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33,694 results on '"Paul, V."'

201. Exponential suppression of bit or phase errors with cyclic error correction

Author

Chen, Zijun, Satzinger, Kevin J, Atalaya, Juan, Korotkov, Alexander N, Dunsworth, Andrew, Sank, Daniel, Quintana, Chris, McEwen, Matt, Barends, Rami, Klimov, Paul V, Hong, Sabrina, Jones, Cody, Petukhov, Andre, Kafri, Dvir, Demura, Sean, Burkett, Brian, Gidney, Craig, Fowler, Austin G, Paler, Alexandru, Putterman, Harald, Aleiner, Igor, Arute, Frank, Arya, Kunal, Babbush, Ryan, Bardin, Joseph C, Bengtsson, Andreas, Bourassa, Alexandre, Broughton, Michael, Buckley, Bob B, Buell, David A, Bushnell, Nicholas, Chiaro, Benjamin, Collins, Roberto, Courtney, William, Derk, Alan R, Eppens, Daniel, Erickson, Catherine, Farhi, Edward, Foxen, Brooks, Giustina, Marissa, Greene, Ami, Gross, Jonathan A, Harrigan, Matthew P, Harrington, Sean D, Hilton, Jeremy, Ho, Alan, Huang, Trent, Huggins, William J, Ioffe, LB, Isakov, Sergei V, Jeffrey, Evan, Jiang, Zhang, Kechedzhi, Kostyantyn, Kim, Seon, Kitaev, Alexei, Kostritsa, Fedor, Landhuis, David, Laptev, Pavel, Lucero, Erik, Martin, Orion, McClean, Jarrod R, McCourt, Trevor, Mi, Xiao, Miao, Kevin C, Mohseni, Masoud, Montazeri, Shirin, Mruczkiewicz, Wojciech, Mutus, Josh, Naaman, Ofer, Neeley, Matthew, Neill, Charles, Newman, Michael, Niu, Murphy Yuezhen, O'Brien, Thomas E, Opremcak, Alex, Ostby, Eric, Pato, Balint, Redd, Nicholas, Roushan, Pedram, Rubin, Nicholas C, Shvarts, Vladimir, Strain, Doug, Szalay, Marco, Trevithick, Matthew D, Villalonga, Benjamin, White, Theodore, Yao, Z Jamie, Yeh, Ping, Yoo, Juhwan, Zalcman, Adam, Neven, Hartmut, Boixo, Sergio, Smelyanskiy, Vadim, Chen, Yu, Megrant, Anthony, and Kelly, Julian

Subjects
Google Quantum AI, General Science & Technology
Abstract

Realizing the potential of quantum computing requires sufficiently low logical error rates1. Many applications call for error rates as low as 10-15 (refs. 2-9), but state-of-the-art quantum platforms typically have physical error rates near 10-3 (refs. 10-14). Quantum error correction15-17 promises to bridge this divide by distributing quantum logical information across many physical qubits in such a way that errors can be detected and corrected. Errors on the encoded logical qubit state can be exponentially suppressed as the number of physical qubits grows, provided that the physical error rates are below a certain threshold and stable over the course of a computation. Here we implement one-dimensional repetition codes embedded in a two-dimensional grid of superconducting qubits that demonstrate exponential suppression of bit-flip or phase-flip errors, reducing logical error per round more than 100-fold when increasing the number of qubits from 5 to 21. Crucially, this error suppression is stable over 50 rounds of error correction. We also introduce a method for analysing error correlations with high precision, allowing us to characterize error locality while performing quantum error correction. Finally, we perform error detection with a small logical qubit using the 2D surface code on the same device18,19 and show that the results from both one- and two-dimensional codes agree with numerical simulations that use a simple depolarizing error model. These experimental demonstrations provide a foundation for building a scalable fault-tolerant quantum computer with superconducting qubits.

Published
2021

202. Structuring Stress for Active Materials Control

Author

Zhang, Rui, Redford, Steven A., Ruijgrok, Paul V., Kumar, Nitin, Mozaffari, Ali, Zemsky, Sasha, Dinner, Aaron R., Vitelli, Vincenzo, Bryant, Zev, Gardel, Margaret L., and de Pablo, Juan J.

Subjects
Condensed Matter - Soft Condensed Matter, Condensed Matter - Materials Science
Abstract

Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means to control and manipulate transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. Simulations and experiments are used to demonstrate that topological defects can be generated at will, and then constrained to move along specified trajectories, by inducing local stresses in an otherwise passive material. These results provide a foundation for design of autonomous and reconfigurable microfluidic systems where transport is controlled by modulating activity with light.

Published
2019
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210. Machine learning active-nematic hydrodynamics

Author

Colen, Jonathan, Han, Ming, Zhang, Rui, Redford, Steven A, Lemma, Linnea M, Morgan, Link, Ruijgrok, Paul V, Adkins, Raymond, Bryant, Zev, Dogic, Zvonimir, Gardel, Margaret L, de Pablo, Juan J, and Vitelli, Vincenzo

Subjects
Bioengineering, Underpinning research, 1.1 Normal biological development and functioning, Affordable and Clean Energy, Hydrodynamics, Machine Learning, deep learning, active turbulence, liquid crystals, topological defects, biomaterials, cond-mat.soft, cond-mat.mtrl-sci, nlin.CD, physics.flu-dyn
Abstract

Hydrodynamic theories effectively describe many-body systems out of equilibrium in terms of a few macroscopic parameters. However, such parameters are difficult to determine from microscopic information. Seldom is this challenge more apparent than in active matter, where the hydrodynamic parameters are in fact fields that encode the distribution of energy-injecting microscopic components. Here, we use active nematics to demonstrate that neural networks can map out the spatiotemporal variation of multiple hydrodynamic parameters and forecast the chaotic dynamics of these systems. We analyze biofilament/molecular-motor experiments with microtubule/kinesin and actin/myosin complexes as computer vision problems. Our algorithms can determine how activity and elastic moduli change as a function of space and time, as well as adenosine triphosphate (ATP) or motor concentration. The only input needed is the orientation of the biofilaments and not the coupled velocity field which is harder to access in experiments. We can also forecast the evolution of these chaotic many-body systems solely from image sequences of their past using a combination of autoencoders and recurrent neural networks with residual architecture. In realistic experimental setups for which the initial conditions are not perfectly known, our physics-inspired machine-learning algorithms can surpass deterministic simulations. Our study paves the way for artificial-intelligence characterization and control of coupled chaotic fields in diverse physical and biological systems, even in the absence of knowledge of the underlying dynamics.

