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4. Safety and efficacy of doravirine as first-line therapy in adults with HIV-1: week 192 results from the open-label extensions of the DRIVE-FORWARD and DRIVE-AHEAD phase 3 trials

Author

Martins, Marcelo D, Cahn, Pedro E, Lopardo, Gustavo D, Porteiro, Norma, Bloch, Mark Theo, Baker, David Alfred, Roth, Norman, Moore, Richard J, Finlayson, Robert James, McMahon, James, Rieger, Armin, Zoufaly, Alexander, Schmied, Brigitte, Hartl, Sylvia, Zangerle, Robert, Smaill, Fiona, Walmsley, Sharon L, Conway, Brian, Rachlis, Anita, Smith, Graham H R, Perez Cortes, Carlos, Afani, Alejandro, Campos Barker, Maria Isabel E, Chahin Anania, Carolina Eugenia, Reyes, Marcelo J. Wolff, Gerstoft, Jan, Weis, Nina, Laursen, Alex Lund, Molina, Jean-Michel, Yazdanpanah, Yazdan, Cotte, Laurent, Raffi, Francois, Slama, Laurence, Morlat, Philippe, Girard, Pierre-Marie, Katlama, Christine, Rockstroh, Juergen K, Arasteh, Keikawus, Esser, Stefan, Stoehr, Albrecht, Stellbrink, Hans-Juergen, Stoll, Matthias, Schuermann, Dirk, Faetkenheuer, Gerd, Bogner, Johannes Richard, Lutz, Thomas, Baumgarten, Axel, Jaeger, Hans, Wiese, Carmen, Gori, Andrea, Migliorino, Guglielmo Marco, Coltan, Gabriel, Constandis, Felicia, Erscoiu, Simona M, Prisacariu, Liviu-Jany, Rugina, Sorin, Streinu-Cercel, Adrian, Pokrovsky, Vadim V, Zakharova, Natalia, Shuldyakov, Andrey Anatolyevich, Ryamova, Elena Pavlovna, Kulagin, Valeriy Viktorovich, Tsybakova, Olga Aleksandrovna, Orlova-Morozova, Elena, Nagimova, Firaya, Voronin, Evgeniy, Shimonova, Tatiana Evgenyevna, Kozyrev, Oleg Anatolyevich, Orrell, Catherine, Lombaard, Johannes Jurgens, Botes, Margaretha Elizabeth, de Jager, Marleen, Segorb, Joaquin Portilla, Gatell Artigas, Josep Maria, Mallolas Masferrer, Josep, Guillen, Santiago Moreno, Perez Elias, Maria Jesus, Arribas Lopez, Jose R, Puigmal, Eugenia Negredo, Podzamczer Palter, Daniel, Ortega, Frederico Pulido, Garcia, Jesus Troya, de los Santos Gil, Ignacio, Berenguer, Juan, Nelson, Mark Richard, Williams, Ian G, Johnson, Margaret A, Khoo, Saye, Schembri, Gabriel, Clarke, Amanda, Gompels, Mark, Fox, Julie Meriel, Lwanga, Julianne, Taylor, Steven John, Dockrell, David Harold, Kegg, Stephen, Hagins, Debbie P, Osiyemi, Olayemi O, Prelutsky, David James, Ramgopal, Moti N, Scarsella, Anthony J, Dretler, Robin, DeJesus, Edwin, Bettacchi, Christopher J, Sims III, James, Clay, Patrick G, Bellos, Nicholaos C, Thompson, Melanie A, Montero, Jose, McDonald, Cheryl K, Creticos, Catherine, Shamblaw, David, Terrelonge, Antonio E, Valdes, Martin, Tashima, Karen T, Robbins, William J, Elion, Richard A, Goldstein, Deborah, Slim, Jihad, Lalezari, Jacob Paul, Pushkin, Richard, Lalla-Reddy, Sujata N, Win, Sanda S, Ruane, Peter Jerome, Mills, Anthony Martin, Cade, Jerry