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1. Human SARS-CoV-2 challenge uncovers local and systemic response dynamics

Author

Lindeboom, Rik G. H., Worlock, Kaylee B., Dratva, Lisa M., Yoshida, Masahiro, Scobie, David, Wagstaffe, Helen R., Richardson, Laura, Wilbrey-Clark, Anna, Barnes, Josephine L., Kretschmer, Lorenz, Polanski, Krzysztof, Allen-Hyttinen, Jessica, Mehta, Puja, Sumanaweera, Dinithi, Boccacino, Jacqueline M., Sungnak, Waradon, Elmentaite, Rasa, Huang, Ni, Mamanova, Lira, Kapuge, Rakesh, Bolt, Liam, Prigmore, Elena, Killingley, Ben, Kalinova, Mariya, Mayer, Maria, Boyers, Alison, Mann, Alex, Swadling, Leo, Woodall, Maximillian N. J., Ellis, Samuel, Smith, Claire M., Teixeira, Vitor H., Janes, Sam M., Chambers, Rachel C., Haniffa, Muzlifah, Catchpole, Andrew, Heyderman, Robert, Noursadeghi, Mahdad, Chain, Benny, Mayer, Andreas, Meyer, Kerstin B., Chiu, Christopher, Nikolić, Marko Z., and Teichmann, Sarah A.

Published
2024
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3. Early human lung immune cell development and its role in epithelial cell fate.

Author

Barnes, Josephine, Yoshida, Masahiro, He, Peng, Worlock, Kaylee, Lindeboom, Rik, Suo, Chenqu, Pett, J, Wilbrey-Clark, Anna, Dann, Emma, Mamanova, Lira, Richardson, Laura, Polanski, Krzysztof, Pennycuick, Adam, Allen-Hyttinen, Jessica, Herczeg, Iván, Arzili, Romina, Hynds, Robert, Teixeira, Vitor, Haniffa, Muzlifah, Lim, Kyungtae, Sun, Dawei, Rawlins, Emma, Oliver, Amanda, Lyons, Paul, Marioni, John, Ruhrberg, Christiana, Tuong, Zewen, Clatworthy, Menna, Reading, James, Janes, Sam, Teichmann, Sarah, Meyer, Kerstin, and Nikolić, Marko

Subjects
Humans, Immunity, Innate, Cell Differentiation, Lung, Killer Cells, Natural, Epithelial Cells
Abstract

Studies of human lung development have focused on epithelial and mesenchymal cell types and function, but much less is known about the developing lung immune cells, even though the airways are a major site of mucosal immunity after birth. An unanswered question is whether tissue-resident immune cells play a role in shaping the tissue as it develops in utero. Here, we profiled human embryonic and fetal lung immune cells using scRNA-seq, smFISH, and immunohistochemistry. At the embryonic stage, we observed an early wave of innate immune cells, including innate lymphoid cells, natural killer cells, myeloid cells, and lineage progenitors. By the canalicular stage, we detected naive T lymphocytes expressing high levels of cytotoxicity genes and the presence of mature B lymphocytes, including B-1 cells. Our analysis suggests that fetal lungs provide a niche for full B cell maturation. Given the presence and diversity of immune cells during development, we also investigated their possible effect on epithelial maturation. We found that IL-1β drives epithelial progenitor exit from self-renewal and differentiation to basal cells in vitro. In vivo, IL-1β-producing myeloid cells were found throughout the lung and adjacent to epithelial tips, suggesting that immune cells may direct human lung epithelial development.

