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258. The missing hydrogen ion, part-1: Historical precedents vs. fundamental concepts

Author

Robert Robergs, Bridgette O'Malley, Sam Torrens, and Jason Siegler

Subjects
Hydrogen ion, Acid, Acidosis, pH, Equilibrium constant (Keq), Ionization, Medicine (General), R5-920
Abstract

The purpose of this review and commentary was to provide an historical and evidence-based account of organic acids and the biochemical and organic chemistry evidence for why cells do not produce metabolites that are acids. The scientific study of acids has a long history dating to the 16th and 17th centuries, and the definition of an acid was proposed in 1884 as a molecule that when in an aqueous solution releases a hydrogen ion (H+). There are three common ionizable functional groups for molecules classified as acids: 1) the carboxyl group, 2) the phosphoryl group and 3) the amine group. The propensity by which a cation will associate or dissociate with a negatively charged atom is quantified by the equilibrium constant (Keq) of the dissociation constant (Kd) of the ionization (Keq ​= ​Kd), which for lactic acid (HLa) vs. lactate (La-) is expressed as: Keq=Kd=[H+][La−][HLa]= 4 677.351 4 (ionic strength ​= ​0.01 Mol⋅L-1, T ​= ​25 ​°C). The negative log10 of the dissociation pKd reveals the pH at which half of the molecules are ionized, which for HLa ​= ​3.67. Thus, knowing the pKd and the pH of the solution at question will reveal the extent of the ionization vs. acidification of molecules that are classified as acids.

Published
2023
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259. Use of Bayesian Optimization to Understand the Structure of Nuclei

Author

Hooker, J., Kovoor, J., Jones, K. L., Kanungo, R., Alcorta, M., Allen, J., Andreoiu, C., Atar, L., Bardayan, D. W., Bhattacharjee, S. S., Blankstein, D., Burbadge, C., Burcher, S., Catford, W. N., Cha, S., Chae, K., Connolly, D., Davids, B., Esker, N., Garcia, F. H., Gillespie, S., Ghimire, R., Gula, A., Hackman, G., Hallam, S., Hellmich, M., Henderson, J., Holl, M., Jassal, P., King, S., Knight, T., Kruecken, R., Lepailleur, A., Liang, J., Morrison, L., O'Malley, P. D., Pain, S. D., Pereira-Lopez, X., Psaltis, A., Radich, A., Shotter, A. C., Vostinar, M., Williams, M., and Workman, O.

Subjects
Physics - Computational Physics, Nuclear Experiment
Abstract

Monte Carlo simulations are widely used in nuclear physics to model experimental systems. In cases where there are significant unknown quantities, such as energies of states, an iterative process of simulating and fitting is often required to describe experimental data. We describe a Bayesian approach to fitting experimental data, designed for data from a $^{12}$Be(d,p) reaction measurement, using simulations made with GEANT4. Q-values from the $^{12}$C(d,p) reaction to well-known states in $^{13}$C are compared with simulations using BayesOpt. The energies of the states were not included in the simulation to reproduce the situation for $^{13}$Be where the states are poorly known. Both cases had low statistics and significant resolution broadening owing to large proton energy losses in the solid deuterium target. Excitation energies of the lowest three excited states in $^{13}$C were extracted to better than 90 keV, paving a way for extracting information on $^{13}$Be., Comment: 8 pages, 6 figures

Published
2021
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260. Factors Associated With Coronary Angiography Performed Within 6 Months of Randomization to the Conservative Strategy in the ISCHEMIA Trial

