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102. Biodiversity recovery of Neotropical secondary forests.

Author

Rozendaal, Danaë MA, Bongers, Frans, Aide, T Mitchell, Alvarez-Dávila, Esteban, Ascarrunz, Nataly, Balvanera, Patricia, Becknell, Justin M, Bentos, Tony V, Brancalion, Pedro HS, Cabral, George AL, Calvo-Rodriguez, Sofia, Chave, Jerome, César, Ricardo G, Chazdon, Robin L, Condit, Richard, Dallinga, Jorn S, de Almeida-Cortez, Jarcilene S, de Jong, Ben, de Oliveira, Alexandre, Denslow, Julie S, Dent, Daisy H, DeWalt, Saara J, Dupuy, Juan Manuel, Durán, Sandra M, Dutrieux, Loïc P, Espírito-Santo, Mario M, Fandino, María C, Fernandes, G Wilson, Finegan, Bryan, García, Hernando, Gonzalez, Noel, Moser, Vanessa Granda, Hall, Jefferson S, Hernández-Stefanoni, José Luis, Hubbell, Stephen, Jakovac, Catarina C, Hernández, Alma Johanna, Junqueira, André B, Kennard, Deborah, Larpin, Denis, Letcher, Susan G, Licona, Juan-Carlos, Lebrija-Trejos, Edwin, Marín-Spiotta, Erika, Martínez-Ramos, Miguel, Massoca, Paulo ES, Meave, Jorge A, Mesquita, Rita CG, Mora, Francisco, Müller, Sandra C, Muñoz, Rodrigo, de Oliveira Neto, Silvio Nolasco, Norden, Natalia, Nunes, Yule RF, Ochoa-Gaona, Susana, Ortiz-Malavassi, Edgar, Ostertag, Rebecca, Peña-Claros, Marielos, Pérez-García, Eduardo A, Piotto, Daniel, Powers, Jennifer S, Aguilar-Cano, José, Rodriguez-Buritica, Susana, Rodríguez-Velázquez, Jorge, Romero-Romero, Marco Antonio, Ruíz, Jorge, Sanchez-Azofeifa, Arturo, de Almeida, Arlete Silva, Silver, Whendee L, Schwartz, Naomi B, Thomas, William Wayt, Toledo, Marisol, Uriarte, Maria, de Sá Sampaio, Everardo Valadares, van Breugel, Michiel, van der Wal, Hans, Martins, Sebastião Venâncio, Veloso, Maria DM, Vester, Hans FM, Vicentini, Alberto, Vieira, Ima CG, Villa, Pedro, Williamson, G Bruce, Zanini, Kátia J, Zimmerman, Jess, and Poorter, Lourens

Subjects
Conservation of Natural Resources, Ecosystem, Biodiversity, Tropical Climate, Geography, Forests
Abstract

Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition. Secondary forests take a median time of five decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both old-growth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modified tropical landscapes.

Published
2019

104. Mesoderm-derived PDGFRA+ cells regulate the emergence of hematopoietic stem cells in the dorsal aorta

Author

Chandrakanthan, Vashe, Rorimpandey, Prunella, Zanini, Fabio, Chacon, Diego, Olivier, Jake, Joshi, Swapna, Kang, Young Chan, Knezevic, Kathy, Huang, Yizhou, Qiao, Qiao, Oliver, Rema A., Unnikrishnan, Ashwin, Carter, Daniel R., Lee, Brendan, Brownlee, Chris, Power, Carl, Brink, Robert, Mendez-Ferrer, Simon, Enikolopov, Grigori, Walsh, William, Göttgens, Berthold, Taoudi, Samir, Beck, Dominik, and Pimanda, John E.