Published
2023

4. An integrated cell atlas of the lung in health and disease

Author

Sikkema, Lisa, Ramírez-Suástegui, Ciro, Strobl, Daniel C, Gillett, Tessa E, Zappia, Luke, Madissoon, Elo, Markov, Nikolay S, Zaragosi, Laure-Emmanuelle, Ji, Yuge, Ansari, Meshal, Arguel, Marie-Jeanne, Apperloo, Leonie, Banchero, Martin, Bécavin, Christophe, Berg, Marijn, Chichelnitskiy, Evgeny, Chung, Mei-i, Collin, Antoine, Gay, Aurore CA, Gote-Schniering, Janine, Hooshiar Kashani, Baharak, Inecik, Kemal, Jain, Manu, Kapellos, Theodore S, Kole, Tessa M, Leroy, Sylvie, Mayr, Christoph H, Oliver, Amanda J, von Papen, Michael, Peter, Lance, Taylor, Chase J, Walzthoeni, Thomas, Xu, Chuan, Bui, Linh T, De Donno, Carlo, Dony, Leander, Faiz, Alen, Guo, Minzhe, Gutierrez, Austin J, Heumos, Lukas, Huang, Ni, Ibarra, Ignacio L, Jackson, Nathan D, Kadur Lakshminarasimha Murthy, Preetish, Lotfollahi, Mohammad, Tabib, Tracy, Talavera-López, Carlos, Travaglini, Kyle J, Wilbrey-Clark, Anna, Worlock, Kaylee B, Yoshida, Masahiro, van den Berge, Maarten, Bossé, Yohan, Desai, Tushar J, Eickelberg, Oliver, Kaminski, Naftali, Krasnow, Mark A, Lafyatis, Robert, Nikolic, Marko Z, Powell, Joseph E, Rajagopal, Jayaraj, Rojas, Mauricio, Rozenblatt-Rosen, Orit, Seibold, Max A, Sheppard, Dean, Shepherd, Douglas P, Sin, Don D, Timens, Wim, Tsankov, Alexander M, Whitsett, Jeffrey, Xu, Yan, Banovich, Nicholas E, Barbry, Pascal, Duong, Thu Elizabeth, Falk, Christine S, Meyer, Kerstin B, Kropski, Jonathan A, Pe’er, Dana, Schiller, Herbert B, Tata, Purushothama Rao, Schultze, Joachim L, Teichmann, Sara A, Misharin, Alexander V, Nawijn, Martijn C, Luecken, Malte D, and Theis, Fabian J

Subjects
Lung, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Respiratory, Good Health and Well Being, Humans, COVID-19, Pulmonary Fibrosis, Lung Neoplasms, Macrophages, Lung Biological Network Consortium, Medical and Health Sciences, Immunology
Abstract

Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.

Published
2023

5. Author Correction: Human SARS-CoV-2 challenge uncovers local and systemic response dynamics

Author

Lindeboom, Rik G. H., Worlock, Kaylee B., Dratva, Lisa M., Yoshida, Masahiro, Scobie, David, Wagstaffe, Helen R., Richardson, Laura, Wilbrey-Clark, Anna, Barnes, Josephine L., Kretschmer, Lorenz, Polanski, Krzysztof, Allen-Hyttinen, Jessica, Mehta, Puja, Sumanaweera, Dinithi, Boccacino, Jacqueline M., Sungnak, Waradon, Elmentaite, Rasa, Huang, Ni, Mamanova, Lira, Kapuge, Rakesh, Bolt, Liam, Prigmore, Elena, Killingley, Ben, Kalinova, Mariya, Mayer, Maria, Boyers, Alison, Mann, Alex, Swadling, Leo, Woodall, Maximillian N. J., Ellis, Samuel, Smith, Claire M., Teixeira, Vitor H., Janes, Sam M., Chambers, Rachel C., Haniffa, Muzlifah, Catchpole, Andrew, Heyderman, Robert, Noursadeghi, Mahdad, Chain, Benny, Mayer, Andreas, Meyer, Kerstin B., Chiu, Christopher, Nikolić, Marko Z., and Teichmann, Sarah A.

Published
2024
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6. A brave new world: Responding to a cyber incident

Author

Clark, Anna Mercado and Snyder, Mitch P.

Subjects
Cyberterrorism -- Management, Company business management, Business, Business, regional
Abstract

Byline: Special to the RBJ It is Monday morning and you arrive at work eager to tackle the day's challenges. You take a sip of your coffee, settle in at [...]

Published
2024

7. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche.

Author

Madissoon, Elo, Oliver, Amanda, Kleshchevnikov, Vitalii, Wilbrey-Clark, Anna, Polanski, Krzysztof, Richoz, Nathan, Ribeiro Orsi, Ana, Mamanova, Lira, Bolt, Liam, Elmentaite, Rasa, Pett, J, Huang, Ni, Xu, Chuan, He, Peng, Dabrowska, Monika, Pritchard, Sophie, Tuck, Liz, Prigmore, Elena, Perera, Shani, Knights, Andrew, Oszlanczi, Agnes, Hunter, Adam, Vieira, Sara, Patel, Minal, Lindeboom, Rik, Campos, Lia, Matsuo, Kazuhiko, Nakayama, Takashi, Yoshida, Masahiro, Worlock, Kaylee, Nikolić, Marko, Georgakopoulos, Nikitas, Mahbubani, Krishnaa, Saeb-Parsy, Kourosh, Bayraktar, Omer, Clatworthy, Menna, Stegle, Oliver, Kumasaka, Natsuhiko, Teichmann, Sarah, and Meyer, Kerstin

Subjects
Humans, Respiratory Mucosa, Lung, Epithelial Cells, B-Lymphocytes, Immunoglobulin A
Abstract

Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new gland-associated immune niche has implications for respiratory health.