Published
2021

212. Author Correction: The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data.

Author

Pastorello, Gilberto, Trotta, Carlo, Canfora, Eleonora, Chu, Housen, Christianson, Danielle, Cheah, You-Wei, Poindexter, Cristina, Chen, Jiquan, Elbashandy, Abdelrahman, Humphrey, Marty, Isaac, Peter, Polidori, Diego, Reichstein, Markus, Ribeca, Alessio, van Ingen, Catharine, Vuichard, Nicolas, Zhang, Leiming, Amiro, Brian, Ammann, Christof, Arain, M Altaf, Ardö, Jonas, Arkebauer, Timothy, Arndt, Stefan K, Arriga, Nicola, Aubinet, Marc, Aurela, Mika, Baldocchi, Dennis, Barr, Alan, Beamesderfer, Eric, Marchesini, Luca Belelli, Bergeron, Onil, Beringer, Jason, Bernhofer, Christian, Berveiller, Daniel, Billesbach, Dave, Black, Thomas Andrew, Blanken, Peter D, Bohrer, Gil, Boike, Julia, Bolstad, Paul V, Bonal, Damien, Bonnefond, Jean-Marc, Bowling, David R, Bracho, Rosvel, Brodeur, Jason, Brümmer, Christian, Buchmann, Nina, Burban, Benoit, Burns, Sean P, Buysse, Pauline, Cale, Peter, Cavagna, Mauro, Cellier, Pierre, Chen, Shiping, Chini, Isaac, Christensen, Torben R, Cleverly, James, Collalti, Alessio, Consalvo, Claudia, Cook, Bruce D, Cook, David, Coursolle, Carole, Cremonese, Edoardo, Curtis, Peter S, D'Andrea, Ettore, da Rocha, Humberto, Dai, Xiaoqin, Davis, Kenneth J, De Cinti, Bruno, de Grandcourt, Agnes, De Ligne, Anne, De Oliveira, Raimundo C, Delpierre, Nicolas, Desai, Ankur R, Di Bella, Carlos Marcelo, di Tommasi, Paul, Dolman, Han, Domingo, Francisco, Dong, Gang, Dore, Sabina, Duce, Pierpaolo, Dufrêne, Eric, Dunn, Allison, Dušek, Jiří, Eamus, Derek, Eichelmann, Uwe, ElKhidir, Hatim Abdalla M, Eugster, Werner, Ewenz, Cacilia M, Ewers, Brent, Famulari, Daniela, Fares, Silvano, Feigenwinter, Iris, Feitz, Andrew, Fensholt, Rasmus, Filippa, Gianluca, Fischer, Marc, Frank, John, Galvagno, Marta, and Gharun, Mana

Abstract

The following authors were omitted from the original version of this Data Descriptor: Markus Reichstein and Nicolas Vuichard. Both contributed to the code development and N. Vuichard contributed to the processing of the ERA-Interim data downscaling. Furthermore, the contribution of the co-author Frank Tiedemann was re-evaluated relative to the colleague Corinna Rebmann, both working at the same sites, and based on this re-evaluation a substitution in the co-author list is implemented (with Rebmann replacing Tiedemann). Finally, two affiliations were listed incorrectly and are corrected here (entries 190 and 193). The author list and affiliations have been amended to address these omissions in both the HTML and PDF versions.

Published
2021

213. Transcatheter closure of large ostium secundum atrial septal defects in symptomatic small children: A single-center retrospective study

Author

Jahangir Ahmed Naseem, Mirza Shohiab Ur Riyaz, Shobhit Priyanshu Joseph, Jesu Krupa, Mayank Agarwal, Pratheesh George Mathen, Oommen K. George, Paul V. George, John Jose, and Viji Samuel Thomson

Subjects
large atrial septal defect, small children, transcatheter device closure, Medicine, Pediatrics, RJ1-570, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background: In general, the risks associated with transcatheter atrial septal defect (ASD) device closure are reported to be relatively low, but the evidence stems from trials involving adults and older children. Current guidelines do not recommend ASD device closure in children with defect sizes >20 mm due to limited data available in this group of patients. This retrospective study sought to determine the clinical and procedural characteristics of successful transcatheter ASD device closure in small children with large defects and assess the complication rates and reasons for unsuccessful device closure. Methods: We retrospectively reviewed the data of all patients who underwent elective transcatheter closure of ostium secundum ASD in our department between September 2013 and February 2022. All children weighing

Published
2023
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214. Prognostic factors associated with improvements in patient-reported outcomes in idiopathic adhesive capsulitis

Author

Paul V. Romeo, BS, Aidan G. Papalia, BS, Matthew G. Alben, BS, Neil Gambhir, BS, Dhruv Shankar, BS, Andrew S. Bi, MD, Joseph D. Zuckerman, MD, and Mandeep S. Virk, MD

Subjects
Adhesive capsulitis, Frozen shoulder, PROMIS, Upper extremity, Factors, Patient-reported outcomes, Orthopedic surgery, RD701-811, Diseases of the musculoskeletal system, RC925-935
Abstract

