Author: "Bennett, Andrew A" / Database: OAIster - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Bennett, Andrew A"' showing total 195 results

Start Over Author "Bennett, Andrew A" Database OAIster

195 results on '"Bennett, Andrew A"'

1. Efficient and Sharp Off-Policy Evaluation in Robust Markov Decision Processes

Author: Bennett, Andrew, Kallus, Nathan, Oprescu, Miruna, Sun, Wen, Wang, Kaiwen, Bennett, Andrew, Kallus, Nathan, Oprescu, Miruna, Sun, Wen, and Wang, Kaiwen
Abstract: We study evaluating a policy under best- and worst-case perturbations to a Markov decision process (MDP), given transition observations from the original MDP, whether under the same or different policy. This is an important problem when there is the possibility of a shift between historical and future environments, due to e.g. unmeasured confounding, distributional shift, or an adversarial environment. We propose a perturbation model that can modify transition kernel densities up to a given multiplicative factor or its reciprocal, which extends the classic marginal sensitivity model (MSM) for single time step decision making to infinite-horizon RL. We characterize the sharp bounds on policy value under this model, that is, the tightest possible bounds given by the transition observations from the original MDP, and we study the estimation of these bounds from such transition observations. We develop an estimator with several appealing guarantees: it is semiparametrically efficient, and remains so even when certain necessary nuisance functions such as worst-case Q-functions are estimated at slow nonparametric rates. It is also asymptotically normal, enabling easy statistical inference using Wald confidence intervals. In addition, when certain nuisances are estimated inconsistently we still estimate a valid, albeit possibly not sharp bounds on the policy value. We validate these properties in numeric simulations. The combination of accounting for environment shifts from train to test (robustness), being insensitive to nuisance-function estimation (orthogonality), and accounting for having only finite samples to learn from (inference) together leads to credible and reliable policy evaluation., Comment: 40 pages, 1 figure
Published: 2024

2. Minimax Instrumental Variable Regression and $L_2$ Convergence Guarantees without Identification or Closedness

Author: Bennett, Andrew, Kallus, Nathan, Mao, Xiaojie, Newey, Whitney, Syrgkanis, Vasilis, Uehara, Masatoshi, Bennett, Andrew, Kallus, Nathan, Mao, Xiaojie, Newey, Whitney, Syrgkanis, Vasilis, and Uehara, Masatoshi
Abstract: In this paper, we study nonparametric estimation of instrumental variable (IV) regressions. Recently, many flexible machine learning methods have been developed for instrumental variable estimation. However, these methods have at least one of the following limitations: (1) restricting the IV regression to be uniquely identified; (2) only obtaining estimation error rates in terms of pseudometrics (\emph{e.g.,} projected norm) rather than valid metrics (\emph{e.g.,} $L_2$ norm); or (3) imposing the so-called closedness condition that requires a certain conditional expectation operator to be sufficiently smooth. In this paper, we present the first method and analysis that can avoid all three limitations, while still permitting general function approximation. Specifically, we propose a new penalized minimax estimator that can converge to a fixed IV solution even when there are multiple solutions, and we derive a strong $L_2$ error rate for our estimator under lax conditions. Notably, this guarantee only needs a widely-used source condition and realizability assumptions, but not the so-called closedness condition. We argue that the source condition and the closedness condition are inherently conflicting, so relaxing the latter significantly improves upon the existing literature that requires both conditions. Our estimator can achieve this improvement because it builds on a novel formulation of the IV estimation problem as a constrained optimization problem., Comment: Under review
Published: 2023

3. Low-Rank MDPs with Continuous Action Spaces

Author: Bennett, Andrew, Kallus, Nathan, Oprescu, Miruna, Bennett, Andrew, Kallus, Nathan, and Oprescu, Miruna
Abstract: Low-Rank Markov Decision Processes (MDPs) have recently emerged as a promising framework within the domain of reinforcement learning (RL), as they allow for provably approximately correct (PAC) learning guarantees while also incorporating ML algorithms for representation learning. However, current methods for low-rank MDPs are limited in that they only consider finite action spaces, and give vacuous bounds as $|\mathcal{A}| \to \infty$, which greatly limits their applicability. In this work, we study the problem of extending such methods to settings with continuous actions, and explore multiple concrete approaches for performing this extension. As a case study, we consider the seminal FLAMBE algorithm (Agarwal et al., 2020), which is a reward-agnostic method for PAC RL with low-rank MDPs. We show that, without any modifications to the algorithm, we obtain a similar PAC bound when actions are allowed to be continuous. Specifically, when the model for transition functions satisfies a H\"older smoothness condition w.r.t. actions, and either the policy class has a uniformly bounded minimum density or the reward function is also H\"older smooth, we obtain a polynomial PAC bound that depends on the order of smoothness., Comment: 25 pages, AISTATS 2024
Published: 2023

4. Source Condition Double Robust Inference on Functionals of Inverse Problems

Author: Bennett, Andrew, Kallus, Nathan, Mao, Xiaojie, Newey, Whitney, Syrgkanis, Vasilis, Uehara, Masatoshi, Bennett, Andrew, Kallus, Nathan, Mao, Xiaojie, Newey, Whitney, Syrgkanis, Vasilis, and Uehara, Masatoshi
Abstract: We consider estimation of parameters defined as linear functionals of solutions to linear inverse problems. Any such parameter admits a doubly robust representation that depends on the solution to a dual linear inverse problem, where the dual solution can be thought as a generalization of the inverse propensity function. We provide the first source condition double robust inference method that ensures asymptotic normality around the parameter of interest as long as either the primal or the dual inverse problem is sufficiently well-posed, without knowledge of which inverse problem is the more well-posed one. Our result is enabled by novel guarantees for iterated Tikhonov regularized adversarial estimators for linear inverse problems, over general hypothesis spaces, which are developments of independent interest.
Published: 2023

5. Kazuo Ishiguro's TV and Film Scripts

Author: Bennett, Andrew, Sloane, Peter, Bennett, Andrew, and Sloane, Peter
Abstract: An essay on Kazuo Ishiguro's works for television and film.
Published: 2022

6. Kazuo Ishiguro's TV and Film Scripts

Author: Bennett, Andrew, Sloane, Peter, Bennett, Andrew, and Sloane, Peter
Abstract: An essay on Kazuo Ishiguro's works for television and film.
Published: 2022

7. Kazuo Ishiguro's TV and Film Scripts

Author: Bennett, Andrew, Sloane, Peter, Bennett, Andrew, and Sloane, Peter
Abstract: An essay on Kazuo Ishiguro's works for television and film.
Published: 2022

8. Provable Safe Reinforcement Learning with Binary Feedback

Author: Bennett, Andrew, Misra, Dipendra, Kallus, Nathan, Bennett, Andrew, Misra, Dipendra, and Kallus, Nathan
Abstract: Safety is a crucial necessity in many applications of reinforcement learning (RL), whether robotic, automotive, or medical. Many existing approaches to safe RL rely on receiving numeric safety feedback, but in many cases this feedback can only take binary values; that is, whether an action in a given state is safe or unsafe. This is particularly true when feedback comes from human experts. We therefore consider the problem of provable safe RL when given access to an offline oracle providing binary feedback on the safety of state, action pairs. We provide a novel meta algorithm, SABRE, which can be applied to any MDP setting given access to a blackbox PAC RL algorithm for that setting. SABRE applies concepts from active learning to reinforcement learning to provably control the number of queries to the safety oracle. SABRE works by iteratively exploring the state space to find regions where the agent is currently uncertain about safety. Our main theoretical results shows that, under appropriate technical assumptions, SABRE never takes unsafe actions during training, and is guaranteed to return a near-optimal safe policy with high probability. We provide a discussion of how our meta-algorithm may be applied to various settings studied in both theoretical and empirical frameworks.
Published: 2022

9. Future-Dependent Value-Based Off-Policy Evaluation in POMDPs

Author: Uehara, Masatoshi, Kiyohara, Haruka, Bennett, Andrew, Chernozhukov, Victor, Jiang, Nan, Kallus, Nathan, Shi, Chengchun, Sun, Wen, Uehara, Masatoshi, Kiyohara, Haruka, Bennett, Andrew, Chernozhukov, Victor, Jiang, Nan, Kallus, Nathan, Shi, Chengchun, and Sun, Wen
Abstract: We study off-policy evaluation (OPE) for partially observable MDPs (POMDPs) with general function approximation. Existing methods such as sequential importance sampling estimators and fitted-Q evaluation suffer from the curse of horizon in POMDPs. To circumvent this problem, we develop a novel model-free OPE method by introducing future-dependent value functions that take future proxies as inputs. Future-dependent value functions play similar roles as classical value functions in fully-observable MDPs. We derive a new Bellman equation for future-dependent value functions as conditional moment equations that use history proxies as instrumental variables. We further propose a minimax learning method to learn future-dependent value functions using the new Bellman equation. We obtain the PAC result, which implies our OPE estimator is consistent as long as futures and histories contain sufficient information about latent states, and the Bellman completeness. Finally, we extend our methods to learning of dynamics and establish the connection between our approach and the well-known spectral learning methods in POMDPs., Comment: This paper was accepted in NeurIPS 2023
Published: 2022

10. The Qualitative Transparency Deliberations: Insights and Implications

Author: Jacobs, Alan, Büthe, Tim, Arjona, Ana, Arriola, Leonardo, Bellin, Eva, Bennett, Andrew, Björkman, Lisa, Bleich, Erik, Elkins, Zachary, Fairfield, Tasha, Gaikwad, Nikhar, Chestnut Greitens, Sheena, Hawkesworth, Mary, Herrera, Veronica, Herrera, Yoshiko M., Johnson, Kimberly S., Karakov, Ekrem, Koivu, Kendra, Kreuzer, Markus, Lake, Milli, Luke, Timothy W., MacLean, Lauren M., Majic, Samantha, Maxwell, Rahsaan, Mampilly, Zachariah, Mickey, Robert, Morgan, Kimberley J., Parkinson, Sarah E., Parsons, Craig, Pearlman, Wendy, Pollack, Mark A., Posner, Elliot, Beatty Riedl, Rachel, Schatz, Edrward, Schneider, Carsten Q., Schwedler, Jillian, Shesterinina, Anastasia, Simmons, Erica S., Singerman, Diane, Soifer, Hillel David, Rush Smith, Nicholas, Spitzer, Scott, Talberg, Jonas, Thomson, Susan, Vázquez-Arroyo, Antonio Y., Vis, Barbara, Wedeen, Lisa, Williams, Juliet A., Wood, Elisabeth Jean, Yashar, Deborah J., Jacobs, Alan, Büthe, Tim, Arjona, Ana, Arriola, Leonardo, Bellin, Eva, Bennett, Andrew, Björkman, Lisa, Bleich, Erik, Elkins, Zachary, Fairfield, Tasha, Gaikwad, Nikhar, Chestnut Greitens, Sheena, Hawkesworth, Mary, Herrera, Veronica, Herrera, Yoshiko M., Johnson, Kimberly S., Karakov, Ekrem, Koivu, Kendra, Kreuzer, Markus, Lake, Milli, Luke, Timothy W., MacLean, Lauren M., Majic, Samantha, Maxwell, Rahsaan, Mampilly, Zachariah, Mickey, Robert, Morgan, Kimberley J., Parkinson, Sarah E., Parsons, Craig, Pearlman, Wendy, Pollack, Mark A., Posner, Elliot, Beatty Riedl, Rachel, Schatz, Edrward, Schneider, Carsten Q., Schwedler, Jillian, Shesterinina, Anastasia, Simmons, Erica S., Singerman, Diane, Soifer, Hillel David, Rush Smith, Nicholas, Spitzer, Scott, Talberg, Jonas, Thomson, Susan, Vázquez-Arroyo, Antonio Y., Vis, Barbara, Wedeen, Lisa, Williams, Juliet A., Wood, Elisabeth Jean, and Yashar, Deborah J.
Abstract: In recent years, a variety of efforts have been made in political science to enable, encourage, or require scholars to be more open and explicit about the bases of their empirical claims and, in turn, make those claims more readily evaluable by others. While qualitative scholars have long taken an interest in making their research open, reflexive, and systematic, the recent push for overarching transparency norms and requirements has provoked serious concern within qualitative research communities and raised fundamental questions about the meaning, value, costs, and intellectual relevance of transparency for qualitative inquiry. In this Perspectives Reflection, we crystallize the central findings of a three-year deliberative process - the Qualitative Transparency Deliberations (QTD) - involving hundreds of political scientists in a broad discussion of these issues. Following an overview of the process and the key insights that emerged, we present summaries of the QTD Working Groups' final reports. Drawing on a series of public, online conversations that unfolded at www.qualtd.net, the reports unpack transparency's promise, practicalities, risks, and limitations in relation to different qualitative methodologies, forms of evidence, and research contexts. Taken as a whole, these reports - the full versions of which can be found in the Supplementary Materials - offer practical guidance to scholars designing and implementing qualitative research, and to editors, reviewers, and funders seeking to develop criteria of evaluation that are appropriate - as understood by relevant research communities - to the forms of inquiry being assessed. We dedicate this Reflection to the memory of our coauthor and QTD working group leader Kendra Koivu.
Published: 2021

