8, pH 7.0, or pH 9.0, or in 20 mM acetate or sorbate at pH 6.5. Genomes of 16 strains revealed over 100 mutations, including single-nucleotide polymorphisms (SNPs), large deletions, and insertion knockouts. Most strains acquired deletions in the benzoate-induced multiple antibiotic resistance (Mar) regulon or in associated regulators such as rob and cpxA, as well as the multidrug resistance (MDR) efflux pumps emrA, emrY, and mdtA Strains also lost or downregulated the Gad acid fitness regulon. In 5 mM benzoate or in 2 mM salicylate (2-hydroxybenzoate), most strains showed increased sensitivity to the antibiotics chloramphenicol and tetracycline; some strains were more sensitive than a marA knockout strain. Thus, our benzoate-evolved strains may reveal additional unknown drug resistance components. Benzoate or salicylate selection pressure may cause general loss of MDR genes and regulators. Benzoate is a common food preservative, and salicylate is the primary active metabolite of aspirin. In the gut microbiome, genetic adaptation to salicylate may involve loss or downregulation of inducible multidrug resistance systems. This discovery implies that aspirin therapy may modulate the human gut microbiome to favor salicylate tolerance at the expense of drug resistance. Similar aspirin-associated loss of drug resistance might occur in bacterial pathogens found in arterial plaques.

