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4. Generative Artificial Intelligence Reproducibility and Consensus

Author

Kim, Edward, Isozaki, Isamu, Sirkin, Naomi, and Robson, Michael

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

We performed a billion locality sensitive hash comparisons between artificially generated data samples to answer the critical question - can we reproduce the results of generative AI models? Reproducibility is one of the pillars of scientific research for verifiability, benchmarking, trust, and transparency. Futhermore, we take this research to the next level by verifying the "correctness" of generative AI output in a non-deterministic, trustless, decentralized network. We generate millions of data samples from a variety of open source diffusion and large language models and describe the procedures and trade-offs between generating more verses less deterministic output. Additionally, we analyze the outputs to provide empirical evidence of different parameterizations of tolerance and error bounds for verification. For our results, we show that with a majority vote between three independent verifiers, we can detect image generated perceptual collisions in generated AI with over 99.89% probability and less than 0.0267% chance of intra-class collision. For large language models (LLMs), we are able to gain 100% consensus using greedy methods or n-way beam searches to generate consensus demonstrated on different LLMs. In the context of generative AI training, we pinpoint and minimize the major sources of stochasticity and present gossip and synchronization training techniques for verifiability. Thus, this work provides a practical, solid foundation for AI verification, reproducibility, and consensus for generative AI applications., Comment: 16 pages

Published
2023

5. Single-cell, whole-embryo phenotyping of mammalian developmental disorders

Author

Huang, Xingfan, Henck, Jana, Qiu, Chengxiang, Sreenivasan, Varun KA, Balachandran, Saranya, Amarie, Oana V, Hrabě de Angelis, Martin, Behncke, Rose Yinghan, Chan, Wing-Lee, Despang, Alexandra, Dickel, Diane E, Duran, Madeleine, Feuchtinger, Annette, Fuchs, Helmut, Gailus-Durner, Valerie, Haag, Natja, Hägerling, Rene, Hansmeier, Nils, Hennig, Friederike, Marshall, Cooper, Rajderkar, Sudha, Ringel, Alessa, Robson, Michael, Saunders, Lauren M, da Silva-Buttkus, Patricia, Spielmann, Nadine, Srivatsan, Sanjay R, Ulferts, Sascha, Wittler, Lars, Zhu, Yiwen, Kalscheuer, Vera M, Ibrahim, Daniel M, Kurth, Ingo, Kornak, Uwe, Visel, Axel, Pennacchio, Len A, Beier, David R, Trapnell, Cole, Cao, Junyue, Shendure, Jay, and Spielmann, Malte

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Human Genome, 1.1 Normal biological development and functioning, Generic health relevance, Animals, Mice, Cell Nucleus, Developmental Disabilities, Embryo, Mammalian, Gain of Function Mutation, Genotype, Loss of Function Mutation, Models, Genetic, Mutation, Phenotype, Single-Cell Gene Expression Analysis, Disease Models, Animal, General Science & Technology
Abstract

Mouse models are a critical tool for studying human diseases, particularly developmental disorders1. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse2. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing3 to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions4,5. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be 'decomposable' through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution.

Published
2023

6. Paclitaxel- or sirolimus-coated balloons used for ArterioVEnous fistulas-2 (PAVE-2): study protocol for a randomised controlled trial to determine the efficacy of paclitaxel- or sirolimus-coated balloons in arteriovenous fistulas used for haemodialysis

Author

Karunanithy, Narayan, Norton, Sam, Calder, Francis, Das, Neelanjan, Dooley, Niamh, Hakobyan, Lusine, Jones, Robert, Padayache, Soundrie, Spriggs, Chloe, Steiner, Kate, Suckling, Rebecca, and Robson, Michael G.

Published
2024
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10. Efficacy and Safety of Ravulizumab in IgA Nephropathy: A Phase 2 Randomized Double-Blind Placebo-Controlled Trial