11. Chlamydial diversity and predictors of infection in a wild Australian parrot, the Crimson Rosella (Platycercus elegans)

Author: Stokes, Helena S., Martens, Johanne M., Jelocnik, Martina, Walder, Ken, Segal, Yonatan, Berg, Mathew L., Bennett, Andrew T.D., Stokes, Helena S., Martens, Johanne M., Jelocnik, Martina, Walder, Ken, Segal, Yonatan, Berg, Mathew L., and Bennett, Andrew T.D.
Published: 2021

12. The Qualitative Transparency Deliberations: Insights and Implications

Author: Politiek en bestuur, UU LEG Research USG Public Matters, Jacobs, Alan, Büthe, Tim, Arjona, Ana, Arriola, Leonardo, Bellin, Eva, Bennett, Andrew, Björkman, Lisa, Bleich, Erik, Elkins, Zachary, Fairfield, Tasha, Gaikwad, Nikhar, Chestnut Greitens, Sheena, Hawkesworth, Mary, Herrera, Veronica, Herrera, Yoshiko M., Johnson, Kimberly S., Karakov, Ekrem, Koivu, Kendra, Kreuzer, Markus, Lake, Milli, Luke, Timothy W., MacLean, Lauren M., Majic, Samantha, Maxwell, Rahsaan, Mampilly, Zachariah, Mickey, Robert, Morgan, Kimberley J., Parkinson, Sarah E., Parsons, Craig, Pearlman, Wendy, Pollack, Mark A., Posner, Elliot, Beatty Riedl, Rachel, Schatz, Edrward, Schneider, Carsten Q., Schwedler, Jillian, Shesterinina, Anastasia, Simmons, Erica S., Singerman, Diane, Soifer, Hillel David, Rush Smith, Nicholas, Spitzer, Scott, Talberg, Jonas, Thomson, Susan, Vázquez-Arroyo, Antonio Y., Vis, Barbara, Wedeen, Lisa, Williams, Juliet A., Wood, Elisabeth Jean, Yashar, Deborah J., Politiek en bestuur, UU LEG Research USG Public Matters, Jacobs, Alan, Büthe, Tim, Arjona, Ana, Arriola, Leonardo, Bellin, Eva, Bennett, Andrew, Björkman, Lisa, Bleich, Erik, Elkins, Zachary, Fairfield, Tasha, Gaikwad, Nikhar, Chestnut Greitens, Sheena, Hawkesworth, Mary, Herrera, Veronica, Herrera, Yoshiko M., Johnson, Kimberly S., Karakov, Ekrem, Koivu, Kendra, Kreuzer, Markus, Lake, Milli, Luke, Timothy W., MacLean, Lauren M., Majic, Samantha, Maxwell, Rahsaan, Mampilly, Zachariah, Mickey, Robert, Morgan, Kimberley J., Parkinson, Sarah E., Parsons, Craig, Pearlman, Wendy, Pollack, Mark A., Posner, Elliot, Beatty Riedl, Rachel, Schatz, Edrward, Schneider, Carsten Q., Schwedler, Jillian, Shesterinina, Anastasia, Simmons, Erica S., Singerman, Diane, Soifer, Hillel David, Rush Smith, Nicholas, Spitzer, Scott, Talberg, Jonas, Thomson, Susan, Vázquez-Arroyo, Antonio Y., Vis, Barbara, Wedeen, Lisa, Williams, Juliet A., Wood, Elisabeth Jean, and Yashar, Deborah J.
Published: 2021

13. Author Correction: Senescence of song revealed by a long-term study of the Seychelles warbler (Acrocephalus sechellensis) (Scientific Reports, (2020), 10, 1, (20479), 10.1038/s41598-020-77405-3)

Author: Berg, Mathew, Beebe, SC, Komdeur, J, Cardilini, Adam, Ribot, Raoul, Bennett, Andrew, Buchanan, Katherine, Berg, Mathew, Beebe, SC, Komdeur, J, Cardilini, Adam, Ribot, Raoul, Bennett, Andrew, and Buchanan, Katherine
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Published: 2021

14. A review of chlamydial infections in wild birds

Author: Stokes, Helena, Berg, Mathew, Bennett, Andrew, Stokes, Helena, Berg, Mathew, and Bennett, Andrew
Abstract: The Chlamydia are a globally distributed genus of bacteria that can infect and cause disease in a range of hosts. Birds are the primary host for multiple chlamydial species. The most well-known of these is Chlamydia psittaci, a zoonotic bacterium that has been identified in a range of wild and domesticated birds. Wild birds are often proposed as a reservoir of Chlamydia psittaci and potentially other chlamydial species. The aim of this review is to present the current knowledge of chlamydial infections in wild avian populations. We focus on C. psittaci but also consider other Chlamydiaceae and Chlamydia-related bacteria that have been identified in wild birds. We summarise the diversity, host range, and clinical signs of infection in wild birds and consider the potential implications of these infections for zoonotic transmission and avian conservation. Chlamydial bacteria have been found in more than 70 species of wild birds, with the greatest chlamydial diversity identified in Europe. The Corvidae and Accipitridae families are emerging as significant chlamydial hosts, in addition to established wild hosts such as the Columbidae. Clarifying the effects of these bacteria on avian host fitness and the zoonotic potential of emerging Chlamydiales will help us to understand the implications of these infections for avian and human health.
Published: 2021

15. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria : Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author: Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il Ryong, Ciuffo, Marina, Clegg, J. Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B.H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas, Gonzalez, Jean Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, Martin H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy H., Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Lǐ, Jiànróng, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R.T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong Zhen, Zhang, Song, Zhang, Jinguo, Zhang, Zhe, Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il Ryong, Ciuffo, Marina, Clegg, J. Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B.H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas, Gonzalez, Jean Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, Martin H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy H., Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Lǐ, Jiànróng, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R.T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong Zhen, Zhang, Song, Zhang, Jinguo, and Zhang, Zhe
Abstract: In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Published: 2021

16. The Qualitative Transparency Deliberations: Insights and Implications

Author: Politiek en bestuur, UU LEG Research USG Public Matters, Jacobs, Alan, Büthe, Tim, Arjona, Ana, Arriola, Leonardo, Bellin, Eva, Bennett, Andrew, Björkman, Lisa, Bleich, Erik, Elkins, Zachary, Fairfield, Tasha, Gaikwad, Nikhar, Chestnut Greitens, Sheena, Hawkesworth, Mary, Herrera, Veronica, Herrera, Yoshiko M., Johnson, Kimberly S., Karakov, Ekrem, Koivu, Kendra, Kreuzer, Markus, Lake, Milli, Luke, Timothy W., MacLean, Lauren M., Majic, Samantha, Maxwell, Rahsaan, Mampilly, Zachariah, Mickey, Robert, Morgan, Kimberley J., Parkinson, Sarah E., Parsons, Craig, Pearlman, Wendy, Pollack, Mark A., Posner, Elliot, Beatty Riedl, Rachel, Schatz, Edrward, Schneider, Carsten Q., Schwedler, Jillian, Shesterinina, Anastasia, Simmons, Erica S., Singerman, Diane, Soifer, Hillel David, Rush Smith, Nicholas, Spitzer, Scott, Talberg, Jonas, Thomson, Susan, Vázquez-Arroyo, Antonio Y., Vis, Barbara, Wedeen, Lisa, Williams, Juliet A., Wood, Elisabeth Jean, Yashar, Deborah J., Politiek en bestuur, UU LEG Research USG Public Matters, Jacobs, Alan, Büthe, Tim, Arjona, Ana, Arriola, Leonardo, Bellin, Eva, Bennett, Andrew, Björkman, Lisa, Bleich, Erik, Elkins, Zachary, Fairfield, Tasha, Gaikwad, Nikhar, Chestnut Greitens, Sheena, Hawkesworth, Mary, Herrera, Veronica, Herrera, Yoshiko M., Johnson, Kimberly S., Karakov, Ekrem, Koivu, Kendra, Kreuzer, Markus, Lake, Milli, Luke, Timothy W., MacLean, Lauren M., Majic, Samantha, Maxwell, Rahsaan, Mampilly, Zachariah, Mickey, Robert, Morgan, Kimberley J., Parkinson, Sarah E., Parsons, Craig, Pearlman, Wendy, Pollack, Mark A., Posner, Elliot, Beatty Riedl, Rachel, Schatz, Edrward, Schneider, Carsten Q., Schwedler, Jillian, Shesterinina, Anastasia, Simmons, Erica S., Singerman, Diane, Soifer, Hillel David, Rush Smith, Nicholas, Spitzer, Scott, Talberg, Jonas, Thomson, Susan, Vázquez-Arroyo, Antonio Y., Vis, Barbara, Wedeen, Lisa, Williams, Juliet A., Wood, Elisabeth Jean, and Yashar, Deborah J.
Published: 2021