Background: The purpose of this study was to identify prognostic factors that are associated with improvements in patient-reported outcomes measures (PROMs) related to upper extremity function and pain in those suffering from idiopathic adhesive capsulitis. Methods: All patients treated conservatively for primary idiopathic adhesive capsulitis were identified from our institutional database between 2019 and 2021. Exclusion criteria included any patients treated surgically, follow-up less than one year, or incomplete survey results. PROMs including Patient-Reported Outcomes Measurement Information System (PROMIS) Upper Extremity Computer Adaptive Test Version 2.0 (P-UE), Pain Interference (P-Interference), Pain Intensity (P-Intensity), and visual analog scale (VAS) pain scores. They were obtained at initial consultation and at one year to assess patient-perceived impact of their condition. Multiple linear and multivariable logistic regressions were performed to identify factors associated with improvement in patient-perceived pain and shoulder function using final PROM scores and difference in PROM scores from initial consultation. An independent t-test was used to compare baseline and one-year minimum follow-up PROMs. Odds ratios and their 95% confidence intervals were calculated for each factor; a P value of < .05 was considered statistically significant. Results: A total of 56 patients (40 females and 16 males) were enrolled in the study with an average age of 54.7 ± 7.7 years. A significant improvement (P

Published
2023
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215. Unraveling Amazon tree community assembly using Maximum Information Entropy: a quantitative analysis of tropical forest ecology

Author

Edwin Pos, Luiz de Souza Coelho, Diogenes de Andrade Lima Filho, Rafael P. Salomão, Iêda Leão Amaral, Francisca Dionízia de Almeida Matos, Carolina V. Castilho, Oliver L. Phillips, Juan Ernesto Guevara, Marcelo de Jesus Veiga Carim, Dairon Cárdenas López, William E. Magnusson, Florian Wittmann, Mariana Victória Irume, Maria Pires Martins, Daniel Sabatier, José Renan da Silva Guimarães, Jean-François Molino, Olaf S. Bánki, Maria Teresa Fernandez Piedade, Nigel C. A. Pitman, Abel Monteagudo Mendoza, José Ferreira Ramos, Joseph E. Hawes, Everton José Almeida, Luciane Ferreira Barbosa, Larissa Cavalheiro, Márcia Cléia Vilela dos Santos, Bruno Garcia Luize, Evlyn Márcia Moraes de Leão Novo, Percy Núñez Vargas, Thiago Sanna Freire Silva, Eduardo Martins Venticinque, Angelo Gilberto Manzatto, Neidiane Farias Costa Reis, John Terborgh, Katia Regina Casula, Euridice N. Honorio Coronado, Juan Carlos Montero, Beatriz S. Marimon, Ben Hur Marimon-Junior, Ted R. Feldpausch, Alvaro Duque, Chris Baraloto, Nicolás Castaño Arboleda, Julien Engel, Pascal Petronelli, Charles Eugene Zartman, Timothy J. Killeen, Rodolfo Vasquez, Bonifacio Mostacedo, Rafael L. Assis, Jochen Schöngart, Hernán Castellanos, Marcelo Brilhante de Medeiros, Marcelo Fragomeni Simon, Ana Andrade, José Luís Camargo, Layon O. Demarchi, William F. Laurance, Susan G. W. Laurance, Emanuelle de Sousa Farias, Maria Aparecida Lopes, José Leonardo Lima Magalhães, Henrique Eduardo Mendonça Nascimento, Helder Lima de Queiroz, Gerardo A. C. Aymard, Roel Brienen, Juan David Cardenas Revilla, Flávia R. C. Costa, Adriano Quaresma, Ima Célia Guimarães Vieira, Bruno Barçante Ladvocat Cintra, Pablo R. Stevenson, Yuri Oliveira Feitosa, Joost F. Duivenvoorden, Hugo F. Mogollón, Leandro Valle Ferreira, James A. Comiskey, Freddie Draper, José Julio de Toledo, Gabriel Damasco, Nállarett Dávila, Roosevelt García-Villacorta, Aline Lopes, Alberto Vicentini, Janaína Costa Noronha, Flávia Rodrigues Barbosa, Rainiellen de Sá Carpanedo, Thaise Emilio, Carolina Levis, Domingos de Jesus Rodrigues, Juliana Schietti, Priscila Souza, Alfonso Alonso, Francisco Dallmeier, Vitor H. F. Gomes, Jon Lloyd, David Neill, Daniel Praia Portela de Aguiar, Alejandro Araujo-Murakami, Luzmila Arroyo, Fernanda Antunes Carvalho, Fernanda Coelho de Souza, Dário Dantas do Amaral, Kenneth J. Feeley, Rogerio Gribel, Marcelo Petratti Pansonato, Jos Barlow, Erika Berenguer, Joice Ferreira, Paul V. A. Fine, Marcelino Carneiro Guedes, Eliana M. Jimenez, Juan Carlos Licona, Maria Cristina Peñuela Mora, Carlos A. Peres, Boris Eduardo Villa Zegarra, Carlos Cerón, Terry W. Henkel, Paul Maas, Marcos Silveira, Juliana Stropp, Raquel Thomas-Caesar, Tim R. Baker, Doug Daly, Kyle G. Dexter, John Ethan Householder, Isau Huamantupa-Chuquimaco, Toby Pennington, Marcos Ríos Paredes, Alfredo Fuentes, José Luis Marcelo Pena, Miles R. Silman, J. Sebastián Tello, Jerome Chave, Fernando Cornejo Valverde, Anthony Di Fiore, Renato Richard Hilário, Juan Fernando Phillips, Gonzalo Rivas-Torres, Tinde R. van Andel, Patricio von Hildebrand, Edelcilio Marques Barbosa, Luiz Carlos de Matos Bonates, Hilda Paulette Dávila Doza, Émile Fonty, Ricardo Zárate Gómez, Therany Gonzales, George Pepe Gallardo Gonzales, Jean-Louis Guillaumet, Bruce Hoffman, André Braga Junqueira, Yadvinder Malhi, Ires Paula de Andrade Miranda, Linder Felipe Mozombite Pinto, Adriana Prieto, Agustín Rudas, Ademir R. Ruschel, Natalino Silva, César I. A. Vela, Vincent Antoine Vos, Egleé L. Zent, Stanford Zent, Bianca Weiss Albuquerque, Angela Cano, Diego F. Correa, Janaina Barbosa Pedrosa Costa, Bernardo Monteiro Flores, Milena Holmgren, Marcelo Trindade Nascimento, Alexandre A. Oliveira, Hirma Ramirez-Angulo, Maira Rocha, Veridiana Vizoni Scudeller, Rodrigo Sierra, Milton Tirado, Maria Natalia Umaña, Geertje van der Heijden, Emilio Vilanova Torre, Corine Vriesendorp, Ophelia Wang, Kenneth R. Young, Manuel Augusto Ahuite Reategui, Cláudia Baider, Henrik Balslev, Sasha Cárdenas, Luisa Fernanda Casas, William Farfan-Rios, Cid Ferreira, Reynaldo Linares-Palomino, Casimiro Mendoza, Italo Mesones, Armando Torres-Lezama, Ligia Estela Urrego Giraldo, Daniel Villarroel, Roderick Zagt, Miguel N. Alexiades, Karina Garcia-Cabrera, Lionel Hernandez, William Milliken, Walter Palacios Cuenca, Susamar Pansini, Daniela Pauletto, Freddy Ramirez Arevalo, Adeilza Felipe Sampaio, Elvis H. Valderrama Sandoval, Luis Valenzuela Gamarra, Gerhard Boenisch, Jens Kattge, Nathan Kraft, Aurora Levesley, Karina Melgaço, Georgia Pickavance, Lourens Poorter, and Hans ter Steege