Published
2023

8. Exploring the value of a global gene drive project registry

Author

Taitingfong, Riley I, Triplett, Cynthia, Vásquez, Váleri N, Rajagopalan, Ramya M, Raban, Robyn, Roberts, Aaron, Terradas, Gerard, Baumgartner, Bridget, Emerson, Claudia, Gould, Fred, Okumu, Fredros, Schairer, Cynthia E, Bossin, Hervé C, Buchman, Leah, Campbell, Karl J, Clark, Anna, Delborne, Jason, Esvelt, Kevin, Fisher, Joshua, Friedman, Robert M, Gronvall, Gigi, Gurfield, Nikos, Heitman, Elizabeth, Kofler, Natalie, Kuiken, Todd, Kuzma, Jennifer, Manrique-Saide, Pablo, Marshall, John M, Montague, Michael, Morrison, Amy C, Opesen, Chris C, Phelan, Ryan, Piaggio, Antoinette, Quemada, Hector, Rudenko, Larisa, Sawadogo, Natéwindé, Smith, Robert, Tuten, Holly, Ullah, Anika, Vorsino, Adam, Windbichler, Nikolai, Akbari, Omar S, Long, Kanya, Lavery, James V, Evans, Sam Weiss, Tountas, Karen, and Bloss, Cinnamon S

Subjects
Gene Drive Technology, Registries, Data Collection
Published
2023

12. Spatially resolved multiomics of human cardiac niches

Author

Kanemaru, Kazumasa, Cranley, James, Muraro, Daniele, Miranda, Antonio M. A., Ho, Siew Yen, Wilbrey-Clark, Anna, Patrick Pett, Jan, Polanski, Krzysztof, Richardson, Laura, Litvinukova, Monika, Kumasaka, Natsuhiko, Qin, Yue, Jablonska, Zuzanna, Semprich, Claudia I., Mach, Lukas, Dabrowska, Monika, Richoz, Nathan, Bolt, Liam, Mamanova, Lira, Kapuge, Rakeshlal, Barnett, Sam N., Perera, Shani, Talavera-López, Carlos, Mulas, Ilaria, Mahbubani, Krishnaa T., Tuck, Liz, Wang, Lu, Huang, Margaret M., Prete, Martin, Pritchard, Sophie, Dark, John, Saeb-Parsy, Kourosh, Patel, Minal, Clatworthy, Menna R., Hübner, Norbert, Chowdhury, Rasheda A., Noseda, Michela, and Teichmann, Sarah A.

Published
2023
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19. Local and systemic responses to SARS-CoV-2 infection in children and adults

Author

Yoshida, Masahiro, Worlock, Kaylee B., Huang, Ni, Lindeboom, Rik G. H., Butler, Colin R., Kumasaka, Natsuhiko, Dominguez Conde, Cecilia, Mamanova, Lira, Bolt, Liam, Richardson, Laura, Polanski, Krzysztof, Madissoon, Elo, Barnes, Josephine L., Allen-Hyttinen, Jessica, Kilich, Eliz, Jones, Brendan C., de Wilton, Angus, Wilbrey-Clark, Anna, Sungnak, Waradon, Pett, J. Patrick, Weller, Juliane, Prigmore, Elena, Yung, Henry, Mehta, Puja, Saleh, Aarash, Saigal, Anita, Chu, Vivian, Cohen, Jonathan M., Cane, Clare, Iordanidou, Aikaterini, Shibuya, Soichi, Reuschl, Ann-Kathrin, Herczeg, Iván T., Argento, A. Christine, Wunderink, Richard G., Smith, Sean B., Poor, Taylor A., Gao, Catherine A., Dematte, Jane E., Reynolds, Gary, Haniffa, Muzlifah, Bowyer, Georgina S., Coates, Matthew, Clatworthy, Menna R., Calero-Nieto, Fernando J., Göttgens, Berthold, O’Callaghan, Christopher, Sebire, Neil J., Jolly, Clare, De Coppi, Paolo, Smith, Claire M., Misharin, Alexander V., Janes, Sam M., Teichmann, Sarah A., Nikolić, Marko Z., and Meyer, Kerstin B.

