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1,115 results on '"Beesley, P."'

1. Measurements of a LYSO crystal array from threshold to 100 MeV

Author

Beesley, O., Carlton, J., Davis-Purcell, B., Ding, D., Foster, S., Frahm, K., Gibbons, L., Gorringe, T., Hertzog, D. W., Hochrein, S., Hui, J., Kammel, P., LaBounty, J., Liu, J., Roehnelt, R., Schwendimann, P., Soter, A., Swanson, E., and Taylor, B.

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment, Nuclear Experiment
Abstract

We report measurements of ten custom-made high-homogeneity LYSO crystals. The investigation is motivated by the need for a compact, high-resolution, and fast electromagnetic calorimeter for a new rare pion decay experiment. Each $2.5\times 2.5 \times 18$ cm$^3$ crystal was first characterized for general light yield properties and then its longitudinal response uniformity and energy resolution were measured using low-energy gamma sources. The ten crystals were assembled as an array and subjected to a 30 - 100 MeV positron beam with excellent momentum definition. The energy and timing resolutions were measured as a function of energy, and the spatial resolution was determined at 70 MeV. An additional measurement using monoenergetic 17.6 MeV gammas produced through a p-Li resonance was later made after the photosensors used in positron testing were improved. As an example of the results, the energy resolution at 70 MeV of 1.80 $\pm$ 0.05% is more than two times better than reported results using previous generation LYSO crystals.

Published
2024

2. Monotonic warpings for additive and deep Gaussian processes

Author

Barnett, Steven D., Beesley, Lauren J., Booth, Annie S., Gramacy, Robert B., and Osthus, Dave

Subjects
Statistics - Computation
Abstract

Gaussian processes (GPs) are canonical as surrogates for computer experiments because they enjoy a degree of analytic tractability. But that breaks when the response surface is constrained, say to be monotonic. Here, we provide a mono-GP construction for a single input that is highly efficient even though the calculations are non-analytic. Key ingredients include transformation of a reference process and elliptical slice sampling. We then show how mono-GP may be deployed effectively in two ways. One is additive, extending monotonicity to more inputs; the other is as a prior on injective latent warping variables in a deep Gaussian process for (non-monotonic, multi-input) non-stationary surrogate modeling. We provide illustrative and benchmarking examples throughout, showing that our methods yield improved performance over the state-of-the-art on examples from those two classes of problems.

Published
2024

3. Mapping Incidence and Prevalence Peak Data for SIR Forecasting Applications

Author

Murph, Alexander C., Gibson, G. Casey, Beesley, Lauren J., Panda, Nishant, Castro, Lauren A., Del Valle, Sara Y., and Osthus, Dave

Subjects
Statistics - Methodology, Statistics - Applications
Abstract

Infectious disease modeling and forecasting have played a key role in helping assess and respond to epidemics and pandemics. Recent work has leveraged data on disease peak infection and peak hospital incidence to fit compartmental models for the purpose of forecasting and describing the dynamics of a disease outbreak. Incorporating these data can greatly stabilize a compartmental model fit on early observations, where slight perturbations in the data may lead to model fits that project wildly unrealistic peak infection. We introduce a new method for incorporating historic data on the value and time of peak incidence of hospitalization into the fit for a Susceptible-Infectious-Recovered (SIR) model by formulating the relationship between an SIR model's starting parameters and peak incidence as a system of two equations that can be solved computationally. This approach is assessed for practicality in terms of accuracy and speed of computation via simulation. To exhibit the modeling potential, we update the Dirichlet-Beta State Space modeling framework to use hospital incidence data, as this framework was previously formulated to incorporate only data on total infections.

Published
2024

5. Moving Towards Automated Interstellar Boundary Explorer Data Selection with LOTUS

Author

Stricklin, Madeline A., Beesley, Lauren J., Weaver, Brian P., Moran, Kelly R., Osthus, Dave, Janzen, Paul H., Meadors, Grant David, and Reisenfeld, Daniel B.

Subjects
Statistics - Applications, Astrophysics - Astrophysics of Galaxies, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics
Abstract

The Interstellar Boundary Explorer (IBEX) satellite collects data on energetic neutral atoms (ENAs) that provide insight into the heliosphere, the region surrounding our solar system and separating it from interstellar space. IBEX collects information on these particles and on extraneous ``background'' particles. While IBEX records how and when the different particles are observed, it does not distinguish between heliospheric ENA particles and incidental background particles. To address this issue, all IBEX data has historically been manually labeled as ``good'' ENA data, or ``bad'' background data. This manual culling process is incredibly time-intensive and contingent on subjective, manually-induced decision thresholds. In this paper, we develop a three-stage automated culling process, called LOTUS, that uses random forests to expedite and standardize the labelling process. In Stage 1, LOTUS uses random forests to obtain probabilities of observing true ENA particles on a per-observation basis. In Stage 2, LOTUS aggregates these probabilities to obtain predictions within small windows of time. In Stage 3, LOTUS refines these predictions. We compare the labels generated by LOTUS to those manually generated by the subject matter expert. We use various metrics to demonstrate that LOTUS is a useful automated process for supplementing and standardizing the manual culling process.

Published
2024

7. USP50 suppresses alternative RecQ helicase use and deleterious DNA2 activity during replication

Author

Mackay, Hannah L., Stone, Helen R., Ronson, George E., Ellis, Katherine, Lanz, Alexander, Aghabi, Yara, Walker, Alexandra K., Starowicz, Katarzyna, Garvin, Alexander J., Van Eijk, Patrick, Koestler, Stefan A., Anthony, Elizabeth J., Piberger, Ann Liza, Chauhan, Anoop S., Conway-Thomas, Poppy, Vaitsiankova, Alina, Vijayendran, Sobana, Beesley, James F., Petermann, Eva, Brown, Eric J., Densham, Ruth M., Reed, Simon H., Dobbs, Felix, Saponaro, Marco, and Morris, Joanna R.

Published
2024
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10. USP50 suppresses alternative RecQ helicase use and deleterious DNA2 activity during replication

Author

Hannah L. Mackay, Helen R. Stone, George E. Ronson, Katherine Ellis, Alexander Lanz, Yara Aghabi, Alexandra K. Walker, Katarzyna Starowicz, Alexander J. Garvin, Patrick Van Eijk, Stefan A. Koestler, Elizabeth J. Anthony, Ann Liza Piberger, Anoop S. Chauhan, Poppy Conway-Thomas, Alina Vaitsiankova, Sobana Vijayendran, James F. Beesley, Eva Petermann, Eric J. Brown, Ruth M. Densham, Simon H. Reed, Felix Dobbs, Marco Saponaro, and Joanna R. Morris

Subjects
Science
Abstract

Abstract Mammalian DNA replication relies on various DNA helicase and nuclease activities to ensure accurate genetic duplication, but how different helicase and nuclease activities are properly directed remains unclear. Here, we identify the ubiquitin-specific protease, USP50, as a chromatin-associated protein required to promote ongoing replication, fork restart, telomere maintenance, cellular survival following hydroxyurea or pyridostatin treatment, and suppression of DNA breaks near GC-rich sequences. We find that USP50 supports proper WRN-FEN1 localisation at or near stalled replication forks. Nascent DNA in cells lacking USP50 shows increased association of the DNA2 nuclease and RECQL4 and RECQL5 helicases and replication defects in cells lacking USP50, or FEN1 are driven by these proteins. Consequently, suppression of DNA2 or RECQL4/5 improves USP50-depleted cell resistance to agents inducing replicative stress and restores telomere stability. These data define an unexpected regulatory protein that promotes the balance of helicase and nuclease use at ongoing and stalled replication forks.

Published
2024
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11. Evaluation of the McGill‐Tongji Blended Education Program for Teacher Leaders in General Practice: The importance of partnership and contextualization in International Primary Care Training Initiatives

Author

Ziyue Wang, Xinxin Zhao, Huixia Shen, Hao Wang, Gemma Cheng, Ya Ning Gao, Wenzhen Zuo, Zhuyin Xu, Francesco Avallone, Anish K. Arora, Manxi Guo, Rachel Simmons, David Lessard, Theresa Beesley, Jialin C. Zheng, Bertrand Lebouché, and Howard Bergman

Subjects
primary care, general practice, continuing professional development, contextualization, international partnership, Public aspects of medicine, RA1-1270
Abstract

Abstract Purpose Strong primary health care (PHC) systems require well‐established PHC education systems to enhance the skills of general practitioners (GPs). However, the literature on the experiences of international collaboration in primary care education in low‐ and middle‐income countries remains limited. The purpose of this study was to evaluate the implementation and perceived impact of the McGill‐Tongji Blended Education Program for Teacher Leaders in General Practice (referred to as the “Tongji Program”). Methods In 2020–2021, the McGill Department of Family Medicine (Montreal, Canada) and Tongji University School of Medicine (TUSM, Shanghai, China) jointly implemented the Tongji Program in Shanghai, China to improve the teaching capacity of PHC teachers. We conducted an exploratory longitudinal case study with a mixed methods design for the evaluation. Quantitative (QUAN) data was collected through questionnaire surveys and qualitative (QUAL) data was collected through focus group discussions. Results The evaluation showed that learners in Tongji Program were primarily female GPs (21/22，95%) with less than 4 years of experience in teaching (16/22，73%). This program was considered a successful learning experience by most participants (19/22, 86%) with higher order learning tasks such as critical thinking and problem‐solving. They also agreed that this program helped them feel more prepared to teach (21/22，95%), and developed a positive attitude toward primary care (21/22，95%). The QUAL interview revealed that both the Tongji and McGill organizers noted that TUSM showed strong leadership in organization, education, and coordination. Both students and teachers agreed that by adapting training content into contextualized delivery formats and settings, the Tongji Program successfully overcame language and technology barriers. Conclusions Committed partnerships and contextualization were key to the success of the Tongji Program. Future research should focus on how international primary care education programs affect learners' behavior in their practice settings, and explore barriers and facilitators to change.

Published
2024
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12. Association of the CHEK2 c.1100delC variant, radiotherapy, and systemic treatment with contralateral breast cancer risk and breast cancer‐specific survival

Author

Morra, Anna, Schreurs, Maartje AC, Andrulis, Irene L, Anton‐Culver, Hoda, Augustinsson, Annelie, Beckmann, Matthias W, Behrens, Sabine, Bojesen, Stig E, Bolla, Manjeet K, Brauch, Hiltrud, Broeks, Annegien, Buys, Saundra S, Camp, Nicola J, Castelao, Jose E, Cessna, Melissa H, Chang‐Claude, Jenny, Chung, Wendy K, Sahlberg, Kristine K, Børresen‐Dale, Anne‐Lise, Gram, Inger Torhild, Olsen, Karina Standahl, Engebråten, Olav, Naume, Bjørn, Geisler, Jürgen, OSBREAC, Alnæs, Grethe I Grenaker, Colonna, Sarah V, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, Dennis, Joe, Devilee, Peter, Dörk, Thilo, Dunning, Alison M, Dwek, Miriam, Easton, Douglas F, Eccles, Diana M, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Fehm, Tanja N, Figueroa, Jonine D, Flyger, Henrik, Gabrielson, Marike, Gago‐Dominguez, Manuela, García‐Closas, Montserrat, García‐Sáenz, José A, Genkinger, Jeanine, Grassmann, Felix, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A, Hamann, Ute, Harrington, Patricia A, Hartikainen, Jaana M, Hoppe, Reiner, Hopper, John L, Houlston, Richard S, Howell, Anthony, Clarke, Christine, Marsh, Deborah, Scott, Rodney, Baxter, Robert, Yip, Desmond, Carpenter, Jane, Davis, Alison, Pathmanathan, Nirmala, Simpson, Peter, Graham, J Dinny, Sachchithananthan, Mythily, Amor, David, Andrews, Lesley, Antill, Yoland, Balleine, Rosemary, Beesley, Jonathan, Bennett, Ian, Bogwitz, Michael, Botes, Leon, Brennan, Meagan, Brown, Melissa, Buckley, Michael, Burke, Jo, Butow, Phyllis, Caldon, Liz, Campbell, Ian, Cao, Michelle, Chakrabarti, Anannya, Chauhan, Deepa, Chauhan, Manisha, Chenevix‐Trench, Georgia, Christian, Alice, Cohen, Paul, Colley, Alison, Crook, Ashley, Cui, James, Courtney, Eliza, Cummings, Margaret, and Dawson, Sarah‐Jane

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Women's Health, Breast Cancer, Clinical Research, Prevention, Cancer, Female, Humans, Breast Neoplasms, Checkpoint Kinase 2, Genetic Predisposition to Disease, Germ-Line Mutation, Heterozygote, Proportional Hazards Models, CHEK2 c.1100delC germline genetic variant, contralateral breast cancer risk, radiotherapy, survival, systemic treatment, NBCS Collaborators, ABCTB Investigators, kConFab Investigators, Biochemistry and Cell Biology, Oncology and carcinogenesis
Abstract

BackgroundBreast cancer (BC) patients with a germline CHEK2 c.1100delC variant have an increased risk of contralateral BC (CBC) and worse BC-specific survival (BCSS) compared to non-carriers.AimTo assessed the associations of CHEK2 c.1100delC, radiotherapy, and systemic treatment with CBC risk and BCSS.MethodsAnalyses were based on 82,701 women diagnosed with a first primary invasive BC including 963 CHEK2 c.1100delC carriers; median follow-up was 9.1 years. Differential associations with treatment by CHEK2 c.1100delC status were tested by including interaction terms in a multivariable Cox regression model. A multi-state model was used for further insight into the relation between CHEK2 c.1100delC status, treatment, CBC risk and death.ResultsThere was no evidence for differential associations of therapy with CBC risk by CHEK2 c.1100delC status. The strongest association with reduced CBC risk was observed for the combination of chemotherapy and endocrine therapy [HR (95% CI): 0.66 (0.55-0.78)]. No association was observed with radiotherapy. Results from the multi-state model showed shorter BCSS for CHEK2 c.1100delC carriers versus non-carriers also after accounting for CBC occurrence [HR (95% CI): 1.30 (1.09-1.56)].ConclusionSystemic therapy was associated with reduced CBC risk irrespective of CHEK2 c.1100delC status. Moreover, CHEK2 c.1100delC carriers had shorter BCSS, which appears not to be fully explained by their CBC risk.