Published
2017

47. Coronal Heating as Determined by the Solar Flare Frequency Distribution Obtained by Aggregating Case Studies

Author

James Paul Mason, Alexandra Werth, Colin G. West, Allison Youngblood, Donald L. Woodraska, Courtney L. Peck, Arvind J. Aradhya, Yijian Cai, David Chaparro, James W. Erikson, Koushik Ganesan, T. R. Geerdts, Thi D Hoang, Thomas M. Horning, Yan Jin, Haixin Liu, Noah Lordi, Zheng Luo, Thanmay S. Menon, Josephine C. Meyer, Emma E Nelson, Kristin A. Oliver, Jorge L Ramirez Ortiz, Andrew Osborne, Alyx Patterson, Nick Pellatz, John Pitten, Nanako Shitara, Daniel Steckhahn, Aseem Visal, Hongda Wang, Chaoran Wang, Evan Wickenden, John Wilson, Mengyu Wu, Nikolay Yegovtsev, Ingrid H Zimmermann, James Holland Aaron, Jumana T. Abdullah, Jonathan M. Abrams, Riley Abrashoff, Andres B. Acevedo, Iker Acha, Daniela M. Meza Acosta, Megan M. Adam, Dante Q. Adams, Kalvyn N Adams, Elena R Adams, Zainab A. Akbar, Ushmi H. Akruwala, Adel Al-Ghazwi, Batool H. Alabbas, Areej A. Alawadhi, Yazeed A. Alharbi, Mohammed S. Alahmed, Mohammed A. Albakr, Yusef J. Albalushi, Jonathan Albaum, Ahmed Aldhamen, Nolan Ales, Mohammad Alesmail, Abdulelah Alhabeeb, Dania Alhamli, Isehaq Alhuseini, Suhail Alkaabi, Tameem Alkhezzi, Mohamed Alkubaisi, Nasser Allanqawi, Martin Allsbrook, Yousef A. Almohsen, Justin Thomas Almquist, Teeb Alnaji, Yousef A Alnasrallah, Nicholas Alonzi, Meshal Alosaimi, Emeen Alqabani, Mohammad Alrubaie, Reema A. Alsinan, Ava L. Altenbern, Abdullah Altokhais, Saleh A. Alyami, Federico Ameijenda, Hamzi Amer, Meggan Amos, Hunter J. Anderson, Carter Andrew, Jesse C Andringa, Abigail Angwin, Gabreece Van Anne, Andrew Aramians, Camila Villamil Arango, Jack. W. Archibald, Brian A. Arias-Robles, Maryam Aryan, Kevin Ash, Justin Astalos, N. S. Atchley-Rivers, Dakota N. Augenstein, Bryce W. Austin, Abhinav Avula, Matthew C. Aycock, Abdulrahman A. Baflah, Sahana Balaji, Brian Balajonda, Leo M Balcer, James O. Baldwin, David J Banda, Titus Bard, Abby Barmore, Grant M. Barnes, Logan D. W. Barnhart, Kevin M. Barone, Jessica L. Bartman, Claire Bassel, Catalina S Bastias, Batchimeg Bat-Ulzii, Jasleen Batra, Lexi Battist, Joshua Bay, Simone Beach, Sara Beard, Quinn I Beato, Ryan Beattie, Thomas Beatty, Tristan De La Beaujardiere, Jacob N. Beauprez, M. G. Beck, Lily Beck, Simone E. Becker, Braden Behr, Timothy A. Behrer, Joshua Beijer, Brennan J. Belei, Annelene L. Belknap, Aislyn Bell, Caden Bence, Evan Benke, Naomi Berhanu, Zachary D. Berriman-Rozen, Chrisanna Bertuccio, Owen A. Berv, Blaine B. Biediger, Samuel J Biehle, Brennen Billig, Jacob Billingsley, Jayce A. Billman, Connor J. Biron, Gabrielle E. Bisacca, Cassidy A. Blake, Guillermo Blandon, Olivia Blevins, Ethan Blouin, Michal Bodzianowski, Taylor A. Boeyink, Matthew Bondar, Lauren Bone, Alberto Espinosa De Los Monteros Bonilla, William T Borelli, Luke R. Borgerding, Troy Bowen, Christine Boyer, Aidan Boyer, Aidan P. Boyle, Tom Boyne, Donovan Branch, Ariana E. Brecl, David J. Brennan, Alexander J Brimhall, Jennifer L. Brockman, Sarah Brookins, Gabriel T. Brown, Cameron L. Brown, Ryan Brown, Jordi Brownlow, Grant Brumage-Heller, Preston J. Brumley, Samuel Bryan, A. Brzostowicz, Maryam Buhamad, Gigi Bullard-Connor, J. R. Ramirez Bunsow, Annemarie C. Burns, John J. Burritt, Nicholas David Burton, Taylor Burton, Celeste Busch, Dylan R. Butler, B. W. Buxton, Malena C. Toups, Carter