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2. Virology—the path forward

Author

Rasmussen, Angela L, Gronvall, Gigi K, Lowen, Anice C, Goodrum, Felicia, Alwine, James, Andersen, Kristian G, Anthony, Simon J, Baines, Joel, Banerjee, Arinjay, Broadbent, Andrew J, Brooke, Christopher B, Campos, Samuel K, Caposio, Patrizia, Casadevall, Arturo, Chan, Gary C, Cliffe, Anna R, Collins-McMillen, Donna, Connell, Nancy, Damania, Blossom, Daugherty, Matthew D, Debbink, Kari, Dermody, Terence S, DiMaio, Daniel, Duprex, W Paul, Emerman, Michael, Galloway, Denise A, Garry, Robert F, Goldstein, Stephen A, Greninger, Alexander L, Hartman, Amy L, Hogue, Brenda G, Horner, Stacy M, Hotez, Peter J, Jung, Jae U, Kamil, Jeremy P, Karst, Stephanie M, Laimins, Lou, Lakdawala, Seema S, Landais, Igor, Letko, Michael, Lindenbach, Brett, Liu, Shan-Lu, Luftig, Micah, McFadden, Grant, Mehle, Andrew, Morrison, Juliet, Moscona, Anne, Mühlberger, Elke, Munger, Joshua, Münger, Karl, Murphy, Eain, Neufeldt, Christopher J, Nikolich, Janko Z, O'Connor, Christine M, Pekosz, Andrew, Permar, Sallie R, Pfeiffer, Julie K, Popescu, Saskia V, Purdy, John G, Racaniello, Vincent R, Rice, Charles M, Runstadler, Jonathan A, Sapp, Martin J, Scott, Rona S, Smith, Gregory A, Sorrell, Erin M, Speranza, Emily, Streblow, Daniel, Tibbetts, Scott A, Toth, Zsolt, Van Doorslaer, Koenraad, Weiss, Susan R, White, Elizabeth A, White, Timothy M, Wobus, Christiane E, Worobey, Michael, Yamaoka, Satoko, and Yurochko, Andrew

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Biomedical and Clinical Sciences, Emerging Infectious Diseases, Infectious Diseases, Prevention, Coronaviruses, Good Health and Well Being, Humans, Containment of Biohazards, COVID-19, United States, Viruses, Virology, Biomedical Research, virology, SARS-CoV-2, oversight, biosafety, emergence, Agricultural and Veterinary Sciences, Medical and Health Sciences, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

In the United States (US), biosafety and biosecurity oversight of research on viruses is being reappraised. Safety in virology research is paramount and oversight frameworks should be reviewed periodically. Changes should be made with care, however, to avoid impeding science that is essential for rapidly reducing and responding to pandemic threats as well as addressing more common challenges caused by infectious diseases. Decades of research uniquely positioned the US to be able to respond to the COVID-19 crisis with astounding speed, delivering life-saving vaccines within a year of identifying the virus. We should embolden and empower this strength, which is a vital part of protecting the health, economy, and security of US citizens. Herein, we offer our perspectives on priorities for revised rules governing virology research in the US.

Published
2024

3. The Analysis of Coade Stone Artefacts

Author

Edwards, Howell G. M., Brooke, Christopher J., van den Berg, Klaas Jan, Series Editor, Burnstock, Aviva, Series Editor, Janssens, Koen, Series Editor, van Langh, Robert, Series Editor, Mass, Jennifer, Series Editor, Nevin, Austin, Series Editor, Lavedrine, Bertrand, Series Editor, Ormsby, Bronwyn, Series Editor, Strlic, Matija, Series Editor, Edwards, Howell G. M., and Brooke, Christopher J.

Published
2024
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4. Historical Myths and Anomalies Associated with Coade Stone

Author

Edwards, Howell G. M., Brooke, Christopher J., van den Berg, Klaas Jan, Series Editor, Burnstock, Aviva, Series Editor, Janssens, Koen, Series Editor, van Langh, Robert, Series Editor, Mass, Jennifer, Series Editor, Nevin, Austin, Series Editor, Lavedrine, Bertrand, Series Editor, Ormsby, Bronwyn, Series Editor, Strlic, Matija, Series Editor, Edwards, Howell G. M., and Brooke, Christopher J.