Author

Lafayette, Richard, Tumlin, James, Fenoglio, Roberta, Kaufeld, Jessica, Pérez Valdivia, Miguel Angel, Wu, Mai-Szu, Susan Huang, Shih-Han, Alamartine, Eric, Kim, Sung Gyun, Yee, Min, Kateifides, Andreas, Rice, Kara, Garlo, Katherine, Barratt, Jonathan, Ranganathan, Dwarakanathan, Wolley, Martin, Tan, Sven-Jean, Chow, Kevin, Tin Law, Mandy Man, Nichols, Kathleen, See, Emily Jan, Steinberg, Adam Glenn, Tiong, Mark, Susan Huang, Shih-Han, Jain, Arsh, Laurin, Louis-Phillipe, Lafrance, Jean-Phillipe, Lamarche, Caroline, Philibert, David, Agharazii, Mohsen, Mac-Way, Fabrice, Alamartine, Eric, Maillard, Nicolas, Mariat, Christophe, Masson, Ingrid, Boffa, Jean-Jacques, Cez, Alexandre, Esteve, Emmanuel, Marchal, Armance, Chauveau, Dominique, Belliere, Julie, Monrozeis, Pauline Bernadet, Colliou, Eloise, Faguer, Stanislas, Huart, Antoine, Ribes, David, Garrouste, Cyril, Heng, Anne-Elisabeth, Mayet, Valentin, Philipponnet, Carole, Moulin, Bruno, Parvez, Laura Braun, Vargas, Gabriela Gautier, Perrin, Peggy, Ohlmann, Sophie, Olagne, Jerome, Haller, Herman, Schmidt-Ott, Kai, Bahlmann-Kroll, Elisabeth, Kaufeld, Jessica, Reinhardt, Martin, Gaeckler, Anja, Dolff, Sebastian, Wilde, Benjamin, Schreiber, Adrian, Koch, Nadine, Seelow, Evelyn, Alberici, Federico, Affatato, Stefania, Mainardi, Allesandro, Mescia, Federica, Scolari, Francesco, Tedesco, Martina, Venturini, Margherita, Cirami, Calogero Lino, Antognoli, Giulia, Caroti, Leonardo, Gualtiero, Gabriele, Moscato, Marcos, Trivioli, Giorgio, La Manna, Gaetano, Baraldi, Olga, Campus, Anita, Stefanini, Carlo, Vischini, Gisella, Roccatello, Dario, Fenoglio, Roberta, Lalloni, Stefania, Sciascia, Savino, Nowicki, Michal, Holub, Tomasz, Kieszek, Błażej, Makówka, Agnieszka, Masajtis, Anna, Piechota, Piotr, Tylski, Maciej, Han, Seung Hyeok, Lee, Sang-Won, Lim, Beon Jin, Pyo, Jung Yoon, Kim, Sung Gyun, An, Jung Nam, Chung, Byung Ha, Kim, Jwa-Kyung, Lee, Hyung Seok, Seo, Young Il, Song, Young Rim, Lee, Hajeong, Park, Sehoon, Han, Seung Seok, Kim, Dong Ki, Kim, Yong Chul, Ryu, Hyunjin, Agraz, Irene, Bolufer, Monica, Hernandez, Josefina Cortés, Gabaldon, Maria Alejandra, Soler, Maria José, Arroyo, David, Carbayo, Javier, Diezhandino, Marian Goicoechea, Perez de Jose, Ana, Guzman, Ursula Verdalles, Moreno, Eduardo Verde, García, Olga Gracia, Albines Fiestas, Zoila Stany, Aladren Gonzalvo, Daniel Joaquin, Gonzalez, Andrea Bernal, Lou Arnal, Luis Miguel, Villarroya, Cristina Medrano, Lopez, Paula Mora, Moncasi, Eduardo Parra, Martin Conde, Maria Luisa, Gonzalez, Jorge, Jatem, Elias, Estor, Aida Moroba, Medrano, Alfons Segarra, Moreno, Antolina Rodriguez, Sanchez de la Nieta, Dolores, Garcia, Clara, Velo, Mercedes, Rocha Castilla, Jose Luis, Bermejo, Sheila, Mendoza, Manuel Lopez, Pérez Valdivia, Miguel Angel, Rojas, Remedios Toledo, Hidalgo, Pilar, Sanchez, Teresa Vazquez, Uriol Rivera, Miguel Giovanni, Fuentes, Mario Lado, Chiu, Yi-Wen, Chang, Jer-Ming, Chen, Hung-Chun, Hsiao, Mei-Ju, Hung, Chi-Chih, Hwang, Shang-Jih, Kuo, Mei Chuan, Kuo, Hung-Tien, Lim, Lee-Moay, Lee, Jia-Jung, Lai, Ping Chin, Chang, David Ray, Chang, Yun-Lun, Chen, I-Ru, Hsieh, Ming-Han, Huang, Chiu-Ching, Kuo, Huey-Liang, Wang, I-Kuan, Wu, Mai-Szu, Chen, Yu-Wei, Chiu, I-Jen, Hsu, Yung-Ho, Hung, Lie-Yee, Laio, Chia-Te, Lin, Gua-Hong, Lin, Yuh-Feng, Wu, Mei-Yi, Zheng, Cai-Mei, Lightstone, Elizabeth, Cairns, Tommy, Mcadoo, Stephen, Medjeral-Thomas, Nicholas, Pickering, Matthew, Robson, Michael, Sinha, Smeeta, Chukwu, Chukwuma, Storrar, Joshua, Ahmed, Sadiq, Cornea, Virgilius, Nadim, Amina, Sims, Tyler, Awad, Ahmed, Aldahan, Mohammed, Clark, Laurie, Lustig, Ryan, Niles, John, Jeyabalan, Anushya, Zonozi, Reza, Tumlin, James, and Paxton, William

