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14,643 results on '"Tim, R."'

1. State- and context-dependent robotic manipulation and grasping via uncertainty-aware imitation learning

Author

Winter, Tim R., Sundaram, Ashok M., Friedl, Werner, Roa, Maximo A., Stulp, Freek, and Silvério, João

Subjects
Computer Science - Robotics, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

Generating context-adaptive manipulation and grasping actions is a challenging problem in robotics. Classical planning and control algorithms tend to be inflexible with regard to parameterization by external variables such as object shapes. In contrast, Learning from Demonstration (LfD) approaches, due to their nature as function approximators, allow for introducing external variables to modulate policies in response to the environment. In this paper, we utilize this property by introducing an LfD approach to acquire context-dependent grasping and manipulation strategies. We treat the problem as a kernel-based function approximation, where the kernel inputs include generic context variables describing task-dependent parameters such as the object shape. We build on existing work on policy fusion with uncertainty quantification to propose a state-dependent approach that automatically returns to demonstrations, avoiding unpredictable behavior while smoothly adapting to context changes. The approach is evaluated against the LASA handwriting dataset and on a real 7-DoF robot in two scenarios: adaptation to slippage while grasping and manipulating a deformable food item.

Published
2024

2. Vegetation-climate feedbacks across scales

Author

Miralles, Diego G., de Arellano, Jordi Vila-Guerau, McVicar, Tim R., and Mahecha, Miguel D.

Subjects
Physics - Atmospheric and Oceanic Physics
Abstract

Vegetation often understood merely as the result of long-term climate conditions. However, vegetation itself plays a fundamental role in shaping Earth's climate by regulating the energy, water, and biogeochemical cycles across terrestrial landscapes. It exerts influence by altering surface roughness, consuming significant water resources through transpiration and interception, lowering atmospheric CO2 concentration, and controlling net radiation and its partitioning into sensible and latent heat fluxes. This influence propagates through the atmosphere, from microclimate scales to the entire atmospheric boundary layer, subsequently impacting large-scale circulation and the global transport of heat and moisture. Understanding the feedbacks between vegetation and atmosphere across multiple scales is crucial for predicting the influence of land use and cover changes and for accurately representing these processes in climate models. This short review aims to discuss the mechanisms through which vegetation modulates climate across spatial and temporal scales. Particularly, we evaluate the influence of vegetation on circulation patterns, precipitation and temperature, both in terms of trends and extreme events, such as droughts and heatwaves. The main goal is to highlight the state of science and review recent studies that may help advance our collective understanding of vegetation feedbacks and the role they play in climate., Comment: In review

Published
2024

3. Self-Recognition in Language Models

Author

Davidson, Tim R., Surkov, Viacheslav, Veselovsky, Veniamin, Russo, Giuseppe, West, Robert, and Gulcehre, Caglar

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

A rapidly growing number of applications rely on a small set of closed-source language models (LMs). This dependency might introduce novel security risks if LMs develop self-recognition capabilities. Inspired by human identity verification methods, we propose a novel approach for assessing self-recognition in LMs using model-generated "security questions". Our test can be externally administered to monitor frontier models as it does not require access to internal model parameters or output probabilities. We use our test to examine self-recognition in ten of the most capable open- and closed-source LMs currently publicly available. Our extensive experiments found no empirical evidence of general or consistent self-recognition in any examined LM. Instead, our results suggest that given a set of alternatives, LMs seek to pick the "best" answer, regardless of its origin. Moreover, we find indications that preferences about which models produce the best answers are consistent across LMs. We additionally uncover novel insights on position bias considerations for LMs in multiple-choice settings., Comment: Accepted to EMNLP 2024, code to reproduce experiments and replicate findings available at https://github.com/trdavidson/self-recognition

Published
2024

4. Assessing the Benefits of Education in Early Childhood: Evidence from a Pre-K Lottery in Georgia. EdWorkingPaper No. 23-880

Author

Annenberg Institute for School Reform at Brown University, Henry Woodyard, Tim R. Sass, and Ishtiaque Fazlul

Abstract

Numerous studies have demonstrated a strong link between participation in pre-K programs and both short-term student achievement and positive later-life outcomes. Existing evidence primarily stems from experimental studies of small-scale, high-quality programs conducted in the 1960s and 1970s and analyses of the federal Head Start program. Meanwhile, evidence on state-funded pre-K programs, with no income restrictions, is scant and inconclusive. Using enrollment lotteries for over-subscribed school-based sites in Georgia's universal pre-K program, we analyze the impact of participation on elementary school outcomes. Lottery winners enter kindergarten more prepared in both math and reading than non-winning peers. Gains fade by the end of kindergarten, and some negative achievement effects emerge by grade 4. Free-andreduced-price meal (FRPM) students benefit more compared to non-FRPM students in later grades, suggesting greater benefits from attendance for disadvantaged students. Although we find no effects for discipline, lottery winners had one fewer absence each grade after kindergarten.