Published
2023

13. Statistical methods for partitioning ribbon and globally-distributed flux using data from the Interstellar Boundary Explorer

Author

Beesley, Lauren J., Osthus, Dave, Moran, Kelly R., Ausdemore, Madeline A., Meadors, Grant David, Janzen, Paul H., Zirnstein, Eric J., Weaver, Brian P., and Reisenfeld, Daniel B.

Subjects
Statistics - Applications, Astrophysics - Astrophysics of Galaxies
Abstract

ASA's Interstellar Boundary Explorer (IBEX) satellite collects data on energetic neutral atoms (ENAs) that can provide insight into the heliosphere boundary between our solar system and interstellar space. Using these data, scientists can construct maps of the ENA intensities (often, expressed in terms of flux) observed in all directions. The ENA flux observed in these maps is believed to come from at least two distinct sources: one source which manifests as a ribbon of concentrated ENA flux and one source (or possibly several) that manifest as smoothly-varying globally-distributed flux. Each ENA source type and its corresponding ENA intensity map is of separate scientific interest. In this paper, we develop statistical methods for separating the total ENA intensity maps into two source-specific maps (ribbon and globally-distributed flux) and estimating corresponding uncertainty. Key advantages of the proposed method include enhanced model flexibility and improved propagation of estimation uncertainty. We evaluate the proposed methods on simulated data designed to mimic realistic data settings. We also propose new methods for estimating the center of the near-elliptical ribbon in the sky, which can be used in the future to study the location and variation of the local interstellar magnetic field.

