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14,444 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

17. 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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20. 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

21. 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

22. 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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23. 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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24. 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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25. 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

26. 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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27. 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

39. 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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40. One sixth of Amazonian tree diversity is dependent on river floodplains

Author

Householder, John Ethan, Wittmann, Florian, Schöngart, Jochen, Piedade, Maria Teresa Fernandez, Junk, Wolfgang J., Latrubesse, Edgardo Manuel, Quaresma, Adriano Costa, Demarchi, Layon O., de S. Lobo, Guilherme, Aguiar, Daniel P. P. de, Assis, Rafael L., Lopes, Aline, Parolin, Pia, Leão do Amaral, Iêda, Coelho, Luiz de Souza, de Almeida Matos, Francisca Dionízia, Lima Filho, Diógenes de Andrade, Salomão, Rafael P., Castilho, Carolina V., Guevara-Andino, Juan Ernesto, Carim, Marcelo de Jesus Veiga, Phillips, Oliver L., Cárdenas López, Dairon, Magnusson, William E., Sabatier, Daniel, Revilla, Juan David Cardenas, Molino, Jean-François, Irume, Mariana Victória, Martins, Maria Pires, Guimarães, José Renan da Silva, Ramos, José Ferreira, Rodrigues, Domingos de Jesus, Bánki, Olaf S., Peres, Carlos A., Pitman, Nigel C. A., Hawes, Joseph E., Almeida, Everton José, Barbosa, Luciane Ferreira, Cavalheiro, Larissa, dos Santos, Márcia Cléia Vilela, Luize, Bruno Garcia, Novo, Evlyn Márcia Moraes de Leão, Núñez Vargas, Percy, Silva, Thiago Sanna Freire, Venticinque, Eduardo Martins, Manzatto, Angelo Gilberto, Reis, Neidiane Farias Costa, Terborgh, John, Casula, Katia Regina, Costa, Flávia R. C., Honorio Coronado, Euridice N., Monteagudo Mendoza, Abel, Montero, Juan Carlos, Feldpausch, Ted R., Aymard C, Gerardo A., Baraloto, Chris, Castaño Arboleda, Nicolás, Engel, Julien, Petronelli, Pascal, Zartman, Charles Eugene, Killeen, Timothy J., Rincón, Lorena Maniguaje, Marimon, Beatriz S., Marimon-Junior, Ben Hur, Schietti, Juliana, Sousa, Thaiane R., Vasquez, Rodolfo, Mostacedo, Bonifacio, Dantas do Amaral, Dário, Castellanos, Hernán, Medeiros, Marcelo Brilhante de, Simon, Marcelo Fragomeni, Andrade, Ana, Camargo, José Luís, Laurance, William F., Laurance, Susan G. W., Farias, Emanuelle de Sousa, Lopes, Maria Aparecida, Magalhães, José Leonardo Lima, Mendonça Nascimento, Henrique Eduardo, Queiroz, Helder Lima de, Brienen, Roel, Stevenson, Pablo R., Araujo-Murakami, Alejandro, Baker, Tim R., Cintra, Bruno Barçante Ladvocat, Feitosa, Yuri Oliveira, Mogollón, Hugo F., Noronha, Janaína Costa, Barbosa, Flávia Rodrigues, de Sá Carpanedo, Rainiellen, Duivenvoorden, Joost F., Silman, Miles R., Ferreira, Leandro Valle, Levis, Carolina, Lozada, José Rafael, Comiskey, James A., Draper, Freddie C., Toledo, José Julio de, Damasco, Gabriel, Dávila, Nállarett, García-Villacorta, Roosevelt, Vicentini, Alberto, Cornejo Valverde, Fernando, Alonso, Alfonso, Arroyo, Luzmila, Dallmeier, Francisco, Gomes, Vitor H. F., Jimenez, Eliana M., Neill, David, Peñuela Mora, Maria Cristina, Carvalho, Fernanda Antunes, Coelho de Souza, Fernanda, Feeley, Kenneth J., Gribel, Rogerio, Pansonato, Marcelo Petratti, Ríos Paredes, Marcos, Barlow, Jos, Berenguer, Erika, Dexter, Kyle G., Ferreira, Joice, Fine, Paul V. A., Guedes, Marcelino Carneiro, Huamantupa-Chuquimaco, Isau, Licona, Juan Carlos, Pennington, Toby, Villa Zegarra, Boris Eduardo, Vos, Vincent Antoine, Cerón, Carlos, Fonty, Émile, Henkel, Terry W., Maas, Paul, Pos, Edwin, Silveira, Marcos, Stropp, Juliana, Thomas, Raquel, Daly, Doug, Milliken, William, Pardo Molina, Guido, Vieira, Ima Célia Guimarães, Albuquerque, Bianca Weiss, Campelo, Wegliane, Emilio, Thaise, Fuentes, Alfredo, Klitgaard, Bente, Marcelo Pena, José Luis, Souza, Priscila F., 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, Doza, Hilda Paulette Dávila, Gómez, Ricardo Zárate, Gonzales, Therany, Gonzales, George Pepe Gallardo, Hoffman, Bruce, Junqueira, André Braga, Malhi, Yadvinder, Miranda, Ires Paula de Andrade, Mozombite-Pinto, Linder Felipe, Prieto, Adriana, Rudas, Agustín, Ruschel, Ademir R., Silva, Natalino, Vela, César I. A., Zent, Stanford, Zent, Egleé L., Cano, Angela, Carrero Márquez, Yrma Andreina, Correa, Diego F., Costa, Janaina Barbosa Pedrosa, Flores, Bernardo Monteiro, Galbraith, David, Holmgren, Milena, Kalamandeen, Michelle, Nascimento, Marcelo Trindade, Oliveira, Alexandre A., Ramirez-Angulo, Hirma, Rocha, Maira, Scudeller, Veridiana Vizoni, Sierra, Rodrigo, Tirado, Milton, Umaña, Maria Natalia, van der Heijden, Geertje, Vilanova Torre, Emilio, 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, 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, and ter Steege, Hans