Author

Pracoń, Radosław, Spertus, John A., Broderick, Samuel, Bangalore, Sripal, Rockhold, Frank W., Ruzyllo, Witold, Demchenko, Elena, Nageh, Thuraia, Grossman, Gabriel Blacher, Mavromatis, Kreton, Manjunath, Cholenahally N., Smanio, Paola E.P., Stone, Gregg W., Mancini, G.B. John, Boden, William E., Newman, Jonathan D., Reynolds, Harmony R., Hochman, Judith S., Maron, David J., Doan, John, Linefsky, Jason, Lee, Raven, Patel, Risha, Miller, Todd, Yang Cho, So, Milbrandt, Susan, Shelstad, Dawn, Banerjee, Subhash, Kamath, Preeti, Tejani, Ishita, Cobos, Stanley E., Quiles, Kirsten J., Dwyer, Raven R., Donnino, Robert M., Espinosa, Dalisa, Phillips, Lawrence M., Saric, Muhamed, Abdul-Nour, Khaled, Schley, Allison, Golden, Heather, Stone, Peter H., Osseni, Hermine, Wiyarand, Charlene, Douglass, Peter, Pomeroy, Hayley, Craft, Alexandra, Harvey, Bethany, Jang, James J., Anaya, Olivia, Yee, Gennie, Goold, Phoebe, Weitz, Steven, Giovannone, Steven, Pritchard, Lori, Arnold, Suzanne, Gans, Rosann, Henry O’Keefe, Jr, James, Kennedy, Paul, Shapiro, Michael D., Ganesan, Shobana, Schlichting, David, Naher, Aynun, El-Hajjar, Mohammad, Sidhu, Mandeep S., Fein, Steven A., Stewart, Wendy L., Torosoff, Mikhail T., Salmi, Kristin M., Lyubarova, Radmila, Mookherjee, Sulagna, Drzymalski, Krzysztof, McFalls, Edward O., Garcia, Santiago A., Bertog, Stefan C., Johnson, Debra K., Siddiqui, Rizwan A., Herrmann, Rebekah R., Ishani, Areef, Hansen, Ronnell A., Georges Khouri, Michel, Arges, Kristine, LeFevre, Melissa, Tomfohr, Jennifer, Goldberg, Jonathan L., Ann Byrne, Kimberly, Zappernick, Taissa, Goldweit, Richard, Canada, Sallie, Kakade, Meghana, Mieses, Patricia, Cobos, Stanley E., Dwyer, Raven R., Cohen, Ronny A., Espinosa, Dalisa, Mirrer, Brooks, Quiles, Kirsten J., Navarro, Victor, Rantinella, Magdalena, Rodriguez, Jessica, Mancilla, Olivia, Winchester, David E., Stinson, Susan, Kronenberg, Marvin, Weyand, Terry, Rogal, Philip, Crook, Sherron C., McFarren, Christopher, Heitner, John F., Ho, Jean, Khan, Saadat, Mohamed, Mahmoud, Dauber, Ira M., Soltau, Mary R., Rose, Delsa K., Wimmer, Rebecca J., Siegel, Kathy E., Derbyshire, Susan, Cannan, Charles, Dixon, Michelle, Leonard, Gerald, Sudarshan, Sriram, Heard, Ciarra, Gabriel, Viviana, Desire, Sukie, Mehta, Puja K., McDaniel, Michael, Rashid, Fauzia, Lerakis, Stamatios, Asier, Senait, Quyyumi, Arshed, Patel, Keyur, Wenger, Nanette K., Hedgepeth, Chester M., Gillis, Jennifer, Hurlburt, Heather, Manocchia, Megan, Rosen, Alan, Moore, Susan, Congdon, Elizabeth, Sahul, Zakir, Brandt, Gail, Marchelletta, Nora, Wippler, Kristina, Booth, David, Taul, Yvonne, Leung, Steve, Isaacs, Jennifer, Abdel-Latif, Ahmed, Bulkley, Viktoria, Reda, Hassan, Rodgers, Caroline, Ziada, Khaled, Setty, Sampoornima, Halverson, Kimberly E., Roraff, Christine, Thorsen, Jonean, Barua, Rajat S., Ojajuni, Amarachi, Olurinde, Oni, Surineni, Kamalakar, Hage, Fadi, Valaiyapathi, Badhma, Caldeira, Christiano, Davies, James E., Leesar, Massoud, Heo, Jaekyeong, Iskandrian, Amy, Al Solaiman, Firas, Singh, Satinder, Dajani, Khaled, Kartje, Carol M., El-Hajjar, Mohammad, Mesropian, Paul Der, Sacco, Joseph, Rawlins, Michele, McCandless, Brian, Thomson, Jennifer, Orgera, Marisa, Sidhu, Mandeep S., Colleen Rogge, Mary, Arif, Imran, Bunke, Julie, Kerr, Hanan, Unterbrink, Kendra, Fannon, Jacqueline, Burman, Cynthia, Trejo, Jorge F., Dubin, Marcia F., Fletcher, Gerald, Lane, Gary E., Neeson, Lynn M., Parikh, Pragnesh P., Pollak, Peter M., Shapiro, Brian P., Landolfo, Kevin, Gemignani, Anthony, Beaudry, Sarah, O’Rourke, Daniel, Meadows, Judith L., Tirado, Stephanie A., Halliday, Janet, Julian, Pamela, Call, Jason T., Lane, Stephanie M., Stanford, Jennifer L., Hannan, Joseph, Bojar, Robert, Arsenault, Patricia, Kumar, Deepti, Sigel, Pamela, Mukai, John, Martin, Edward T., Brooks, Miriam, Vorobiof, Gabriel, Douangvila, Ladda, Gevorgyan, Rubine, Moorman, Alec, Ranjbaran, Fatima, Smith, Bryn, Ohmart, Carly, Kinlay, Scott, Hamburger, Robert J., Rocco, Thomas P., Ly, Samantha, Bhatt, Deepak L., Quinn, Margot C., Croce, Kevin, Temiyasathit, Sara, Quin, Jacquelyn A, Do, Jacquelyn, Anumpa, Jati, Tobin, Desiree, Zenati, Marco, Faxon, David P, Rayos, Glenn, Langdon, Jennifer, Werner Bayer, Marcia, Seedhom, Ashraf, O’Malley, Amanda, Sullenberger, Lance, Orvis, Erin, Kumkumian, Gregory, Murphy, Mandy, Greenberg, Ann, Iraola, Margaret, Sedlis, Steven P., Maranan, Leandro C., Donnino, Robert M., Lorin, Jeffrey, Tamis-Holland, Jacqueline E., Malinay, Ammy, Kornberg, Robert, Leber, Robert, Saba, Souheil, Edillo, Candice P., Lee, Michael W., Small, Delano R., Nona, Wassim, Alexander, Patrick B., Rehman, Iram, Badami, Umesh, Ostrander, Ann, Wasmiller, Stephanie, Marzo, Kevin, Drewes, Wendy, Patel, Dipti, Robbins, Inga H., Levite, Howard A., White, Jackie M, Shetty, Sanjay, Hallam, Alison, Patel, Mayuri, Hamroff, Glenn S., Spooner, Benjamin J, Hollenweger, Linda M, Little, Raymond W., Little, Holly, Zimbelman, Brandi D., Little, Tiffany, Lui, Charles Y., Eskelson, Nona A, Smith, Brigham R., Vezina, Daniel P., Khor, Lillian L., Abraham, Josephine D., Bull, David A., McKellar, Stephen H., Booth, David, Taul, Yvonne, Kotter, John, Rodgers, Caroline, Abdel-Latif, Ahmed, Isaacs, Jennifer, Bulkley, Viktoria, Hu, Bob, Kaneshiro, Renee, Labovitz, Arthur J., Berlowitz, Michael, Kirby, Bonnie J., Rogal, Philip, Tran, Nhi N., McFarren, Christopher, Jahrsdorfer, Catherine, Matar, Fadi, Caldeira, Christiano, Rodriguez, Fatima, Yunis, Reem, Schnittger, Ingela, Patro, Jhina, Fearon, William F., Deedwania, Prakash, Vega, Antonia, Reddy, Kiran, Sweeny, Joseph, Bloise-Adames, Hugo, Jimenez, Santa, Saint Vrestil, Nicole, Bhandari, Reyna, Spizzieri, Christopher, Schade, Danielle, Yost, Roxanne, Hochberg, Claudia P, Beardsley, Paula, Fine, Denise, Salerno, William D., Tancredi, Jana, Arakelian, Patricia, Mathus, Susan, O’Neill, Deborah, Wyman, Ray, Burkhardt, Joy, Hosino, Suellen, Lubyanaya, Oksana A., Salas, Jose D., Zarka, Amer, Aguirre, Maria, Shah, Anil V., Dhawan, Manu, Parra, Diana, Tran, Tri, Haldis, Thomas, Weick, Catherine, Fowler-Lehman, Katie, Spitzer, Natalie, Riedberger, Casey, Weick, Catherine, Kohn, Jeffrey A., Cobos, Stanley E., Dwyer, Raven R., Espinosa, Dalisa, Quiles, Kirsten J., Girotra, Saket, Drum, Carrie, Miller-Cox, Kimberly, Ollinger, Amy, Almousalli, Omar, Capasso-Gulve, Elizabeth, Melanie Loehr, Alaine, Mosley, Marlowe, Krishnam, Mayil S., Heydari, Shirin, Milliken, Jeffrey C., Lundeen, Andrea M., Patel, Pranav M., Karanjah, Edgar, Seto, Arnold H., Marfori, Wanda C., Harley, Kevin T., Hernandez-Rangel, Eduardo, Gibson, Michael A., Singh, Pam, Allen, Byron J., Coram, Rita, Marie Webb, Anne, Fridell, Ellie, Wilson, Heidi, Thomas, Sabu, Kim, Angela, Schwartz, Ronald G, Wilmot, Patrick, Chen, Wei, El Shahawy, Mahfouz, Stevens, Ramona, Stafford, James, Black, Loriane, Abernethy, William B., Hull, Amber B., Lim, Olivia J., Tucker, Helen C., Putnam, Natasha C., Hall, Linda L., Cauthren, Tia, Tucker, Trish, Zurick, Andrew, Horton, Hollie, Orga, Jan, Meyer, Thomas M., White, Joyce R., Morford, Ronald G., Baumann, Cynthia, Rutkin, Bruce, Seeratan, Vidya, Bokhari, Sabahat, Jimenez, Magnolia, Sokol, Seth I., Schultz, Cidney, Meisner, Jay, Russo, Jeanne, Hamzeh, Ihab, Misra, Arunima, Huda, Zohra, Wall, Matthew, Boan, Araceli, Lenges De Rosen, Veronica, Alam, Mahboob, Turner, Michael C., Hinton, Christine R, Mulhearn, Thomas J., Good, Arnold P., Archer, Beth A., Dionne, Julia S., Allardyce, Cheryl A., Sikora, Lindsey N., Czerniak, Jennifer H., Mull, Jennifer A., Ferguson, Elizabeth, Laube, Frances, Shammas, Nicolas W., Shammas, Gail A, Christensen, Lori, Park, Holly, Chilton, Robert, Hecht, Joan, Nguyen, Patricia K., Vo, Davis, Hirsch, James, Jezior, Matthew, Bindeman, Jody, Salkind, Sara, Espinosa, Dalisa, Desimone, Lori-Ann, Gordon, Paul C., Felix-Stern, Lina, Crain, Thomas, Gomes, Jassira, Gordon, Catherine, Stenberg, Robert, Mann, Aimee, McCreary, Theresa, Pedalino, Ronald P., Cobos, Stanley E., Dwyer, Raven R., Espinosa, Dalisa, Quiles, Kirsten J., Wiesel, Joseph, Cobos, Stanley E., Dwyer, Raven R., Espinosa, Dalisa, Quiles, Kirsten