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5,465 results on '"Tim, R."'

1. 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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9. 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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12. 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

13. 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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14. 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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15. 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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16. 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

17. 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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19. 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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25. 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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29. 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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30. 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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33. 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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34. 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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35. 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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36. 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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37. 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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38. 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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39. 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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41. Efficacy and safety of three antiretroviral therapy regimens started in pregnancy up to 50 weeks post partum: a multicentre, open-label, randomised, controlled, phase 3 trial

Author

Chinula, Lameck, Ziemba, Lauren, Brummel, Sean, McCarthy, Katie, Coletti, Anne, Krotje, Chelsea, Johnston, Benjamin, Knowles, Kevin, Moyo, Sikhulile, Stranix-Chibanda, Lynda, Hoffman, Risa, Sax, Paul E, Stringer, Jeffrey, Chakhtoura, Nahida, Jean-Philippe, Patrick, Korutaro, Violet, Cassim, Haseena, Fairlie, Lee, Masheto, Gaerolwe, Boyce, Ceejay, Frenkel, Lisa M, Amico, K Rivet, Purdue, Lynette, Shapiro, Roger, Mmbaga, Blandina Theophil, Patel, Faeezah, van Wyk, Jean, Rooney, James F, Currier, Judith S, Lockman, Shahin, Best, Brookie M, Blanchette, Cheryl D, Browning, Renee, Jaliaah, Nagawa, Mirochnick, Mark, Murtaugh, William A, Patras, Emmanuel, Whalen, Frances, Momper, Jeremiah D, Ponatshego, Ponego L, Tirelo, Lesedi, Seme, Boitshepo J, Modise, Georginah O, Raesi, Mpho S, Budu, Marian E, Ramogodiri, Moakanyi, Oliveira, Ricardo H, Hofe, Cristina B, de Abreu, Thalita Fernandes, Pestanha, Lorena M, João, Esaú, Sidi, Leon C, Fuller, Trevon, Cruz, Maria LS, Pinto, Jorge, Ferreira, Flãvia, Correa, Mãrio, Romeiro, Juliana, Pilotto, Jose H, Fernandes, Luis EBC, Moreira, Luiz F, Gomes, Ivete M, Naik, Shilpa, Nevrekar, Neetal, Mave, Vidya, Kinikar, Aarti, Horne, Elizea, Soma-Kasiram, Hamisha, Violari, Avy, Mathiba, Sisinyana R, Nyati, Mandisa, Theron, Gerhard, de Jager, Jeanne, Rossouw, Magdel, Rossouw, Lindie, Hanley, Sherika, Desmond, Alicia C, Gazu, Rosemary, Govender, Vani, Chalermchockcharoenkit, Amphan, Thamkhantho, Manopchai, Werarak, Peerawong, Rungmaitree, Supattra, Achalapong, Jullapong, Sitiritkawin, Lukkana, Cressey, Tim R, Sukrakanchana, Pra-ornsuda, Aurpibul, Linda, Tongprasert, Fuanglada, Khamrong, Chintana, Kiattivej, Sopida, Wabwire, Deo, Kabugo, Enid, Maena, Joel, Nakayiwa, Frances, Ndyanabangi, Victoria, Nagaddya, Beatrice, Sekabira, Rogers, Ashaba, Justus, and Mitchell, Charles D

