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1. Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis

Author

Xie, Ouli, Morris, Jacqueline M., Hayes, Andrew J., Towers, Rebecca J., Jespersen, Magnus G., Lees, John A., Ben Zakour, Nouri L., Berking, Olga, Baines, Sarah L., Carter, Glen P., Tonkin-Hill, Gerry, Schrieber, Layla, McIntyre, Liam, Lacey, Jake A., James, Taylah B., Sriprakash, Kadaba S., Beatson, Scott A., Hasegawa, Tadao, Giffard, Phil, Steer, Andrew C., Batzloff, Michael R., Beall, Bernard W., Pinho, Marcos D., Ramirez, Mario, Bessen, Debra E., Dougan, Gordon, Bentley, Stephen D., Walker, Mark J., Currie, Bart J., Tong, Steven Y. C., McMillan, David J., and Davies, Mark R.

Published
2024
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2. Quantifying the common genetic variability of bacterial traits

Author

Mai, T. Tien, Tonkin-Hill, Gerry, Lees, John A., and Corander, Jukka

Subjects
Quantitative Biology - Genomics
Abstract

The study of common heritability, or co-heritability, among multiple traits has been widely established in quantitative and molecular genetics. However, in bacteria, genome-based estimation of heritability has only been considered very recently and no methods are currently available for considering co-heritability. Here we introduce such a method and demonstrate its usefulness by multi-trait analyses of the three major human pathogens \textit{Escherichia coli}, \textit{Neisseria gonorrhoeae} and \textit{Streprococcus pneumoniae}. We anticipate that the increased availability of high-throughput genomic and phenotypic screens of bacterial populations will spawn ample future opportunities to understand the common molecular basis of different traits in bacteria.

Published
2023

3. Inferring the heritability of bacterial traits in the era of machine learning

Author

Mai, The Tien, Lees, John A, Gladstone, Rebecca A, and Corander, Jukka

Subjects
Statistics - Applications, Quantitative Biology - Genomics
Abstract

Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for assessing the heritability of a trait have been developed in the field of quantitative genetics. However, the rise of modern population genomics with large sample sizes has led to the development of several new machine learning based approaches to inferring heritability. In this paper, we systematically summarize recent advances in machine learning which can be used to infer heritability. We focus on an application of these methods to bacterial genomes, where heritability plays a key role in understanding phenotypes such as antibiotic resistance and virulence, which are particularly important due to the rising frequency of antimicrobial resistance. By designing a heritability model incorporating realistic patterns of genome-wide linkage disequilibrium for a frequently recombining bacterial pathogen, we test the performance of a wide spectrum of different inference methods, including also GCTA. In addition to the synthetic data benchmark, we present a comparison of the methods for antibiotic resistance traits for multiple bacterial pathogens. Insights from the benchmarking and real data analyses indicate a highly variable performance of the different methods and suggest that heritability inference would likely benefit from tailoring of the methods to the specific genetic architecture of the target organism.

Published
2022
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4. A Not-Knowing, Values-Based and Relational Approach to Counselling Education

Author

Proctor, Gillian, Cahill, Jane, Gore, Stuart, Lees, John, and Shloim, Netalie

Abstract

In this paper, we present our development of a previously articulated approach to counselling education of transformational learning through a relational dynamic approach (Macaskie et al., 2013). We replace the idea of integration with a values-based approach and supplement the notion of transformational relational learning with a not-knowing attitude. This perspective on education and learning in counselling parallels the attitude within psychotherapy that we teach our students. We argue that this unites relational approaches to learning and psychotherapy across modalities and offers a trans-theoretical approach that could explain the common factors research in psychotherapy.