17. The Qualitative Transparency Deliberations : Insights and Implications

Author: Jacobs, Alan M., Büthe, Tim, Arjona, Ana, Arriola, Leonardo R., Bellin, Eva, Bennett, Andrew, Björkman, Lisa, Bleich, Erik, Elkins, Zachary, Fairfield, Tasha, Gaikwad, Nikhar, Greitens, Sheena Chestnut, Hawkesworth, Mary, Herrera, Veronica, Herrera, Yoshiko M., Johnson, Kimberley S., Karakoç, Ekrem, Koivu, Kendra, Kreuzer, Marcus, Lake, Milli, Luke, Timothy W., MacLean, Lauren M., Majic, Samantha, Maxwell, Rahsaan, Mampilly, Zachariah, Mickey, Robert, Morgan, Kimberly J., Parkinson, Sarah E., Parsons, Craig, Pearlman, Wendy, Pollack, Mark A., Posner, Elliot, Riedl, Rachel Beatty, Schatz, Edward, Schneider, Carsten Q., Schwedler, Jillian, Shesterinina, Anastasia, Simmons, Erica S., Singerman, Diane, Soifer, Hillel David, Smith, Nicholas Rush, Spitzer, Scott, Tallberg, Jonas, Thomson, Susan, Vázquez-Arroyo, Antonio Y., Vis, Barbara, Wedeen, Lisa, Williams, Juliet A., Wood, Elisabeth Jean, Yashar, Deborah J., Jacobs, Alan M., Büthe, Tim, Arjona, Ana, Arriola, Leonardo R., Bellin, Eva, Bennett, Andrew, Björkman, Lisa, Bleich, Erik, Elkins, Zachary, Fairfield, Tasha, Gaikwad, Nikhar, Greitens, Sheena Chestnut, Hawkesworth, Mary, Herrera, Veronica, Herrera, Yoshiko M., Johnson, Kimberley S., Karakoç, Ekrem, Koivu, Kendra, Kreuzer, Marcus, Lake, Milli, Luke, Timothy W., MacLean, Lauren M., Majic, Samantha, Maxwell, Rahsaan, Mampilly, Zachariah, Mickey, Robert, Morgan, Kimberly J., Parkinson, Sarah E., Parsons, Craig, Pearlman, Wendy, Pollack, Mark A., Posner, Elliot, Riedl, Rachel Beatty, Schatz, Edward, Schneider, Carsten Q., Schwedler, Jillian, Shesterinina, Anastasia, Simmons, Erica S., Singerman, Diane, Soifer, Hillel David, Smith, Nicholas Rush, Spitzer, Scott, Tallberg, Jonas, Thomson, Susan, Vázquez-Arroyo, Antonio Y., Vis, Barbara, Wedeen, Lisa, Williams, Juliet A., Wood, Elisabeth Jean, and Yashar, Deborah J.
Abstract: In recent years, a variety of efforts have been made in political science to enable, encourage, or require scholars to be more open and explicit about the bases of their empirical claims and, in turn, make those claims more readily evaluable by others. While qualitative scholars have long taken an interest in making their research open, reflexive, and systematic, the recent push for overarching transparency norms and requirements has provoked serious concern within qualitative research communities and raised fundamental questions about the meaning, value, costs, and intellectual relevance of transparency for qualitative inquiry. In this Perspectives Reflection, we crystallize the central findings of a three-year deliberative process-the Qualitative Transparency Deliberations (QTD)-involving hundreds of political scientists in a broad discussion of these issues. Following an overview of the process and the key insights that emerged, we present summaries of the QTD Working Groups' final reports. Drawing on a series of public, online conversations that unfolded at www.qualtd.net, the reports unpack transparency's promise, practicalities, risks, and limitations in relation to different qualitative methodologies, forms of evidence, and research contexts. Taken as a whole, these reports-the full versions of which can be found in the Supplementary Materials-offer practical guidance to scholars designing and implementing qualitative research, and to editors, reviewers, and funders seeking to develop criteria of evaluation that are appropriate-as understood by relevant research communities-to the forms of inquiry being assessed. We dedicate this Reflection to the memory of our coauthor and QTD working group leader Kendra Koivu.(1)
Published: 2021
Full Text: View/download PDF

18. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.

Author: Kuhn, Jens H, Kuhn, Jens H, Adkins, Scott, Agwanda, Bernard R, Al Kubrusli, Rim, Alkhovsky, Sergey V, Amarasinghe, Gaya K, Avšič-Županc, Tatjana, Ayllón, María A, Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J, Basler, Christopher F, Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J, Bente, Dennis A, Bergeron, Éric, Bird, Brian H, Blair, Carol D, Blasdell, Kim R, Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B, Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A, Brown, Judith K, Buchholz, Ursula J, Buchmeier, Michael J, Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H, Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N, Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il-Ryong, Ciuffo, Marina, Clegg, J Christopher S, Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L, Debat, Humberto, Dheilly, Nolwenn M, Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G, Digiaro, Michele, Dolnik, Olga, Drebot, Michael A, Drexler, J Felix, Dundon, William G, Duprex, W Paul, Dürrwald, Ralf, Dye, John M, Easton, Andrew J, Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W, Fooks, Anthony R, Forgia, Marco, Formenty, Pierre BH, Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R, Gaskin, Thomas, Gonzalez, Jean-Paul J, Griffiths, Anthony, Goldberg, Tony L, Groschup, Martin H, Günther, Stephan, Hall, Roy A, Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S, Hu, Tao, Hughes, Holly R, Hüttner, Florian, Kuhn, Jens H, Kuhn, Jens H, Adkins, Scott, Agwanda, Bernard R, Al Kubrusli, Rim, Alkhovsky, Sergey V, Amarasinghe, Gaya K, Avšič-Županc, Tatjana, Ayllón, María A, Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J, Basler, Christopher F, Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J, Bente, Dennis A, Bergeron, Éric, Bird, Brian H, Blair, Carol D, Blasdell, Kim R, Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B, Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A, Brown, Judith K, Buchholz, Ursula J, Buchmeier, Michael J, Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H, Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N, Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il-Ryong, Ciuffo, Marina, Clegg, J Christopher S, Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L, Debat, Humberto, Dheilly, Nolwenn M, Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G, Digiaro, Michele, Dolnik, Olga, Drebot, Michael A, Drexler, J Felix, Dundon, William G, Duprex, W Paul, Dürrwald, Ralf, Dye, John M, Easton, Andrew J, Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W, Fooks, Anthony R, Forgia, Marco, Formenty, Pierre BH, Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R, Gaskin, Thomas, Gonzalez, Jean-Paul J, Griffiths, Anthony, Goldberg, Tony L, Groschup, Martin H, Günther, Stephan, Hall, Roy A, Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S, Hu, Tao, Hughes, Holly R, and Hüttner, Florian
Abstract: In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Published: 2021

19. The Qualitative Transparency Deliberations: Insights and Implications

Author: Politiek en bestuur, UU LEG Research USG Public Matters, Jacobs, Alan, Büthe, Tim, Arjona, Ana, Arriola, Leonardo, Bellin, Eva, Bennett, Andrew, Björkman, Lisa, Bleich, Erik, Elkins, Zachary, Fairfield, Tasha, Gaikwad, Nikhar, Chestnut Greitens, Sheena, Hawkesworth, Mary, Herrera, Veronica, Herrera, Yoshiko M., Johnson, Kimberly S., Karakov, Ekrem, Koivu, Kendra, Kreuzer, Markus, Lake, Milli, Luke, Timothy W., MacLean, Lauren M., Majic, Samantha, Maxwell, Rahsaan, Mampilly, Zachariah, Mickey, Robert, Morgan, Kimberley J., Parkinson, Sarah E., Parsons, Craig, Pearlman, Wendy, Pollack, Mark A., Posner, Elliot, Beatty Riedl, Rachel, Schatz, Edrward, Schneider, Carsten Q., Schwedler, Jillian, Shesterinina, Anastasia, Simmons, Erica S., Singerman, Diane, Soifer, Hillel David, Rush Smith, Nicholas, Spitzer, Scott, Talberg, Jonas, Thomson, Susan, Vázquez-Arroyo, Antonio Y., Vis, Barbara, Wedeen, Lisa, Williams, Juliet A., Wood, Elisabeth Jean, Yashar, Deborah J., Politiek en bestuur, UU LEG Research USG Public Matters, Jacobs, Alan, Büthe, Tim, Arjona, Ana, Arriola, Leonardo, Bellin, Eva, Bennett, Andrew, Björkman, Lisa, Bleich, Erik, Elkins, Zachary, Fairfield, Tasha, Gaikwad, Nikhar, Chestnut Greitens, Sheena, Hawkesworth, Mary, Herrera, Veronica, Herrera, Yoshiko M., Johnson, Kimberly S., Karakov, Ekrem, Koivu, Kendra, Kreuzer, Markus, Lake, Milli, Luke, Timothy W., MacLean, Lauren M., Majic, Samantha, Maxwell, Rahsaan, Mampilly, Zachariah, Mickey, Robert, Morgan, Kimberley J., Parkinson, Sarah E., Parsons, Craig, Pearlman, Wendy, Pollack, Mark A., Posner, Elliot, Beatty Riedl, Rachel, Schatz, Edrward, Schneider, Carsten Q., Schwedler, Jillian, Shesterinina, Anastasia, Simmons, Erica S., Singerman, Diane, Soifer, Hillel David, Rush Smith, Nicholas, Spitzer, Scott, Talberg, Jonas, Thomson, Susan, Vázquez-Arroyo, Antonio Y., Vis, Barbara, Wedeen, Lisa, Williams, Juliet A., Wood, Elisabeth Jean, and Yashar, Deborah J.
Published: 2021

20. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author: 0000-0002-7800-6045, 0000-0003-0095-8414, 0000-0003-4135-4537, 0000-0001-6913-5841, 0000-0002-0418-9707, 0000-0001-6243-0688, Ayllón, María A. [0000-0001-7893-6106], 0000-0001-7572-4300, Balkema-Buschmann, A. [0000-0001-7613-9592], 0000-0001-7453-8725, 0000-0003-4195-425X, 0000-0001-8424-5635, 0000-0002-0598-5254, 0000-0002-7851-3506, 0000-0003-1032-4781, 0000-0003-3398-8628, 0000-0001-8170-8710, 0000-0002-2803-0354, 0000-0003-2121-0376, 0000-0001-5490-3334, 0000-0001-5972-0844, 0000-0002-1985-751X, 0000-0002-9106-1014, 0000-0002-4819-8963, 0000-0002-6697-7688, 0000-0003-4669-8443, 0000-0002-2329-3198, 0000-0002-2387-9287, 0000-0002-0342-4824, 0000-0002-7238-7799, 0000-0002-2086-2594, 0000-0003-0396-262X, 0000-0003-1840-1198, 0000-0003-0232-7077, 0000-0002-7675-8251, 0000-0002-7565-8881, Chiapello, M. [0000-0001-7768-3047], 0000-0003-0422-408X, 0000-0003-2485-4011, 0000-0002-8171-8115, De Swart, Rik L. [0000-0003-3599-8969], 0000-0003-3056-3739, 0000-0002-3675-5013, 0000-0002-9694-3913, 0000-0003-2822-704X, 0000-0002-7772-2250, 0000-0001-7739-4798, Drexler, J. Felix [0000-0002-3509-0232], 0000-0002-2776-169X, 0000-0003-1716-6376, 0000-0002-3432-0438, 0000-0002-0883-5016, 0000-0002-2288-3882, 0000-0002-2576-9735, 0000-0003-2211-7907, 0000-0001-5422-1982, 0000-0002-3243-6154, 0000-0003-0101-1046, 0000-0002-9482-5411, 0000-0001-8451-1454, 0000-0002-0506-6880, 0000-0002-1084-2119, 0000-0001-6468-6943, 0000-0002-6551-1827, 0000-0003-3034-6400, 0000-0003-3063-1770, 0000-0001-5435-8364, 0000-0003-3962-4913, Groschup, M. H. [0000-0003-0215-185X], 0000-0002-6562-0230, 0000-0001-5778-1387, 0000-0001-7593-747X, 0000-0001-5699-214X, 0000-0003-2273-3152, 0000-0002-1285-4455, 0000-0003-4682-7698, 0000-0003-3003-4140, 0000-0003-1380-8263, Von Bargen, Susanne [0000-0001-8321-1572], Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avsic-Zupanc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, A., Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven B., Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, M., Choi, Il-Ryong, Ciuffo, Marina, Clegg, J Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, J. C., de Lamballerie, Xavier, De Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B.H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas R., Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, M. H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy, Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, B., Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Li, Jianrong, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, N., Nunes, Márcio R.T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, Van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, Von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong-Zhen, Zhang, Song, Zhang, Jinguo, Zhang, Zhe, Zhou, Xueping, 0000-0002-7800-6045, 0000-0003-0095-8414, 0000-0003-4135-4537, 0000-0001-6913-5841, 0000-0002-0418-9707, 0000-0001-6243-0688, Ayllón, María A. [0000-0001-7893-6106], 0000-0001-7572-4300, Balkema-Buschmann, A. [0000-0001-7613-9592], 0000-0001-7453-8725, 0000-0003-4195-425X, 0000-0001-8424-5635, 0000-0002-0598-5254, 0000-0002-7851-3506, 0000-0003-1032-4781, 0000-0003-3398-8628, 0000-0001-8170-8710, 0000-0002-2803-0354, 0000-0003-2121-0376, 0000-0001-5490-3334, 0000-0001-5972-0844, 0000-0002-1985-751X, 0000-0002-9106-1014, 0000-0002-4819-8963, 0000-0002-6697-7688, 0000-0003-4669-8443, 0000-0002-2329-3198, 0000-0002-2387-9287, 0000-0002-0342-4824, 0000-0002-7238-7799, 0000-0002-2086-2594, 0000-0003-0396-262X, 0000-0003-1840-1198, 0000-0003-0232-7077, 0000-0002-7675-8251, 0000-0002-7565-8881, Chiapello, M. [0000-0001-7768-3047], 0000-0003-0422-408X, 0000-0003-2485-4011, 0000-0002-8171-8115, De Swart, Rik L. [0000-0003-3599-8969], 0000-0003-3056-3739, 0000-0002-3675-5013, 0000-0002-9694-3913, 0000-0003-2822-704X, 0000-0002-7772-2250, 0000-0001-7739-4798, Drexler, J. Felix [0000-0002-3509-0232], 0000-0002-2776-169X, 0000-0003-1716-6376, 0000-0002-3432-0438, 0000-0002-0883-5016, 0000-0002-2288-3882, 0000-0002-2576-9735, 0000-0003-2211-7907, 0000-0001-5422-1982, 0000-0002-3243-6154, 0000-0003-0101-1046, 0000-0002-9482-5411, 0000-0001-8451-1454, 0000-0002-0506-6880, 0000-0002-1084-2119, 0000-0001-6468-6943, 0000-0002-6551-1827, 0000-0003-3034-6400, 0000-0003-3063-1770, 0000-0001-5435-8364, 0000-0003-3962-4913, Groschup, M. H. [0000-0003-0215-185X], 0000-0002-6562-0230, 0000-0001-5778-1387, 0000-0001-7593-747X, 0000-0001-5699-214X, 0000-0003-2273-3152, 0000-0002-1285-4455, 0000-0003-4682-7698, 0000-0003-3003-4140, 0000-0003-1380-8263, Von Bargen, Susanne [0000-0001-8321-1572], Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avsic-Zupanc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, A., Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven B., Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, M., Choi, Il-Ryong, Ciuffo, Marina, Clegg, J Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, J. C., de Lamballerie, Xavier, De Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B.H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas R., Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, M. H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy, Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, B., Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Li, Jianrong, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, N., Nunes, Márcio R.T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, Van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, Von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong-Zhen, Zhang, Song, Zhang, Jinguo, Zhang, Zhe, and Zhou, Xueping
Abstract: Unfortunately, the inclusion of original names (in non-Latin script) of the following authors caused problems with author name indexing in PubMed. Therefore, these original names were removed from XML data to correct the PubMed record. Mengji Cao, Yuya Chiaki, Hideki Ebihara, Jingjing Fu, George Fú Gāo, Tong Han, Jiang Hong, Ni Hong, Seiji Hongo, Masayuki Horie, Dàohóng Jiāng, Fujio Kadono, Hideki Kondō, Kenji Kubota, Shaorong Li, Longhui Li, Jiànróng Lǐ, Huazhen Liu, Tomohide Natsuaki, Sergey V. Netesov, Anna Papa, Sofia Paraskevopoulou, Liying Qi, Takahide Sasaya, Mang Shi, Xiǎohóng Shí, Zhènglì Shí, Yoshifumi Shimomoto, Jin‑Won Song, Ayato Takada, Shigeharu Takeuchi, Yasuhiro Tomitaka, Keizō Tomonaga, Shinya Tsuda, Changchun Tu, Tomio Usugi, Nikos Vasilakis, Jiro Wada, Lin‑Fa Wang, Guoping Wang, Yanxiang Wang, Yaqin Wang, Tàiyún Wèi, Shaohua Wen, Jiangxiang Wu, Lei Xu, Hironobu Yanagisawa, Caixia Yang, Zuokun Yang, Lifeng Zhai, Yong‑Zhen Zhang, Song Zhang, Jinguo Zhang, Zhe Zhang, Xueping Zhou. In addition, the publication call-out in the supplementary material was updated from issue 11 to issue 12. The original article has been corrected.
Published: 2021

21. Proximal Reinforcement Learning: Efficient Off-Policy Evaluation in Partially Observed Markov Decision Processes

Author: Bennett, Andrew, Kallus, Nathan, Bennett, Andrew, and Kallus, Nathan
Abstract: In applications of offline reinforcement learning to observational data, such as in healthcare or education, a general concern is that observed actions might be affected by unobserved factors, inducing confounding and biasing estimates derived under the assumption of a perfect Markov decision process (MDP) model. Here we tackle this by considering off-policy evaluation in a partially observed MDP (POMDP). Specifically, we consider estimating the value of a given target policy in a POMDP given trajectories with only partial state observations generated by a different and unknown policy that may depend on the unobserved state. We tackle two questions: what conditions allow us to identify the target policy value from the observed data and, given identification, how to best estimate it. To answer these, we extend the framework of proximal causal inference to our POMDP setting, providing a variety of settings where identification is made possible by the existence of so-called bridge functions. We then show how to construct semiparametrically efficient estimators in these settings. We term the resulting framework proximal reinforcement learning (PRL). We demonstrate the benefits of PRL in an extensive simulation study and on the problem of sepsis management.
Published: 2021

22. Consequences to patients, clinicians, and manufacturers when very serious adverse drug reactions are identified (1997–2019):A qualitative analysis from the Southern Network on Adverse Reactions (SONAR)

Author: Bennett, Charles L., Hoque, Shamia, Olivieri, Nancy, Taylor, Matthew A., Aboulafia, David, Lubaczewski, Courtney, Bennett, Andrew C., Vemula, Jay, Schooley, Benjamin, Witherspoon, Bartlett J., Godwin, Ashley C., Ray, Paul S., Yarnold, Paul R., Ausdenmoore, Henry C., Fishman, Marc, Herring, Georgne, Ventrone, Anne, Aldaco, Juan, Hrushesky, William J., Restaino, John, Thomsen, Henrik S., Marx, Robert, Migliorati, Cesar, Ruggiero, Salvatore, Nabhan, Chadi, Carson, Kenneth R., McKoy, June M., Yang, Y. Tony, Schoen, Martin W., Knopf, Kevin, Martin, Linda, Sartor, Oliver, Rosen, Steven, Smith, William K., Bennett, Charles L., Hoque, Shamia, Olivieri, Nancy, Taylor, Matthew A., Aboulafia, David, Lubaczewski, Courtney, Bennett, Andrew C., Vemula, Jay, Schooley, Benjamin, Witherspoon, Bartlett J., Godwin, Ashley C., Ray, Paul S., Yarnold, Paul R., Ausdenmoore, Henry C., Fishman, Marc, Herring, Georgne, Ventrone, Anne, Aldaco, Juan, Hrushesky, William J., Restaino, John, Thomsen, Henrik S., Marx, Robert, Migliorati, Cesar, Ruggiero, Salvatore, Nabhan, Chadi, Carson, Kenneth R., McKoy, June M., Yang, Y. Tony, Schoen, Martin W., Knopf, Kevin, Martin, Linda, Sartor, Oliver, Rosen, Steven, and Smith, William K.
Abstract: Background: Adverse drug/device reactions (ADRs) can result in severe patient harm. We define very serious ADRs as being associated with severe toxicity, as measured on the Common Toxicity Criteria Adverse Events (CTCAE)) scale, following use of drugs or devices with large sales, large financial settlements, and large numbers of injured persons. We report on impacts on patients, clinicians, and manufacturers following very serious ADR reporting. Methods: We reviewed clinician identified very serious ADRs published between 1997 and 2019. Drugs and devices associated with reports of very serious ADRs were identified. Included drugs or devices had market removal discussed at Food and Drug Advisory (FDA) Advisory Committee meetings, were published by clinicians, had sales > $1 billion, were associated with CTCAE Grade 4 or 5 toxicity effects, and had either >$1 billion in settlements or >1,000 injured patients. Data sources included journals, Congressional transcripts, and news reports. We reviewed data on: 1) timing of ADR reports, Boxed warnings, and product withdrawals, and 2) patient, clinician, and manufacturer impacts. Binomial analysis was used to compare sales pre- and post-FDA Advisory Committee meetings. Findings: Twenty very serious ADRs involved fifteen drugs and one device. Legal settlements totaled $38.4 billion for 753,900 injured persons. Eleven of 18 clinicians (61%) reported harms, including verbal threats from manufacturer (five) and loss of a faculty position (one). Annual sales decreased 94% from $29.1 billion pre-FDA meeting to $4.9 billion afterwards (p<0.0018). Manufacturers of four drugs paid $1.7 billion total in criminal fines for failing to inform the FDA and physicians about very serious ADRs. Following FDA approval, the median time to ADR reporting was 7.5 years (Interquartile range 3,13 years). Twelve drugs received Box warnings and one drug received a warning (median, 7.5 years following ADR reporting (IQR 5,11 years). Six
Published: 2021

23. Have you tried Neural Topic Models? Comparative Analysis of Neural and Non-Neural Topic Models with Application to COVID-19 Twitter Data

Author: Bennett, Andrew, Misra, Dipendra, Than, Nga, Bennett, Andrew, Misra, Dipendra, and Than, Nga
Abstract: Topic models are widely used in studying social phenomena. We conduct a comparative study examining state-of-the-art neural versus non-neural topic models, performing a rigorous quantitative and qualitative assessment on a dataset of tweets about the COVID-19 pandemic. Our results show that not only do neural topic models outperform their classical counterparts on standard evaluation metrics, but they also produce more coherent topics, which are of great benefit when studying complex social problems. We also propose a novel regularization term for neural topic models, which is designed to address the well-documented problem of mode collapse, and demonstrate its effectiveness.
Published: 2021

24. Consequences to patients, clinicians, and manufacturers when very serious adverse drug reactions are identified (1997–2019):A qualitative analysis from the Southern Network on Adverse Reactions (SONAR)

Author: Bennett, Charles L., Hoque, Shamia, Olivieri, Nancy, Taylor, Matthew A., Aboulafia, David, Lubaczewski, Courtney, Bennett, Andrew C., Vemula, Jay, Schooley, Benjamin, Witherspoon, Bartlett J., Godwin, Ashley C., Ray, Paul S., Yarnold, Paul R., Ausdenmoore, Henry C., Fishman, Marc, Herring, Georgne, Ventrone, Anne, Aldaco, Juan, Hrushesky, William J., Restaino, John, Thomsen, Henrik S., Marx, Robert, Migliorati, Cesar, Ruggiero, Salvatore, Nabhan, Chadi, Carson, Kenneth R., McKoy, June M., Yang, Y. Tony, Schoen, Martin W., Knopf, Kevin, Martin, Linda, Sartor, Oliver, Rosen, Steven, Smith, William K., Bennett, Charles L., Hoque, Shamia, Olivieri, Nancy, Taylor, Matthew A., Aboulafia, David, Lubaczewski, Courtney, Bennett, Andrew C., Vemula, Jay, Schooley, Benjamin, Witherspoon, Bartlett J., Godwin, Ashley C., Ray, Paul S., Yarnold, Paul R., Ausdenmoore, Henry C., Fishman, Marc, Herring, Georgne, Ventrone, Anne, Aldaco, Juan, Hrushesky, William J., Restaino, John, Thomsen, Henrik S., Marx, Robert, Migliorati, Cesar, Ruggiero, Salvatore, Nabhan, Chadi, Carson, Kenneth R., McKoy, June M., Yang, Y. Tony, Schoen, Martin W., Knopf, Kevin, Martin, Linda, Sartor, Oliver, Rosen, Steven, and Smith, William K.
Abstract: Background: Adverse drug/device reactions (ADRs) can result in severe patient harm. We define very serious ADRs as being associated with severe toxicity, as measured on the Common Toxicity Criteria Adverse Events (CTCAE)) scale, following use of drugs or devices with large sales, large financial settlements, and large numbers of injured persons. We report on impacts on patients, clinicians, and manufacturers following very serious ADR reporting. Methods: We reviewed clinician identified very serious ADRs published between 1997 and 2019. Drugs and devices associated with reports of very serious ADRs were identified. Included drugs or devices had market removal discussed at Food and Drug Advisory (FDA) Advisory Committee meetings, were published by clinicians, had sales > $1 billion, were associated with CTCAE Grade 4 or 5 toxicity effects, and had either >$1 billion in settlements or >1,000 injured patients. Data sources included journals, Congressional transcripts, and news reports. We reviewed data on: 1) timing of ADR reports, Boxed warnings, and product withdrawals, and 2) patient, clinician, and manufacturer impacts. Binomial analysis was used to compare sales pre- and post-FDA Advisory Committee meetings. Findings: Twenty very serious ADRs involved fifteen drugs and one device. Legal settlements totaled $38.4 billion for 753,900 injured persons. Eleven of 18 clinicians (61%) reported harms, including verbal threats from manufacturer (five) and loss of a faculty position (one). Annual sales decreased 94% from $29.1 billion pre-FDA meeting to $4.9 billion afterwards (p<0.0018). Manufacturers of four drugs paid $1.7 billion total in criminal fines for failing to inform the FDA and physicians about very serious ADRs. Following FDA approval, the median time to ADR reporting was 7.5 years (Interquartile range 3,13 years). Twelve drugs received Box warnings and one drug received a warning (median, 7.5 years following ADR reporting (IQR 5,11 years). Six
Published: 2021