Published
2023

5. The AI Review Lottery: Widespread AI-Assisted Peer Reviews Boost Paper Scores and Acceptance Rates

Author

Latona, Giuseppe Russo, Ribeiro, Manoel Horta, Davidson, Tim R., Veselovsky, Veniamin, and West, Robert

Subjects
Computer Science - Computers and Society
Abstract

Journals and conferences worry that peer reviews assisted by artificial intelligence (AI), in particular, large language models (LLMs), may negatively influence the validity and fairness of the peer-review system, a cornerstone of modern science. In this work, we address this concern with a quasi-experimental study of the prevalence and impact of AI-assisted peer reviews in the context of the 2024 International Conference on Learning Representations (ICLR), a large and prestigious machine-learning conference. Our contributions are threefold. Firstly, we obtain a lower bound for the prevalence of AI-assisted reviews at ICLR 2024 using the GPTZero LLM detector, estimating that at least $15.8\%$ of reviews were written with AI assistance. Secondly, we estimate the impact of AI-assisted reviews on submission scores. Considering pairs of reviews with different scores assigned to the same paper, we find that in $53.4\%$ of pairs the AI-assisted review scores higher than the human review ($p = 0.002$; relative difference in probability of scoring higher: $+14.4\%$ in favor of AI-assisted reviews). Thirdly, we assess the impact of receiving an AI-assisted peer review on submission acceptance. In a matched study, submissions near the acceptance threshold that received an AI-assisted peer review were $4.9$ percentage points ($p = 0.024$) more likely to be accepted than submissions that did not. Overall, we show that AI-assisted reviews are consequential to the peer-review process and offer a discussion on future implications of current trends, Comment: Manoel Horta Ribeiro, Tim R. Davidson, and Veniamin Veselovsky contributed equally to this work

Published
2024

6. Spectral density of complex eigenvalues and associated mean eigenvector self-overlaps at the edge of elliptic Ginibre ensembles

Author

Crumpton, Mark J. and Würfel, Tim R.

Subjects
Mathematical Physics
Abstract

We consider the density of complex eigenvalues, $\rho(z)$, and the associated mean eigenvector self-overlaps, $\mathcal{O}(z)$, at the spectral edge of $N \times N$ real and complex elliptic Ginibre matrices, as $N \to \infty$. Two different regimes of ellipticity are studied: strong non-Hermiticity, keeping the ellipticity parameter $\tau$ fixed and weak non-Hermiticity with $\tau \rightarrow 1 $ as $N \rightarrow \infty$. At strong non-Hermiticity, we find that both $\rho(z)$ and $\mathcal{O}(z)$ have the same leading order behaviour across the elliptic Ginibre ensembles, establishing the expected universality. In the limit of weak non-Hermiticity, we find different results for $\rho(z)$ and $\mathcal{O}(z)$ across the two ensembles. This paper is the final of three papers that we have presented addressing the mean self-overlap of eigenvectors in these ensembles., Comment: 22 pages, 5 figures

Published
2024

7. Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma

Author

Smith, Nicola J, Reddin, Ian, Policelli, Paige, Oh, Sunwoo, Zainal, Nur, Howes, Emma, Jenkins, Benjamin, Tracy, Ian, Edmond, Mark, Sharpe, Benjamin, Amendra, Damian, Zheng, Ke, Egawa, Nagayasu, Doorbar, John, Rao, Anjali, Mahadevan, Sangeetha, Carpenter, Michael A, Harris, Reuben S, Ali, Simak, Hanley, Christopher, Buisson, Rémi, King, Emma, Thomas, Gareth J, and Fenton, Tim R

Published
2024
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13. Mean eigenvector self-overlap in the real and complex elliptic Ginibre ensembles at strong and weak non-Hermiticity

Author

Crumpton, Mark J., Fyodorov, Yan V., and Würfel, Tim R.