Published
2023

15. Stratified analyses refine association between TLR7 rare variants and severe COVID-19

Author

Jannik Boos, Caspar I. van der Made, Gayatri Ramakrishnan, Eamon Coughlan, Rosanna Asselta, Britt-Sabina Löscher, Luca V.C. Valenti, Rafael de Cid, Luis Bujanda, Antonio Julià, Erola Pairo-Castineira, J. Kenneth Baillie, Sandra May, Berina Zametica, Julia Heggemann, Agustín Albillos, Jesus M. Banales, Jordi Barretina, Natalia Blay, Paolo Bonfanti, Maria Buti, Javier Fernandez, Sara Marsal, Daniele Prati, Luisa Ronzoni, Nicoletta Sacchi, Joachim L. Schultze, Olaf Riess, Andre Franke, Konrad Rawlik, David Ellinghaus, Alexander Hoischen, Axel Schmidt, Kerstin U. Ludwig, Valeria Rimoldi, Elvezia M. Paraboschi, Alessandra Bandera, Flora Peyvandi, Giacomo Grasselli, Francesco Blasi, Francesco Malvestiti, Serena Pelusi, Cristiana Bianco, Lorenzo Miano, Angela Lombardi, Pietro Invernizzi, Alessio Gerussi, Giuseppe Citerio, Andrea Biondi, Maria Grazia Valsecchi, Marina Elena Cazzaniga, Giuseppe Foti, Ilaria Beretta, Mariella D'Angiò, Laura Rachele Bettini, Xavier Farré, Susana Iraola-Guzmán, Manolis Kogevinas, Gemma Castaño-Vinyals, Koldo Garcia-Etxebarria, Beatriz Nafria, Mauro D'Amato, Adriana Palom, Colin Begg, Sara Clohisey, Charles Hinds, Peter Horby, Julian Knight, Lowell Ling, David Maslove, Danny McAuley, Johnny Millar, Hugh Montgomery, Alistair Nichol, Peter J.M. Openshaw, Alexandre C. Pereira, Chris P. Ponting, Kathy Rowan, Malcolm G. Semple, Manu Shankar-Hari, Charlotte Summers, Timothy Walsh, Latha Aravindan, Ruth Armstrong, Heather Biggs, Ceilia Boz, Adam Brown, Richard Clark, Audrey Coutts, Judy Coyle, Louise Cullum, Sukamal Das, Nicky Day, Lorna Donnelly, Esther Duncan, Angie Fawkes, Paul Fineran, Max Head Fourman, Anita Furlong, James Furniss, Bernadette Gallagher, Tammy Gilchrist, Ailsa Golightly, Fiona Griffiths, Katarzyna Hafezi, Debbie Hamilton, Ross Hendry, Andy Law, Dawn Law, Rachel Law, Sarah Law, Rebecca Lidstone-Scott, Louise Macgillivray, Alan Maclean, Hanning Mal, Sarah McCafferty, Ellie Mcmaster, Jen Meikle, Shona C. Moore, Kirstie Morrice, Lee Murphy, Sheena Murphy, Mybaya Hellen, Wilna Oosthuyzen, Chenqing Zheng, Jiantao Chen, Nick Parkinson, Trevor Paterson, Katherine Schon, Andrew Stenhouse, Mihaela Das, Maaike Swets, Helen Szoor-McElhinney, Filip Taneski, Lance Turtle, Tony Wackett, Mairi Ward, Jane Weaver, Nicola Wrobel, Marie Zechner, Gill Arbane, Aneta Bociek, Sara Campos, Neus Grau, Tim Owen Jones, Rosario Lim, Martina Marotti, Marlies Ostermann, Christopher Whitton, Zoe Alldis, Raine Astin-Chamberlain, Fatima Bibi, Jack Biddle, Sarah Blow, Matthew Bolton, Catherine Borra, Ruth Bowles, Maudrian Burton, Yasmin Choudhury, David Collier, Amber Cox, Amy Easthope, Patrizia Ebano, Stavros Fotiadis, Jana Gurasashvili, Rosslyn Halls, Pippa Hartridge, Delordson Kallon, Jamila Kassam, Ivone Lancoma-Malcolm, Maninderpal Matharu, Peter May, Oliver Mitchelmore, Tabitha Newman, Mital Patel, Jane Pheby, Irene Pinzuti, Zoe Prime, Oleksandra Prysyazhna, Julian Shiel, Melanie Taylor, Carey Tierney, Suzanne Wood, Anne Zak, Olivier Zongo, Stephen Bonner, Keith Hugill, Jessica Jones, Steven Liggett, Evie Headlam, Nageswar Bandla, Minnie Gellamucho, Michelle Davies, Christopher Thompson, Marwa Abdelrazik, Dhanalakshmi Bakthavatsalam, Munzir Elhassan, Arunkumar Ganesan, Anne Haldeos, Jeronimo Moreno-Cuesta, Dharam Purohit, Rachel Vincent, Kugan Xavier, Kumar Rohit, Frater Alasdair, Malik Saleem, Carter David, Jenkins Samuel, Zoe Lamond, Wall Alanna, Jaime Fernandez-Roman, David O. Hamilton, Emily Johnson, Brian Johnston, Maria Lopez Martinez, Suleman Mulla, David Shaw, Alicia A.C. Waite, Victoria Waugh, Ingeborg D. Welters, Karen Williams, Anna Cavazza, Maeve Cockrell, Eleanor Corcoran, Maria Depante, Clare Finney, Ellen Jerome, Mark McPhail, Monalisa Nayak, Harriet Noble, Kevin O'Reilly, Evita Pappa, Rohit Saha, Sian Saha, John Smith, Abigail Knighton, David Antcliffe, Dorota Banach, Stephen Brett, Phoebe Coghlan, Ziortza Fernandez, Anthony Gordon, Roceld Rojo, Sonia Sousa Arias, Maie Templeton, Megan Meredith, Lucy Morris, Lucy Ryan, Amy Clark, Julia Sampson, Cecilia Peters, Martin Dent, Margaret Langley, Saima Ashraf, Shuying Wei, Angela Andrew, Archana Bashyal, Neil Davidson, Paula Hutton, Stuart McKechnie, Jean Wilson, David Baptista, Rebecca Crowe, Rita Fernandes, Rosaleen Herdman-Grant, Anna Joseph, Denise O'Connor, Meryem Allen, Adam Loveridge, India McKenley, Eriko Morino, Andres Naranjo, Richard Simms, Kathryn Sollesta, Andrew Swain, Harish Venkatesh, Jacyntha Khera, Jonathan Fox, Gillian Andrew, Lucy Barclay, Marie Callaghan, Rachael Campbell, Sarah Clark, Dave Hope, Lucy Marshall, Corrienne McCulloch, Kate Briton, Jo Singleton, Sohphie Birch, Lutece Brimfield, Zoe Daly, David Pogson, Steve Rose, Ceri Battle, Elaine Brinkworth, Rachel Harford, Carl Murphy, Luke Newey, Tabitha Rees, Marie Williams, Sophie Arnold, Petra Polgarova, Katerina Stroud, Eoghan Meaney, Megan Jones, Anthony Ng, Shruti Agrawal, Nazima Pathan, Deborah White, Esther Daubney, Kay Elston, Lina Grauslyte, Musarat Hussain, Mandeep Phull, Tatiana Pogreban, Lace Rosaroso, Erika Salciute, George Franke, Joanna Wong, Aparna George, Laura Ortiz-Ruiz de Gordoa, Emily Peasgood, Claire Phillips, Michelle Bates, Jo Dasgin, Jaspret Gill, Annette Nilsson, James Scriven, Carlos Castro Delgado, Deborah Dawson, Lijun Ding, Georgia Durrant, Obiageri Ezeobu, Sarah Farnell-Ward, Abiola Harrison, Rebecca Kanu, Susannah Leaver, Elena Maccacari, Soumendu Manna, Romina Pepermans Saluzzio, Joana Queiroz, Tinashe Samakomva, Christine Sicat, Joana Texeira, Edna Fernandes Da Gloria, Ana Lisboa, John Rawlins, Jisha Mathew, Ashley Kinch, William James Hurt, Nirav Shah, Victoria Clark, Maria Thanasi, Nikki Yun, Kamal Patel, Sara Bennett, Emma Goodwin, Matthew Jackson, Alissa Kent, Clare Tibke, Wiesia Woodyatt, Ahmed Zaki, Azmerelda Abraheem, Peter Bamford, Kathryn Cawley, Charlie Dunmore, Maria Faulkner, Rumanah Girach, Helen Jeffrey, Rhianna Jones, Emily London, Imrun Nagra, Farah Nasir, Hannah Sainsbury, Clare Smedley, Tahera Patel, Matthew Smith, Srikanth Chukkambotla, Aayesha Kazi, Janice Hartley, Joseph Dykes, Muhammad Hijazi, Sarah Keith, Meherunnisa Khan, Janet Ryan-Smith, Philippa Springle, Jacqueline Thomas, Nick Truman, Samuel Saad, Dabheoc Coleman, Christopher Fine, Roseanna Matt, Bethan Gay, Jack Dalziel, Syamlan Ali, Drew Goodchild, Rhiannan Harling, Ravi Bhatterjee, Wendy Goddard, Chloe Davison, Stephen Duberly, Jeanette Hargreaves, Rachel Bolton, Miriam Davey, David Golden, Rebecca Seaman, Shiney Cherian, Sean Cutler, Anne Emma Heron, Anna Roynon-Reed, Tamas Szakmany, Gemma Williams, Owen Richards, Yusuf Cheema, Hollie Brooke, Sarah Buckley, Jose Cebrian Suarez, Ruth Charlesworth, Karen Hansson, John Norris, Alice Poole, Alastair Rose, Rajdeep Sandhu, Brendan Sloan, Elizabeth Smithson, Muthu Thirumaran, Veronica Wagstaff, Alexandra Metcalfe, Mark Brunton, Jess Caterson, Holly Coles, Matthew Frise, Sabi Gurung Rai, Nicola Jacques, Liza Keating, Emma Tilney, Shauna Bartley, Parminder Bhuie, Sian Gibson, Amanda Lyle, Fiona McNeela, Jayachandran Radhakrishnan, Alistair Hughes, Bryan Yates, Jessica Reynolds, Helen Campbell, Maria Thompsom, Steve Dodds, Stacey Duffy, Sandra Greer, Karen Shuker, Ascanio Tridente, Reena Khade, Ashok Sundar, George Tsinaslanidis, Isobel Birkinshaw, Joseph Carter, Kate Howard, Joanne Ingham, Rosie Joy, Harriet Pearson, Samantha Roche, Zoe Scott, Hollie Bancroft, Mary Bellamy, Margaret Carmody, Jacqueline Daglish, Faye Moore, Joanne Rhodes, Mirriam Sangombe, Salma Kadiri, Maria Croft, Ian White, Victoria Frost, Maia Aquino, Rajeev Jha, Vinodh Krishnamurthy, Lai Lim, Li Lim, Edward Combes, Teishel Joefield, Sonja Monnery, Valerie Beech, Sallyanne Trotman, Christine Almaden-Boyle, Pauline Austin, Louise Cabrelli, Stephen Cole, Matt Casey, Susan Chapman, Clare Whyte, Yolanda Baird, Aaron Butler, Indra Chadbourn, Linda Folkes, Heather Fox, Amy Gardner, Raquel Gomez, Gillian Hobden, Luke Hodgson, Kirsten King, Michael Margarson, Tim Martindale, Emma Meadows, Dana Raynard, Yvette Thirlwall, David Helm, Jordi Margalef, Kristine Criste, Rebecca Cusack, Kim Golder, Hannah Golding, Oliver Jones, Samantha Leggett, Michelle Male, Martyna Marani, Kirsty Prager, Toran Williams, Belinda Roberts, Karen Salmon, Peter Anderson, Katie Archer, Karen Austin, Caroline Davis, Alison Durie, Olivia Kelsall, Jessica Thrush, Charlie Vigurs, Laura Wild, Hannah-Louise Wood, Helen Tranter, Alison Harrison, Nicholas Cowley, Michael McAlindon, Andrew Burtenshaw, Stephen Digby, Emma Low, Aled Morgan, Naiara Cother, Tobias Rankin, Sarah Clayton, Alex McCurdy, Cecilia Ahmed, Balvinder Baines, Sarah Clamp, Julie Colley, Risna Haq, Anne Hayes, Jonathan Hulme, Samia Hussain, Sibet Joseph, Rita Kumar, Zahira Maqsood, Manjit Purewal, Leonie Benham, Zena Bradshaw, Joanna Brown, Melanie Caswell, Jason Cupitt, Sarah Melling, Stephen Preston, Nicola Slawson, Emma Stoddard, Scott Warden, Bethan Deacon, Ceri Lynch, Carla Pothecary, Lisa Roche, Gwenllian Sera Howe, Jayaprakash Singh, Keri Turner, Hannah Ellis, Natalie Stroud, Jodie Hunt, Joy Dearden, Emma Dobson, Andy Drummond, Michelle Mulcahy, Sheila Munt, Grainne O'Connor, Jennifer Philbin, Chloe Rishton, Redmond Tully, Sarah Winnard, Susanne Cathcart, Katharine Duffy, Alex Puxty, Kathryn Puxty, Lynne Turner, Jane Ireland, Gary Semple, Kate Long, Simon Whiteley, Elizabeth Wilby, Bethan Ogg, Amanda Cowton, Andrea Kay, Melanie Kent, Kathryn Potts, Ami Wilkinson, Suzanne Campbell, Ellen Brown, Julie Melville, Jay Naisbitt, Rosane Joseph, Maria Lazo, Olivia Walton, Alan Neal, Peter Alexander, Schvearn Allen, Joanne Bradley-Potts, Craig Brantwood, Jasmine Egan, Timothy Felton, Grace Padden, Luke Ward, Stuart Moss, Susannah Glasgow, Lynn Abel, Michael Brett, Brian Digby, Lisa Gemmell, James Hornsby, Patrick MacGoey, Pauline O'Neil, Richard Price, Natalie Rodden, Kevin Rooney, Radha Sundaram, Nicola Thomson, Bridget Hopkins, Laura Thrasyvoulou, Heather Willis, Martyn Clark, Martina Coulding, Edward Jude, Jacqueline McCormick, Oliver Mercer, Darsh Potla, Hafiz Rehman, Heather Savill, Victoria Turner, Charlotte Downes, Kathleen Holding, Katie Riches, Mary Hilton, Mel Hayman, Deepak Subramanian, Priya Daniel, Oluronke Adanini, Nikhil Bhatia, Maines Msiska, Rebecca Collins, Ian Clement, Bijal Patel, A. Gulati, Carole Hays, K. Webster, Anne Hudson, Andrea Webster, Elaine Stephenson, Louise McCormack, Victoria Slater, Rachel Nixon, Helen Hanson, Maggie Fearby, Sinead Kelly, Victoria Bridgett, Philip Robinson, Julie Camsooksai, Charlotte Humphrey, Sarah Jenkins, Henrik Reschreiter, Beverley Wadams, Yasmin Death, Victoria Bastion, Daphene Clarke, Beena David, Harriet Kent, Rachel Lorusso, Gamu Lubimbi, Sophie Murdoch, Melchizedek Penacerrada, Alastair Thomas, Jennifer Valentine, Ana Vochin, Retno Wulandari, Brice Djeugam, Gillian Bell, Katy English, Amro Katary, Louise Wilcox, Michelle Bruce, Karen Connolly, Tracy Duncan, Helen T-Michael, Gabriella Lindergard, Samuel Hey, Claire Fox, Jordan Alfonso, Laura Jayne Durrans, Jacinta Guerin, Bethan Blackledge, Jade Harris, Martin Hruska, Ayaa Eltayeb, Thomas Lamb, Tracey Hodgkiss, Lisa Cooper, Joanne Rothwell, Angela Allan, Felicity Anderson, Callum Kaye, Jade Liew, Jasmine Medhora, Teresa Scott, Erin Trumper, Adriana Botello, Liana Lankester, Nikitas Nikitas, Colin Wells, Bethan Stowe, Kayleigh Spencer, Craig Brandwood, Lara Smith, Katie Birchall, Laurel Kolakaluri, Deborah Baines, Anila Sukumaran, Elena Apetri, Cathrine Basikolo, Laura Catlow, Bethan Charles, Paul Dark, Reece Doonan, Alice Harvey, Daniel Horner, Karen Knowles, Stephanie Lee, Diane Lomas, Chloe Lyons, Tracy Marsden, Danielle McLaughlan, Liam McMorrow, Jessica Pendlebury, Jane Perez, Maria Poulaka, Nicola Proudfoot, Melanie Slaughter, Kathryn Slevin, Vicky Thomas, Danielle Walker, Angiy Michael, Matthew Collis, Tracey Cosier, Gemma Millen, Neil Richardson, Natasha Schumacher, Heather Weston, James Rand, Nicola Baxter, Steven Henderson, Sophie Kennedy-Hay, Christopher McParland, Laura Rooney, Malcolm Sim, Gordan McCreath, Louise Akeroyd, Shereen Bano, Matt Bromley, Lucy Gurr, Tom Lawton, James Morgan, Kirsten Sellick, Deborah Warren, Brian Wilkinson, Janet McGowan, Camilla Ledgard, Amelia Stacey, Kate Pye, Ruth Bellwood, Michael Bentley, Jeremy Bewley, Zoe Garland, Lisa Grimmer, Bethany Gumbrill, Rebekah Johnson, Katie Sweet, Denise Webster, Georgia Efford, Karen Convery, Deirdre Fottrell-Gould, Lisa Hudig, Jocelyn Keshet-Price, Georgina Randell, Katie Stammers, Maria Bokhari, Vanessa Linnett, Rachael Lucas, Wendy McCormick, Jenny Ritzema, Amanda Sanderson, Helen Wild, Anthony Rostron, Alistair Roy, Lindsey Woods, Sarah Cornell, Fiona Wakinshaw, Kimberley Rogerson, Jordan Jarmain, Robert Parker, Amie Reddy, Ian Turner-Bone, Laura Wilding, Peter Harding, Caroline Abernathy, Louise Foster, Andrew Gratrix, Vicky Martinson, Priyai Parkinson, Elizabeth Stones, Llucia Carbral-Ortega, Georgia Bercades, David Brealey, Ingrid Hass, Niall MacCallum, Gladys Martir, Eamon Raith, Anna Reyes, Deborah Smyth, Letizia Zitter, Sarah Benyon, Suzie Marriott, Linda Park, Samantha Keenan, Elizabeth Gordon, Helen Quinn, Kizzy Baines, Lenka Cagova, Adama Fofano, Lucie Garner, Helen Holcombe, Sue Mepham, Alice Michael Mitchell, Lucy Mwaura, Krithivasan Praman, Alain Vuylsteke, Julie Zamikula, Bally Purewal, Vanessa Rivers, Stephanie Bell, Hayley Blakemore, Borislava Borislavova, Beverley Faulkner, Emma Gendall, Elizabeth Goff, Kati Hayes, Matt Thomas, Ruth Worner, Kerry Smith, Deanna Stephens, Louise Mew, Esther Mwaura, Richard Stewart, Felicity Williams, Lynn Wren, Sara-Beth Sutherland, Emily Bevan, Jane Martin, Dawn Trodd, Geoff Watson, Caroline Wrey Brown, Amy Collins, Waqas Khaliq, Estefania Treus Gude, Olugbenga Akinkugbe, Alasdair Bamford, Emily Beech, Holly Belfield, Michael Bell, Charlene Davies, Gareth A.L. Jones, Tara McHugh, Hamza Meghari, Lauran O'Neill, Mark J. Peters, Samiran Ray, Ana Luisa Tomas, Iona Burn, Geraldine Hambrook, Katarina Manso, Ruth Penn, Pradeep Shanmugasundaram, Julie Tebbutt, Danielle Thornton, Jade Cole, Rhys Davies, Donna Duffin, Helen Hill, Ben Player, Emma Thomas, Angharad Williams, Denise Griffin, Nycola Muchenje, Mcdonald Mupudzi, Richard Partridge, Jo-Anna Conyngham, Rachel Thomas, Mary Wright, Maria Alvarez Corral, Reni Jacob, Cathy Jones, Craig Denmade, Sarah Beavis, Katie Dale, Rachel Gascoyne, Joanne Hawes, Kelly Pritchard, Lesley Stevenson, Amanda Whileman, Patricia Doble, Joanne Hutter, Corinne Pawley, Charmaine Shovelton, Marius Vaida, Deborah Butcher, Susie O'Sullivan, Nicola Butterworth-Cowin, Norfaizan Ahmad, Joann Barker, Kris Bauchmuller, Sarah Bird, Kay Cawthron, Kate Harrington, Yvonne Jackson, Faith Kibutu, Becky Lenagh, Shamiso Masuko, Gary H. Mills, Ajay Raithatha, Matthew Wiles, Jayne Willson, Helen Newell, Alison Lye, Lorenza Nwafor, Claire Jarman, Sarah Rowland-Jones, David Foote, Joby Cole, Roger Thompson, James Watson, Lisa Hesseldon, Irene Macharia, Luke Chetam, Jacqui Smith, Amber Ford, Samantha Anderson, Kathryn Birchall, Kay Housley, Sara Walker, Leanne Milner, Helena Hanratty, Helen Trower, Patrick Phillips, Simon Oxspring, Ben Donne, Catherine Jardine, Dewi Williams, Alasdair Hay, Rebecca Flanagan, Gareth Hughes, Scott Latham, Emma McKenna, Jennifer Anderson, Robert Hull, Kat Rhead, Carina Cruz, Natalie Pattison, Rob Charnock, Denise McFarland, Denise Cosgrove, Ashar Ahmed, Anna Morris, Srinivas Jakkula, Asifa Ali, Megan Brady, Sam Dale, Annalisa Dance, Lisa Gledhill, Jill Greig, Kathryn Hanson, Kelly Holdroyd, Marie Home, Diane Kelly, Ross Kitson, Lear Matapure, Deborah Melia, Samantha Mellor, Tonicha Nortcliffe, Jez Pinnell, Matthew Robinson, Lisa Shaw, Ryan Shaw, Lesley Thomis, Alison Wilson, Tracy Wood, Lee-Ann Bayo, Ekta Merwaha, Tahira Ishaq, Sarah Hanley, Meg Hibbert, Dariusz Tetla, Chrsitopher Woodford, Latha Durga, Gareth Kennard-Holden, Debbie Branney, Jordan Frankham, Sally Pitts, Nigel White, Shondipon Laha, Mark Verlander, Alexandra Williams, Abdelhakim Altabaibeh, Ana Alvaro, Kayleigh Gilbert, Louise Ma, Loreta Mostoles, Chetan Parmar, Kathryn Simpson, Champa Jetha, Lauren Booker, Anezka Pratley, Colene Adams, Anita Agasou, Tracie Arden, Amy Bowes, Pauline Boyle, Mandy Beekes, Heather Button, Nigel Capps, Mandy Carnahan, Anne Carter, Danielle Childs, Denise Donaldson, Kelly Hard, Fran Hurford, Yasmin Hussain, Ayesha Javaid, James Jones, Sanal Jose, Michael Leigh, Terry Martin, Helen Millward, Nichola Motherwell, Rachel Rikunenko, Jo Stickley, Julie Summers, Louise Ting, Helen Tivenan, Louise Tonks, Rebecca Wilcox, Maureen Holland, Natalie Keenan, Marc Lyons, Helen Wassall, Chris Marsh, Mervin Mahenthran, Emma Carter, Thomas Kong, Helen Blackman, Ben Creagh-Brown, Sinead Donlon, Natalia Michalak-Glinska, Sheila Mtuwa, Veronika Pristopan, Armorel Salberg, Eleanor Smith, Sarah Stone, Charles Piercy, Jerik Verula, Dorota Burda, Rugia Montaser, Lesley Harden, Irving Mayangao, Cheryl Marriott, Paul Bradley, Celia Harris, Susan Anderson, Eleanor Andrews, Janine Birch, Emma Collins, Kate Hammerton, Ryan O'Leary, Michele Clark, Sarah Purvis, Russell Barber, Claire Hewitt, Annette Hilldrith, Karen Jackson-Lawrence, Sarah Shepardson, Maryanne Wills, Susan Butler, Silvia Tavares, Amy Cunningham, Julia Hindale, Sarwat Arif, Sarah Bean, Karen Burt, Michael Spivey, Carrie Demetriou, Charlotte Eckbad, Sarah Hierons, Lucy Howie, Sarah Mitchard, Lidia Ramos, Alfredo Serrano-Ruiz, Katie White, Fiona Kelly, Daniele Cristiano, Natalie Dormand, Zohreh Farzad, Mahitha Gummadi, Kamal Liyanage, Brijesh Patel, Sara Salmi, Geraldine Sloane, Vicky Thwaites, Mathew Varghese, Anelise C. Zborowski, John Allan, Tim Geary, Gordon Houston, Alistair Meikle, Peter O'Brien, Miranda Forsey, Agilan Kaliappan, Anne Nicholson, Joanne Riches, Mark Vertue, Elizabeth Allan, Kate Darlington, Ffyon Davies, Jack Easton, Sumit Kumar, Richard Lean, Daniel Menzies, Richard Pugh, Xinyi Qiu, Llinos Davies, Hannah Williams, Jeremy Scanlon, Gwyneth Davies, Callum Mackay, Joannne Lewis, Stephanie Rees, Metod Oblak, Monica Popescu, Mini Thankachen, Andrew Higham, Kerry Simpson, Jayne Craig, Rosie Baruah, Sheila Morris, Susie Ferguson, Amy Shepherd, Luke Stephen Prockter Moore, Marcela Paola Vizcaychipi, Laura Gomes de Almeida Martins, Jaime Carungcong, Inthakab Ali Mohamed Ali, Karen Beaumont, Mark Blunt, Zoe Coton, Hollie Curgenven, Mohamed Elsaadany, Kay Fernandes, Sameena Mohamed Ally, Harini Rangarajan, Varun Sarathy, Sivarupan Selvanayagam, Dave Vedage, Matthew White, Mandy Gill, Paul Paul, Valli Ratnam, Sarah Shelton, Inez Wynter, Siobhain Carmody, Valerie Joan Page, Claire Marie Beith, Karen Black, Suzanne Clements, Alan Morrison, Dominic Strachan, Margaret Taylor, Michelle Clarkson, Stuart D'Sylva, Kathryn Norman, Fiona Auld, Joanne Donnachie, Ian Edmond, Lynn Prentice, Nikole Runciman, Dario Salutous, Lesley Symon, Anne Todd, Patricia Turner, Abigail Short, Laura Sweeney, Euan Murdoch, Dhaneesha Senaratne, Michaela Hill, Thogulava Kannan, Wild Laura, Rikki Crawley, Abigail Crew, Mishell Cunningham, Allison Daniels, Laura Harrison, Susan Hope, Ken Inweregbu, Sian Jones, Nicola Lancaster, Jamie Matthews, Alice Nicholson, Gemma Wray, Helen Langton, Rachel Prout, Malcolm Watters, Catherine Novis, Anthony Barron, Ciara Collins, Sundeep Kaul, Heather Passmore, Claire Prendergast, Anna Reed, Paula Rogers, Rajvinder Shokkar, Meriel Woodruff, Hayley Middleton, Oliver Polgar, Claire Nolan, Kanta Mahay, Dawn Collier, Anil Hormis, Victoria Maynard, Cheryl Graham, Rachel Walker, Ellen Knights, Alicia Price, Alice Thomas, Chris Thorpe, Teresa Behan, Caroline Burnett, Jonathan Hatton, Elaine Heeney, Atideb Mitra, Maria Newton, Rachel Pollard, Rachael Stead, Vishal Amin, Elena Anastasescu, Vikram Anumakonda, Komala Karthik, Rizwana Kausar, Karen Reid, Jacqueline Smith, Janet Imeson-Wood, Denise Skinner, Jane Gaylard, Dee Mullan, Julie Newman, Alison Brown, Vikki Crickmore, Gabor Debreceni, Joy Wilkins, Liz Nicol, Rosie Reece-Anthony, Mark Birt, Alison Ghosh, Emma Williams, Louise Allen, Eva Beranova, Nikki Crisp, Joanne Deery, Tracy Hazelton, Alicia Knight, Carly Price, Sorrell Tilbey, Salah Turki, Sharon Turney, Joshua Cooper, Cheryl Finch, Sarah Liderth, Alison Quinn, Natalia Waddington, Tina Coventry, Susan Fowler, Michael MacMahon, Amanda McGregor, Anne Cowley, Judith Highgate, Jane Gregory, Susan O'Connell, Tim Smith, Luigi Barberis, Shameer Gopal, Nichola Harris, Victoria Lake, Stella Metherell, Elizabeth Radford, Amelia Daniel, Joanne Finn, Rajnish Saha, Nikki White, Phil Donnison, Fiona Trim, Beena Eapen, Jenny Birch, Laura Bough, Josie Goodsell, Rebecca Tutton, Patricia Williams, Sarah Williams, Barbara Winter-Goodwin, Ailstair Nichol, Kathy Brickell, Michelle Smyth, Lorna Murphy, Samantha Coetzee, Alistair Gales, Igor Otahal, Meena Raj, Craig Sell, Paula Hilltout, Jayne Evitts, Amanda Tyler, Joanne Waldron, Kate Beesley, Sarah Board, Agnieszka Kubisz-Pudelko, Alison Lewis, Jess Perry, Lucy Pippard, Di Wood, Clare Buckley, Peter Barry, Neil Flint, Patel Rekha, Dawn Hales, Lara Bunni, Claire Jennings, Monica Latif, Rebecca Marshall, Gayathri Subramanian, Peter J. McGuigan, Christopher Wasson, Stephanie Finn, Jackie Green, Erin Collins, Bernadette King, Andy Campbell, Sara Smuts, Joseph Duffield, Oliver Smith, Lewis Mallon, Watkins Claire, Liam Botfield, Joanna Butler, Catherine Dexter, Jo Fletcher, Atul Garg, Aditya Kuravi, Poonam Ranga, Emma Virgilio, Zakaula Belagodu, Bridget Fuller, Anca Gherman, Olumide Olufuwa, Remi Paramsothy, Carmel Stuart, Naomi Oakley, Charlotte Kamundi, David Tyl, Katy Collins, Pedro Silva, June Taylor, Laura King, Charlotte Coates, Maria Crowley, Phillipa Wakefield, Jane Beadle, Laura Johnson, Janet Sargeant, Madeleine Anderson, Ailbhe Brady, Rebekah Chan, Jeff Little, Shane McIvor, Helena Prady, Helen Whittle, Bijoy Mathew, Ben Attwood, Penny Parsons, Geraldine Ward, Pamela Bremmer, West Joe, Baird Tracy, Ruddy Jim, Ellie Davies, Sonia Sathe, Catherine Dennis, Alastair McGregor, Victoria Parris, Sinduya Srikaran, Anisha Sukha, Noreen Clarke, Jonathan Whiteside, Mairi Mascarenhas, Avril Donaldson, Joanna Matheson, Fiona Barrett, Marianne O'Hara, Laura Okeefe, Clare Bradley, Christine Eastgate-Jackson, Helder Filipe, Daniel Martin, Amitaa Maharajh, Sara Mingo Garcia, Glykeria Pakou, Mark De Neef, Kathy Dent, Elizabeth Horsley, Muhmmad Nauman Akhtar, Sandra Pearson, Dorota Potoczna, Sue Spencer, Melanie Clapham, Rosemary Harper, Una Poultney, Polly Rice, Rachel Mutch, Lisa Armstrong, Hayley Bates, Emma Dooks, Fiona Farquhar, Brigid Hairsine, Chantal McParland, Sophie Packham, Rehana Bi, Barney Scholefield, Lydia Ashton, Linsha George, Sophie Twiss, David Wright, Manish Chablani, Amy Kirkby, Kimberley Netherton, Kim Davies, Linda O'Brien, Zohra Omar, Emma Perkins, Tracy Lewis, Isobel Sutherland, Karen Burns, Dr Ben Chandler, Kerry Elliott, Janine Mallinson, Alison Turnbull, Prisca Gondo, Bernard Hadebe, Abdul Kayani, Bridgett Masunda, Taya Anderson, Dan Hawcutt, Laura O'Malley, Laura Rad, Naomi Rogers, Paula Saunderson, Kathryn Sian Allison, Deborah Afolabi, Jennifer Whitbread, Dawn Jones, Rachael Dore, Matthew Halkes, Pauline Mercer, Lorraine Thornton, Joy Dawson, Sweyn Garrioch, Melanie Tolson, Jonathan Aldridge, Ritoo Kapoor, David Loader, Karen Castle, Sally Humphreys, Ruth Tampsett, Katherine Mackintosh, Amanda Ayers, Wendy Harrison, Julie North, Suzanne Allibone, Roman Genetu, Vidya Kasipandian, Amit Patel, Ainhi Mac, Anthony Murphy, Parisa Mahjoob, Roonak Nazari, Lucy Worsley, Andrew Fagan, Thomas Bemand, Ethel Black, Arnold Dela Rosa, Ryan Howle, Shaman Jhanji, Ravishankar Rao Baikady, Kate Colette Tatham, Benjamin Thomas, Dina Bell, Rosalind Boyle, Katie Douglas, Lynn Glass, Emma Lee, Liz Lennon, Austin Rattray, Abigail Taylor, Rachel Anne Hughes, Helen Thomas, Alun Rees, Michaela Duskova, Janet Phipps, Suzanne Brooks, Michelle Edwards, Sheena Quaid, Ekaterina Watson, Adam Brayne, Emma Fisher, Jane Hunt, Peter Jackson, Duncan Kaye, Nicholas Love, Juliet Parkin, Victoria Tuckey, Lynne Van Koutrik, Sasha Carter, Benedict Andrew, Louise Findlay, Katie Adams, Jen Service, Alison Williams, Claire Cheyne, Anne Saunderson, Sam Moultrie, Miranda Odam, Kathryn Hall, Isheunesu Mapfunde, Charlotte Willis, Alex Lyon, Chunda Sri-Chandana, Joslan Scherewode, Lorraine Stephenson, Sarah Marsh, John Hardy, Henry Houlden, Eleanor Moncur, Ambreen Tariq, Arianna Tucci, Maria Hobrok, Ronda Loosley, Heather McGuinness, Helen Tench, Rebecca Wolf-Roberts, Val Irvine, Benjamin Shelley, Claire Gorman, Abhinav Gupta, Elizabeth Timlick, Rebecca Brady, Barry Milligan, Arianna Bellini, Jade Bryant, Anton Mayer, Amy Pickard, Nicholas Roe, Jason Sowter, Alex Howlett, Katy Fidler, Emma Tagliavini, and Kevin Donnelly