25. Author Correction: A consensus-based transparency checklist.

Author: Aczel, Balazs, Aczel, Balazs, Szaszi, Barnabas, Sarafoglou, Alexandra, Kekecs, Zoltan, Kucharský, Šimon, Benjamin, Daniel, Chambers, Christopher D, Fisher, Agneta, Gelman, Andrew, Gernsbacher, Morton A, Ioannidis, John P, Johnson, Eric, Jonas, Kai, Kousta, Stavroula, Lilienfeld, Scott O, Lindsay, D Stephen, Morey, Candice C, Munafò, Marcus, Newell, Benjamin R, Pashler, Harold, Shanks, David R, Simons, Daniel J, Wicherts, Jelte M, Albarracin, Dolores, Anderson, Nicole D, Antonakis, John, Arkes, Hal R, Back, Mitja D, Banks, George C, Beevers, Christopher, Bennett, Andrew A, Bleidorn, Wiebke, Boyer, Ty W, Cacciari, Cristina, Carter, Alice S, Cesario, Joseph, Clifton, Charles, Conroy, Ronán M, Cortese, Mike, Cosci, Fiammetta, Cowan, Nelson, Crawford, Jarret, Crone, Eveline A, Curtin, John, Engle, Randall, Farrell, Simon, Fearon, Pasco, Fichman, Mark, Frankenhuis, Willem, Freund, Alexandra M, Gaskell, M Gareth, Giner-Sorolla, Roger, Green, Don P, Greene, Robert L, Harlow, Lisa L, de la Guardia, Fernando Hoces, Isaacowitz, Derek, Kolodner, Janet, Lieberman, Debra, Logan, Gordon D, Mendes, Wendy B, Moersdorf, Lea, Nyhan, Brendan, Pollack, Jeffrey, Sullivan, Christopher, Vazire, Simine, Wagenmakers, Eric-Jan, Aczel, Balazs, Aczel, Balazs, Szaszi, Barnabas, Sarafoglou, Alexandra, Kekecs, Zoltan, Kucharský, Šimon, Benjamin, Daniel, Chambers, Christopher D, Fisher, Agneta, Gelman, Andrew, Gernsbacher, Morton A, Ioannidis, John P, Johnson, Eric, Jonas, Kai, Kousta, Stavroula, Lilienfeld, Scott O, Lindsay, D Stephen, Morey, Candice C, Munafò, Marcus, Newell, Benjamin R, Pashler, Harold, Shanks, David R, Simons, Daniel J, Wicherts, Jelte M, Albarracin, Dolores, Anderson, Nicole D, Antonakis, John, Arkes, Hal R, Back, Mitja D, Banks, George C, Beevers, Christopher, Bennett, Andrew A, Bleidorn, Wiebke, Boyer, Ty W, Cacciari, Cristina, Carter, Alice S, Cesario, Joseph, Clifton, Charles, Conroy, Ronán M, Cortese, Mike, Cosci, Fiammetta, Cowan, Nelson, Crawford, Jarret, Crone, Eveline A, Curtin, John, Engle, Randall, Farrell, Simon, Fearon, Pasco, Fichman, Mark, Frankenhuis, Willem, Freund, Alexandra M, Gaskell, M Gareth, Giner-Sorolla, Roger, Green, Don P, Greene, Robert L, Harlow, Lisa L, de la Guardia, Fernando Hoces, Isaacowitz, Derek, Kolodner, Janet, Lieberman, Debra, Logan, Gordon D, Mendes, Wendy B, Moersdorf, Lea, Nyhan, Brendan, Pollack, Jeffrey, Sullivan, Christopher, Vazire, Simine, and Wagenmakers, Eric-Jan
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Published: 2020

26. A consensus-based transparency checklist.

Author: Aczel, Balazs, Aczel, Balazs, Szaszi, Barnabas, Sarafoglou, Alexandra, Kekecs, Zoltan, Kucharský, Šimon, Benjamin, Daniel, Chambers, Christopher D, Fisher, Agneta, Gelman, Andrew, Gernsbacher, Morton A, Ioannidis, John P, Johnson, Eric, Jonas, Kai, Kousta, Stavroula, Lilienfeld, Scott O, Lindsay, D Stephen, Morey, Candice C, Munafò, Marcus, Newell, Benjamin R, Pashler, Harold, Shanks, David R, Simons, Daniel J, Wicherts, Jelte M, Albarracin, Dolores, Anderson, Nicole D, Antonakis, John, Arkes, Hal R, Back, Mitja D, Banks, George C, Beevers, Christopher, Bennett, Andrew A, Bleidorn, Wiebke, Boyer, Ty W, Cacciari, Cristina, Carter, Alice S, Cesario, Joseph, Clifton, Charles, Conroy, Ronán M, Cortese, Mike, Cosci, Fiammetta, Cowan, Nelson, Crawford, Jarret, Crone, Eveline A, Curtin, John, Engle, Randall, Farrell, Simon, Fearon, Pasco, Fichman, Mark, Frankenhuis, Willem, Freund, Alexandra M, Gaskell, M Gareth, Giner-Sorolla, Roger, Green, Don P, Greene, Robert L, Harlow, Lisa L, de la Guardia, Fernando Hoces, Isaacowitz, Derek, Kolodner, Janet, Lieberman, Debra, Logan, Gordon D, Mendes, Wendy B, Moersdorf, Lea, Nyhan, Brendan, Pollack, Jeffrey, Sullivan, Christopher, Vazire, Simine, Wagenmakers, Eric-Jan, Aczel, Balazs, Aczel, Balazs, Szaszi, Barnabas, Sarafoglou, Alexandra, Kekecs, Zoltan, Kucharský, Šimon, Benjamin, Daniel, Chambers, Christopher D, Fisher, Agneta, Gelman, Andrew, Gernsbacher, Morton A, Ioannidis, John P, Johnson, Eric, Jonas, Kai, Kousta, Stavroula, Lilienfeld, Scott O, Lindsay, D Stephen, Morey, Candice C, Munafò, Marcus, Newell, Benjamin R, Pashler, Harold, Shanks, David R, Simons, Daniel J, Wicherts, Jelte M, Albarracin, Dolores, Anderson, Nicole D, Antonakis, John, Arkes, Hal R, Back, Mitja D, Banks, George C, Beevers, Christopher, Bennett, Andrew A, Bleidorn, Wiebke, Boyer, Ty W, Cacciari, Cristina, Carter, Alice S, Cesario, Joseph, Clifton, Charles, Conroy, Ronán M, Cortese, Mike, Cosci, Fiammetta, Cowan, Nelson, Crawford, Jarret, Crone, Eveline A, Curtin, John, Engle, Randall, Farrell, Simon, Fearon, Pasco, Fichman, Mark, Frankenhuis, Willem, Freund, Alexandra M, Gaskell, M Gareth, Giner-Sorolla, Roger, Green, Don P, Greene, Robert L, Harlow, Lisa L, de la Guardia, Fernando Hoces, Isaacowitz, Derek, Kolodner, Janet, Lieberman, Debra, Logan, Gordon D, Mendes, Wendy B, Moersdorf, Lea, Nyhan, Brendan, Pollack, Jeffrey, Sullivan, Christopher, Vazire, Simine, and Wagenmakers, Eric-Jan
Published: 2020

27. A consensus-based transparency checklist

Author: Aczel, Balazs, Szaszi, Barnabas, Sarafoglou, Alexandra, Kekecs, Zoltan, Kucharský, Šimon, Benjamin, Daniel, Chambers, Christopher D., Fisher, Agneta, Gelman, Andrew, Gernsbacher, Morton A., Ioannidis, John P., Johnson, Eric, Jonas, Kai, Kousta, Stavroula, Lilienfeld, Scott O., Lindsay, D. Stephen, Morey, Candice C., Munafò, Marcus, Newell, Benjamin R., Pashler, Harold, Shanks, David R., Simons, Daniel J., Wicherts, Jelte M., Albarracin, Dolores, Anderson, Nicole D., Antonakis, John, Arkes, Hal R., Back, Mitja D., Banks, George C., Beevers, Christopher, Bennett, Andrew A., Bleidorn, Wiebke, Boyer, Ty W., Cacciari, Cristina, Carter, Alice S., Cesario, Joseph, Clifton, Charles, Conroy, Ronán M., Cortese, Mike, Cosci, Fiammetta, Cowan, Nelson, Crawford, Jarret, Crone, Eveline A., Curtin, John, Engle, Randall, Farrell, Simon, Fearon, Pasco, Fichman, Mark, Frankenhuis, Willem, Freund, Alexandra M., Gaskell, M. Gareth, Giner-Sorolla, Roger, Green, Don P., Greene, Robert L., Harlow, Lisa L., de la Guardia, Fernando Hoces, Isaacowitz, Derek, Kolodner, Janet, Lieberman, Debra, Logan, Gordon D., Mendes, Wendy B., Moersdorf, Lea, Nyhan, Brendan, Pollack, Jeffrey, Sullivan, Christopher, Vazire, Simine, Wagenmakers, Eric Jan, Aczel, Balazs, Szaszi, Barnabas, Sarafoglou, Alexandra, Kekecs, Zoltan, Kucharský, Šimon, Benjamin, Daniel, Chambers, Christopher D., Fisher, Agneta, Gelman, Andrew, Gernsbacher, Morton A., Ioannidis, John P., Johnson, Eric, Jonas, Kai, Kousta, Stavroula, Lilienfeld, Scott O., Lindsay, D. Stephen, Morey, Candice C., Munafò, Marcus, Newell, Benjamin R., Pashler, Harold, Shanks, David R., Simons, Daniel J., Wicherts, Jelte M., Albarracin, Dolores, Anderson, Nicole D., Antonakis, John, Arkes, Hal R., Back, Mitja D., Banks, George C., Beevers, Christopher, Bennett, Andrew A., Bleidorn, Wiebke, Boyer, Ty W., Cacciari, Cristina, Carter, Alice S., Cesario, Joseph, Clifton, Charles, Conroy, Ronán M., Cortese, Mike, Cosci, Fiammetta, Cowan, Nelson, Crawford, Jarret, Crone, Eveline A., Curtin, John, Engle, Randall, Farrell, Simon, Fearon, Pasco, Fichman, Mark, Frankenhuis, Willem, Freund, Alexandra M., Gaskell, M. Gareth, Giner-Sorolla, Roger, Green, Don P., Greene, Robert L., Harlow, Lisa L., de la Guardia, Fernando Hoces, Isaacowitz, Derek, Kolodner, Janet, Lieberman, Debra, Logan, Gordon D., Mendes, Wendy B., Moersdorf, Lea, Nyhan, Brendan, Pollack, Jeffrey, Sullivan, Christopher, Vazire, Simine, and Wagenmakers, Eric Jan
Published: 2020