Published
2022
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109. Roughness-dependent tribology effects on discontinuous shear thickening

Author

Hsu, Chiao-Peng, Ramakrishna, Shivaprakash N., Zanini, Michele, Spencer, Nicholas D., and Isa, Lucio

Subjects
Condensed Matter - Soft Condensed Matter
Abstract

Surface roughness affects many properties of colloids, from depletion [1] and capillary interactions [2], to their dispersibility [3] and use as emulsion stabilizers [4]. It also impacts particle-particle frictional contacts, which have recently emerged as being responsible for the discontinuous shear thickening (DST) of dense suspensions [5-17]. Tribological properties of these contacts have been rarely experimentally accessed [6, 15, 17, 18], especially for non-spherical particles. Here, we systematically tackle the effect of nanoscale surface roughness by producing a library of all-silica, raspberry-like colloids [19] and linking their rheology to their tribology. Rougher surfaces lead to a significant anticipation of DST onset, both in terms of shear rate and solid loading. Strikingly, they also eliminate continuous thickening. DST is here due to the interlocking of asperities, which we have identified as "stick-slip" frictional contacts by measuring the sliding of the same particles via lateral force microscopy (LFM). Direct measurements of particle-particle friction therefore highlight the value of an engineering-tribology approach to tuning the thickening of suspensions.

Published
2018
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110. Balanced Viscosity solutions to a rate-independent system for damage

Author

Knees, Dorothee, Rossi, Riccarda, and Zanini, Chiara

Subjects
Mathematics - Analysis of PDEs
Abstract

This article is the third one in a series of papers by the authors on vanishing-viscosity solutions to rate-independent damage systems. While in the first two papers [KRZ13, KRZ15] the assumptions on the spatial domain $\Omega$ were kept as general as possible (i.e. nonsmooth domain with mixed boundary conditions), we assume here that $\partial\Omega$ is smooth and that the type of boundary conditions does not change. This smoother setting allows us to derive enhanced regularity spatial properties both for the displacement and damage fields. Thus, we are in a position to work with a stronger solution notion at the level of the viscous approximating system. The vanishing-viscosity analysis then leads us to obtain the existence of a stronger solution concept for the rate-independent limit system. Furthermore, in comparison to [KRZ13, KRZ15], in our vanishing-viscosity analysis we do not switch to an artificial arc-length parameterization of the trajectories but we stay with the true physical time. The resulting concept of Balanced Viscosity solution to the rate-independent damage system thus encodes a more explicit characterization of the system behavior at time discontinuities of the solution.

Published
2017
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116. STAT3 induces breast cancer growth via ANGPTL4, MMP13 and STC1 secretion by cancer associated fibroblasts

Author

Avalle, Lidia, Raggi, Laura, Monteleone, Emanuele, Savino, Aurora, Viavattene, Daniele, Statello, Luisa, Camperi, Andrea, Stabile, Simona Aversano, Salemme, Vincenzo, De Marzo, Niccolò, Marino, Francesca, Guglielmi, Chiara, Lobascio, Andrea, Zanini, Cristina, Forni, Marco, Incarnato, Danny, Defilippi, Paola, Oliviero, Salvatore, and Poli, Valeria

Published
2022
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121. Influenza Vaccination Can Broadly Activate the HIV Reservoir During Antiretroviral Therapy

Author

Christensen-Quick, Aaron, Chaillon, Antoine, Yek, Christina, Zanini, Fabio, Jordan, Parris, Ignacio, Caroline, Caballero, Gemma, Gianella, Sara, and Smith, Davey

Subjects
Biomedical and Clinical Sciences, Epidemiology, Public Health, Clinical Sciences, Health Sciences, Adolescent, Adult, Anti-Retroviral Agents, Female, HIV, HIV Infections, Humans, Influenza Vaccines, Influenza, Human, Male, Middle Aged, Virus Activation, Young Adult, Public Health and Health Services, Virology, Clinical sciences, Public health
Published
2018

122. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

Author

Schaum, Nicholas, Karkanias, Jim, Neff, Norma F, May, Andrew P, Quake, Stephen R, Wyss-Coray, Tony, Darmanis, Spyros, Batson, Joshua, Botvinnik, Olga, Chen, Michelle B, Chen, Steven, Green, Foad, Jones, Robert C, Maynard, Ashley, Penland, Lolita, Pisco, Angela Oliveira, Sit, Rene V, Stanley, Geoffrey M, Webber, James T, Zanini, Fabio, Baghel, Ankit S, Bakerman, Isaac, Bansal, Ishita, Berdnik, Daniela, Bilen, Biter, Brownfield, Douglas, Cain, Corey, Cho, Min, Cirolia, Giana, Conley, Stephanie D, Demers, Aaron, Demir, Kubilay, de Morree, Antoine, Divita, Tessa, du Bois, Haley, Dulgeroff, Laughing Bear Torrez, Ebadi, Hamid, Espinoza, F Hernán, Fish, Matt, Gan, Qiang, George, Benson M, Gillich, Astrid, Genetiano, Geraldine, Gu, Xueying, Gulati, Gunsagar S, Hang, Yan, Hosseinzadeh, Shayan, Huang, Albin, Iram, Tal, Isobe, Taichi, Ives, Feather, Kao, Kevin S, Karnam, Guruswamy, Kershner, Aaron M, Kiss, Bernhard M, Kong, William, Kumar, Maya E, Lam, Jonathan Y, Lee, Davis P, Lee, Song E, Li, Guang, Li, Qingyun, Liu, Ling, Lo, Annie, Lu, Wan-Jin, Manjunath, Anoop, May, Kaia L, May, Oliver L, McKay, Marina, Metzger, Ross J, Mignardi, Marco, Min, Dullei, Nabhan, Ahmad N, Ng, Katharine M, Noh, Joseph, Patkar, Rasika, Peng, Weng Chuan, Puccinelli, Robert, Rulifson, Eric J, Sikandar, Shaheen S, Sinha, Rahul, Szade, Krzysztof, Tan, Weilun, Tato, Cristina, Tellez, Krissie, Travaglini, Kyle J, Tropini, Carolina, Waldburger, Lucas, and van Weele, Linda J

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Animals, Cell Biology, Endothelial Cells, Female, Flow Cytometry, Gene Expression Profiling, Male, Mice, Mice, Inbred C57BL, Microfluidics, Organ Specificity, Single-Cell Analysis, T-Lymphocytes, Transcription Factors, Transcriptome, Tabula Muris Consortium, Overall coordination, Logistical coordination, Organ collection and processing, Library preparation and sequencing, Computational data analysis, Cell type annotation, Writing group, Supplemental text writing group, Principal investigators, General Science & Technology
Abstract

Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3'-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.

Published
2018

126. Innate immunity changes in soccer players after whole-body cryotherapy

Author

Selleri, Valentina, Mattioli, Marco, Lo Tartaro, Domenico, Paolini, Annamaria, Zanini, Giada, De Gaetano, Anna, D’Alisera, Roberta, Roli, Laura, Melegari, Alessandra, Maietta, Pasqualino, Tripi, Ferdinando, Guerra, Emanuele, Chester, Johanna, Savino, Gustavo, Trenti, Tommaso, Cossarizza, Andrea, Mattioli, Anna Vittoria, Pinti, Marcello, and Nasi, Milena

Published
2022
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127. The HHIP-AS1 lncRNA promotes tumorigenicity through stabilization of dynein complex 1 in human SHH-driven tumors

Author

Bartl, Jasmin, Zanini, Marco, Bernardi, Flavia, Forget, Antoine, Blümel, Lena, Talbot, Julie, Picard, Daniel, Qin, Nan, Cancila, Gabriele, Gao, Qingsong, Nath, Soumav, Koumba, Idriss Mahoungou, Wolter, Marietta, Kuonen, François, Langini, Maike, Beez, Thomas, Munoz, Christopher, Pauck, David, Marquardt, Viktoria, Yu, Hua, Souphron, Judith, Korsch, Mascha, Mölders, Christina, Berger, Daniel, Göbbels, Sarah, Meyer, Frauke-Dorothee, Scheffler, Björn, Rotblat, Barak, Diederichs, Sven, Ramaswamy, Vijay, Suzuki, Hiromishi, Oro, Anthony, Stühler, Kai, Stefanski, Anja, Fischer, Ute, Leprivier, Gabriel, Willbold, Dieter, Steger, Gerhard, Buell, Alexander, Kool, Marcel, Lichter, Peter, Pfister, Stefan M., Northcott, Paul A., Taylor, Michael D., Borkhardt, Arndt, Reifenberger, Guido, Ayrault, Olivier, and Remke, Marc