C. Cabbage, Breonna Cage, Jackson R. Cahn, Andrew J Campbell, Braden P. Canales, Alejandro R. Cancio, Luke Carey, Emma L. Carillion, Michael Andrew Carpender, Emily Carpenter, Shivank Chadda, Paige Chambers, Jasey Chanders, Olivia M. Chandler, Ethan C. Chang, Mitchell G. Chapman, Logan T. Chapman, S. Chavali, Luis Chavez, Kevin Chen, Lily Chen, Sam Chen, Judy Chen, Jenisha Chhetri, Bradyn Chiles, Kayla M. Chizmar, Katherine E Christiansen, Nicholas A. Cisne, Alexis Cisneros, David B. Clark, Evelyn Clarke, Peter C Clarkson, Alexis R. Clausi, Brooke Cochran, Ryan W. Coe, Aislinn Coleman-Plante, Jake R. Colleran, Zachary Colleran, Curran Collier, Nathaniel A. Collins, Sarah Collins, Jack C. Collins, Michael Colozzi, Aurora Colter, Rebecca A. Cone, Thomas C. Conroy, Reese Conti, Charles J. Contizano, Destiny J. Cool, Nicholas M. Cooper, Jessica S Corbitt, Jonas Courtney, Olivia Courtney, Corben L. Cox, Wilmsen B. Craig, Joshua B. Creany, Anastasia Crews, K. A. Crocker, A. J. Croteau, Christian J. Crow, Zoe Cruse, Avril Cruz, Tyler L. Curnow, Hayden Current, Riley T. Curry, Libby Cutler, Aidan St. Cyr, Frederick M. Dabberdt, Johnston Daboub, Olivia Damgaard, Swagatam Das, Emma A. B. Davis, Elyse Debarros, Sean Deel, Megan E. Delasantos, Tianyue Deng, Zachary Derwin, Om Desai, Kai Dewey, John S. Dias, Kenzie A. Dice, R. Dick, Cyrus A. Dicken, Henry Dietrick, Alexis M. Dinser, Alyssa M. Dixon, Thomas J. Dixon, Helen C. Do, Chris H Doan, Connor Doane, Joshua Dodrill, Timothy Doermer, Lizbeth Montoya Dominguez, J. Dominguez, Emerson N. Domke, Caroline R. Doran, Jackson A. Dorr, Philip Dorricott, Danielle C. Dresdner, Michael Driscoll, Kailer H. Driscoll, Sheridan J. Duncan, Christian Dunlap, Gabrielle M. Dunn, Tien Q. Duong, Tomi Oshima Dupeyron, Peter Dvorak, Andrew East, Andrew N. East, Bree Edwards, Lauren Ehrlich, Sara I. Elbashir, Rasce Engelhardt, Jacob Engelstad, Colin England, Andrew Enrich, Abbey Erickson, Benjamin Erickson, Nathan Evans, Calvin A Ewing, Elizabeth A. Eyeson, Ian Faber, Avery M. Fails, John T Fauntleroy, Kevin Fell, Zitian Feng, Logan D. Fenwick, Nikita Feoktistov, Ryann Fife, John Alfred D. Figueirinhas, Jean-Paul Fisch, Emmalee Fischer, Jules Fischer-White, Aidan F. Fitton, Alexander Fix, Lydia Flackett, Fernando Flores, Aidan Floyd, Leonardo Del Foco, Adeduni Folarin, Aidan E. Forbes, Elise Fortino, Benjamin L. Fougere, Alexandra A. Fowler, Margaret Fox, James M. French, Katherine V. French, Florian G. Frick, Calvin R. Fuchs, Bethany E. S. Fuhrman, Sebastian Furney, Moutamen Gabir, Gabriela Galarraga, Skylar Gale, Keala C. Gapin, A. J. Garscadden, Rachel Gasser, Lily Gayou, Emily E. Gearhart, Jane Geisman, Julianne R. Geneser, Sl Genne, Julia G Gentile, Eleanor Gentry, Jacob D. George, Nathaniel James Georgiades, Phillip Gerhardstein, Clint Gersabeck, Bandar Abu Ghaith, Dorsa Ghiassi, B. C. Giebner, Dalton Gilmartin, Connor B. Gilpatrick, Michael Gjini, Olivia Golden, Nathan T. Golding, C. A. Goldsberry, Angel R. Gomez, Angel A. Gomez, Sean Gopalakrishnan, Mariam Gopalani, Nicholas Gotlib, Alaina S. Graham, Michael J Gray, Alannah H. Gregory, Joshua A. Gregory, Kristyn Grell, Justus Griego, Nicholas F. Griffin, Kyle J. Griffin, Matt Guerrero, Nicole Gunderson, Mutian Guo, E. R. Gustavsson, Grace K. Hach, L. N. Haile, Jessica Haines, Jack J. Mc Hale, Ryder Buchanan Hales, Mark S. Haley, Jacqueline L. Hall, Sean R. Hamilton, Soonhee