28. Senescence of song revealed by a long-term study of the Seychelles warbler (Acrocephalus sechellensis)

Author: Berg, Mathew L., Beebe, Sarah C., Komdeur, Jan, Cardilini, Adam P. A., Ribot, Raoul F. H., Bennett, Andrew T. D., Buchanan, Katherine L., Berg, Mathew L., Beebe, Sarah C., Komdeur, Jan, Cardilini, Adam P. A., Ribot, Raoul F. H., Bennett, Andrew T. D., and Buchanan, Katherine L.
Abstract: Senescence is widespread in nature, often resulting in diminishing survival or reproduction with age, but its role in age-dependent variation in sexual traits is often poorly understood. One reason is that few studies of sexual traits consider non-linear relationships with age, or only consider a narrow range of years relative to the life span of the species. Birdsong has evolved to allow assessment of conspecific quality in numerous bird species. Whilst theory and empirical work suggests that song may become more elaborate with age, there are a paucity of long-term studies testing whether song is associated with age or longevity. In particular, the occurrence of song senescence has rarely been demonstrated. Using an exceptional long-term dataset for the Seychelles warbler (Acrocephalus sechellensis), we analysed relationships between male song, age, survival, and longevity. This species is a long-lived songbird with early life increases, followed by senescent declines, in survival and reproduction. The study population (Cousin Island, Seychelles) is a closed population, with no depredation of adults, providing an excellent opportunity to study senescence in free-living animals. We tested whether song traits were related to age at recording, future survival, longevity, and territory quality. We found age-dependent changes in five song traits (duration, maximum frequency, peak frequency of songs, and duration and frequency bandwidth of trills). Relationships with age were quadratic, indicating reversal in the expression of song coinciding with the onset of senescence in reproduction and survival in this species. One song trait (trill bandwidth) had a quadratic relationship with future survival, but no song traits were related to longevity, suggesting age-related patterns were not the result of selective disappearance. Our study provides one of the first examples of functional senescence in song, offering new insights into avian senescence.
Published: 2020

29. Species, sex and geographic variation in chlamydial prevalence in abundant wild Australian parrots

Author: Stokes, Helena S., Martens, Johanne M., Walder, Ken, Segal, Yonatan, Berg, Mathew L., Bennett, Andrew T. D., Stokes, Helena S., Martens, Johanne M., Walder, Ken, Segal, Yonatan, Berg, Mathew L., and Bennett, Andrew T. D.
Abstract: Chlamydia psittaci (order: Chlamydiales) is a globally distributed zoonotic bacterium that can cause potentially fatal disease in birds and humans. Parrots are a major host, yet prevalence and risk factors for infection in wild parrots are largely unknown. Additionally, recent research suggests there is a diverse range of novel Chlamydiales circulating in wildlife. We therefore sampled seven abundant parrot species in south-eastern Australia, taking cloacal swabs and serum from n = 132 wild adults. We determined C. psittaci and Chlamydiales prevalence and seroprevalence, and tested for host species, sex, geographical and seasonal differences, and temporal changes in individual infection status. Across all species, Chlamydiales prevalence was 39.8% (95% CI 31.6, 48.7), C. psittaci prevalence was 9.8% (95% CI 5.7, 16.3) and C. gallinacea prevalence was 0.8% (95% CI 0.1, 4.5). Other Chlamydiales species were not identified to species level. We identified two C. psittaci strains within the 6BC clade, which is highly virulent in humans. Seroprevalence was 37.0% (95% CI 28.5, 46.4). Host species (including crimson rosellas, galahs, sulphur-crested cockatoos and blue-winged parrots) differed in seroprevalence and Chlamydiales prevalence. Galahs had both highest Chlamydiales prevalence (54.8%) and seroprevalence (74.1%). Seroprevalence differed between sites, with a larger difference in males (range 20–63%) than females (29–44%). We reveal a higher chlamydial prevalence than previously reported in many wild parrots, with implications for potential reservoirs, and transmission risks to humans and other avian hosts.
Published: 2020

30. A non-invasive method to assess environmental contamination with avian pathogens: beak and feather disease virus (BFDV) detection in nest boxes

Author: Martens, Johanne M., Stokes, Helena S., Berg, Mathew L., Walder, Ken, Raidal, Shane R., Magrath, Michael J.L., Bennett, Andrew T.D., Martens, Johanne M., Stokes, Helena S., Berg, Mathew L., Walder, Ken, Raidal, Shane R., Magrath, Michael J.L., and Bennett, Andrew T.D.
Published: 2020

31. Seasonal fluctuation of beak and feather disease virus (BFDV) infection in wild Crimson Rosellas (Platycercus elegans)

Author: Martens, Johanne M, Stokes, Helena S, Berg, Mathew L, Walder, Ken, Bennett, Andrew TD, Martens, Johanne M, Stokes, Helena S, Berg, Mathew L, Walder, Ken, and Bennett, Andrew TD
Published: 2020

32. Author Correction: A consensus-based transparency checklist.

Author: Aczel, Balazs, Aczel, Balazs, Szaszi, Barnabas, Sarafoglou, Alexandra, Kekecs, Zoltan, Kucharský, Šimon, Benjamin, Daniel, Chambers, Christopher D, Fisher, Agneta, Gelman, Andrew, Gernsbacher, Morton A, Ioannidis, John P, Johnson, Eric, Jonas, Kai, Kousta, Stavroula, Lilienfeld, Scott O, Lindsay, D Stephen, Morey, Candice C, Munafò, Marcus, Newell, Benjamin R, Pashler, Harold, Shanks, David R, Simons, Daniel J, Wicherts, Jelte M, Albarracin, Dolores, Anderson, Nicole D, Antonakis, John, Arkes, Hal R, Back, Mitja D, Banks, George C, Beevers, Christopher, Bennett, Andrew A, Bleidorn, Wiebke, Boyer, Ty W, Cacciari, Cristina, Carter, Alice S, Cesario, Joseph, Clifton, Charles, Conroy, Ronán M, Cortese, Mike, Cosci, Fiammetta, Cowan, Nelson, Crawford, Jarret, Crone, Eveline A, Curtin, John, Engle, Randall, Farrell, Simon, Fearon, Pasco, Fichman, Mark, Frankenhuis, Willem, Freund, Alexandra M, Gaskell, M Gareth, Giner-Sorolla, Roger, Green, Don P, Greene, Robert L, Harlow, Lisa L, de la Guardia, Fernando Hoces, Isaacowitz, Derek, Kolodner, Janet, Lieberman, Debra, Logan, Gordon D, Mendes, Wendy B, Moersdorf, Lea, Nyhan, Brendan, Pollack, Jeffrey, Sullivan, Christopher, Vazire, Simine, Wagenmakers, Eric-Jan, Aczel, Balazs, Aczel, Balazs, Szaszi, Barnabas, Sarafoglou, Alexandra, Kekecs, Zoltan, Kucharský, Šimon, Benjamin, Daniel, Chambers, Christopher D, Fisher, Agneta, Gelman, Andrew, Gernsbacher, Morton A, Ioannidis, John P, Johnson, Eric, Jonas, Kai, Kousta, Stavroula, Lilienfeld, Scott O, Lindsay, D Stephen, Morey, Candice C, Munafò, Marcus, Newell, Benjamin R, Pashler, Harold, Shanks, David R, Simons, Daniel J, Wicherts, Jelte M, Albarracin, Dolores, Anderson, Nicole D, Antonakis, John, Arkes, Hal R, Back, Mitja D, Banks, George C, Beevers, Christopher, Bennett, Andrew A, Bleidorn, Wiebke, Boyer, Ty W, Cacciari, Cristina, Carter, Alice S, Cesario, Joseph, Clifton, Charles, Conroy, Ronán M, Cortese, Mike, Cosci, Fiammetta, Cowan, Nelson, Crawford, Jarret, Crone, Eveline A, Curtin, John, Engle, Randall, Farrell, Simon, Fearon, Pasco, Fichman, Mark, Frankenhuis, Willem, Freund, Alexandra M, Gaskell, M Gareth, Giner-Sorolla, Roger, Green, Don P, Greene, Robert L, Harlow, Lisa L, de la Guardia, Fernando Hoces, Isaacowitz, Derek, Kolodner, Janet, Lieberman, Debra, Logan, Gordon D, Mendes, Wendy B, Moersdorf, Lea, Nyhan, Brendan, Pollack, Jeffrey, Sullivan, Christopher, Vazire, Simine, and Wagenmakers, Eric-Jan
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Published: 2020

33. A consensus-based transparency checklist.

Author: Aczel, Balazs, Aczel, Balazs, Szaszi, Barnabas, Sarafoglou, Alexandra, Kekecs, Zoltan, Kucharský, Šimon, Benjamin, Daniel, Chambers, Christopher D, Fisher, Agneta, Gelman, Andrew, Gernsbacher, Morton A, Ioannidis, John P, Johnson, Eric, Jonas, Kai, Kousta, Stavroula, Lilienfeld, Scott O, Lindsay, D Stephen, Morey, Candice C, Munafò, Marcus, Newell, Benjamin R, Pashler, Harold, Shanks, David R, Simons, Daniel J, Wicherts, Jelte M, Albarracin, Dolores, Anderson, Nicole D, Antonakis, John, Arkes, Hal R, Back, Mitja D, Banks, George C, Beevers, Christopher, Bennett, Andrew A, Bleidorn, Wiebke, Boyer, Ty W, Cacciari, Cristina, Carter, Alice S, Cesario, Joseph, Clifton, Charles, Conroy, Ronán M, Cortese, Mike, Cosci, Fiammetta, Cowan, Nelson, Crawford, Jarret, Crone, Eveline A, Curtin, John, Engle, Randall, Farrell, Simon, Fearon, Pasco, Fichman, Mark, Frankenhuis, Willem, Freund, Alexandra M, Gaskell, M Gareth, Giner-Sorolla, Roger, Green, Don P, Greene, Robert L, Harlow, Lisa L, de la Guardia, Fernando Hoces, Isaacowitz, Derek, Kolodner, Janet, Lieberman, Debra, Logan, Gordon D, Mendes, Wendy B, Moersdorf, Lea, Nyhan, Brendan, Pollack, Jeffrey, Sullivan, Christopher, Vazire, Simine, Wagenmakers, Eric-Jan, Aczel, Balazs, Aczel, Balazs, Szaszi, Barnabas, Sarafoglou, Alexandra, Kekecs, Zoltan, Kucharský, Šimon, Benjamin, Daniel, Chambers, Christopher D, Fisher, Agneta, Gelman, Andrew, Gernsbacher, Morton A, Ioannidis, John P, Johnson, Eric, Jonas, Kai, Kousta, Stavroula, Lilienfeld, Scott O, Lindsay, D Stephen, Morey, Candice C, Munafò, Marcus, Newell, Benjamin R, Pashler, Harold, Shanks, David R, Simons, Daniel J, Wicherts, Jelte M, Albarracin, Dolores, Anderson, Nicole D, Antonakis, John, Arkes, Hal R, Back, Mitja D, Banks, George C, Beevers, Christopher, Bennett, Andrew A, Bleidorn, Wiebke, Boyer, Ty W, Cacciari, Cristina, Carter, Alice S, Cesario, Joseph, Clifton, Charles, Conroy, Ronán M, Cortese, Mike, Cosci, Fiammetta, Cowan, Nelson, Crawford, Jarret, Crone, Eveline A, Curtin, John, Engle, Randall, Farrell, Simon, Fearon, Pasco, Fichman, Mark, Frankenhuis, Willem, Freund, Alexandra M, Gaskell, M Gareth, Giner-Sorolla, Roger, Green, Don P, Greene, Robert L, Harlow, Lisa L, de la Guardia, Fernando Hoces, Isaacowitz, Derek, Kolodner, Janet, Lieberman, Debra, Logan, Gordon D, Mendes, Wendy B, Moersdorf, Lea, Nyhan, Brendan, Pollack, Jeffrey, Sullivan, Christopher, Vazire, Simine, and Wagenmakers, Eric-Jan
Abstract: We present a consensus-based checklist to improve and document the transparency of research reports in social and behavioural research. An accompanying online application allows users to complete the form and generate a report that they can submit with their manuscript or post to a public repository.
Published: 2020

