Search Results - [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment by Lensink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen-You, Schneidman-Duhovny, Dina, Segura, Joan, Fernandez-Fuentes, Narcis, Viswanath, Shruthi, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Rie Lee, Gyu, Seok, Chaok, Qin, Sanbo, Zhou, Huan-Xiang, Ritchie, David W., Maigret, Bernard, Devignes, Marie-Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël A.G., Bates, Paul A., Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra S., Weng, Zhiping, Vreven, Thom, Pierce, Brian G., Borrman, Tyler M., Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Rodrigues, João P.G.L.M., van Zundert, Gydo, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien S.J., Visscher, Koen, Kastritis, Panagiotis L., Bonvin, Alexandre M.J.J., Xu, Xianjin, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna X., Kim, Hyung-Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil J., Fuller, Jonathan C., Wade, Rebecca C., Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A., Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain H., Férnandez-Recio, Juan, Joung, Jong Young, Kim, Jong Yun, Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David R., Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, Del Carpio, Carlos A., Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Gray, Jeffrey J., Chermak, Edrisse, Cavallo, Luigi, Oliva, Romina, Tovchigrechko, Andrey, Wodak, Shoshana J.

“…ABSTRACT We present the results for CAPRI Round 30, the first joint CASP‐CAPRI experiment, which brought together experts from the protein structure prediction…”
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On the Mechanisms of Biliary Flux by Vartak, Nachiket, Drasdo, Dirk, Geisler, Fabian, Itoh, Tohru, P.J.Oude Elferink, Ronald, Graaf, Stan F.J., Chiang, John, Keitel, Verena, Trauner, Michael, Jansen, Peter, Hengstler, Jan G.

“…Since the late 1950s, transport of bile in the liver has been described by the “osmotic concept,” according to which bile flows into the canaliculi toward the…”
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Adjusting D-dimer to Lung Disease Extent to Exclude Pulmonary Embolism in COVID-19 Patients (Co-LEAD) by Planquette, Benjamin, Khider, Lina, Berre, Alice Le, Soudet, Simon, Pernod, Gilles, Mao, Raphaël Le, Besutti, Matthieu, Gendron, Nicolas, Yanoutsos, Alexandra, Smadja, David M., Goudot, Guillaume, Kahf, Salma Al, Mohamedi, Nassim, Hamoud, Antoine Al, Philippe, Aurélien, Fournier, Laure, Rance, Bastien, Diehl, Jean-Luc, Mirault, Tristan, Messas, Emmanuel, Emmerich, Joseph, Chocron, Richard, Couturaud, Francis, Ferretti, Gilbert, Sevestre, Marie Antoinette, Meneveau, Nicolas, Chatellier, Gilles, Sanchez, Olivier

“…Abstract Objective  D-dimer measurement is a safe tool to exclude pulmonary embolism (PE), but its specificity decreases in coronavirus disease 2019 (COVID-19)…”
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Randomly stacked open cylindrical shells as functional mechanical energy absorber by Sano, Tomohiko G., Hohnadel, Emile, Kawata, Toshiyuki, Métivet, Thibaut, Bertails-Descoubes, Florence

“… Combining experiments and simulations, we demonstrate that the stacked shells can absorb and store mechanical energy upon compression by exploiting…”
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Pragmatic Coarse-Graining of Proteins: Models and Applications by Borges-Araújo, Luís, Patmanidis, Ilias, Singh, Akhil P, Santos, Lucianna H S, Sieradzan, Adam K, Vanni, Stefano, Czaplewski, Cezary, Pantano, Sergio, Shinoda, Wataru, Monticelli, Luca, Liwo, Adam, Marrink, Siewert J, Souza, Paulo C T

“… For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein…”
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MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation by Vuillemot, Rémi, Mirzaei, Alex, Harastani, Mohamad, Hamitouche, Ilyes, Fréchin, Léo, Klaholz, Bruno P., Miyashita, Osamu, Tama, Florence, Rouiller, Isabelle, Jonic, Slavica