Published
2023
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10. CELEBRIMBOR: Pangenomes from metagenomes

Author

Hellewell, Joel, primary, Horsfield, Samuel T., additional, von Wachsmann, Johanna, additional, Gurbich, Tatiana, additional, Finn, Robert D., additional, Iqbal, Zamin, additional, Roberts, Leah W., additional, and Lees, John A., additional

Published
2024
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11. Fear of Losing It: An Auto-Ethnographic Case Study Exploring Re-Triggered Loss Experiences during Psychotherapy Training

Author

Bateson, Karen, Lees, John, Proctor, Gillian, and Shloim, Netalie

Abstract

The aim of this article is to explore loss experiences within a counselling and psychotherapy training arena, an environment that effects individual change. We use an auto-ethnographic case study format and data in the form of photographs, hybridised client material, journal entries and commentaries in order to reflexively consider loss material. We do this with a view to creating a narrative that enables readers to consider their emotions, thoughts and reactions to the material presented. We conclude that loss and grief can be re-triggered. Loss is inevitable. However, hidden loss affects the ability to manage change and has the potential to create transgenerational patterns.

Published
2021
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14. The Predictive Moment: Reverie, Connection and Predictive Processing

Author

McVey, Lynn, Nolan, Greg, and Lees, John

Abstract

According to the theory of predictive processing, understanding in the present involves non-consciously representing the immediate future, based on probabilistic inference shaped by learning from the past. This paper suggests links between this neuroscientific theory and the psychoanalytic concept of reverie -- an empathic, containing attentional state -- and considers implications for the ways therapists intuit implicit material in their clients. Using findings from a study about therapists' experiences of this state, we propose that reverie can offer practitioners from diverse theoretical backgrounds a means to enter the predictive moment deeply, making use of its subtle contents to connect with clients.

Published
2020
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18. Host and pathogen genetics associated with pneumococcal meningitis

Author

Lees, John Andrew, Bentley, Stephen Damien, Barrett, Jeffrey, and Parkhill, Julian

Subjects
616.8, meningitis, genome-wide association study, streptococcus pneumoniae, neisseria meningitidis, pneumococcus, bacteremia, human genetics, pathogen genomics, statistical genetics, within-host evolution, asymptomatic carriage, carriage duration, invasive disease
Abstract

Meningitis is an infection of the meninges, a layer of tissue surrounding the brain. In cases of pneumococcal meningitis (where the bacterium Streptococcus pneumoniae is the causat- ive agent) this causes severe inflammation, requiring intensive care and rapid antibiotic treatment. The contribution of variation in host and pathogen genetics to pneumococcal meningitis is unknown. In this thesis I develop and apply statistical genetics techniques to identify genomic variation associated with the various stages of pneumococcal meningitis, including colonisation, invasion and severity. I start by describing the development of a method to perform genome-wide association studies (GWAS) in bacteria, which can find variation in bacterial genomes associated with bacterial traits such as antibiotic resistance and virulence. I then applied this method to longitudinal samples from asymptomatic carriage, and found lineages and specific variants associated with altered duration of carriage. To assess meningitis versus carriage samples I applied similar analysis techniques, and found that the bacterial genome is crucial in determining invasive potential. As well as bacterial serotype, which I found to be the main effect, I discovered many independent sequence variants associated with disease. Separately, I analysed within host-diversity during the invasive phase of disease and found it to be of less relevance to disease progression. Finally, I analysed host genotype data from four independent studies using GWAS and heritability estimates to determine the contribution of human sequence variation to pneumococcal meningitis. Host sequence accounted for some variation in susceptibility to and severity of meningitis. The work concludes with a combined analysis of pairs of bacterial and human sequences from meningitis cases, and finds variation correlated between the two.

Published
2017
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19. Database of epidemic trends and control measures during the first wave of COVID-19 in mainland China

