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1. Windowing Regularization Techniques for Unsteady Aerodynamic Shape Optimization

Author

Schotthöfer, Steffen, Zhou, Beckett Y., Albring, Tim, and Gauger, Nicolas R.

Subjects
Mathematics - Numerical Analysis
Abstract

Unsteady Aerodynamic Shape Optimization presents new challenges in terms of sensitivity analysis of time-dependent objective functions. In this work, we consider periodic unsteady flows governed by the URANS equations. Hence, the resulting output functions acting as objective or constraint functions of the optimization are themselves periodic with unknown period length, that may depend on the design parameter of said optimization. Sensitivity Analysis on the time-average of a function with these properties turns out to be difficult. Therefore, we explore methods to regularize the time average of such a function with the so called windowing-approach. Furthermore, we embed these regularizers into the discrete adjoint solver for the URANS equations of the multi-physics and optimization software SU2. Finally, we exhibit a comparison study between the classical non regularized optimization procedure and the ones enhanced with regularizers of different smoothness and show that the latter result in a more robust optimization.

Published
2024
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3. Dynamic proportional loss of functional connectivity revealed change of left superior frontal gyrus in subjective cognitive decline: an explanatory study based on Chinese and Western cohorts

Author

Wang, Luyao, Hu, Wenjing, Dong, Fan, Sheng, Can, Wu, Jinglong, Han, Ying, Jiang, Jiehui, Weiner, Michael W., Aisen, Paul, Petersen, Ronald, Jack, Clifford R., Jagust, William, Trojanowski, John Q., Toga, Arthur W., Beckett, Laurel, Green, Robert C., Saykin, Andrew J., Morris, John, Shaw, Leslie M., Khachaturian, Zaven, Sorensen, Greg, Kuller, Lew, Raichle, Marcus, Paul, Steven, Davies, Peter, Fillit, Howard, Hefti, Franz, Holtzman, David, Mesulam, Marek M., Potter, William, Snyder, Peter, Schwartz, Adam, Montine, Tom, Thomas, Ronald G., Donohue, Michael, Walter, Sarah, Gessert, Devon, Sather, Tamie, Jiminez, Gus, Harvey, Danielle, Bernstein, Matthew, Thompson, Paul, Schuff, Norbert, Borowski, Bret, Gunter, Jeff, Senjem, Matt, Vemuri, Prashanthi, Jones, David, Kantarci, Kejal, Ward, Chad, Koeppe, Robert A., Foster, Norm, Reiman, Eric M., Chen, Kewei, Mathis, Chet, Landau, Susan, Cairns, Nigel J., Householder, Erin, Taylor-Reinwald, Lisa, Lee, Virginia, Korecka, Magdalena, Figurski, Michal, Crawford, Karen, Neu, Scott, Foroud, Tatiana M., Potkin, Steven G., Shen, Li, Faber, Kelley, Kim, Sungeun, Nho, Kwangsik, Thal, Leon, Buckholtz, Neil, Albert, Marylyn, Frank, Richard, Hsiao, John, Kaye, Jeffrey, Quinn, Joseph, Lind, Betty, Carter, Raina, Dolen, Sara, Schneider, Lon S., Pawluczyk, Sonia, Beccera, Mauricio, Teodoro, Liberty, Spann, Bryan M., Brewer, James, Vanderswag, Helen, Fleisher, Adam, Heidebrink, Judith L., Lord, Joanne L., Mason, Sara S., Albers, Colleen S., Knopman, David, Johnson, Kris, Doody, Rachelle S., Villanueva-Meyer, Javier, Chowdhury, Munir, Rountree, Susan, Dang, Mimi, Stern, Yaakov, Honig, Lawrence S., Bell, Karen L., Ances, Beau, Carroll, Maria, Leon, Sue, Mintun, Mark A., Schneider, Stacy, Oliver, Angela, Marson, Daniel, Griffith, Randall, Clark, David, Geldmacher, David, Brockington, John, Roberson, Erik, Grossman, Hillel, Mitsis, Effie, de