Published
2024
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11. Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development

Author

Henck, Jana, Huang, Xingfan, Qiu, Chengxiang, Sreenivasan, Varun, Ulferts, Sascha, Behncke, Rose, Hansmeier, Nils, Haegerling, Rene, Despang, Alexandra, Ibrahim, Daniel, Ringel, Alessa, Robson, Michael, Wittler, Lars, Kalscheuer, Vera, Kornak, Uwe, Haag, Natja, Kurth, Ingo, Chan, Wing-Lee, Beier, David, Saunders, Lauren, Trapnell, Cole, Dickel, Diane, Visel, Axel, Pennacchio, Len, Cao, Junyue, Shendure, Jay, and Spielmann, Malte

Subjects
Genetics, Clinical Sciences, Genetics & Heredity, Clinical sciences
Published
2023

14. An Open-Publishing Response to the COVID-19 Infodemic

Author

Rando, Halie M., Boca, Simina M., McGowan, Lucy D'Agostino, Himmelstein, Daniel S., Robson, Michael P., Rubinetti, Vincent, Velazquez, Ryan, Consortium, COVID-19 Review, Greene, Casey S., and Gitter, Anthony

Subjects
Computer Science - Digital Libraries, Quantitative Biology - Quantitative Methods
Abstract

The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures present unique challenges to collaborative science. We applied a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators summarized and critiqued COVID-19 literature, creating a review manuscript. Manubot automatically compiled citation information for referenced preprints, journal publications, websites, and clinical trials. Continuous integration workflows retrieved up-to-date data from online sources nightly, regenerating some of the manuscript's figures and statistics. Manubot rendered the manuscript into PDF, HTML, LaTeX, and DOCX outputs, immediately updating the version available online upon the integration of new content. Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,500 sources and developed seven literature reviews. While many efforts from the computational community have focused on mining COVID-19 literature, our project illustrates the power of open publishing to organize both technical and non-technical scientists to aggregate and disseminate information in response to an evolving crisis., Comment: 10 pages, 4 figures

Published
2021

21. The impact of treatment with avacopan on health-related quality of life in antineutrophil cytoplasmic antibody-associated vasculitis: a post-hoc analysis of data from the ADVOCATE trial