Author

Fu, Han, Wang, Haowei, Xi, Xiaoyue, Boonyasiri, Adhiratha, Wang, Yuanrong, Hinsley, Wes, Fraser, Keith J., McCabe, Ruth, Olivera Mesa, Daniela, Skarp, Janetta, Ledda, Alice, Dewé, Tamsin, Dighe, Amy, Winskill, Peter, van Elsland, Sabine L., Ainslie, Kylie E.C., Baguelin, Marc, Bhatt, Samir, Boyd, Olivia, Brazeau, Nicholas F., Cattarino, Lorenzo, Charles, Giovanni, Coupland, Helen, Cucunuba, Zulma M., Cuomo-Dannenburg, Gina, Donnelly, Christl A., Dorigatti, Ilaria, Eales, Oliver D., FitzJohn, Richard G., Flaxman, Seth, Gaythorpe, Katy A.M., Ghani, Azra C., Green, William D., Hamlet, Arran, Hauck, Katharina, Haw, David J., Jeffrey, Benjamin, Laydon, Daniel J., Lees, John A., Mellan, Thomas, Mishra, Swapnil, Nedjati-Gilani, Gemma, Nouvellet, Pierre, Okell, Lucy, Parag, Kris V., Ragonnet-Cronin, Manon, Riley, Steven, Schmit, Nora, Thompson, Hayley A., Unwin, H.Juliette T., Verity, Robert, Vollmer, Michaela A.C., Volz, Erik, Walker, Patrick G.T., Walters, Caroline E., Watson, Oliver J., Whittaker, Charles, Whittles, Lilith K., Imai, Natsuko, Bhatia, Sangeeta, and Ferguson, Neil M.

Published
2021
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22. Potential impact of the COVID-19 pandemic on HIV, tuberculosis, and malaria in low-income and middle-income countries: a modelling study

Author

Hogan, Alexandra B, Jewell, Britta L, Sherrard-Smith, Ellie, Vesga, Juan F, Watson, Oliver J, Whittaker, Charles, Hamlet, Arran, Smith, Jennifer A, Winskill, Peter, Verity, Robert, Baguelin, Marc, Lees, John A, Whittles, Lilith K, Ainslie, Kylie E C, Bhatt, Samir, Boonyasiri, Adhiratha, Brazeau, Nicholas F, Cattarino, Lorenzo, Cooper, Laura V, Coupland, Helen, Cuomo-Dannenburg, Gina, Dighe, Amy, Djaafara, Bimandra A, Donnelly, Christl A, Eaton, Jeff W, van Elsland, Sabine L, FitzJohn, Richard G, Fu, Han, Gaythorpe, Katy A M, Green, William, Haw, David J, Hayes, Sarah, Hinsley, Wes, Imai, Natsuko, Laydon, Daniel J, Mangal, Tara D, Mellan, Thomas A, Mishra, Swapnil, Nedjati-Gilani, Gemma, Parag, Kris V, Thompson, Hayley A, Unwin, H Juliette T, Vollmer, Michaela A C, Walters, Caroline E, Wang, Haowei, Wang, Yuanrong, Xi, Xiaoyue, Ferguson, Neil M, Okell, Lucy C, Churcher, Thomas S, Arinaminpathy, Nimalan, Ghani, Azra C, Walker, Patrick G T, and Hallett, Timothy B

Published
2020
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23. Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications

Author

Timme, Ruth E., primary, Karsch-Mizrachi, Ilene, additional, Waheed, Zahra, additional, Arita, Masanori, additional, MacCannell, Duncan, additional, Maguire, Finlay, additional, Petit III, Robert, additional, Page, Andrew J., additional, Mendes, Catarina Inês, additional, Nasar, Muhammad Ibtisam, additional, Oluniyi, Paul, additional, Tyler, Andrea D., additional, Raphenya, Amogelang R., additional, Guthrie, Jennifer L., additional, Olawoye, Idowu, additional, Rinck, Gabriele, additional, O’Cathail, Colman, additional, Lees, John, additional, Cochrane, Guy, additional, Cummins, Carla, additional, Brister, J. Rodney, additional, Klimke, William, additional, Feldgarden, Michael, additional, and Griffiths, Emma, additional

Published
2023
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26. Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillinresistant Staphylococcus aureus

Author

Copin, Richard, Sause, William E., Fulmer, Yi, Balasubramanian, Divya, Dyzenhaus, Sophie, Ahmed, Jamil M., Kumar, Krishan, Lees, John, Stachel, Anna, Fisher, Jason C., Drlica, Karl, Phillips, Michael, Weiser, Jeffrey N., Planet, Paul J., Uhlemann, Anne-Catrin, Altman, Deena R., Sebra, Robert, van Bakel, Harm, Lighter, Jennifer, Torres, Victor J., and Shopsin, Bo