Published
2022
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24. Dosimetric impact of contour editing on CT and MRI deep‐learning autosegmentation for brain OARs.

Author

Alzahrani, Nouf M., Henry, Ann M., Clark, Anna K., Al‐Qaisieh, Bashar M., Murray, Louise J., and Nix, Michael G.

Subjects
MEDICAL dosimetry, PEARSON correlation (Statistics), ACROMIOCLAVICULAR joint, MAGNETIC resonance imaging
Abstract

Purpose: To establish the clinical applicability of deep‐learning organ‐at‐risk autocontouring models (DL‐AC) for brain radiotherapy. The dosimetric impact of contour editing, prior to model training, on performance was evaluated for both CT and MRI‐based models. The correlation between geometric and dosimetric measures was also investigated to establish whether dosimetric assessment is required for clinical validation. Method: CT and MRI‐based deep learning autosegmentation models were trained using edited and unedited clinical contours. Autosegmentations were dosimetrically compared to gold standard contours for a test cohort. D1%, D5%, D50%, and maximum dose were used as clinically relevant dosimetric measures. The statistical significance of dosimetric differences between the gold standard and autocontours was established using paired Student's t‐tests. Clinically significant cases were identified via dosimetric headroom to the OAR tolerance. Pearson's Correlations were used to investigate the relationship between geometric measures and absolute percentage dose changes for each autosegmentation model. Results: Except for the right orbit, when delineated using MRI models, the dosimetric statistical analysis revealed no superior model in terms of the dosimetric accuracy between the CT DL‐AC models or between the MRI DL‐AC for any investigated brain OARs. The number of patients where the clinical significance threshold was exceeded was higher for the optic chiasm D1% than other OARs, for all autosegmentation models. A weak correlation was consistently observed between the outcomes of dosimetric and geometric evaluations. Conclusions: Editing contours before training the DL‐AC model had no significant impact on dosimetry. The geometric test metrics were inadequate to estimate the impact of contour inaccuracies on dose. Accordingly, dosimetric analysis is needed to evaluate the clinical applicability of DL‐AC models in the brain. [ABSTRACT FROM AUTHOR]

Published
2024
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25. Childhood-Onset Asthma is Characterized by Airway Epithelial Hillock-to-Squamous Differentiation in Early Life

Author

Kersten, Elin T.G., primary, Pett, J. Patrick, additional, Malmström, Kristiina, additional, Chun, Yoojin, additional, Jonker, Marnix R., additional, Wilbrey-Clark, Anna, additional, Worlock, Kaylee B., additional, van den Berge, Maarten, additional, Vermeulen, Roel C.H., additional, Vonk, Judith, additional, Sebire, Neil J., additional, Lohi, Jouko, additional, Timens, W., additional, Teichmann, Sarah, additional, Bunyavanich, Supinda, additional, Nikolić, Marko Z., additional, Nawijn, Martijn C., additional, Makela, Mika, additional, Meyer, Kerstin, additional, and Koppelman, Gerard, additional

Published
2024
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28. Single cell derived mRNA signals across human kidney tumors

Author

Young, Matthew D., Mitchell, Thomas J., Custers, Lars, Margaritis, Thanasis, Morales-Rodriguez, Francisco, Kwakwa, Kwasi, Khabirova, Eleonora, Kildisiute, Gerda, Oliver, Thomas R. W., de Krijger, Ronald R., van den Heuvel-Eibrink, Marry M., Comitani, Federico, Piapi, Alice, Bugallo-Blanco, Eva, Thevanesan, Christine, Burke, Christina, Prigmore, Elena, Ambridge, Kirsty, Roberts, Kenny, Braga, Felipe A. Vieira, Coorens, Tim H. H., Del Valle, Ignacio, Wilbrey-Clark, Anna, Mamanova, Lira, Stewart, Grant D., Gnanapragasam, Vincent J., Rampling, Dyanne, Sebire, Neil, Coleman, Nicholas, Hook, Liz, Warren, Anne, Haniffa, Muzlifah, Kool, Marcel, Pfister, Stefan M., Achermann, John C., He, Xiaoling, Barker, Roger A., Shlien, Adam, Bayraktar, Omer A., Teichmann, Sarah A., Holstege, Frank C., Meyer, Kerstin B., Drost, Jarno, Straathof, Karin, and Behjati, Sam

Published
2021
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29. Just a matter of time: reviewing temporality in Australian historiography.