Subjects
Medicine, Science
Abstract

Abstract In a time of rapid global change, the question of what determines patterns in species abundance distribution remains a priority for understanding the complex dynamics of ecosystems. The constrained maximization of information entropy provides a framework for the understanding of such complex systems dynamics by a quantitative analysis of important constraints via predictions using least biased probability distributions. We apply it to over two thousand hectares of Amazonian tree inventories across seven forest types and thirteen functional traits, representing major global axes of plant strategies. Results show that constraints formed by regional relative abundances of genera explain eight times more of local relative abundances than constraints based on directional selection for specific functional traits, although the latter does show clear signals of environmental dependency. These results provide a quantitative insight by inference from large-scale data using cross-disciplinary methods, furthering our understanding of ecological dynamics.

Published
2023
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216. Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity

Author

Wei-Hung Chen, Agnes Hajduczki, Elizabeth J. Martinez, Hongjun Bai, Hanover Matz, Thomas M. Hill, Eric Lewitus, William C. Chang, Layla Dawit, Caroline E. Peterson, Phyllis A. Rees, Adelola B. Ajayi, Emily S. Golub, Isabella Swafford, Vincent Dussupt, Sapna David, Sandra V. Mayer, Sandrine Soman, Caitlin Kuklis, Courtney Corbitt, Jocelyn King, Misook Choe, Rajeshwer S. Sankhala, Paul V. Thomas, Michelle Zemil, Lindsay Wieczorek, Tricia Hart, Debora Duso, Larry Kummer, Lianying Yan, Spencer L. Sterling, Eric D. Laing, Christopher C. Broder, Jazmean K. Williams, Edgar Davidson, Benjamin J. Doranz, Shelly J. Krebs, Victoria R. Polonis, Dominic Paquin-Proulx, Morgane Rolland, William W. Reiley, Gregory D. Gromowski, Kayvon Modjarrad, Helen Dooley, and M. Gordon Joyce

Subjects
Science
Abstract

SARS-CoV-2 variants of concern continue to emerge, reducing vaccine efficacy and limiting therapeutic options. Here, Chen and colleagues describe the identification and design of shark nanobodies with pansarbecovirus activity.

Published
2023
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224. Pegcetacoplan for the treatment of geographic atrophy secondary to age-related macular degeneration (OAKS and DERBY): two multicentre, randomised, double-masked, sham-controlled, phase 3 trials