Han, Tyler Hand, Luke C. Hanley, Connor M Hansen, Joshua A. Hansen, Jonathan Hansson, Tony Yunfei Hao, Nicholas Haratsaris, Isabelle Hardie, Dillon F. Hardwick, Cameron T. Hares, Logan Swous Harris, Coyle M. Harris, Omer Hart, Kyle Hashiro, Elsie Hattendorf, Calder Haubrich, Elijah Hawat, Griffin A. Hayrynen, Danielle A. Heintz, Tim Hellweg, Angel Hernandez, Emanuel Herrera, Robert N. Herrington, Tim Herwig, Troy M. Hesse, Quinn Hiatt, Lea Pearl Hibbard, Imari R. Hicks, Andrew J. Hicks, Nigel Highhouse, Annalise K. Hildebrand, Paula Hill, Hallie Hill, Evan Hintsa, Anna E. Hirschmann, Travis Hitt, Ella Ho, Isabelle J. Hoff, Alex Hoffman, Blake A. Hogen, Linda Horne, Timothy J Houck, Noah H. Howell, E. M. Hrudka, J. Hu, Jianyang Huang, Chenqi Huang, Shancheng Huang, Zachary A. Hudson, Nathan C. Hudson, Tyler J. Huebsch, Owen Hull, Samuel C Hunter, Troy Husted, Abigail P. Hutabarat, Leslie Huynh, Antonio E. Samour Ii, Yolande Idoine, Julia A. Ingram, Taro Iovan, Samuel A. Isert, Antonio Salcido-Alcontar, Thomas Jacobsen, Alan A Jaimes, Connor Jameson, J. R. Jarriel, Sam Jarvis, Josh Jenkins, Alexander V. Jensen, Jacob Jeong, Luke A. Jeseritz, Trevor Jesse, Soo Yeun Ji, Yufan Jiang, Owen Johnson, Matthew Johnson, Sawyer Johnson, Julia Johnston, Braedon Y. Johnston, Olivia M. Jones, M. R. Jones, Tara Jourabchi, Tony A. House, Parker Juels, Sabrina J. H. T. Kainz, Emily Kaiser, Nicolas Ian Kallemeyn, Madison H. Kalmus, Etash Kalra, Margaret Kamenetskiy, Jeerakit Kanokthippayakun, Shaun D. Kapla, Brennan J. Karsh, Caden J. Keating, Morgan A. Kelley, Michael P. Kelley, Nicholas Kelly, James Kelly, Teagan Kelly, Christopher M Kelly, Kellen Kennedy, Cayla J. Kennedy, Forrest Kennedy, Abigail Kennedy, Liana Kerr-Layton, Marilyn Ketterer, Ibraheem A. Khan, Usman Khan, Sapriya Khanal, Jack L. Kiechlin, Dominic Killian, Kevin Kim, Brian T. Kim, Matthew M. Kim, Jake Kim, Aspen Kimlicko, Isabel M Kipp, Hunter B. Kirkpatrick, Natalie Kissner, Emily R. Kite, Olivia R. Kleinhaus, Philip Whiting Knott, Will Koch, Greta Koenig, Emily Koke, Thomas Kokes, Yash S. Kothamdi, Zack Krajnak, Zoe M. Kresek, Dylan Kriegman, Jake E. Kritzberg, Davis J. Krueger, Bartlomiej Kubiak, Kirsten Kuehl, Chrisanne Kuester, Nicolas A. Kuiper, Aman Priyadarshi Kumar, Connor Kuybus, Daniel Kwiatkowski, Quintin Y. Lafemina, Kevin Lacjak, Kyle Lahmers, Antonia Lam, Kalin Landrey, Maxwell B. Lantz, Zachary Larter, Benjamin P. Lau, Megan Lauzon, Rian Lawlor, Tyler Learned, E. C. Lee, Junwon Lee, Adrianna J. Lee, Justin Lee, Alexis Ying-Shan Lee, Christian J Lee, Nathaniel F. Lee, Linzhi Leiker, Dylan Lengerich, Cecilia Leoni, Adrienne R. Lezak, David Y. Li, Isaac Li, Ryan Z. Liao, Bridget Linders, Morgan I Linger, Katherine B. Linnane, Sam Lippincott, Barrett Lister, Shelby D Litton, Nianzi Liu, Steven Y. Liu, Timothy W. Logan, Nathan Londres, Mia C. Lonergan, Emily Lookhoff, N. E. Loomis, Christian Lopez, Justin Loring, Jeffrey Lucca, Dax Lukianow, Nathan M. Cheang, William Macdonald, Claire A. Madonna, Kasey O. Madsen, Tiffany E. Maksimuk, Macguire Mallory, Ryan A. Malone, Blake Maly, Xander R. Manzanares, Aimee S. Maravi, Serafima M. Marcus, Nasreen Marikar, Josie A. Marquez, Mathew J. Marquez, Lauren Marsh, Toni Marsh, Logan S. Martin, Alexa M. Martinez, Jose R. Martinez, Hazelia K. Martinez, Cara Martyr, Mirna Masri, Giorgio Matessi, Adam Izz Khan Mohd Reduan Mathavan, Randi M. Mathieson, Kabir