Subjects
Reproductive Medicine, Biomedical and Clinical Sciences, Mental Health, Infectious Diseases, Pediatric, HIV/AIDS, Clinical Research, Clinical Trials and Supportive Activities, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Reproductive health and childbirth, Infection, Good Health and Well Being, Pregnancy, Child, Female, Humans, Male, HIV Infections, Anti-HIV Agents, Tenofovir, Benzoxazines, Emtricitabine, Adenine, RNA, Viral Load, IMPAACT 2010/VESTED Study Team and Investigators, Medical and Health Sciences, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundDrugs taken during pregnancy can affect maternal and child health outcomes, but few studies have compared the safety and virological efficacy of different antiretroviral therapy (ART) regimens. We report the primary safety outcomes from enrolment up to 50 weeks post partum and a secondary virological efficacy outcome at 50 weeks post partum of three commonly used ART regimens for HIV-1.MethodsIn this multicentre, open-label, randomised, controlled, phase 3 trial, we enrolled pregnant women aged 18 years or older with confirmed HIV-1 infection at 14-28 weeks of gestation. Women were enrolled at 22 clinical research sites in nine countries (Botswana, Brazil, India, South Africa, Tanzania, Thailand, Uganda, the USA, and Zimbabwe). Participants were randomly assigned (1:1:1) to one of three oral regimens: dolutegravir, emtricitabine, and tenofovir alafenamide; dolutegravir, emtricitabine, and tenofovir disoproxil fumarate; or efavirenz, emtricitabine, and tenofovir disoproxil fumarate. Up to 14 days of antepartum ART before enrolment was permitted. Women with known multiple gestation, fetal anomalies, acute significant illness, transaminases more than 2·5 times the upper limit of normal, or estimated creatinine clearance of less than 60 mL/min were excluded. Primary safety analyses were pairwise comparisons between ART regimens of the proportion of maternal and infant adverse events of grade 3 or higher up to 50 weeks post partum. Secondary efficacy analyses at 50 weeks post partum included a comparison of the proportion of women with plasma HIV-1 RNA of less than 200 copies per mL in the combined dolutegravir-containing groups versus the efavirenz-containing group. Analyses were done in the intention-to-treat population, which included all randomly assigned participants with available data. This trial was registered with ClinicalTrials.gov, NCT03048422.FindingsBetween Jan 19, 2018, and Feb 8, 2019, we randomly assigned 643 pregnant women to the dolutegravir, emtricitabine, and tenofovir alafenamide group (n=217), the dolutegravir, emtricitabine, and tenofovir disoproxil fumarate group (n=215), and the efavirenz, emtricitabine, and tenofovir disoproxil fumarate group (n=211). At enrolment, median gestational age was 21·9 weeks (IQR 18·3-25·3), median CD4 count was 466 cells per μL (308-624), and median HIV-1 RNA was 903 copies per mL (152-5183). 607 (94%) women and 566 (92%) of 617 liveborn infants completed the study. Up to the week 50 post-partum visit, the estimated probability of experiencing an adverse event of grade 3 or higher was 25% in the dolutegravir, emtricitabine, and tenofovir alafenamide group; 31% in the dolutegravir, emtricitabine, and tenofovir disoproxil fumarate group; and 28% in the efavirenz, emtricitabine, and tenofovir disoproxil fumarate group (no significant difference between groups). Among infants, the estimated probability of experiencing at least one adverse event of grade 3 or higher by postnatal week 50 was 28% overall, with small and non-statistically significant differences between groups. By postnatal week 50, 14 infants whose mothers were in the efavirenz-containing group (7%) died, compared with six in the combined dolutegravir groups (1%). 573 (89%) women had HIV-1 RNA data available at 50 weeks post partum: 366 (96%) in the dolutegravir-containing groups and 186 (96%) in the efavirenz-containing group had HIV-1 RNA less than 200 copies per mL, with no significant difference between groups.InterpretationSafety and efficacy data during pregnancy and up to 50 weeks post partum support the current recommendation of dolutegravir-based ART (particularly in combination with emtricitabine and tenofovir alafenamide) rather than efavirenz, emtricitabine, and tenofovir disoproxil fumarate, when started in pregnancy.FundingNational Institute of Allergy and Infectious Diseases, the Eunice Kennedy Shriver National Institute of Child Health and Human Development, and the National Institute of Mental Health.

Published
2023

43. Learning-Mode Choice, Student Engagement, and Achievement Growth during the COVID-19 Pandemic

Author

Darling-Aduana, Jennifer, Woodyard, Henry T., Sass, Tim R., and Barry, Sarah S.