Published
2022
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128. Correction: The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

Author

Butler-Laporte, Guillaume, Gonzalez-Kozlova, Edgar, Su, Chen-Yang, Zhou, Sirui, Nakanishi, Tomoko, Brunet-Ratnasingham, Elsa, Morrison, David, Laurent, Laetitia, Aflalo, Jonathan, Aflalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A., Schadt, Eric, Nie, Kai, Simons, Nicole W., Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Greenwood, Celia M. T., Paterson, Clare, Hinterberg, Michael, Langenberg, Claudia, Forgetta, Vincenzo, Mooser, Vincent, Marron, Thomas, Beckmann, Noam D., Kenigsberg, Ephraim, Charney, Alexander W., Kim-schulze, Seunghee, Merad, Miriam, Kaufmann, Daniel E., Gnjatic, Sacha, and Richards, J. Brent

Published
2022
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129. The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

Author

Butler-Laporte, Guillaume, Gonzalez-Kozlova, Edgar, Su, Chen-Yang, Zhou, Sirui, Nakanishi, Tomoko, Brunet-Ratnasingham, Elsa, Morrison, David, Laurent, Laetitia, Afilalo, Jonathan, Afilalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A., Schadt, Eric, Nie, Kai, Simons, Nicole W., Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Greenwood, Celia M. T., Paterson, Clare, Hinterberg, Michael, Langenberg, Claudia, Forgetta, Vincenzo, Mooser, Vincent, Marron, Thomas, Beckmann, Noam, Kenigsberg, Ephraim, Charney, Alexander W., Kim-schulze, Seunghee, Merad, Miriam, Kaufmann, Daniel E., Gnjatic, Sacha, and Richards, J Brent

Published
2022
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136. Establishment and stability of the latent HIV-1 DNA reservoir

Author

Brodin, Johanna, Zanini, Fabio, Thebo, Lina, Lanz, Christa, Bratt, Göran, Neher, Richard A., and Albert, Jan

Subjects
Quantitative Biology - Populations and Evolution
Abstract

HIV-1 infection currently cannot be cured because the virus persists as integrated proviral DNA in long-lived cells despite years of suppressive antiretroviral therapy (ART). To characterize establishment, turnover, and evolution of viral DNA reservoirs we deep-sequenced the p17gag region of the HIV-1 genome from samples obtained after 3-18 years of suppressive ART from 10 patients. For each of these patients, whole genome deep-sequencing data of HIV-1 RNA populations before onset of ART were available from 6-12 longitudinal plasma samples spanning 5-8 years of untreated infection. This enabled a detailed analysis of the dynamics and origin of proviral DNA during ART. A median of 14% (range 0-42%) of the p17gag DNA sequences were overtly defective due to G-to-A hypermutation. The remaining sequences were remarkably similar to previously observed RNA sequences and showed no evidence of evolution over many years of suppressive ART. Most sequences from the DNA reservoirs were very similar to viruses actively replicating in plasma (RNA sequences) shortly before start of ART. The results do not support persistent HIV-1 replication as a mechanism to maintain the HIV-1 reservoir during suppressive therapy. Rather, the data indicate that viral DNA variants are turning over as long as patients are untreated and that suppressive ART halts this turnover.