L, Campo, Rafael, Dietz, Craig A, Hoffman-Terry, Margaret, Blick, Gary, Rubin, David Scott, Mayer, Cynthia, Rondon, Juan Carlos, Cook, Paul P, Daar, Eric, Kumar, Princy N, Swindells, Susan, Castro, Jose Guillermo, Morales-Ramirez, Javier O, Santiago, Lizette, Santana-Bagur, Jorge L, Vandekerckhove, Linos, Florence, Eric, De Wit, Stephane, Derdelinckx, Inge, Vandercam, Bernard, Belkhir, Leila, De Wet, Joseph, Lebouche, Bertrand, Trottier, Benoit, Longpre, Daniele, Szabo, Jason, LeBlanc, Roger P, Jensen, Werner, Gonzalez, Alvaro Rojas, Beltran, Carlos, Sussmann, Otto Alberto, Velez, Juan Diego, Onate, Jose Millan, Nielsen, Henrik, Degen, Olaf, Stephan, Christoph, Arathoon, Eduardo, Lopez, Rudy Manuel, Rojas Alvarado, Evelyn Michelle, Gonzalez Patzan, Luis Demetrio, Meija, Carlos R, Pinzon, Rodolfo, Parchment, Charles, Sthoeger, Zev, Chowers, Michal, Riesenberg, Klaris, Shahar, Eduardo, Levy, Itzchak, Quintero Perez, Nora Patricia, Andrade-Villanueva, Jaime Federico, Crabtree Ramirez, Brenda Eloisa, Rijnders, Bart, den Hollander, Jan G, Handy, Rupert, Morales, Nilo Bonifacio, Hidalgo, Jose Alfredo, Infante, Rosa Mercedes, Matos Prado, Eduardo Demetrio, Campos, Pablo E, Ticona Chaves, Eduardo Romulo, Pinedo, Yvett, Pacheco, Patricia, Maltez, Fernando Manuel, Cunha, Jose, Neves, Isabel, Serrao, Rosario, Melendez-Rivera, Ivan, Mendoza-Rodriguez, Rafael O, Maldonado-Rivera, Sandra, Ortiz-Lasanta, Grisell, Kizhlo, Svetlana, Freud, Hernando Knobel, Moreno, Jose Sanz, Mendez, Francisco Vera, Mohapi, Lerato, Mitha, Essack Aziz, Mahomed, Akbar Anvar, Fouche, Leon Frederik, Kaplan, Richard, Siddique, Naeem, Hoosen, Farzana, Rassool, Mohammed Siddique, Baraldi, Ezio, Calmy, Alexandra, Cavassini, Matthias, Fehr, Jan, Tsai, Hung-Chin, Lin, Hsi-Hsun, Huang, Chun-Kai, Ko, Wen-Chien, Lin, Yu-Hui, Chen, Su-Jung, Hung, Chien-Ching, Avihingsanon, Anchalee, Kiertiburanakul, Sasisopin, Ratanasuwan, Winai, Supparatpinyo, Khuanchai, Chetchotisakd, Ploenchan, Changpradub, Dhitiwat, Orkin, Chloe, Fox, Ashini, Winston, Alan, Ustianowski, Andrew, Yangco, Bienvenido G, Asmuth, David Michael, Vigil, Karen J, Berger, Daniel S, Bhatti, Laveeza, Campbell, Thomas, Casey, Kathleen K, Liu, Edward, Crofoot, Gordon E, Cunningham, Douglas, Feinberg, Judith, Fichtenbaum, Carl, Balamban Felizarta, Franco Antonio, Jefferson, Thomas T, Johnson, Marc Alexander, Lewis, Stanley T, Luque, Amneris E, Novak, Richard M, Sloan, Louis, Sweet, Donna E, Towner, William J, Zane, Ryan, Riedel, David J, Loftus, Richard Anton, Shon, Alyssa So Young, Mogyoros, Miguel, Tebas, Pablo, Scott, Mia Louise, Parenti, David M, Inciarte Portillo, Alexy, Cahn, Pedro, Lombaard, Johannes, Kumar, Sushma, Campbell, Havilland, Wan, Hong, Teal, Valerie, Jin Xu, Zhi, Asante-Appiah, Ernest, Sklar, Peter, Teppler, Hedy, and Lahoulou, Rima