Abstract

The COVID-19 pandemic resulted in an unanticipated, near-universal shift from in-person to virtual instruction in the spring of 2020. During the 2020-21 school year, schools began to reopen, and families were faced with decisions regarding the instructional mode for their children. We leverage administrative, survey, and virtual-learning data to examine the determinants of family learning-mode choice and associations between virtual education, student engagement, and academic achievement. Family preference for virtual (versus face-to-face) instruction was highly associated with subsequent school-level infection rates and appeared relatively uniform within schools. We find that students assigned to a higher proportion of instructional days in virtual mode experienced higher rates of attendance but negative achievement growth compared to students who were assigned a higher proportion of instructional days in face-to-face mode. Insights from this study can be used to better understand family preferences as well as to target and refine virtual learning in a post-COVID-19 society.

Published
2022

44. Using marine protected areas to assess the status and recovery of the spiny lobster Jasus edwardsii fishery in the Hauraki Gulf, Aotearoa New Zealand

Author

Hayley R. Nessia, Benn J. Hanns, Tim R. Haggitt, and Nick T. Shears

Subjects
marine protected areas, marine reserves, Jasus edwardsii, spiny lobster, fisheries, fisheries-independent data, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

The value of no-take marine protected areas (MPAs) in providing fisheries-independent information to evaluate the status of adjacent fish stocks is increasingly being recognised. However, to ensure robust assessments of fisheries using this approach, MPAs need to be representative of the wider fished area and sampling should include multiple MPA and fished locations spanning the area of interest. The spiny lobster Jasus edwardsii fishery in Aotearoa New Zealand’s Hauraki Gulf has been in decline since the late 1990s, but latest stock estimates suggest a dramatic recovery following catch reductions in 2018. We compared J. edwardsii populations on shallow reefs (

Published
2024
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45. Novel Approaches to Postnatal Prophylaxis to Eliminate Vertical Transmission of HIV

Author

Ruel, Theodore, Penazzato, Martina, Zech, Jennifer M, Archary, Moherndran, Cressey, Tim R, Goga, Ameena, Harwell, Joseph, Landovitz, Raphael J, Lain, Maria Grazia, Lallemant, Marc, Namusoke-Magongo, Eleanor, Mukui, Irene, Permar, Sallie R, Prendergast, Andrew J, Shapiro, Roger, and Abrams, Elaine J

Subjects
Health Services and Systems, Public Health, Health Sciences, Sexually Transmitted Infections, Clinical Research, Pediatric, Pediatric AIDS, Clinical Trials and Supportive Activities, Prevention, HIV/AIDS, Infectious Diseases, 5.1 Pharmaceuticals, 6.1 Pharmaceuticals, Infection, Good Health and Well Being, Humans, Infant, Female, HIV Infections, Anti-HIV Agents, Infectious Disease Transmission, Vertical, Breast Feeding, Health services and systems, Public health
Abstract

Despite progress in providing antiretroviral therapy to pregnant women living with HIV, a substantial number of vertical transmissions continue to occur. Novel approaches leveraging modern potent, safe, and well-tolerated antiretroviral drugs are urgently needed.

Published
2023

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

Author

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

Subjects
Science
Abstract

Abstract Gram-negative bacteria (GNB) are a major cause of neonatal sepsis in low- and middle-income countries (LMICs). Although the World Health Organization (WHO) reports that over 80% of these sepsis deaths could be prevented through improved treatment, the efficacy of the currently recommended first- and second-line treatment regimens for this condition is increasingly affected by high rates of drug resistance. Here we assess three well known antibiotics, fosfomycin, flomoxef and amikacin, in combination as potential antibiotic treatment regimens by investigating the drug resistance and genetic profiles of commonly isolated GNB causing neonatal sepsis in LMICs. The five most prevalent bacterial isolates in the NeoOBS study (NCT03721302) are Klebsiella pneumoniae, Acinetobacter baumannii, E. coli, Serratia marcescens and Enterobacter cloacae complex. Among these isolates, high levels of ESBL and carbapenemase encoding genes are detected along with resistance to ampicillin, gentamicin and cefotaxime, the current WHO recommended empiric regimens. The three new combinations show excellent in vitro activity against ESBL-producing K. pneumoniae and E. coli isolates. Our data should further inform and support the clinical evaluation of these three antibiotic combinations for the treatment of neonatal sepsis in areas with high rates of multidrug-resistant Gram-negative bacteria.