Published
2016

137. In-vivo mutation rates and fitness landscape of HIV-1

Author

Zanini, Fabio, Puller, Vadim, Brodin, Johanna, Albert, Jan, and Neher, Richard

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding of evolution. Using whole genome deep sequencing data from longitudinal samples during untreated HIV-1 infection, we estimated mutation rates and fitness costs in HIV-1 from the temporal dynamics of genetic variation. At approximately neutral sites, mutations accumulate with a rate of 1.2 x 10^-5 per site per day, in agreement with the rate measured in cell cultures. The rate from G to A is largest, followed by the other transitions C to T, T to C, and A to G, while transversions are more rare. At non-neutral sites, most mutations reduce virus replication; using a model of mutation selection balance, we estimated the fitness cost of mutations at every site in the HIV-1 genome. About half of all nonsynonymous mutations have large fitness costs (greater than 10\%), while most synonymous mutations have costs below 1\%. The cost of synonymous mutations is especially low in most of gag and pol, while much higher costs are observed in important RNA structures and regulatory regions. The intrapatient fitness cost estimates are consistent across multiple patients, suggesting that the deleterious part of the fitness landscape is universal and explains a large fraction of global HIV-1 group M diversity.

Published
2016

138. 2024 Standardization of Polysomnography Reports – A Consensus of the Brazilian Sleep Association

Author

Palombini, Luciana de Oliveira, Mello, Luciane Impellizieri Luna de, Santos-Silva, Rogério, Assis, Márcia, Cunha, Thays Crosara Abrahão, Drager, Luciano Ferreira, Zancanella, Edilson, Alves, Rosana Cardoso, Bacelar, Andrea, Bagnato, Mauricio da Cunha, Balsalobre, Rafael de Andrade, Bianchini, Esther Mandelbaum Gonçalves, Brasil, Evelyn Lucien, Coelho, Fernando Morgadinho Santos, Duarte, Bruno Bernardo, Eckeli, Alan Luiz, Fabbro, Cibele Dal, Franco, Aline Marques, Genta, Pedro Rodrigues, Giannasi, Lilian Chrystiane, Miguel, Mário André Leocadio, Moreira, Gustavo Antonio, Naufel, Maria Fernanda, Pereira, Luciana Moraes Studart, Poyares, Dalva, Pradella-Hallinan, Marcia, Soares, Carolina Ferraz de Paula, Soster, Leticia Azevedo, Zanini, Marcio Andrei, and Pires, Gabriel Natan

Published
2024
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148. Population genomics of intrapatient HIV-1 evolution

Author

Zanini, Fabio, Brodin, Johanna, Thebo, Lina, Lanz, Christa, Bratt, Göran, Albert, Jan, and Neher, Richard A.

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics
Abstract

Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are essential. We performed whole-genome deep sequencing of HIV-1 populations in 9 untreated patients, with 6-12 longitudinal samples per patient spanning 5-8 years of infection. We show that patterns of minor diversity are reproducible between patients and mirror global HIV-1 diversity, suggesting a universal landscape of fitness costs that control diversity. Reversions towards the ancestral HIV-1 sequence are observed throughout infection and account for almost one third of all sequence changes. Reversion rates depend strongly on conservation. Frequent recombination limits linkage disequilibrium to about 100bp in most of the genome, but strong hitch-hiking due to short range linkage limits diversity.

Published
2015
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149. A Diachronic Perspective on Formality in Students' Writing: Empirical Findings from the UK

Author

Constantinou, Filio, Chambers, Lucy, Zanini, Nadir, and Klir, Nicole

Abstract

One of the missions of language education internationally is to enable students to use language in a context-appropriate manner. Against this backdrop, students' ability to linguistically encode formality emerges as an important issue. Using extracts of writing produced by 16-year-old students in 2004 and 2014, this study sought to investigate whether the level of formality in students' writing changed over time. The 858 extracts of writing sampled were composed as part of a high-stakes examination in English Language. The linguistic analysis carried out focused on a number of features serving either as discriminators between spoken and written discourse (e.g. lexical diversity, lexical sophistication), or as markers of informal electronic communication (e.g. abbreviations, omitted stops, non-capitalised sentences). A statistical comparison of the prevalence of these features in the 2004 and 2014 corpora indicated that students' writing underwent informalisation. This trend was found to be stronger among lower attaining students.

Published
2020
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