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2,101 results on '"d'Andréa, R."'

103. Tunable Approximations to Control Time-to-Solution in an HPC Molecular Docking Mini-App

Author

Gadioli, Davide, Palermo, Gianluca, Cherubin, Stefano, Vitali, Emanuele, Agosta, Giovanni, Manelfi, Candida, Beccari, Andrea R., Cavazzoni, Carlo, Sanna, Nico, and Silvano, Cristina

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the three-dimensional pose of a given molecule when it interacts with the target protein binding site. This task is often done for virtual screening a huge set of molecules to find the most promising ones, which will be forwarded to the later stages of the drug discovery process. Given the huge complexity of the problem, molecular docking cannot be solved by exploring the entire space of the ligand poses. State-of-the-art approaches face the problem by sampling the space of the ligand poses to generate results in a reasonable time budget. In this work, we improve the geometric approach to molecular docking by introducing tunable approximations. In particular, we analyzed and enriched the original implementation with tunable software knobs to explore and control the performance-accuracy tradeoffs. We modeled time-to-solution of the virtual screening task as a function of software knobs, input data features, and available computational resources. Therefore, the application can autotune its configuration according to a user-defined time budget. We used a Mini-App derived by LiGenDock - a state-of-the-art molecular docking application - to validate the proposed approach. We run the enhanced Mini-App on an HPC system by using a very large database of pockets and ligands. The proposed approach exposes a time-to-solution interval spanning more than one order of magnitude with accuracy degradation up to 30%, more in general providing different accuracy levels according to the needs of the virtual screening campaign.

Published
2019

104. The ANTAREX Domain Specific Language for High Performance Computing

Author

Silvano, Cristina, Agosta, Giovanni, Bartolini, Andrea, Beccari, Andrea R., Benini, Luca, Besnard, Loïc, Bispo, João, Cmar, Radim, Cardoso, João M. P., Cavazzoni, Carlo, Cesarini, Daniele, Cherubin, Stefano, Ficarelli, Federico, Gadioli, Davide, Golasowski, Martin, Libri, Antonio, Martinovič, Jan, Palermo, Gianluca, Pinto, Pedro, Rohou, Erven, Slaninová, Kateřina, and Vitali, Emanuele

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

The ANTAREX project relies on a Domain Specific Language (DSL) based on Aspect Oriented Programming (AOP) concepts to allow applications to enforce extra functional properties such as energy-efficiency and performance and to optimize Quality of Service (QoS) in an adaptive way. The DSL approach allows the definition of energy-efficiency, performance, and adaptivity strategies as well as their enforcement at runtime through application autotuning and resource and power management. In this paper, we present an overview of the key outcome of the project, the ANTAREX DSL, and some of its capabilities through a number of examples, including how the DSL is applied in the context of the project use cases.

Published
2019

106. Resuspension

Author

Ferro, Andrea R., Zhang, Yinping, editor, Hopke, Philip K., editor, and Mandin, Corinne, editor

Published
2022
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107. Nonmarket Strategy

Author

Hugill, Andrea R., Wolfolds, Sarah E., Fleisher, Craig, Section editor, Harris, Phil, editor, Bitonti, Alberto, editor, Fleisher, Craig S., editor, and Binderkrantz, Anne Skorkjær, editor

Published
2022
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108. Identifying Student Struggle by Analyzing Facial Movement During Asynchronous Video Lecture Viewing: Towards an Automated Tool to Support Instructors

Author

Linson, Adam, Xu, Yucheng, English, Andrea R., Fisher, Robert B., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Rodrigo, Maria Mercedes, editor, Matsuda, Noburu, editor, Cristea, Alexandra I., editor, and Dimitrova, Vania, editor

Published
2022
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117. Combined 70- and 80-gene signatures identify tumors with genomically luminal biology responsive to neoadjuvant endocrine therapy and are prognostic of 5-year outcome in early-stage breast cancer

Author

Pellicane, James V., Beitsch, Peter D., Rock, David T., Budway, Raye J., Dul, Carrie L., Kelemen, Pond R., Ashikari, Andrew Y., Baron, Paul L., Weinstein, Paul D., Mislowsky, Angela, Lee, Laura A., Beatty, Jennifer, Murray, Mary K., Dupree, Beth B., Finn, Christine, Corcoran, Kate, Wang, Shiyu, Menicucci, Andrea R., Yoder, Erin B., Blumencranz, Lisa E., Dauer, Patricia, Audeh, William, and Whitworth, Pat W.