Subjects
SARS-CoV-2, host genetics, toll-like receptor 7, targeted sequencing, rare variants, variant collapsing analysis, Genetics, QH426-470
Abstract

Summary: Despite extensive global research into genetic predisposition for severe COVID-19, knowledge on the role of rare host genetic variants and their relation to other risk factors remains limited. Here, 52 genes with prior etiological evidence were sequenced in 1,772 severe COVID-19 cases and 5,347 population-based controls from Spain/Italy. Rare deleterious TLR7 variants were present in 2.4% of young (

Published
2024
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16. Towards Improved Heliosphere Sky Map Estimation with Theseus

Author

Osthus, Dave, Weaver, Brian P., Beesley, Lauren J., Moran, Kelly R., Ausdemore, Madeline A., Zirnstein, Eric J., Janzen, Paul H., and Reisenfeld, Daniel B.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Statistics - Applications
Abstract

The Interstellar Boundary Explorer (IBEX) satellite has been in orbit since 2008 and detects energy-resolved energetic neutral atoms (ENAs) originating from the heliosphere. Different regions of the heliosphere generate ENAs at different rates. It is of scientific interest to take the data collected by IBEX and estimate spatial maps of heliospheric ENA rates (referred to as sky maps) at higher resolutions than before. These sky maps will subsequently be used to discern between competing theories of heliosphere properties that are not currently possible. The data IBEX collects present challenges to sky map estimation. The two primary challenges are noisy and irregularly spaced data collection and the IBEX instrumentation's point spread function. In essence, the data collected by IBEX are both noisy and biased for the underlying sky map of inferential interest. In this paper, we present a two-stage sky map estimation procedure called Theseus. In Stage 1, Theseus estimates a blurred sky map from the noisy and irregularly spaced data using an ensemble approach that leverages projection pursuit regression and generalized additive models. In Stage 2, Theseus deblurs the sky map by deconvolving the PSF with the blurred map using regularization. Unblurred sky map uncertainties are computed via bootstrapping. We compare Theseus to a method closely related to the one operationally used today by the IBEX Science Operation Center (ISOC) on both simulated and real data. Theseus outperforms ISOC in nearly every considered metric on simulated data, indicating that Theseus is an improvement over the current state of the art., Comment: 38 pages, 18 figures, 3 tables