Published
2024
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5. The Cryptosporidium parvum Kinome

Author

Artz Jennifer D, Wernimont Amy K, Allali-Hassani Abdellah, Zhao Yong, Amani Mehrnaz, Lin Yu-Hui, Senisterra Guillermo, Wasney Gregory A, Fedorov Oleg, King Oliver, Roos Annette, Lunin Vlad V, Qiu Wei, Finerty Patrick, Hutchinson Ashley, Chau Irene, von Delft Frank, MacKenzie Farrell, Lew Jocelyne, Kozieradzki Ivona, Vedadi Masoud, Schapira Matthieu, Zhang Chao, Shokat Kevan, Heightman Tom, and Hui Raymond

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Hundreds of millions of people are infected with cryptosporidiosis annually, with immunocompromised individuals suffering debilitating symptoms and children in socioeconomically challenged regions at risk of repeated infections. There is currently no effective drug available. In order to facilitate the pursuit of anti-cryptosporidiosis targets and compounds, our study spans the classification of the Cryptosporidium parvum kinome and the structural and biochemical characterization of representatives from the CDPK family and a MAP kinase. Results The C. parvum kinome comprises over 70 members, some of which may be promising drug targets. These C. parvum protein kinases include members in the AGC, Atypical, CaMK, CK1, CMGC, and TKL groups; however, almost 35% could only be classified as OPK (other protein kinases). In addition, about 25% of the kinases identified did not have any known orthologues outside of Cryptosporidium spp. Comparison of specific kinases with their Plasmodium falciparum and Toxoplasma gondii orthologues revealed some distinct characteristics within the C. parvum kinome, including potential targets and opportunities for drug design. Structural and biochemical analysis of 4 representatives of the CaMK group and a MAP kinase confirms features that may be exploited in inhibitor design. Indeed, screening CpCDPK1 against a library of kinase inhibitors yielded a set of the pyrazolopyrimidine derivatives (PP1-derivatives) with IC50 values of < 10 nM. The binding of a PP1-derivative is further described by an inhibitor-bound crystal structure of CpCDPK1. In addition, structural analysis of CpCDPK4 identified an unprecedented Zn-finger within the CDPK kinase domain that may have implications for its regulation. Conclusions Identification and comparison of the C. parvum protein kinases against other parasitic kinases shows how orthologue- and family-based research can be used to facilitate characterization of promising drug targets and the search for new drugs.

Published
2011
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6. Spatial interactions and oscillatory tragedies of the commons

Author

Lin, Yu-Hui and Weitz, Joshua S.

Subjects
Quantitative Biology - Populations and Evolution, Physics - Biological Physics
Abstract

A tragedy of the commons (TOC) occurs when individuals acting in their own self-interest deplete commonly-held resources, leading to a worse outcome than had they cooperated. Over time, the depletion of resources can change incentives for subsequent actions. Here, we investigate long-term feedback between game and environment across a continuum of incentives in an individual-based framework. We identify payoff-dependent transition rules that lead to oscillatory TOC-s in stochastic simulations and the mean field limit. Further extending the stochastic model, we find that spatially explicit interactions can lead to emergent, localized dynamics, including the propagation of cooperative wave fronts and cluster formation of both social context and resources. These dynamics suggest new mechanisms underlying how TOCs arise and how they might be averted., Comment: 5 pages and 3 figures in main text, 9 pages and 4 figures in supplementary material

Published
2019
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14. Performance of new 8-inch photomultiplier tube used for the Tibet muon-detector array

Author

Zhang, Ying, Huang, Jing, Chen, Ding, Zhai, Liu-Ming, Chen, Xu, Hu, Xiao-Bin, Lin, Yu-Hui, Zhang, Xue-Yao, Feng, Cun-Feng, Jia, Huan-Yu, Zhou, Xun-Xiu, Dan-Zen, Luo-bu, Chen, Tian-Lu, Laba, Ci-Ren, Mao-Yuan, Gao, Qi, and Zha-xi, Ci-ren