Author

Cole, Abosede O, Gerstenblith, Adam T, Kotagiri, Ajay, Edwards, Albert O, Zambrano, Alberto D, Eaton, Alexander M, Rubowitz, Alexander, Lyon, Alice T, Chiang, Allen, Ho, Allen, Hu, Allen Y, Guerami, Amir H, Dessouki, Amr L, de Carvalho, André Corrêa Maia, Emanuelli, Andrés, Chang, Andrew A, Antoszyk, Andrew N, Francone, Anibal Andrés, Prasad, Anita, Wolf, Armin, Khanani, Arshad M, Abbey, Ashkan Michael, Moulana, Asma, Wihelm, Barbara, Sikorski, Bartosz L, Kuppermann, Baruch D, Wolff, Benjamin, Jewart, Brian H, Do, Brian K, Chan-Kai, Brian T, Mein, Calvin, Hoyng, Carel B, Awh, Carl C, Regillio, Carl, Zeolite, Carlos, Baumal, Caroline R, Creuzot-Garcher, Catherine, Maury, Catherine Français, Wykoff, Charles C, Newell, Charles K, Jhaveri, Chirag, Lohmann, Chris P, Dinah, Christiana B, Ma, Colin, Crawford, Courtney, Parke, D Wilkin, Lavinsky, Daniel, Roth, Daniel, Pieramici, Dante J, Moshfeghi, Darius M, Levin, Darrin, Saperstein, David A, Brown, David, Gaucher, David, Lally, David R, Liao, David S, Brown, David Warren, Goldstein, Debra, Marcus, Dennis, Chan, Derek G, Dhoot, Dilsher, Tacite, Domingo, Zalewski, Dominik, Espana, Edgar M, Lad, Eleonora M, Souied, Eric H, Suan, Eric P, Eting, Eva, Sola, Federico Furno, de Bats, Flore, Bandello, Francesco, Gómez-Ulla, Francisco, Devin, François, Holz, Frank G, Chen, Fred K, Makkouk, Fuad, Dyer, Gawain, Spital, George, Staurenghi, Giovanni, Stoller, Glenn, Cousins, Gwen, Salehi-Had, Hani, Agostini, Hansjürgen, Eleftheriadis, Haralabos, Weiss, Harold, Sultan, Harris C, Massé, Hélène, Pearce, Ian, Dias, Indra, Barbazetto, Irene, Rosenblatt, Irit, Suñer, Ivan J, Kovach, Jaclyn L, Kaluzny, Jakub, Borthwick, James, Howard, James G, Wong, James, Ernest, Jan, Němčanský, Jan, Ysasaga, Jason Edward, Handza, Jason M, Moreno, Javier Antonio Montero, Korobelnik, Jean-François, Heier, Jeffrey S, Arnold, Jennifer J, Brown, Jeremiah, Bafalluy, Joaquin, Pearlman, Joel, Pitcher, John D, Kitchens, John, Carlson, John P, Gilhotra, Jolly, Fein, Jordana, Monés, Jordi M, Luna, José Domingo, Moreno, José María Ruiz, Coney, Joseph M, Sallum, Juliana Maria Ferraz, Olsen, Karl R, Blobner, Katharina, Macoul, Katherine A, Oh, Kean T, Malik, Khurram Javed, Hattenbach, Lars-Olof, Kodjikian, Laurent, Neto, Laurentino Biccas, Singerman, Lawrence J, Altay, Lebriz, Sheck, Leo-H, Feiner, Leonard, Harris, Lindsey D, Chishold, Lionel D, Rao, Llewelyn J, Nehemy, Márcio Bittar, Elizalde, Maria Jose Capella, Gamulescu, Maria-Andreea, Saravia, Mario J, Johnson, Mark W, McKibbin, Martin, Maccumber, Mathew, Vidosevich, Matko, Ohr, Matthew P, Samuel, Michael A, Singer, Michael A, Cassell, Michael, Dollin, Michael, Elman, Michael J, Ip, Michael S, Goldstein, Michaella, Busquets, Miguel, Mititelu, Mihai, Shah, Milan, Veith, Miroslav, Fineman, Mitchell, Varano, Monica, Christmas, Nancy, Steinle, Nathan C, Chaudhry, Nauman, Chinskey, Nicholas D, Eter, Nicole, London, Nikolas J S, Mathalone, Nurit, Schlottmann, Patricio G, Coady, Patrick, Higgins, Patrick M, Raskauskas, Paul A, Yates, Paul A, Bernstein, Paul, Mitchell, Paul, Monsour, Paul, Raphaelian, Paul V, Stanga, Paulo E, Stodulka, Pavel, Issa, Peter Charbel, Pavan, Peter, Ferrone, Phil J, Oleksy, Piotr, Abraham, Prema, Mruthyunjaya, Prithvi, Nguyen, Quan Dong, Reddy, Rahul K, Khurana, Rahul N, Tuli, Raman, Tadayoni, Ramin, Katz, Randy Steven, Arora, Rashi, Schlingemann, Reinier O, Rosen, Richard B, Gale, Richard, Scartozzi, Richard, Isernharge, Ricky, Singh, Rishi P, Stoltz, Robert A, Avery, Robert L, Wirthlin, Robert S, Guymer, Robyn, Goldberg, Roger A, Frenkel, Ronald, Belfort, Rubens Jr, Mohand-Said, Saddek, Grisanti, Salvatore, Razavi, Sam, Fraser-Bell, Samantha, Shah, Sandeep N, Wickremasinghe, Sanjeewa, Haug, Sara Joy, Adrean, Sean D, Priglinger, Siegfried G, Esposti, Simona Degli, Guest, Stephen, Huddleston, Stephen, Itty, Sujit, Moon, Suk Jin, Bhatia, Sumit P, Gupta, Sunil, Patel, Sunil S, Garg, Sunir J, Joshi, Sunir, Nghiem-Buffet, Sylvia, Johnson, T Mark, Jaouni, Tareq, Ach, Thomas, Williams, Thomas R, Sheidow, Thomas, Cleland, Timothy P, You, Timothy T, Peto, Tunde, Konidaris, Vasileios, Gonzalez, Victor H, Korda, Vladimir, Freeman, William R, Bridges, William Z, Barak, Yoreh, Zagorski, Zbigniew, Yehoshua, Zohar, Dubska, Zora, Rosenfeld, Philip J, Guymer, Robyn H, Boyer, David, Grossi, Federico, Korobelnik, Jean-Francois, Slakter, Jason S, Waheed, Nadia K, Metlapally, Ravi, Steinle, Nathan, Francone, Anibal A, Hu, Allen, Deschatelets, Pascal, Francois, Cedric, Bliss, Caleb, Monés, Jordi, and Ribeiro, Ramiro

Published
2023
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229. Cytoreductive Nephrectomy for Patients with Metastatic Sarcomatoid and/or Rhabdoid Renal Cell Carcinoma Treated with Immune Checkpoint Therapy

Author

Hahn, Andrew W., Kotecha, Ritesh R., Viscuse, Paul V., Pieretti, Alberto C., Wiele, Andrew J., Jonasch, Eric, Lee, Chung-Han, Gao, Jianjun, Zurita, Amado J., Shah, Amishi Y., Campbell, Matthew T., Sharma, Padmanee, Motzer, Robert J., Russo, Paul, Wood, Christopher G., Tannir, Nizar M., Voss, Martin H., Karam, Jose A., Hakimi, A. Ari, and Msaouel, Pavlos