Published
2022
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126. Single nucleotide polymorphisms and chromosomal copy number variation may impact the Sporothrix brasiliensis antifungal susceptibility and sporotrichosis clinical outcomes

Author

Teixeira, Marcus M., Almeida-Paes, Rodrigo, Bernardes-Engemann, Andréa R., Nicola, André M., de Macedo, Priscila M., Valle, Antonio Carlos F., Gutierrez-Galhardo, Maria Clara, Freitas, Dayvison F.S., Barker, Bridget M., Matute, Daniel R., Stajich, Jason E., and Zancopé-Oliveira, Rosely M.

Published
2022
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128. Glaucoma Genetic Risk Scores in the Million Veteran Program

Author

Gaziano, J. Michael, Ramoni, Rachel, Breeling, Jim, Chang, Kyong-Mi, Huang, Grant, Muralidhar, Sumitra, O’Donnell, Christopher J., Tsao, Philip S., Moser, Jennifer, Whitbourne, Stacey B., Brewer, Jessica V., Concato, John, Warren, Stuart, Argyres, Dean P., Stephens, Brady, Brophy, Mary T., Humphries, Donald E., Do, Nhan, Shayan, Shahpoor, Nguyen, Xuan-Mai T., Pyarajan, Saiju, Cho, Kelly, Hauser, Elizabeth, Sun, Yan, Zhao, Hongyu, Wilson, Peter, McArdle, Rachel, Dellitalia, Louis, Harley, John, Whittle, Jeffrey, Beckham, Jean, Wells, John, Gutierrez, Salvador, Gibson, Gretchen, Kaminsky, Laurence, Villareal, Gerardo, Kinlay, Scott, Xu, Junzhe, Hamner, Mark, Haddock, Kathlyn Sue, Bhushan, Sujata, Iruvanti, Pran, Godschalk, Michael, Ballas, Zuhair, Buford, Malcolm, Mastorides, Stephen, Klein, Jon, Ratcliffe, Nora, Florez, Hermes, Swann, Alan, Murdoch, Maureen, Sriram, Peruvemba, Yeh, Shing Shing, Washburn, Ronald, Jhala, Darshana, Aguayo, Samuel, Cohen, David, Sharma, Satish, Callaghan, John, Oursler, Kris Ann, Whooley, Mary, Ahuja, Sunil, Gutierrez, Amparo, Schifman, Ronald, Greco, Jennifer, Rauchman, Michael, Servatius, Richard, Oehlert, Mary, Wallbom, Agnes, Fernando, Ronald, Morgan, Timothy, Stapley, Todd, Sherman, Scott, Anderson, Gwenevere, Tsao, Philip, Sonel, Elif, Boyko, Edward, Meyer, Laurence, Gupta, Samir, Fayad, Joseph, Hung, Adriana, Lichy, Jack, Hurley, Robin, Robey, Brooks, Striker, Robert, Waksmunski, Andrea R., Kinzy, Tyler G., Cruz, Lauren A., Nealon, Cari L., Halladay, Christopher W., Simpson, Piana, Canania, Rachael L., Anthony, Scott A., Roncone, David P., Sawicki Rogers, Lea, Leber, Jenna N., Dougherty, Jacquelyn M., Greenberg, Paul B., Sullivan, Jack M., Wu, Wen-Chih, Iyengar, Sudha K., Crawford, Dana C., Peachey, Neal S., and Cooke Bailey, Jessica N.