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract

A new hybrid experiment has been constructed to measure the chemical composition of cosmic rays around the "knee" in the wide energy range by the Tibet AS$\gamma$ collaboration at Tibet, China, since 2014. They consist of a high-energy air-shower-core array (YAC-II), a high-density air-shower array (Tibet-III) and a large underground water-Cherenkov muon-detector array (MD). In order to obtain the primary proton, helium and iron spectra and their "knee" positions in the energy range lower than $10^{16}$ eV, each of PMTs equipped to the MD cell is required to measure the number of photons capable of covering a wide dynamic range of 100 - $10^{6}$ photoelectrons (PEs) according to Monte Carlo simulations. In this paper, we firstly compare the characteristic features between R5912-PMT made by Japan Hamamatsu and CR365-PMT made by Beijing Hamamatsu. This is the first comparison between R5912-PMT and CR365-PMT. If there exists no serious difference, we will then add two 8-inch-in-diameter PMTs to meet our requirements in each MD cell, which are responsible for the range of 100 - 10000 PEs and 2000 - 1000000 PEs, respectively. That is, MD cell is expected to be able to measure the number of muons over 6 orders of magnitude., Comment: 5 pages, 8 figures

Published
2016
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17. Use of rippling to automate Event-B invariant preservation proofs

Author

Lin, Yu Hui, Bundy, Alan, Maclean, Ewen, and Gudmund, Grov

Subjects
004.01, Event-B
Abstract

The use of formal method techniques can contribute to the production of more reliable and dependable systems. However, a common bottleneck for the industrial adoption of formal methods techniques is proof automation. To address the challenge of proof automation, we aim to improve it by using automated theorem proving techniques. We set one popular formal method technique as our working domain in this thesis, that is, Event-B. More specifically, we target a family of proofs, i.e. invariant preservation (INV) proofs, which can account for a significant part of the proofs that needs human interactions. We apply one of the most successful automated theorem proving techniques, which is rippling, to improve the proof automation of Event-B INV POs. Rippling uses metalevel guidance to automate proofs, and it is in particular useful to develop proof patches to recover proofs based on the meta-level guidance when proof attempts fail. We are especially interested in the case when lemmas are required to recover failed proofs. We combine a scheme-based theory-exploration system, i.e. IsaScheme, with rippling to develop a proof patch for lemma discovery, i.e. ahLemma. In addition to ahLemma, we also develop two proof patches to suggest case-splits and to simplify the goal and hypotheses by rewriting. The combining use of rippling and these proof patches can improve the proof automation of INV POs.

Published
2015

20. Quantitative two-dimensional phase-contrast magnetic resonance imaging characterization of lower extremity venous disease: venous reflux versus venous obstruction

Author

Huang, Yao-Kuang, primary, Hsu, Yin-Chen, additional, Tseng, Yuan-Hsi, additional, Kao, Chih-Chen, additional, Ngo, Yeh Giin, additional, Lee, Chung-Yuan, additional, Yang, Teng-Yao, additional, Chang, Kuo-Song, additional, Chen, Pang-Yen, additional, Wang, Shih-Chung, additional, Chen, Sheng-Ya, additional, Lin, Yu-Hui, additional, and Chen, Chien-Wei, additional

Published
2023
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22. Safety and efficacy of doravirine as first-line therapy in adults with HIV-1: week 192 results from the open-label extensions of the DRIVE-FORWARD and DRIVE-AHEAD phase 3 trials

