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4,641 results on '"Thomson, A. J."'

1. Multidimensional fatigue and its impact on work productivity, mood and quality of life in long-term survivors following definitive intensity-modulated radiotherapy for oropharyngeal cancer: A cross-sectional study

Author

Iyizoba-Ebozue, Zsuzsanna, Nicklin, Emma, Currie, Stuart, Price, James, Baldwin, J. P. C., Prestwich, Robin, Brown, Sarah, Hall, Emma, Lilley, John, Lowe, Matthew, Thomson, David J., Slevin, Finbar, Tyyger, Marcus, Murray, Louise, and Boele, Florien

Published
2025
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9. Systematic analysis of biomolecular conformational ensembles with PENSA.

Author

Vögele, Martin, Thomson, Neil J., Truong, Sang T., McAvity, Jasper, Zachariae, Ulrich, and Dror, Ron O.

Subjects
*CONFORMATIONAL analysis, *MOLECULAR conformation, *NUCLEIC acids, *FEATURE selection, *FLEXIBLE packaging
Abstract

Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions—for example, with various mutations or bound ligands—in order to identify differences between the molecular conformations adopted under these conditions. However, the large amount of data produced by simulations of ever larger and more complex systems often renders it difficult to identify the structural features that are relevant to a particular biochemical phenomenon. We present a flexible software package named Python ENSemble Analysis (PENSA) that enables a comprehensive and thorough investigation into biomolecular conformational ensembles. It provides featurization and feature transformations that allow for a complete representation of biomolecules such as proteins and nucleic acids, including water and ion binding sites, thus avoiding the bias that would come with manual feature selection. PENSA implements methods to systematically compare the distributions of molecular features across ensembles to find the significant differences between them and identify regions of interest. It also includes a novel approach to quantify the state-specific information between two regions of a biomolecule, which allows, for example, tracing information flow to identify allosteric pathways. PENSA also comes with convenient tools for loading data and visualizing results, making them quick to process and easy to interpret. PENSA is an open-source Python library maintained at https://github.com/drorlab/pensa along with an example workflow and a tutorial. We demonstrate its usefulness in real-world examples by showing how it helps us determine molecular mechanisms efficiently. [ABSTRACT FROM AUTHOR]

Published
2025
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10. Running Through the Haze: How Wildfire Smoke Affects Physical Activity and Mental Well-Being.

Author

Giles, Luisa V., Thomson, Cynthia J., Lesser, Iris, and Brandenburg, Jason P.

Subjects
GLOBAL warming, MENTAL health, AIR pollution, AIR quality, PHYSICAL activity
Abstract

Background: With a warming climate, extreme wildfires are more likely to occur, which may adversely affect air quality, physical activity (PA), and therefore, mental well-being. Methods: We assessed PA engagement and mental well-being between periods with and without wildfire smoke, and whether there were associations between changes in PA behavior and mental well-being. Questionnaires on PA and mental well-being during a period of wildfire smoke were completed by 348 participants; of these participants, 162 also completed a follow-up PA and mental well-being questionnaire during a period without wildfire smoke. Data were analyzed using generalized/linear mixed models. Relationships between mental well-being and PA were analyzed using repeated-measures correlations. Results: Leisure-time walking, moderate PA, and vigorous PA were all significantly lower during periods of smoke compared to periods without smoke. Participants also experienced significantly higher symptoms of stress (11.63 [1.91] vs 10.20 [1.70], P =.039), anxiety (7.75 [2.24] vs 4.38 [1.32], P <.001), and depression (9.67 [0.90] vs 7.27 [0.76], P <.001) during the period of wildfire smoke. Vigorous PA, the proportion of PA time spent outdoors, and the sum of PA during leisure time, were significantly negatively correlated with mental well-being, therefore, it is possible that PA could be used as a tool during times of wildfire smoke. Conclusions: These data suggest that PA and mental well-being are adversely impacted during wildfire smoke events. Future research should consider the impact of strategies to support PA during wildfire events on PA and mental well-being. [ABSTRACT FROM AUTHOR]

Published
2024
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17. A Pre–Post Study Design Exploring the Potential Benefits of a Hiking Intervention for Active and Inactive Older Adults.

Author

Lesser, Iris A. and Thomson, Cynthia J.

Abstract

Introduction: Physical activity (PA) is essential for healthy aging, yet PA levels are low in older adults. Group-based nature programming may be an ideal opportunity for engaging older adults in PA and improving health-related quality of life. Methods: Twenty-seven older adults, 55–75 years of age (n = 14 active and n = 13 previously inactive), enrolled in a biweekly 8-week hiking program. At baseline, participants completed online questionnaires on health-related quality of life, behavioral and psychological outcomes, and a one-mile walk test to assess cardiorespiratory fitness. Results: Average attendance was 81% in the previously inactive groups and 74% in the active group. There was a significant increase in the physical component of quality of life over time in the previously inactive group (p =.03, d = 0.71). Participants significantly improved their cardiorespiratory fitness (p =.003, d = 0.77) and competency (p =.005, d = 0.41) as assessed by the Basic Psychological Needs for Exercise Scale. The previously inactive group additionally increased their self-efficacy for exercise (p =.001, d = 1.43). Both active and previously inactive groups exercised at a similar relative intensity during the hikes based on heart rate; however, perceived exertion at the end of the hike on average was lower among active participants (p =.014). Conclusion: Group-based hiking for previously inactive older adults significantly improved physical health-related quality of life over an 8-week biweekly intervention. Hiking at an individualized pace may allow for hiking to be an appropriate PA program in previously inactive older adults. [ABSTRACT FROM AUTHOR]