Published
2024
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47. Assessment of Grapefruit Expressing Anti-NodT Antibody for Huanglongbing Resistance

Author

Chad Vosburg, Judith P. Sinn, Vladimir Orbovic, Rhuanito Soranz Ferrarezi, J. Martin Zapien Macias, Earl L. Taylor, Mark Hilf, Greg McCollum, Tim R. Gottwald, Ed Stover, and Timothy W. McNellis

Subjects
citrus greening, HLB, single-chain antibody, transformation, Plant culture, SB1-1110, Botany, QK1-989
Abstract

Growers rely on broad-spectrum agrochemicals to manage one of the most economically important fruit tree diseases, huanglongbing (HLB, citrus greening disease), presumptively caused by the gram-negative bacterium ‘Candidatus Liberibacter asiaticus’ (CLas). Although genetic resistance would be an attractive alternative to chemical management, this option is not yet available for HLB. Here, we tested whether a single chain variable fragment (scFv) antibody targeting the predicted CLas outer membrane transporter NodT can inhibit CLas growth or HLB disease development when expressed in ‘Duncan’ grapefruit (Citrus × paradisi). CLas NodT is similar to TolC and could be involved in Type I secretion and virulence. The scFv antibody was expressed in grapefruit trees as a C-terminal translational fusion to the Flowering Locus T protein of Poncirus trifoliata (FT-scFv) to promote expression in the phloem. Wild-type and FT-scFv-expressing transgenic lines were challenged with CLas using three inoculation approaches: psyllid-mediated inoculation, vegetative graft inoculation, and natural exposure in grove-like conditions. With the first two approaches, HLB symptom expression and CLas bacterial titers in FT-scFv grapefruit lines were not significantly different from wild-type controls. In the grove trial, one FT-scFv line exhibited a slight, but significant, reduction in canopy chlorosis compared to wild-type controls. Wild-type and FT-scFv lines were similar in all other metrics. We conclude that the expression of anti-NodT FT-scFv antibody in grapefruit did not decrease HLB susceptibility. Although our approach was unsuccessful, we hope that documenting our results will be useful for those seeking to develop HLB-resistant citrus germplasm in the future. [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Published
2024
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48. A universal molecular control for DNA, mRNA and protein expression

Author

Helen M. Gunter, Scott E. Youlten, Andre L. M. Reis, Tim McCubbin, Bindu Swapna Madala, Ted Wong, Igor Stevanovski, Arcadi Cipponi, Ira W. Deveson, Nadia S. Santini, Sarah Kummerfeld, Peter I. Croucher, Esteban Marcellin, and Tim R. Mercer

Subjects
Science
Abstract

Abstract The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.

Published
2024
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49. Structural changes in Florida citrus production, 1980-2021 and associated consequences of weather events and disease.

Author

Taylor, Earl L, Gottwald, Tim R, and Adkins, Scott

Subjects
Florida citrus production, freeze events, hurricane, Asiatic citrus canker (ACC), Huanglongbing (HLB), structural change
Abstract

Florida citrus production from 1980-2021 was examined and modeled to determine the impacts associated with weather events and disease introductions.  Specifically, the study examined the effects of North Atlantic hurricanes, freezes events and two disease introductions -- Asiatic citrus canker (ACC), and Huanglongbing (HLB) -- on productions levels and on the structure of the Florida citrus industry.  The models estimated quantified the effects on production associated with the weather events and disease introductions.  Using the deterministic model generated, forecasts were generated to identify future implications of HLB on Florida citrus production.  Theses generated forecasts were compared to actual production levels and the USDA Crop forecast to test and validate the model.  Whereas testing indicated a significant structural change in the Florida citrus industry resulting from adverse weather events and disease introductions, published economic impact studies were examined and reviewed to gage the resulting reduction in total economic impact.

Published
2023

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