J., Juang, George J., Gopaul, Candace, Hultberg, Karen, Huk, Tauqir, Hussain, Afshan, Al-Amoodi, Mohammed, Zambrano, Yesenia, Medina Rodriguez, Sarah, Milner, Trudie, Wohns, David, Mulder, Abbey, Van Oosterhout, Stacie, Lader, Ellis W., Meyer, Martha, Mumma, Michael, Clapp, Nancy L., Barrentine, Heather, Dharmarajan, Lekshmi, Jose, Jenne M., Cobos, Stanley E., Dwyer, Raven R., Espinosa, Dalisa, Quiles, Kirsten J., Manchery, Jenne, McGarvey Jr, Joseph F.X., McKinney, Vera, Schwarz, Linda, Downes, Thomas R., Kaczkowski, Scott M., Luckasen, Gary J., Jaskowiak, Adam J., Klitch, Joel, Cheong, Benjamin, Dees, Debra, Potluri, Srinivasa, Vasquez, Precilia, Mastouri, Ronald A., Breall, Jeffery A., Hannemann, Elise L., Revtyak, George E., Mae Foltz, Judy, Bazeley, Jonathan W., Li, Dayuan, DeRosa, Emily, Jorgenson, Beth, Riestenberg-Smith, Joyce, Giedd, Kenneth, Old, Wayne, Bariciano, Rebecca, Burt, Francis, Sokhon, Kozhaya, Waldron, Jessica, Mayon, Michelle, Gopal, Deepika, Valeti, Uma S., Ann Peichel, Gretchen, Kobashigawa, Jon, Starks, Brandy, Garcia, Lucilla, Thottam, Maria, Bhargava, Balram, Anand, Anjali, Chakanalil Govindan, Sajeev, Raj, Janitha, Gopalan Nair, Rajesh, Ravindran, Reshma, Rajalekshmi, VS, Nataraj, Nandita, Moorthy, Nagaraja, Nayak, Soundarya, Mylarappa, Mahevamma, Narayanappa, Suryaprakash, Pandit, Neeraj, Bajaj, Sheromani, Kumar Nath, Ranjit, Yadav, Vandana, Mishra, Girish, Dwivedi, S.K., Tewari, Roma, Narain, V.S., Mishra, Meenakshi, Chandra, Sharad, Patel, Shivali, Singh, Suman, Wander, Gurpreet S., Tandon, Rohit, Ralhan, Sarju, Kaur, Baljeet, Aslam, Naved, Gupta, Sonika, Goyal, Abhishek, Bhargava, Balram, Suvarna, Chandini, Karthikeyan, G., Ramakrishnan, S., Seth, Sandeep, Yadav, Rakesh, Singh, Sandeep, Roy, Ambuj, Parakh, Neeraj, Kumar Verma, Sunil, Narang, Rajiv, Mishra, Sundeep, Naik, Nitish, Sharma, Gautam, Kumar Choudhary, Shiv, Patel, Chetan, Gulati, Gurpreet, Sharma, Sanjeev, Bahl, V K, Mathew, Anoop, Mannekkattukudy Kurian, Binoy, Punnoose, Eapen, Avdhoot Gadkari, Milind, Rupesh Karwa, Sheetal, Gadage, Siddharth, Kolhe, Suvarna, Umesh Pillay, Tapan, Satheesh, Santhosh, Vindhya, R. J., Jain, Peeyush, Seth, Ashok, Singh Meharwal, Zile, Mathur, Atul, Verma, Atul, Kaul, Upendra, Bhatia, Mona, Sachdeva, Ankush, Indira Devi, Thounaojam, Jungla, Nungshi, Christopher, Johann, Manjula Rani, K., Menon, Rajeev, Sowjanya Reddy, M., Kumar, Nirmal, Preethi, K., Oomman, Abraham, sidh, Rinu R, Mao, Robert, Ramakrishnan, T., Solomon, Hilda, Francis, Rajesh, Naik, Sudhir, Vamshi, Priya P., Parveen Khan, Sajeeda, Christopher, Johann, Preethi, Kotiboinna, Kumar, Nirmal, Grant, Purvez, Hande, Shweta, Sonawane, Poonam, Kachru, Ranjan, Dubey, Abhishek, Rawat, Kavita, Kumar, Ajit, Ganapathi, Sanjay, K, Jayakumar, CP, Vineeth, Sivadasanpillai, Harikrishnan, Chacko, Manas, Sasidharan, Bijulal, Babu, Suresh, TR, Kapilamoorthy, Christopher, Johann, Reddy, Sowjanya, Polamuri, Praneeth, Rani, Manjula, Kaul, Upendra, Arambam, Priyadarshani, Singh, Bebek, Senior, Roxy, Fox, Keith AA, Young, Grace M., Carruthers, Kathryn, Senior, Roxy, Elghamaz, Ahmed, Gurunathan, Sothinathan, Karogiannis, Nikolaos, Young, Grace M., Shah, Benoy N, Kinsey, Christopher, Trimlett, Richard HJ, Kavalakkat, Raisa, Rubens, Michael B, Evans, Jo, Nicol, Edward D, Hassan, Ikraam, Mittal, Tarun K, Hampson, Reinette, Andreas Gamma, Reto, Williams, Sarah, Holland, Kim, Swan, Karen, de Belder, Mark A, Atkinson, Bev, Thambyrajah, Jeet, Kunhunny, Swapna, Davies, John R, Lindsay, Steven J., Atkinson, Craig, Kurian, John, Krannila, Carita, Jamil, Haqeel, Vinod, Manitha, Raheem, Osama, Hoye, Angela, Chaytor, Lisa, Cox, Leanne, Morrow, Julie, Rowe, Kay, Donnelly, Patrick, Kelly, Stephanie, Valecka, Bernardas, Regan, Susan, Turnbull, Dawn, Chauhan, Anoop, Fleming, Catherine, Ghosh, Arijit, Gratrix, Karen, Preston, Stephen, Barr, Craig, Cartwright, Anne, Alfakih, Khaled, Knighton, Abigail, Byrne, Jonathan, Martin, Katherine, Webb, Ian, Henriksen, Peter, Flint, Laura, Harrison, James, OKane, Peter, Lakeman, Nicki, Ljubez, Anja, de Silva, Ramesh, Conway, Dwayne S. G., Wright, Judith, Exley, Donna, Sirker, Alexander A, Andiapen, Mervyn, Richards, Amy J., Hoole, Stephen P, Wong, Lisa, Witherow, Fraser N., Munro, Melanie J., Johnston, Nicola, Harbinson, Mark, McEvoy, Michelle, Walsh, Simon, Brown, Caroline, Douglas, Hanna, Luckie, Matthew, Charles, Thabitha, Kolakaluri, Laurel, Phillips, Hannah, Sobolewska, Jolanta, Morby, Louise, Hallett, Karen, Corbett, Carolyn, Winstanley, Lynne, Jeetley, Paramjit, Smit, Angelique, Patel, Niket, Kotecha, Tushar, Travill, Christopher, Gent, Susan, Karimullah, Iqbal, Hussain, Nafisa, Al-Bustami, Mahmud, Braganza, Denise, Haines, Fiona, Taaffe, Joanne, Henderson, Robert, Burton, Jane, Pointon, Kate, Colton, Maria, Naik, Surendra, King, Rachel, Mathew, Thomas, Brown, Ammani, Docherty, Andrew, Berry, Colin, McCloy, Lisa, Collison, Damien, Robb, Kate, Roditi, Giles, Paterson, Craig, Crawford, Wenda, Kelly, Joanne, McGregor, Lorraine, Moriarty, Andrew J, Mackin, Anne, Glover, Jason D., Knight, Janet P, Pradhan, Jiwan, Mikhail, Ghada, Bose, Tuhina, Francis, Darrel P., Dzavik, Vladimir, Goodman, Shaun, Gosselin, Gilbert, Gosselin, Gilbert, Proietti, Anna, Brousseau, Myriam, Corfias, Magalie, Blaise, Patricia, Harvey, Luc, Diaz, Ariel, Rheault, Philippe, Barrero, Miguel, Gagné, Carl-Éric, Alarie, Patricia, Pépin-Dubois, Yanek, Arcand, Linda, Costa, Ricardo, Roy, Isabelle, Tung Sia, Ying, Montpetit, Estelle, Lemay, Catherine, Gisbert, Alejandro, Gervais, Pierre, Rheault, Alain, Drouin, Katia, Carl Phaneuf, Denis, Bergeron, Christine, Gosselin, Gilbert, Shelley, Christine, Masson, Christine, Garg, Pallav, Carr, Sandy, Bone, Catherine, Chow, Benjamin J.W., Moga, Ermina, Hessian, Renee C., Kourzenkova, Janetta, Beanlands, Rob S., Walter, Olga, Davies, Richard F., Bainey, Kevin R., Hogg, Norma, Welsh, Suzanne, Cheema, Asim N., Bagai, Akshay, Wald, Ron, Goodman, Shaun, Kushniriuk, Khrystyna, Joseph Graham, John, Hussain, Mohammed, Peterson, Mark, Bello, Olugbenga, Chow, Chi-Ming, Abramson, Beth, Nazir Cheema, Asim, Syed, Ishba, Hussain, Mohammed, Kushniriuk, Khrystyna, Cha, James, Otis, Judy, Otis, Rebecca, Howarth, Andrew G, Seib, Michelle M, Rivest, Sandra M, Sandonato, Rosa, Wong, Graham, Chow, Jackie, Starovoytov, Andrew, Uchida, Naomi, Meadows, Ngaire, Uxa, Amar, Asif, Nadia, Tavares, Suzana, Galiwango, Paul, Bozek, Bev, Kassam, Saleem, Shier, Maria, Mukherjee, Ashok, Larmand, Lori-Ann, Ricci, A. Joseph, Janmohamed, Amir, Hart, Brenda, Lam, Andy, Marucci, Jane, Tai, Sharon, Mehta, Shamir, Brons, Sonya, Beck, Chris, Wong, Glenda, Etherington, Krystal, Arumairajah, Thippeekaa, Udell, Jacob, Aprile, Maria, Karlsson, Sara, Webber, Susan, Généreux, Philippe, Mercure, Chantale, Hameed, Adnan, Aedy, Nancy, Daba, Ledjalem, Farquharson, Fran, Siddiqui, Anam, Carlos Carvalho, Antonio, Lopes, Renato D., Hueb, Whady, Emy Takiuti, Myrthes, Cury Rezende, Paulo, Eustáquio Ribeiro Silva, Expedito, Ciappina Hueb, Alexandre, Pizzol Caetano, Leonardo, Schaan de Quadros, Alexandre, Abdala Karam Kalil, Renato, Peixoto Deiro, Aline, Luiz da Costa Vieira, José, Manica Muller, Alice, Antonieta Pereira de Moraes, Maria, Píccaro de Oliveira, Pedro, Maria Ascoli, Bruna, Bridi, Leonardo, Zottis Poletti, Sílvia, Savaris, Simone, Vitola, João V, Cerci, Rodrigo J, Zier, Sandra S., Farias, Fabio R, Veiga Jr, Vilmar, Fernandes, Miguel M, Antonio Marin-Neto, José, Schmidt, André, de Oliveira Lima Filho, Moysés, Franca da Cunha, Diego, Mendes Oliveira, Ricardo, Reynaldo Abbud Chierice, João, Polanczyk, Carísi A., Rucatti, Guilherme G, Furtado, Mariana V., Igansi, Fernanda, Smidt, Luis F., Haeffner, Mauren P, Carlos Carvalho, Antonio, Almeida, Viviane, Pucci, Gustavo, Sanchez de Souza, Gabriela, Lyra, Flavio, Rabelo Alves Junior, Alvaro, Almeida, Mayana, dos Santos, Viviane, Dracoulakis, Marianna D. A., Oliveira, Natalia S, Lima, Rodolfo G. S. 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2024
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263. Light response of poly(ethylene 2,6-naphthalate) to neutrons