Published
2023
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231. Global transpiration data from sap flow measurements: the SAPFLUXNET database

Author

Poyatos, Rafael, Granda, Víctor, Flo, Víctor, Adams, Mark A, Adorján, Balázs, Aguadé, David, Aidar, Marcos PM, Allen, Scott, Alvarado-Barrientos, M Susana, Anderson-Teixeira, Kristina J, Aparecido, Luiza Maria, Arain, M Altaf, Aranda, Ismael, Asbjornsen, Heidi, Baxter, Robert, Beamesderfer, Eric, Berry, Z Carter, Berveiller, Daniel, Blakely, Bethany, Boggs, Johnny, Bohrer, Gil, Bolstad, Paul V, Bonal, Damien, Bracho, Rosvel, Brito, Patricia, Brodeur, Jason, Casanoves, Fernando, Chave, Jérôme, Chen, Hui, Cisneros, Cesar, Clark, Kenneth, Cremonese, Edoardo, Dang, Hongzhong, David, Jorge S, David, Teresa S, Delpierre, Nicolas, Desai, Ankur R, C., Frederic, Dohnal, Michal, Domec, Jean-Christophe, Dzikiti, Sebinasi, Edgar, Colin, Eichstaedt, Rebekka, El-Madany, Tarek S, Elbers, Jan, Eller, Cleiton B, Euskirchen, Eugénie S, Ewers, Brent, Fonti, Patrick, Forner, Alicia, Forrester, David I, Freitas, Helber C, Galvagno, Marta, Garcia-Tejera, Omar, Ghimire, Chandra Prasad, Gimeno, Teresa E, Grace, John, Granier, André, Griebel, Anne, Guangyu, Yan, Gush, Mark B, Hanson, Paul J, Hasselquist, Niles J, Heinrich, Ingo, Hernandez-Santana, Virginia, Herrmann, Valentine, Hölttä, Teemu, Holwerda, Friso, Irvine, James, Ayutthaya, Supat Isarangkool Na, Jarvis, Paul G, Jochheim, Hubert, Joly, Carlos A, Kaplick, Julia, Kim, Hyun Seok, Klemedtsson, Leif, Kropp, Heather, Lagergren, Fredrik, Lane, Patrick, Lang, Petra, Lapenas, Andrei, Lechuga, Víctor, Lee, Minsu, Leuschner, Christoph, Limousin, Jean-Marc, Linares, Juan Carlos, Linderson, Maj-Lena, Lindroth, Anders, Llorens, Pilar, López-Bernal, Álvaro, Loranty, Michael M, Lüttschwager, Dietmar, Macinnis-Ng, Cate, Maréchaux, Isabelle, Martin, Timothy A, Matheny, Ashley, McDowell, Nate, McMahon, Sean, Meir, Patrick, and Mészáros, Ilona

Subjects
Life on Land, Atmospheric Sciences, Geochemistry, Physical Geography and Environmental Geoscience
Abstract

Plant transpiration links physiological responses of vegetation to water supply and demand with hydrological, energy, and carbon budgets at the land-atmosphere interface. However, despite being the main land evaporative flux at the global scale, transpiration and its response to environmental drivers are currently not well constrained by observations. Here we introduce the first global compilation of whole-plant transpiration data from sap flow measurements (SAPFLUXNET, https://sapfluxnet.creaf.cat/, last access: 8 June 2021). We harmonized and quality-controlled individual datasets supplied by contributors worldwide in a semi-automatic data workflow implemented in the R programming language. Datasets include sub-daily time series of sap flow and hydrometeorological drivers for one or more growing seasons, as well as metadata on the stand characteristics, plant attributes, and technical details of the measurements. SAPFLUXNET contains 202 globally distributed datasets with sap flow time series for 2714 plants, mostly trees, of 174 species. SAPFLUXNET has a broad bioclimatic coverage, with woodland/shrubland and temperate forest biomes especially well represented (80% of the datasets). The measurements cover a wide variety of stand structural characteristics and plant sizes. The datasets encompass the period between 1995 and 2018, with 50% of the datasets being at least 3 years long. Accompanying radiation and vapour pressure deficit data are available for most of the datasets, while on-site soil water content is available for 56% of the datasets. Many datasets contain data for species that make up 90% or more of the total stand basal area, allowing the estimation of stand transpiration in diverse ecological settings. SAPFLUXNET adds to existing plant trait datasets, ecosystem flux networks, and remote sensing products to help increase our understanding of plant water use, plant responses to drought, and ecohydrological processes. SAPFLUXNET version 0.1.5 is freely available from the Zenodo repository (10.5281/zenodo.3971689; Poyatos et al., 2020a). The "sapfluxnetr"R package-designed to access, visualize, and process SAPFLUXNET data-is available from CRAN.

Published
2021

232. Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2

Author

Azumaya, Caleigh M, Braxton, Julian R, Brilot, Axel F, Gupta, Meghna, Li, Fei, Lopez, Kyle E, Melo, Arthur, Merz, Gregory E, Moss, Frank, Paulino, Joana, Pospiech, Thomas H, Pourmal, Sergei, Puchades, Cristina, Rizo, Alexandrea N, Smith, Amber M, Sun, Ming, Thomas, Paul V, Wang, Feng, Yu, Zanlin, Asarnow, Daniel, Campbell, Melody G, Chio, Cynthia M, Chio, Un Seng, Dickinson, Miles Sasha, Diwanji, Devan, Faust, Bryan, Hoppe, Nick, Jin, Mingliang, Li, Junrui, Liu, Yanxin, Nguyen, Henry C, Sangwan, Smriti, Trenker, Raphael, Trinidad, Donovan, Tse, Eric, Zhang, Kaihua, Zhou, Fengbo, Billesboelle, Christian, Bowen, Alisa, Li, Yen-Li, Nguyen, Phuong, Nowotny, Carlos, Safari, Mali, Schaefer, Kaitlin, Tsui, Tsz Kin Martin, Whitis, Natalie, Zhao, Jianhua, Kim, Kate, Moritz, Michelle, Owens, Tristan W, Peters, Jessica K, Biel, Justin, Deshpande, Ishan, Herrera, Nadia, Kratochvil, Huong T, Liu, Xi, Schulze-Gahmen, Ursula, Young, Iris D, Chen, Jen, Diallo, Amy, Doan, Loan, Flores, Sebastian, Lam, Victor L, Li, Yang, Lo, Megan, Thwin, Aye C, Titus, Erron W, Zhang, Yang, and Bulkley, David