Author

Au Peh, Chen, Chakera, Aron, Cooper, Bruce, Kurtkoti, Jagadeesh, Langguth, Daman, Levidiotis, Vicki, Luxton, Grant, Mount, Peter, Mudge, David, Noble, Euan, Phoon, Richard, Ranganathan, Dwarakanathan, Ritchie, Angus, Ryan, Jessica, Suranyi, Michael, Rosenkranz, Alexander, Lhotta, Karl, Kronbichler, Andreas, Demoulin, Nathalie, Bovy, Christophe, Hellemans, Rachel, Hougardy, Jean-Michel, Sprangers, Ben, Wissing, Karl Martin, Pagnoux, Christian, Barbour, Sean, Brachemi, Soumeya, Cournoyer, Serge, Girard, Louis-Philippe, Laurin, Louis-Philippe, Liang, Patrick, Philibert, David, Walsh, Michael, Tesar, Vladimir, Becvar, Radim, Horak, Pavel, Rychlik, Ivan, Szpirt, Wladimir, Dieperink, Hans, Gregersen, Jon Waarst, Ivarsen, Per, Krarup, Elizabeth, Lyngsoe, Cecilie, Rigothier, Claire, Augusto, Jean-Francois, Belot, Alexandre, Chauveau, Dominique, Cornec, Divi, Jourde-Chiche, Noemie, Ficheux, Maxence, Karras, Alexandre, Klein, Alexandre, Maurier, Francois, Mesbah, Rafik, Moranne, Olivier, Neel, Antoine, Quemeneur, Thomas, Saadoun, David, Terrier, Benjamin, Zaoui, Philippe, Schaier, Matthias, Benck, Urs Tobias, Bergner, Raoul, Busch, Martin, Floege, Juergen, Grundmann, Franziska, Haller, Hermann, Haubitz, Marion, Hellmich, Bernhard, Henes, Joerg Christoph, Hohenstein, Bernd, Hugo, Christian, Iking-Konert, Christof, Arndt, Fabian, Kubacki, T, Kotter, Ina, Lamprecht, Peter, Lindner, Tom, Halbritter, Jan, Mehling, Heidrun, Schönermarck, Ulf, Venhoff, Nils, Vielhauer, Volker, Witzke, Oliver, Szombati, Istvan, Szucs, Gabriella, Garibotto, Giacomo, Alberici, Federico, Brunetta, Enrico, Dagna, Lorenzo, De Vita, Salvatore, Emmi, Giacomo, Gabrielli, Armando, Manenti, Lucio, Pieruzzi, Federico, Roccatello, Dario, Salvarani, Carlo, Harigai, Masayoshi, Dobashi, Hiroaki, Atsumi, Tatsuya, Fujimoto, Shoichi, Hagino, Noboru, Ihata, Atsushi, Kaname, Shinya, Kaneko, Yuko, Katagiri, Akira, Katayama, Masao, Kirino, Yohei, Kitagawa, Kiyoki, Komatsuda, Atsushi, Kono, Hajime, Kurasawa, Takahiko, Matsumura, Ryutaro, Mimura, Toshihide, Morinobu, Akio, Murakawa, Yohko, Naniwa, Taio, Nanki, Toshihiro, Ogawa, Noriyoshi, Oshima, Hisaji, Sada, Kenei, Sugiyama, Eiji, Takeuchi, Tohru, Taki, Hirofumi, Tamura, Naoto, Tsukamoto, Tatsuo, Yamagata, Kunihiro, Yamamura, Masahiro, van Daele, Paulus Leon Arthur, Rutgers, Abraham, Teng, Y.K. Onno, Walker, Robert, Chua, Ignatius, Collins, Michael, Rabindranath, Kannaiyan, de Zoysa, Janak, Svensson, My Hanna Sofia, Grevbo, Bard-Waldum, Kalstad, Synove, Little, Mark, Clarkson, Michael, Molloy, Eamonn, Agraz Pamplona, Irene, Anton, Jordi, Barrio Lucia, Vicente, Ciggaran, Secundino, Cinta Cid, Maria, Diaz Encarnacion, Montserrat, Fulladosa Oliveras, Xavier, Jose Soler, Maria, Marco Rusinol, Helena, Praga, Manuel, Quintana Porras, Luis, Segarra, Alfons, Bruchfeld, Annette, Segelmark, Marten, Soveri, Inga, Thomaidi, Eleni, Westman, Kerstin, Neumann, Thomas, Burnier, Michel, Daikeler, Thomas, Dudler, Jean, Hauser, Thomas, Seeger, Harald, Vogt, Bruno, Burton, James, Al Jayyousi, Reem, Amin, Tania, Andrews, Jacqueline, Baines, Laura Anne, Brogan, Paul, Dasgupta, Bhaskar, Doulton, Timothy William Ronald, Flossmann, Oliver, Griffin, Sian V., Harper, Janice Marian, Harper, Lorraine, Kidder, Dana, Klocke, Rainer, Lanyon, Peter Charles, Luqmani, Raashid, McLaren, John Stuart, Makanjuola, David Osagie, McCann, Liza, Nandagudi, Anupama C., Selvan, Shilpa, O'Riordan, Edmond, Patel, Mumtaz, Patel, Rajan Kantilal, Pusey, Charles Dickson, Rajakariar, Ravindra, Robson, Joanna C., Robson, Michael, Salama, Alan David, Smyth, Lucy, Sznajd, Jan, Taylor, Joanne, Sreih, Antonie G., Belilos, Elise, Bomback, Andrew S., Carlin, Jeffrey, Chang Chen Lin, Yih, Derebail, Vimal K., Dragoi, Serban, Dua, Anisha, Forbess, Lindsy, Geetha, Duvuru, Gipson, Patrick, Gohh, Reginald, Greenwood, Gregory Todd, Hugenberg, Steven T., Jimenez, Richard A.H., Kaskas, Marwan Omar, Kermani, Tanaz, Kivitz, Alan J., Koening, Curry, Langford, Carol A., Marder, Galina, Mohamed, Amr Ahmed El-Huesseini, Monach, Paul, Neyra, Nilda Roxana, Niemer, Gregory W., Niles, John, Obi, Reginald, Owens, Charles, Parks, Deborah L., Podoll, Amber S., Rovin, Brad, Sam, R, Shergy, William Julius, Silva, Arnold Lawrence, Specks, Ulrich, Spiera, Robert, Springer, Jason M., Striebich, Christopher Charles, Swarup, Areena, Thakar, Surabhi, Tiliakos, Athan N., Tsai, Yong, Waguespack, Dia R., Chester Wasko, Mary, Strand, Vibeke, Jayne, David R W, Horomanski, Audra, Yue, Huibin, Bekker, Pirow, and Merkel, Peter A