Published
2022
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129. Biomarkers and Echocardiographic Predictors of Cardiovascular Outcome in Patients With Chronic Chagas Disease

Author

Veronica G. Mendes, Lorena Rimolo, Ana Carolina B. de Lima, Roberto R. Ferreira, Luciano S. Oliveira, Lindice M. Nisimura, Samuel I. M. Horita, Andréa R. Costa, Gilberto Marcelo S. da Silva, Luiz Henrique C. Sangenis, Fernanda S. N. S. Mendes, Andrea S. Sousa, Henrique H. Veloso, Marcelo T. Holanda, Mauro F. F. Mediano, Mariana C. Waghabi, Luciana R. Garzoni, Otacílio C. Moreira, Constança Britto, Ademir B. Cunha, Alejandro Marcel Hasslocher‐Moreno, and Roberto M. Saraiva

Subjects
2‐dimensional strain analysis, 3‐dimensional echocardiography, Chagas disease, mortality, prognosis, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background Chagas disease (CD) presents an ominous prognosis. The predictive value of biomarkers and new echocardiogram parameters in adjusted models have not been well studied. Methods and Results There were 361 patients with chronic CD (57.6% men, 61±11 years of age, clinical forms: indeterminate 27.1%, cardiac 56.6%, digestive 3.6%, cardiodigestive 12.7%) included in this single‐center, observational, prospective longitudinal study. Echocardiographic evaluation included strain analyses of left atrial, left ventricular (LV), and right ventricular and 3‐dimensional analyses of left atrial and LV volumes. Biomarkers included cardiac troponin I, brain natriuretic peptide, transforming growth factor β1, tumor necrosis factor, matrix metalloproteinases, and Trypanosoma cruzi polymerase chain reaction. The studied end point was a composite of CD‐related mortality, heart transplant, hospital admission due to worsening heart failure, or new cardiac device insertion. Event‐free survival was analyzed by multivariable regression analyses adjusted for competing risks. P values

Published
2023
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135. Baricitinib versus dexamethasone for adults hospitalised with COVID-19 (ACTT-4): a randomised, double-blind, double placebo-controlled trial