Subjects
Mathematical Physics
Abstract

We study the mean diagonal overlap of left and right eigenvectors associated with complex eigenvalues in $N\times N$ non-Hermitian random Gaussian matrices. In well known works by Chalker and Mehlig the expectation of this (self-)overlap was computed for the complex Ginibre ensemble as $N\to \infty$. In the present work, we consider the same quantity in the real and complex elliptic Ginibre ensembles characterized by correlations between off-diagonal entries controlled by a parameter $\tau\in[0,1]$, with $\tau=1$ corresponding to the Hermitian limit. We derive exact expressions for the mean diagonal overlap in both ensembles at any finite $N$, for any eigenvalue off the real axis. We further investigate several scaling regimes as $N\rightarrow \infty$, both in the limit of strong non-Hermiticity keeping a fixed $\tau\in[0,1)$ and in the weak non-Hermiticity limit, with $\tau$ approaching unity in such a way that $N(1-\tau)$ remains finite., Comment: 29 pages, 6 figures

Published
2024

14. Evaluating Language Model Agency through Negotiations

Author

Davidson, Tim R., Veselovsky, Veniamin, Josifoski, Martin, Peyrard, Maxime, Bosselut, Antoine, Kosinski, Michal, and West, Robert

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

We introduce an approach to evaluate language model (LM) agency using negotiation games. This approach better reflects real-world use cases and addresses some of the shortcomings of alternative LM benchmarks. Negotiation games enable us to study multi-turn, and cross-model interactions, modulate complexity, and side-step accidental evaluation data leakage. We use our approach to test six widely used and publicly accessible LMs, evaluating performance and alignment in both self-play and cross-play settings. Noteworthy findings include: (i) only closed-source models tested here were able to complete these tasks; (ii) cooperative bargaining games proved to be most challenging to the models; and (iii) even the most powerful models sometimes "lose" to weaker opponents, Comment: Accepted to ICLR 2024, code and link to project data are made available at https://github.com/epfl-dlab/LAMEN

Published
2024

15. Ultraviolet finite resummation of perturbative quantum gravity

Author

Morris, Tim R.

Subjects
High Energy Physics - Theory, General Relativity and Quantum Cosmology
Abstract

If the metric is chosen to depend exponentially on the conformal factor, and if one works in a gauge where the conformal factor has the wrong sign propagator, perturbative quantum gravity corrections can be partially resummed into a series of terms each of which is ultraviolet finite. These new terms however are not perturbative in some small parameter, and are not individually BRST invariant, or background diffeomorphism invariant. With appropriate parametrisation, the finiteness property holds true also for a full phenomenologically relevant theory of quantum gravity coupled to (beyond the standard model) matter fields, provided massive tadpole corrections are set to zero by a trivial renormalisation., Comment: 39 pages. Further comments and clarifications added. Version accepted for publication in Jour Class and Quant Gravity

Published
2024

18. An assessment of federal alcohol policies in Canada and priority recommendations: Results from the 3rd Canadian Alcohol Policy Evaluation Project

Author

Farkouh, Elizabeth K., Vallance, Kate, Wettlaufer, Ashley, Giesbrecht, Norman, Asbridge, Mark, Farrell-Low, Amanda M., Gagnon, Marilou, Price, Tina R., Priore, Isabella, Shelley, Jacob, Sherk, Adam, Shield, Kevin D., Solomon, Robert, Stockwell, Tim R., Thompson, Kara, Vishnevsky, Nicole, and Naimi, Timothy S.

Published
2024
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21. Mean left-right eigenvector self-overlap in the real Ginibre ensemble

Author

Würfel, Tim R., Crumpton, Mark J., and Fyodorov, Yan V.

Subjects
Mathematical Physics
Abstract

We study analytically the Chalker-Mehlig mean diagonal overlap $\mathcal{O}(z)$ between left and right eigenvectors associated with a complex eigenvalue $z$ of $N\times N$ matrices in the real Ginibre ensemble (GinOE). We first derive a general finite $N$ expression for the mean overlap and then investigate several scaling regimes in the limit $N\rightarrow \infty$. While in the generic spectral bulk and edge of the GinOE the limiting expressions for $\mathcal{O}(z)$ are found to coincide with the known results for the complex Ginibre ensemble (GinUE), in the region of eigenvalue depletion close to the real axis the asymptotic for the GinOE is considerably different. We also study numerically the distribution of diagonal overlaps and conjecture that it is the same in the bulk and at the edge of both the GinOE and GinUE, but essentially different in the depletion region of the GinOE., Comment: 23 pages, 7 figures