Published
2022

17. Single-cell guided prenatal derivation of primary fetal epithelial organoids from human amniotic and tracheal fluids

Author

Gerli, Mattia Francesco Maria, Calà, Giuseppe, Beesley, Max Arran, Sina, Beatrice, Tullie, Lucinda, Sun, Kylin Yunyan, Panariello, Francesco, Michielin, Federica, Davidson, Joseph R., Russo, Francesca Maria, Jones, Brendan C., Lee, Dani Do Hyang, Savvidis, Savvas, Xenakis, Theodoros, Simcock, Ian C., Straatman-Iwanowska, Anna A., Hirst, Robert A., David, Anna L., O’Callaghan, Christopher, Olivo, Alessandro, Eaton, Simon, Loukogeorgakis, Stavros P., Cacchiarelli, Davide, Deprest, Jan, Li, Vivian S. W., Giobbe, Giovanni Giuseppe, and De Coppi, Paolo

Published
2024
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18. Evaluating the effectiveness of sulfidated nano zerovalent iron and sludge co-application for reducing metal mobility in contaminated soil

Author

Omolola Ojo, Zuzana Vaňková, Luke Beesley, Niluka Wickramasinghe, and Michael Komárek

Subjects
Medicine, Science
Abstract

Abstract Sewage sludge has long been applied to soils as a fertilizer yet may be enriched with leachable metal(loid)s and other pollutants. Sulfidated nanoscale zerovalent iron (S-nZVI) has proven effective at metal sorption; however, risks associated with the use of engineered nanoparticles cannot be neglected. This study investigated the effects of the co-application of composted sewage sludge with S-nZVI for the stabilization of Cd, Pb, Fe, Zn. Five treatments (control, Fe grit, composted sludge, S-nZVI, composted sludge and S-nZVI), two leaching fluids; synthetic precipitation leaching procedure (SPLP) and toxicity characteristic leaching procedure (TCLP) fluid were used, samples were incubated at different time intervals of 1 week, 1, 3, and 6 months. Fe grit proved most efficient in reducing the concentration of extractable metals in the batch experiment; the mixture of composted sludge and S-nZVI was the most effective in reducing the leachability of metals in the column systems, while S-nZVI was the most efficient for reducing about 80% of Zn concentration in soil solution. Thus, the combination of two amendments, S-nZVI incorporated with composted sewage sludge and Fe grit proved most effective at reducing metal leaching and possibly lowering the associated risks. Future work should investigate the longer-term efficiency of this combination.

Published
2024
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19. Active eDNA Is More Cost‐Effective Than Fyke Nets or Passive eDNA Collection When Monitoring the Invasion of an Alien Freshwater Fish

Author

Lenore Morris, Leah S. Beesley, Emma R. Stevens, Daniel C. Gwinn, Josephine Hyde, Suzanne Thompson, Deirdre B. Gleeson, and Michael M. Douglas

Subjects
active eDNA, alien species, Canning River, freshwater, management, passive eDNA, Environmental sciences, GE1-350, Microbial ecology, QR100-130
Abstract

ABSTRACT Monitoring alien species is critical to their management. However, early detection of invading alien freshwater fish can be challenging due to the difficulty of observing fish in low abundance. Environmental DNA (eDNA) has emerged as a new and potentially more sensitive method for sampling invasive species as compared to conventional methods, but the comparative financial cost is not often assessed. Adoption of eDNA by managers requires studies that showcase its cost‐effectiveness relative to conventional approaches. Here we use eDNA to assist in the management of an aggressive alien fish, the pearl cichlid (Geophagus brasiliensis), that is invading an urban river in south‐western Australia. We applied an occupancy model to survey data collected 6 years apart (2015, 2021) to assess how the species' distribution had changed and to evaluate whether an instream barrier had the potential to limit upstream invasion. To understand the effectiveness of eDNA, we used our model to quantify the relative efficiency (capture probability) of two eDNA sampling methods (active eDNA and passive eDNA) and fyke netting, as well as the number of replicate samples required per site to deliver >95% detection. We coupled the number of replicates needed with the cost per replicate to determine the cost‐efficiency of each method. We found that G. brasiliensis abundance was higher in downstream reaches in both survey years, and there was no evidence that its distribution had changed through time. However, G. brasiliensis was present above the instream barrier. Active eDNA sampling was considerably better at detecting G. brasiliensis than the other methods, making it the most cost‐effective method. Fyke nets came in a close second, and passive eDNA was a very distant third. Our results directly inform management in the study river and broadly highlight the cost‐effectiveness of active eDNA as a freshwater biosecurity tool.

Published
2024
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20. Implementing Linkage Quality Assessments in Large-Scale Privacy Preserving Infrastructure: Did we kill them a second time and why are there zombies?

Author

Kenneth Gersing, Jasmin Phua, Shaun Grannis, Sara Rogovin, Saad Ljazouli, Sam Michael, and Chris Beesley

Subjects
Demography. Population. Vital events, HB848-3697
Abstract

The National Clinical Cohort Collaborative (N3C) uses privacy-preserving record linkage (PPRL) to formulate longitudinal patient histories and for de-duplication across disparate data including electronic health records, administrative claims, and mortality data. The N3C employs a linkage honest broker implementation model which separates the entity holding de-identified PPRL tokens, from the entity holding the substantive data payloads. As a result of this data governance structure, linkage quality assessments are necessarily distributed into 2 distinct processes: 1) Linkage Honest Broker receipt and processing of linkages, 2) Data Aggregation entity assembling data based on received linkage crosswalks. Data is released on a weekly basis. This presentation will focus on Step 2 for the Mortality data linkages where the downstream data linkage pipelines must assess linkage quality across several dimensions of quality, focused on plausibility. There are 4 types of mortality data spanning the electronic health record, government Social Security Administration death master files, third-party obituary data, and administrative claims. Each of these sources has different levels of authoritativeness and data latency, compounding the challenges of reconciling fact of death including accurate death reporting dates. To address these challenges, we implemented an automated linkage quality pipeline which generates reports that assess linkage plausibility across the various data types, classifying concordance and discordance between data sources including age, dates of death, surfacing plausible and non-plausible activities post-death. Sharing our real-world implementation will aid conference attendees in understanding how to plan for such activities when considering specific implementation models for privacy-preserving linkages.

Published
2024
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21. Data sharing in cancer research: A qualitative study exploring community members' preferences

Author

Elizabeth A. Johnston, Xanthia E. Bourdaniotis, Susannah K. Ayre, Leah Zajdlewicz, Vanessa L. Beesley, and Belinda C. Goodwin

Subjects
clinical cancer research, community outreach, ethical considerations, translational research, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Advancements in cancer treatment and survivorship rely on participation in research and access to health records. Methods This study explored preferences for data access and sharing in 14 workshops with 42 community members, most of whom were a cancer survivor or carer. Various scenarios for data access and sharing were presented and discussed, with participants' preferences summarized using descriptive statistics. Reasons underlying these preferences were identified through a thematic analysis of workshop transcripts. Results Most participants indicated a willingness for researchers to use their self‐report data and current health records for a specific research project (86%). Many were also willing for their self‐report data and current (62%) or all future (44%) health records to be shared with other researchers for use in other studies if made aware of this. Willingness to consent to data access and sharing data in cancer research was influenced by: (i) the potential for data sharing to advance medical discoveries and benefit people impacted by cancer in the future, (ii) transparency around researchers' credibility and their intentions for data sharing, (iii) level of ownership and control over data sharing, and (iv) protocols for privacy and confidentiality in data sharing. Conclusions Based on these themes, we present practical strategies for optimizing data access and sharing in cancer research.

Published
2024
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22. Designing for Diversity Part 3: Implementation of the Equity and Inclusion Curriculum Development Approach--The Role of State and Local Education Agencies. Brief

Author

National Comprehensive Center (NCC), Westat, Inc., Alozie, Nonye, Yang, Hui, and Beesley, Andrea

Abstract

This is the third whitepaper in the National Comprehensive Center's series on designing curricula for diversity. It provides state and local education leaders recommendations on the use of the Equity and Inclusion Framework for Curriculum Development in the design and adaptation of STEM+CS [science, technology, engineering, mathematics, and computer science] curriculum materials. [For Part 1, see ED615692. For Part 2, see ED615694.]

Published
2021

23. Copy Number Variants Are Ovarian Cancer Risk Alleles at Known and Novel Risk Loci

Author

DeVries, Amber A, Dennis, Joe, Tyrer, Jonathan P, Peng, Pei-Chen, Coetzee, Simon G, Reyes, Alberto L, Plummer, Jasmine T, Davis, Brian D, Chen, Stephanie S, Dezem, Felipe Segato, Aben, Katja KH, Anton-Culver, Hoda, Antonenkova, Natalia N, Beckmann, Matthias W, Beeghly-Fadiel, Alicia, Berchuck, Andrew, Bogdanova, Natalia V, Bogdanova-Markov, Nadja, Brenton, James D, Butzow, Ralf, Campbell, Ian, Chang-Claude, Jenny, Chenevix-Trench, Georgia, Cook, Linda S, DeFazio, Anna, Doherty, Jennifer A, Dörk, Thilo, Eccles, Diana M, Eliassen, A Heather, Fasching, Peter A, Fortner, Renée T, Giles, Graham G, Goode, Ellen L, Goodman, Marc T, Gronwald, Jacek, Webb, P, DeFazio, A, Friedlander, M, Obermair, A, Grant, P, Nagle, C, Beesley, V, Chevenix-Trench, G, Bowtell, D, Blomfield, P, Brand, A, Davis, A, Leung, Y, Nicklin, J, Quinn, M, Livingstone, K, O'Neill, H, Williams, M, Black, A, Hadley, A, Glasgow, A, Garrett, A, Rao, A, Shannon, C, Steer, C, Allen, D, Neesham, D, Otton, G, Au-Yeung, G, Goss, G, Wain, G, Gard, G, Robertson, G, Lombard, J, Tan, J, McNeilage, J, Power, J, Coward, J, Miller, J, Carter, J, Lamont, J, Wong, KM, Reid, K, Perrin, L, Milishkin, L, Nascimento, M, Buck, M, Bunting, M, Harrison, M, Chetty, N, Hacker, N, McNally, O, Harnett, P, Beale, P, Awad, R, Mohan, R, Farrell, R, McIntosh, R, Rome, R, Sayer, R, Houghton, R, Hogg, R, Land, R, Baron-Hay, S, and Paramasivum, S

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Human Genome, Genetic Testing, Clinical Research, Ovarian Cancer, Rare Diseases, Prevention, Women's Health, Cancer, Genetics, 2.1 Biological and endogenous factors, Female, Humans, Carcinoma, Ovarian Epithelial, Genome-Wide Association Study, Alleles, DNA Copy Number Variations, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Ovarian Neoplasms, OPAL Study Group, AOCS Group, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

BackgroundKnown risk alleles for epithelial ovarian cancer (EOC) account for approximately 40% of the heritability for EOC. Copy number variants (CNVs) have not been investigated as EOC risk alleles in a large population cohort.MethodsSingle nucleotide polymorphism array data from 13 071 EOC cases and 17 306 controls of White European ancestry were used to identify CNVs associated with EOC risk using a rare admixture maximum likelihood test for gene burden and a by-probe ratio test. We performed enrichment analysis of CNVs at known EOC risk loci and functional biofeatures in ovarian cancer-related cell types.ResultsWe identified statistically significant risk associations with CNVs at known EOC risk genes; BRCA1 (PEOC = 1.60E-21; OREOC = 8.24), RAD51C (Phigh-grade serous ovarian cancer [HGSOC] = 5.5E-4; odds ratio [OR]HGSOC = 5.74 del), and BRCA2 (PHGSOC = 7.0E-4; ORHGSOC = 3.31 deletion). Four suggestive associations (P

Published
2022

24. Investigating Anthrax-Associated Virulence Genes among Archival and Contemporary Bacillus cereus Group Genomes

Author

Susanna J. Sabin, Cari A. Beesley, Chung K. Marston, Taylor K. Paisie, Christopher A. Gulvik, Gregory A. Sprenger, Jay E. Gee, Rita M. Traxler, Melissa E. Bell, John R. McQuiston, and Zachary P. Weiner

Subjects
anthrax, Bacillus anthracis, Bacillus cereus group, genomics, pseudogenes, gene decay, Medicine
Abstract

Bacillus anthracis causes anthrax through virulence factors encoded on two plasmids. However, non-B. anthracis organisms within the closely related, environmentally ubiquitous Bacillus cereus group (BCG) may cause an anthrax-like disease in humans through the partial adoption of anthrax-associated virulence genes, challenging the definition of anthrax disease. To elucidate these phenomena and their evolutionary past, we performed whole-genome sequencing on non-anthracis BCG isolates, including 93 archival (1967–2003) and 5 contemporary isolates (2019–2023). We produced annotated genomic assemblies and performed a pan-genome analysis to identify evidence of virulence gene homology and virulence gene acquisition by linear inheritance or horizontal gene transfer. At least one anthrax-associated virulence gene was annotated in ten isolates. Most homologous sequences in archival isolates showed evidence of pseudogenization and subsequent gene loss. The presence or absence of accessory genes, including anthrax-associated virulence genes, aligned with the phylogenetic structure of the BCG core genome. These findings support the hypothesis that anthrax-associated virulence genes were inherited from a common ancestor in the BCG and were retained or lost across different lineages, and contribute to a growing body of work informing public health strategies related to anthrax surveillance and identification.