Published
2019

27. Reduction in mobility and COVID-19 transmission

Author

Nouvellet, Pierre, Bhatia, Sangeeta, Cori, Anne, Ainslie, Kylie E. C., Baguelin, Marc, Bhatt, Samir, Boonyasiri, Adhiratha, Brazeau, Nicholas F., Cattarino, Lorenzo, Cooper, Laura V., Coupland, Helen, Cucunuba, Zulma M., Cuomo-Dannenburg, Gina, Dighe, Amy, Djaafara, Bimandra A., Dorigatti, Ilaria, Eales, Oliver D., van Elsland, Sabine L., Nascimento, Fabricia F., FitzJohn, Richard G., Gaythorpe, Katy A. M., Geidelberg, Lily, Green, William D., Hamlet, Arran, Hauck, Katharina, Hinsley, Wes, Imai, Natsuko, Jeffrey, Benjamin, Knock, Edward, Laydon, Daniel J., Lees, John A., Mangal, Tara, Mellan, Thomas A., Nedjati-Gilani, Gemma, Parag, Kris V., Pons-Salort, Margarita, Ragonnet-Cronin, Manon, Riley, Steven, Unwin, H. Juliette T., Verity, Robert, Vollmer, Michaela A. C., Volz, Erik, Walker, Patrick G. T., Walters, Caroline E., Wang, Haowei, Watson, Oliver J., Whittaker, Charles, Whittles, Lilith K., Xi, Xiaoyue, Ferguson, Neil M., and Donnelly, Christl A.

Published
2021
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28. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Author

Pöntinen, Anna K., Top, Janetta, Arredondo-Alonso, Sergio, Tonkin-Hill, Gerry, Freitas, Ana R., Novais, Carla, Gladstone, Rebecca A., Pesonen, Maiju, Meneses, Rodrigo, Pesonen, Henri, Lees, John A., Jamrozy, Dorota, Bentley, Stephen D., Lanza, Val F., Torres, Carmen, Peixe, Luisa, Coque, Teresa M., Parkhill, Julian, Schürch, Anita C., Willems, Rob J. L., and Corander, Jukka

Published
2021
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30. Immune exclusion by naturally acquired secretory IgA against pneumococcal pilus-1

Author

Binsker, Ulrike, Lees, John A., Hammond, Alexandria J., and Weiser, Jeffrey N.

Subjects
Thermo Fisher Scientific Inc., GraphPad Software Inc., Immunoglobulin A -- Health aspects, Software industry -- Health aspects, Scientific equipment industry -- Health aspects, Pathogenic microorganisms, Streptococcus pneumoniae, Health care industry
Abstract

Successful infection by mucosal pathogens requires overcoming the mucus barrier. To better understand this key step, we performed a survey of the interactions between human respiratory mucus and the human pathogen Streptococcus pneumoniae. Pneumococcal adherence to adult human nasal fluid was seen only by isolates expressing pilus-1. Robust binding was independent of pilus-1 adhesive properties but required Fab-dependent recognition of RrgB, the pilus shaft protein, by naturally acquired secretory IgA (sIgA). Pilus-1 binding by specific sIgA led to bacterial agglutination, but adherence required interaction of agglutinated pneumococci and entrapment in mucus particles. To test the effect of these interactions in vivo, pneumococci were preincubated with human sIgA before intranasal challenge in a mouse model of colonization. sIgA treatment resulted in rapid immune exclusion of pilus-expressing pneumococci. Our findings predict that immune exclusion would select for nonpiliated isolates in individuals who acquired RrgB-specific sIgA from prior episodes of colonization with piliated strains. Accordingly, genomic data comparing isolates carried by mothers and their children showed that mothers are less likely to be colonized with pilus-expressing strains. Our study provides a specific example of immune exclusion involving naturally acquired antibody in the human host, a major factor driving pneumococcal adaptation., Introduction Airway mucus plays a critical role in host defense by providing a physicochemical barrier that protects the underlying respiratory epithelium from inhaled particulate matter, including infectious agents (1, 2). [...]

