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2. Frontmatter

Author

Johnson, Lauri, Finn, Mary E., and Lewis, Rebecca

Published
2005

3. Index

Author

Johnson, Lauri, Finn, Mary E., and Lewis, Rebecca

Published
2005

6. Contributors

Author

Johnson, Lauri, Finn, Mary E., and Lewis, Rebecca

Published
2005

19. Preface

Author

Johnson, Lauri, Finn, Mary E., and Lewis, Rebecca

Published
2005

25. Title Page

Author

Johnson, Lauri, Finn, Mary E., and Lewis, Rebecca

Published
2005

27. High-dimensional inference and confidence sets of models

Author

Lewis, Rebecca and Battey, Heather

Abstract

In high-dimensional regression problems, a key aim is to identify a sparse model that fits the data well. This may be used to form accurate predictions or to gain subject-matter understanding. When strong dependence is present among covariates, it is common for many models to fit the data equally well. Whilst it is sufficient to report a single model for prediction, when the goal is to gain subject-matter understanding, Cox & Battey (2017) argue that a confidence set of models - a set consisting of all models of appropriate fit - should be reported and propose a method to achieve this aim. This thesis provides a theoretical elucidation of this approach, and based on the results, explores further ideas in high-dimensional data analysis.

Published
2023
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28. Do mating traits evolve ex situ and should we care?

Author

Lewis, Rebecca, Shultz, Susanne, and Gilman, Robert

Subjects
Zoos, Birds, Conservation, Behaviour, Bioacoustics
Abstract

As a group, birds are facing continued declines in conservation status. As such, ex situ management is becoming a more widely used and important tool in conservation programmes. However, adaptation to captivity and behavioural change during ex situ breeding programmes may reduce the success of these interventions. Changes in mating traits, such as vocal behaviour, may be particularly important. In this thesis, I examine the potential for vocal evolution during ex situ conservation to determine how it could impact conservation efforts, focusing on the Java sparrow (Lonchura oryzivora), an endangered estrildid finch. Firstly, I examine the existing literature to determine how vocal behaviour could impact on conservation actions and how potential problems could be mitigated (Chapter 2). Vocal learning and the formation of population dialects have particular significance in conservation programmes due to their effects on important behaviours, such as mate choice. Java sparrows learn a number of components of their song, including song complexity and note acoustic structure (Chapter 3). Birds also learned many temporal features of song, such as tempo, the inheritance of which has been less frequently studied (Chapter 4). Given the importance of vocal learning in song development, there is a high potential for vocal change and population divergence during ex situ breeding in this species. Such differences are important for mate preference; Java sparrow females preferred familiar, over unfamiliar, songs (Chapter 5). Preference for familiar songs may result in assortative mating between individuals of different population origin during conservation efforts, reducing the effectiveness of conservation programmes. As well as behavioural changes, other phenotypic changes may occur in captivity. Captive Java sparrows were both larger and had greater sexual size dimorphism than those of wild origin (Chapter 6). Morphological changes during captive breeding may reduce the performance of captive-bred individuals in wild environments, as well as affecting other, correlated traits, such as vocal behaviour. Vocal behaviour may also be affected by altered sound environments experienced by birds during ex situ breeding programmes. Human presence has a significant effect on the zoo soundscape; reduction in human presence during the COVID-19 lockdown was associated with a number of changes in the sound environment (Chapter 7). Overall, there is significant potential for vocal evolution during the captive breeding of Java sparrows, mediated by cultural processes resulting from social learning of vocalizations, environmental differences, and other, correlated changes. Changes in vocal behaviour in the Java sparrow could affect conservation programmes due to preferences for familiar vocalizations in this species by contributing to assortative mating. The findings from this species suggest that vocal behaviour can have an important role in the success of conservation efforts and requires further investigation in this and other species.

Published
2023

30. Mindfulness as Art Education, Self-Inquiry, and Artmaking

Author

Graham, Mark A. and Lewis, Rebecca

Abstract

This article presents an overview and continuation of a study investigating how artist awareness and critical response might provide a better understanding of mindfulness and its practice within art education. While there are distinct advantages to mindfulness practices in education, these practices might also have problematic aspects, such as helping people conform to oppressive structures in education rather than questioning them. The pandemic of 2020-2021 accentuated student concerns with social, emotional, and mental health and illuminated possible benefits of mindfulness practice. Results show that preservice art education students used mindfulness and data visualization to connect art and self-inquiry. Important findings included the positive impact mindfulness practices had on students' social-emotional learning and a refined distinction between mindfulness as a therapeutic educational intervention versus mindfulness an art educational experience.