Published
2025
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18. Distinct cell death pathways induced by granzymes collectively protect against intestinal Salmonella infection

Author

Chawla, Amanpreet Singh, Vandereyken, Maud, Arias, Maykel, Santiago, Llipsy, Dikovskaya, Dina, Nguyen, Chi, Skariah, Neema, Wenner, Nicolas, Golovchenko, Natasha B., Thomson, Sarah J., Ondari, Edna, Garzón-Tituaña, Marcela, Anderson, Christopher J., Bergkessel, Megan, C. D. Hinton, Jay, Edelblum, Karen L., Pardo, Julian, and Swamy, Mahima

Published
2024
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26. Assessment of endpoint definitions in curative-intent trials for mucosal head and neck squamous cell carcinomas: Head and Neck Cancer International Group consensus recommendations

Author

Lim, Annette M, McDowell, Lachlan, Hurt, Chris, Le Tourneau, Christophe, Homma, Akihiro, Shenouda, George, Thomson, David J, Moya-Plana, Antoine, Henson, Christina, Szturz, Petr, Day, Andrew T, Bates, James E, Lazarakis, Smaro, Thariat, Juliette, Psyrri, Amanda, Mehanna, Hisham, and Yom, Sue S

Published
2024
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29. Journalism Employability in the Modern Newsroom: Insights from Applicant Resumes and Cover Letters

Author

Thomson, T. J. and Sternberg, Jason

Abstract

What skills, attributes, and experiences are needed for a visual journalism job in a contemporary print and digital newsroom? Previous attempts at answering this question examine it through insights from hiring managers or news editors, often collected retrospectively or at arbitrary times of the year through surveys; analyses of position descriptions, which are often framed in normative terms; or through analyzing journalism curricula, which perpetually struggle to adapt nimbly to evolving industry demands. This signaling theory study adopts a novel approach by examining, through qualitative thematic analysis, all applicants' resumes and cover letters submitted by candidates for a visual journalism job posted in 2019. The hiring organization sought a candidate who could not only tell newsworthy stories through images but also one who could "write their own stories," "have strong organizational skills," and be "knowledgeable about current digital technology and applications for smartphone photography." The results provide insight into the types of applicants who apply to such a position; the skills, attributes, and experiences employers regard as worthy of shortlisting; and the strategies candidates adopted in addressing the position description and selection criteria.

Published
2022
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41. TORPEdO: A phase III trial of intensity-modulated proton beam therapy versus intensity-modulated radiotherapy for multi-toxicity reduction in oropharyngeal cancer

Author

Thomson, David J., Cruickshank, Clare, Baines, Helen, Banner, Russell, Beasley, Matthew, Betts, Guy, Bulbeck, Helen, Charlwood, Frances, Christian, Judith, Clarke, Matthew, Donnelly, Olly, Foran, Bernadette, Gillies, Callum, Griffin, Clare, Homer, Jarrod J., Langendijk, Johannes A., Lee, Lip Wai, Lester, James, Lowe, Matthew, McPartlin, Andrew, Miles, Elizabeth, Nutting, Christopher, Palaniappan, Nachi, Prestwich, Robin, Price, James M., Roberts, Clare, Roe, Justin, Shanmugasundaram, Ramkumar, Simões, Rita, Thompson, Anna, West, Catharine, Wilson, Lorna, Wolstenholme, Jane, and Hall, Emma

Published
2023
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45. Meta-GWAS identifies the heritability of acute radiation-induced toxicities in head and neck cancer

Author

Naderi, Elnaz, Schack, Line M.H., Welsh, Ceilidh, Sim, Adelene Y.L., Aguado-Barrera, Miguel E., Dudding, Tom, Summersgil, Holly, Martínez-Calvo, Laura, Ong, Enya H.W., Odding, Yasmin, Varela-Pazos, Ana, Steenbakkers, Roel J.H.M., Crijns, Anne P.G., Jena, Rajesh, Pring, Miranda, Dennis, Joe, Lobato-Busto, Ramón, Alsner, Jan, Ness, Andy, Nutting, Christopher, Thomson, David J, Gómez-Caamaño, Antonio, Eriksen, Jesper G., Thomas, Steve J., Bates, Amy M., Overgaard, Jens, Cascallar-Caneda, Luis M., Duprez, Fréderic, Barnett, Gillian C., Dorling, Leila, Chua, Melvin L.K., Vega, Ana, West, Catharine M.L., Langendijk, Johannes A., Nicolaj Andreassen, Christian, and Alizadeh, Behrooz Z.

Published
2022
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49. Surviving winter on the Qinghai-Tibetan Plateau : Pikas suppress energy demands and exploit yak feces to survive winter

Author

Speakman, John R., Chi, Qingsheng, Ołdakowski, Łukasz, Fu, Haibo, Fletcher, Quinn E., Hambly, Catherine, Togo, Jacques, Liu, Xinyu, Piertney, Stuart B., Wang, Xinghao, Zhang, Liangzhi, Redman, Paula, Wang, Lu, Tang, Gangbin, Li, Yongguo, Cui, Jianguo, Thomson, Peter J., Wang, Zengli, Glover, Paula, Robertson, Olivia C., Zhang, Yanming, and Wang, Dehua

Published
2021

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