Published
2023
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25. SARS-CoV-2 Research in Dogs (Canis lupus familiaris) and Felines (Felis silvestris catus) Domiciled in an International Border Region (Paraguay and Brazil).

Author

Rey, Laisa Marina Rosa, Delai, Robson Michael, Batista, Aline Cristiane Cechinel Assing, Ferreira, Leonardo, Santos, Isabela Carvalho dos, Del Vecchio, Marco Aurélio Cunha, Andrade, Ana Cláudia Souza, Teles, Pedro, Pereira, Ulisses de Pádua, Gerber, Alexandra Lehmkuhl, Guimarães, Ana Paula de Campos, Almeida, Luiz Gonzaga Paula de, Lamarca, Alessandra Pavan, Vasconcelos, Ana Tereza Ribeiro de, and Gonçalves, Daniela Dib

Subjects
*CATS, *COVID-19, *SARS-CoV-2 Delta variant, *SCIENTIFIC literature, *COMMUNICABLE diseases
Abstract

Introduction: COVID-19 is an infectious disease caused by SARS-CoV-2 that has become a serious threat to public health owing to its rapid spread from aerosols from infected people. Despite being considered a strictly human disease, there are reports in the literature about animals with confirmed presence of the virus. Aim: Owing to the scarcity of scientific literature on the potential for infection of animals and their importance for One Health, the objective of this work was to research SARS-CoV-2 RNA in felines (Felis silvestris catus) and dogs (Canis lupus familiaris) domiciled. Materials and Methods: Oropharyngeal swabs were collected from domestic dogs and cats belonging to patients diagnosed with COVID-19 from August to October 2021 and residents of the northwest and west regions of Paraná, Brazil. Results: Of the 34 samples collected, 14 were from dogs and 20 from cats. Three of these samples tested positive in real-time PCR, and two of them were also positive in the immunochromatographic test. After testing positive in real-time PCR, the samples underwent genetic sequencing using the Illumina COVIDSeq test. Of the 34 samples collected, three (9%), all of them female and from the feline species, tested positive in real-time PCR, with two of these (67%) also testing positive in the immunochromatographic test. Regarding sequencing, it was possible to sequence the three samples aligned with the AY.101 lineage, corresponding to the Delta variant. Conclusion: The occurrence of SARS-CoV-2 infection in dogs and cats is seen as an unintended event with significant implications for public health, including its potential transmission to other animal species. Further research is required to enhance our understanding of how this disease spreads among these animals and its broader impact on One Health initiatives. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Missing History of a Modern Domesticate: Historical Demographics and Genetic Diversity in Farm-bred Red Fox Populations

Author

Rando, Halie, primary, Alexander, Emmarie P, additional, Preckler-Quisquater, Sophie, additional, Quinn, Cate B, additional, Stutchman, Jeremy T, additional, Johnson, Jennifer L, additional, Bastounes, Estelle R, additional, Horecka, Beata, additional, Black, Kristina L, additional, Robson, Michael P, additional, Shepeleva, Darya V, additional, Herbeck, Yury E, additional, Kharlamova, Anastasiya V, additional, Trut, Lyudmila N, additional, Pauli, Jonathan N, additional, Sacks, Benjamin N, additional, and Kukekova, Anna V, additional

Published
2024
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34. Entomo-virological surveillance followed by serological active survey of symptomatic individuals is helpful to identify hotspots of early arbovirus transmission