“…•It uses MD-simulation-based 3D-to-2D flexible fitting of an atomic structure to images.•It refines conformational landscapes using principal motion directions learned iteratively…”
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ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets by Brozovic, Matija, Dantec, Christelle, Dardaillon, Justine, Dauga, Delphine, Faure, Emmanuel, Gineste, Mathieu, Louis, Alexandra, Naville, Magali, Nitta, Kazuhiro R, Piette, Jacques, Reeves, Wendy, Scornavacca, Céline, Simion, Paul, Vincentelli, Renaud, Bellec, Maelle, Aicha, Sameh Ben, Fagotto, Marie, Guéroult-Bellone, Marion, Haeussler, Maximilian, Jacox, Edwin, Lowe, Elijah K, Mendez, Mickael, Roberge, Alexis, Stolfi, Alberto, Yokomori, Rui, Brown, C Titus, Cambillau, Christian, Christiaen, Lionel, Delsuc, Frédéric, Douzery, Emmanuel, Dumollard, Rémi, Kusakabe, Takehiro, Nakai, Kenta, Nishida, Hiroki, Satou, Yutaka, Swalla, Billie, Veeman, Michael, Volff, Jean-Nicolas, Lemaire, Patrick

“…Abstract ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to…”
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Identification of biological regulatory networks from Process Hitting models by Folschette, Maxime, Paulevé, Loïc, Inoue, Katsumi, Magnin, Morgan, Roux, Olivier

“…Qualitative formalisms offer a well-established alternative to the more traditionally used differential equation models of Biological Regulatory Networks…”
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Finite-displacement computation of the electron-phonon interaction within the projector augmented-wave method by Chaput, L., Togo, Atsushi, Tanaka, Isao

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Relating Near-Infrared Light Path-Length Modifications to the Water Content of Scattering Media in Near-Infrared Spectroscopy: Toward a New Bouguer-Beer-Lambert Law by Mallet, Alexandre, Tsenkova, Roumiana, Muncan, Jelena, Charnier, Cyrille, Latrille, Éric, Bendoula, Ryad, Steyer, Jean-Philippe, Roger, Jean-Michel

“…In near-infrared spectroscopy (NIRS), the linear relationship between absorbance and an absorbing compound concentration has been strictly defined by the…”
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Inclusive fitness theory and eusociality by Abe, Jun, Alcock, John, Andre, Jean-Baptiste, van Baalen, Minus, Balloux, Francois, Balshine, Sigal, Barton, Nick, Beukeboom, Leo W., Biernaskie, Jay M., Breed, Michael, Brown, Sam, Bshary, Redouan, Buckling, Angus, Burley, Nancy T., Burton-Chellew, Max N., Cant, Michael A., Chapuisat, Michel, Clutton-Brock, Tim, Cosmides, Leda, Coyne, Jerry A., Crespi, Bernard, Curry, Robert L., Dall, Sasha R. X., Dickinson, Janis L., Dugatkin, Lee Alan, Mouden, Claire El, Emlen, Stephen T., Evans, Jay, Ferriere, Regis, Field, Jeremy, Foster, Kevin, Foster, William A., Fox, Charles W., Gadau, Juergen, Gardner, Andy, Gardner, Michael G., Getty, Thomas, Grafen, Alan, Grosberg, Rick, Grozinger, Christina M., Gouyon, Pierre-Henri, Gwynne, Darryl, Harvey, Paul H., Hatchwell, Ben J., Helantera, Heikki, Helms, Ken R., Hill, Kim, Jiricny, Natalie, Johnstone, Rufus A., Kacelnik, Alex, Kiers, E. Toby, Komdeur, Jan, Korb, Judith, Kronauer, Daniel, Kümmerli, Rolf, Lehmann, Laurent, Lion, Sébastien, Lyon, Bruce, Marshall, James A. R., McElreath, Richard, Michod, Richard E., Mock, Douglas, Montgomerie, Robert, Moore, Allen J., Mueller, Ulrich G., Pamilo, Pekka, Pedersen, Jes S., Pfennig, David, Reece, Sarah E., Reeve, Hudson K., Reuter, Max, Roberts, Gilbert, Robson, Simon K. A., Roze, Denis, Rousset, Francois, Sachs, Joel L., Santorelli, Lorenzo, Schmid-Hempel, Paul, Shellmann-Sherman, Janet, Sherman, Paul W., Shuker, David M., Smith, Jeff, Spagna, Joseph C., Strassmann, Beverly, Sundström, Liselotte, Taborsky, Michael, Thompson, Graham, Tooby, John, Tsuji, Kazuki, Turillazzi, Stefano, Úbeda, Francisco, Vargo, Edward L., Voelkl, Bernard, Wenseleers, Tom, West, Stuart A., Westneat, David F., Wild, Geoff, Wrangham, Richard, Zeh, David W., Zink, Andrew