Author

Clark, Anna

Subjects
*HISTORIOGRAPHY, *PHILOSOPHY of time, *HISTORICITY, *HISTORICAL research, AUSTRALIAN history
Abstract

Time is a foundational concept in historical studies. The past is located 'in time', of course, such that time guides and bounds 'what happened' to a 'when'. There have also been increasing theorisations that understand 'time' itself as temporally and culturally bound. As well as historicising, then, time itself must be historicised. Using Australian historiography as a case study, this paper explores the changing concept of 'time' over time. It sets out a provisional timeline of Australian history's understanding and deployment of historical time, contributing a much-needed historicisation of time to a growing field of historical theory. In charting a history of time in Australian historiography, it demonstrates the historicity of 'time'. This paper shows how the concept of time not only reflects, but in turn shapes and defines, historical practice and research. [ABSTRACT FROM AUTHOR]

Published
2024
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31. A framework for identifying fertility gene targets for mammalian pest control.

Author

Clark, Anna C., Edison, Rey, Esvelt, Kevin, Kamau, Sebastian, Dutoit, Ludovic, Champer, Jackson, Champer, Samuel E., Messer, Philipp W., Alexander, Alana, and Gemmell, Neil J.

Subjects
*PEST control, *GENE targeting, *FERTILITY, *GENE expression, *COMPARATIVE genomics, *CATTLE fertility, *KNOCKOUT mice
Abstract

Fertility‐targeted gene drives have been proposed as an ethical genetic approach for managing wild populations of vertebrate pests for public health and conservation benefit. This manuscript introduces a framework to identify and evaluate target gene suitability based on biological gene function, gene expression and results from mouse knockout models. This framework identified 16 genes essential for male fertility and 12 genes important for female fertility that may be feasible targets for mammalian gene drives and other non‐drive genetic pest control technology. Further, a comparative genomics analysis demonstrates the conservation of the identified genes across several globally significant invasive mammals. In addition to providing important considerations for identifying candidate genes, our framework and the genes identified in this study may have utility in developing additional pest control tools such as wildlife contraceptives. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Decoding the epithelial-T helper cell signalling axis in human asthmatic airways one cell at a time

Author

Oliver, Amanda, primary, Madissoon, Elo, additional, Sungnak, Waradon, additional, Berg, Marijn, additional, Kapuge, Rakeshlal, additional, Richardson, Laura, additional, Semprich, Claudi, additional, Wilbrey-Clark, Anna, additional, Gillet, Tessa, additional, Meyer, Kerstin, additional, Nawijn, Martijn, additional, and Teichmann, Sarah, additional

Published
2023
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35. Childhood-onset asthma is characterized by airway epithelial hillock-to-squamous differentiation in early life

Author

Kersten, Elin T.G., primary, Pett, Jan Patrick, additional, Malmstrom, Kristiina, additional, Chun, Yoojin, additional, Jonker, Marnix R., additional, Wilbrey-Clark, Anna L, additional, Worlock, Kaylee B., additional, van den Berge, Maarten, additional, Vermeulen, Roel C.H., additional, Vonk, Judith M, additional, Sebire, Neil, additional, Lohi, Jouko, additional, Timens, Wim, additional, Teichmann, Sarah, additional, Bunyavanich, Supinda, additional, Nikolic, Marko Z, additional, Nawijn, Martijn C., additional, Makela, Mika, additional, Meyer, Kerstin B, additional, and Koppelman, Gerard H., additional

Published
2023
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36. Data privacy and security concerns with rise of online betting, gaming

Author

Clark, Anna Mercado

Subjects
Online gambling -- Information management -- Safety and security measures -- Laws, regulations and rules, Data security -- Methods -- Laws, regulations and rules, Gambling industry -- Information management -- Safety and security measures -- Laws, regulations and rules, Personal information -- Access control -- Laws, regulations and rules, Government regulation, Sports/gambling game, Company systems management, Data security issue, Business, Business, regional
Abstract

Byline: Special to the RBJ As of January 8, 2022, New York State joined the ranks of more than a dozen states that have legalized online and mobile sports betting [...]