Published
2024
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43. Generalised unitary group integrals of Ingham-Siegel and Fisher-Hartwig type

Author

Akemann, Gernot, Aygün, Noah, and Würfel, Tim R.

Subjects
Mathematical Physics, Condensed Matter - Statistical Mechanics, High Energy Physics - Theory
Abstract

We generalise well-known integrals of Ingham-Siegel and Fisher-Hartwig type over the unitary group $U(N)$ with respect to Haar measure, for finite $N$ and including fixed external matrices. When depending only on the eigenvalues of the unitary matrix, they can be related to a Toeplitz determinant with jump singularities. After introducing fixed deterministic matrices as external sources, the integrals can no longer be solved using Andr\'ei\'ef's integration formula. Resorting to the character expansion as put forward by Balantekin, we derive explicit determinantal formulae containing Kummer's confluent and Gauss' hypergeometric function. They depend only on the eigenvalues of the deterministic matrices and are analytic in the parameters of the jump singularities. Furthermore, unitary two-matrix integrals of the same type are proposed and solved in the same manner. When making part of the deterministic matrices random and integrating over them, we obtain similar formulae in terms of Pfaffian determinants. This is reminiscent to a unitary group integral found recently by Kanazawa and Kieburg., Comment: 23 pages

Published
2023
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44. Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence

Author

Sam C. Went, David M. Picton, Richard D. Morgan, Andrew Nelson, Aisling Brady, Giuseppina Mariano, David T. F. Dryden, Darren L. Smith, Nicolas Wenner, Jay C. D. Hinton, and Tim R. Blower

Subjects
Science
Abstract

Abstract Bacteria have evolved a broad range of systems that provide defence against their viral predators, bacteriophages. Bacteriophage Exclusion (BREX) systems recognise and methylate 6 bp non-palindromic motifs within the host genome, and prevent replication of non-methylated phage DNA that encodes these same motifs. How BREX recognises cognate motifs has not been fully understood. In this study we characterise BREX from pathogenic Salmonella and present X-ray crystallographic structures of the conserved BREX protein, PglX. The PglX N-terminal domain encodes the methyltransferase, whereas the C-terminal domain is for motif recognition. We also present the structure of PglX bound to the phage-derived DNA mimic, Ocr, an inhibitor of BREX activity. Our analyses propose modes for DNA-binding by PglX and indicate that both methyltransferase activity and defence require larger BREX complexes. Through rational engineering of PglX we broaden both the range of phages targeted, and the host motif sequences that are methylated by BREX. Our data demonstrate that PglX is used to recognise specific DNA sequences for BREX activity, contributing to motif recognition for both phage defence and host methylation.

Published
2024
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45. Population Pharmacokinetic Modeling of Abacavir/Dolutegravir/Lamivudine to Support a Fixed-Dose Combination in Children with HIV-1

Author

Hardik Chandasana, Sven C. van Dijkman, Rashmi Mehta, Mark Bush, Helena Rabie, Patricia Flynn, Tim R. Cressey, Edward P. Acosta, Kristina M. Brooks, and for the IMPAACT 2019 Study Team