Published
2024
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5. Introduction—Coade Artificial Stone and Its Marks

Author

Edwards, Howell G. M., Brooke, Christopher J., van den Berg, Klaas Jan, Series Editor, Burnstock, Aviva, Series Editor, Janssens, Koen, Series Editor, van Langh, Robert, Series Editor, Mass, Jennifer, Series Editor, Nevin, Austin, Series Editor, Lavedrine, Bertrand, Series Editor, Ormsby, Bronwyn, Series Editor, Strlic, Matija, Series Editor, Edwards, Howell G. M., and Brooke, Christopher J.

Published
2024
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6. The Mineralogy of Fired Ceramics

Author

Edwards, Howell G. M., Brooke, Christopher J., van den Berg, Klaas Jan, Series Editor, Burnstock, Aviva, Series Editor, Janssens, Koen, Series Editor, van Langh, Robert, Series Editor, Mass, Jennifer, Series Editor, Nevin, Austin, Series Editor, Lavedrine, Bertrand, Series Editor, Ormsby, Bronwyn, Series Editor, Strlic, Matija, Series Editor, Edwards, Howell G. M., and Brooke, Christopher J.

Published
2024
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7. Case Studies: Coade Stone

Author

Edwards, Howell G. M., Brooke, Christopher J., van den Berg, Klaas Jan, Series Editor, Burnstock, Aviva, Series Editor, Janssens, Koen, Series Editor, van Langh, Robert, Series Editor, Mass, Jennifer, Series Editor, Nevin, Austin, Series Editor, Lavedrine, Bertrand, Series Editor, Ormsby, Bronwyn, Series Editor, Strlic, Matija, Series Editor, Edwards, Howell G. M., and Brooke, Christopher J.

Published
2024
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8. Artificial Stone: The Precursors, Contemporaries and Later Variations of Coade Stone

Author

Edwards, Howell G. M., Brooke, Christopher J., van den Berg, Klaas Jan, Series Editor, Burnstock, Aviva, Series Editor, Janssens, Koen, Series Editor, van Langh, Robert, Series Editor, Mass, Jennifer, Series Editor, Nevin, Austin, Series Editor, Lavedrine, Bertrand, Series Editor, Ormsby, Bronwyn, Series Editor, Strlic, Matija, Series Editor, Edwards, Howell G. M., and Brooke, Christopher J.

Published
2024
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9. Conclusions

Author

Edwards, Howell G. M., Brooke, Christopher J., van den Berg, Klaas Jan, Series Editor, Burnstock, Aviva, Series Editor, Janssens, Koen, Series Editor, van Langh, Robert, Series Editor, Mass, Jennifer, Series Editor, Nevin, Austin, Series Editor, Lavedrine, Bertrand, Series Editor, Ormsby, Bronwyn, Series Editor, Strlic, Matija, Series Editor, Edwards, Howell G. M., and Brooke, Christopher J.

Published
2024
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10. Factors That Influenced the Success of Coade Stone

Author

Edwards, Howell G. M., Brooke, Christopher J., van den Berg, Klaas Jan, Series Editor, Burnstock, Aviva, Series Editor, Janssens, Koen, Series Editor, van Langh, Robert, Series Editor, Mass, Jennifer, Series Editor, Nevin, Austin, Series Editor, Lavedrine, Bertrand, Series Editor, Ormsby, Bronwyn, Series Editor, Strlic, Matija, Series Editor, Edwards, Howell G. M., and Brooke, Christopher J.

Published
2024
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11. Virology under the Microscope-a Call for Rational Discourse.