Published
2023
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31. What are oxytocin assays measuring? Epitope mapping, metabolites, and comparisons of wildtype & knockout mouse urine.

Author

Gnanadesikan, Gitanjali, Hammock, Elizabeth, Tecot, Stacey, Lewis, Rebecca, Hart, Russ, MacLean, Evan, and Carter, Cameron

Subjects
ELISA, Knockout mice, Matrix interference, Oxytocin, Solid-phase extraction, Urine, Animals, Epitope Mapping, Epitopes, Immunoassay, Mice, Mice, Knockout, Oxytocin
Abstract

Oxytocin has become a popular analyte in behavioral endocrinology in recent years, due in part to its roles in social behavior, stress physiology, and cognition. Urine samples have the advantage of being non-invasive and minimally disruptive to collect, allowing for oxytocin measurements even in some wild populations. However, methods for urinary oxytocin immunoassay have not been sufficiently optimized and rigorously assessed for their potential limitations. Using samples from oxytocin knockout (KO) and wildtype (WT) mice, we find evidence of considerable interference in unextracted urine samples, with similar distributions of measured oxytocin in both genotypes. Importantly, although this interference can be reduced by a reversed-phase solid-phase extraction (SPE), this common approach is not sufficient for eliminating false-positive signal on three immunoassay kits. To better understand the source of the observed interference, we conducted epitope mapping of the Arbor Assays antibody and assessed its cross-reactivity with known, biologically active fragments of oxytocin. We found considerable cross-reactivity (0.5-52% by-molarity) for three fragments of oxytocin that share the core epitope, with more cross-reactivity for longer fragments. Given the presence of some cross-reactivity for even the tripeptide MIF-1, it is likely that many small protein metabolites might be sufficiently similar to the epitope that at high concentrations they interfere with immunoassays. We present a new mixed-mode cation-exchange SPE method that minimizes interference-with knockout samples measuring below the assays limit of detection-while effectively retaining oxytocin from the urine of wildtype mice. This method demonstrates good parallelism and spike recovery across multiple species (mice, dogs, sifakas, humans). Our results suggest that immunoassays of urine samples may be particularly susceptible to interference, even when using common extraction protocols, but that this interference can be successfully managed using a novel mixed-mode cation exchange extraction. These findings imply that previous conclusions based on urinary oxytocin measurements-especially those involving unextracted samples-may need to be reassessed.

Published
2022

32. Large Comparative Analyses of Primate Body Site Microbiomes Indicate that the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates

Author

Asangba, Abigail E, Mugisha, Lawrence, Rukundo, Joshua, Lewis, Rebecca J, Halajian, Ali, Cortés-Ortiz, Liliana, Junge, Randall E, Irwin, Mitchell T, Karlson, Johan, Perkin, Andrew, Watsa, Mrinalini, Erkenswick, Gideon, Bales, Karen L, Patton, Dorothy L, Jasinska, Anna J, Fernandez-Duque, Eduardo, Leigh, Steven R, and Stumpf, Rebecca M

Subjects
Microbiology, Biological Sciences, Genetics, Dental/Oral and Craniofacial Disease, Human Genome, Aetiology, 2.2 Factors relating to the physical environment, Animals, Bacteria, Gastrointestinal Microbiome, Mammals, Microbiota, Phylogeny, Primates, microbiome, nonhuman primates, variation
Abstract