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Hackett, Brennan, deBoer, Richard, Efremenko, Yuri, Febbraro, Michael, Nattress, Jason, Bardayan, Dan, Boomershine, Chevelle, Brandenburg, Kristyn, Dede, Stefania, Derkin, Joseph, Fang, Ruoyu, Fritsch, Adam, Gula, August, György, Gyürky, Hamad, Gulakhshan, Jones-Alberty, Yenuel, Kelmar, Beka, Manukyan, Khachatur, Matney, Miriam, McDonaugh, John, Moylan, Shane, O’Malley, Patrick, Shahina, Shahina, and Singh, Nisha

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2024
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267. Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium

Author

Chaput, Gina, Ford, Jacob, DeDiego, Lani, Narayanan, Achala, Tam, Yin, Whalen, Meghan, Huntemann, Marcel, Clum, Alicia, Spunde, Alex, Pillay, Manoj, Palaniappan, Krishnaveni, Varghese, Neha, Mikhailova, Natalia, Chen, I-Min, Stamatis, Dimitrios, Reddy, TBK, O’Malley, Ronan, Daum, Chris, Shapiro, Nicole, Ivanova, Natalia, Kyrpides, Nikos C, Woyke, Tanja, del Rio, Tijana Glavina, and DeAngelis, Kristen M

Subjects
Microbiology, Biological Sciences, Genetics, Biotechnology, Anaerobiosis, Animals, Bacterial Typing Techniques, DNA, Bacterial, Enterobacteriaceae, Lignin, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Symbiosis, endosymbionts, aromatic metabolism, lignocellulosic biofuel, anaerobic catabolic pathways, aromatic compounds
Abstract

Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and enriched under anoxic conditions with organosolv lignin as the sole carbon source, we successfully isolated a novel bacterium, designated 159R. Based on the 16S rRNA gene, the isolate belongs to the genus Sodalis in the family Bruguierivoracaceae. Whole-genome sequencing revealed a genome size of 6.38 Mbp and a GC content of 55 mol%. To resolve the phylogenetic position of 159R, its phylogeny was reconstructed using (i) 16S rRNA genes of its closest relatives, (ii) multilocus sequence analysis (MLSA) of 100 genes, (iii) 49 clusters of orthologous groups (COG) domains, and (iv) 400 conserved proteins. Isolate 159R was closely related to the deadwood associated Sodalis guild rather than the tsetse fly and other insect endosymbiont guilds. Estimated genome-sequence-based digital DNA-DNA hybridization (dDDH), genome percentage of conserved proteins (POCP), and an alignment analysis between 159R and the Sodalis clade species further supported that isolate 159R was part of the Sodalis genus and a strain of Sodalis ligni. We proposed the name Sodalis ligni str. 159R (=DSM 110549 = ATCC TSD-177). IMPORTANCE Currently, in the paper industry, paper mill pulping relies on unsustainable and costly processes to remove lignin from lignocellulosic material. A greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. Anaerobic bacteria are a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable by-products. We presented Sodalis ligni str. 159R and its characteristics as another example of potential mechanisms that can be developed for lignocellulosic applications.

Published
2022

268. Thousands of small, novel genes predicted in global phage genomes

Author

Fremin, Brayon J, Bhatt, Ami S, Kyrpides, Nikos C, Consortium, Global Phage Small Open Reading Frame, Sengupta, Aditi, Sczyrba, Alexander, da Silva, Aline Maria, Buchan, Alison, Gaudin, Amelie, Brune, Andreas, Hirsch, Ann M, Neumann, Anthony, Shade, Ashley, Visel, Axel, Campbell, Barbara, Baker, Brett, Hedlund, Brian P, Crump, Byron C, Currie, Cameron, Kelly, Charlene, Craft, Chris, Hazard, Christina, Francis, Christopher, Schadt, Christopher W, Averill, Colin, Mobilian, Courtney, Buckley, Dan, Hunt, Dana, Noguera, Daniel, Beck, David, Valentine, David L, Walsh, David, Sumner, Dawn, Lymperopoulou, Despoina, Bhaya, Devaki, Bryant, Donald A, Morrison, Elise, Brodie, Eoin, Young, Erica, Lilleskov, Erik, Högfors-Rönnholm, Eva, Chen, Feng, Stewart, Frank, Nicol, Graeme W, Teeling, Hanno, Beller, Harry R, Dionisi, Hebe, Liao, Hui-Ling, Beman, J Michael, Stegen, James, Tiedje, James, Jansson, Janet, VanderGheynst, Jean, Norton, Jeanette, Dangl, Jeff, Blanchard, Jeffrey, Bowen, Jennifer, Macalady, Jennifer, Pett-Ridge, Jennifer, Rich, Jeremy, Payet, Jérôme P, Gladden, John D, Raff, Jonathan D, Klassen, Jonathan L, Tarn, Jonathan, Neufeld, Josh, Gravuer, Kelly, Hofmockel, Kirsten, Chen, Ko-Hsuan, Konstantinidis, Konstantinos, DeAngelis, Kristen M, Partida-Martinez, Laila P, Meredith, Laura, Chistoserdova, Ludmila, Moran, Mary Ann, Scarborough, Matthew, Schrenk, Matthew, Sullivan, Matthew, David, Maude, O'Malley, Michelle A, Medina, Monica, Habteselassie, Mussie, Ward, Nicholas D, Pietrasiak, Nicole, Mason, Olivia U, Sorensen, Patrick O, de los Santos, Paulina Estrada, Baldrian, Petr, McKay, R Michael, Simister, Rachel, Stepanauskas, Ramunas, Neumann, Rebecca, Malmstrom, Rex, Cavicchioli, Ricardo, Kelly, Robert, Hatzenpichler, Roland, Stocker, Roman, Cattolico, Rose Ann, Ziels, Ryan, and Vilgalys, Rytas

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 2.1 Biological and endogenous factors, Generic health relevance, Bacteriophages, Genome, Viral, Genomics, Microbiota, Phylogeny, Global Phage Small Open Reading Frame (GP-SmORF) Consortium, CP: Microbiology, MetaRibo-Seq, comparative genomics, gene families, microbiome, phage, sORFs, small genes, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

Small genes (40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

Published
2022

269. Blind Optimism and Student Loan Debt

Author

Thomas C. O’Malley and Brian C. Payne

Abstract

This paper analyses potential links between extreme optimism and student loan debt. Prior work finds extreme optimism to be associated with imprudent household savings and investment decisions. This paper explores whether these findings are relevant to student loan decisions. Using the most recent administration of the Survey of Consumer Finances (SCF), we present evidence that extreme optimists tend to be over-indebted with higher student loan balances, in absolute terms and relative to income. They are less likely to make payments on their student loan debt or reduce their loan balance. Extreme optimists are also more likely to take out loans for a degree they do not obtain and to enroll in income-based repayment plans. [This paper was presented virtually on September 27, 2022 at the 2022 Academy of Financial Services (AFS) Annual Meeting.]

Published
2023

270. 'It's Our Own Community Where We Can Educate Other People and Educate Each Other': Youth Perspectives on Staffing a Textline

Author

O'Malley, Teagen L. and Horowitz, Katie Rose

Abstract

Peer education is a valued strategy for sexuality education and health promotion. Innovative approaches beyond traditional classroom settings offer critical opportunities to support adolescent sexual health. Yet, such models have been rarely used. "It's OK to Ask Someone (IOTAS)" is the first to use customized software to enable youth to both ask and answer sexual health questions using cell phones. This article describes an evaluation aimed to understand high school peer educators' experience staffing "IOTAS" and perception of how participation impacted their peer education training. Our findings suggest a value in direct peer education opportunities for participants through "IOTAS" in expanded education and skill development. The health promotion impact of sexuality education using cell phone interventions could be far-reaching for both peer education students and young people outside program participation.

Published
2023
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271. Challenges and Lessons Learned Conducting a Formative Evaluation of a Multicomponent Care Delivery Intervention

Author

Keith, Rosalind E., Heitkamp, Shannon, Little, Jasmine, Peebles, Victoria, Sarwar, Rumin, Petersen, Dana M., and O'Malley, Ann S.

Abstract

Formative evaluation provides stakeholders with timely feedback to support an intervention's improvement during implementation to maximize its effectiveness. We describe the qualitative methods that guided one study within a formative evaluation of a multicomponent care delivery intervention. We then describe the challenges and lessons learned that emerged from this study, organizing them by the study's four overarching challenges: (1) addressing multiple research questions, (2) working with a large interdisciplinary team, (3) triangulating qualitative results with quantitative results, and (4) studying implementation in real-world delivery settings. Overall, the evaluation generated important findings to support improvement of the intervention during implementation. We hope that sharing the lessons learned will increase the rigor and efficiency with which formative evaluations of complex care delivery interventions are conducted and the likelihood that they will improve implementation in real time. We also hope the lessons learned will enhance the satisfaction of the researchers working on these evaluations.