Published
2024
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25. Addressing delayed case reporting in infectious disease forecast modeling

Author

Beesley, Lauren J, Osthus, Dave, and Del Valle, Sara Y

Subjects
Statistics - Methodology, Statistics - Applications
Abstract

Infectious disease forecasting is of great interest to the public health community and policymakers, since forecasts can provide insight into disease dynamics in the near future and inform interventions. Due to delays in case reporting, however, forecasting models may often underestimate the current and future disease burden. In this paper, we propose a general framework for addressing reporting delay in disease forecasting efforts with the goal of improving forecasts. We propose strategies for leveraging either historical data on case reporting or external internet-based data to estimate the amount of reporting error. We then describe several approaches for adapting general forecasting pipelines to account for under- or over-reporting of cases. We apply these methods to address reporting delay in data on dengue fever cases in Puerto Rico from 1990 to 2009 and to reports of influenza-like illness (ILI) in the United States between 2010 and 2019. Through a simulation study, we compare method performance and evaluate robustness to assumption violations. Our results show that forecasting accuracy and prediction coverage almost always increase when correction methods are implemented to address reporting delay. Some of these methods required knowledge about the reporting error or high quality external data, which may not always be available. Provided alternatives include excluding recently-reported data and performing sensitivity analysis. This work provides intuition and guidance for handling delay in disease case reporting and may serve as a useful resource to inform practical infectious disease forecasting efforts., Comment: 6 figures and Supplement provided

Published
2021
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26. The Western Channel Observatory: a century of physical, chemical and biological data compiled from pelagic and benthic habitats in the western English Channel

Author

A. J. McEvoy, A. Atkinson, R. L. Airs, R. Brittain, I. Brown, E. S. Fileman, H. S. Findlay, C. L. McNeill, C. Ostle, T. J. Smyth, P. J. Somerfield, K. Tait, G. A. Tarran, S. Thomas, C. E. Widdicombe, E. M. S. Woodward, A. Beesley, D. V. P. Conway, J. Fishwick, H. Haines, C. Harris, R. Harris, P. Hélaouët, D. Johns, P. K. Lindeque, T. Mesher, A. McQuatters-Gollop, J. Nunes, F. Perry, A. M. Queiros, A. Rees, S. Rühl, D. Sims, R. Torres, and S. Widdicombe

Subjects
Environmental sciences, GE1-350, Geology, QE1-996.5
Abstract

The Western Channel Observatory (WCO) comprises a series of pelagic, benthic and atmospheric sampling sites within 40 km of Plymouth, UK, that have been sampled by the Plymouth institutes on a regular basis since 1903. This longevity of recording and the high frequency of observations provide a unique combination of data; for example temperature data were first collected in 1903, and the reference station L4, where nearly 400 planktonic taxa have been enumerated, has been sampled on a weekly basis since 1988. While the component datasets have been archived, here we provide the first summary database bringing together a wide suite of the observations. This provides monthly average values of some of the key pelagic and benthic measurements for the inshore site L4 (50∘15.00′ N, 4∘13.02′ W; approx. depth 55 m), the offshore site E1 (50∘02.00′ N, 4∘22.00′ W; approx. depth 75 m) and the intermediate L5 site (50∘10.80′ N, 4∘18.00′ W; approx. depth 58 m). In brief, these data include the following: water temperature (from 1903); macronutrients (from 1934); dissolved inorganic carbon and total alkalinity (from 2008); methane and nitrous oxide (from 2011); chlorophyll a (from 1992); high-performance liquid chromatography (HPLC)-derived pigments (from 1999); µm plankton by flow cytometry, including bacteria (8 functional groups from 2007); phytoplankton by microscopy (6 functional groups from 1992); microplankton and mesozooplankton from FlowCam (6 groups from 2012); Noctiluca sp. dinoflagellate (from 1997); mesozooplankton by microscopy (8 groups from 1988); Calanus helgolandicus egg production rates (from 1992); fish larvae from the Young Fish Trawl survey (4 groups from 1924); benthic macrofauna (4 groups from 2008); demersal fish (19 families from 2008); blue shark, Prionace glauca (from 1958); and 16S alpha diversity for sediment and water column (from 2012). These data have varying coverage with respect to time and depth resolution. The metadata tables describe each dataset and provide pointers to the source data and other related Western Channel Observatory datasets and outputs not compiled here. We provide summaries of the main trends in seasonality and some major climate-related shifts that have been revealed over the last century. The data are available from the Data Archive for Seabed Species and Habitats (DASSH): https://doi.org/10.17031/645110fb81749 (McEvoy and Atkinson, 2023). Making these data fully accessible and including units of both abundance and biomass will stimulate a variety of uptakes. These may include uses as an educational resource for projects, for models and budgets, for the analysis of seasonality and long-term change in a coupled benthic–pelagic system, or for supporting UK and north-eastern Atlantic policy and management.

Published
2023
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27. Mechanisms of synthetic lethality between BRCA1/2 and 53BP1 deficiencies and DNA polymerase theta targeting

Author

George E. Ronson, Katarzyna Starowicz, Elizabeth J. Anthony, Ann Liza Piberger, Lucy C. Clarke, Alexander J. Garvin, Andrew D. Beggs, Celina M. Whalley, Matthew J. Edmonds, James F. J. Beesley, and Joanna R. Morris

Subjects
Science
Abstract

Abstract A synthetic lethal relationship exists between disruption of polymerase theta (Polθ), and loss of either 53BP1 or homologous recombination (HR) proteins, including BRCA1; however, the mechanistic basis of these observations are unclear. Here we reveal two distinct mechanisms of Polθ synthetic lethality, identifying dual influences of 1) whether Polθ is lost or inhibited, and 2) the underlying susceptible genotype. Firstly, we find that the sensitivity of BRCA1/2- and 53BP1-deficient cells to Polθ loss, and 53BP1-deficient cells to Polθ inhibition (ART558) requires RAD52, and appropriate reduction of RAD52 can ameliorate these phenotypes. We show that in the absence of Polθ, RAD52 accumulations suppress ssDNA gap-filling in G2/M and encourage MRE11 nuclease accumulation. In contrast, the survival of BRCA1-deficient cells treated with Polθ inhibitor are not restored by RAD52 suppression, and ssDNA gap-filling is prevented by the chemically inhibited polymerase itself. These data define an additional role for Polθ, reveal the mechanism underlying synthetic lethality between 53BP1, BRCA1/2 and Polθ loss, and indicate genotype-dependent Polθ inhibitor mechanisms.

Published
2023
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28. Brief floodplain inundation provides growth and survival benefits to a young-of-year fish in an intermittent river threatened by water development

Author

Oliver P. Pratt, Leah S. Beesley, Bradley J. Pusey, Daniel C. Gwinn, Chris S. Keogh, and Michael M. Douglas

Subjects
Medicine, Science
Abstract

Abstract Riverine floodplains are highly productive habitats that often act as nurseries for fish but are threatened by flow regulation. The Fitzroy River in northern Australia is facing development, but uncertainty exists regarding the extent to which floodplain habitats deliver benefits to fish, particularly given the brevity of seasonal floodplain inundation. We investigated the growth rate of young-of-year bony bream (Nematalosa erebi) in main channel and ephemeral floodplain habitats using age derived from otolith daily increments. We also investigated potential mechanisms influencing growth and modelled the consequences of differential growth rate on survival. Our results revealed higher growth occurred exclusively on the floodplain and that zooplankton biomass was the best predictor of growth rate. Modelling indicated that elevated growth rate in high-growth floodplain pools (top 25th percentile) could translate into substantial increases in survivorship. The positive effect of zooplankton biomass on growth was moderated under highly turbid conditions. Temperature had a minor influence on growth, and only in floodplain habitats. Our results indicate ephemeral floodplain habitats can deliver substantial growth and survival benefits to young-of-year fish even when floodplain inundation is brief. This study highlights the need to ensure that water policy safeguards floodplain habitats due to their important ecological role.

Published
2023
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29. ‘The current mental health status of children and young people with JIA, and their wider family’: a charity partner collaboration survey

Author

Polly Livermore, S. Ainsworth, R. Beesley, S. Douglas, E. Earle, D. Wilson, L. Woolley, and J. Clinch

Subjects
Paediatric rheumatology, Adolescent, JIA, Mental health, Support, Parents, Pediatrics, RJ1-570, Diseases of the musculoskeletal system, RC925-935
Abstract

Abstract Background This paper presents insight into the scale of mental health concerns for families who have a child or young person with a diagnosis of Juvenile Idiopathic Arthritis (JIA) living in any of the four nations of the United Kingdom (UK). The study’s objective is to share the current experiences of those that responded to a charity survey and consider future work to improve mental health support. Methods This work was initiated and led by five UK charity partner organisations working with families affected by JIA. Parents/carers of a child or young person with JIA, and young people with JIA, submitted self-completion online questionnaires. The questionnaire asked 19 core questions, with a focus on the mental health impact of having and living with a JIA diagnosis. Questionnaires were delivered via charity partner UK-wide mailing lists and social media. Results Questionnaire were completed by 291 participants over a 3-week period in February 2022. The majority of respondents were parents (229, 79%), 103 children had been diagnosed for over six years (35%), and 131 (45%) received shared care between paediatric rheumatology centres. In total, 168 (59%) children and young people with JIA had received, were currently receiving or were waiting for mental health support. Parents reported that their child’s diagnosis impacted their own mental health (218, 82%). Children and young people reported never being offered mental health support during appointments for JIA (157, 54%), and 71 (50%) of these had never received support. Conclusion Children and young people with JIA have significant mental health sequelae from their diagnosis. Our findings found that nearly 60% of our respondents have had or are requiring mental health support, with significant numbers of parents/carers reporting difficulties in accessing care for their child’s mental health or their own mental health, due to their child’s diagnosis. This unique collaborative charity-led study, illustrates the importance of timely and accessible mental health support. Further work is needed to understand why best practice guidance for mental health support is not being met consistently and to identify how to embed it into standard rheumatology care.

Published
2023
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30. Reconstructing magnetic deflections from sets of proton images using differential evolution

Author

Levesque, Joseph M. and Beesley, Lauren J.

Subjects
Physics - Data Analysis, Statistics and Probability, Physics - Plasma Physics
Abstract

Proton imaging is a powerful technique for imaging electromagnetic fields within an experimental volume, in which spatial variations in proton fluence are a result of deflections to proton trajectories due to interaction with the fields. When deflections are large, proton trajectories can overlap, and this nonlinearity creates regions of greatly increased proton fluence on the image, known as caustics. The formation of caustics has been a persistent barrier to reconstructing the underlying fields from proton images. We have developed a new method for reconstructing the path-integrated magnetic fields which begins to address the problem posed by caustics. Our method uses multiple proton images of the same object, each image at a different energy, to fill in the information gaps and provide some uniqueness when reconstructing caustic features. We use a differential evolution algorithm to iteratively estimate the underlying deflection function which accurately reproduces the observed proton fluence at multiple proton energies simultaneously. We test this reconstruction method using synthetic proton images generated for three different, cylindrically symmetric field geometries at various field amplitudes and levels of proton statistics, and present reconstruction results from a set of experimental images. The method we propose requires no assumption of deflection linearity and can reliably solve for fields underlying linear, nonlinear, and caustic proton image features for the selected geometries, and is shown to be fairly robust to noise in the input proton intensity.

Published
2021
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31. Multiple imputation with missing data indicators

Author

Beesley, Lauren J, Bondarenko, Irina, Elliott, Michael R, Kurian, Allison W, Katz, Steven J, and Taylor, Jeremy M G

Subjects
Statistics - Methodology
Abstract

Multiple imputation is a well-established general technique for analyzing data with missing values. A convenient way to implement multiple imputation is sequential regression multiple imputation (SRMI), also called chained equations multiple imputation. In this approach, we impute missing values using regression models for each variable, conditional on the other variables in the data. This approach, however, assumes that the missingness mechanism is missing at random, and it is not well-justified under not-at-random missingness without additional modification. In this paper, we describe how we can generalize the SRMI imputation procedure to handle not-at-random missingness (MNAR) in the setting where missingness may depend on other variables that are also missing. We provide algebraic justification for several generalizations of standard SRMI using Taylor series and other approximations of the target imputation distribution under MNAR. Resulting regression model approximations include indicators for missingness, interactions, or other functions of the MNAR missingness model and observed data. In a simulation study, we demonstrate that the proposed SRMI modifications result in reduced bias in the final analysis compared to standard SRMI, with an approximation strategy involving inclusion of an offset in the imputation model performing the best overall. The method is illustrated in a breast cancer study, where the goal is to estimate the prevalence of a specific genetic pathogenic variant., Comment: See also: Supplemental Material

Published
2021

32. Accounting for not-at-random missingness through imputation stacking

Author

Beesley, Lauren J and Taylor, Jeremy M G

Subjects
Statistics - Methodology
Abstract

Not-at-random missingness presents a challenge in addressing missing data in many health research applications. In this paper, we propose a new approach to account for not-at-random missingness after multiple imputation through weighted analysis of stacked multiple imputations. The weights are easily calculated as a function of the imputed data and assumptions about the not-at-random missingness. We demonstrate through simulation that the proposed method has excellent performance when the missingness model is correctly specified. In practice, the missingness mechanism will not be known. We show how we can use our approach in a sensitivity analysis framework to evaluate the robustness of model inference to different assumptions about the missingness mechanism, and we provide R package StackImpute to facilitate implementation as part of routine sensitivity analyses. We apply the proposed method to account for not-at-random missingness in human papillomavirus test results in a study of survival for patients diagnosed with oropharyngeal cancer., Comment: See also: Supplementary Materials

Published
2021

33. Elementary Students' Mathematics Identity: Findings from a Longitudinal Study in an Out-of-School Setting

Author

Michaela Gulemetova, Andrea D. Beesley, Cheri Fancsali, and Uttara Balakrishnan

Abstract

This study presents findings from a randomized controlled trial of an afterschool program intended to develop mathematics identity for students from grades 4 and 5 in groups underrepresented in STEM. Mathematics identity refers to the ways that students think about themselves in relation to mathematics and the extent to which they have developed a commitment to, and have come to see value in, mathematics. While the impact analyses showed no effects of the intervention on mathematics identity or achievement, the exploration of the longitudinal data collected over 2 years provided several insights. On average, student mathematics identity remained constant over the study period; however, the overall averages mask large variations in individual students and sites. Some students saw improvement in mathematics identity, while others saw decreases. Counter to findings in previous literature, we found no overall differences by gender suggesting that boys and girls report similar mathematics identity. Importantly, we found a positive relationship between mathematics identity and achievement. This finding holds in both directions and suggests that boosting mathematics identity could lead to improving mathematics achievement and vice versa. This study contributes to our understanding of mathematics identity, how it is measured, how it evolves over time, what relationship it has to mathematics achievement, and what its potential for development in afterschool environments could be.