Published
2020
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31. The potential public health consequences of COVID-19 on malaria in Africa

Author

Sherrard-Smith, Ellie, Hogan, Alexandra B., Hamlet, Arran, Watson, Oliver J., Whittaker, Charlie, Winskill, Peter, Ali, Fatima, Mohammad, Audu B., Uhomoibhi, Perpetua, Maikore, Ibrahim, Ogbulafor, Nnenna, Nikau, Jamilu, Kont, Mara D., Challenger, Joseph D., Verity, Robert, Lambert, Ben, Cairns, Matthew, Rao, Bhargavi, Baguelin, Marc, Whittles, Lilith K., Lees, John A., Bhatia, Sangeeta, Knock, Edward S., Okell, Lucy, Slater, Hannah C., Ghani, Azra C., Walker, Patrick G. T., Okoko, Okefu Oyale, and Churcher, Thomas S.

Published
2020
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32. Indices of Change: Analysing the Indexical Properties of Data from Psychotherapy Case Work to Discern Patterns of Therapeutic Change Over Time

Author

Hills, John, Cahill, Jane, Lees, John, Freshwater, Dawn, Kacprzyk, Janusz, Series editor, Pal, Nikhil R., Advisory editor, Bello Perez, Rafael, Advisory editor, Corchado, Emilio S., Advisory editor, Hagras, Hani, Advisory editor, Kóczy, László T., Advisory editor, Kreinovich, Vladik, Advisory editor, Lin, Chin-Teng, Advisory editor, Lu, Jie, Advisory editor, Melin, Patricia, Advisory editor, Nedjah, Nadia, Advisory editor, Nguyen, Ngoc Thanh, Advisory editor, Wang, Jun, Advisory editor, Costa, António Pedro, editor, Reis, Luís Paulo, editor, Souza, Francislê Neri de, editor, and Moreira, António, editor

Published
2018
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33. Psychosoma in Crisis: An Autoethnographic Study of Medically Unexplained Symptoms and Their Diverse Contexts

Author

Hills, John, Lees, John, Freshwater, Dawn, and Cahill, Jane

Abstract

In this study, we examine autoethnographic data from three critical incidents as experienced by the first author demonstrating the importance of context in understanding medically unexplained symptoms, their incidence and underlying patterns. We make the case for ethnographies as a crucial research strand in discerning the finer aspects of the patient or client experience; aspects that might be missed where people are directed along protocolised pathways of care. The article describes care as fragmented and depersonalising, leading to disembodied exchanges, as reflected in other autoethnographic studies, particularly those that highlight the complex relationship and controversies surrounding diagnostic uncertainty. We observe that psychological therapists, given the quality of the therapeutic relationship and sustained attention to the person's experience, are well placed to assist in the necessary processes of re-contextualisation and re-embodiment.

Published
2018
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34. Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study