Published
2022

37. A framework for identifying fertility gene targets for mammalian pest control

Author

Clark, Anna C, Alexander, Alana, Edison, Rey, Esvelt, Kevin, Kamau, Sebastian, Dutoit, Ludovic, Champer, Jackson, Champer, Samuel E, Messer, Philipp W, and Gemmell, Neil J

Subjects
Article
Abstract

1. Fertility-targeted gene drives have been proposed as an ethical genetic approach for managing wild populations of vertebrate pests for public health and conservation benefit. 2. This manuscript introduces a framework to identify and evaluate target gene suitability based on biological gene function, gene expression, and results from mouse knockout models. 3. This framework identified 16 genes essential for male fertility and 12 genes important for female fertility that may be feasible targets for mammalian gene drives and other non-drive genetic pest control technology. Further, a comparative genomics analysis demonstrates the conservation of the identified genes across several globally significant invasive mammals. 4. In addition to providing important considerations for identifying candidate genes, our framework and the genes identified in this study may have utility in developing additional pest control tools such as wildlife contraceptives.

Published
2023

38. Human SARS-CoV-2 challenge resolves local and systemic response dynamics

Author

Lindeboom, Rik G H, primary, Worlock, Kaylee B, additional, Dratva, Lisa M, additional, Yoshida, Masahiro, additional, Scobie, David, additional, Wagstaffe, Helen R, additional, Richardson, Laura, additional, Wilbrey-Clark, Anna L, additional, Barnes, Josephine L, additional, Polanski, Krzysztof, additional, Allen-Hyttinen, Jessica, additional, Mehta, Puja, additional, Sumanaweera, Dinithi, additional, Boccacino, Jacqueline M, additional, Sungnak, Waradon, additional, Huang, Ni, additional, Mamanova, Lira, additional, Kapuge, Rakeshlal, additional, Bolt, Liam, additional, Prigmore, Elena, additional, Killingley, Ben, additional, Kalinova, Mariya, additional, Mayer, Maria, additional, Boyers, Alison, additional, Mann, Alex, additional, Teixeira, Vitor H, additional, Janes, Sam M, additional, Chambers, Rachel C, additional, Haniffa, Muzlifah, additional, Catchpole, Andrew, additional, Heyderman, Robert S, additional, Noursadeghi, Mahdad, additional, Chain, Benny, additional, Mayer, Andreas, additional, Meyer, Kerstin B, additional, Chiu, Christopher, additional, Nikolić, Marko Z, additional, and Teichmann, Sarah A, additional

Published
2023
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39. Spatially resolved multiomics of human cardiac niches

Author

Kanemaru, Kazumasa, primary, Cranley, James, additional, Muraro, Daniele, additional, Miranda, Antonio M.A., additional, Pett, Jan Patrick, additional, Litvinukova, Monika, additional, Kumasaka, Natsuhiko, additional, Ho, Siew Yen, additional, Polanski, Krzysztof, additional, Richardson, Laura, additional, Mach, Lukas, additional, Dabrowska, Monika, additional, Richoz, Nathan, additional, Barnett, Sam N., additional, Perera, Shani, additional, Wilbrey-Clark, Anna L, additional, Talavera-López, Carlos, additional, Mulas, Ilaria, additional, Mahbubani, Krishnaa T., additional, Bolt, Liam, additional, Mamanova, Lira, additional, Tuck, Liz, additional, Wang, Lu, additional, Huang, Margaret M., additional, Prete, Martin, additional, Pritchard, Sophie, additional, Dark, John, additional, Saeb-Parsy, Kourosh, additional, Patel, Minal, additional, Clatworthy, Menna R., additional, Chowdhury, Rasheda A., additional, Noseda, Michela, additional, and Teichmann, Sarah A., additional

Published
2023
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42. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

Author

Madissoon, Elo, primary, Oliver, Amanda J., additional, Kleshchevnikov, Vitalii, additional, Wilbrey-Clark, Anna, additional, Polanski, Krzysztof, additional, Richoz, Nathan, additional, Ribeiro Orsi, Ana, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Elmentaite, Rasa, additional, Pett, J. Patrick, additional, Huang, Ni, additional, Xu, Chuan, additional, He, Peng, additional, Dabrowska, Monika, additional, Pritchard, Sophie, additional, Tuck, Liz, additional, Prigmore, Elena, additional, Perera, Shani, additional, Knights, Andrew, additional, Oszlanczi, Agnes, additional, Hunter, Adam, additional, Vieira, Sara F., additional, Patel, Minal, additional, Lindeboom, Rik G. H., additional, Campos, Lia S., additional, Matsuo, Kazuhiko, additional, Nakayama, Takashi, additional, Yoshida, Masahiro, additional, Worlock, Kaylee B., additional, Nikolić, Marko Z., additional, Georgakopoulos, Nikitas, additional, Mahbubani, Krishnaa T., additional, Saeb-Parsy, Kourosh, additional, Bayraktar, Omer Ali, additional, Clatworthy, Menna R., additional, Stegle, Oliver, additional, Kumasaka, Natsuhiko, additional, Teichmann, Sarah A., additional, and Meyer, Kerstin B., additional