Published
2022
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34. Association of germline genetic variants with breast cancer-specific survival in patient subgroups defined by clinic-pathological variables related to tumor biology and type of systemic treatment

Author

Morra, Anna, Escala-Garcia, Maria, Beesley, Jonathan, Keeman, Renske, Canisius, Sander, Ahearn, Thomas U, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Auer, Paul L, Augustinsson, Annelie, Beane Freeman, Laura E, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Bojesen, Stig E, Bolla, Manjeet K, Brenner, Hermann, Brüning, Thomas, Buys, Saundra S, Caan, Bette, Campa, Daniele, Canzian, Federico, Castelao, Jose E, Chang-Claude, Jenny, Chanock, Stephen J, Cheng, Ting-Yuan David, Clarke, Christine L, Colonna, Sarah V, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, Dennis, Joe, Dörk, Thilo, Dossus, Laure, Dunning, Alison M, Dwek, Miriam, Eccles, Diana M, Ekici, Arif B, Eliassen, A Heather, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Flyger, Henrik, Fritschi, Lin, Gago-Dominguez, Manuela, García-Sáenz, José A, Giles, Graham G, Grip, Mervi, Guénel, Pascal, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hart, Steven N, Hartikainen, Jaana M, Hartmann, Arndt, He, Wei, Hooning, Maartje J, Hoppe, Reiner, Hopper, John L, Howell, Anthony, Hunter, David J, Jager, Agnes, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Jung, Audrey Y, Kaaks, Rudolf, Keupers, Machteld, Kitahara, Cari M, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N, Kurian, Allison W, Lacey, James V, Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Linet, Martha, Luben, Robert N, Lubiński, Jan, Lush, Michael, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martens, John WM, Martinez, Maria Elena, Mavroudis, Dimitrios, Michailidou, Kyriaki, Milne, Roger L, Mulligan, Anna Marie, Muranen, Taru A, Nevanlinna, Heli, Newman, William G, and Nielsen, Sune F

Subjects
Clinical Research, Cancer, Breast Cancer, Human Genome, Genetics, 2.1 Biological and endogenous factors, Aetiology, Breast Neoplasms, Female, Genome-Wide Association Study, Germ-Line Mutation, Humans, Polymorphism, Single Nucleotide, Prognosis, Survival Analysis, Common germline genetic variants, Breast cancer-specific survival, Patient subgroups, Tumor biology, Systemic treatment, NBCS Collaborators, ABCTB Investigators, kConFab Investigators, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

BackgroundGiven the high heterogeneity among breast tumors, associations between common germline genetic variants and survival that may exist within specific subgroups could go undetected in an unstratified set of breast cancer patients.MethodsWe performed genome-wide association analyses within 15 subgroups of breast cancer patients based on prognostic factors, including hormone receptors, tumor grade, age, and type of systemic treatment. Analyses were based on 91,686 female patients of European ancestry from the Breast Cancer Association Consortium, including 7531 breast cancer-specific deaths over a median follow-up of 8.1 years. Cox regression was used to assess associations of common germline variants with 15-year and 5-year breast cancer-specific survival. We assessed the probability of these associations being true positives via the Bayesian false discovery probability (BFDP

Published
2021

35. Germline variants and breast cancer survival in patients with distant metastases at primary breast cancer diagnosis.

Author

Escala-Garcia, Maria, Canisius, Sander, Keeman, Renske, Beesley, Jonathan, Anton-Culver, Hoda, Arndt, Volker, Augustinsson, Annelie, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Bermisheva, Marina, Bojesen, Stig E, Bolla, Manjeet K, Brenner, Hermann, Canzian, Federico, Castelao, Jose E, Chang-Claude, Jenny, Chanock, Stephen J, Couch, Fergus J, Czene, Kamila, Daly, Mary B, Dennis, Joe, Devilee, Peter, Dörk, Thilo, Dunning, Alison M, Easton, Douglas F, Ekici, Arif B, Eliassen, A Heather, Fasching, Peter A, Flyger, Henrik, Gago-Dominguez, Manuela, García-Closas, Montserrat, García-Sáenz, José A, Geisler, Jürgen, Giles, Graham G, Grip, Mervi, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hartikainen, Jaana M, Heemskerk-Gerritsen, Bernadette AM, Hollestelle, Antoinette, Hoppe, Reiner, Hopper, John L, Hunter, David J, Jacot, William, Jakubowska, Anna, John, Esther M, Jung, Audrey Y, Kaaks, Rudolf, Khusnutdinova, Elza, Koppert, Linetta B, Kraft, Peter, Kristensen, Vessela N, Kurian, Allison W, Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Luben, Robert N, Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mavroudis, Dimitrios, Muranen, Taru A, Nevanlinna, Heli, Olshan, Andrew F, Olsson, Håkan, Park-Simon, Tjoung-Won, Patel, Alpa V, Peterlongo, Paolo, Pharoah, Paul DP, Punie, Kevin, Radice, Paolo, Rennert, Gad, Rennert, Hedy S, Romero, Atocha, Roylance, Rebecca, Rüdiger, Thomas, Ruebner, Matthias, Saloustros, Emmanouil, Sawyer, Elinor J, Schmutzler, Rita K, Schoemaker, Minouk J, Scott, Christopher, Southey, Melissa C, Surowy, Harald, Swerdlow, Anthony J, Tamimi, Rulla M, Teras, Lauren R, Thomas, Emilie, Tomlinson, Ian, Troester, Melissa A, Vachon, Celine M, Wang, Qin, Winqvist, Robert, and Wolk, Alicja

Subjects
kConFab/AOCS Investigators, Cancer, Genetics, Breast Cancer, Prevention, 2.1 Biological and endogenous factors, 4.1 Discovery and preclinical testing of markers and technologies
Abstract

Breast cancer metastasis accounts for most of the deaths from breast cancer. Identification of germline variants associated with survival in aggressive types of breast cancer may inform understanding of breast cancer progression and assist treatment. In this analysis, we studied the associations between germline variants and breast cancer survival for patients with distant metastases at primary breast cancer diagnosis. We used data from the Breast Cancer Association Consortium (BCAC) including 1062 women of European ancestry with metastatic breast cancer, 606 of whom died of breast cancer. We identified two germline variants on chromosome 1, rs138569520 and rs146023652, significantly associated with breast cancer-specific survival (P = 3.19 × 10-8 and 4.42 × 10-8). In silico analysis suggested a potential regulatory effect of the variants on the nearby target genes SDE2 and H3F3A. However, the variants showed no evidence of association in a smaller replication dataset. The validation dataset was obtained from the SNPs to Risk of Metastasis (StoRM) study and included 293 patients with metastatic primary breast cancer at diagnosis. Ultimately, larger replication studies are needed to confirm the identified associations.

Published
2021

36. Immediate effect of the COVID-19 pandemic on patient health, health-care use, and behaviours: results from an international survey of people with rheumatic diseases

Author

Hausmann, Jonathan S, Kennedy, Kevin, Simard, Julia F, Liew, Jean W, Sparks, Jeffrey A, Moni, Tarin T, Harrison, Carly, Larché, Maggie J, Levine, Mitchell, Sattui, Sebastian E, Semalulu, Teresa, Foster, Gary, Surangiwala, Salman, Thabane, Lehana, Beesley, Richard P, Durrant, Karen L, Mateus, Elsa F, Mingolla, Serena, Nudel, Michal, Palmerlee, Candace A, Richards, Dawn P, Liew, David FL, Hill, Catherine L, Bhana, Suleman, Costello, Wendy, Grainger, Rebecca, Machado, Pedro M, Robinson, Philip C, Sufka, Paul, Wallace, Zachary S, Yazdany, Jinoos, Sirotich, Emily, Alliance, COVID-19 Global Rheumatology, Sufka, Paul H, Singh, Namrata, Howard, Richard A, Kim, Alfred HJ, Westrich-Robertson, Tiffany, Tsui, Edmund, Duarte-Garcia, Ali, Tam, Herman, Jayatilleke, Arundathi, Konig, Maximilian F, Graef, Elizabeth R, Putman, Michael S, Syed, Reema H, Korsten, Peter, Mateus, Elsa, Laura, Upton A, Adam, Kilian, Chock, Yu Pei Eugenia, White, Douglas W, Zamora, Geraldine T, Traboco, Lisa S, Patel, Aarat M, Ugarte-Gil, Manuel F, Gianfrancesco, Milena A, Amigues, Isabelle, Sanchez-Alvarez, Catalina, Trupin, Laura, Jacobsohn, Lindsay R, Hoyer, Bimba F, Makan, Kavita, Gossec, Laure, Priyank, Chaudhary, Leipe, Jan, Wallace, Beth, Angeles-Han, Sheila T, Almaghlouth, Ibrahim A, Katherine, Wysham D, Padula, Anthony S, Berenbaum, Francis, Treemarcki, Erin M, Sinha, Rashmi, Lewandowski, Laura B, Webb, Kate, Young, Kristen J, Bulina, Inita, Uribe, Sebastian Herrera, Rubinstein, Tamar B, Nolan, Marc W, Ang, Elizabeth Y, Venuturupalli, Swamy R, Dubreuil, Maureen, Pisoni, Cecilia N, Cosatti, Micaela A, Campos, Jose, and Conway, Richard

Subjects
Arthritis, Aging, Autoimmune Disease, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Inflammatory and immune system, Good Health and Well Being, COVID-19 Global Rheumatology Alliance
Abstract

BackgroundThe impact and consequences of the COVID-19 pandemic on people with rheumatic disease are unclear. We developed the COVID-19 Global Rheumatology Alliance Patient Experience Survey to assess the effects of the COVID-19 pandemic on people with rheumatic disease worldwide.MethodsSurvey questions were developed by key stakeholder groups and disseminated worldwide through social media, websites, and patient support organisations. Questions included demographics, rheumatic disease diagnosis, COVID-19 diagnosis, adoption of protective behaviours to mitigate COVID-19 exposure, medication access and changes, health-care access and communication with rheumatologists, and changes in employment or schooling. Adults age 18 years and older with inflammatory or autoimmune rheumatic diseases were eligible for inclusion. We included participants with and without a COVID-19 diagnosis. We excluded participants reporting only non-inflammatory rheumatic diseases such as fibromyalgia or osteoarthritis.Findings12 117 responses to the survey were received between April 3 and May 8, 2020, and of these, 10 407 respondents had included appropriate age data. We included complete responses from 9300 adults with rheumatic disease (mean age 46·1 years; 8375 [90·1%] women, 893 [9·6%] men, and 32 [0·3%] participants who identified as non-binary). 6273 (67·5%) of respondents identified as White, 1565 (16·8%) as Latin American, 198 (2·1%) as Black, 190 (2·0%) as Asian, and 42 (0·5%) as Native American or Aboriginal or First Nation. The most common rheumatic disease diagnoses included rheumatoid arthritis (3636 [39·1%] of 9300), systemic lupus erythematosus (2882 [31·0%]), and Sjögren's syndrome (1290 [13·9%]). Most respondents (6921 [82·0%] of 8441) continued their antirheumatic medications as prescribed. Almost all (9266 [99·7%] of 9297) respondents adopted protective behaviours to limit SARS-CoV-2 exposure. A change in employment status occurred in 2524 (27·1%) of 9300) of respondents, with a 13·6% decrease in the number in full-time employment (from 4066 to 3514).InterpretationPeople with rheumatic disease maintained therapy and followed public health advice to mitigate the risks of COVID-19. Substantial employment status changes occurred, with potential implications for health-care access, medication affordability, mental health, and rheumatic disease activity.FundingAmerican College of Rheumatology.