34. Blood contains circulating cell-free respiratory competent mitochondria.

Author: Al Amir Dache, Zahra, Otandault, Amaëlle, Tanos, Rita, Pastor, Brice, Meddeb, Romain, Sanchez, Cynthia, Arena, Giuseppe, Lasorsa, Laurence, Bennett, Andrew, Grange, Thierry, El Messaoudi, Safia, Mazard, Thibault, Prevostel, Corinne, Thierry, Alain R., Al Amir Dache, Zahra, Otandault, Amaëlle, Tanos, Rita, Pastor, Brice, Meddeb, Romain, Sanchez, Cynthia, Arena, Giuseppe, Lasorsa, Laurence, Bennett, Andrew, Grange, Thierry, El Messaoudi, Safia, Mazard, Thibault, Prevostel, Corinne, and Thierry, Alain R.
Abstract: Mitochondria are considered as the power-generating units of the cell due to their key role in energy metabolism and cell signaling. However, mitochondrial components could be found in the extracellular space, as fragments or encapsulated in vesicles. In addition, this intact organelle has been recently reported to be released by platelets exclusively in specific conditions. Here, we demonstrate for the first time, that blood preparation with resting platelets, contains whole functional mitochondria in normal physiological state. Likewise, we show, that normal and tumor cultured cells are able to secrete their mitochondria. Using serial centrifugation or filtration followed by polymerase chain reaction-based methods, and Whole Genome Sequencing, we detect extracellular full-length mitochondrial DNA in particles over 0.22 µm holding specific mitochondrial membrane proteins. We identify these particles as intact cell-free mitochondria using fluorescence-activated cell sorting analysis, fluorescence microscopy, and transmission electron microscopy. Oxygen consumption analysis revealed that these mitochondria are respiratory competent. In view of previously described mitochondrial potential in intercellular transfer, this discovery could greatly widen the scope of cell-cell communication biology. Further steps should be developed to investigate the potential role of mitochondria as a signaling organelle outside the cell and to determine whether these circulating units could be relevant for early detection and prognosis of various diseases.
Published: 2020

35. Off-policy Evaluation in Infinite-Horizon Reinforcement Learning with Latent Confounders

Author: Bennett, Andrew, Kallus, Nathan, Li, Lihong, Mousavi, Ali, Bennett, Andrew, Kallus, Nathan, Li, Lihong, and Mousavi, Ali
Abstract: Off-policy evaluation (OPE) in reinforcement learning is an important problem in settings where experimentation is limited, such as education and healthcare. But, in these very same settings, observed actions are often confounded by unobserved variables making OPE even more difficult. We study an OPE problem in an infinite-horizon, ergodic Markov decision process with unobserved confounders, where states and actions can act as proxies for the unobserved confounders. We show how, given only a latent variable model for states and actions, policy value can be identified from off-policy data. Our method involves two stages. In the first, we show how to use proxies to estimate stationary distribution ratios, extending recent work on breaking the curse of horizon to the confounded setting. In the second, we show optimal balancing can be combined with such learned ratios to obtain policy value while avoiding direct modeling of reward functions. We establish theoretical guarantees of consistency, and benchmark our method empirically.
Published: 2020

36. Efficient Policy Learning from Surrogate-Loss Classification Reductions

Author: Bennett, Andrew, Kallus, Nathan, Bennett, Andrew, and Kallus, Nathan
Abstract: Recent work on policy learning from observational data has highlighted the importance of efficient policy evaluation and has proposed reductions to weighted (cost-sensitive) classification. But, efficient policy evaluation need not yield efficient estimation of policy parameters. We consider the estimation problem given by a weighted surrogate-loss classification reduction of policy learning with any score function, either direct, inverse-propensity weighted, or doubly robust. We show that, under a correct specification assumption, the weighted classification formulation need not be efficient for policy parameters. We draw a contrast to actual (possibly weighted) binary classification, where correct specification implies a parametric model, while for policy learning it only implies a semiparametric model. In light of this, we instead propose an estimation approach based on generalized method of moments, which is efficient for the policy parameters. We propose a particular method based on recent developments on solving moment problems using neural networks and demonstrate the efficiency and regret benefits of this method empirically.
Published: 2020

37. The Variational Method of Moments

Author: Bennett, Andrew, Kallus, Nathan, Bennett, Andrew, and Kallus, Nathan
Abstract: The conditional moment problem is a powerful formulation for describing structural causal parameters in terms of observables, a prominent example being instrumental variable regression. A standard approach reduces the problem to a finite set of marginal moment conditions and applies the optimally weighted generalized method of moments (OWGMM), but this requires we know a finite set of identifying moments, can still be inefficient even if identifying, or can be theoretically efficient but practically unwieldy if we use a growing sieve of moment conditions. Motivated by a variational minimax reformulation of OWGMM, we define a very general class of estimators for the conditional moment problem, which we term the variational method of moments (VMM) and which naturally enables controlling infinitely-many moments. We provide a detailed theoretical analysis of multiple VMM estimators, including ones based on kernel methods and neural nets, and provide conditions under which these are consistent, asymptotically normal, and semiparametrically efficient in the full conditional moment model. We additionally provide algorithms for valid statistical inference based on the same kind of variational reformulations, both for kernel- and neural-net-based varieties. Finally, we demonstrate the strong performance of our proposed estimation and inference algorithms in a detailed series of synthetic experiments.
Published: 2020

38. Fire and biodiversity in the Anthropocene

Author: Centre Tecnològic Forestal de Catalunya, University of Melbourne, Australian Research Council, Xunta de Galicia, Foundation for Science and Technology, European Commission, Ministerio de Economía y Competitividad (España), Kelly, Luke T., Giljohann, Katherine M., Duane, Andrea, Aquilué, Núria, Archibald, Sally, Batllori, Enric, Bennett, Andrew F., Buckland, Stephen T., Canelles, Quim, Clarke, Michael F., Fortin, Marie-Josée, Hermoso, Virgilio, Herrando, Sergi, Keane, Robert E., Lake, Frank K., McCarthy, Michael A., Morán-Ordóñez, Alejandra, Parr, Catherine L., Pausas, J. G., Penman, Trent D., Regos, Adrián, Rumpff, Libby, Santos, Julianna L., Smith, Annabel L., Syphard, Alexandra D., Tingley, Morgan W., Brotons, Lluís, Centre Tecnològic Forestal de Catalunya, University of Melbourne, Australian Research Council, Xunta de Galicia, Foundation for Science and Technology, European Commission, Ministerio de Economía y Competitividad (España), Kelly, Luke T., Giljohann, Katherine M., Duane, Andrea, Aquilué, Núria, Archibald, Sally, Batllori, Enric, Bennett, Andrew F., Buckland, Stephen T., Canelles, Quim, Clarke, Michael F., Fortin, Marie-Josée, Hermoso, Virgilio, Herrando, Sergi, Keane, Robert E., Lake, Frank K., McCarthy, Michael A., Morán-Ordóñez, Alejandra, Parr, Catherine L., Pausas, J. G., Penman, Trent D., Regos, Adrián, Rumpff, Libby, Santos, Julianna L., Smith, Annabel L., Syphard, Alexandra D., Tingley, Morgan W., and Brotons, Lluís
Abstract: Fire has been a source of global biodiversity for millions of years. However, interactions with anthropogenic drivers such as climate change, land use, and invasive species are changing the nature of fire activity and its impacts. We review how such changes are threatening species with extinction and transforming terrestrial ecosystems. Conservation of Earth’s biological diversity will be achieved only by recognizing and responding to the critical role of fire. In the Anthropocene, this requires that conservation planning explicitly includes the combined effects of human activities and fire regimes. Improved forecasts for biodiversity must also integrate the connections among people, fire, and ecosystems. Such integration provides an opportunity for new actions that could revolutionize how society sustains biodiversity in a time of changing fire activity.
Published: 2020

39. Plumage coloration follows Gloger's rule in a ring species

Author: Ribot, Raoul FH, Ribot, Raoul FH, Berg, Mathew L, Schubert, Emanuel, Endler, John A, Bennett, Andrew TD, Ribot, Raoul FH, Ribot, Raoul FH, Berg, Mathew L, Schubert, Emanuel, Endler, John A, and Bennett, Andrew TD
Published: 2019

40. Plumage coloration follows Gloger's rule in a ring species

Author: Ribot, Raoul FH, Berg, Mathew L, Schubert, Emanuel, Endler, John A, Bennett, Andrew TD, Ribot, Raoul FH, Berg, Mathew L, Schubert, Emanuel, Endler, John A, and Bennett, Andrew TD
Published: 2019

41. Animal movements in fire-prone landscapes

Author: Nimmo, Dale G., Avitabile, Sarah, Banks, Sam C., Bird, Rebecca Bliege, Callister, Kate, Clarke, Michael F., Dickman, Chris R., Doherty, Tim S., Driscoll, Don A., Greenville, Aaron C., Haslem, Angie, Kelly, Luke T., Kenny, Sally A., Lahoz-Monfort, Jose J., Moore, Harry, Newsome, Thomas, Ritchie, Euan G., Watson, Simon, Bennett, Andrew F., Nimmo, Dale G., Avitabile, Sarah, Banks, Sam C., Bird, Rebecca Bliege, Callister, Kate, Clarke, Michael F., Dickman, Chris R., Doherty, Tim S., Driscoll, Don A., Greenville, Aaron C., Haslem, Angie, Kelly, Luke T., Kenny, Sally A., Lahoz-Monfort, Jose J., Moore, Harry, Newsome, Thomas, Ritchie, Euan G., Watson, Simon, and Bennett, Andrew F.
Published: 2019

42. Description and evaluation of the Community Ice Sheet Model (CISM) v2.1

Author: Lipscomb, William H. (author), Price, Stephen F. (author), Hoffman, Matthew J. (author), Leguy, Gunter R. (author), Bennett, Andrew R. (author), Bradley, S.L. (author), Evans, Katherine J. (author), Fyke, Jeremy G. (author), Kennedy, Joseph H. (author), Lipscomb, William H. (author), Price, Stephen F. (author), Hoffman, Matthew J. (author), Leguy, Gunter R. (author), Bennett, Andrew R. (author), Bradley, S.L. (author), Evans, Katherine J. (author), Fyke, Jeremy G. (author), and Kennedy, Joseph H. (author)
Abstract: We describe and evaluate version 2.1 of the Community Ice Sheet Model (CISM). CISM is a parallel, 3-D thermomechanical model, written mainly in Fortran, that solves equations for the momentum balance and the thickness and temperature evolution of ice sheets. CISM's velocity solver incorporates a hierarchy of Stokes flow approximations, including shallow-shelf, depth-integrated higher order, and 3-D higher order. CISM also includes a suite of test cases, links to third-party solver libraries, and parameterizations of physical processes such as basal sliding, iceberg calving, and sub-ice-shelf melting. The model has been verified for standard test problems, including the Ice Sheet Model Intercomparison Project for Higher-Order Models (ISMIP-HOM) experiments, and has participated in the initMIP-Greenland initialization experiment. In multimillennial simulations with modern climate forcing on a 4 km grid, CISM reaches a steady state that is broadly consistent with observed flow patterns of the Greenland ice sheet. CISM has been integrated into version 2.0 of the Community Earth System Model, where it is being used for Greenland simulations under past, present, and future climates. The code is open-source with extensive documentation and remains under active development., Physical and Space Geodesy
Published: 2019
Full Text: View/download PDF