Author

Goodrum, Felicia, Lowen, Anice C, Lakdawala, Seema, Alwine, James, Casadevall, Arturo, Imperiale, Michael J, Atwood, Walter, Avgousti, Daphne, Baines, Joel, Banfield, Bruce, Banks, Lawrence, Bhaduri-McIntosh, Sumita, Bhattacharya, Deepta, Blanco-Melo, Daniel, Bloom, David, Boon, Adrianus, Boulant, Steeve, Brandt, Curtis, Broadbent, Andrew, Brooke, Christopher, Cameron, Craig, Campos, Samuel, Caposio, Patrizia, Chan, Gary, Cliffe, Anna, Coffin, John, Collins, Kathleen, Damania, Blossom, Daugherty, Matthew, Debbink, Kari, DeCaprio, James, Dermody, Terence, Dikeakos, Jimmy, DiMaio, Daniel, Dinglasan, Rhoel, Duprex, W Paul, Dutch, Rebecca, Elde, Nels, Emerman, Michael, Enquist, Lynn, Fane, Bentley, Fernandez-Sesma, Ana, Flenniken, Michelle, Frappier, Lori, Frieman, Matthew, Frueh, Klaus, Gack, Michaela, Gaglia, Marta, Gallagher, Tom, Galloway, Denise, García-Sastre, Adolfo, Geballe, Adam, Glaunsinger, Britt, Goff, Stephen, Greninger, Alexander, Hancock, Meaghan, Harris, Eva, Heaton, Nicholas, Heise, Mark, Heldwein, Ekaterina, Hogue, Brenda, Horner, Stacy, Hutchinson, Edward, Hyser, Joseph, Jackson, William, Kalejta, Robert, Kamil, Jeremy, Karst, Stephanie, Kirchhoff, Frank, Knipe, David, Kowalik, Timothy, Lagunoff, Michael, Laimins, Laimonis, Langlois, Ryan, Lauring, Adam, Lee, Benhur, Leib, David, Liu, Shan-Lu, Longnecker, Richard, Lopez, Carolina, Luftig, Micah, Lund, Jennifer, Manicassamy, Balaji, McFadden, Grant, McIntosh, Michael, Mehle, Andrew, Miller, W Allen, Mohr, Ian, Moody, Cary, Moorman, Nathaniel, Moscona, Anne, Mounce, Bryan, Munger, Joshua, Münger, Karl, Murphy, Eain, Naghavi, Mojgan, Nelson, Jay, Neufeldt, Christopher, Nikolich, Janko, and O'Connor, Christine

Subjects
COVID-19, Coronavirus, DURC, Gain of function, SARS-CoV-2, biosafety, influenza, pandemic, vaccines, zoonosis, Infectious Diseases, Prevention, Vaccine Related, Immunization, Infection, Good Health and Well Being, Biological Sciences, Medical and Health Sciences, Microbiology
Abstract

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.

Published
2023

14. Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness

Author

Ke, Ruian, Martinez, Pamela P., Smith, Rebecca L., Gibson, Laura L., Mirza, Agha, Conte, Madison, Gallagher, Nicholas, Luo, Chun Huai, Jarrett, Junko, Zhou, Ruifeng, Conte, Abigail, Liu, Tongyu, Farjo, Mireille, Walden, Kimberly K. O., Rendon, Gloria, Fields, Christopher J., Wang, Leyi, Fredrickson, Richard, Edmonson, Darci C., Baughman, Melinda E., Chiu, Karen K., Choi, Hannah, Scardina, Kevin R., Bradley, Shannon, Gloss, Stacy L., Reinhart, Crystal, Yedetore, Jagadeesh, Quicksall, Jessica, Owens, Alyssa N., Broach, John, Barton, Bruce, Lazar, Peter, Heetderks, William J., Robinson, Matthew L., Mostafa, Heba H., Manabe, Yukari C., Pekosz, Andrew, McManus, David D., and Brooke, Christopher B.

Published
2022
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17. Mitigation of SARS-CoV-2 transmission at a large public university