The study of the mammalian microbiome serves as a critical tool for understanding host-microbial diversity and coevolution and the impact of bacterial communities on host health. While studies of specific microbial systems (e.g., in the human gut) have rapidly increased, large knowledge gaps remain, hindering our understanding of the determinants and levels of variation in microbiomes across multiple body sites and host species. Here, we compare microbiome community compositions from eight distinct body sites among 17 phylogenetically diverse species of nonhuman primates (NHPs), representing the largest comparative study of microbial diversity across primate host species and body sites. Analysis of 898 samples predominantly acquired in the wild demonstrated that oral microbiomes were unique in their clustering, with distinctive divergence from all other body site microbiomes. In contrast, all other body site microbiomes clustered principally by host species and differentiated by body site within host species. These results highlight two key findings: (i) the oral microbiome is unique compared to all other body site microbiomes and conserved among diverse nonhuman primates, despite their considerable dietary and phylogenetic differences, and (ii) assessments of the determinants of host-microbial diversity are relative to the level of the comparison (i.e., intra-/inter-body site, -host species, and -individual), emphasizing the need for broader comparative microbial analyses across diverse hosts to further elucidate host-microbial dynamics, evolutionary and biological patterns of variation, and implications for human-microbial coevolution. IMPORTANCE The microbiome is critical to host health and disease, but much remains unknown about the determinants, levels, and evolution of host-microbial diversity. The relationship between hosts and their associated microbes is complex. Most studies to date have focused on the gut microbiome; however, large gaps remain in our understanding of host-microbial diversity, coevolution, and levels of variation in microbiomes across multiple body sites and host species. To better understand the patterns of variation and evolutionary context of host-microbial communities, we conducted one of the largest comparative studies to date, which indicated that the oral microbiome was distinct from the microbiomes of all other body sites and convergent across host species, suggesting conserved niche specialization within the Primates order. We also show the importance of host species differences in shaping the microbiome within specific body sites. This large, comparative study contributes valuable information on key patterns of variation among hosts and body sites, with implications for understanding host-microbial dynamics and human-microbial coevolution.

Published
2022

37. A national multicentre study of outcomes and patient satisfaction with the virtual fracture clinic and the influence of the COVID-19 pandemic: The MAVCOV study