Published
2023
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272. Monitoring the Future National Survey Results on Drug Use, 1975-2019. Volume II, College Students & Adults Ages 19-60

Author

University of Michigan, Institute for Social Research, Schulenberg, John E., Johnston, Lloyd D., O'Malley, Patrick M., Bachman, Jerald G., Miech, Richard A., and Patrick, Megan E.

Abstract

The present volume presents new 2019 findings from the U.S. national Monitoring the Future (MTF) follow-up study concerning substance use among the nation's college students and adults from ages 19 through 60. This report includes 2019 prevalence estimates on numerous illicit and licit substances, examines how substance use differs across this age span, and shows how substance use and related behaviors and attitudes have changed over the past four decades. MTF, now in its 46th year, is a research program conducted at the University of Michigan's Institute for Social Research under a series of investigator-initiated, competing research grants from the National Institute on Drug Abuse -- one of the National Institutes of Health. The integrated MTF study comprises several ongoing series of annual surveys of nationally representative samples of 8th and 10th grade students (begun in 1991), 12th grade students (begun in 1975), and high school graduates followed into adulthood (begun in 1976). Note that the data reported in this volume were collected before the COVID-19 pandemic. The authors report the results of the repeated cross-sectional surveys of all high school graduating classes since 1976 and follow them into their adult years. Segments of the general adult population represented in these follow-up surveys include: (1) U.S. college students; (2) same-aged youth who also are graduates from high school but not attending college full time, sometimes in the past called the "forgotten half"; (3) all young adult high school graduates of modal ages 19 to 30 (or 19-28 for trend estimates), to whom we refer as the "young adult" sample; and (4) high school graduates at the specific later modal ages of 35, 40, 45, 50, 55, and 60. This volume emphasizes historical and developmental changes in substance use and related attitudes and beliefs occurring at these age strata. [For "Monitoring the Future National Survey Results on Drug Use, 1975-2019. Volume I, Secondary School Students," see ED608265. For the report from the previous year, see ED599071.]

Published
2020

273. Monitoring the Future National Survey Results on Drug Use, 1975-2019. Volume I, Secondary School Students

Author

University of Michigan, Institute for Social Research, Miech, Richard A., Johnston, Lloyd D., O'Malley, Patrick M., Bachman, Jerald G., Schulenberg, John E., and Patrick, Megan E.

Abstract

Substance use is a leading cause of preventable morbidity and mortality; it is in large part why, among 17 high-income nations, people in the U.S. have the highest probability of dying by age 50. Substance use is also an important contributor to many social ills including child and spousal abuse, violence more generally, theft, suicide, and more; and it typically is initiated during adolescence. It warrants our sustained attention. Monitoring the Future (MTF) is designed to give such attention to substance use among the nation's youth and adults. It is an investigator-initiated study that originated with, and is conducted by, a team of research professors at the University of Michigan's Institute for Social Research. Since its onset in 1975, MTF has been funded continuously by the National Institute on Drug Abuse -- one of the National Institutes of Health -- under a series of peer-reviewed, competitive research grants. The 2019 survey, reported here, is the 45th consecutive survey of 12th grade students and the 29th such survey of 8th and 10th graders. Two of the major topics included in the present volume are: (1) the prevalence and frequency of use of a great many substances, both licit and illicit, among U.S. secondary school students in 8th , 10th, and 12th grades; and (2) historical trends in use by students in those grades. Distinctions are made among important demographic subgroups in these populations based on gender, college plans, region of the country, population density, parent education, and race/ethnicity. MTF has demonstrated that key attitudes and beliefs about drug use are important determinants of usage trends, in particular the amount of risk to the user perceived to be associated with the various drugs and disapproval of using them; thus, those measures also are tracked over time, as are students' perceptions of certain relevant aspects of the social environment--in particular, perceived availability, peer norms, use by friends, and exposure to use by others of the various drugs. Data on grade of first use, discontinuation of use, trends in use in lower grades, and intensity of use are also reported here. [For "Monitoring the Future National Survey Results on Drug Use, 1975-2019. Volume II, College Students & Adults Ages 19-60," see ED608266. For the report from the previous year, see ED599067.]

Published
2020

274. PhotoVoice: An Innovative Qualitative Method in Research and Classroom Teaching

Author

O'Malley, Lori J. and Munsell, Sonya E.

Abstract

The purpose of this workshop was to inform participants of the multiple uses of a qualitative research method called Photovoice. Both presenters have utilized this method extensively in their own academic research, in their research methods courses, and in their nonresearch related courses. In this method, participants are provided with a series of questions (or topics) and asked to take photographs that capture their responses to these questions/topics. Once these photographs have been taken, participants meet with researchers/instructors to discuss the photographs in a semi-structured or focus group format. Photovoice allows participants to take an active role in research and allows their perspectives to be visually displayed for enhanced discussion.

Published
2020

275. Demographic Subgroup Trends among Adolescents in the Use of Various Licit and Illicit Drugs, 1975-2019. Monitoring the Future Occasional Paper Series. Paper 94

Author

University of Michigan, Institute for Social Research, Johnston, Lloyd D., Miech, Richard A., O'Malley, Patrick M., Bachman, Jerald G., Schulenberg, John E., and Patrick, Megan E.

Abstract

This occasional paper presents national demographic subgroup data for the 1975-2019 Monitoring the Future (MTF) national survey results on 8th, 10th, and 12th graders' use of drugs, alcohol, and tobacco. The 2018 subgroup data presented in this report accompany the "Monitoring the Future National Survey Results on Drug Use: 1975-2019: Overview, Key Findings on Adolescent Drug Use" (see ED604018) and the "Monitoring the Future National Survey Results on Drug Use, 1975-2018: Volume I, Secondary School Students" (see ED599067). The trends presented in this occasional paper in tabular and graphic forms cover demographic subgroups based on: (1) Gender; (2) College plans; (3) Region of the country; (4) Population density; (5) Education level of the parents (a proxy for socioeconomic level); and (6) Racial/ethnic identification. Detailed descriptions of the demographic categories are provided. The graphs and tables in this occasional paper present trend data for 8th-, 10th-, and 12th-grade respondents separately. Data for 12th grade begins with 1975, the first year in which a nationally representative sample of high school seniors was surveyed. Data for 8th and 10th grades begin with 1991, when the study's nationally representative annual surveys were expanded to include those lower grade levels.

Published
2020

276. Demographic Subgroup Trends among Young Adults in the Use of Various Licit and Illicit Drugs, 1988-2019. Monitoring the Future Occasional Paper Series. Paper 95

Author

University of Michigan, Institute for Social Research, Johnston, Lloyd D., Schulenberg, John E., O'Malley, Patrick M., Bachman, Jerald G., Miech, Richard A., and Patrick, Megan E.

Abstract

This occasional paper presents subgroup findings from the Monitoring the Future (MTF) study on levels of, and trends in, the use of a number of substances for nationally representative samples of high school graduates ages 19-30, "Monitoring the Future National Survey Results on Drug Use, 1975-2018. Volume II, College Students & Adults Ages 19-60" (see ED599071). The data have been gathered in a series of follow-up surveys of representative subsamples of high school seniors who were first surveyed in 12th grade as part of the MTF study. The subgroup trends shown in this occasional paper complement the last section of Chapter 5 (Trends in Drug Use in Early and Middle Adulthood) of that monograph by presenting the trend data for young adult subgroups in both graphic and tabular form. The results are described and discussed in Chapter 5, but the extensive set of tables and figures is provided in this occasional paper for the reader who wishes to view the figures and the underlying numerical values. Three demographic dimensions are differentiated: gender, region of the country, and population density. Gender includes trends for males and females; region describes trends for each of the four major regions defined by the U.S. Census; and population density differentiates trends for five levels of community size. The Table of Contents and List of Figures in this occasional paper contain links to the content and figures. Following each figure is a table giving the numerical values associated with each trend line in that figure.