Author

Wahid, Lana, Walter, Emmanuel B., Belur, Akhila G., Dreyer, Grace, Patterson, Jan E., Bowling, Jason E., Dixon, Danielle O., Hewlett, Angela, Odrobina, Robert, Pupaibool, Jakrapun, Mocherla, Satish, Lazarte, Suzana, Cayabyab, Meilani, Hussein, Rezhan H., Golamari, Reshma R., Krill, Kaleigh L., Rajme, Sandra, Riska, Paul F., Zingman, Barry S., Mertz, Gregory, Sosa, Nestor, Goepfert, Paul A., Berhe, Mezgebe, Dishner, Emma, Fayed, Mohamed, Hubel, Kinsley, Martinez-Orozco, José Arturo, Bautista Felix, Nora, Elmor, Sammy T., Bechnak, Amer Ryan, Saklawi, Youssef, Van Winkle, Jason W., Zea, Diego F., Laguio-Vila, Maryrose, Walsh, Edward E., Falsey, Ann R., Carvajal, Karen, Hyzy, Robert C., Hanna, Sinan, Olbrich, Norman, Traenkner, Jessica J., Kraft, Colleen S., Tebas, Pablo, Baron, Jillian T, Levine, Corri, Nock, Joy, Billings, Joanne, Kim, Hyun, Elie-Turenne, Marie-Carmelle, Whitaker, Jennifer A., Luetkemeyer, Anne F., Dwyer, Jay, Bainbridge, Emma, Gyun Choe, Pyoeng, Kyung Kang, Chang, Jilg, Nikolaus, Cantos, Valeria D, Bhamidipati, Divya R., Nithin Gopalsamy, Srinivasa, Chary, Aarthi, Jung, Jongtak, Song, Kyoung-Ho, Kim, Hong Bin, Benson, Constance A., McConnell, Kimberly, Wang, Jennifer P., Wessolossky, Mireya, Perez, Katherine, Eubank, Taryn A, Berjohn, Catherine, Utz, Gregory C., Jackson, Patrick E.H., Bell, Taison D., Haughey, Heather M., Moanna, Abeer, Cribbs, Sushma, Harrison, Telisha, Colombo, Christopher J., Schofield, Christina, Colombo, Rhonda E., Tapson, Victor F., Grein, Jonathan, Sutterwala, Fayyaz, Ince, Dilek, Winokur, Patricia L., Fung, Monica, Jang, Hannah, Wyles, David, Frank, Maria G., Sarcone, Ellen, Neumann, Henry, Viswanathan, Anand, Hochman, Sarah, Mulligan, Mark, Eckhardt, Benjamin, Carmody, Ellie, Ahuja, Neera, Nadeau, Kari, Svec, David, Macaraeg, Jeffrey C., Morrow, Lee, Quimby, Dave, Bessesen, Mary, Nicholson, Lindsay, Adams, Jill, Kumar, Princy, Lambert, Allison A., Arguinchona, Henry, Alicic, Radica Z., Saito, Sho, Ohmagari, Norio, Mikami, Ayako, Chien Lye, David, Hong Lee, Tau, Ying Chia, Po, Hsieh, Lanny, Amin, Alpesh N., Watanabe, Miki, Candiotti, Keith A., Castro, Jose G., Antor, Maria A., Lee, Tida, Lalani, Tahaniyat, Novak, Richard M., Wendrow, Andrea, Borgetti, Scott A., George, Sarah L., Hoft, Daniel F., Brien, James D., Cohen, Stuart H., Thompson, George R., 3rd, Chakrabarty, Melony, Guirgis, Faheem, Davey, Richard T., Voell, Jocelyn, Strich, Jeffrey R., Lindholm, David A., Mende, Katrin, Wellington, Trevor R., Rapaka, Rekha R., Husson, Jennifer S., Levine, Andrea R., Yen Tan, Seow, Shafi, Humaira, Chien, Jaime M F, Hostler, David C., Hostler, Jordanna M., Shahan, Brian T., Adams, David H., Osinusi, Anu, Cao, Huyen, Burgess, Timothy H., Rozman, Julia, Chung, Kevin K., Nieuwoudt, Christina, El-Khorazaty, Jill A., Hill, Heather, Pettibone, Stephanie, Gettinger, Nikki, Engel, Theresa, Lewis, Teri, Wang, Jing, Deye, Gregory A., Nomicos, Effie, Pikaart-Tautges, Rhonda, Elsafy, Mohamed, Jurao, Robert, Koo, Hyung, Proschan, Michael, Yokum, Tammy, Arega, Janice, Florese, Ruth, Wolfe, Cameron R, Tomashek, Kay M, Patterson, Thomas F, Gomez, Carlos A, Marconi, Vincent C, Jain, Mamta K, Yang, Otto O, Paules, Catharine I, Palacios, Guillermo M Ruiz, Grossberg, Robert, Harkins, Michelle S, Mularski, Richard A, Erdmann, Nathaniel, Sandkovsky, Uriel, Almasri, Eyad, Pineda, Justino Regalado, Dretler, Alexandra W, de Castilla, Diego Lopez, Branche, Angela R, Park, Pauline K, Mehta, Aneesh K, Short, William R, McLellan, Susan L F, Kline, Susan, Iovine, Nicole M, El Sahly, Hana M, Doernberg, Sarah B, Oh, Myoung-don, Huprikar, Nikhil, Hohmann, Elizabeth, Kelley, Colleen F, Holodniy, Mark, Kim, Eu Suk, Sweeney, Daniel A, Finberg, Robert W, Grimes, Kevin A, Maves, Ryan C, Ko, Emily R, Engemann, John J, Taylor, Barbara S, Ponce, Philip O, Larson, LuAnn, Melendez, Dante Paolo, Seibert, Allan M, Rouphael, Nadine G, Strebe, Joslyn, Clark, Jesse L, Julian, Kathleen G, de Leon, Alfredo Ponce, Cardoso, Anabela, de Bono, Stephanie, Atmar, Robert L, Ganesan, Anuradha, Ferreira, Jennifer L, Green, Michelle, Makowski, Mat, Bonnett, Tyler, Beresnev, Tatiana, Ghazaryan, Varduhi, Dempsey, Walla, Nayak, Seema U, Dodd, Lori E, Beigel, John H, and Kalil, Andre C

Published
2022
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140. A phase 2 randomized, double-blinded, placebo-controlled, multicenter trial evaluating the efficacy and safety of raloxifene for patients with mild to moderate COVID-19

Author

Nicastri, Emanuele, Marinangeli, Franco, Pivetta, Emanuele, Torri, Elena, Reggiani, Francesco, Fiorentino, Giuseppe, Scorzolini, Laura, Vettori, Serena, Marsiglia, Carolina, Gavioli, Elizabeth Marie, Beccari, Andrea R., Terpolilli, Giuseppe, De Pizzol, Maria, Goisis, Giovanni, Mantelli, Flavio, Vaia, Francesco, and Allegretti, Marcello

Published
2022
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146. Moderators of treatment outcomes for LGBTQ+ military veterans in the PRIDE in All Who Served health promotion group.