Author

Brooks, Abdullah W, Corso, Alejandra, Davydov, Alexander, Maguire, Alison, Pollard, Andrew, Kiran, Anmol, Skoczynska, Anna, Moiane, Benild, Beall, Bernard, Sigauque, Betuel, Aanensen, David, Lehmann, Deborah, Faccone, Diego, Foster-Nyarko, Ebenezer, Bojang, Ebrima, Egorova, Ekaterina, Voropaeva, Elena, Sampane-Donkor, Eric, Sadowy, Ewa, Bigogo, Godfrey, Mucavele, Helio, Belabbès, Houria, Diawara, Idrissa, Moïsi, Jennifer, Verani, Jennifer, Keenan, Jeremy, Nair Thulasee Bhai, Jyothish N, Ndlangisa, Kedibone M, Zerouali, Khalid, Ravikumar, K L, Titov, Leonid, De Gouveia, Linda, Alaerts, Maaike, Ip, Margaret, de Cunto Brandileone, Maria Cristina, Hasanuzzaman, Md, Paragi, Metka, Nurse-Lucas, Michele, Ali, Mushal, Elmdaghri, Naima, Croucher, Nicholas, Wolter, Nicole, Porat, Nurit, Eser, Özgen Köseoglu, Akpaka, Patrick E, Turner, Paul, Gagetti, Paula, Tientcheu, Peggy-Estelle, Carter, Philip E, Mostowy, Rafal, Kandasamy, Rama, Ford, Rebecca, Henderson, Rebecca, Malaker, Roly, Shakoor, Sadia, Grassi Almeida, Samanta Cristine, Saha, Samir K, Doiphode, Sanjay, Madhi, Shabir A, Devi Sekaran, Shamala, Srifuengfung, Somporn, Obaro, Stephen, Clarke, Stuart C, Nzenze, Susan A, Kastrin, Tamara, Ochoa, Theresa J, Balaji, Veeraraghavan, Hryniewicz, Waleria, Urban, Yulia, Lo, Stephanie W, Gladstone, Rebecca A, van Tonder, Andries J, Lees, John A, du Plessis, Mignon, Benisty, Rachel, Givon-Lavi, Noga, Hawkins, Paulina A, Cornick, Jennifer E, Kwambana-Adams, Brenda, Law, Pierra Y, Ho, Pak Leung, Antonio, Martin, Everett, Dean B, Dagan, Ron, von Gottberg, Anne, Klugman, Keith P, McGee, Lesley, Breiman, Robert F, and Bentley, Stephen D

Published
2019
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37. Inter-species gene flow drives ongoing evolution ofStreptococcus pyogenesandStreptococcus dysgalactiaesubsp.equisimilis

Author

Xie, Ouli, primary, Morris, Jacqueline M., additional, Hayes, Andrew J., additional, Towers, Rebecca J., additional, Jespersen, Magnus G., additional, Lees, John A., additional, Ben Zakour, Nouri L., additional, Berking, Olga, additional, Baines, Sarah L., additional, Carter, Glen P., additional, Tonkin-Hill, Gerry, additional, Schrieber, Layla, additional, McIntyre, Liam, additional, Lacey, Jake A., additional, James, Taylah B., additional, Sriprakash, Kadaba S., additional, Beatson, Scott A., additional, Hasegawa, Tadao, additional, Giffard, Phil, additional, Steer, Andrew C., additional, Batzloff, Michael R., additional, Beall, Bernie W., additional, Pinho, Marcos D., additional, Ramirez, Mario, additional, Bessen, Debra E., additional, Dougan, Gordon, additional, Bentley, Stephen D., additional, Walker, Mark J., additional, Currie, Bart J., additional, Tong, Steven Y. C., additional, McMillan, David J., additional, and Davies, Mark R., additional

Published
2023
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39. Seasonal adaptations in the energetics and biomechanics of locomotion in the Svalbard rock ptarmigan (Lagopus muta hyperborea)

Author

Lees, John, Ennos, Anthony, and Codd, Jonathan

Subjects
598.6, Respirometry, Birds, Sexual selection, Locomotion, Jumping, Energetics, Arctic, Ptarmigan
Abstract