Published
2020

277. Monitoring the Future National Survey Results on Drug Use, 1975-2019: Overview, Key Findings on Adolescent Drug Use

Author

University of Michigan, Institute for Social Research, Johnston, Lloyd D., Miech, Richard A., O'Malley, Patrick M., Bachman, Jerald G., Schulenberg, John E., and Patrick, Megan E.

Abstract

Monitoring the Future (MTF) is a long-term study of substance use and related factors among U.S. adolescents, college students, and adult high school graduates through age 60. It is conducted annually and supported by the National Institute on Drug Abuse. MTF findings identify emerging substance use problems, track substance use trends, and inform national policy and intervention strategies. The key findings regarding use of various substances by 8th, 10th, and 12th graders surveyed across the coterminous U.S. in 2019 are summarized. [For "Monitoring the Future National Survey Results on Drug Use, 1975-2018: Overview, Key Findings on Adolescent Drug Use," see ED594190.]

Published
2020

278. Monitoring the Future National Survey Results: HIV/AIDS Risk & Protective Behaviors among Adults Ages 21 to 30 in the U.S., 2004-2019

Author

University of Michigan, Institute for Social Research, Johnston, Lloyd D., O'Malley, Patrick M., Bachman, Jerald G., Schulenberg, John E., Patrick, Megan E., and Miech, Richard A.

Abstract

Monitoring the Future (MTF) is a long-term study of American adolescents, college students, and adult high school graduates through age 60. The study is funded under a series of investigator-initiated, competing research grants from the National Institute on Drug Abuse and has been conducted annually by the University of Michigan's Institute for Social Research since 1975. The present monograph focuses on a range of behaviors, including certain forms of substance use, related to the spread of the human immunodeficiency virus (HIV), which is responsible for acquired immunodeficiency syndrome (AIDS). The ages covered in this study contain the two age bands with the highest rates of newly diagnosed HIV infection in the United States: namely, ages 20-24 and 25-29. High school graduates who fall into this age range each year have been surveyed annually since 2004. The present volume is the fourth monograph in the MTF series of annual reports. [For the first three monographs, see ED604018 (Overview of Key Findings), ED608265 (Volume 1), and ED608266 (Volume 2). For "Monitoring the Future National Survey Results: HIV/AIDS Risk & Protective Behaviors among Adults Ages 21 to 30 in the U.S., 2004-2018," see ED611901.]

Published
2020

279. Coping with COVID

Author

Munsell, Sonya E., O'Malley, Lori, and Mackey, Christi

Abstract

The recent COVID-19 pandemic has brought with it an unprecedented amount of change to the daily lives of individuals around the world. Stay at home/safer at home measures have drastically limited individuals' face to face contact. College students have had to quickly adapt to new modes of instruction, including various forms of distance learning. Many colleges have yet to make final decisions regarding how instruction will be delivered in the coming semester. The uncertainty COVID-19 brings in regard to daily living and higher education pursuits may lead to a variety of negative outcomes for college students, including increased stress and anxiety and decreased academic performance. The current research examines how undergraduate students attending a small college in the Southwestern United States are coping with the pandemic compared to the general adult population. 289 participants completed survey items related to coping, hope, and personality. Results reveal that college students employ significantly more maladaptive coping strategies than the general population in response to the stress surrounding the pandemic. Additionally, they have significantly lower levels of hope and possess lower levels of conscientiousness, emotional engagement, and openness to new experiences. The results of this study have important implications for higher education institutions, who should take these findings into consideration as they make plans for the coming academic year.

Published
2020

281. Yeats and Lu Xun: Postcolonised Modernists?

Author

O’Malley-Sutton, Simone, Chao, Shun-liang, Series Editor, Clark, Steve, Series Editor, Connolly, Tristanne, Series Editor, Watson, Alex, Series Editor, Williams, Laurence, Series Editor, and O’Malley-Sutton, Simone

Published
2023
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292. Continuous conditional generative adversarial networks for data-driven solutions of poroelasticity with heterogeneous material properties

Author

Kadeethum, T., O'Malley, D., Choi, Y., Viswanathan, H. S., Bouklas, N., and Yoon, H.

Subjects
Computer Science - Computational Engineering, Finance, and Science, Mathematics - Numerical Analysis
Abstract

Machine learning-based data-driven modeling can allow computationally efficient time-dependent solutions of PDEs, such as those that describe subsurface multiphysical problems. In this work, our previous approach of conditional generative adversarial networks (cGAN) developed for the solution of steady-state problems involving highly heterogeneous material properties is extended to time-dependent problems by adopting the concept of continuous cGAN (CcGAN). The CcGAN that can condition continuous variables is developed to incorporate the time domain through either element-wise addition or conditional batch normalization. We note that this approach can accommodate other continuous variables (e.g., Young's modulus) similar to the time domain, which makes this framework highly flexible and extendable. Moreover, this framework can handle training data that contain different timestamps and then predict timestamps that do not exist in the training data. As a numerical example, the transient response of the coupled poroelastic process is studied in two different permeability fields: Zinn \& Harvey transformation and a bimodal transformation. The proposed CcGAN uses heterogeneous permeability fields as input parameters while pressure and displacement fields over time are model output. Our results show that the model provides sufficient accuracy with computational speed-up. This robust framework will enable us to perform real-time reservoir management and robust uncertainty quantification in realistic problems.

Published
2021
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293. A Conformer-based ASR Frontend for Joint Acoustic Echo Cancellation, Speech Enhancement and Speech Separation

Author

O'Malley, Tom, Narayanan, Arun, Wang, Quan, Park, Alex, Walker, James, and Howard, Nathan

Subjects
Electrical Engineering and Systems Science - Audio and Speech Processing, Computer Science - Sound
Abstract

We present a frontend for improving robustness of automatic speech recognition (ASR), that jointly implements three modules within a single model: acoustic echo cancellation, speech enhancement, and speech separation. This is achieved by using a contextual enhancement neural network that can optionally make use of different types of side inputs: (1) a reference signal of the playback audio, which is necessary for echo cancellation; (2) a noise context, which is useful for speech enhancement; and (3) an embedding vector representing the voice characteristic of the target speaker of interest, which is not only critical in speech separation, but also helpful for echo cancellation and speech enhancement. We present detailed evaluations to show that the joint model performs almost as well as the task-specific models, and significantly reduces word error rate in noisy conditions even when using a large-scale state-of-the-art ASR model. Compared to the noisy baseline, the joint model reduces the word error rate in low signal-to-noise ratio conditions by at least 71% on our echo cancellation dataset, 10% on our noisy dataset, and 26% on our multi-speaker dataset. Compared to task-specific models, the joint model performs within 10% on our echo cancellation dataset, 2% on the noisy dataset, and 3% on the multi-speaker dataset., Comment: Will appear in IEEE-ASRU 2021