Author

Brown, Jonathon, Lim, Jun Wei, Smith, Matthew, Lau, Nicole, Kamaraj, Achi, Zhou, Andrew, Lim, Jiang An, Jenkins, Lydia, Tennyson, Maria, Khan, Wasim, Foster, Amy, Rutherfoord, Catharine, Nathoo, Nikita, Domos, Peter, Padwick, Thomas, White, William, Robinson, Andrew, Vusirikala, Anuhya, Ensor, David, Akula, Maheswara, Vignaraja, Vikram, Rogers, Benedict, Kalabi, Fatemeh, Chan, Gareth, Clayton-Yeomans, Jacob, Gibbs, James, Titheradge, Rachel, Spalvieri, Stefano, Nair, Abhinav, Nathwani, Dinesh, Selvakumar, Jashan, Wihba, Kinan, Zakieh, Omar, Park, Andrew, Crewe, Claire, Ayeni, Funbi, Prowse, James, Kumar, Pradeep, Akinyemi, Tosin, Solim, Zahirah Nahaboo, Shaerf, Daniel, Sheikh, Hamza, Poustie, Mark, Rai, Sumnima, Birole, Umesh, Russell, Aimee, Loh, Cheryl, Drury, Colin, Cemm, Nicholas, Pravinkumar, Ruth, Baig, Saira, Bigsby, Ewan, Sellers, Grace, Dow, Joseph, Jenner, Lydia, Rogers, Michaela, Rankin, Sally, Mangtani, Anisha, Brameier, Devon, Rooker, Jemma, Anwer, Mohammed Azher, Kumar, Nakulan Nantha, Lam, Ryan, Andronic, Adrian, Phillips, Hannah, Attwood, Joe, Sturdee, Simon, Panagiotopoulos, Andreas, McVie, James, Boylan, Luke, Reid, Michael, Cheekoty, Prashasth, Edwards, Rebecca, Lindh, Amy, Kettle, Sarah, Genena, Ahmed, Hourston, George, Gopaul, Steven, Garg, Sunil, Gowers, Benjamin, Lennox-Warburton, Hannah, Sambhwani, Sharan, Shyamsundar, Srinivasan, Srinivasan, Suresh, Tavakkolizadeh, Adel, Petohazi, Alexandra, O'Hanlon, Ciaran, Everton, Harry Donkin, Pilkington, Isobel, Graziadei, Vivien, Anwar, Walid, Wignall, Alice, Jassal, Arun, Ilyas, Haris, Palan, Jeya, Monkhouse, Ray, Nijamudeen, Aysha, Caruana, Ethan, Gilbody, Julian, Malik, Maymunah, Saadat, Waqar, Yusuf, Karshe, Davies, Kimberley, Mueller, Marion, Tint, Pyi Han, Sengupta, Shreya, James, Andrew, Virji, Faizan, Bond, Gemma, Thumbadoo, Ruben, Teng, Wai Huang, Gee, Christopher, Warren, Craig, Nair, Gopikrishnan, Bohler, Iain, Periasamy, Kumar, Liao, Quintin, Ramasubbu, Rohan, Baston, Tessa, Witek, Alexander, Parwaiz, Hammad, Williams, James, Aboelmagd, Karim, Haines, Samuel, Bänziger, Carina, Harrold, Fraser, Abishek, Joshua, Davies, Peter, Pennington, Rachel, Parulekar, Ramaa, Sinnerton, Robert, Ravury, Sheetal, Macdonald, Angus, Emmerson, Benjamin, Inman, Dominic, Moedbeck, Edwina, Barber, Margaret, Jaiswal, Sharlene, Lewis, Rebecca, Downie, Samantha, Ng, Samantha, Shue, Wan Nee, Fosu, Augustine, Ko, Chai Chi, Lewis, Charlotte, Thiruchandran, Gajendiran, Jain, Siddharth, Ng, Zhаn, Wilson, Christopher, Toh, Ching, Miller, Gillian, Duncan, Katherine, McKee, Lesley, Mitchell, Martin, Ferguson, David, Hambidge, John, Wickramarachchi, Lilanthi, Abouelela, Amr, Hong, Anna, Oo, Aung Phyo, Kitsis, Christos, Elgalli, Mosab, Aros-Atolagbe, Robert, Clement, Adeline, Gibb, Catriona, Goffin, Joaquim, Jalal, Murtadhah, Leung, Billy, Neal-Smith, Gregory, Khatkar, Harman, Maher, Mark, Davies, Neville, Aboelmagd, Tariq, Jarrat, Jeremy, McKay, Joseph, Walmsley, Matthew, Greenhalgh, Michael, McCabe-Robinson, Olivia, Berry, Alexander, Iftinca, Dorin, Easwaran, Palakkad, Patel, Akash, Awow, Fatima, Pan, Myat, Patel, Nikhil, Khanal, Pragalva, Wagner, Boris, Athawes, Kirsten, Makaram, Navnit, Hegde, Rutwik, White, Tim, Williamson, Thomas, McAskill, Victoria, Stevens, Chloe, Malagelada, Francesc, Nasser, Mohammad Zeeshan, Ogunfuye, Omodolapo, Zahoor, Ubaid, Rogers, Gareth, Telford, Jeremy, Cowie, Jonathan, Hoggett, Lee, Havenhand, Tom, Do, Anh Duy, Cross, Charlotte, Morris, James, Hunter, Joel, Nabahin, Maram, Choudhary, Tashi, Campbell, Aaron, Mercer, Alexandra, Deyermond, Chloe, Fowler, Chris, McGoldrick, Peter, McCormac, Philip, Kakar, Sahil, McKenna, Sean, Boutros, Ihab, Vial, Izziddine, Bhullar, Samraj, Lyle, Victoria, Thomas, Alexander, Shean, Kate, Jacobs, Neal, Townsend, Oliver, Sharma, Akshara, van der Broeck, Alyssa, Hartley, Laura, O'Riordan, Marguerite, Gella, Sreenadh, Adlawan, Anjeli, Ijaz, Arhum, Al-kamali, Aws, Livesey, Jon, Yeshitila, Natania, Thayaparan, Anthony, Hayter, Edward, McLean, Elizabeth, Davies, Jessica, Walker, Joseph, Anakwe, Raymond, Fell, Adam, Haque, Aniqa, Sobti, Anshul, Jacob, Joshua, Moore, Thomas, Bhandari, Farzaan, Boitnott, Jasmine, Cheong, Jeremy, Lim, Wei Boon, Michla, Yusuf, Gilmore, Catherine, McConway, Jim, Elliott, Jonathan, Khan, Azizah, Madhu, Divine, Yusuf, Hannah, Gibby, Mary Louise, Thomas, Phillip, Abdel-Fattah, Areej, Martinson, Eliott, Akhtar, Muhammad Adeel, Hossain, Fahad, Ismayl, Ghiath, Khadabadi, Nikhil, Moores, Thomas, Goude, William, Ibrahim, Edward, Sivaganesh, Karthikeyan, Ogunjimi, Michael, Wilson, Michael, Shah, Sachi, McCluskey, Aled, Zakaria, Benjamin, Berber, Onur, Cuthbert, Rory, Mergia, Teresa, Khawaja, Abdullah, Hayman, Gregory, Relwani, Jai, Shaeir, Mohammed, Shah, Sohail, Peach, Christopher, Cook, Edward, Helston, Olivia, Koh, Yun Jee, Ng, Zhan H., Makaram, Navnit S., Kolhe, Shivam N., Mackenzie, Samuel P., Clement, Nick D., Duckworth, Andrew D., and White, Tim O.

Published
2024
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