P. Mathur, Graham Mauer, Victoria A. Mayer, Liam Mazzotta, Glen S. Mccammon, Rowan Mcconvey, Tyler Mccormick, Andrew Mccoy, Kelleen Mcentee, Meaghan V. Mcgarvey, Riley M. Mcgill, James K. Mcintyre, Finbar K. Mckemey, Zane Mcmorris, Jesse J. Mcmullan, Ella Mcquaid, Caden Mcvey, Kyle Mccurry, Mateo M. Medellin, Melissa Medialdea, Amar Mehidic, Stella Meillon, Jonah B. Meiselman-Ashen, Sarah Mellett, Dominic Menassa, Citlali Mendez, Patricia Mendoza-Anselmi, Riley Menke, Sarah Mesgina, William J. Mewhirter, Ethan Meyer, Aya M. Miften, Ethan J. Miles, Andrew Miller, Joshua B. Miller, Emily B. Millican, Sarah J. Millican, Dylan P. Mills, Josh Minimo, Jay H. Misener, Alexander J. Mitchell, Alexander Z. Mizzi, Luis Molina-Saenz, Tyler S Moll, Hayden Moll, Maximus Montano, Michael Montoya, Eli Monyek, Jacqueline Rodriguez Mora, Gavin Morales, Genaro Morales, Annalise M. Morelock, Cora Morency, Angel J. Moreno, Remy Morgan, Alexander P. Moss, Brandon A. Muckenthaler, Alexander Mueller, Owen T. Mulcahy, Aria T. Mundy, Alexis A. Muniz, Maxwell J. Murphy, Madalyn C. Murphy, Ryan C. Murphy, Tyler Murrel, Andrew J. Musgrave, Michael S. Myer, Kshmya Nandu, Elena R. Napoletano, Abdulaziz Naqi, Anoothi Narayan, Liebe Nasser, Brenna K Neeland, Molly Nehring, Maya Li Nelson, Lena P. Nguyen, Lena Nguyen, Leonardo Nguyen, Valerie A. Nguyen, Khoa D Nguyen, Kelso Norden, Cooper Norris, Dario Nunes-Valdes, Rosemary O. Nussbaum, Cian O’Sullivan, Ian O’Neill, S. H. Oakes, Anand Odbayar, Caleb Ogle, Sean Oishi-Holder, Nicholas Olguin, Nathaniel P. Olson, Jason Ong, Elena N. Opp, Dan Orbidan, Ryan Oros, Althea E. Ort, Matthew Osborn, Austin Osogwin, Grant Otto, Jessica Oudakker, Igor Overchuk, Hannah M. Padgette, Jacqueline Padilla, Mallory Palizzi, Madeleine L. Palmgren, Adler Palos, Luke J. Pan, Nathan L. Parker, Sasha R. Parker, Evan J. Parkinson, Anish Parulekar, Paige J. Pastor, Kajal Patel, Akhil Patel, Neil S. Patel, Samuel Patti, Catherine Patton, Genevieve K. Payne, Matthew P. Payne, Harrison M. Pearl, Charles B. Beck Von Peccoz, Alexander J. Pedersen, Lily M. Pelster, Munisettha E. Peou, J. S. Perez, Freddy Perez, Anneliese Pesce, Audrey J. Petersen, B. Peterson, Romeo S. L. Petric, Joshua Pettine, Ethan J. Phalen, Alexander V. Pham, Denise M. Phan, Callie C Pherigo, Lance Phillips, Justin Phillips, Krista Phommatha, Alex Pietras, Tawanchai P. Pine, Sedique Pitsuean-Meier, Andrew M. Pixley, Will Plantz, William C. Plummer, Kaitlyn E. Plutt, Audrey E. Plzak, Kyle Pohle, Hyden Polikoff, Matthew Pollard, Madelyn Polly, Trevor J. Porter, David Price, Nicholas K. Price, Gale H. Prinster, Henry Austin Propper, Josh Quarderer, Megan S. Quinn, Oliver Quinonez, Devon Quispe, Cameron Ragsdale, Anna L. Rahn, M. Rakhmonova, Anoush K Ralapanawe, Nidhi Ramachandra, Nathaniel Ramirez, Ariana C. Ramirez, Sacha Ramirez, Parker Randolph, Anurag Ranjan, Frederick C Rankin, Sarah Grace Rapaport, Nicholas O Ratajczyk, Mia G. V. Ray, Brian D. Reagan, John C. Recchia, Brooklyn J. Reddy, Joseph Reed, Charlie Reed, Justin Reeves, Eileen N. Reh, Ferin J. Von Reich, Andrea B. Reyna, Alexander Reynolds, Hope Reynolds, Matthew Rippel, Guillermo A. Rivas, Anna Linnea Rives, Amanda M. Robert, Samuel M. Robertson, Maeve Rodgers, Stewart Rojec, Andres C. Romero, Ryan Rosasco, Beth Rossman, Michael Rotter, Tyndall Rounsefell, Charlotte Rouse, Allie C. Routledge, Marc G. Roy, Zoe A. Roy, Ryan