Published
2021

294. Cross-attention conformer for context modeling in speech enhancement for ASR

Author

Narayanan, Arun, Chiu, Chung-Cheng, O'Malley, Tom, Wang, Quan, and He, Yanzhang

Subjects
Electrical Engineering and Systems Science - Audio and Speech Processing, Computer Science - Sound
Abstract

This work introduces \emph{cross-attention conformer}, an attention-based architecture for context modeling in speech enhancement. Given that the context information can often be sequential, and of different length as the audio that is to be enhanced, we make use of cross-attention to summarize and merge contextual information with input features. Building upon the recently proposed conformer model that uses self attention layers as building blocks, the proposed cross-attention conformer can be used to build deep contextual models. As a concrete example, we show how noise context, i.e., short noise-only audio segment preceding an utterance, can be used to build a speech enhancement feature frontend using cross-attention conformer layers for improving noise robustness of automatic speech recognition., Comment: Will appear in IEEE-ASRU 2021

Published
2021

295. First Measurement of the $B(E2; 3/2^- \rightarrow 1/2^-)$ Transition Strength in $^7$Be: Testing Ab Initio Predictions for $A=7$ Nuclei

Author

Henderson, S. L., Ahn, T., Caprio, M. A., Fasano, P. J., Simon, A., Tan, W., O'Malley, P., Allen, J., Bardayan, D. W., Blankstein, D., Frentz, B., Hall, M. R., Kolata, J. J., McCoy, A. E., Moylan, S., Reingold, C. S., Strauss, S. Y., and Torres-Isea, R. O.

Subjects
Nuclear Experiment, Nuclear Theory
Abstract

Electromagnetic observables are able to give insight into collective and emergent features in nuclei, including nuclear clustering. These observables also provide strong constraints for ab initio theory, but comparison of these observables between theory and experiment can be difficult due to the lack of convergence for relevant calculated values, such as $E2$ transition strengths. By comparing the ratios of $E2$ transition strengths for mirror transitions, we find that a wide range of ab initio calculations give robust and consistent predictions for this ratio. To experimentally test the validity of these ab initio predictions, we performed a Coulomb excitation experiment to measure the $B(E2; 3/2^- \rightarrow 1/2^-)$ transition strength in $^7$Be for the first time. A $B(E2; 3/2^- \rightarrow 1/2^-)$ value of $26(6)(3) \, e^2 \mathrm{fm}^4$ was deduced from the measured Coulomb excitation cross section. This result is used with the experimentally known $^7$Li $B(E2; 3/2^- \rightarrow 1/2^-)$ value to provide an experimental ratio to compare with the ab initio predictions. Our experimental value is consistent with the theoretical ratios within $1 \sigma$ uncertainty, giving experimental support for the value of these ratios. Further work in both theory and experiment can give insight into the robustness of these ratios and their physical meaning., Comment: 9 pages, 7 figures

Published
2021
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296. Remeasuring the anomalously enhanced $B(E2; 2^+ \rightarrow 1^+)$ in $^8\mathrm{Li}$

Author

Henderson, S. L., Ahn, T., Fasano, P. J., McCoy, A. E., Aguilar, S., Blankstein, D. T., Caves, L., Dombos, A. C., Grzywacz, R. K., Jones, K. L., Jin, S., Kelmar, R., Kolata, J. J., O'Malley, P. D., Reingold, C. S., Simon, A., and Smith, K.

Subjects
Nuclear Experiment, Nuclear Theory
Abstract

The large reported $E2$ strength between the $2^+$ ground state and $1^+$ first excited state of $\isotope[8]{Li}$, $B(E2; 2^+ \rightarrow 1^+)= 55(15)\,e^2\fm^4$, presents a puzzle. Unlike in neighboring $A=7\text{--}9$ isotopes, where enhanced $E2$ strengths may be understood to arise from deformation as rotational in-band transitions, the $2^+\rightarrow1^+$ transition in $^8$Li cannot be understood in any simple way as a rotational in-band transition. Moreover, the reported strength exceeds \textit{ab initio} predictions by an order of magnitude. In light of this discrepancy, we revisited the Coulomb excitation measurement of this strength, now using particle-$\gamma$ coincidences, yielding a revised $B(E2; 2^+ \rightarrow 1^+)$ of $19(^{+7}_{-6})(2)$~e$^2$fm$^4$. We explore how this value compares to what might be expected in the limits of rotational models. While the present value is about a factor of three smaller than previously reported, it remains anomalously enhanced., Comment: 21 pages, 5 figures

Published
2021

297. Frequency of Children Diagnosed with Perinatal Hepatitis C, United States, 2018-2020

Author

Newton, Suzanne M., Woodworth, Kate R., Chang, Daniel, Sizemore, Lindsey, Wingate, Heather, Pinckney, Leah, Osinski, Anthony, Orkis, Lauren, Reynolds, Bethany D., Carpentieri, Cynthia, Halai, Umme-Aiman, Lyu, Caleb, Longcore, Nicole, Thomas, Nadia, Wills, Aprielle, Akosa, Amanda, Olsen, Emily O'Malley, Panagiotakopoulos, Lakshmi, Thompson, Nicola D., Gilboa, Suzanne M., and Tong, Van T.

Subjects
United States. Centers for Disease Control and Prevention -- Analysis, Viral antibodies -- Analysis, Hepatitis C virus -- Analysis, Infants -- Analysis, Infection -- Prevention, RNA -- Analysis, Disease transmission -- Prevention, Public health -- Analysis, Antibodies -- Analysis, Health
Abstract

Hepatitis C virus (HCV) can be transmitted perinatally (1). Rates of acute HCV infection have increased recently (2), but few children perinatally exposed to HCV are tested and referred to [...]

Published
2024

298. Niraparib Population Pharmacokinetics and Exposure-Response Relationships in Patients With Newly Diagnosed Advanced Ovarian Cancer

Author

Monk, Bradley J., Romero, Ignacio, Graybill, Whitney, Churruca, Cristina, O'Malley, David M., Knudsen, Anja Ør, Yap, Oi Wah Stephanie, Baurain, Jean-François, Rose, Peter G., Denys, Hannelore, Ghamande, Sharad, Pisano, Carmela, Fabbro, Michel, Braicu, Elena Ioana, Calvert, Paula M., Amit, Amnon, Prendergast, Emily, Taylor, Adekemi, Kheibarshekan, Leila, Zhang, Zhi-Yi, Zajic, Stefan, Jewell, Roxanne C., Gupta, Divya, and González-Martín, Antonio

Published
2024
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299. A phase 2 trial exploring the significance of homologous recombination status in patients with platinum sensitive or platinum resistant relapsed ovarian cancer receiving combination cediranib and olaparib

Author

Liu, Joyce F., Xiong, Niya, Wenham, Robert M., Wahner-Hendrickson, Andrea, Armstrong, Deborah K., Chan, Nancy, O'Malley, David M., Lee, Jung-Min, Penson, Richard T., Cristea, Mihaela C., Abbruzzese, James L., Matsuo, Koji, Olawaiye, Alexander B., Barry, William T., Cheng, Su-Chun, Polak, Madeline, Swisher, Elizabeth M., Shapiro, Geoffrey I., Kohn, Elise C., Ivy, S. Percy, and Matulonis, Ursula A.

Published
2024
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