Author

André de Souza Leandro, Renata Defante Lopes, Caroline Amaral Martins, Robson Michael Delai, Daniel A. M. Villela, and Rafael Maciel-de-Freitas

Subjects
entomo-virological surveillance, dengue, chikungunya, early-warning system, Aedes aegpyti, vector-borne diseases, Public aspects of medicine, RA1-1270
Abstract

Arboviruses transmitted by Aedes aegypti in urban environments have spread rapidly worldwide, causing great impacts on public health. The development of reliable and timely alert signals is among the most important steps in designing accurate surveillance systems for vector-borne diseases. In July and September 2017, we conducted a pilot study to improve an existing integrated surveillance system by using entomo-virological surveillance to prioritize areas to conduct active searches for individuals with arbovirus infection symptoms. Foz do Iguaçu City has a permanent entomo-virological surveillance system with approximately 3,500 traps to capture Aedes sp. in the adult stage. The Aedes aegypti females are captured alive and human samples are submitted to RT-qPCR (real-time qPCR) screening for DENV, ZIKV, and CHIKV diagnosis. Of the 55 Ae. aegypti mosquitoes tested in July 2017, seven (12.7%) were considered positive for DENV-2 and three (5.4%) for CHIKV. In September, we tested a sample of 54 mosquitoes, and 15 (27.7%) were considered infected by DENV-2. We created 25 circumferences with 150-m radius each to perform an active survey to identify symptomatic householders. In July, we selected one circumference, and five (35.7%) patients were positive for DENV, whereas two (14.3%) for CHIKV. In September, we selected four circumferences, and, from the 21 individuals sampled, nine (42.8%) were positive for DENV-2. A statistical model with a binomial response was used to estimate the number of cases in areas without active surveys, i.e., 20 circumferences. We estimated an additional 83 symptomatic patients (95% CI: 45–145) to be found in active searches, with 38 (95% CI: 18–72) of them confirming arbovirus infection. Arbovirus detection and serotyping in mosquitoes, but also in symptomatic individuals during active surveys, can provide an alert signal of early arbovirus transmission.

Published
2022
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35. A multicenter randomized controlled trial indicates that paclitaxel-coated balloons provide no benefit for arteriovenous fistulas

Author

Karunanithy, Narayan, Robinson, Emily J., Ahmad, Farhan, Burton, James O., Calder, Francis, Coles, Simon, Das, Neelanjan, Dorling, Anthony, Forman, Colin, Jaffer, Ounali, Lawman, Sarah, Lakshminarayan, Raghuram, Lewlellyn, Rhys, Peacock, Janet L., Ramnarine, Raymond, Mesa, Irene Rebollo, Shaikh, Shoaib, Simpson, James, Steiner, Kate, Suckling, Rebecca, Szabo, Laszlo, Turner, Douglas, Wadoodi, Ashar, Wang, Yanzhong, Weir, Graeme, Wilkins, C. Jason, Gardner, Leanne M., and Robson, Michael G.

Published
2021
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39. WHO's Robson platform for data-sharing on caesarean section rates

Author

Opiyo, Newton, Torloni, Maria Regina, Robson, Michael, Ladfors, Lars, Gholbzouri, Karima, Kacerauskiene, Justina, Vila-Candel, Rafael, Kessler, Joerg, Lucovnik, Miha, and Betran, Ana Pilar

Subjects
Cesarean section -- Health aspects, Obstetrics -- Health aspects, Health
Abstract

Optimizing caesarean section use is a global health priority, given the maternal and perinatal morbidity and mortality associated with caesarean underuse and overuse. (1,2) Monitoring caesarean section rates is important [...]

Published
2022
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40. The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub

Author

Alessandra P. Lamarca, Ueric José Borges de Souza, Filipe Romero Rebello Moreira, Luiz G. P. de Almeida, Mariane Talon de Menezes, Adrieli Barboza de Souza, Alessandro Clayton de Souza Ferreira, Alexandra L. Gerber, Aline B. de Lima, Ana Paula de C. Guimarães, Andréa Cony Cavalcanti, Aryel B. Paz e Silva, Bruna Israel Lima, Cirley Lobato, Cristiane Gomes Da Silva, Cristiane P. T. B. Mendonça, Daniel Costa Queiroz, Danielle Alves Gomes Zauli, Diego Menezes, Fábio Sossai Possebon, Franciano Dias Pereira Cardoso, Frederico Scott Varella Malta, Isabela Braga-Paz, Joice do Prado Silva, Jorge Gomes Goulart Ferreira, Jucimária Dantas Galvão, Leandro Magalhães de Souza, Leonardo Ferreira, Lia Gonçalves Possuelo, Liliane Tavares de Faria Cavalcante, Luige B. Alvim, Luiz Fellype Alves de Souza, Luiza C. G. de Araújo E Santos, Rillery Calixto Dias, Rutilene Barbosa Souza, Thaís Regina y Castro, Andréia Rosane de Moura Valim, Fabrício Souza Campos, João Pessoa Araujo, Priscila de Arruda Trindade, Renato S. Aguiar, Robson Michael Delai, and Ana Tereza R de Vasconcelos

Subjects
COVID-19, phylodynamics, variant of concern, genome, viral evolution, dispersal, Microbiology, QR1-502
Abstract

Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation.

Published
2023
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41. Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator

Author

Allou, Lila, Balzano, Sara, Magg, Andreas, Quinodoz, Mathieu, Royer-Bertrand, Beryl, Schöpflin, Robert, Chan, Wing-Lee, Speck-Martins, Carlos E., Carvalho, Daniel Rocha, Farage, Luciano, Lourenço, Charles Marques, Albuquerque, Regina, Rajagopal, Srilakshmi, Nampoothiri, Sheela, Campos-Xavier, Belinda, Chiesa, Carole, Niel-Bütschi, Florence, Wittler, Lars, Timmermann, Bernd, Spielmann, Malte, Robson, Michael I., Ringel, Alessa, Heinrich, Verena, Cova, Giulia, Andrey, Guillaume, Prada-Medina, Cesar A., Pescini-Gobert, Rosanna, Unger, Sheila, Bonafé, Luisa, Grote, Phillip, Rivolta, Carlo, Mundlos, Stefan, and Superti-Furga, Andrea

Published
2021
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42. Incomplete transcriptional dosage compensation of chicken and platypus sex chromosomes is balanced by post-transcriptional compensation.

Author

Lister, Nicholas C., Milton, Ashley M., Patel, Hardip R., Waters, Shafagh A., Hanrahan, Benjamin J., McIntyre, Kim L., Livernois, Alexandra M., Horspool, William B., Lee Kian Wee, Ringel, Alessa R., Mundlos, Stefan, Robson, Michael I., Shearwin-Whyatt, Linda, Grützner, Frank, Graves, Jennifer A. Marshall, Ruiz-Herrera, Aurora, and Waters, Paul D.

Subjects
SEX chromosomes, CHICKENS, PLATYPUS, EPIGENETICS, MAMMALS
Abstract

Heteromorphic sex chromosomes (XY or ZW) present problems of gene dosage imbalance between sexes and with autosomes. A need for dosage compensation has long been thought to be critical in vertebrates. However, this was questioned by findings of unequal mRNA abundance measurements in monotreme mammals and birds. Here, we demonstrate unbalanced mRNA levels of X genes in platypus males and females and a correlation with differential loading of histone modifications. We also observed unbalanced transcripts of Z genes in chicken. Surprisingly, however, we found that protein abundance ratios were 1:1 between the sexes in both species, indicating a post-transcriptional layer of dosage compensation. We conclude that sex chromosome output is maintained in chicken and platypus (and perhaps many other non therian vertebrates) via a combination of transcriptional and post-transcriptional control, consistent with a critical importance of sex chromosome dosage compensation. [ABSTRACT FROM AUTHOR]

Published
2024
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47. Implementing the QUALI-DEC project in Argentina, Burkina Faso, Thailand and Viet Nam: a process delineation and theory-driven process evaluation protocol

Author

Cleeve, Amanda, primary, Annerstedt, Kristi Sidney, additional, Betrán, Ana Pilar, additional, Mölsted Alvesson, Helle, additional, Kaboré Wendyam, Charles, additional, Carroli, Guillermo, additional, Lumbiganon, Pisake, additional, Nhu Hung, Mac Quoc, additional, Zamboni, Karen, additional, Opiyo, Newton, additional, Bohren, Meghan A., additional, El Halabi, Soha, additional, Gialdini, Celina, additional, Vila Ortiz, Mercedes, additional, Escuriet, Ramón, additional, Robson, Michael, additional, Dumont, Alexandre, additional, and Hanson, Claudia, additional