Ruger, Kendall Ruggles-Delgado, Ian C. Rule, Madigan Rumley, Brenton M. Runyon, Collin Ruprecht, Bowman Russell, Sloan Russell, Diana Ryder, David Saeb, J. Salazar, Violeta Salazar, Maxwell Saldi, Jose A. Salgado, Adam D. Salindeho, Ethan S. Sanchez, Gustavo Sanchez-Sanchez, Darian Sarfaraz, Sucheta Sarkar, Ginn A. Sato, Carl Savage, Marcus T. Schaller, Benjamin T. Scheck, Jared A. W. Schlenker, Matthew J Schofer, Stephanie H. Schubert, Courtney Schultze, Grace K Schumacher, Kasper Seglem, Lauren Serio, Octave Seux, Hannan Shahba, Callie D. Shannahan, Shajesh Sharma, Nathan Shaver, Timothy Shaw, Arlee K. Shelby, Emma Shelby, Grace Shelchuk, Tucker Sheldrake, Daniel P. Sherry, Kyle Z. Shi, Amanda M. Shields, Kyungeun Shin, Michael C. Shockley, Dominick Shoha, Jadon Shortman, Mitchell Shuttleworth, Lisa Sibrell, Molly G. Sickler, Nathan Siles, H. K. Silvester, Conor Simmons, Dylan M. Simone, Anna Simone, Savi Singh, Maya A. Singh, Madeline Sinkovic, Leo Sipowicz, Chris Sjoroos, Ryan Slocum, Colin Slyne, Korben Smart, Alexandra N. Smith, Kelly Smith, Corey Smith, Elena K. Smith, Samantha M. Smith, Percy Smith, Trevor J Smith, G. L. Snyder, Daniel A. Soby, Arman S. Sohail, William J. Solorio, Lincoln Solt, Caitlin Soon, Ava A Spangler, Benjamin C. Spicer, Ashish Srivastava, Emily Stamos, Peter Starbuck, Ethan K. Stark, Travis Starling, Caitlyn Staudenmier, Sheen L. Steinbarth, Christopher H. Steinsberger, Tyler Stepaniak, Ellie N. Steward, Trey Stewart, T. C. Stewart, Cooper N. Stratmeyer, Grant L. Stratton, Jordin L. Stribling, S. A Sulaiman, Brandon J Sullivan, M. E. Sundell, Sohan N. Sur, Rohan Suri, Jason R. Swartz, Joshua D. Sweeney, Konner Syed, Emi Szabo, Philip Szeremeta, Michael-Tan D. Ta, Nolan C. Tanguma, Kyle Taulman, Nicole Taylor, Eleanor Taylor, Liam C. Taylor, K. E. Tayman, Yesica Tellez, Richard Terrile, Corey D Tesdahl, Quinn N. Thielmann, Gerig Thoman, Daniel Thomas, Jeffrey J. Thomas, William N. Thompson, Noah R. Thornally, Darien P. Tobin, Kelly Ton, Nathaniel J. Toon, Kevin Tran, Bryn Tran, Maedee Trank-Greene, Emily D. Trautwein, Robert B. Traxler, Judah Tressler, Tyson R. Trofino, Thomas Troisi, Benjamin L. Trunko, Joshua K. Truong, Julia Tucker, Thomas D Umbricht, C. H. Uphoff, Zachary T. Upthegrove, Shreenija Vadayar, Whitney Valencia, Mia M. Vallery, Eleanor Vanetten, John D. Vann, Ilian Varela, Alexandr Vassilyev, Nicholas J. Vaver, Anjali A. Velamala, Evan Vendetti, Nancy Ortiz Venegas, Aditya V. Vepa, Marcus T. Vess, Jenna S. Veta, Andrew Victory, Jessica Vinson, Connor Maklain Vogel, Michaela Wagoner, Steven P. Wallace, Logan Wallace, Caroline Waller, Jiawei Wang, Keenan Warble, N. R. D. Ward-Chene, James Adam Watson, Robert J. Weber, Aidan B. Wegner, Anthony A Weigand, Amanda M. Weiner, Ayana West, Ethan Benjamin Wexler, Nicola H. Wheeler, Jamison R. White, Zachary White, Oliver S. White, Lloyd C. Whittall, Isaac Wilcove, Blake C. Wilkinson, John S. Willard, Abigail K. Williams, Sajan Williams, Orion K. Wilson, Evan M. Wilson, Timothy R. Wilson, Connor B. Wilson, Briahn Witkoff, Aubrey M. Wolfe, Jackson R. Wolle, Travis M. Wood, Aiden L. Woodard, Katelynn Wootten, Catherine Xiao, Jianing Yang, Zhanchao Yang, Trenton J. Young, Isabel Young, Thomas Zenner, Jiaqi Zhang, Tianwei Zhao, Tiannie Zhao, Noah Y. Zhao, Chongrui Zhou, Josh J Ziebold, Lucas J. Ziegler, James C. Zygmunt, Jinhua Zhang, and H. J. Lewandowski