Toledo-Morrell, Leyla, Shah, Raj C., Duara, Ranjan, Varon, Daniel, Greig, Maria T., Roberts, Peggy, Onyike, Chiadi, D’Agostino, Daniel, Kielb, Stephanie, Galvin, James E., Cerbone, Brittany, Michel, Christina A., Rusinek, Henry, de Leon, Mony J., Glodzik, Lidia, De Santi, Susan, Doraiswamy, PMurali, Petrella, Jeffrey R., Wong, Terence Z., Arnold, Steven E., Karlawish, Jason H., Wolk, David, Smith, Charles D., Jicha, Greg, Hardy, Peter, Sinha, Partha, Oates, Elizabeth, Conrad, Gary, Lopez, Oscar L., Oakley, MaryAnn, Simpson, Donna M., Porsteinsson, Anton P., Goldstein, Bonnie S., Martin, Kim, Makino, Kelly M., Ismail, MSaleem, Brand, Connie, Mulnard, Ruth A., Thai, Gaby, McAdams-Ortiz, Catherine, Womack, Kyle, Mathews, Dana, Quiceno, Mary, Diaz-Arrastia, Ramon, King, Richard, Weiner, Myron, Martin-Cook, Kristen, DeVous, Michael, Levey, Allan I., Lah, James J., Cellar, Janet S., Burns, Jeffrey M., Anderson, Heather S., Swerdlow, Russell H., Apostolova, Liana, Tingus, Kathleen, Woo, Ellen, Silverman, Daniel H. S., Lu, Po H., Bartzokis, George, Graff-Radford, Neill R., Parfitt, Francine, Kendall, Tracy, Johnson, Heather, Farlow, Martin R., Hake, Ann Marie, Matthews, Brandy R., Herring, Scott, Hunt, Cynthia, van Dyck, Christopher H., Carson, Richard E., MacAvoy, Martha G., Chertkow, Howard, Bergman, Howard, Hosein, Chris, Hsiung, Ging-Yuek Robin, Feldman, Howard, Mudge, Benita, Assaly, Michele, Bernick, Charles, Munic, Donna, Kertesz, Andrew, Rogers, John, Trost, Dick, Kerwin, Diana, Lipowski, Kristine, Wu, Chuang-Kuo, Johnson, Nancy, Sadowsky, Carl, Martinez, Walter, Villena, Teresa, Turner, Raymond Scott, Johnson, Kathleen, Reynolds, Brigid, Sperling, Reisa A., Johnson, Keith A., Marshall, Gad, Frey, Meghan, Lane, Barton, Rosen, Allyson, Tinklenberg, Jared, Sabbagh, Marwan N., Belden, Christine M., Jacobson, Sandra A., Sirrel, Sherye A., Kowall, Neil, Killiany, Ronald, Budson, Andrew E., Norbash, Alexander, Johnson, Patricia Lynn, Allard, Joanne, Lerner, Alan, Ogrocki, Paula, Hudson, Leon, Fletcher, Evan, Carmichae, Owen, Olichney, John, DeCarli, Charles, Kittur, Smita, Borrie, Michael, Lee, T.-Y., Bartha, Rob, Johnson, Sterling, Asthana, Sanjay, Carlsson, Cynthia M., Preda, Adrian, Nguyen, Dana, Tariot, Pierre, Reeder, Stephanie, Bates, Vernice, Capote, Horacio, Rainka, Michelle, Scharre, Douglas W., Kataki, Maria, Adeli, Anahita, Zimmerman, Earl A., Celmins, Dzintra, Brown, Alice D., Pearlson, Godfrey D., Blank, Karen, Anderson, Karen, Santulli, Robert B., Kitzmiller, Tamar J., Schwartz, Eben S., Sink, Kaycee M., Williamson, Jeff D., Garg, Pradeep, Watkins, Franklin, Ott, Brian R., Querfurth, Henry, Tremont, Geoffrey, Salloway, Stephen, Malloy, Paul, Correia, Stephen, Rosen, Howard J., Miller, Bruce L., Mintzer, Jacobo, Spicer, Kenneth, Bachman, David, Pasternak, Stephen, Rachinsky, Irina, Drost, Dick, Pomara, Nunzio, Hernando, Raymundo, Sarrael, Antero, Schultz, Susan K., Ponto, Laura L. Boles, Shim, Hyungsub, Smith, Karen Elizabeth, Relkin, Norman, Chaing, Gloria, Raudin, Lisa, Smith, Amanda, Fargher, Kristin, Raj, Balebail Ashok, Neylan, Thomas, Grafman, Jordan, Davis, Melissa, Morrison, Rosemary, Hayes, Jacqueline, Finley, Shannon, Friedl, Karl, Fleischman, Debra, Arfanakis, Konstantinos, James, Olga, Massoglia, Dino, Fruehling, JJay, Harding, Sandra, Peskind, Elaine R., Petrie, Eric C., Li, Gail, Yesavage, Jerome A., Taylor, Joy L., and Furst, Ansgar J.