“…Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson Nature466, 1057–1062 (2010)10.1038/nature09205 ; Nowak et al. reply Nowak et al. 1 argue that inclusive…”
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High Throughput/Gate AES Hardware Architectures Based on Datapath Compression by Ueno, Rei, Homma, Naofumi, Morioka, Sumio, Miura, Noriyuki, Matsuda, Kohei, Nagata, Makoto, Bhasin, Shivam, Mathieu, Yves, Graba, Tarik, Danger, Jean-Luc

“…This article proposes highly efficient Advanced Encryption Standard (AES) hardware architectures that support encryption and both encryption and decryption…”
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Global Distribution of Zooplankton Biomass Estimated by In Situ Imaging and Machine Learning by Drago, Laetitia, Panaïotis, Thelma, Irisson, Jean-Olivier, Babin, Marcel, Biard, Tristan, Carlotti, François, Coppola, Laurent, Guidi, Lionel, Hauss, Helena, Karp-Boss, Lee, Lombard, Fabien, McDonnell, Andrew M. P., Picheral, Marc, Rogge, Andreas, Waite, Anya M., Stemmann, Lars, Kiko, Rainer

“…Zooplankton plays a major role in ocean food webs and biogeochemical cycles, and provides major ecosystem services as a main driver of the biological carbon…”
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Modification of endothelial nitric oxide synthase by 4-oxo-2(E)-nonenal(ONE) in preeclamptic placentas by Guerby, Paul, Swiader, Audrey, Tasta, Oriane, Pont, Frédéric, Rodriguez, Frédéric, Parant, Olivier, Vayssière, Christophe, Shibata, Takahiro, Uchida, Koji, Salvayre, Robert, Negre-Salvayre, Anne

“…Preeclampsia (PE) is a leading cause of pregnancy complications, affecting 3–7% of pregnant women worldwide. The pathophysiology of preeclampsia involves a…”
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Economic burden in non‐Hodgkin lymphoma survivors: The French Lymphoma Study Association SIMONAL cross‐sectional study by Nerich, Virginie, Guyeux, Christophe, Henry‐Amar, Michel, Couturier, Raphaël, Thieblemont, Catherine, Ribrag, Vincent, Tilly, Hervé, Haioun, Corinne, Casasnovas, René‐Olivier, Morschhauser, Franck, Feugier, Pierre, Sibon, David, Ysebaert, Loic, Nicolas‐Virelizier, Emmanuelle, Broussais‐Guillaumot, Florence, Damaj, Gandhi L., Jais, Jean‐Philippe, Salles, Gilles, Woronoff‐Lemsi, Macha, Mounier, Nicolas

“…Background No study has focused on the economic burden in non‐Hodgkin lymphoma (NHL) survivors, even though this knowledge is essential. This study reports on…”
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A survey of impact on industrial parks caused by the 2011 Great East Japan earthquake and tsunami by Yu, Junlei, Cruz, Ana Maria, Piatyszek, Eric, Lesbats, Michel, Tardy, Alicja, Hokugo, Akihiko, Tatano, Hirokazu

“…During the 2011 Great East Japan Earthquake and Tsunami (GEJET), many industrial facilities were affected to different extents by the earthquake and/or…”
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Numerical investigation of floating zone silicon using Halbach array magnets by Han, Xue-Feng, Kakimoto, Koichi, Alradi, Samah, Zaidat, Kader

“…•The application of Halbach array magnets for FZ process is proposed.•Magnetic field in the melt provided by Halbach array magnets is adequately…”
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Thermal analysis of fractures at Cerberus Fossae, Mars: Detection of air convection in the porous debris apron by Antoine, R., Lopez, T., Baratoux, D., Rabinowicz, M., Kurita, K.

“…► Analysis of thermal data of the surface of Mars. ► Role of gas circulation in the ground in controlling surface temperature. ► Thermal anomalies at Cerberus…”
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Generic HTR Models for Medieval Manuscripts. The CREMMALab Project by Pinche, Ariane

“…In the Humanities, the emergence of digital methods has opened up research questions to quantitative analysis. This is why HTR technology is increasingly…”
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Measuring phenology uncertainty with large scale image processing by Alles, Guilherme, Comba, João, Vincent, Jean-Marc, Nagai, Shin, Schnorr, Lucas Mello

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