Subjects
Dolutegravir, Abacavir, Lamivudine, Population pharmacokinetics, HIV-1, Pediatrics, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Introduction Once-daily fixed-dose combinations (FDC) containing abacavir (ABC), dolutegravir (DTG), and lamivudine (3TC) have been approved in the US for adults and children with HIV weighing ≥ 6 kg. This analysis assessed the ability of previously developed ABC, DTG, and 3TC pediatric population pharmacokinetic (PopPK) models using multiple formulations to describe and predict PK data in young children using dispersible tablet (DT) and tablet formulations of ABC/DTG/3TC FDC in the IMPAACT 2019 study. Methods IMPAACT 2019 was a Phase I/II study assessing the PK, safety, tolerability, and efficacy of ABC/DTG/3TC FDC in children with HIV-1. Intensive and sparse PK samples were collected over 48 weeks. Existing drug-specific pediatric PopPK models for ABC (2-compartment), DTG (1-compartment), and 3TC (1-compartment) were applied to the IMPAACT 2019 drug concentration data without re-estimation (external validation) of PopPK parameters. Drug exposures were then simulated across World Health Organization weight bands for children weighing ≥ 6 to

Published
2024
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46. Tidal and seasonal influence on cold seep activity and methanotroph efficiency in the North Sea

Author

Tim R. de Groot, Malika Menoud, Judith van Bleijswijk, Sonja M. van Leeuwen, J. van der Molen, Victor Hernando-Morales, Helen Czerski, Hossein Maazallahi, Sylvia Walter, Darci Rush, Thomas Röckmann, and Helge Niemann

Subjects
Geology, QE1-996.5, Environmental sciences, GE1-350
Abstract

Abstract The ocean’s methane emission to the atmosphere is dominated by continental shelves where cold seeps are globally common features. Seeps emit methane into the hydrosphere, but temporal variations and controls of seep activity and the efficiency of the microbial methane filter in the water column are scarce. Here we address these knowledge gaps by measuring whole water column methane inventories and methanotrophic activity at a temporal resolution of 2 hours at a North Sea cold seep (Doggerbank) in summer and autumn. We found that bottom water methane inventories were 68% (summer) and 11% (autumn) higher during low tide compared to high tide coinciding with increased methanotrophic activity. The activity of methanotrophs was reduced during autumn when the water column was fully mixed and matched by higher methane emissions to the atmosphere. Our results show that tides are underappreciated controls on seepage and methanotrophic activity and methane sea–atmosphere fluxes.

Published
2024
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47. Receiving home care forms and the risk for emergency department visits in community-dwelling Dutch older adults, a retrospective cohort study using national data

Author

Oscar S Smeekes, Tim R De Boer, Robert D Van Der Mei, Bianca M Buurman, and Hanna C Willems

Subjects
Home care, Emergency department, Risk, Older adults, National data, Public aspects of medicine, RA1-1270
Abstract

Abstract Background Older adults receiving home care have a higher risk of visiting the emergency department (ED) than community-dwelling older adults not receiving home care. This may result from a higher incidence of comorbidities and reduced functional autonomy in home care recipients. Since people receive different types of home care because of their different comorbidities and autonomy profiles, it is possible that distinguishing between the form of home care can help identify subpopulations with different risks for ED visits and help develop targeted interventions. This study aimed to compare the risk of visiting the ED in older adults receiving different forms of home care with those living at home without receiving home care in a national cohort in one year. Methods A retrospective cohort study using claims data collected in 2019 on the Dutch population aged ≥ 65 years (N = 3,314,440) was conducted. Participants were classified as follows: no claimed home care (NO), household help (HH), personal care (PC), HH + PC, and nursing home care at home (NHH). The primary outcome was the number of individuals that visited the ED. Secondary outcomes were the number of individuals whose home care changed, who were institutionalized, or who died. Exploratory logistic regression was applied. Results There were 2,758,093 adults in the NO group, 131,260 in the HH group, 154,462 in the PC group, 96,526 in the HH + PC group, and 34,612 in the NHH group. More ED visits were observed in the home care groups than in the NO group, and this risk increased to more than two-fold for the PC groups. There was a significant change to a more intensive form of home care, institutionalization, or death in all groups. Conclusions Distinguishing between the form of home care older adults receive identifies subpopulations with different risks for ED visits compared with community-dwelling older adults not receiving home care on a population level. Home care transitions are frequent and mostly involve more intensive care or death. Although older adults not receiving home care have a lower risk of ED visits, they contribute most to the absolute volume of ED visits.