Author

Hilgeman, Michelle M., Cramer, Robert J., Kaniuka, Andréa R., Robertson, Ryan A., Bishop, Teddy, Wilson, Sarah M., Sperry, Heather A., and Lange, Tiffany M.

Subjects
LGBTQ+ people, VETERANS, MINORITIES, MINORITY stress, SEXUAL orientation, LGBTQ+ youth, TRANSGENDER youth
Abstract

Background: Veterans who identify as lesbian, gay, bisexual, transgender, queer, questioning, and related identities (LGBTQ+) have faced discrimination that puts them at increased risk for depression, anxiety, and suicide. Upstream interventions like the PRIDE in All Who Served program can improve internalized prejudice, suicidality, symptoms of depression, and symptoms of anxiety by addressing minority stress, facilitating social connection, and promoting engagement with the healthcare system. Yet, little is known about who benefits most from these types of services. Methods and materials: Sixty-six US military veterans (Mean age = 47.06, SD = 13.74) provided outcome surveys before and after a 10-week health promotion group for LGBTQ+ individuals at one of 10 Veterans Health Administration (VA) Medical Centers. Subscales of a coping self-efficacy measure (e.g., problem-solving, social support, thought-stopping), and demographic factors were examined as moderators of treatment outcomes. Results: Coping self-efficacy moderated effects across treatment outcomes with those lower in coping self-efficacy beliefs reporting the greatest benefit of the intervention. Reduction in anxiety symptoms was moderated only by problem-solving coping self-efficacy, while suicidality was moderated only by social support. Reduction of internalized prejudice and depression symptoms were moderated by both problem-solving and social support coping self-efficacy, while thought-stopping (a frequent target of traditional cognitive therapies) only moderated internalized prejudice, but not clinical symptom indicators. Most demographic factors (e.g., age, race, gender) did not impact treatment outcomes; however, sexual orientation was significant such that those who identified as bisexual, queer, or something else (e.g., pansexual) had greater reductions in internalized prejudice than their single gender-attracted peers. Discussion and conclusion: Individual differences like coping self-efficacy and sexual orientation are rarely considered in clinical care settings when shaping policy or implementing tailored programs. Understanding implications for who is most likely to improve could inform program refinement and implementation of affirming interventions for minoritized people. [ABSTRACT FROM AUTHOR]

Published
2024
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147. SARS-CoV-2 mRNA vaccine induced higher antibody affinity and IgG titers against variants of concern in post-partum vs non-post-partum women

Author

Lee, Youri, Grubbs, Gabrielle, Ramelli, Sabrina C., Levine, Andrea R., Bathula, Allison, Saharia, Kapil, Purcell, Madeleine, Singireddy, Shreya, Dugan, Colleen L., Kirchoff, Lindsey, Lankford, Allison, Cipriano, Sarah, Curto, Ryan A., Wu, Jocelyn, Raja, Katherine, Kelley, Emily, Herr, Daniel, Vannella, Kevin M., Ravichandran, Supriya, Tang, Juanjie, Harris, Anthony, Sajadi, Mohammad, Chertow, Daniel S., Grazioli, Alison, and Khurana, Surender

Published
2022
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149. Two-dimensional strain derived parameters provide independent predictors of progression to Chagas cardiomyopathy and mortality in patients with Chagas disease

Author

Saraiva, Roberto M., Mediano, Mauro Felippe F., Quintana, Marcel S.B., Sperandio da Silva, Gilberto Marcelo, Costa, Andréa R., Sousa, Andréa S., Sangenis, Luiz Henrique C., Mendes, Fernanda S.N.S., Veloso, Henrique H., Xavier, Sergio S., Holanda, Marcelo T., and Hasslocher-Moreno, Alejandro Marcel

Published
2022
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