Author

Ranoa, Diana Rose E., Holland, Robin L., Alnaji, Fadi G., Green, Kelsie J., Wang, Leyi, Fredrickson, Richard L., Wang, Tong, Wong, George N., Uelmen, Johnny, Maslov, Sergei, Weiner, Zachary J., Tkachenko, Alexei V., Zhang, Hantao, Liu, Zhiru, Ibrahim, Ahmed, Patel, Sanjay J., Paul, John M., Vance, Nickolas P., Gulick, Joseph G., Satheesan, Sandeep Puthanveetil, Galvan, Isaac J., Miller, Andrew, Grohens, Joseph, Nelson, Todd J., Stevens, Mary P., Hennessy, P Mark, Parker, Jr, Robert C., Santos, Edward, Brackett, Charles, Steinman, Julie D., Fenner, Jr, Melvin R., Dohrer, Kirstin, DeLorenzo, Michael, Wilhelm-Barr, Laura, Brauer, Brian R., Best-Popescu, Catherine, Durack, Gary, Wetter, Nathan, Kranz, David M., Breitbarth, Jessica, Simpson, Charlie, Pryde, Julie A., Kaler, Robin N., Harris, Chris, Vance, Allison C., Silotto, Jodi L., Johnson, Mark, Valera, Enrique Andres, Anton, Patricia K., Mwilambwe, Lowa, Bryan, Stephen P., Stone, Deborah S., Young, Danita B., Ward, Wanda E., Lantz, John, Vozenilek, John A., Bashir, Rashid, Moore, Jeffrey S., Garg, Mayank, Cooper, Julian C., Snyder, Gillian, Lore, Michelle H., Yocum, Dustin L., Cohen, Neal J., Novakofski, Jan E., Loots, Melanie J., Ballard, Randy L., Band, Mark, Banks, Kayla M., Barnes, Joseph D., Bentea, Iuliana, Black, Jessica, Busch, Jeremy, Conte, Abigail, Conte, Madison, Curry, Michael, Eardley, Jennifer, Edwards, April, Eggett, Therese, Fleurimont, Judes, Foster, Delaney, Fouke, Bruce W., Gallagher, Nicholas, Gastala, Nicole, Genung, Scott A., Glueck, Declan, Gray, Brittani, Greta, Andrew, Healy, Robert M., Hetrick, Ashley, Holterman, Arianna A., Ismail, Nahed, Jasenof, Ian, Kelly, Patrick, Kielbasa, Aaron, Kiesel, Teresa, Kindle, Lorenzo M., Lipking, Rhonda L., Manabe, Yukari C., Mayes, Jade ́, McGuffin, Reubin, McHenry, Kenton G., Mirza, Agha, Moseley, Jada, Mostafa, Heba H., Mumford, Melody, Munoz, Kathleen, Murray, Arika D., Nolan, Moira, Parikh, Nil A., Pekosz, Andrew, Pflugmacher, Janna, Phillips, Janise M., Pitts, Collin, Potter, Mark C., Quisenberry, James, Rear, Janelle, Robinson, Matthew L., Rosillo, Edith, Rye, Leslie N., Sherwood, MaryEllen, Simon, Anna, Singson, Jamie M., Skadden, Carly, Skelton, Tina H., Smith, Charlie, Stech, Mary, Thomas, Ryan, Tomaszewski, Matthew A., Tyburski, Erika A., Vanwingerden, Scott, Vlach, Evette, Watkins, Ronald S., Watson, Karriem, White, Karen C., Killeen, Timothy L., Jones, Robert J., Cangellaris, Andreas C., Martinis, Susan A., Vaid, Awais, Brooke, Christopher B., Walsh, Joseph T., Elbanna, Ahmed, Sullivan, William C., Smith, Rebecca L., Goldenfeld, Nigel, Fan, Timothy M., Hergenrother, Paul J., and Burke, Martin D.

Published
2022
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18. Stratification of viral shedding patterns in saliva of COVID-19 patients

Author

Park, Hyeongki, primary, Yoshimura, Raiki, additional, Iwanami, Shoya, additional, Kim, Kwang Su, additional, Ejima, Keisuke, additional, Nakamura, Naotoshi, additional, Aihara, Kazuyuki, additional, Miyazaki, Yoshitsugu, additional, Umeyama, Takashi, additional, Miyazawa, Ken, additional, Morita, Takeshi, additional, Watashi, Koichi, additional, Brooke, Christopher B., additional, Ke, Ruian, additional, Iwami, Shingo, additional, and Miyazaki, Taiga, additional

Published
2024
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19. Influenza A viral burst size from thousands of infected single cells using droplet quantitative PCR (dqPCR).