Published
2023
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48. NETS coordinate genome organisation and gene expression changes in T-cells and during myogenesis

Author

Robson, Michael Ian, Schirmer, Eric, and Bickmore, Wendy

Subjects
572.8, nuclear envelope transmembrane proteins, NETs, genome organisation, gene expression, development, myogenesis, DamID, FISH
Abstract

Gene positioning changes with respect to the nuclear periphery correlate with their activation in a number of tissues during development. However, the determination of the function this serves or the mechanism through which this was achieved has been remarkably difficult to resolve. It may now be possible to address these questions due to the recent identification of a number of tissue-specific nuclear envelope transmembrane proteins (NETs) which are capable of promoting the repositioning of specific subsets of chromosomes and concomitantly inducing changes to gene expression (Zuleger et al,. 2013). In this thesis I describe the role of NETs in the positioning of genes to the nuclear envelope (NE) during muscle differentiation and the role this activity plays in the optimisation of myogenic gene expression in as myoblasts (MTs) differentiate to myotubes (MTs). To do this I identified four NETs with the capacity to reposition a chromosome to the periphery that are present specifically in the NEs of skeletal muscle. Using a combination of genome-wide gene expression analysis and DamID I determined that depletion of these NETs disrupted myogenic gene expression and, more significantly, prevented the targeting to and silencing of normally repressed genes at the NE. I also investigated an analogous role for the blood-specific NET TAPBPL in the regulation of the critical T-cell regulator interleukin 2 (IL-2) at the NE in T-cells. Depletion of this NET caused release of the IL2 locus from the periphery and promoted its inappropriate and long-term activation. Interestingly, depletion of TAPBPL also prevented IL2 silencing following the end of T-cell activation, suggesting this genome organisation activity is critical for the maintenance of normal T-cell function. Collectively, the results discussed herein describe a new role for NETs in the regulation of gene expression through the manipulation of spatial genome organisation and may serve as an additional layer of higher order tissue-specific gene regulation in higher organisms.

Published
2015

49. ‘Candidatus Mycoplasma haemoalbiventris’ and tick-borne pathogens screening in white-eared opossums (Didelphis albiventris) from Curitiba and Foz do Iguaçu Cities, Paraná State, southern Brazil

Author

Renata Prestes Antonangelo de Oliveira, Flávia Carolina Meira Collere, Larissa Dantas Roeder Ferrari, Vanessa dos Santos Coradi, Nathália de Albuquerque Soares, André de Souza Leandro, Wagner Fabiano de Oliveira, Sandro Roberto Galvão, Rosinei Kafka, Robson Michael Delai, Rafaella Martini, André Saldanha, Leonardo Pereira dos Santos, Zalmir Silvino Cubas, Rogério Ribas Lange, Thállitha Samih Wischral Jayme Vieira, and Rafael Felipe da Costa Vieira

Subjects
Marsupials, hemotropic mycoplasmas, hemoplasmas, Animal culture, SF1-1100
Abstract

Abstract Hemoplasmas are epierythrocytic bacteria that infect mammals. ‘Candidatus Mycoplasma haemoalbiventris’ was detected in white-eared opossums (Didelphis albiventris) from southern and central-western Brazil. The present study aimed at: i) screening opossums for tick-borne (TBP) pathogens (Piroplasmida and Anaplasmataceae) and ii) detecting and characterizing hemoplasma species infecting opossums from Curitiba and Foz do Iguaçu cities in the Paraná State, southern Brazil. Thirty blood samples from white-eared opossums were evaluated by PCR assays. Animals were not infested by ectoparasites. The mammalian endogenous gapdh gene was consistently amplified in all samples. All opossums tested negative for Theileria/Babesia spp. and Ehrlichia/Anaplasma spp. by PCR based on 18S rRNA and 16S rRNA genes, respectively. A genus-specific PCR assay based on the 16S rRNA gene of hemoplasmas showed that three/13 (23.08%; CI 95%: 8.18-50.26%) opossums from Foz do Iguaçu were positive for hemotropic Mycoplasma sp. All opossums from Curitiba tested negative for hemoplasmas. Sequencing of both the 16S and 23S rRNA genes revealed that the animals were infected by ‘Ca. M. haemoalbiventris’. Although ‘Ca. M. haemoalbiventris’ is prevalent in opossums in Brazil, clinical signs associated with its infection and its putative vectors remain unknown.

Published
2021
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