Published
2025
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5. High-definition imaging of a filamentary connection between a close quasar pair at z = 3

Author

Tornotti, Davide, Fumagalli, Michele, Fossati, Matteo, Benitez-Llambay, Alejandro, Izquierdo-Villalba, David, Travascio, Andrea, Arrigoni Battaia, Fabrizio, Cantalupo, Sebastiano, Beckett, Alexander, Bonoli, Silvia, Dayal, Pratika, D’Odorico, Valentina, Dutta, Rajeshwari, Lusso, Elisabeta, Peroux, Celine, Rafelski, Marc, Revalski, Mitchell, Spinoso, Daniele, and Swinbank, Mark

Published
2025
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15. Spaceflight alters host-gut microbiota interactions

Author

Gonzalez, E., Lee, M. D., Tierney, B. T., Lipieta, N., Flores, P., Mishra, M., Beckett, L., Finkelstein, A., Mo, A., Walton, P., Karouia, F., Barker, R., Jansen, R. J., Green, S. J., Weging, S., Kelliher, J., Singh, N. K., Bezdan, D., Galazska, J., and Brereton, N. J. B.

Published
2024
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20. Sepsis endotypes identified by host gene expression across global cohorts

Author

Chenoweth, Josh G., Brandsma, Joost, Striegel, Deborah A., Genzor, Pavol, Chiyka, Elizabeth, Blair, Paul W., Krishnan, Subramaniam, Dogbe, Elliot, Boakye, Isaac, Fogel, Gary B., Tsalik, Ephraim L., Woods, Christopher W., Owusu-Ofori, Alex, Oppong, Chris, Oduro, George, Vantha, Te, Letizia, Andrew G., Beckett, Charmagne G., Schully, Kevin L., and Clark, Danielle V.

Published
2024
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23. Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre

Author

Beckett, Stephen J., Demory, David, Coenen, Ashley R., Casey, John R., Dugenne, Mathilde, Follett, Christopher L., Connell, Paige, Carlson, Michael C. G., Hu, Sarah K., Wilson, Samuel T., Muratore, Daniel, Rodriguez-Gonzalez, Rogelio A., Peng, Shengyun, Becker, Kevin W., Mende, Daniel R., Armbrust, E. Virginia, Caron, David A., Lindell, Debbie, White, Angelicque E., Ribalet, François, and Weitz, Joshua S.

Published
2024
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24. Unravelling the transcriptomic symphony of muscle ageing: key pathways and hub genes altered by ageing and caloric restriction in rat muscle revealed by RNA sequencing

Author

Gulam Altab, Brian J. Merry, Charles W. Beckett, Priyanka Raina, Inês Lopes, Katarzyna Goljanek-Whysall, and João Pedro de Magalhães