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biodefense, Vaccine Related, Clinical Research, Prevention, Lung, Emerging Infectious Diseases, Infectious Diseases, Pneumonia & Influenza, Pneumonia, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, Good Health and Well Being, Angiotensin-Converting Enzyme 2, Animals, Antibodies, Neutralizing, Antibodies, Viral, Binding Sites, Antibody, Chlorocebus aethiops, Cryoelectron Microscopy, HEK293 Cells, Humans, Models, Molecular, Peptide Library, Protein Binding, Protein Conformation, alpha-Helical, Protein Conformation, beta-Strand, Protein Interaction Domains and Motifs, SARS-CoV-2, Single-Chain Antibodies, Spike Glycoprotein, Coronavirus, Vero Cells, QCRG Structural Biology Consortium, Medicinal and Biomolecular Chemistry, Biochemistry and Cell Biology, Biochemistry & Molecular Biology, Biochemistry and cell biology, Medicinal and biomolecular chemistry
Abstract

Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1,400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with a half-maximal inhibitory concentration (IC50) of 4.0 nM (180 ng ml-1). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy.

Published
2021

241. Additional Skills Acquisition Programme (ASAP) Project: The Case of an Employability Enhancement Initiative in India

Author

M., Nimmi P., Mathew, Paul V., and Donald, William E.

Abstract

Purpose: The purpose of this paper is to explore an employability enhancement initiative, the Additional Skills Acquisition Programme (ASAP) project in the state of Kerala, India, as a case for the inclusive development of employability in college and university students. Design/methodology/approach: ASAP is applied as a case study to examine the employability enhancement initiative in India. Findings: Participation in the ASAP project led to increased measures of employability. These increases were most pronounced in women and individuals living below the poverty line. Partnerships between educational institutions and organisations focusing on students' technical and skill development can help overcome local and national talent shortages. Originality/value: The theoretical implications come from addressing the lack of representation of skills based employability initiatives among students from India in the vocational behaviour literature. Practical implications come from knowledge sharing of innovative strategies to enhance the employability outcomes of individuals entering the labour market. New ways to overcome the reported mismatch in business education between curriculum content and the development of employability skills in graduates are presented. Benefits for diversity and inclusion are also provided.

Published
2022
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242. An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike

Author

Schoof, Michael, Faust, Bryan, Saunders, Reuben A, Sangwan, Smriti, Rezelj, Veronica, Hoppe, Nick, Boone, Morgane, Billesbølle, Christian B, Puchades, Cristina, Azumaya, Caleigh M, Kratochvil, Huong T, Zimanyi, Marcell, Deshpande, Ishan, Liang, Jiahao, Dickinson, Sasha, Nguyen, Henry C, Chio, Cynthia M, Merz, Gregory E, Thompson, Michael C, Diwanji, Devan, Schaefer, Kaitlin, Anand, Aditya A, Dobzinski, Niv, Zha, Beth Shoshana, Simoneau, Camille R, Leon, Kristoffer, White, Kris M, Chio, Un Seng, Gupta, Meghna, Jin, Mingliang, Li, Fei, Liu, Yanxin, Zhang, Kaihua, Bulkley, David, Sun, Ming, Smith, Amber M, Rizo, Alexandrea N, Moss, Frank, Brilot, Axel F, Pourmal, Sergei, Trenker, Raphael, Pospiech, Thomas, Gupta, Sayan, Barsi-Rhyne, Benjamin, Belyy, Vladislav, Barile-Hill, Andrew W, Nock, Silke, Liu, Yuwei, Krogan, Nevan J, Ralston, Corie Y, Swaney, Danielle L, García-Sastre, Adolfo, Ott, Melanie, Vignuzzi, Marco, Walter, Peter, Manglik, Aashish, Braxton, Julian R, Lopez, Kyle E, Melo, Arthur, Paulino, Joana, Pospiech, Thomas H, Thomas, Paul V, Wang, Feng, Yu, Zanlin, Dickinson, Miles Sasha, Asarnow, Daniel, Campbell, Melody G, Li, Junrui, Tsui, Tsz Kin Martin, Trinidad, Donovan, Tse, Eric, Zhou, Fengbo, Herrera, Nadia, and Schulze-Gahmen, Ursula

Subjects
Biochemistry and Cell Biology, Biological Sciences, Lung, Vaccine Related, Prevention, Infectious Diseases, Pneumonia, Pneumonia & Influenza, Biodefense, Emerging Infectious Diseases, Angiotensin-Converting Enzyme 2, Animals, Antibodies, Neutralizing, Antibodies, Viral, Antibody Affinity, Chlorocebus aethiops, Cryoelectron Microscopy, Humans, Neutralization Tests, Protein Binding, Protein Stability, Single-Domain Antibodies, Spike Glycoprotein, Coronavirus, Vero Cells, QCRG Structural Biology Consortium, General Science & Technology
Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus enters host cells via an interaction between its Spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2). By screening a yeast surface-displayed library of synthetic nanobody sequences, we developed nanobodies that disrupt the interaction between Spike and ACE2. Cryo-electron microscopy (cryo-EM) revealed that one nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains locked into their inaccessible down state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains function after aerosolization, lyophilization, and heat treatment, which enables aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia.