One of the most striking things about many animals is that they can be defined by the ways in which they move. Moving costs metabolic energy and is a significant contributor to the daily energy balance of organisms and therefore fitness. Balancing energy needs is critically important to species inhabiting areas of limited resources. The metabolic cost of locomotion is influenced by physiological, morphological and behavioural factors that vary across species. The influence of these factors within species is less well understood. The objective of my PhD is to elucidate the potential for variation in locomotor performance, in particular the energy consumed and the biomechanics of locomotion within a species, in response to differences in season, sex, age and the nature of the terrain. The Svalbard ptarmigan (Lagopus muta hyperborea) is the only year-round avian resident of the Arctic archipelago of Svalbard. Svalbard is characterized by extreme photoperiodic and climatic conditions, with 24 hours of daylight in summer and continuous darkness in winter, when ice makes food unpredictable. As a result, ptarmigan annually gain significant fat stores, as much as doubling their body mass in winter. The consequences of such large gains in mass upon the metabolic cost and biomechanics of terrestrial locomotion are yet to be quantified. The Svalbard ptarmigan represents a unique opportunity to gain insight into avian adaptations.Using respirometry, I present evidence that winter birds are able to carry their fat stores at no metabolic cost. Using kinematic and force plate data, I show that acquiring fat results in reduced locomotor performance in terms of speed and take-off ability. As well as exhibiting phenotypic variation, male and female Svalbard ptarmigan are behaviourally very different. I present evidence that these behavioural differences are reflected in the metabolic cost of locomotion. In particular, males are both more efficient and faster than female birds during both summer and winter. I suggest that this results from sexual selection upon male locomotor performance. Furthermore, I present data demonstrating that sub-adult males experiencing their first winter possess the same metabolic and speed capabilities of adults. These data may indicate that selection for improved male locomotor performance may act upon sub-adult birds. Regardless of season, age or sex, Svalbard ptarmigan must locomote on a predominantly sloping terrain. The influence of inclines upon the metabolic cost of locomotion in birds is poorly understood. I provide evidence that at the same degree of incline, the cost of lifting 1 kg by 1 vertical metre is similar regardless of season and is therefore dictated by increased positive work. However, this cost varies according to the degree of incline and may be influenced by gait.The principal findings of the 5 first author papers presented are that behavioural, physiological and morphological variation within a species can have significant impacts upon the metabolic cost of locomotion and other aspects of locomotor performance. The potential for intraspecific differences should therefore be taken into account in future research regarding the patterns of energy expenditure in animals.

Published
2013

40. Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

Author

Davies, Mark R., McIntyre, Liam, Mutreja, Ankur, Lacey, Jake A., Lees, John A., Towers, Rebecca J., Duchêne, Sebastián, Smeesters, Pierre R., Frost, Hannah R., Price, David J., Holden, Matthew T. G., David, Sophia, Giffard, Philip M., Worthing, Kate A., Seale, Anna C., Berkley, James A., Harris, Simon R., Rivera-Hernandez, Tania, Berking, Olga, Cork, Amanda J., Torres, Rosângela S. L. A., Lithgow, Trevor, Strugnell, Richard A., Bergmann, Rene, Nitsche-Schmitz, Patric, Chhatwal, Gusharan S., Bentley, Stephen D., Fraser, John D., Moreland, Nicole J., Carapetis, Jonathan R., Steer, Andrew C., Parkhill, Julian, Saul, Allan, Williamson, Deborah A., Currie, Bart J., Tong, Steven Y. C., Dougan, Gordon, and Walker, Mark J.

Published
2019
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42. State-level tracking of COVID-19 in the United States

Author

Unwin, H. Juliette T., Mishra, Swapnil, Bradley, Valerie C., Gandy, Axel, Mellan, Thomas A., Coupland, Helen, Ish-Horowicz, Jonathan, Vollmer, Michaela A. C., Whittaker, Charles, Filippi, Sarah L., Xi, Xiaoyue, Monod, Mélodie, Ratmann, Oliver, Hutchinson, Michael, Valka, Fabian, Zhu, Harrison, Hawryluk, Iwona, Milton, Philip, Ainslie, Kylie E. C., Baguelin, Marc, Boonyasiri, Adhiratha, Brazeau, Nick F., Cattarino, Lorenzo, Cucunuba, Zulma, Cuomo-Dannenburg, Gina, Dorigatti, Ilaria, Eales, Oliver D., Eaton, Jeffrey W., van Elsland, Sabine L., FitzJohn, Richard G., Gaythorpe, Katy A. M., Green, William, Hinsley, Wes, Jeffrey, Benjamin, Knock, Edward, Laydon, Daniel J., Lees, John, Nedjati-Gilani, Gemma, Nouvellet, Pierre, Okell, Lucy, Parag, Kris V., Siveroni, Igor, Thompson, Hayley A., Walker, Patrick, Walters, Caroline E., Watson, Oliver J., Whittles, Lilith K., Ghani, Azra C., Ferguson, Neil M., Riley, Steven, Donnelly, Christl A., Bhatt, Samir, and Flaxman, Seth

Published
2020
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45. A contribution to developing the counselling and psychotheraphy profession : a reflexive action research study

Author

Lees, John and Freshwater, Dawn

Subjects
616.89, RC Internal medicine
Abstract

This study has a manifest and a latent aspect. The manifest aspect tells a story about some key developments within the counselling and psychotherapy professions in recent years. 1 begin by looking at three phenomena which have been referred to as Schoolism, the research-practice gap and the hierarchy of evidence. I argue that it is important to address these phenomena as the profession moves towards statutory registration under the aegis of the Health Professions Council. I also argue that, in order to achieve this and develop a cohesive profession, traditional research methodologies which the profession promotes in, for example, such journals as Counselling and Psychotherapy Research, need to be supplemented by 'psychotherapeutic' research methodologies (or what, in academic terms, I have referred to as reflexive action research). In other words I posit that the adoption of both traditional and psychotherapeutic/reflexive action research methods will further the development of the profession, meet the aims of such organizations as the British Association for Counselling and Psychotherapy and address the issues of Schoolism, the gap and the hierarchy of evidence. I use psychotherapeutic/reflexive action research methodology as an integrating framework for examining professional experiential data with a view to bringing about change and transformation within the profession and as a way of incorporating a bricolage of methodologies - autobiographical and autoethnographic, heuristic, narrative, deconstructive, phenomenological, reflexive and action research. The latent aspect of the study engages in a discursive examination of some key discourses and knowledge systems within the profession. In so doing, I argue for an approach to research which emancipates practitioners from the confining web of professional discourses and methodological systems so that they can get in touch with their lived embodied professional experience. I thus examine the powerful influence of professional discourses, including my own, and incorporate the principles of critical theory as a means of becoming aware of the influence of these discourses and encouraging practitioners to liberate themselves from them in order to promote change and transformation within the profession. I also take the view that our understanding and activities are influenced for better or worse by our beliefs. Consequently all aspects of the study are influenced by my core belief – a spiritual monistic belief system called Anthroposophy - and, towards the end of the investigation, I attempt to make the relevance of this belief to research transparent and also engage in some reflection on the role of belief in professional life and activity generally and some of the contradictions and tensions in the text.

Published
2005

47. Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs

Author

Kuronen, Juri, Horsfield, Samuel T., Po¨ntinen, Anna K., Mallawaarachchi, Sudaraka, Arredondo-Alonso, Sergio, Thorpe, Harry, Gladstone, Rebecca A., Willems, Rob J.L., Bentley, Stephen D., Croucher, Nicholas J., Pensar, Johan, Lees, John A., Tonkin-Hill, Gerry, and Corander, Jukka

Abstract

Studies of bacterial adaptation and evolution are hampered by the difficulty of measuring traits such as virulence, drug resistance, and transmissibility in large populations. In contrast, it is now feasible to obtain high-quality complete assemblies of many bacterial genomes thanks to scalable high-accuracy long-read sequencing technologies. To exploit this opportunity, we introduce a phenotype- and alignment-free method for discovering coselected and epistatically interacting genomic variation from genome assemblies covering both core and accessory parts of genomes. Our approach uses a compact colored de Bruijn graph to approximate the intragenome distances between pairs of loci for a collection of bacterial genomes to account for the impacts of linkage disequilibrium (LD). We demonstrate the versatility of our approach to efficiently identify associations between loci linked with drug resistance and adaptation to the hospital niche in the major human bacterial pathogens Streptococcus pneumoniaeand Enterococcus faecalis.

Published
2024
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50. Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study

Author

Hadjirin, Nazreen F., primary, van Tonder, Andries J., additional, Blane, Beth, additional, Lees, John A., additional, Kumar, Narender, additional, Delappe, Niall, additional, Brennan, Wendy, additional, McGrath, Elaine, additional, Parkhill, Julian, additional, Cormican, Martin, additional, Peacock, Sharon J., additional, and Ludden, Catherine, additional

Published
2023
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