Published
2023
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48. Pandemic Pivots for the Internship Game

Author

Tanner, Preston J.

Abstract

The COVID-19 pandemic dramatically impacted opportunities for internships in parks, recreation, tourism, and sports. The government mandated numerous agencies to close. Many agencies that remained open reduced staff, froze budgets, shifted programs online, and discontinued internships. The senior internship for Parks, Recreation, and Tourism students at the University of Utah is an important capstone experience. The purpose of the senior internship is for students to integrate and apply knowledge, skills, and abilities learned through their undergraduate education. With this purpose in mind, the department made multiple pivots to facilitate meaningful learning opportunities within the community or on behalf of the community. This article will describe the custom learning paths developed for graduating seniors, the communication required to coordinate the adapted plans, and the lessons learned from implementing these changes.

Published
2023
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50. A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts

Author

Matthew Chung, Preston J. Basting, Rayanna S. Patkus, Alexandra Grote, Ashley N. Luck, Elodie Ghedin, Barton E. Slatko, Michelle Michalski, Jeremy M. Foster, Casey M. Bergman, and Julie C. Dunning Hotopp

Subjects
wolbachia, transcriptomics, rna-seq, meta-analysis, intracellular, bacteria, Genetics, QH426-470
Abstract

Wolbachia is a genus containing obligate, intracellular endosymbionts with arthropod and nematode hosts. Numerous studies have identified differentially expressed transcripts in Wolbachia endosymbionts that potentially inform the biological interplay between these endosymbionts and their hosts, albeit with discordant results. Here, we re-analyze previously published Wolbachia RNA-Seq transcriptomics data sets using a single workflow consisting of the most up-to-date algorithms and techniques, with the aim of identifying trends or patterns in the pan-Wolbachia transcriptional response. We find that data from one of the early studies in filarial nematodes did not allow for robust conclusions about Wolbachia differential expression with these methods, suggesting the original interpretations should be reconsidered. Across datasets analyzed with this unified workflow, there is a general lack of global gene regulation with the exception of a weak transcriptional response resulting in the upregulation of ribosomal proteins in early larval stages. This weak response is observed across diverse Wolbachia strains from both nematode and insect hosts suggesting a potential pan-Wolbachia transcriptional response during host development that diverged more than 700 million years ago.

Published
2020
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