Published
2022
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43. Early human lung immune cell development and its role in epithelial cell fate

Author

Barnes, Josephine L., primary, He, Peng, additional, Yoshida, Masahiro, additional, Worlock, Kaylee B., additional, Lindeboom, Rik G.H., additional, Suo, Chenqu, additional, Pett, J. Patrick, additional, Wilbrey-Clark, Anna, additional, Dann, Emma, additional, Mamanova, Lira, additional, Richardson, Laura, additional, Oliver, Amanda J., additional, Pennycuick, Adam, additional, Allen-Hyttinen, Jessica, additional, Herczeg, Iván T., additional, Hynds, Robert E., additional, Teixeira, Vitor H., additional, Haniffa, Muzlifah, additional, Lim, Kyungtae, additional, Sun, Dawei, additional, Rawlins, Emma L., additional, Polanski, Krzysztof, additional, Lyons, Paul A., additional, Marioni, John C., additional, Tuong, Zewen Kelvin, additional, Clatworthy, Menna R., additional, Reading, James L., additional, Janes, Sam M., additional, Teichmann, Sarah A., additional, Meyer, Kerstin B., additional, and Nikolić, Marko Z., additional

Published
2022
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44. Exploring the value of a global gene drive project registry

Author

Taitingfong, Riley I., primary, Triplett, Cynthia, additional, Vásquez, Váleri N., additional, Rajagopalan, Ramya M., additional, Raban, Robyn, additional, Roberts, Aaron, additional, Terradas, Gerard, additional, Baumgartner, Bridget, additional, Emerson, Claudia, additional, Gould, Fred, additional, Okumu, Fredros, additional, Schairer, Cynthia E., additional, Bossin, Hervé C., additional, Buchman, Leah, additional, Campbell, Karl J., additional, Clark, Anna, additional, Delborne, Jason, additional, Esvelt, Kevin, additional, Fisher, Joshua, additional, Friedman, Robert M., additional, Gronvall, Gigi, additional, Gurfield, Nikos, additional, Heitman, Elizabeth, additional, Kofler, Natalie, additional, Kuiken, Todd, additional, Kuzma, Jennifer, additional, Manrique-Saide, Pablo, additional, Marshall, John M., additional, Montague, Michael, additional, Morrison, Amy C., additional, Opesen, Chris C., additional, Phelan, Ryan, additional, Piaggio, Antoinette, additional, Quemada, Hector, additional, Rudenko, Larisa, additional, Sawadogo, Natéwindé, additional, Smith, Robert, additional, Tuten, Holly, additional, Ullah, Anika, additional, Vorsino, Adam, additional, Windbichler, Nikolai, additional, Akbari, Omar S., additional, Long, Kanya, additional, Lavery, James V., additional, Evans, Sam Weiss, additional, Tountas, Karen, additional, and Bloss, Cinnamon S., additional

Published
2022
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45. A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates

Author

He, Peng, primary, Lim, Kyungtae, additional, Sun, Dawei, additional, Pett, Jan Patrick, additional, Jeng, Quitz, additional, Polanski, Krzysztof, additional, Dong, Ziqi, additional, Bolt, Liam, additional, Richardson, Laura, additional, Mamanova, Lira, additional, Dabrowska, Monika, additional, Wilbrey-Clark, Anna, additional, Madissoon, Elo, additional, Tuong, Zewen Kelvin, additional, Dann, Emma, additional, Suo, Chenqu, additional, Goh, Isaac, additional, Yoshida, Masahiro, additional, Nikolić, Marko Z., additional, Janes, Sam M., additional, He, Xiaoling, additional, Barker, Roger A., additional, Teichmann, Sarah A., additional, Marioni, John C., additional, Meyer, Kerstin B., additional, and Rawlins, Emma L., additional

Published
2022
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47. Cherish Farrah

Author

Clark, Anna

Subjects
Cherish Farrah (Novel) -- Morrow, Bethany C., Books -- Book reviews, Library and information science
Abstract

Morrow, Bethany C. Cherish Farrah. Penguin Random House Audio. Feb. 2022. 11:08 hrs. ISBN 9780593509005. $20. THRILLER Farrah Turner and Cherish Whitman are the only two Black girls in their [...]