Subjects
Sarcopenia, Diet, Functional genomics, Nutrigenomics, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Age-related muscle wasting, sarcopenia is an extensive loss of muscle mass and strength with age and a major cause of disability and accidents in the elderly. Mechanisms purported to be involved in muscle ageing and sarcopenia are numerous but poorly understood, necessitating deeper study. Hence, we employed high-throughput RNA sequencing to survey the global changes in protein-coding gene expression occurring in skeletal muscle with age. Caloric restriction (CR) is a known prophylactic intervention against sarcopenia. Therefore, total RNA was isolated from the muscle tissue of both rats fed ad libitum and CR rats. RNA-seq data were subjected to Gene Ontology, pathway, co-expression, and interaction network analyses. This revealed the functional pathways most activated by both ageing and CR, as well as the key “hub” proteins involved in their activation. RNA-seq revealed 442 protein-coding genes to be upregulated and 377 to be downregulated in aged muscle, compared to young muscle. Upregulated genes were commonly involved in protein folding and immune responses; meanwhile, downregulated genes were often related to developmental biology. CR was found to suppress 69.7% and rescue 57.8% of the genes found to be upregulated and downregulated in aged muscle, respectively. In addition, CR uniquely upregulated 291 and downregulated 304 protein-coding genes. Hub genes implicated in both ageing and CR included Gc, Plg, Irf7, Ifit3, Usp18, Rsad2, Blm and RT1-A2, whilst those exclusively implicated in CR responses included Alb, Apoa1, Ambp, F2, Apoh, Orm1, Mx1, Oasl2 and Rtp4. Hub genes involved in ageing but unaffected by CR included Fgg, Fga, Fgb and Serpinc1. In conclusion, this comprehensive RNA sequencing study highlights gene expression patterns, hub genes and signalling pathways most affected by ageing in skeletal muscle. This data may provide the initial evidence for several targets for potential future therapeutic interventions against sarcopenia.

Published
2025
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25. Examining change and permanence in traditional earthen construction in Ghana: a case study of Tamale and Wa

Author

Irene Appeaning Addo, Ibrahim Yakubu, Alexandre S. Gagnon, Christopher T. S. Beckett, Yuner Huang, Frederick Owusu-Nimo, and Ana Margarida Armada Brás

Subjects
Change, Permanence, Preservation, Earthen construction, Transformation, Cultural heritage, Architecture, NA1-9428
Abstract

Abstract The architectural style found in Wa and Tamale is renowned for its distinctive use of earthen construction, which features square buildings with flat roofs and circular compounds with conical thatch roofs. Recently, there has been a growing inclination towards the use of alternative construction techniques in which nontraditional materials such as cement, bitumen, and used car engine oil are utilised to render wall surfaces. These structures show how the materials and design in northern Ghana have substantially evolved. However, what forces drive the changes in cob construction in this region? Furthermore, how might these changes impact the preservation of cultural heritage in Ghana? To explore the factors that contribute to the departure from traditional earthen building methods that rely on local materials, this study employs a constructivist research approach. Participants in a survey that informed this study revealed that they struggled to access building materials to construct their houses. While most of the people who responded to the survey have resided in buildings constructed with a mixture of beini and dawadawa, they hesitate to use plant-based biostabilisers in new constructions. Factors that hinder the ongoing construction and preservation of earthen buildings include shifting cultural and social norms, environmental changes, difficulties accessing local building resources, flood risks, regular maintenance requirements, and societal influences. Thus, this study concludes that if communities are empowered to take ownership and recognise the value of their cultural heritage, they are likely to be increasingly aware and appreciative of their architectural heritage. Thus, their local heritage will be preserved.

Published
2025
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26. Prepartum skeletal muscle reserves and branched-chain volatile fatty acid supplementation have minimal effects in response to intravenous glucose tolerance tests in periparturient dairy cattle