Published
2021

37. The Unique Challenges of Afterschool Research: A Practical Guide for Evaluators and Practitioners

Author

Murchison, Lizzie, Brohawn, Katie, Fanscali, Cheri, Beesley, Andrea D., and Stafford, Erin

Abstract

Funders and policymakers are increasingly recognizing the afterschool field for its vital role in supporting the social and emotional growth and academic achievement of school-age youth. Although this recognition is welcome, it often comes with increased expectations for high-quality research demonstrating the value of programming. To satisfy these demands and make the most of funding opportunities, practitioners must develop strong partnerships with external evaluators. However, developing afterschool evaluation partnerships that work well for all parties is often far more difficult than program directors or evaluators anticipate. When research is conducted in K-12 schools, educators often bring some experience in assessment methods, and researchers often have at least a basic knowledge of pedagogy. In contrast, in the out-of-school time (OST) field, program directors with little formal research experience are frequently paired with evaluators who lack experience in OST programs. This research-practice gap, if not addressed, can translate into frustrating evaluation experiences for practitioners and evaluators alike. Program directors may finish an evaluation feeling that they did not learn anything new or that the study was entirely for the benefit of the funder. Evaluators may find themselves stymied by data collection issues and communication challenges they are unprepared to solve. The literature offers little practical guidance about developing and conducting research in OST settings, beyond instruments for possible use in evaluation. This article addresses this gap by providing candid advice for evaluators seeking to transition from K-12 to afterschool research. This advice may also help program directors and other stakeholders who want to make the research process work more effectively for them. We aim to help evaluators understand what is and is not possible (or advisable) in afterschool evaluations and to help practitioners serve as more effective partners by anticipating evaluator assumptions and other challenges that can derail a study. The authors bring a variety of experience in researching and evaluating OST programs. They have conducted mixed-method evaluation studies for general programmatic improvement as well as rigorous randomized control trials for federal agencies, including the National Science Foundation and the U.S. Department of Education. Some of them have studied community-based afterschool programs generally, while others have concentrated on specific initiatives in STEM, literacy, and social and emotional learning. Many of the afterschool programs they have researched have taken place in schools, though a few have been located in spaces such as community centers, museums, libraries, and maker labs. This article addresses a broad spectrum of research designs, from formative assessments to confirmatory analyses, in varied OST settings. In their experience, regardless of the intended audience for the report or the level of rigor in the study design, evaluators transitioning to afterschool are challenged by a common set of issues related to data collection and communication. This article addresses those challenges. First, they describe how afterschool is unique--and particularly how it is different from K-12 education. Next, they recommend ways to take those unique features into account when designing and implementing an afterschool study. The final section addresses best practices for forming and maintaining strong partnerships between evaluators and practitioners to produce results that meet the needs not only of funders but also of the program and its staff, students, and families.

Published
2019

39. Adenosine metabolized from extracellular ATP ameliorates organ injury by triggering A2BR signaling

Author

Taha Kelestemur, Zoltán H. Németh, Pal Pacher, Jennet Beesley, Simon C. Robson, Holger K. Eltzschig, and György Haskó

Subjects
CD39, CD73, A2BR, Adenosine, Acute lung injury, Trauma hemorrhagic shock, Diseases of the respiratory system, RC705-779
Abstract

Abstract Background Trauma and a subsequent hemorrhagic shock (T/HS) result in insufficient oxygen delivery to tissues and multiple organ failure. Extracellular adenosine, which is a product of the extracellular degradation of adenosine 5’ triphosphate (ATP) by the membrane-embedded enzymes CD39 and CD73, is organ protective, as it participates in signaling pathways, which promote cell survival and suppress inflammation through adenosine receptors including the A2BR. The aim of this study was to evaluate the role of CD39 and CD73 delivering adenosine to A2BRs in regulating the host’s response to T/HS. Methods T/HS shock was induced by blood withdrawal from the femoral artery in wild-type, global knockout (CD39, CD73, A2BR) and conditional knockout (intestinal epithelial cell-specific deficient VillinCre-A2BRfl/fl) mice. At 3 three hours after resuscitation, blood and tissue samples were collected to analyze organ injury. Results T/HS upregulated the expression of CD39, CD73, and the A2BR in organs. ATP and adenosine levels increased after T/HS in bronchoalveolar lavage fluid. CD39, CD73, and A2BR mimics/agonists alleviated lung and liver injury. Antagonists or the CD39, CD73, and A2BR knockout (KO) exacerbated lung injury, inflammatory cytokines, and chemokines as well as macrophage and neutrophil infiltration and accumulation in the lung. Agonists reduced the levels of the liver enzymes aspartate transferase and alanine transaminase in the blood, whereas antagonist administration or CD39, CD73, and A2BR KO enhanced enzyme levels. In addition, intestinal epithelial cell-specific deficient VillinCre-A2BRfl/fl mice showed increased intestinal injury compared to their wild-type VillinCre controls. Conclusion In conclusion, the CD39-CD73-A2BR axis protects against T/HS-induced multiple organ failure.

Published
2023
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40. Associations between body mass index and episodic memory for recent eating, mindful eating, and cognitive distraction: A cross‐sectional study

Author

Elanor C. Hinton, Victoria Beesley, Sam D. Leary, and Danielle Ferriday

Subjects
adults, appetite, body mass index, cognitive distraction, eating behaviors, episodic memory for recent eating, Internal medicine, RC31-1245
Abstract

Abstract Objectives Eating while distracted has been associated with a higher body mass index (BMI), whereas mindful eating and episodic memory for recent eating have shown the opposite pattern. This pre‐registered, global study (https://osf.io/rdjzk) compared the relative association between these variables (and four “positive controls”: restraint, disinhibition, emotional eating, plate clearing) and self‐reported BMI. The timing of data collection (April–May 2020) during the SARS‐CoV‐2 pandemic enabled an investigation of the impact of stay‐at‐home restrictions imposed on the UK population on the measures of eating behavior. Methods An online survey was completed, including: (i) demographic data (e.g., self‐reported BMI), (ii) Likert ratings assessing episodic memory for recent eating, mindful eating, cognitive distraction, restrained eating, emotional eating, disinhibition and plate clearing over the last 12 months and the last 7 days (during the first UK COVID‐19 lockdown), and (iii) the Mindful Eating Questionnaire (MEQ). Results A large adult sample participated (N = 846; mean (SD) age = 33.0 (14.3) years; mean (SD) BMI = 24.6 (5.6) kg/m2). Mindful eating (MEQ‐total score) was associated with a lower self‐reported BMI (β = −0.12; 95% CI = −0.20, −0.04; p = 0.004), whereas disinhibited eating was associated with a higher self‐reported BMI (β = 0.30; 95% CI = 0.21, 0.38; p

Published
2024
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42. Identifying predictors and determining mortality rates of septic cardiomyopathy and sepsis-related cardiogenic shock: A retrospective, observational study.

Author

Kathryn W Hendrickson, Meghan M Cirulis, Rebecca E Burk, Michael J Lanspa, Ithan D Peltan, Hunter Marshall, Danielle Groat, Al Jephson, Sarah J Beesley, and Samuel M Brown

Subjects
Medicine, Science
Abstract

IntroductionSeptic shock is a severe form of sepsis that has a high mortality rate, and a substantial proportion of these patients will develop cardiac dysfunction, often termed septic cardiomyopathy (SCM). Some SCM patients may develop frank cardiac failure, termed sepsis-related cardiogenic shock (SeRCS). Little is known of SeRCS. This study describes baseline characteristics of patients with SCM and SeRCS compared to patients with septic shock without cardiac dysfunction. We compare clinical outcomes among SCM, SeRCS, and septic shock, and identify risk factors for the development of SCM and SeRCS.MethodsSeptic patients admitted to the ICU with an echocardiogram obtained within 72 hours were included. Left ventricular ejection fraction of ≤55% was used to define SCM, and cardiac index ≤2.1 L/min/m2 among patients with SCM defined SeRCS. Machine learning was used to identify risk factors for development of SCM and SeRCS. Logistic regression was used to compare mortality among groups.ResultsAmong 1229 patients, 977 patients had septic shock without cardiac dysfunction, 207 had SCM, and 45 had SeRCS. In patients with septic shock, the strongest predictor for developing SCM and SeRCs was a prior history of cardiac dysfunction. Mortality did not significantly differ among the three groups.ConclusionsSCM and SeRCS affect a minority of patients with septic shock, disproportionately affecting individuals with a history of cardiac disease. We did not identify a mortality difference associated with SCM or SeRCS. Additional work is needed to define further subtypes and treatment options for this patient population.

Published
2024
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43. Pre-post feasibility trial of a telephone-delivered exercise intervention for patients during chemotherapy for recurrent ovarian cancer: the ECHO-R trial protocol

Author

Andreas Obermair, Monika Janda, Sandra C Hayes, Elizabeth Eakin, Marcelo Nascimento, Dimitrios Vagenas, Jermaine Coward, Louisa G Gordon, Catherine Shannon, James Nicklin, Jeffrey Goh, Vanessa L Beesley, Penny Webb, Merran Williams, Sheree Rye, Rosalind R Spence, Helene O’Neill, Melissa J Newton, Sara Baniahmadi, and Andrea Garret

Subjects
Medicine
Abstract

Introduction The benefits of exercise in reducing treatment-related morbidity and improving quality of life following a primary diagnosis of cancer have been well documented and have led to exercise being recommended by oncology societies for all people with a cancer diagnosis. However, these recommendations are derived from research typically involving cohorts with more common cancers and relatively good prognosis, such as breast and prostate. Evidence from these cancers may not apply to women with recurrent ovarian cancer. Therefore, the primary objective of this trial is to evaluate the feasibility and safety of a home-based, telephone-delivered exercise intervention for women undergoing chemotherapy for recurrent ovarian cancer.Methods and analysis The Exercise During Chemotherapy for Recurrent Ovarian Cancer (ECHO-R) trial is a single-arm, phase II, pre/postintervention trial of a 6-month, telephone-delivered exercise intervention (consistent with recommended exercise oncology prescription). The target sample size is 80 women who are currently undergoing (or are scheduled to receive) chemotherapy for recurrent ovarian cancer. Recruitment is through participating hospital sites in Queensland, Australia, or via self-referral. The exercise intervention comprises 12 telephone sessions over a 6-month period delivered by trial-trained exercise professionals and supplemented (where feasible) by five sessions face to face. Exercise prescription is individualised and works towards an overall goal of achieving a weekly target of 150 min of moderate-intensity, mixed-mode exercise. Assessments via self-administered survey and physical fitness and function tests occur at baseline and then at 6 and 9 months postbaseline. Data to inform feasibility and safety are recorded as case notes by the exercise professional during each session.Ethics and dissemination Ethics approval for the ECHO-R trial was granted by the Metro North Human Research Ethics Committee (HREC/2020/QRBW/67223) on 6 November 2020. Findings from the trial are planned to be disseminated via peer-reviewed publications and both national and international exercise and oncology conferences.Trial registration number ACTRN12621000042842.

Published
2024
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44. Patient Recruitment Using Electronic Health Records Under Selection Bias: a Two-phase Sampling Framework

Author

Zhang, Guanghao, Beesley, Lauren J., Mukherjee, Bhramar, and Shi, Xu

Subjects
Statistics - Methodology
Abstract

Electronic health records (EHRs) are increasingly recognized as a cost-effective resource for patient recruitment in clinical research. However, how to optimally select a cohort from millions of individuals to answer a scientific question of interest remains unclear. Consider a study to estimate the mean or mean difference of an expensive outcome. Inexpensive auxiliary covariates predictive of the outcome may often be available in patients' health records, presenting an opportunity to recruit patients selectively which may improve efficiency in downstream analyses. In this paper, we propose a two-phase sampling design that leverages available information on auxiliary covariates in EHR data. A key challenge in using EHR data for multi-phase sampling is the potential selection bias, because EHR data are not necessarily representative of the target population. Extending existing literature on two-phase sampling design, we derive an optimal two-phase sampling method that improves efficiency over random sampling while accounting for the potential selection bias in EHR data. We demonstrate the efficiency gain from our sampling design via simulation studies and an application to evaluating the prevalence of hypertension among US adults leveraging data from the Michigan Genomics Initiative, a longitudinal biorepository in Michigan Medicine.

Published
2020

45. Variable selection with multiply-imputed datasets: choosing between stacked and grouped methods

Author

Du, Jiacong, Boss, Jonathan, Han, Peisong, Beesley, Lauren J, Goutman, Stephen A, Batterman, Stuart, Feldman, Eva L, and Mukherjee, Bhramar

Subjects
Statistics - Methodology, Statistics - Applications, Statistics - Computation
Abstract

Penalized regression methods, such as lasso and elastic net, are used in many biomedical applications when simultaneous regression coefficient estimation and variable selection is desired. However, missing data complicates the implementation of these methods, particularly when missingness is handled using multiple imputation. Applying a variable selection algorithm on each imputed dataset will likely lead to different sets of selected predictors, making it difficult to ascertain a final active set without resorting to ad hoc combination rules. In this paper we consider a general class of penalized objective functions which, by construction, force selection of the same variables across multiply-imputed datasets. By pooling objective functions across imputations, optimization is then performed jointly over all imputed datasets rather than separately for each dataset. We consider two objective function formulations that exist in the literature, which we will refer to as "stacked" and "grouped" objective functions. Building on existing work, we (a) derive and implement efficient cyclic coordinate descent and majorization-minimization optimization algorithms for both continuous and binary outcome data, (b) incorporate adaptive shrinkage penalties, (c) compare these methods through simulation, and (d) develop an R package miselect for easy implementation. Simulations demonstrate that the "stacked" objective function approaches tend to be more computationally efficient and have better estimation and selection properties. We apply these methods to data from the University of Michigan ALS Patients Repository (UMAPR) which aims to identify the association between persistent organic pollutants and ALS risk., Comment: 23 pages, 6 figures. This paper has been submitted to Statistics in Medicine

Published
2020

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