Published
2022

48. Local and systemic responses to SARS-CoV-2 infection in children and adults

Author

Yoshida, Masahiro, Worlock, Kaylee B., Huang, Ni, Lindeboom, Rik G. H., Butler, Colin R., Kumasaka, Natsuhiko, Dominguez Conde, Cecilia, Mamanova, Lira, Bolt, Liam, Richardson, Laura, Polanski, Krzysztof, Madissoon, Elo, Barnes, Josephine L., Allen-Hyttinen, Jessica, Kilich, Eliz, Jones, Brendan C., de Wilton, Angus, Wilbrey-Clark, Anna, Sungnak, Waradon, Pett, J. Patrick, Weller, Juliane, Prigmore, Elena, Yung, Henry, Mehta, Puja, Saleh, Aarash, Saigal, Anita, Chu, Vivian, Cohen, Jonathan M., Cane, Clare, Iordanidou, Aikaterini, Shibuya, Soichi, Reuschl, Ann-Kathrin, Herczeg, Iván T., Argento, A. Christine, Wunderink, Richard G., Smith, Sean B., Poor, Taylor A., Gao, Catherine A., Dematte, Jane E., Budinger, G. R. Scott, Donnelly, Helen K., Markov, Nikolay S., Lu, Ziyan, Reynolds, Gary, Haniffa, Muzlifah, Bowyer, Georgina S., Coates, Matthew, Clatworthy, Menna R., Calero-Nieto, Fernando J., Göttgens, Berthold, O’Callaghan, Christopher, Sebire, Neil J., Jolly, Clare, De Coppi, Paolo, Smith, Claire M., Misharin, Alexander V., Janes, Sam M., Teichmann, Sarah A., Nikolić, Marko Z., and Meyer, Kerstin B.

Subjects
Multidisciplinary Sciences, Science & Technology, Multidisciplinary, Science & Technology - Other Topics, COVID-19, CELL
Abstract

It is not fully understood why COVID-19 is typically milder in children1–3. Here, to examine the differences between children and adults in their response to SARS-CoV-2 infection, we analysed paediatric and adult patients with COVID-19 as well as healthy control individuals (total n = 93) using single-cell multi-omic profiling of matched nasal, tracheal, bronchial and blood samples. In the airways of healthy paediatric individuals, we observed cells that were already in an interferon-activated state, which after SARS-CoV-2 infection was further induced especially in airway immune cells. We postulate that higher paediatric innate interferon responses restrict viral replication and disease progression. The systemic response in children was characterized by increases in naive lymphocytes and a depletion of natural killer cells, whereas, in adults, cytotoxic T cells and interferon-stimulated subpopulations were significantly increased. We provide evidence that dendritic cells initiate interferon signalling in early infection, and identify epithelial cell states associated with COVID-19 and age. Our matching nasal and blood data show a strong interferon response in the airways with the induction of systemic interferon-stimulated populations, which were substantially reduced in paediatric patients. Together, we provide several mechanisms that explain the milder clinical syndrome observed in children.

Published
2021

49. A Vexing To-Do List for Michigan's Gretchen Whitmer.

Author

Clark, Anna

Subjects
EARNED income tax credit, FLINT water crisis, Flint, Michigan, 2014-2019, FREEDOM of Information Act (U.S.), ECONOMIC development projects, LABOR union members, ABORTION laws, REFERENDUM, PUBLIC records
Abstract

Michigan Governor Gretchen Whitmer, who gained popularity for her commonsense approach to governance, is facing challenges in fulfilling key campaign promises. These promises include fixing the state's roads, bringing transparency to government, fighting for a $15 minimum wage, repealing the emergency manager law, and regulating companies that extract Michigan groundwater. While Whitmer has made progress on some priorities, such as codifying abortion rights and enacting policies to prevent gun violence, there are still unfulfilled promises. Advocates and allies are waiting for Whitmer to take action on these issues, especially since Democrats currently have control over the state government. However, it remains unclear if Whitmer will address these promises during the busy election season or after leaving the Democratic National Convention. [Extracted from the article]

Published
2024

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