Author

Orkin, Chloe, Molina, Jean-Michel, Cahn, Pedro, Lombaard, Johannes, Supparatpinyo, Khuanchai, Kumar, Sushma, Campbell, Havilland, Wan, Hong, Teal, Valerie, Jin Xu, Zhi, Asante-Appiah, Ernest, Sklar, Peter, Teppler, Hedy, Lahoulou, Rima, Martins, Marcelo D, Cahn, Pedro E, Lopardo, Gustavo D, Porteiro, Norma, Bloch, Mark Theo, Baker, David Alfred, Roth, Norman, Moore, Richard J, Finlayson, Robert James, McMahon, James, Rieger, Armin, Zoufaly, Alexander, Schmied, Brigitte, Hartl, Sylvia, Zangerle, Robert, Smaill, Fiona, Walmsley, Sharon L, Conway, Brian, Rachlis, Anita, Smith, Graham H R, Perez Cortes, Carlos, Afani, Alejandro, Campos Barker, Maria Isabel E, Chahin Anania, Carolina Eugenia, Reyes, Marcelo J. Wolff, Gerstoft, Jan, Weis, Nina, Laursen, Alex Lund, Molina, Jean-Michel, Yazdanpanah, Yazdan, Cotte, Laurent, Raffi, Francois, Slama, Laurence, Morlat, Philippe, Girard, Pierre-Marie, Katlama, Christine, Rockstroh, Juergen K, Arasteh, Keikawus, Esser, Stefan, Stoehr, Albrecht, Stellbrink, Hans-Juergen, Stoll, Matthias, Schuermann, Dirk, Faetkenheuer, Gerd, Bogner, Johannes Richard, Lutz, Thomas, Baumgarten, Axel, Jaeger, Hans, Wiese, Carmen, Gori, Andrea, Migliorino, Guglielmo Marco, Coltan, Gabriel, Constandis, Felicia, Erscoiu, Simona M, Prisacariu, Liviu-Jany, Rugina, Sorin, Streinu-Cercel, Adrian, Pokrovsky, Vadim V, Zakharova, Natalia, Shuldyakov, Andrey Anatolyevich, Ryamova, Elena Pavlovna, Kulagin, Valeriy Viktorovich, Tsybakova, Olga Aleksandrovna, Orlova-Morozova, Elena, Nagimova, Firaya, Voronin, Evgeniy, Shimonova, Tatiana Evgenyevna, Kozyrev, Oleg Anatolyevich, Orrell, Catherine, Lombaard, Johannes Jurgens, Botes, Margaretha Elizabeth, de Jager, Marleen, Segorb, Joaquin Portilla, Gatell Artigas, Josep Maria, Mallolas Masferrer, Josep, Guillen, Santiago Moreno, Perez Elias, Maria Jesus, Arribas Lopez, Jose R, Puigmal, Eugenia Negredo, Podzamczer Palter, Daniel, Ortega, Frederico Pulido, Garcia, Jesus Troya, de los Santos Gil, Ignacio, Berenguer, Juan, Nelson, Mark Richard, Williams, Ian G, Johnson, Margaret A, Khoo, Saye, Schembri, Gabriel, Clarke, Amanda, Gompels, Mark, Fox, Julie Meriel, Lwanga, Julianne, Taylor, Steven John, Dockrell, David Harold, Kegg, Stephen, Hagins, Debbie P, Osiyemi, Olayemi O, Prelutsky, David James, Ramgopal, Moti N, Scarsella, Anthony J, Dretler, Robin, DeJesus, Edwin, Bettacchi, Christopher J, Sims III, James, Clay, Patrick G, Bellos, Nicholaos C, Thompson, Melanie A, Montero, Jose, McDonald, Cheryl K, Creticos, Catherine, Shamblaw, David, Terrelonge, Antonio E, Valdes, Martin, Tashima, Karen T, Robbins, William J, Elion, Richard A, Goldstein, Deborah, Slim, Jihad, Lalezari, Jacob Paul, Pushkin, Richard, Lalla-Reddy, Sujata N, Win, Sanda S, Ruane, Peter Jerome, Mills, Anthony Martin, Cade, Jerry L, Campo, Rafael, Dietz, Craig A, Hoffman-Terry, Margaret, Blick, Gary, Rubin, David