Author

Zath, Geoffrey K., Thomas, Mallory M., Loveday, Emma K., Bikos, Dimitri A., Sanche, Steven, Ke, Ruian, Brooke, Christopher B., and Chang, Connie B.

Subjects
INFLUENZA, INFLUENZA A virus, H3N2 subtype, INFLUENZA viruses, INFLUENZA A virus, VIRAL transmission
Abstract

An important aspect of how viruses spread and infect is the viral burst size, or the number of new viruses produced by each infected cell. Surprisingly, this value remains poorly characterized for influenza A virus (IAV), commonly known as the flu. In this study, we screened tens of thousands of cells using a microfluidic method called droplet quantitative PCR (dqPCR). The high-throughput capability of dqPCR enabled the measurement of a large population of infected cells producing progeny virus. By measuring the fully assembled and successfully released viruses from these infected cells, we discover that the viral burst sizes for both the seasonal H3N2 and the 2009 pandemic H1N1 strains vary significantly, with H3N2 ranging from 101 to 104 viruses per cell, and H1N1 ranging from 101 to 103 viruses per cell. Some infected cells produce average numbers of new viruses, while others generate extensive number of viruses. In fact, we find that only 10% of the single-cell infections are responsible for creating a significant portion of all the viruses. This small fraction produced approximately 60% of new viruses for H3N2 and 40% for H1N1. On average, each infected cell of the H3N2 flu strain produced 709 new viruses, whereas for H1N1, each infected cell produced 358 viruses. This novel method reveals insights into the flu virus and can lead to improved strategies for managing and preventing the spread of viruses. Author summary: Viruses infect and exploit host cells to reproduce and spread. The viral burst size, or the number of viral particles released from an infected cell, plays a critical role in understanding infection dynamics and overall viral fitness. However, accurately determining burst size for many single cells using conventional laboratory methods can be challenging. Here, we introduce dqPCR, a droplet microfluidic method for the rapid measurement of influenza virus numbers produced by thousands of individual cells. Our findings revealed that only a small proportion of infected cells are responsible for producing a significant portion of the total viral population. By utilizing this method in future studies, we can gain a deeper understanding of the role of diversity in rapidly evolving viruses. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Feeding Ecology of Large Browsing and Grazing Herbivores

Author

Venter, Jan A., Vermeulen, Mika M., Brooke, Christopher F., Canadell, Josep G., Series Editor, Díaz, Sandra, Series Editor, Heldmaier, Gerhard, Series Editor, Jackson, Robert B., Series Editor, Levia, Delphis F., Series Editor, Schulze, Ernst-Detlef, Series Editor, Sommer, Ulrich, Series Editor, Wardle, David A., Series Editor, Gordon, Iain J., editor, and Prins, Herbert H. T., editor

Published
2019
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23. Correction for Rasmussen et al., “Virology—the path forward”

Author

Rasmussen, Angela L., primary, Gronvall, Gigi K., additional, Lowen, Anice C., additional, Goodrum, Felicia, additional, Alwine, James, additional, Andersen, Kristian G., additional, Anthony, Simon J., additional, Baines, Joel, additional, Banerjee, Arinjay, additional, Broadbent, Andrew J., additional, Brooke, Christopher B., additional, Campos, Samuel K., additional, Caposio, Patrizia, additional, Casadevall, Arturo, additional, Chan, Gary C., additional, Cliffe, Anna R., additional, Collins-McMillen, Donna, additional, Connell, Nancy, additional, Damania, Blossom, additional, Daugherty, Matthew D., additional, Debbink, Kari, additional, Dermody, Terence S., additional, DiMaio, Daniel, additional, Duprex, W. Paul, additional, Emerman, Michael, additional, Galloway, Denise A., additional, Garry, Robert F., additional, Goldstein, Stephen A., additional, Greninger, Alexander L., additional, Hartman, Amy L., additional, Hogue, Brenda G., additional, Horner, Stacy M., additional, Hotez, Peter J., additional, Jung, Jae U., additional, Kamil, Jeremy P., additional, Karst, Stephanie M., additional, Laimins, Lou, additional, Lakdawala, Seema S., additional, Landais, Igor, additional, Letko, Michael, additional, Lindenbach, Brett, additional, Liu, Shan-Lu, additional, Luftig, Micah, additional, McFadden, Grant, additional, Mehle, Andrew, additional, Morrison, Juliet, additional, Moscona, Anne, additional, Mühlberger, Elke, additional, Munger, Joshua, additional, Münger, Karl, additional, Murphy, Eain, additional, Neufeldt, Christopher J., additional, Nikolich, Janko Z., additional, O'Connor, Christine M., additional, Pekosz, Andrew, additional, Permar, Sallie R., additional, Pfeiffer, Julie K., additional, Popescu, Saskia V., additional, Purdy, John G., additional, Racaniello, Vincent R., additional, Rice, Charles M., additional, Runstadler, Jonathan A., additional, Sapp, Martin J., additional, Scott, Rona S., additional, Smith, Gregory A., additional, Sorrell, Erin M., additional, Speranza, Emily, additional, Streblow, Daniel, additional, Tibbetts, Scott A., additional, Toth, Zsolt, additional, Van Doorslaer, Koenraad, additional, Weiss, Susan R., additional, White, Elizabeth A., additional, White, Timothy M., additional, Wobus, Christiane E., additional, Worobey, Michael, additional, Yamaoka, Satoko, additional, and Yurochko, Andrew, additional

Published
2024
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26. Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection

Author

Farjo, Mireille, primary, Koelle, Katia, additional, Martin, Michael A., additional, Gibson, Laura L., additional, Walden, Kimberly K. O., additional, Rendon, Gloria, additional, Fields, Christopher J., additional, Alnaji, Fadi G., additional, Gallagher, Nicholas, additional, Luo, Chun Huai, additional, Mostafa, Heba H., additional, Manabe, Yukari C., additional, Pekosz, Andrew, additional, Smith, Rebecca L., additional, McManus, David D., additional, and Brooke, Christopher B., additional

Published
2024
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30. Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome

Author

Ranum, Jordan N, primary, Ledwith, Mitchell P, additional, Alnaji, Fadi G, additional, Diefenbacher, Meghan, additional, Orton, Richard, additional, Sloan, Elisabeth, additional, Guereca, Melissa, additional, Feltman, Elizabeth M, additional, Smollett, Katherine, additional, da Silva Filipe, Ana, additional, Conley, Michaela, additional, Russell, Alistair B, additional, Brooke, Christopher B, additional, Hutchinson, Edward, additional, and Mehle, Andrew, additional

Published
2023
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31. Leveraging vaccination-induced protective antibodies to define conserved epitopes on influenza N2 neuraminidase

Author

Lei, Ruipeng, primary, Kim, Wooseob, additional, Lv, Huibin, additional, Mou, Zongjun, additional, Scherm, Michael J., additional, Schmitz, Aaron J., additional, Turner, Jackson S., additional, Tan, Timothy J.C., additional, Wang, Yiquan, additional, Ouyang, Wenhao O., additional, Liang, Weiwen, additional, Rivera-Cardona, Joel, additional, Teo, Chuyun, additional, Graham, Claire S., additional, Brooke, Christopher B., additional, Presti, Rachel M., additional, Mok, Chris K.P., additional, Krammer, Florian, additional, Dai, Xinghong, additional, Ellebedy, Ali H., additional, and Wu, Nicholas C., additional

Published
2023
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36. Drivers of large mammal distribution: an overview and modelling approach for palaeoecological reconstructions of extinct ecosystems.

Author

Brooke, Christopher F, Marean, Curtis W, Wren, Colin D, Bergin, Sean, Fahey, B Patrick, and Venter, Jan A

Subjects
*PALEOECOLOGY, *ANIMAL ecology, *HABITAT selection, *SEA level, *ATMOSPHERIC models
Abstract

One of the primary goals of the palaeosciences is to produce robust understandings of palaeoecologies of extinct ecosystems. The time has arrived where such palaeoecologies can be significantly improved—agent-based models (ABMs) that synthesize our modern understandings of animal ecology with past conditions provide a unique opportunity for this. The Palaeo-Agulhas Plain (PAP), a now submerged landscape off the south coast of South Africa, formed a novel ecosystem during the lower sea levels of the Pleistocene. Here we provide a review of the utility of ABMs for understanding herbivores in prehistoric environments using the Paleoscape Model. The Paleoscape Model is fortunate to have features models of climate, geology and vegetation upon which we can understand how herbivores used the PAP environment. To incorporate aspects of herbivore behaviour and habitat suitability into the model requires analogies from extant systems. In addition to reconstructions of the availability of resources and associated risks, data on herbivore behaviour and physiology are imperative to our understanding of these systems. Behaviour, driven by changes in the environment, is interpreted by species, leading to selection of suitable habitats ultimately driving the herbivore's decisions within ABMs. Finally, we discuss herbivore integration into these models that can be used in numerous other scenarios (past, present and future). [ABSTRACT FROM AUTHOR]

Published
2024
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40. Virology under the Microscope—a Call for Rational Discourse

Author

Goodrum, Felicia, primary, Lowen, Anice C., additional, Lakdawala, Seema, additional, Alwine, James, additional, Casadevall, Arturo, additional, Imperiale, Michael J., additional, Atwood, Walter, additional, Avgousti, Daphne, additional, Baines, Joel, additional, Banfield, Bruce, additional, Banks, Lawrence, additional, Bhaduri-McIntosh, Sumita, additional, Bhattacharya, Deepta, additional, Blanco-Melo, Daniel, additional, Bloom, David, additional, Boon, Adrianus, additional, Boulant, Steeve, additional, Brandt, Curtis, additional, Broadbent, Andrew, additional, Brooke, Christopher, additional, Cameron, Craig, additional, Campos, Samuel, additional, Caposio, Patrizia, additional, Chan, Gary, additional, Cliffe, Anna, additional, Coffin, John, additional, Collins, Kathleen, additional, Damania, Blossom, additional, Daugherty, Matthew, additional, Debbink, Kari, additional, DeCaprio, James, additional, Dermody, Terence, additional, Dikeakos, Jimmy, additional, DiMaio, Daniel, additional, Dinglasan, Rhoel, additional, Duprex, W. Paul, additional, Dutch, Rebecca, additional, Elde, Nels, additional, Emerman, Michael, additional, Enquist, Lynn, additional, Fane, Bentley, additional, Fernandez-Sesma, Ana, additional, Flenniken, Michelle, additional, Frappier, Lori, additional, Frieman, Matthew, additional, Frueh, Klaus, additional, Gack, Michaela, additional, Gaglia, Marta, additional, Gallagher, Tom, additional, Galloway, Denise, additional, García-Sastre, Adolfo, additional, Geballe, Adam, additional, Glaunsinger, Britt, additional, Goff, Stephen, additional, Greninger, Alexander, additional, Hancock, Meaghan, additional, Harris, Eva, additional, Heaton, Nicholas, additional, Heise, Mark, additional, Heldwein, Ekaterina, additional, Hogue, Brenda, additional, Horner, Stacy, additional, Hutchinson, Edward, additional, Hyser, Joseph, additional, Jackson, William, additional, Kalejta, Robert, additional, Kamil, Jeremy, additional, Karst, Stephanie, additional, Kirchhoff, Frank, additional, Knipe, David, additional, Kowalik, Timothy, additional, Lagunoff, Michael, additional, Laimins, Laimonis, additional, Langlois, Ryan, additional, Lauring, Adam, additional, Lee, Benhur, additional, Leib, David, additional, Liu, Shan-Lu, additional, Longnecker, Richard, additional, Lopez, Carolina, additional, Luftig, Micah, additional, Lund, Jennifer, additional, Manicassamy, Balaji, additional, McFadden, Grant, additional, McIntosh, Michael, additional, Mehle, Andrew, additional, Miller, W. Allen, additional, Mohr, Ian, additional, Moody, Cary, additional, Moorman, Nathaniel, additional, Moscona, Anne, additional, Mounce, Bryan, additional, Munger, Joshua, additional, Münger, Karl, additional, Murphy, Eain, additional, Naghavi, Mojgan, additional, Nelson, Jay, additional, Neufeldt, Christopher, additional, Nikolich, Janko, additional, O'Connor, Christine, additional, Ono, Akira, additional, Orenstein, Walter, additional, Ornelles, David, additional, Ou, Jing-hsiung, additional, Parker, John, additional, Parrish, Colin, additional, Pekosz, Andrew, additional, Pellett, Philip, additional, Pfeiffer, Julie, additional, Plemper, Richard, additional, Polyak, Stephen, additional, Purdy, John, additional, Pyeon, Dohun, additional, Quinones-Mateu, Miguel, additional, Renne, Rolf, additional, Rice, Charles, additional, Schoggins, John, additional, Roller, Richard, additional, Russell, Charles, additional, Sandri-Goldin, Rozanne, additional, Sapp, Martin, additional, Schang, Luis, additional, Schmid, Scott, additional, Schultz-Cherry, Stacey, additional, Semler, Bert, additional, Shenk, Thomas, additional, Silvestri, Guido, additional, Simon, Viviana, additional, Smith, Gregory, additional, Smith, Jason, additional, Spindler, Katherine, additional, Stanifer, Megan, additional, Subbarao, Kanta, additional, Sundquist, Wesley, additional, Suthar, Mehul, additional, Sutton, Troy, additional, Tai, Andrew, additional, Tarakanova, Vera, additional, tenOever, Benjamin, additional, Tibbetts, Scott, additional, Tompkins, Stephen, additional, Toth, Zsolt, additional, van Doorslaer, Koenraad, additional, Vignuzzi, Marco, additional, Wallace, Nicholas, additional, Walsh, Derek, additional, Weekes, Michael, additional, Weinberg, Jason, additional, Weitzman, Matthew, additional, Weller, Sandra, additional, Whelan, Sean, additional, White, Elizabeth, additional, Williams, Bryan, additional, Wobus, Christiane, additional, Wong, Scott, additional, and Yurochko, Andrew, additional

Published
2023
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43. From Lisbon to The Last Man

Author

Brooke, Christopher, Brooke, Christopher [0000-0002-0524-8457], and Apollo - University of Cambridge Repository

Abstract

According to Eileen Hunt in her excellent new book, Artificial Life after Frankenstein, Mary Shelley is the fountainhead of the tradition of ‘modern political science fiction’, which she describes as imaginative works ‘with a distinctively futuristic and political orientation’ whose ‘stories and allegories draw on facts gleaned through science and history to construct powerful counterfactual narrative premises’. Behind Shelley stand both of her parents, Mary Wollstonecraft and William Godwin, and behind them in turn stands Jean-Jacques Rousseau. The point Hunt wants to emphasise is that these predecessors’ political novels—Maria (1798), Caleb Williams (1794), and Émile (1762) respectively—showcased this specifically counterfactual approach. The ‘almost preposterous scenario’ of Émile allows Rousseau ‘to test the hypothesis that a poor system of education causes the vices of modern civilization’; and Wollstonecraft and Godwin both followed in Rousseau’s footsteps, imagining ‘alternate political realities in which disenfranchised and disempowered people such as Caleb and Maria nevertheless find ways to struggle against the injustices of the eighteenth-century British legal system’. We know that Shelley was reading all three authors in 1814-15, ‘the first year of her elopement with Percy’; Hunt’s view is that Émile ‘may have been the most important source for the counterfactual form of Shelley’s Frankenstein and The Last Man’.

Published
2022
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44. Characterizing SARS-CoV-2 Transcription of Subgenomic and Genomic RNAs During Early Human Infection Using Multiplexed Droplet Digital Polymerase Chain Reaction

Author

Hwang, Hyon S, primary, Lo, Che-Min, additional, Murphy, Michael, additional, Grudda, Tanner, additional, Gallagher, Nicholas, additional, Luo, Chun Huai, additional, Robinson, Matthew L, additional, Mirza, Agha, additional, Conte, Madison, additional, Conte, Abigail, additional, Zhou, Ruifeng, additional, Vergara, Candelaria, additional, Brooke, Christopher B, additional, Pekosz, Andrew, additional, Mostafa, Heba H, additional, Manabe, Yukari C, additional, Thio, Chloe L, additional, and Balagopal, Ashwin, additional

Published
2022
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