Published
2024
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48. Variability and trends of near-surface wind speed over the Tibetan Plateau: The role played by the westerly and Asian monsoon

Author

Gang-Feng Zhang, Cesar Azorin-Molina, Deliang Chen, Tim R. McVicar, Jose A. Guijarro, Kai-Qiang Deng, Lorenzo Minola, Jaeyeon Lee, Seok-Woo Son, Heng Ma, and Pei-Jun Shi

Subjects
Tibetan Plateau, Wind speed, Decadal change, Atmospheric circulation, Physical processes, Meteorology. Climatology, QC851-999, Social sciences (General), H1-99
Abstract

Near-surface wind speed exerts profound impacts on many environmental issues, while the long-term (≥60 years) trend and multidecadal variability in the wind speed and its underlying causes in global high-elevation and mountainous areas (e.g., Tibetan Plateau) remain largely unknown. Here, by examining homogenized wind speed data from 104 meteorological stations over the Tibetan Plateau for 1961–2020 and ERA5 reanalysis datasets, we investigated the variability and long-term trend in the near-surface wind speed and revealed the role played by the westerly and Asian monsoon. The results show that the homogenized annual wind speed displays a decreasing trend (−0.091 m s−1 per decade, p

Published
2024
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49. Camtrap DP: an open standard for the FAIR exchange and archiving of camera trap data

Author

Jakub W. Bubnicki, Ben Norton, Steven J. Baskauf, Tom Bruce, Francesca Cagnacci, Jim Casaer, Marcin Churski, Joris P. G. M. Cromsigt, Simone Dal Farra, Christian Fiderer, Tavis D. Forrester, Heidi Hendry, Marco Heurich, Tim R. Hofmeester, Patrick A. Jansen, Roland Kays, Dries P. J. Kuijper, Yorick Liefting, John D. C. Linnell, Matthew S. Luskin, Christopher Mann, Tanja Milotic, Peggy Newman, Jürgen Niedballa, Damiano Oldoni, Federico Ossi, Tim Robertson, Francesco Rovero, Marcus Rowcliffe, Lorenzo Seidenari, Izabela Stachowicz, Dan Stowell, Mathias W. Tobler, John Wieczorek, Fridolin Zimmermann, and Peter Desmet

Subjects
Biodiversity data, camera traps, data exchange, data sharing, information standards, Technology, Ecology, QH540-549.5
Abstract

Abstract Camera trapping has revolutionized wildlife ecology and conservation by providing automated data acquisition, leading to the accumulation of massive amounts of camera trap data worldwide. Although management and processing of camera trap‐derived Big Data are becoming increasingly solvable with the help of scalable cyber‐infrastructures, harmonization and exchange of the data remain limited, hindering its full potential. There is currently no widely accepted standard for exchanging camera trap data. The only existing proposal, “Camera Trap Metadata Standard” (CTMS), has several technical shortcomings and limited adoption. We present a new data exchange format, the Camera Trap Data Package (Camtrap DP), designed to allow users to easily exchange, harmonize and archive camera trap data at local to global scales. Camtrap DP structures camera trap data in a simple yet flexible data model consisting of three tables (Deployments, Media and Observations) that supports a wide range of camera deployment designs, classification techniques (e.g., human and AI, media‐based and event‐based) and analytical use cases, from compiling species occurrence data through distribution, occupancy and activity modeling to density estimation. The format further achieves interoperability by building upon existing standards, Frictionless Data Package in particular, which is supported by a suite of open software tools to read and validate data. Camtrap DP is the consensus of a long, in‐depth, consultation and outreach process with standard and software developers, the main existing camera trap data management platforms, major players in the field of camera trapping and the Global Biodiversity Information Facility (GBIF). Under the umbrella of the Biodiversity Information Standards (TDWG), Camtrap DP has been developed openly, collaboratively and with version control from the start. We encourage camera trapping users and developers to join the discussion and contribute to the further development and adoption of this standard.

Published
2024
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50. Genomic and taxonomic evaluation of 38 Treponema prophage sequences

Author

Rachel Ridgway, Hanshuo Lu, Tim R. Blower, Nicholas James Evans, and Stuart Ainsworth

Subjects
Bacteriophages, Prophages, Treponema, Bioinformatics, Treponema phages, Genomic analysis, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Despite Spirochetales being a ubiquitous and medically important order of bacteria infecting both humans and animals, there is extremely limited information regarding their bacteriophages. Of the genus Treponema, there is just a single reported characterised prophage. Results We applied a bioinformatic approach on 24 previously published Treponema genomes to identify and characterise putative treponemal prophages. Thirteen of the genomes did not contain any detectable prophage regions. The remaining eleven contained 38 prophage sequences, with between one and eight putative prophages in each bacterial genome. The prophage regions ranged from 12.4 to 75.1 kb, with between 27 and 171 protein coding sequences. Phylogenetic analysis revealed that 24 of the prophages formed three distinct sequence clusters, identifying putative myoviral and siphoviral morphology. ViPTree analysis demonstrated that the identified sequences were novel when compared to known double stranded DNA bacteriophage genomes. Conclusions In this study, we have started to address the knowledge gap on treponeme bacteriophages by characterising 38 prophage sequences in 24 treponeme genomes. Using bioinformatic approaches, we have been able to identify and compare the prophage-like elements with respect to other bacteriophages, their gene content, and their potential to be a functional and inducible bacteriophage, which in turn can help focus our attention on specific prophages to investigate further.

Published
2024
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