Scott, Mayer, Cynthia, Rondon, Juan Carlos, Cook, Paul P, Daar, Eric, Kumar, Princy N, Swindells, Susan, Castro, Jose Guillermo, Morales-Ramirez, Javier O, Santiago, Lizette, Santana-Bagur, Jorge L, Vandekerckhove, Linos, Florence, Eric, De Wit, Stephane, Derdelinckx, Inge, Vandercam, Bernard, Belkhir, Leila, De Wet, Joseph, Lebouche, Bertrand, Trottier, Benoit, Longpre, Daniele, Szabo, Jason, LeBlanc, Roger P, Jensen, Werner, Gonzalez, Alvaro Rojas, Beltran, Carlos, Sussmann, Otto Alberto, Velez, Juan Diego, Onate, Jose Millan, Nielsen, Henrik, Degen, Olaf, Stephan, Christoph, Arathoon, Eduardo, Lopez, Rudy Manuel, Rojas Alvarado, Evelyn Michelle, Gonzalez Patzan, Luis Demetrio, Meija, Carlos R, Pinzon, Rodolfo, Parchment, Charles, Sthoeger, Zev, Chowers, Michal, Riesenberg, Klaris, Shahar, Eduardo, Levy, Itzchak, Quintero Perez, Nora Patricia, Andrade-Villanueva, Jaime Federico, Crabtree Ramirez, Brenda Eloisa, Rijnders, Bart, den Hollander, Jan G, Handy, Rupert, Morales, Nilo Bonifacio, Hidalgo, Jose Alfredo, Infante, Rosa Mercedes, Matos Prado, Eduardo Demetrio, Campos, Pablo E, Ticona Chaves, Eduardo Romulo, Pinedo, Yvett, Pacheco, Patricia, Maltez, Fernando Manuel, Cunha, Jose, Neves, Isabel, Serrao, Rosario, Melendez-Rivera, Ivan, Mendoza-Rodriguez, Rafael O, Maldonado-Rivera, Sandra, Ortiz-Lasanta, Grisell, Kizhlo, Svetlana, Freud, Hernando Knobel, Moreno, Jose Sanz, Mendez, Francisco Vera, Mohapi, Lerato, Mitha, Essack Aziz, Mahomed, Akbar Anvar, Fouche, Leon Frederik, Kaplan, Richard, Siddique, Naeem, Hoosen, Farzana, Rassool, Mohammed Siddique, Baraldi, Ezio, Calmy, Alexandra, Cavassini, Matthias, Fehr, Jan, Tsai, Hung-Chin, Lin, Hsi-Hsun, Huang, Chun-Kai, Ko, Wen-Chien, Lin, Yu-Hui, Chen, Su-Jung, Hung, Chien-Ching, Avihingsanon, Anchalee, Kiertiburanakul, Sasisopin, Ratanasuwan, Winai, Supparatpinyo, Khuanchai, Chetchotisakd, Ploenchan, Changpradub, Dhitiwat, Orkin, Chloe, Fox, Ashini, Winston, Alan, Ustianowski, Andrew, Yangco, Bienvenido G, Asmuth, David Michael, Vigil, Karen J, Berger, Daniel S, Bhatti, Laveeza, Campbell, Thomas, Casey, Kathleen K, Liu, Edward, Crofoot, Gordon E, Cunningham, Douglas, Feinberg, Judith, Fichtenbaum, Carl, Balamban Felizarta, Franco Antonio, Jefferson, Thomas T, Johnson, Marc Alexander, Lewis, Stanley T, Luque, Amneris E, Novak, Richard M, Sloan, Louis, Sweet, Donna E, Towner, William J, Zane, Ryan, Riedel, David J, Loftus, Richard Anton, Shon, Alyssa So Young, Mogyoros, Miguel, Tebas, Pablo, Scott, Mia Louise, Parenti, David M, and Inciarte Portillo, Alexy

Abstract

In two phase 3 trials for first-line therapy in adults with HIV-1, doravirine showed non-inferior efficacy, a favourable safety profile, and a superior lipid profile to darunavir and efavirenz through to 48 and 96 weeks. Here we report 192-week results from both studies.

Published
2024
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