Published
2023

22. Efficacy, Safety, and Tolerability of Doravirine/Lamivudine/Tenofovir Disoproxil Fumarate Fixed-Dose Combination Tablets in Adolescents Living With HIV: Results Through Week 96 from IMPAACT 2014

Author

Rungmaitree, Supattra, Aurpibul, Linda, Best, Brookie M, Li, Xiang, Warshaw, Meredith G, Wan, Hong, Tobin, Nicole H, Jumes, Patricia, Leavitt, Randi, McCarthy, Katie, Scheckter, Rachel, Ounchanum, Pradthana, Violari, Avy, Teppler, Hedy, Campbell, Havilland, Krotje, Chelsea, Townley, Ellen, Moye, Jack, Melvin, Ann J, Beck, Justine, Sise, Thucuma, Kapogiannis, Bill G, George, Kathleen, Morgan, Patricia, Woolwine-Cunningham, Yvonne, Leblanc, Rebecca, Trabert, Kathleen, Mendell, Jeanne, Alvero, Carmelita, Farhad, Mona, Pasyar, Sarah, Muresan, Petronella, Patel, Nehali, English, Adrienne, Heince, Ryan, Jones, Sandra, Cooper, Ellen, McLaud, Debra, McFarland, Elizabeth, Hays, Shane Curran, Dunn, Jennifer, Navarro, Kacey, Robson, Amanda, Ndiwani, Hilda, Mathiba, Ruth, Ramsagar, Nastassja, Chotirosniramit, Nuntisa, Khamrong, Chintana, Chantong, Jiraporn, Srita, Angkana, Cressey, Tim R, Sukrakanchana, Praornsuda, Kaewmamuang, Kanyanee, Thaweesombat, Yupawan, Vanprapar, Nirun, Chokephaibulkit, Kulkanya, Kongstan, Nantaka, and Lermankul, Watcharee

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Pediatric, HIV/AIDS, Infectious Diseases, Clinical Trials and Supportive Activities, Clinical Research, Sexually Transmitted Infections, 6.1 Pharmaceuticals, Infection, Good Health and Well Being, Adolescent, Female, Humans, Male, Anti-HIV Agents, Anti-Retroviral Agents, HIV Infections, HIV Seropositivity, Lamivudine, RNA, Tenofovir, Treatment Outcome, adolescents, doravirine, HIV-1, MK-1439A, IMPAACT 2014 study team, Medical microbiology, Paediatrics
Abstract

BackgroundIMPAACT 2014 study is a phase I/II, multicenter, open-label, nonrandomized study of doravirine (DOR) co-formulated with lamivudine (3TC) and tenofovir disoproxil fumarate (TDF) as fixed-dose combination (DOR FDC) in adolescents with HIV-1. We report the efficacy, safety, and tolerability of DOR FDC through 96 weeks.MethodsParticipants were adolescents aged 12 to

Published
2023

23. Nucleotidyltransferase toxin MenT extends aminoacyl acceptor ends of serine tRNAs to control Mycobacterium tuberculosis growth

Author

Xibing Xu, Roland Barriot, Bertille Voisin, Tom J. Arrowsmith, Ben Usher, Claude Gutierrez, Xue Han, Carine Pagès, Peter Redder, Tim R. Blower, Olivier Neyrolles, and Pierre Genevaux

Subjects
Science
Abstract

Abstract Toxins of toxin-antitoxin systems use diverse mechanisms to inhibit bacterial growth. In this study, we characterize the translation inhibitor toxin MenT3 of Mycobacterium tuberculosis, the bacterium responsible for tuberculosis in humans. We show that MenT3 is a robust cytidine specific tRNA nucleotidyltransferase in vitro, capable of modifying the aminoacyl acceptor ends of most tRNA but with a marked preference for tRNASer, to which long stretches of cytidines are added. Furthermore, transcriptomic-wide analysis of MenT3 targets in M. tuberculosis identifies tRNASer as the sole target of MenT3 and reveals significant detoxification attempts by the essential CCA-adding enzyme PcnA in response to MenT3. Finally, under physiological conditions, only in the presence the native menAT3 operon, an active pool of endogenous MenT3 targeting tRNASer in M. tuberculosis is detected, likely reflecting the importance of MenT3 during infection.

Published
2024
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24. The biogeography of the Amazonian tree flora

Author

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

Subjects
Biology (General), QH301-705.5
Abstract

Abstract We describe the geographical variation in tree species composition across Amazonian forests and show how environmental conditions are associated with species turnover. Our analyses are based on 2023 forest inventory plots (1 ha) that provide abundance data for a total of 5188 tree species. Within-plot species composition reflected both local environmental conditions (especially soil nutrients and hydrology) and geographical regions. A broader-scale view of species turnover was obtained by interpolating the relative tree species abundances over Amazonia into 47,441 0.1-degree grid cells. Two main dimensions of spatial change in tree species composition were identified. The first was a gradient between western Amazonia at the Andean forelands (with young geology and relatively nutrient-rich soils) and central–eastern Amazonia associated with the Guiana and Brazilian Shields (with more ancient geology and poor soils). The second gradient was between the wet forests of the northwest and the drier forests in southern Amazonia. Isolines linking cells of similar composition crossed major Amazonian rivers, suggesting that tree species distributions are not limited by rivers. Even though some areas of relatively sharp species turnover were identified, mostly the tree species composition changed gradually over large extents, which does not support delimiting clear discrete biogeographic regions within Amazonia.

Published
2024
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25. Inducible auto-phosphorylation regulates a widespread family of nucleotidyltransferase toxins

Author

Tom J. Arrowsmith, Xibing Xu, Shangze Xu, Ben Usher, Peter Stokes, Megan Guest, Agnieszka K. Bronowska, Pierre Genevaux, and Tim R. Blower

Subjects
Science
Abstract

Abstract Nucleotidyltransferases (NTases) control diverse physiological processes, including RNA modification, DNA replication and repair, and antibiotic resistance. The Mycobacterium tuberculosis NTase toxin family, MenT, modifies tRNAs to block translation. MenT toxin activity can be stringently regulated by diverse MenA antitoxins. There has been no unifying mechanism linking antitoxicity across MenT homologues. Here we demonstrate through structural, biochemical, biophysical and computational studies that despite lacking kinase motifs, antitoxin MenA1 induces auto-phosphorylation of MenT1 by repositioning the MenT1 phosphoacceptor T39 active site residue towards bound nucleotide. Finally, we expand this predictive model to explain how unrelated antitoxin MenA3 is similarly able to induce auto-phosphorylation of cognate toxin MenT3. Our study reveals a conserved mechanism for the control of tuberculosis toxins, and demonstrates how active site auto-phosphorylation can regulate the activity of widespread NTases.

Published
2024
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26. Off-shell divergences in quantum gravity

Author

Mandric, Vlad-Mihai, Morris, Tim R., and Stulga, Dalius

Subjects
High Energy Physics - Theory, General Relativity and Quantum Cosmology
Abstract

We investigate off-shell perturbative renormalisation of pure quantum gravity for both background metric and quantum fluctuations. We show that at each new loop order, the divergences that do not vanish on-shell are constructed from only the total metric, whilst those that vanish on-shell are renormalised by canonical transformations involving the quantum fields. Purely background metric divergences do not separately appear, and the background metric does not get renormalised. We highlight that renormalisation group identities play a crucial role ensuring consistency in the renormalisation of BRST transformations beyond one loop order. We verify these assertions by computing leading off-shell divergences to two loops, exploiting off-shell BRST invariance and the renormalisation group equations. Although some divergences can be absorbed by field redefinitions, we explain why this does not lead to finite beta-functions for the corresponding field., Comment: 45 pages

Published
2023

27. Universal scaling dimensions for highly irrelevant operators in the Local Potential Approximation

Author

Mandric, Vlad-Mihai, Morris, Tim R., and Stulga, Dalius

Subjects
High Energy Physics - Theory
Abstract

We study $d$-dimensional scalar field theory in the Local Potential Approximation of the functional renormalization group. Sturm-Liouville methods allow the eigenoperator equation to be cast as a Schrodinger-type equation. Combining solutions in the large field limit with the Wentzel-Kramers-Brillouin approximation, we solve analytically for the scaling dimension $d_n$ of high dimension potential-type operators $\mathcal{O}_n(\varphi)$ around a non-trivial fixed point. We find that $d_n = n(d-d_\varphi)$ to leading order in $n$ as $n \to \infty$, where $d_\varphi=\frac{1}{2}(d-2+\eta)$ is the scaling dimension of the field, $\varphi$, and determine the power-law growth of the subleading correction. For $O(N)$ invariant scalar field theory, the scaling dimension is just double this, for all fixed $N\geq0$ and additionally for $N=-2,-4,\ldots \,.$ These results are universal, independent of the choice of cutoff function which we keep general throughout, subject only to some weak constraints., Comment: 23 pages, no figures. Clarifications added. Version published in PRD

Published
2023
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28. Pharmacokinetics and safety of first-line tuberculosis drugs rifampin, isoniazid, ethambutol, and pyrazinamide during pregnancy and postpartum: results from IMPAACT P1026s

Author

Van Schalkwyk, Marije, Bekker, Adrie, Decloedt, Eric, Wang, Jiajia, Theron, Gerhard B, Cotton, Mark F, Eke, Ahizechukwu C, Cressey, Tim R, Shapiro, David E, Bacon, Kira, Knowles, Kevin, George, Kathleen, Browning, Renee, Chakhtoura, Nahida, Rungruengthanakit, Kittipong, Wiesner, Lubbe, Capparelli, Edmund V, Stek, Alice M, Mirochnick, Mark, Best, Brookie M, and Team, on behalf of the IMPAACT P1026s Protocol

Subjects
Reproductive Medicine, Biomedical and Clinical Sciences, Clinical Research, Tuberculosis, HIV/AIDS, Rare Diseases, Infectious Diseases, Prevention, Clinical Trials and Supportive Activities, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Infection, Good Health and Well Being, IMPAACT P1026s Protocol Team, drug-susceptible tuberculosis, ethambutol, isoniazid, pharmacokinetics, pregnancy, pyrazinamide, rifampin, Microbiology, Medical Microbiology, Pharmacology and Pharmaceutical Sciences, Medical microbiology, Pharmacology and pharmaceutical sciences
Abstract

Physiological changes during pregnancy may alter the pharmacokinetics (PK) of antituberculosis drugs. The International Maternal Pediatric Adolescent AIDS Clinical Trials Network P1026s was a multicenter, phase IV, observational, prospective PK and safety study of antiretroviral and antituberculosis drugs administered as part of clinical care in pregnant persons living with and without HIV. We assessed the effects of pregnancy on rifampin, isoniazid, ethambutol, and pyrazinamide PK in pregnant and postpartum (PP) persons without HIV treated for drug-susceptible tuberculosis disease. Daily antituberculosis treatment was prescribed following World Health Organization-recommended weight-band dosing guidelines. Steady-state 12-hour PK profiles of rifampin, isoniazid, ethambutol, and pyrazinamide were performed during second trimester (2T), third trimester (3T), and 2-8 of weeks PP. PK parameters were characterized using noncompartmental analysis, and comparisons were made using geometric mean ratios (GMRs) with 90% confidence intervals (CI). Twenty-seven participants were included: 11 African, 9 Asian, 3 Hispanic, and 4 mixed descent. PK data were available for 17, 21, and 14 participants in 2T, 3T, and PP, respectively. Rifampin and pyrazinamide AUC0-24 and C max in pregnancy were comparable to PP with the GMR between 0.80 and 1.25. Compared to PP, isoniazid AUC0-24 was 25% lower and C max was 23% lower in 3T. Ethambutol AUC0-24 was 39% lower in 3T but limited by a low PP sample size. In summary, isoniazid and ethambutol concentrations were lower during pregnancy compared to PP concentrations, while rifampin and pyrazinamide concentrations were similar. However, the median AUC0-24 for rifampin, isoniazid, and pyrazinamide met the therapeutic targets. The clinical impact of lower isoniazid and ethambutol exposure during pregnancy needs to be determined.

Published
2023

38. Unravelling the physicochemical and antimicrobial mechanisms of human serum albumin/tannic acid coatings for medical-grade polycaprolactone scaffolds

Author

Silvia Cometta, Bogdan C. Donose, Alfredo Juárez-Saldivar, Akhilandeshwari Ravichandran, Yanan Xu, Nathalie Bock, Tim R. Dargaville, Aleksandar D. Rakić, and Dietmar W. Hutmacher

Subjects
Bacterial infection, Biofilm, Human serum albumin, Tannic acid, Polycaprolactone, 3D printing, Materials of engineering and construction. Mechanics of materials, TA401-492, Biology (General), QH301-705.5
Abstract

Biofilm-related biomaterial infections are notoriously challenging to treat and can lead to chronic infection and persisting inflammation. To date, a large body of research can be reviewed for coatings which potentially prevent bacterial infection while promoting implant integration. Yet only a very small number has been translated from bench to bedside. This study provides an in-depth analysis of the stability, antibacterial mechanism, and biocompatibility of medical grade polycaprolactone (mPCL), coated with human serum albumin (HSA), the most abundant protein in blood plasma, and tannic acid (TA), a natural polyphenol with antibacterial properties. Molecular docking studies demonstrated that HSA and TA interact mainly through hydrogen-bonding, ionic and hydrophobic interactions, leading to smooth and regular assemblies. In vitro bacteria adhesion testing showed that coated scaffolds maintained their antimicrobial properties over 3 days by significantly reducing S. aureus colonization and biofilm formation. Notably, amplitude modulation-frequency modulation (AMFM) based viscoelasticity mapping and transmission electron microscopy (TEM) data suggested that HSA/TA-coatings cause morphological and mechanical changes on the outer cell membrane of S. aureus leading to membrane disruption and cell death while proving non-toxic to human primary cells. These results support this antibiotic-free approach as an effective and biocompatible strategy to prevent biofilm-related biomaterial infections.

Published
2024
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40. The biogeography of the Amazonian tree flora

Author

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

Published
2024
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46. Assessment of three antibiotic combination regimens against Gram-negative bacteria causing neonatal sepsis in low- and middle-income countries

Author

Kakaraskoska Boceska, Biljana, Vilken, Tuba, Xavier, Basil Britto, Kostyanev, Tomislav, Lin, Qiang, Lammens, Christine, Ellis, Sally, O’Brien, Seamus, da Costa, Renata Maria Augusto, Cook, Aislinn, Russell, Neal, Bielicki, Julia, Riddell, Amy, Stohr, Wolfgang, Walker, Ann Sarah, Berezin, Eitan Naaman, Roilides, Emmanuel, De Luca, Maia, Romani, Lorenza, Ballot, Daynia, Dramowski, Angela, Wadula, Jeannette, Lochindarat, Sorasak, Boonkasidecha, Suppawat, Namiiro, Flavia, Ngoc, Hoang Thi Bich, Tran, Minh Dien, Cressey, Tim R., Preedisripipat, Kanchana, Berkley, James A., Musyimi, Robert, Zarras, Charalampos, Nana, Trusha, Whitelaw, Andrew, da Silva, Cely Barreto, Jaglal, Prenika, Ssengooba, Willy, Saha, Samir K., Islam, Mohammad Shahidul, Mussi-Pinhata, Marisa Marcia, Carvalheiro, Cristina Gardonyi, Piddock, Laura J. V., Heath, Paul T., Malhotra-Kumar, Surbhi, Sharland, Michael, Glupczynski, Youri, and Goossens, Herman

Published
2024
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50. Mammal responses to global changes in human activity vary by trophic group and landscape

Author

Burton, A. Cole, Beirne, Christopher, Gaynor, Kaitlyn M., Sun, Catherine, Granados, Alys, Allen, Maximilian L., Alston, Jesse M., Alvarenga, Guilherme C., Calderón, Francisco Samuel Álvarez, Amir, Zachary, Anhalt-Depies, Christine, Appel, Cara, Arroyo-Arce, Stephanny, Balme, Guy, Bar-Massada, Avi, Barcelos, Daniele, Barr, Evan, Barthelmess, Erika L., Baruzzi, Carolina, Basak, Sayantani M., Beenaerts, Natalie, Belmaker, Jonathan, Belova, Olgirda, Bezarević, Branko, Bird, Tori, Bogan, Daniel A., Bogdanović, Neda, Boyce, Andy, Boyce, Mark, Brandt, LaRoy, Brodie, Jedediah F., Brooke, Jarred, Bubnicki, Jakub W., Cagnacci, Francesca, Carr, Benjamin Scott, Carvalho, João, Casaer, Jim, Černe, Rok, Chen, Ron, Chow, Emily, Churski, Marcin, Cincotta, Connor, Ćirović, Duško, Coates, T. D., Compton, Justin, Coon, Courtney, Cove, Michael V., Crupi, Anthony P., Farra, Simone Dal, Darracq, Andrea K., Davis, Miranda, Dawe, Kimberly, De Waele, Valerie, Descalzo, Esther, Diserens, Tom A., Drimaj, Jakub, Duľa, Martin, Ellis-Felege, Susan, Ellison, Caroline, Ertürk, Alper, Fantle-Lepczyk, Jean, Favreau, Jorie, Fennell, Mitch, Ferreras, Pablo, Ferretti, Francesco, Fiderer, Christian, Finnegan, Laura, Fisher, Jason T., Fisher-Reid, M. Caitlin, Flaherty, Elizabeth A., Fležar, Urša, Flousek, Jiří, Foca, Jennifer M., Ford, Adam, Franzetti, Barbara, Frey, Sandra, Fritts, Sarah, Frýbová, Šárka, Furnas, Brett, Gerber, Brian, Geyle, Hayley M., Giménez, Diego G., Giordano, Anthony J., Gomercic, Tomislav, Gompper, Matthew E., Gräbin, Diogo Maia, Gray, Morgan, Green, Austin, Hagen, Robert, Hagen, Robert (Bob), Hammerich, Steven, Hanekom, Catharine, Hansen, Christopher, Hasstedt, Steven, Hebblewhite, Mark, Heurich, Marco, Hofmeester, Tim R., Hubbard, Tru, Jachowski, David, Jansen, Patrick A., Jaspers, Kodi Jo, Jensen, Alex, Jordan, Mark, Kaizer, Mariane C., Kelly, Marcella J., Kohl, Michel T., Kramer-Schadt, Stephanie, Krofel, Miha, Krug, Andrea, Kuhn, Kellie M., Kuijper, Dries P. J., Kuprewicz, Erin K., Kusak, Josip, Kutal, Miroslav, Lafferty, Diana J. R., LaRose, Summer, Lashley, Marcus, Lathrop, Richard, Lee, Jr, Thomas E., Lepczyk, Christopher, Lesmeister, Damon B., Licoppe, Alain, Linnell, Marco, Loch, Jan, Long, Robert, Lonsinger, Robert C., Louvrier, Julie, Luskin, Matthew Scott, MacKay, Paula, Maher, Sean, Manet, Benoît, Mann, Gareth K. H., Marshall, Andrew J., Mason, David, McDonald, Zara, McKay, Tracy, McShea, William J., Mechler, Matt, Miaud, Claude, Millspaugh, Joshua J., Monteza-Moreno, Claudio M., Moreira-Arce, Dario, Mullen, Kayleigh, Nagy, Christopher, Naidoo, Robin, Namir, Itai, Nelson, Carrie, O’Neill, Brian, O’Mara, M. Teague, Oberosler, Valentina, Osorio, Christian, Ossi, Federico, Palencia, Pablo, Pearson, Kimberly, Pedrotti, Luca, Pekins, Charles E., Pendergast, Mary, Pinho, Fernando F., Plhal, Radim, Pocasangre-Orellana, Xochilt, Price, Melissa, Procko, Michael, Proctor, Mike D., Ramalho, Emiliano Esterci, Ranc, Nathan, Reljic, Slaven, Remine, Katie, Rentz, Michael, Revord, Ronald, Reyna-Hurtado, Rafael, Risch, Derek, Ritchie, Euan G., Romero, Andrea, Rota, Christopher, Rovero, Francesco, Rowe, Helen, Rutz, Christian, Salvatori, Marco, Sandow, Derek, Schalk, Christopher M., Scherger, Jenna, Schipper, Jan, Scognamillo, Daniel G., Şekercioğlu, Çağan H., Semenzato, Paola, Sevin, Jennifer, Shamon, Hila, Shier, Catherine, Silva-Rodríguez, Eduardo A., Sindicic, Magda, Smyth, Lucy K., Soyumert, Anil, Sprague, Tiffany, St. Clair, Colleen Cassady, Stenglein, Jennifer, Stephens, Philip A., Stępniak, Kinga Magdalena, Stevens, Michael, Stevenson, Cassondra, Ternyik, Bálint, Thomson, Ian, Torres, Rita T., Tremblay, Joan, Urrutia, Tomas, Vacher, Jean-Pierre, Visscher, Darcy, Webb, Stephen L., Weber, Julian, Weiss, Katherine C. B., Whipple, Laura S., Whittier, Christopher A., Whittington, Jesse, Wierzbowska, Izabela, Wikelski, Martin, Williamson, Jacque, Wilmers, Christopher C., Windle, Todd, Wittmer, Heiko U., Zharikov, Yuri, Zorn, Adam, and Kays, Roland

Published
2024
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