43. LIVVkit 2.1: Automated and extensible ice sheet model validation

Author: Evans, Katherine J. (author), Kennedy, Joseph H. (author), Lu, Dan (author), Forrester, Mary M. (author), Price, Stephen (author), Fyke, Jeremy (author), Bennett, Andrew R. (author), Hoffman, Matthew J. (author), Tezaur, Irina (author), Zender, Charles S. (author), Vizcaino, M. (author), Evans, Katherine J. (author), Kennedy, Joseph H. (author), Lu, Dan (author), Forrester, Mary M. (author), Price, Stephen (author), Fyke, Jeremy (author), Bennett, Andrew R. (author), Hoffman, Matthew J. (author), Tezaur, Irina (author), Zender, Charles S. (author), and Vizcaino, M. (author)
Abstract: A collection of scientific analyses, metrics, and visualizations for robust validation of ice sheet models is presented using the Land Ice Verification and Validation toolkit (LIVVkit), version 2.1, and the LIVVkit Extensions repository (LEX), version 0.1. This software collection targets stand-alone ice sheet or coupled Earth system models, and handles datasets and analyses that require high-performance computing and storage. LIVVkit aims to enable efficient and fully reproducible workflows for postprocessing, analysis, and visualization of observational and model-derived datasets in a shareable format, whereby all data, methodologies, and output are distributed to users for evaluation. Extending from the initial LIVVkit software framework, we demonstrate Greenland ice sheet simulation validation metrics using the coupled Community Earth System Model (CESM) as well as an idealized stand-alone high-resolution Community Ice Sheet Model, version 2 (CISM2), coupled to the Albany/FELIX velocity solver (CISM-Albany or CISM-A). As one example of the capability, LIVVkit analyzes the degree to which models capture the surface mass balance (SMB) and identifies potential sources of bias, using recently available in situ and remotely sensed data as comparison. Related fields within atmosphere and land surface models, e.g., surface temperature, radiation, and cloud cover, are also diagnosed. Applied to the CESM1.0, LIVVkit identifies a positive SMB bias that is focused largely around Greenland's southwest region that is due to insufficient ablation., Physical and Space Geodesy
Published: 2019
Full Text: View/download PDF

44. The response of wild bees to tree cover and rural land use is mediated by species' traits

Author: Hall, Mark A, Nimmo, Dale G, Cunningham, Saul, Walker, Kenneth, Bennett, Andrew F., Hall, Mark A, Nimmo, Dale G, Cunningham, Saul, Walker, Kenneth, and Bennett, Andrew F.
Abstract: Worldwide, bees have an important role in ecosystem function and the provision of ecosystem services through their role as pollinators. The diversity of bee species in rural landscapes is influenced by the type of landscape features present, and by land-use and management practices. A key challenge is to understand and predict how species vary across the landscape; and the role of functional traits in determining compositional patterns. We systematically sampled wild bees in four types of landscape feature – open farmland, scattered farmland trees, roadside vegetation and streamside vegetation – in rural landscapes in southern Australia. Landscapes were selected to represent wooded or non-wooded combinations of these site types (e.g. roadside vegetation with or without trees), embedded in farmland with different land-uses (e.g. cropping, grazing). The species richness and abundance of bees was greater at sites containing little or no tree cover; and the cumulative richness of species was greater for tree-less sites than for those with trees. In contrast, species evenness was greatest in wooded site types, indicating these were less dominated by abundant generalist species. Open farmland and treeless roadsides had greater functional diversity (based on species traits) than wooded site types. Strong species trait associations were more numerous with open parts of the landscape, reflecting the greater functional diversity of open site types. These results suggest that a suite of the extant bee fauna can exploit large-scale transformation from former extensively wooded ecosystems to open agricultural landscapes. However, not all species are able to exploit modified landscapes and may disappear with further loss of wooded vegetation. Trait-based approaches provide insight into how changes in landscape pattern affect the bee fauna. Failure to adequately cater for multiple functional groups of bees across all landscape features could mean a substantial loss in species that
Published: 2019

45. Plumage coloration follows Gloger's rule in a ring species

Author: Ribot, Raoul FH, Ribot, Raoul FH, Berg, Mathew L, Schubert, Emanuel, Endler, John A, Bennett, Andrew TD, Ribot, Raoul FH, Ribot, Raoul FH, Berg, Mathew L, Schubert, Emanuel, Endler, John A, and Bennett, Andrew TD
Published: 2019

46. Description and evaluation of the Community Ice Sheet Model (CISM) v2.1

Author: Lipscomb, William H. (author), Price, Stephen F. (author), Hoffman, Matthew J. (author), Leguy, Gunter R. (author), Bennett, Andrew R. (author), Bradley, S.L. (author), Evans, Katherine J. (author), Fyke, Jeremy G. (author), Kennedy, Joseph H. (author), Lipscomb, William H. (author), Price, Stephen F. (author), Hoffman, Matthew J. (author), Leguy, Gunter R. (author), Bennett, Andrew R. (author), Bradley, S.L. (author), Evans, Katherine J. (author), Fyke, Jeremy G. (author), and Kennedy, Joseph H. (author)
Abstract: We describe and evaluate version 2.1 of the Community Ice Sheet Model (CISM). CISM is a parallel, 3-D thermomechanical model, written mainly in Fortran, that solves equations for the momentum balance and the thickness and temperature evolution of ice sheets. CISM's velocity solver incorporates a hierarchy of Stokes flow approximations, including shallow-shelf, depth-integrated higher order, and 3-D higher order. CISM also includes a suite of test cases, links to third-party solver libraries, and parameterizations of physical processes such as basal sliding, iceberg calving, and sub-ice-shelf melting. The model has been verified for standard test problems, including the Ice Sheet Model Intercomparison Project for Higher-Order Models (ISMIP-HOM) experiments, and has participated in the initMIP-Greenland initialization experiment. In multimillennial simulations with modern climate forcing on a 4 km grid, CISM reaches a steady state that is broadly consistent with observed flow patterns of the Greenland ice sheet. CISM has been integrated into version 2.0 of the Community Earth System Model, where it is being used for Greenland simulations under past, present, and future climates. The code is open-source with extensive documentation and remains under active development., Physical and Space Geodesy
Published: 2019
Full Text: View/download PDF

47. LIVVkit 2.1: Automated and extensible ice sheet model validation

Author: Evans, Katherine J. (author), Kennedy, Joseph H. (author), Lu, Dan (author), Forrester, Mary M. (author), Price, Stephen (author), Fyke, Jeremy (author), Bennett, Andrew R. (author), Hoffman, Matthew J. (author), Tezaur, Irina (author), Zender, Charles S. (author), Vizcaino, M. (author), Evans, Katherine J. (author), Kennedy, Joseph H. (author), Lu, Dan (author), Forrester, Mary M. (author), Price, Stephen (author), Fyke, Jeremy (author), Bennett, Andrew R. (author), Hoffman, Matthew J. (author), Tezaur, Irina (author), Zender, Charles S. (author), and Vizcaino, M. (author)
Abstract: A collection of scientific analyses, metrics, and visualizations for robust validation of ice sheet models is presented using the Land Ice Verification and Validation toolkit (LIVVkit), version 2.1, and the LIVVkit Extensions repository (LEX), version 0.1. This software collection targets stand-alone ice sheet or coupled Earth system models, and handles datasets and analyses that require high-performance computing and storage. LIVVkit aims to enable efficient and fully reproducible workflows for postprocessing, analysis, and visualization of observational and model-derived datasets in a shareable format, whereby all data, methodologies, and output are distributed to users for evaluation. Extending from the initial LIVVkit software framework, we demonstrate Greenland ice sheet simulation validation metrics using the coupled Community Earth System Model (CESM) as well as an idealized stand-alone high-resolution Community Ice Sheet Model, version 2 (CISM2), coupled to the Albany/FELIX velocity solver (CISM-Albany or CISM-A). As one example of the capability, LIVVkit analyzes the degree to which models capture the surface mass balance (SMB) and identifies potential sources of bias, using recently available in situ and remotely sensed data as comparison. Related fields within atmosphere and land surface models, e.g., surface temperature, radiation, and cloud cover, are also diagnosed. Applied to the CESM1.0, LIVVkit identifies a positive SMB bias that is focused largely around Greenland's southwest region that is due to insufficient ablation., Physical and Space Geodesy
Published: 2019
Full Text: View/download PDF

48. Policy Evaluation with Latent Confounders via Optimal Balance

Author: Bennett, Andrew, Kallus, Nathan, Bennett, Andrew, and Kallus, Nathan
Abstract: Evaluating novel contextual bandit policies using logged data is crucial in applications where exploration is costly, such as medicine. But it usually relies on the assumption of no unobserved confounders, which is bound to fail in practice. We study the question of policy evaluation when we instead have proxies for the latent confounders and develop an importance weighting method that avoids fitting a latent outcome regression model. We show that unlike the unconfounded case no single set of weights can give unbiased evaluation for all outcome models, yet we propose a new algorithm that can still provably guarantee consistency by instead minimizing an adversarial balance objective. We further develop tractable algorithms for optimizing this objective and demonstrate empirically the power of our method when confounders are latent.
Published: 2019

49. Darwin Wasps: a new name heralds renewed efforts to unravel the evolutionary history of Ichneumonidae

Author: Klopfstein, Seraina, Santos, Bernardo, Shaw, Mark, Alvarado, Mabel, Bennett, Andrew, Dal Pos, Davide, Giannotta, Madalene, Florez, Andres, Karlsson, Dave, Khalaim, Andrey, Lima, Alessandro, Miko, Istvan, Sääksjärvi, Ilari, Shimizu, So, Spasojevic, Tamara, van Noort, Simon, Vilhelmsen, Lars, Broad, Gavin, Klopfstein, Seraina, Santos, Bernardo, Shaw, Mark, Alvarado, Mabel, Bennett, Andrew, Dal Pos, Davide, Giannotta, Madalene, Florez, Andres, Karlsson, Dave, Khalaim, Andrey, Lima, Alessandro, Miko, Istvan, Sääksjärvi, Ilari, Shimizu, So, Spasojevic, Tamara, van Noort, Simon, Vilhelmsen, Lars, and Broad, Gavin
Published: 2019

50. Darwin Wasps: a new name heralds renewed efforts to unravel the evolutionary history of Ichneumonidae

Author: Klopfstein, Seraina, Santos, Bernardo, Shaw, Mark, Alvarado, Mabel, Bennett, Andrew, Dal Pos, Davide, Giannotta, Madalene, Florez, Andres, Karlsson, Dave, Khalaim, Andrey, Lima, Alessandro, Miko, Istvan, Sääksjärvi, Ilari, Shimizu, So, Spasojevic, Tamara, van Noort, Simon, Vilhelmsen, Lars, Broad, Gavin, Klopfstein, Seraina, Santos, Bernardo, Shaw, Mark, Alvarado, Mabel, Bennett, Andrew, Dal Pos, Davide, Giannotta, Madalene, Florez, Andres, Karlsson, Dave, Khalaim, Andrey, Lima, Alessandro, Miko, Istvan, Sääksjärvi, Ilari, Shimizu, So, Spasojevic, Tamara, van Noort, Simon, Vilhelmsen, Lars, and Broad, Gavin
Published: 2019

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Publication Year Range

Publication Type

Journal

Database

Publisher

195 results on '"Bennett, Andrew A"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources