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1. Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces

Author

Pluske John R, Gill Bhupinder P, Prosser James I, Aminov Rustam I, Bailey Mick, Lewis Marie, Stokes Christopher R, Schmidt Bettina, Mulder Imke E, Mayer Claus-Dieter, Musk Corran C, and Kelly Denise

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Background Early microbial colonization of the gut reduces the incidence of infectious, inflammatory and autoimmune diseases. Recent population studies reveal that childhood hygiene is a significant risk factor for development of inflammatory bowel disease, thereby reinforcing the hygiene hypothesis and the potential importance of microbial colonization during early life. The extent to which early-life environment impacts on microbial diversity of the adult gut and subsequent immune processes has not been comprehensively investigated thus far. We addressed this important question using the pig as a model to evaluate the impact of early-life environment on microbe/host gut interactions during development. Results Genetically-related piglets were housed in either indoor or outdoor environments or in experimental isolators. Analysis of over 3,000 16S rRNA sequences revealed major differences in mucosa-adherent microbial diversity in the ileum of adult pigs attributable to differences in early-life environment. Pigs housed in a natural outdoor environment showed a dominance of Firmicutes, in particular Lactobacillus, whereas animals housed in a hygienic indoor environment had reduced Lactobacillus and higher numbers of potentially pathogenic phylotypes. Our analysis revealed a strong negative correlation between the abundance of Firmicutes and pathogenic bacterial populations in the gut. These differences were exaggerated in animals housed in experimental isolators. Affymetrix microarray technology and Real-time Polymerase Chain Reaction revealed significant gut-specific gene responses also related to early-life environment. Significantly, indoor-housed pigs displayed increased expression of Type 1 interferon genes, Major Histocompatibility Complex class I and several chemokines. Gene Ontology and pathway analysis further confirmed these results. Conclusion Early-life environment significantly affects both microbial composition of the adult gut and mucosal innate immune function. We observed that a microbiota dominated by lactobacilli may function to maintain mucosal immune homeostasis and limit pathogen colonization.

Published
2009
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2. Preventing Avoidable Rehospitalizations through Standardizing Management of Chronic Conditions in Skilled Nursing Facilities

Author

Brown, Patty, Rothman, Paul, Berkowitz, Scott, Baumgartner, William, Bellantoni, Michele, Beranek, Ed, Blum, Robert, Brotman, Daniel, Colmers, John, Deutschendorf, Amy, Dunbar, Linda, Durso, Samuel Chris, Erdman, Stuart, Everett, Anita, Ford, Daniel, Greene, Peter, Haldeman, Dalal, Hellmann, David, Howell, Eric, Kravet, Steven, Lyketsos, Constantine, Mandell, Steven, Parker, David, Reel, Stephanie, Reitz, Judy, Sylvester, Carol, Zollinger, Raymond, Lepley, Diane, Meyers, Mary, Richardson, Melissa, Boonyasai, Romsai Tony, Leung, Curtis, Andon, Lindsay, Bailey, Jenny, Fingerhood, Michael, Hebert, Lindsay, Hickman, Debra, Kachur, Sarah, Langley, Anne, Novak, Tracy, Petinga, Michelle, Purnell, Leon, Richardson, Regina, Truant, Vince, Young, Hunter, Filbert, Lisa, Reuland, Melissa, Torres, Laura, Murphy, Shannon, Frick, Kevin, Hough, Doug, Sylvia, Martha, Lu, Yanyan, Huang, Xuan, Appel, Lawrence, Hill-Briggs, Felicia, Durkin, Nola, Ephraim, Patti, Yeh, Jessica, Bass, Eric, Wu, Albert, Hsiao, Ya Luan, Weston, Christine, Wilson, Lisa, Pulcinella, Abigail, Ibe, Chidinma, Frazier, Demetrius, Knight, Brian, Rogers, Mike, Smith, Ernest, Bass, Eric B., Wu, Albert W., Kelly, Denise, and Berkowitz, Scott A.

Published
2023
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3. Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020.

Author

LaPelusa, Michael, Donoviel, Dorit, Branzini, Sergio E, Carlson, Paul E, Culler, Stephanie, Cheema, Amrita K, Kaddurah-Daouk, Rima, Kelly, Denise, de Cremoux, Isabelle, Knight, Rob, Krajmalnik-Brown, Rosa, Mayo, Stephen L, Mazmanian, Sarkis K, Mayer, Emeran A, Petrosino, Joseph F, and Garrison, Keith

Subjects
Animals, Humans, Mars, Space Flight, Astronauts, Delivery of Health Care, Microbiota, Gastrointestinal Microbiome, Autism spectrum disorder, Behavior, Fecal microbiota transplants, Gut-brain axis, Live biotherapeutic products, Metabolome, Microbiome, Multiple sclerosis, Radiation, Sequencing, Spaceflight, Vaccine Related, Immunization, Infectious Diseases, Prevention, Emerging Infectious Diseases, Influenza, Pneumonia & Influenza, Clinical Research, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Infection, Ecology, Microbiology, Medical Microbiology
Abstract

The inaugural "Microbiome for Mars" virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duration human space travel. The conference focused on surveying current microbiome research, future endeavors, and how this growing field could broadly impact human health and space exploration. This report summarizes each speaker's presentation in the order presented at the workshop.

Published
2021

4. Adaptive immunity and neutralizing antibodies against SARS-CoV-2 variants of concern following vaccination in patients with cancer: the CAPTURE study

Author

Fendler, Annika, Shepherd, Scott T. C., Au, Lewis, Wilkinson, Katalin A., Wu, Mary, Byrne, Fiona, Cerrone, Maddalena, Schmitt, Andreas M., Joharatnam-Hogan, Nalinie, Shum, Benjamin, Tippu, Zayd, Rzeniewicz, Karolina, Boos, Laura Amanda, Harvey, Ruth, Carlyle, Eleanor, Edmonds, Kim, Del Rosario, Lyra, Sarker, Sarah, Lingard, Karla, Mangwende, Mary, Holt, Lucy, Ahmod, Hamid, Korteweg, Justine, Foley, Tara, Bazin, Jessica, Gordon, William, Barber, Taja, Emslie-Henry, Andrea, Xie, Wenyi, Gerard, Camille L., Deng, Daqi, Wall, Emma C., Agua-Doce, Ana, Namjou, Sina, Caidan, Simon, Gavrielides, Mike, MacRae, James I., Kelly, Gavin, Peat, Kema, Kelly, Denise, Murra, Aida, Kelly, Kayleigh, O’Flaherty, Molly, Dowdie, Lauren, Ash, Natalie, Gronthoud, Firza, Shea, Robyn L., Gardner, Gail, Murray, Darren, Kinnaird, Fiona, Cui, Wanyuan, Pascual, Javier, Rodney, Simon, Mencel, Justin, Curtis, Olivia, Stephenson, Clemency, Robinson, Anna, Oza, Bhavna, Farag, Sheima, Leslie, Isla, Rogiers, Aljosja, Iyengar, Sunil, Ethell, Mark, Messiou, Christina, Cunningham, David, Chau, Ian, Starling, Naureen, Turner, Nicholas, Welsh, Liam, van As, Nicholas, Jones, Robin L., Droney, Joanne, Banerjee, Susana, Tatham, Kate C., O’Brien, Mary, Harrington, Kevin, Bhide, Shreerang, Okines, Alicia, Reid, Alison, Young, Kate, Furness, Andrew J. S., Pickering, Lisa, Swanton, Charles, Gandhi, Sonia, Gamblin, Steve, Bauer, David L. V., Kassiotis, George, Kumar, Sacheen, Yousaf, Nadia, Jhanji, Shaman, Nicholson, Emma, Howell, Michael, Walker, Susanna, Wilkinson, Robert J., Larkin, James, and Turajlic, Samra

Published
2021
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5. Time in early modern English theatre and culture

Author

Kelly, Denise

Subjects
792
Abstract

This thesis explores the emergence of the theatre in England as significantly congruent with the horological evolutions of the late sixteenth to mid-seventeenth centuries. It examines the cultural texture of England's shifting notion of time, and demonstrates that the theatre was not simply an event that occurred within time, but a powerful cultural institution that actively deployed it. Through an exploration of the works of playwrights such as William Shakespeare, Ben Johnson, John Fletcher, Robert Green, Margaret Cavendish, and William Davenant, and an engagement with a range of theoretical paradigms, this thesis resituates early modern England and the theatre in the horological narrative and establishes the theatre as a significant time-keeping institution.

Published
2015

11. Preventing Avoidable Rehospitalizations through Standardizing Management of Chronic Conditions in Skilled Nursing Facilities

Author

Hsiao, Ya Luan, primary, Bass, Eric B., additional, Wu, Albert W., additional, Kelly, Denise, additional, Sylvester, Carol, additional, Berkowitz, Scott A., additional, Bellantoni, Michele, additional, Brown, Patty, additional, Rothman, Paul, additional, Berkowitz, Scott, additional, Baumgartner, William, additional, Beranek, Ed, additional, Blum, Robert, additional, Brotman, Daniel, additional, Colmers, John, additional, Deutschendorf, Amy, additional, Dunbar, Linda, additional, Durso, Samuel Chris, additional, Erdman, Stuart, additional, Everett, Anita, additional, Ford, Daniel, additional, Greene, Peter, additional, Haldeman, Dalal, additional, Hellmann, David, additional, Howell, Eric, additional, Kravet, Steven, additional, Lyketsos, Constantine, additional, Mandell, Steven, additional, Parker, David, additional, Reel, Stephanie, additional, Reitz, Judy, additional, Zollinger, Raymond, additional, Lepley, Diane, additional, Meyers, Mary, additional, Richardson, Melissa, additional, Boonyasai, Romsai Tony, additional, Leung, Curtis, additional, Andon, Lindsay, additional, Bailey, Jenny, additional, Fingerhood, Michael, additional, Hebert, Lindsay, additional, Hickman, Debra, additional, Kachur, Sarah, additional, Langley, Anne, additional, Novak, Tracy, additional, Petinga, Michelle, additional, Purnell, Leon, additional, Richardson, Regina, additional, Truant, Vince, additional, Young, Hunter, additional, Filbert, Lisa, additional, Reuland, Melissa, additional, Torres, Laura, additional, Murphy, Shannon, additional, Frick, Kevin, additional, Hough, Doug, additional, Sylvia, Martha, additional, Lu, Yanyan, additional, Huang, Xuan, additional, Appel, Lawrence, additional, Hill-Briggs, Felicia, additional, Durkin, Nola, additional, Ephraim, Patti, additional, Yeh, Jessica, additional, Bass, Eric, additional, Wu, Albert, additional, Hsiao, Ya Luan, additional, Weston, Christine, additional, Wilson, Lisa, additional, Pulcinella, Abigail, additional, Ibe, Chidinma, additional, Frazier, Demetrius, additional, Knight, Brian, additional, Rogers, Mike, additional, and Smith, Ernest, additional

Published
2023
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12. Data from Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways

Author

Spain, Lavinia, primary, Coulton, Alexander, primary, Lobon, Irene, primary, Rowan, Andrew, primary, Schnidrig, Desiree, primary, Shepherd, Scott T.C., primary, Shum, Benjamin, primary, Byrne, Fiona, primary, Goicoechea, Maria, primary, Piperni, Elisa, primary, Au, Lewis, primary, Edmonds, Kim, primary, Carlyle, Eleanor, primary, Hunter, Nikki, primary, Renn, Alexandra, primary, Messiou, Christina, primary, Hughes, Peta, primary, Nobbs, Jaime, primary, Foijer, Floris, primary, van den Bos, Hilda, primary, Wardenaar, Rene, primary, Spierings, Diana C.J., primary, Spencer, Charlotte, primary, Schmitt, Andreas M., primary, Tippu, Zayd, primary, Lingard, Karla, primary, Grostate, Lauren, primary, Peat, Kema, primary, Kelly, Kayleigh, primary, Sarker, Sarah, primary, Vaughan, Sarah, primary, Mangwende, Mary, primary, Terry, Lauren, primary, Kelly, Denise, primary, Biano, Jennifer, primary, Murra, Aida, primary, Korteweg, Justine, primary, Lewis, Charlotte, primary, O'Flaherty, Molly, primary, Cattin, Anne-Laure, primary, Emmerich, Max, primary, Gerard, Camille L., primary, Pallikonda, Husayn Ahmed, primary, Lynch, Joanna, primary, Mason, Robert, primary, Rogiers, Aljosja, primary, Xu, Hang, primary, Huebner, Ariana, primary, McGranahan, Nicholas, primary, Al Bakir, Maise, primary, Murai, Jun, primary, Naceur-Lombardelli, Cristina, primary, Borg, Elaine, primary, Mitchison, Miriam, primary, Moore, David A., primary, Falzon, Mary, primary, Proctor, Ian, primary, Stamp, Gordon W.H., primary, Nye, Emma L., primary, Young, Kate, primary, Furness, Andrew J.S., primary, Pickering, Lisa, primary, Stewart, Ruby, primary, Mahadeva, Ula, primary, Green, Anna, primary, Larkin, James, primary, Litchfield, Kevin, primary, Swanton, Charles, primary, Jamal-Hanjani, Mariam, primary, and Turajlic, Samra, primary

Published
2023
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13. Supplementary Tables S1-S8 from Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways

Author

Spain, Lavinia, primary, Coulton, Alexander, primary, Lobon, Irene, primary, Rowan, Andrew, primary, Schnidrig, Desiree, primary, Shepherd, Scott T.C., primary, Shum, Benjamin, primary, Byrne, Fiona, primary, Goicoechea, Maria, primary, Piperni, Elisa, primary, Au, Lewis, primary, Edmonds, Kim, primary, Carlyle, Eleanor, primary, Hunter, Nikki, primary, Renn, Alexandra, primary, Messiou, Christina, primary, Hughes, Peta, primary, Nobbs, Jaime, primary, Foijer, Floris, primary, van den Bos, Hilda, primary, Wardenaar, Rene, primary, Spierings, Diana C.J., primary, Spencer, Charlotte, primary, Schmitt, Andreas M., primary, Tippu, Zayd, primary, Lingard, Karla, primary, Grostate, Lauren, primary, Peat, Kema, primary, Kelly, Kayleigh, primary, Sarker, Sarah, primary, Vaughan, Sarah, primary, Mangwende, Mary, primary, Terry, Lauren, primary, Kelly, Denise, primary, Biano, Jennifer, primary, Murra, Aida, primary, Korteweg, Justine, primary, Lewis, Charlotte, primary, O'Flaherty, Molly, primary, Cattin, Anne-Laure, primary, Emmerich, Max, primary, Gerard, Camille L., primary, Pallikonda, Husayn Ahmed, primary, Lynch, Joanna, primary, Mason, Robert, primary, Rogiers, Aljosja, primary, Xu, Hang, primary, Huebner, Ariana, primary, McGranahan, Nicholas, primary, Al Bakir, Maise, primary, Murai, Jun, primary, Naceur-Lombardelli, Cristina, primary, Borg, Elaine, primary, Mitchison, Miriam, primary, Moore, David A., primary, Falzon, Mary, primary, Proctor, Ian, primary, Stamp, Gordon W.H., primary, Nye, Emma L., primary, Young, Kate, primary, Furness, Andrew J.S., primary, Pickering, Lisa, primary, Stewart, Ruby, primary, Mahadeva, Ula, primary, Green, Anna, primary, Larkin, James, primary, Litchfield, Kevin, primary, Swanton, Charles, primary, Jamal-Hanjani, Mariam, primary, and Turajlic, Samra, primary

Published
2023
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14. Supplementary Figures S1-S25 from Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways

Author

Spain, Lavinia, primary, Coulton, Alexander, primary, Lobon, Irene, primary, Rowan, Andrew, primary, Schnidrig, Desiree, primary, Shepherd, Scott T.C., primary, Shum, Benjamin, primary, Byrne, Fiona, primary, Goicoechea, Maria, primary, Piperni, Elisa, primary, Au, Lewis, primary, Edmonds, Kim, primary, Carlyle, Eleanor, primary, Hunter, Nikki, primary, Renn, Alexandra, primary, Messiou, Christina, primary, Hughes, Peta, primary, Nobbs, Jaime, primary, Foijer, Floris, primary, van den Bos, Hilda, primary, Wardenaar, Rene, primary, Spierings, Diana C.J., primary, Spencer, Charlotte, primary, Schmitt, Andreas M., primary, Tippu, Zayd, primary, Lingard, Karla, primary, Grostate, Lauren, primary, Peat, Kema, primary, Kelly, Kayleigh, primary, Sarker, Sarah, primary, Vaughan, Sarah, primary, Mangwende, Mary, primary, Terry, Lauren, primary, Kelly, Denise, primary, Biano, Jennifer, primary, Murra, Aida, primary, Korteweg, Justine, primary, Lewis, Charlotte, primary, O'Flaherty, Molly, primary, Cattin, Anne-Laure, primary, Emmerich, Max, primary, Gerard, Camille L., primary, Pallikonda, Husayn Ahmed, primary, Lynch, Joanna, primary, Mason, Robert, primary, Rogiers, Aljosja, primary, Xu, Hang, primary, Huebner, Ariana, primary, McGranahan, Nicholas, primary, Al Bakir, Maise, primary, Murai, Jun, primary, Naceur-Lombardelli, Cristina, primary, Borg, Elaine, primary, Mitchison, Miriam, primary, Moore, David A., primary, Falzon, Mary, primary, Proctor, Ian, primary, Stamp, Gordon W.H., primary, Nye, Emma L., primary, Young, Kate, primary, Furness, Andrew J.S., primary, Pickering, Lisa, primary, Stewart, Ruby, primary, Mahadeva, Ula, primary, Green, Anna, primary, Larkin, James, primary, Litchfield, Kevin, primary, Swanton, Charles, primary, Jamal-Hanjani, Mariam, primary, and Turajlic, Samra, primary

Published
2023
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15. Sotrovimab restores neutralization against current Omicron subvariants in patients with blood cancer

Author

Wu, Mary Y., primary, Shepherd, Scott T.C., additional, Fendler, Annika, additional, Carr, Edward J., additional, Au, Lewis, additional, Harvey, Ruth, additional, Dowgier, Giulia, additional, Hobbs, Agnieszka, additional, Herman, Lou S., additional, Ragno, Martina, additional, Adams, Lorin, additional, Schmitt, Andreas M., additional, Tippu, Zayd, additional, Shum, Benjamin, additional, Farag, Sheima, additional, Rogiers, Aljosja, additional, O’Reilly, Nicola, additional, Bawumia, Philip, additional, Smith, Callie, additional, Carlyle, Eleanor, additional, Edmonds, Kim, additional, Del Rosario, Lyra, additional, Lingard, Karla, additional, Mangwende, Mary, additional, Holt, Lucy, additional, Ahmod, Hamid, additional, Korteweg, Justine, additional, Foley, Tara, additional, Barber, Taja, additional, Hepworth, Stephanie, additional, Emslie-Henry, Andrea, additional, Caulfield-Lynch, Niamh, additional, Byrne, Fiona, additional, Deng, Daqi, additional, Williams, Bryan, additional, Brown, Michael, additional, Caidan, Simon, additional, Gavrielides, Mike, additional, MacRae, James I., additional, Kelly, Gavin, additional, Peat, Kema, additional, Kelly, Denise, additional, Murra, Aida, additional, Kelly, Kayleigh, additional, O’Flaherty, Molly, additional, Popat, Sanjay, additional, Yousaf, Nadia, additional, Jhanji, Shaman, additional, Tatham, Kate, additional, Cunningham, David, additional, Van As, Nicholas, additional, Young, Kate, additional, Furness, Andrew J.S., additional, Pickering, Lisa, additional, Beale, Rupert, additional, Swanton, Charles, additional, Gandhi, Sonia, additional, Gamblin, Steve, additional, Bauer, David L.V., additional, Kassiotis, George, additional, Howell, Michael, additional, Walker, Susanna, additional, Nicholson, Emma, additional, Larkin, James, additional, Wall, Emma C., additional, and Turajlic, Samra, additional

Published
2023
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16. Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways

Author

Spain, Lavinia, Coulton, Alexander, Lobon, Irene, Rowan, Andrew, Schnidrig, Desiree, Shepherd, Scott TC, Shum, Benjamin, Byrne, Fiona, Goicoechea, Maria, Piperni, Elisa, Au, Lewis, Edmonds, Kim, Carlyle, Eleanor, Hunter, Nikki, Renn, Alexandra, Messiou, Christina, Hughes, Peta, Nobbs, Jaime, Foijer, Floris, van den Bos, Hilda, Wardenaar, Rene, Spierings, Diana CJ, Spencer, Charlotte, Schmitt, Andreas M, Tippu, Zayd, Lingard, Karla, Grostate, Lauren, Peat, Kema, Kelly, Kayleigh, Sarker, Sarah, Vaughan, Sarah, Mangwende, Mary, Terry, Lauren, Kelly, Denise, Biano, Jennifer, Murra, Aida, Korteweg, Justine, Lewis, Charlotte, OFlaherty, Molly, Cattin, Anne-Laure, Emmerich, Max, Gerard, Camille L, Pallikonda, Husayn Ahmed, Lynch, Joanna, Mason, Robert, Rogiers, Aljosja, Xu, Hang, Huebner, Ariana, McGranahan, Nicholas, Al Bakir, Maise, Murai, Jun, Naceur-Lombardelli, Cristina, Borg, Elaine, Mitchison, Miriam, Moore, David A, Falzon, Mary, Proctor, Ian, Stamp, Gordon WH, Nye, Emma L, Young, Kate, Furness, Andrew JS, Pickering, Lisa, Stewart, Ruby, Mahadeva, Ula, Green, Anna, Larkin, James, Litchfield, Kevin, Swanton, Charles, Jamal-Hanjani, Mariam, Consortium, The PEACE, and Turajlic, Samra

Subjects
Chemical Biology & High Throughput, Signalling & Oncogenes, Human Biology & Physiology, Ecology,Evolution & Ethology, Genome Integrity & Repair, Tumour Biology, Genetics & Genomics, Computational & Systems Biology
Abstract

Understanding the evolutionary pathways to metastasis and resistance to immune checkpoint inhibitors (ICI) in melanoma is critical for improving outcomes. Here we present the most comprehensive intra-patient metastatic melanoma dataset assembled to date as part of the PEACE research autopsy programme, including 222 exome, 493 panel-sequenced, 161 RNA-seq, and 22 single-cell whole-genome sequencing samples from 14 ICI-treated patients. We observed frequent whole-genome doubling and widespread loss of heterozygosity, often involving antigen presentation machinery. We found KIT extrachromosomal DNA may have contributed to the lack of response to KIT inhibitors of a KIT-driven melanoma. At the lesion-level, MYC amplifications were enriched in ICI non-responders. Single-cell sequencing revealed polyclonal seeding of metastases originating from clones with different ploidy in one of the patients. Finally, we observed that brain metastases that diverged early in molecular evolution emerge late in disease. Overall, our study illustrates the diverse evolutionary landscape of advanced melanoma.

Published
2023
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17. Functional immune responses against SARS-CoV-2 variants of concern after fourth COVID-19 vaccine dose or infection in patients with blood cancer

Author

Fendler, Annika, primary, Shepherd, Scott T.C., additional, Au, Lewis, additional, Wu, Mary, additional, Harvey, Ruth, additional, Wilkinson, Katalin A., additional, Schmitt, Andreas M., additional, Tippu, Zayd, additional, Shum, Benjamin, additional, Farag, Sheima, additional, Rogiers, Aljosja, additional, Carlyle, Eleanor, additional, Edmonds, Kim, additional, Del Rosario, Lyra, additional, Lingard, Karla, additional, Mangwende, Mary, additional, Holt, Lucy, additional, Ahmod, Hamid, additional, Korteweg, Justine, additional, Foley, Tara, additional, Barber, Taja, additional, Emslie-Henry, Andrea, additional, Caulfield-Lynch, Niamh, additional, Byrne, Fiona, additional, Deng, Daqi, additional, Kjaer, Svend, additional, Song, Ok-Ryul, additional, Queval, Christophe J., additional, Kavanagh, Caitlin, additional, Wall, Emma C., additional, Carr, Edward J., additional, Caidan, Simon, additional, Gavrielides, Mike, additional, MacRae, James I., additional, Kelly, Gavin, additional, Peat, Kema, additional, Kelly, Denise, additional, Murra, Aida, additional, Kelly, Kayleigh, additional, O’Flaherty, Molly, additional, Shea, Robyn L., additional, Gardner, Gail, additional, Murray, Darren, additional, Popat, Sanjay, additional, Yousaf, Nadia, additional, Jhanji, Shaman, additional, Tatham, Kate, additional, Cunningham, David, additional, Van As, Nicholas, additional, Young, Kate, additional, Furness, Andrew J.S., additional, Pickering, Lisa, additional, Beale, Rupert, additional, Swanton, Charles, additional, Gandhi, Sonia, additional, Gamblin, Steve, additional, Bauer, David L.V., additional, Kassiotis, George, additional, Howell, Michael, additional, Nicholson, Emma, additional, Walker, Susanna, additional, Wilkinson, Robert J., additional, Larkin, James, additional, and Turajlic, Samra, additional

Published
2022
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19. Recommendations and Guidelines for Creating Scholarly Journals: A Scoping Review

Author

Jeremy Y. Ng, Kelly Denise Cobey, Saad Ahmed, Valerie Chow, Sharleen G. Maduranayagam, Lucas J. Santoro, Lindsey Sikora, Ana Marusic, Daniel Shanahan, Randy Townsend, Alan Ehrlich, Alfonso Iorio, and David Moher

Abstract

Background: Scholarly journals play a key role in the dissemination of research findings. However, little focus is given to the process of establishing new, credible journals and the obstacles faced in achieving this. This scoping review aimed to identify and describe existing guidelines for starting a biomedical scholarly journal. Methods: We searched five bibliographic databases: OVID Medline + Medline in Process, Embase Classic + Embase, ERIC, APA PsycINFO, and Web of Science on January 14, 2022. A related grey literature search was conducted on March 19, 2022. Eligible sources were those published in English in any year, of any format, and that described guidance for starting a biomedical journal. Titles and abstracts of obtained sources were screened. We extracted descriptive characteristics including author name, year and country of publication, journal name, and source type, and any recommendations from the included sources discussing guidance for starting a biomedical journal. These recommendations were categorized and thematically grouped.Results: A total of 5626 unique sources were obtained. Thirty-three sources met our inclusion criteria. Most sources were blog posts (10/33; 30.30%), and only 10 sources were supported by evidence. We extracted 51 unique recommendations from these 33 sources, which we thematically classified into nine themes which were: journal operations, editorial review processes, peer review processes, open access publishing, copyediting/typesetting, production, archiving/indexing/metrics, marketing/promotion, and funding. Conclusions: There is little formal guidance regarding how to start a scholarly journal. The development of an evidence-based guideline may help uphold scholarly publishing quality, provide insight into obstacles new journals will face, and equip novice publishers with the tools to meet best practices.

Published
2022
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20. Recommendations and Guidelines for Creating Scholarly Journals: A Scoping Review

Author

Ng, Jeremy Y., primary, Cobey, Kelly Denise, additional, Ahmed, Saad, additional, Chow, Valerie, additional, Maduranayagam, Sharleen G., additional, Santoro, Lucas J., additional, Sikora, Lindsey, additional, Marusic, Ana, additional, Shanahan, Daniel, additional, Townsend, Randy, additional, Ehrlich, Alan, additional, Iorio, Alfonso, additional, and Moher, David, additional

Published
2022
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21. Epidemiological characteristics and prevalence rates of research reproducibility across disciplines: A scoping review

Author

Kelly Denise Cobey, Christophe A. Fehlmann, Marina Christ Franco, Ana Patricia Ayala, Lindsey Sikora, Danielle B Rice, Chenchen Xu, John P.A. Ioannidis, Manoj Mathew Lalu, Alixe Menard, Andrew Neitzel, Bea Nguyen, Nino Tsertsvadze, and David Moher

Abstract

Background: Reproducibility is a central tenant of research. Explicit reproducibility checks are made across different disciplines trying to assess the replication of previously published studies. We aimed to synthesize the literature on reproducibility and describe its epidemiological characteristics, including how reproducibility is defined and assessed. We also aimed to determine and compare estimates for reproducibility across different fields.Methods and Findings: We conducted a scoping review to identify English language replication studies published between 2018-2019 in economics, education, psychology, health sciences and biomedicine. We searched Medline, Embase, PsycINFO, Cumulative Index of Nursing and Allied Health Literature – CINAHL, Education Source via EBSCOHost, ERIC, EconPapers, International Bibliography of the Social Sciences (IBSS), and EconLit. Documents retrieved were screened in duplicate against our inclusion criteria. We extracted year of publication, number of authors, country of affiliation of the corresponding author, and whether the study was funded. For the individual replication studies, we recorded whether a registered protocol was used, whether there was contact between the replicating team and the original authors, what study design was used, and what the primary outcome was. Finally, we recorded how replication was defined by the authors, and whether the assessed study(ies) successfully replicated based on this definition. Extraction was done by a single reviewer and quality controlled by a second reviewer. Our search identified 11,224 unique documents, of which 47 were included in this review. Most studies were related to either psychology (48.6%) or health sciences (23.7%). Among these 47 documents, 36 described a single replication study while the remaining 11 reported at least two replications in the same paper. Less than the half of the studies referred to a registered protocol. There was variability in the definitions of replication success. In total, across the 47 documents 177 studies were reported. Based on the definition used by the author of each study, 95 of 177 (53.7%) studies replicated. Conclusion: This study gives an overview of research across five disciplines that explicitly set out to replicate previous research. Such replication studies are extremely scarce, the definition of a success in replication is ambiguous, and the replication rate is overall modest.

Published
2022
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22. Omicron neutralising antibodies after third COVID-19 vaccine dose in patients with cancer

Author

Fendler, Annika, Shepherd, Scott T C, Au, Lewis, Wu, Mary, Harvey, Ruth, Schmitt, Andreas M, Tippu, Zayd, Shum, Benjamin, Farag, Sheima, Rogiers, Aljosja, Carlyle, Eleanor, Edmonds, Kim, Del Rosario, Lyra, Lingard, Karla, Mangwende, Mary, Holt, Lucy, Ahmod, Hamid, Korteweg, Justine, Foley, Tara, Barber, Taja, Emslie-Henry, Andrea, Caulfield-Lynch, Niamh, Byrne, Fiona, Deng, Daqi, Kjaer, Svend, Song, Ok-Ryul, Queval, Christophe, Kavanagh, Caitlin, Wall, Emma C, Carr, Edward J, Caidan, Simon, Gavrielides, Mike, MacRae, James I, Kelly, Gavin, Peat, Kema, Kelly, Denise, Murra, Aida, Kelly, Kayleigh, O'Flaherty, Molly, Shea, Robyn L, Gardner, Gail, Murray, Darren, Yousaf, Nadia, Jhanji, Shaman, Tatham, Kate, Cunningham, David, Van As, Nicholas, Young, Kate, Furness, Andrew J S, Pickering, Lisa, Beale, Rupert, Swanton, Charles, Gandhi, Sonia, Gamblin, Steve, Bauer, David L V, Kassiotis, George, Howell, Michael, Nicholson, Emma, Walker, Susanna, Larkin, James, and Turajlic, Samra

Published
2022
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23. Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging

Author

Turroni, Francesca, Bottacini, Francesca, Foroni, Elena, Mulder, Imke, Kim, Jae-Han, Zomer, Aldert, Sánchez, Borja, Bidossi, Alessandro, Ferrarini, Alberto, Giubellini, Vanessa, Delledonne, Massimo, Henrissat, Bernard, Coutinho, Pedro, Oggioni, Marco, Fitzgerald, Gerald F., Mills, David, Margolles, Abelardo, Kelly, Denise, van Sinderen, Douwe, Ventura, Marco, and Klaenhammer, Todd R.

Published
2010

24. Peroxisome proliferator-activated receptor gamma activation is required for maintenance of innate antimicrobial immunity in the colon

Author

Peyrin-Biroulet, Laurent, Beisner, Julia, Wang, Guoxing, Nuding, Sabine, Oommen, Sajit Thottathil, Kelly, Denise, Parmentier-Decrucq, Erika, Dessein, Rodrigue, Merour, Emilie, Chavatte, Philipe, Grandjean, Teddy, Bressenot, Aude, Desreumaux, Pierre, Colombel, Jean-Frédéric, Desvergne, Béatrice, Stange, Eduard F., Wehkamp, Jan, and Chamaillard, Mathias

Published
2010

25. Immune responses following third COVID-19 vaccination are reduced in patients with hematological malignancies compared to patients with solid cancer

Author

Fendler, Annika, Shepherd, Scott T.C., Au, Lewis, Wilkinson, Katalin A., Wu, Mary, Schmitt, Andreas M., Tippu, Zayd, Farag, Sheima, Rogiers, Aljosja, Harvey, Ruth, Carlyle, Eleanor, Edmonds, Kim, Del Rosario, Lyra, Lingard, Karla, Mangwende, Mary, Holt, Lucy, Ahmod, Hamid, Korteweg, Justine, Foley, Tara, Barber, Taja, Emslie-Henry, Andrea, Caulfield-Lynch, Niamh, Byrne, Fiona, Shum, Benjamin, Gerard, Camille L., Deng, Daqi, Kjaer, Svend, Song, Ok-Ryul, Queval, Christophe, Kavanagh, Caitlin, Wall, Emma C., Carr, Edward J., Namjou, Sina, Caidan, Simon, Gavrielides, Mike, MacRae, James I., Kelly, Gavin, Peat, Kema, Kelly, Denise, Murra, Aida, Kelly, Kayleigh, O’Flaherty, Molly, Shea, Robyn L., Gardner, Gail, Murray, Darren, Popat, Sanjay, Yousaf, Nadia, Jhanji, Shaman, Van As, Nicholas, Young, Kate, Furness, Andrew J.S., Pickering, Lisa, Beale, Rupert, Swanton, Charles, Gandhi, Sonia, Gamblin, Steve, Bauer, David L.V., Kassiotis, George, Howell, Michael, Nicholson, Emma, Walker, Susanna, Wilkinson, Robert J., Larkin, James, and Turajlic, Samra

Published
2022
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28. Epidemiological characteristics and prevalence rates of research reproducibility across disciplines: A scoping review

Author

Cobey, Kelly Denise, primary, Fehlmann, Christophe A., additional, Franco, Marina Christ, additional, Ayala, Ana Patricia, additional, Sikora, Lindsey, additional, Rice, Danielle B, additional, Xu, Chenchen, additional, Ioannidis, John P.A., additional, Lalu, Manoj Mathew, additional, Menard, Alixe, additional, Neitzel, Andrew, additional, Nguyen, Bea, additional, Tsertsvadze, Nino, additional, and Moher, David, additional

Published
2022
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29. Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay

Author

Orlando, Francesco, Romanel, Alessandro, Trujillo, Blanca, Sigouros, Michael, Wetterskog, Daniel, Quaini, Orsetta, Leone, Gianmarco, Xiang, Jenny Z, Wingate, Anna, Tagawa, Scott, Jayaram, Anuradha, Linch, Mark, Swanton, Charles, Jamal-Hanjani, Mariam, Abbosh, Chris, Zaccaria, Simone, Hessey, Sonya, Shiu, Kai-Keen, Bridgewater, John, Hochhauser, Daniel, Forster, Martin, Lee, Siow-Ming, Ahmad, Tanya, Papadatos-Pastos, Dionysis, Janes, Sam, Van Loo, Peter, Enfield, Katey, McGranahan, Nicholas, Huebner, Ariana, Quezada, Sergio, Beck, Stephan, Parker, Peter, Enver, Tariq, Hynds, Robert E, Dijkstra, Krijn, Pearce, David R, Falzon, Mary, Proctor, Ian, Sinclair, Ron, Lok, Chi-wah, Rhodes, Zoe, Moore, David, Marafioti, Teresa, Mitchison, Miriam, Ellery, Peter, Sivakumar, Monica, Brandner, Sebastian, Rowan, Andrew, Hiley, Crispin, Veeriah, Selvaraju, Shaw, Heather, Attard, Gert, Naceur-Lombardelli, Cristina, Toncheva, Antonia, Prymas, Paulina, Watkins, Tom, Bailey, Chris, Ruiz, Carlos Martinez, Litchfield, Kevin, Al-Bakir, Maise, Kanu, Nnenna, Ward, Sophie, Lim, Emilia, Reading, James, Chain, Benny, Alba, Blanca Trujillo, Akay, Melek, Flanagan, Adrienne, Biswas, Dhruva, Pich, Oriol, Dietzen, Michelle, Puttick, Clare, Colliver, Emma, Magness, Alistair, Angelova, Mihaela, Black, James, Lucas, Olivia, Hill, William, Liu, Wing-Kin, Frankell, Alexander, Magno, Neil, Athanasopoulou, Foteini, Wilson, Gareth, Rosenthal, Rachel, Salgado, Roberto, Lee, Claudia, Grigoriadis, Kristiana, Al-Sawaf, Othman, Karasaki, Takahiro, Bunkum, Abigail, Noorani, Imran, Benafif, Sarah, Barbe, Vittorio, Bola, Supreet, Vainauskas, Osvaldas, Hasan, Mahedi, Lise, Stefano, Leone, GianMarco, Alifrangis, Constantine, McGovern, Ursula, Thol, Kerstin, Gamble, Samuel, Ung, Seng Kuong, Sahwangarrom, Teerapon, Marin, Claudia Peinador, Wong, Sophia, Pawlik, Piotr, Gishen, Faye, Tookman, Adrian, Stone, Paddy, Stirling, Caroline, Turajlic, Samra, Larkin, James, Pickering, Lisa, Furness, Andrew, Young, Kate, Drake, Will, Edmonds, Kim, Hunter, Nikki, Mangwende, Mary, Pearce, Karla, Grostate, Lauren, Au, Lewis, Spain, Lavinia, Shepherd, Scott, Yan, Haixi, Shum, Ben, Tippu, Zayd, Hanley, Brian, Spencer, Charlotte, Emmerich, Max, Gerard, Camille, Schmitt, Andreas Michael, Del Rosario, Lyra, Carlyle, Eleanor, Lewis, Charlotte, Holt, Lucy, Lucanas, Analyn, O'Flaherty, Molly, Hazell, Steve, Mudhar, Hardeep, Messiou, Christina, Latifoltojar, Arash, Fendler, Annika, Byrne, Fiona, Pallinkonda, Husayn, Lobon, Irene, Coulton, Alex, Cattin, Anne Laure, Deng, Daqi, Feng, Geoffrey Hugang, Rowan, Andew, Yousaf, Nadia, Popat, Sanjay, Curtis, Olivia, Milner-Watts, Charlotte, Stamp, Gordon, Nye, Emma, Murra, Aida, Korteweg, Justine, Kelly, Denise, Terry, Lauren, Biano, Jennifer, Peat, Kema, Kelly, Kayleigh, Hill, Peter, Josephs, Debra, Irshad, Sheeba, Chandra, Ashish, Spicer, James, Mahadeva, Ula, Green, Anna, Stewart, Ruby, Iredale, Lara-Rose, Mackay, Tina, Deakin, Ben, Enting, Debra, Rudman, Sarah, Ghosh, Sharmistha, Karapagniotou, Lena, Pintus, Elias, Tutt, Andrew, Howlett, Sarah, Michalarea, Vasiliki, Brenton, James, Caldas, Carlos, Fitzgerald, Rebecca, Jimenez-Linan, Merche, Provenzano, Elena, Cluroe, Alison, Paterson, Anna, Aitken, Sarah, Allinson, Kieren, Stewart, Grant, McDermott, Ultan, Beddowes, Emma, Maughan, Tim, Ansorge, Olaf, Campbell, Peter, Roxburgh, Patricia, Fraser, Sioban, Kidd, Andrew, Blyth, Kevin, Le Quesne, John, Krebs, Matthew, Blackhall, Fiona, Summers, Yvonne, Oliveira, Pedro, Ortega-Franco, Ana, Dive, Caroline, Gomes, Fabio, Carter, Mat, Dransfield, Jo, Thomas, Anne, Fennell, Dean, Shaw, Jacqui, Naidu, Babu, Baijal, Shobhit, Tanchel, Bruce, Langman, Gerald, Robinson, Andrew, Collard, Martin, Cockcroft, Peter, Ferris, Charlotte, Bancroft, Hollie, Kerr, Amy, Middleton, Gary, Webb, Joanne, Kadiri, Salma, Colloby, Peter, Olisemeke, Bernard, Wilson, Rodelaine, Tomlinson, Ian, McNeish, Iain, Jogai, Sanjay, Holden, Samantha, Fernandes, Tania, Hampton, Blanche, McKenzie, Mairead, Hackshaw, Allan, Sharp, Abby, Chan, Kitty, Farrelly, Laura, Bridger, Hayley, Leslie, Rachel, Consortium, PEACE, Rubin, Mark A, Wyatt, Alexander W, Beltran, Himisha, Attard, Gerhardt, and Demichelis, Francesca

Subjects
Chemical Biology & High Throughput, Signalling & Oncogenes, Human Biology & Physiology, Ecology,Evolution & Ethology, Genome Integrity & Repair, Tumour Biology, Genetics & Genomics, Computational & Systems Biology
Abstract

Sequencing of cell-free DNA (cfDNA) in cancer patients’ plasma offers a minimally-invasive solution to detect tumor cell genomic alterations to aid real-time clinical decision-making. The reliability of copy number detection decreases at lower cfDNA tumor fractions, limiting utility at earlier stages of the disease. To test a novel strategy for detection of allelic imbalance, we developed a prostate cancer bespoke assay, PCF_SELECT, that includes an innovative sequencing panel covering ∼25 000 high minor allele frequency SNPs and tailored analytical solutions to enable allele-informed evaluation. First, we assessed it on plasma samples from 50 advanced prostate cancer patients. We then confirmed improved detection of genomic alterations in samples with

Published
2022
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30. Adaptive immunity and neutralizing antibodies against SARS-CoV-2 variants of concern following vaccination in patients with cancer: the CAPTURE study

Author

Fendler, Annika, Shepherd, Scott TC, Au, Lewis, Wilkinson, Katalin A, Wu, Mary, Byrne, Fiona, Cerrone, Maddalena, Schmitt, Andreas M, Joharatnam-Hogan, Nalinie, Shum, Benjamin, Tippu, Zayd, Rzeniewicz, Karolina, Boos, Laura Amanda, Harvey, Ruth, Carlyle, Eleanor, Edmonds, Kim, Del Rosario, Lyra, Sarker, Sarah, Lingard, Karla, Mangwende, Mary, Holt, Lucy, Ahmod, Hamid, Korteweg, Justine, Foley, Tara, Bazin, Jessica, Gordon, William, Barber, Taja, Emslie-Henry, Andrea, Xie, Wenyi, Gerard, Camille L, Deng, Daqi, Wall, Emma C, Agua-Doce, Ana, Namjou, Sina, Caidan, Simon, Gavrielides, Mike, MacRae, James I, Kelly, Gavin, Peat, Kema, Kelly, Denise, Murra, Aida, Kelly, Kayleigh, O���Flaherty, Molly, Dowdie, Lauren, Ash, Natalie, Gronthoud, Firza, Shea, Robyn L, Gardner, Gail, Murray, Darren, Kinnaird, Fiona, Cui, Wanyuan, Pascual, Javier, Rodney, Simon, Mencel, Justin, Curtis, Olivia, Stephenson, Clemency, Robinson, Anna, Oza, Bhavna, Farag, Sheima, Leslie, Isla, Rogiers, Aljosja, Iyengar, Sunil, Ethell, Mark, Messiou, Christina, Cunningham, David, Chau, Ian, Starling, Naureen, Turner, Nicholas, Welsh, Liam, van As, Nicholas, Jones, Robin L, Droney, Joanne, Banerjee, Susana, Tatham, Kate C, O���Brien, Mary, Harrington, Kevin, Bhide, Shreerang, Okines, Alicia, Reid, Alison, Young, Kate, Furness, Andrew JS, Pickering, Lisa, Swanton, Charles, Consortium, The Crick COVID-19, Gandhi, Sonia, Gamblin, Steve, Bauer, David LV, Kassiotis, George, Kumar, Sacheen, Yousaf, Nadia, Jhanji, Shaman, Nicholson, Emma, Howell, Michael, Walker, Susanna, Wilkinson, Robert J, Larkin, James, Turajlic, Samra, and Consortium, The CAPTURE

Subjects
Model organisms, Chemical Biology & High Throughput, Human Biology & Physiology, FOS: Clinical medicine, Stem Cells, Genome Integrity & Repair, Immunology, Neurosciences, Infectious Disease, Cell Biology, Tumour Biology, Biochemistry & Proteomics, Signalling & Oncogenes, Metabolism, Ecology,Evolution & Ethology, Cell Cycle & Chromosomes, Genetics & Genomics, Developmental Biology, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

Coronavirus disease 2019 (COVID-19) antiviral response in a pan-tumor immune monitoring (CAPTURE) (NCT03226886) is a prospective cohort study of COVID-19 immunity in patients with cancer. Here we evaluated 585 patients following administration of two doses of BNT162b2 or AZD1222 vaccines, administered 12 weeks apart. Seroconversion rates after two doses were 85% and 59% in patients with solid and hematological malignancies, respectively. A lower proportion of patients had detectable titers of neutralizing antibodies (NAbT) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) versus wild-type (WT) SARS-CoV-2. Patients with hematological malignancies were more likely to have undetectable NAbT and had lower median NAbT than those with solid cancers against both SARS-CoV-2 WT and VOC. By comparison with individuals without cancer, patients with hematological, but not solid, malignancies had reduced neutralizing antibody (NAb) responses. Seroconversion showed poor concordance with NAbT against VOC. Previous SARS-CoV-2 infection boosted the NAb response including against VOC, and anti-CD20 treatment was associated with undetectable NAbT. Vaccine-induced T cell responses were detected in 80% of patients and were comparable between vaccines or cancer types. Our results have implications for the management of patients with cancer during the ongoing COVID-19 pandemic.

Published
2022
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31. Identifying Potential Barriers and Solutions to Patient Partner Compensation (Payment) in Research

Author

Dawn P. Richards, Kelly Denise Cobey, Laurie Proulx, Shoba Dawson, Maarten de Wit, and Karine Toupin April

Subjects
Patient partner, Health (social science), Patient and public involvement, General Health Professions, Patient engagement, Institutional barriers, Patient research partner, Payment, Compensation, Barriers
Abstract

Research that engages patients on the research team is often supported by grant funding from different organizations and, in some cases, principal investigators (who control the grant funding) provide patient partners with compensation (or payment) for their contributions. However, we have noted a gap in resources that identify and address barriers to compensating patient partners (no matter the size, degree or length of their engagement). In this paper, we present thoughts and experiences related to barriers to compensating patient partners with the goal of helping individuals identify and find solutions to these obstacles. Based on our experiences as individuals who live with chronic conditions and are patient partners, and those who are researchers who engage patient partners, we have identified eight barriers to compensating patient partners. We discuss each of these barriers: lack of awareness about patient partnership, institutional inflexibility, policy guidance from funders, compensation not prioritized in research budgets, leadership hesitancy to create a new system, culture of research teams, preconceived beliefs about the skills and abilities of patient partners, and expectations placed on patient partners. We demonstrate these barriers with real life examples and we offer some solutions. To further demonstrate these barriers, we ask readers to reflect on some scenarios that present realistic parallel situations to those that patient partners face. The intention is to illustrate, through empathy or putting yourself in someone else's shoes, how we might all do better with respect to institutional barriers related to patient partner compensation. Last, we issue a call to action to share resources and identify actions to overcome these barriers from which we will create an online resource repository.Research teams that engage patients as partners sometimes provide compensation or payment to these patient partners for their contributions. There does not seem to be many resources that identify and tackle barriers to compensating patient partners. Based on our experiences as people who live with chronic conditions and who are patient partners, and as researchers who engage patient partners, we have identified eight barriers to compensating patient partners. We discuss each of these barriers: lack of awareness about patient partnership, institutional inflexibility, policy guidance from funders, compensation not prioritized in research budgets, leadership hesitancy to create a new system, culture on research teams, preconceived beliefs about patient partners’ skills and abilities, and expectations placed on patient partners. We illustrate these with real-life scenarios and we offer some solutions. Last, we issue a call to action to the global community that engages patient partners in their research teams to share resources and identify actions to overcome these barriers. By doing so, we can begin to create an online resource repository and help patient partners and researchers focus on working together rather than wasting energy navigating a system that is not well adapted to engaging patient partners.

Published
2021
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34. COVID-19 Encephalitis with SARS-CoV-2 Detected in Cerebrospinal Fluid Presenting as a Stroke Mimic

Author

Glavin, Diarmuid, Kelly, Denise, Wood, Greta Karen, McCausland, Beth MS, Ellul, Mark Alexander, Varatharaj, Aravinthan, Galea, Ian, Thomas, Rhys Huw, Michael, Benedict Daniel, Gallen, Brian, and Grp, CoroNerve Study Management

Subjects
Stroke mimic, medicine.medical_specialty, Pediatrics, Neurology, SARS-Cov-2, medicine.medical_treatment, Case Report, Electroencephalography, 03 medical and health sciences, 0302 clinical medicine, Cerebrospinal fluid, Neuroimaging, medicine, medicine.diagnostic_test, business.industry, Rehabilitation, COVID-19, Respiratory infection, Thrombolysis, medicine.disease, Encephalitis, Surgery, Neurology (clinical), Differential diagnosis, Cardiology and Cardiovascular Medicine, business, 030217 neurology & neurosurgery
Abstract

We report the case of a 35-year-old male with COVID-19 encephalitis presenting as a stroke mimic with sudden-onset expressive and receptive dysphasia, mild confusion and right arm incoordination. The patient received thrombolysis for a suspected ischaemic stroke, but later became febrile and SARS-CoV-2 was detected in cerebrospinal fluid. Electroencephalography demonstrated excess in slow waves, but neuroimaging was reported as normal. Respiratory symptoms were absent throughout and nasopharyngeal swab was negative for SARS-CoV-2. At the most recent follow-up, the patient had made a full neurological recovery. Clinicians should therefore consider testing for SARS-CoV-2 in CSF in patients who present with acute focal neurology, confusion and fever during the pandemic, even when there is no evidence of respiratory infection.

Published
2021

35. Immune responses following third COVID-19 vaccination are reduced in patients with hematologic malignancies compared to patients with solid cancer

Author

Fendler, Annika, primary, Shepherd, Scott T.C., additional, Au, Lewis, additional, Wilkinson, Katalin A., additional, Wu, Mary, additional, Schmitt, Andreas M., additional, Tippu, Zayd, additional, Farag, Sheima, additional, Rogiers, Aljosja, additional, Harvey, Ruth, additional, Carlyle, Eleanor, additional, Edmonds, Kim, additional, Rosario, Lyra Del, additional, Lingard, Karla, additional, Mangwende, Mary, additional, Holt, Lucy, additional, Ahmod, Hamid, additional, Korteweg, Justine, additional, Foley, Tara, additional, Barber, Taja, additional, Emslie-Henry, Andrea, additional, Caulfield-Lynch, Niamh, additional, Byrne, Fiona, additional, Shum, Benjamin, additional, Gerard, Camille L., additional, Deng, Daqi, additional, Kjaer, Svend, additional, Song, Ok-Ryul, additional, Queval, Christophe, additional, Kavanagh, Caitlin, additional, Wall, Emma C., additional, Carr, Edward J., additional, Namjou, Sina, additional, Caidan, Simon, additional, Gavrielidis, Mike, additional, McRae, James, additional, Kelly, Gavin, additional, Peat, Kema, additional, Kelly, Denise, additional, Murra, Aida, additional, Kelly, Kayleigh, additional, O'Flaherty, Molly, additional, Shea, Robyn L., additional, Gardner, Gail, additional, Murray, Darren, additional, Yousaf, Nadia, additional, Jhanji, Shaman, additional, As, Nicholas Van, additional, Young, Kate, additional, Furness, Andre J.S., additional, Pickering, Lisa, additional, Beale, Rupert, additional, Swanton, Charles, additional, Ghandi, Sonia, additional, Gamblin, Steve, additional, Bauer, David L.V., additional, Kassiotis, George, additional, Howell, Michael, additional, Nicholson, Emma, additional, Wilkinson, Robert J., additional, Larkin, James, additional, and Turajlic, Samra, additional

Published
2021
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37. Following the Franklin: using film footage ethnographically to study archaeological practice in Tasmania

Author

Kelly Denise Wiltshire

Subjects
Archeology, History, Actor–network theory, World heritage, History of archaeology, Archaeology, Knowledge production
Abstract

When archaeologists Rhys Jones, Jim Allen and others undertook archaeological investigations in the newly proclaimed World Heritage Area in southwest Tasmania following the Franklin River Dam campa...

Published
2019
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41. Adaptive immunity and neutralizing antibodies against SARS-CoV-2 variants of concern following vaccination in patients with cancer: The CAPTURE study

Author

Fendler, Annika, primary, Shepherd, Scott, additional, Au, Lewis, additional, Wilkinson, Katalin, additional, Wu, Mary, additional, Byrne, Fiona, additional, Cerrone, Maddalena, additional, Schmitt, Andreas, additional, Joharatnam-Hogan, Nalinie, additional, Shum, Ben, additional, Tippu, Zayd, additional, Rzeniewicz, Karolina, additional, Boos, Laura, additional, Harvey, Ruth, additional, Carlyle, Eleanor, additional, Edmonds, Kim, additional, Rosario, Lyra Del, additional, Sarker, Sarah, additional, Lingard, Karla, additional, Mangwende, Mary, additional, Holt, Lucy, additional, Ahmod, Hamid, additional, Koreweg, Justine, additional, Foley, Tara, additional, Bazin, Jessica, additional, Gordon, William, additional, Barber, Taja, additional, Emslie-Henry, Andrea, additional, Xie, Wenyi, additional, Gerard, Camille, additional, Deng, Daqi, additional, Wall, Emma, additional, Agua-Doce, Ana, additional, Namjou, Sina, additional, Caidan, Simon, additional, Gavrielides, Mike, additional, MacRae, James, additional, Kelly, Gavin, additional, Peat, Kema, additional, Kelly, Denise, additional, Murra, Aida, additional, Kelly, Kayleigh, additional, O'Flaherty, Molly, additional, Dowdie, Lauren, additional, Ash, Natalie, additional, Grounthoud, Firza, additional, Shea, Robyn, additional, Gardner, Gail, additional, Murray, Darren, additional, Kinnaird, Fiona, additional, Cui, Wanyuan, additional, Pascual, Javier, additional, Rodney, Simon, additional, Mencel, Justin, additional, Curtis, Olivia, additional, Stephenson, Clemency, additional, Robinson, Anna, additional, Oza, Bhavna, additional, Farag, Sheima, additional, Leslie, Isla, additional, Rogiers, Aljosja, additional, Lyengar, Sunil, additional, Ethell, Mark, additional, Messiou, Christina, additional, Cunningham, David, additional, Chau, Ian, additional, Starling, Naureen, additional, Turner, Nicholas, additional, Welsh, Liam, additional, As, Nicholas van, additional, Jones, Robin, additional, DRoney, Joanne, additional, Banerjee, Susana, additional, Tatham, Kate, additional, O'Brien, Mary, additional, Harrington, Kevin, additional, Bhide, Shreerang, additional, Okines, Alicia, additional, Reid, Alison, additional, Young, Kate, additional, Furness, Andrew, additional, Pickering, Lisa, additional, Swanton, Charles, additional, Gandhi, Sonia, additional, Gamblin, Steve, additional, Bauer, David, additional, Kassiotis, George, additional, Kumar, Sacheen, additional, Yousaf, Nadia, additional, Jhanji, Shaman, additional, Nicholson, Emma, additional, Howell, Michael, additional, Walker, Susanna, additional, Wilkinson, Robert, additional, Larkin, James, additional, and Turajlic, Samra, additional

Published
2021
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43. Does the ICMJE guideline for authorship need revising to support and recognize patient partnership? A cross-sectional survey of journal editor-in chief

Author

Kelly Denise Cobey, Zarah Monfaredi, Evelyn Poole, Laurie Proulx, Dean Ferguson, and David Moher

Abstract

Objectives: To measure medical journal Editor-in-Chiefs’ perceptions regarding including patients as (co-)authors on research publications and to measure their views on the application of the ICMJE authorship criteria to patient partners.Design: Cross-sectional survey co-developed with a patient partner Participants: Editor-in-Chiefs of medical journals were identified via a random sample of journals obtained from the Scopus source list, which contains all MEDLINE and EMBASE content. We restricted the Scopus source list to journals with a classification code of ‘Medicine’ and that were listed as active. Editor-in-Chiefs contact names and contact details were manually extracted from journal websites or obtained via online searching. Main outcome measures: The key outcome measures were whether Editor-in-Chiefs believed: 1) patient partners should be (co-)authors and; 2) whether they felt the ICMJE criteria for authorship required modification for use with patient partners. We also measured Editor-in-Chiefs description of how their journal’s operations incorporate patient partner perspectives. Results: 112 Editor-in-Chiefs responded to our survey (18.7% response rate; 66.69% male). Participants were able to skip any questions they did not want to answer, so there is missing data for some items. 69.2% (N = 74) of Editor-in-Chiefs indicated it was acceptable for patient partners to be authors or co-authors on published biomedical research articles, with the remaining 30.8% (N = 33) indicating this would not be appropriate. When asked specifically about the ICMJE authorship criteria, and whether this should be revised to be more inclusive of patient partners, 35.8% (N = 39) indicated it should be revised, 35.8% (N = 39) indicated it should not be revised, and 28.4% (N = 31) were unsure about a revision. Acceptability of the individual components of the ICMJE authorship criteria by Editor-in-Chiefs varied. 67.9% (N=74) of Editor-in-Chiefs felt a patient partner would likely be able to “give final approval a manuscript to be published” but only 42.6% (N = 46) of Editor-in-chiefs felt patient partners could be “accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved”. 74.1% (N = 80) of Editor-in-Chiefs did not think patients should be required to have an academic affiliation to published while 16.7% (N = 18) and 9.3% (N = 10) indicated they should or were unsure, respectively. 3.6% (N = 4) of Editor-in-Chiefs indicated their journal had a policy that specifies how patients or patient partners should be considered as authors. Conclusions: We found that a substantial proportion of medical journal Editor-in-Chiefs do not agree that patient partners should act as authors on publications, and that there is little consensus as to whether the ICMJE authorship criteria is appropriate for use with patient partners. Further, few journals involve patient or patient partners in the operations of their journal or have independent policy guidance around how authorship might apply to these groups. Access to, and awareness of, appropriate authorship criteria is an important right for patient partners to recognize contributions to research. Our findings highlight gaps that may act as barriers to patient partner participation in research.

Published
2021
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44. Sex-specific effects of aging on the humoral immune response to repeat vaccination with the high-dose seasonal influenza vaccine in older adults

Author

Shapiro, Janna R., primary, Li, Huifen, additional, Morgan, Rosemary, additional, Chen, Yiyin, additional, Kuo, Helen, additional, Ning, Xiaoxuan, additional, Shea, Patrick, additional, Wu, Cunjin, additional, Merport, Katherine, additional, Saldanha, Rayna, additional, Liu, Suifeng, additional, Abrams, Engle, additional, Chen, Yan, additional, Kelly, Denise C., additional, Sheridan-Malone, Eileen, additional, Wang, Lan, additional, Zeger, Scott L., additional, Klein, Sabra L., additional, and Leng, Sean X., additional

Published
2021
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45. Desarrollo de estrategias para la infraestructura de vecindarios sostenibles de la ciudad Cuenca-Ecuador a partir de marcos internacionales de evaluación

Author

Quesada Molina, Juan Felipe, Fernández Ochoa, Kelly Denise, Tobar Palacios, María Inés, Quesada Molina, Juan Felipe, Fernández Ochoa, Kelly Denise, and Tobar Palacios, María Inés

Abstract

In Latin America, residential areas located far from urban centers present limited conditions of basic infrastructure and utilities such as: energy, telecommunications, water resources and sanitation, which hinders local sustainable development. The development of sustainable infrastructure strategies is proposed, based on the international NSA (Neighborhood Sustainability Assessment Tools). With this goal in mind, the methodology of this thesis begins with studying the tools and applying their assessment to determine the level of sustainability of two case studies from Cuenca-Ecuador. Based on this, verifiable infrastructure strategies are proposed as guidelines and intervention proposals to improve the sustainability of the neighborhood with the most unfavorable rating. It is shown that by applying strategies based on the assessment tools, the level of sustainability of the selected neighborhood would be improved. These strategies can be applied in similar neighborhoods in Cuenca-Ecuador that aim to approach the ideal sustainable neighborhood. Finally, the implementation of urban design strategies for the infrastructure of neighborhoods based on the indicators of the NSA tools manages to promote sustainable development in the city.

Published
2021

46. Developing service provision for patients in primary care

Author

Martin, Jeannett, Black, Gillian, Cleverdon, Stephen, Kelly, Denise, Shanahan, Hilary, Kinnair, Donna, Southon, Sue, and Webb, Sue

Subjects
Methods, Laws, regulations and rules, Government regulation, Patient care -- Methods -- Laws, regulations and rules, Primary care nursing -- Laws, regulations and rules -- Methods, Community health services -- Laws, regulations and rules -- Methods, Patients -- Care and treatment, Primary nursing -- Laws, regulations and rules -- Methods
Abstract

Summary This article outlines the government's changes to the way that primary and community health services will be commissioned and provided. It also discusses the opportunities that exist for nurses [...]

Published
2007

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