Published
2020

247. The Magnitude and Impact of Food Allergens and the Potential of AI-Based Non-Destructive Testing Methods in Their Detection and Quantification

Author

Akinbode A. Adedeji, Paul V. Priyesh, and Adeniyi A. Odugbemi

Subjects
food allergens, ELISA, biosensors, non-destructive method, celiac, eliciting doses, Chemical technology, TP1-1185
Abstract

Reaction to food allergens is on the increase and so is the attending cost on consumers, the food industry, and society at large. According to FDA, the “big-eight” allergens found in foods include wheat (gluten), peanuts, egg, shellfish, milk, tree nuts, fish, and soybeans. Sesame was added to the list in 2023, making the target allergen list nine instead of eight. These allergenic foods are major ingredients in many food products that can cause severe reactions in those allergic to them if found at a dose that can elicit a reaction. Defining the level of contamination that can elicit sensitivity is a work in progress. The first step in preventing an allergic reaction is reliable detection, then an effective quantification method. These are critical steps in keeping contaminated foods out of the supply chain of foods with allergen-free labels. The conventional methods of chemical assay, DNA-PCR, and enzyme protocols like enzyme-linked immunosorbent assay are effective in allergen detection but slow in providing a response. Most of these methods are incapable of quantifying the level of allergen contamination. There are emerging non-destructive methods that combine the power of sensors and machine learning to provide reliable detection and quantification. This review paper highlights some of the critical information on the types of prevalent food allergens, the mechanism of an allergic reaction in humans, the measure of allergenic sensitivity and eliciting doses, and the conventional and emerging AI-based methods of detection and quantification—the merits and downsides of each type.

Published
2024
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248. Impaired IgM Memory B Cell Function Is Common in Coeliac Disease but Conjugate Pneumococcal Vaccination Induces Robust Protective Immunity

Author

Olivia G. Moscatelli, Amy K. Russell, Lee M. Henneken, Melinda Y. Hardy, Nadia Mazarakis, Rachel Higgins, Jesse Ekin, Harry McLeod, Paul Simkin, Paul V. Licciardi, Vanessa L. Bryant, and Jason A. Tye-Din

Subjects
coeliac disease, IgM memory B cells, hyposplenism, pneumococcal vaccination, Medicine
Abstract

Coeliac disease (CD) is associated with hyposplenism, an acquired impairment of spleen function associated with reduced IgM memory B cells and increased susceptibility to serious pneumococcal infection. Little is known about the immune implications of hyposplenism in CD or the optimal pneumococcal vaccination strategy. In this study, the immune effects of hyposplenism in CD, and the accuracy of screening approaches and protective responses induced by two different pneumococcal vaccines were examined. Active and treated CD cohorts, and healthy and surgically splenectomised controls underwent testing for the presence of Howell–Jolly bodies and pitted red cells, spleen ultrasound, and immune assessment of IgM memory B cell frequency and IgM memory B cell responses to T cell-dependent (TD) or T cell-independent (TI) stimulation. Responses following conjugate (TD) and polysaccharide (TI) pneumococcal vaccination were compared using ELISA and opsonophagocytic assays. Although hyposplenism is rare in treated CD (5.1%), functional B cell defects are common (28–61%) and are not detected by current clinical tests. Conjugate pneumococcal vaccination induced superior and sustained protection against clinically relevant serotypes. Clinical practice guidelines in CD should recommend routine pneumococcal vaccination, ideally with a conjugate vaccine, of all patients in lieu of hyposplenism screening.

Published
2024
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250. Altered sphingolipid pathway in SARS-CoV-2 infected human lung tissue

Author

Rabisa J. Khan, Sierra L. Single, Christopher S. Simmons, Mohammad Athar, Yuelong Liu, Sandeep Bodduluri, Paul V. Benson, Kayla F. Goliwas, and Jessy S. Deshane

Subjects
sphingolipid signaling, SARS-CoV-2, COVID-19, COVID-19 convalescence, lung structural remodeling, Immunologic diseases. Allergy, RC581-607
Abstract

IntroductionThe SARS-CoV-2 mediated COVID-19 pandemic has impacted millions worldwide. Hyper-inflammatory processes, including cytokine storm, contribute to long-standing tissue injury and damage in COVID-19. The metabolism of sphingolipids as regulators of cell survival, differentiation, and proliferation has been implicated in inflammatory signaling and cytokine responses. Sphingosine-kinase-1 (SK1) and ceramide-synthase-2 (CERS2) generate metabolites that regulate the anti- and pro-apoptotic processes, respectively. Alterations in SK1 and CERS2 expression may contribute to the inflammation and tissue damage during COVID-19. The central objective of this study is to evaluate structural changes in the lung post-SARS-CoV-2 infection and to investigate whether the sphingolipid rheostat is altered in response to SARS-CoV-2 infection.MethodsCentral and peripheral lung tissues from COVID-19+ or control autopsies and resected lung tissue from COVID-19 convalescents were subjected to histologic evaluation of airspace and collagen deposisiton, and immunohistochemical evaluation of SK1 and CERS2.ResultsHere, we report significant reduction in air space and increase in collagen deposition in lung autopsy tissues from patients who died from COVID-19 (COVID-19+) and COVID-19 convalescent individuals. SK1 expression increased in the lungs of COVID-19+ autopsies and COVID-19 convalescent lung tissue compared to controls and was mostly associated with Type II pneumocytes and alveolar macrophages. No significant difference in CERS2 expression was noted. SARS-CoV-2 infection upregulates SK1 and increases the ratio of SK1 to CERS2 expression in lung tissues of COVID-19 autopsies and COVID-19 convalescents.DiscussionThese data suggest an alteration in the sphingolipid rheostat in lung tissue during COVID-19, suggesting a potential contribution to the inflammation and tissue damage associated with viral infection.

Published
2023
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