Author

K.M. Gouveia, L.M. Beckett, M.N. Flinders, T.M. Casey, and J.P. Boerman

Subjects
Dairy processing. Dairy products, SF250.5-275
Abstract

Periparturient dairy cows experience metabolic adaptations to prepare for increased nutrient requirements of the fetus and the onset of lactation. Adaptations include increased peripheral tissue insulin resistance, which can be evaluated experimentally using intravenous glucose tolerance tests (IVGTT). The objective of this study was to determine if prepartum skeletal muscle reserves and supplementation of branched-chain volatile fatty acids (BCVFA) in the prepartum period affected blood glucose, β-hydroxybutyrate (BHB), and insulin concentrations 2 wk prepartum and 1 wk postpartum utilizing an IVGTT. At 42 d before expected calving (BEC), the longissimus dorsi muscle depth was measured from an ultrasound image, and based on muscle depth, cows were assigned to either the high muscle (HM; >4.6 cm, n = 17) or low muscle (LM; ≤4.6 cm, n = 17) group. Cows were randomly assigned to either the branched-chain volatile fatty acid (BCVFA) treatment (fed as 39.1 g/d isobutyrate product; 19.4 g/d isovalerate product; 19.6 g/d 2-methylbutyrate product, all on a DM basis) or control (73.0 g/d soyhull pellets on a DM basis) treatment, which were top-dressed daily. Assignment to muscle group and treatment resulted in a 2 × 2 factorial design and the following 4 combinations: HM-CON (n = 7), HM-BCVFA (n = 10), LM-CON (n = 9), and LM-BCVFA (n = 8). On 14 d BEC and 7 DIM an IVGTT was performed following a 1 h fasting period. Baseline blood samples were taken −15 and −5 min before dextrose administration (250 mg/kg BW); blood was then collected at 12 time points over a 3-h time period. Skeletal muscle reserves had no impact on glucose or insulin response across the IVGTT period, whereas BCVFA supplementation increased glucose area under the curve (AUC) in the prepartum period but had no effect in the postpartum period. Prepartum glucose and insulin AUC were higher than the postpartum glucose and insulin AUC. Findings indicate that muscle reserves in the prepartum period do not affect insulin and glucose clearance in periparturient dairy cows, reflecting no differences in insulin sensitivity in response to IVGTT. Changes observed in glucose and insulin AUC between pre- and postpartum IVGTT reflect normal metabolic adaptations to increased energetic requirements of dairy cows between late gestation and early lactation.

Published
2025
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27. Co-design and content validation of psychosis care assessment material for medical, pharmacy, nursing, and occupational therapy curricula

Author

Jenny Chen, Jack Charles Collins, Justin Newton Scanlan, Andrea McCloughen, Rosa Howard, Claire Ashton-James, Claire L. O’Reilly, Rebekah J. Moles, Tina X. Ung, Carl R. Schneider, Bandana Saini, Jennifer Ong, Paul Beckett, Karen Watson, Margaret McGrath, Timothy F. Chen, and Sarira El-Den

Subjects
Mental health first aid, Psychosis, Co-design, Simulation, Content validation, Healthcare education, Special aspects of education, LC8-6691, Medicine
Abstract

Abstract Background Despite high disease burden and heightened suicide risk associated with psychosis, psychosis education is lacking in healthcare curricula, potentially hindering students’ willingness, and confidence to provide psychosis care as future healthcare professionals. This study aimed to co-design and content validate psychosis care assessment material for medical, pharmacy, nursing, and occupational therapy curricula. Methods A nominal group technique (NGT) meeting was conducted to generate and rank ideas among people with lived/living experience of mental illness. Prioritised ideas were used to create simulated role-play scenarios for each discipline, by discipline experts. The developed scenarios underwent content validation by content experts, whereby the content validity index was computed for relevance and clarity. Results The four highest ranked ideas based on rank scores and accumulated rank score sums were selected during the NGT meeting and used to guide the development of four role-play scenarios focusing on antipsychotic medication side effects, suicide risk, paranoia and delusions, and visual hallucinations. Discipline experts created scenario outlines and rubrics for each selected idea. Content validity indices of all items were deemed satisfactory, ranging from 0.8 to 1. Written feedback for each role-play scenario was considered and scenarios/rubrics were modified accordingly. Conclusion Overall, this study provides a framework for partnering with mental health stakeholders to co-design and validate psychosis care assessment material for healthcare curricula. Through the integral contribution of people with lived/living experience and clinicians, authentic scenarios which reflect real-life practice have been developed. Future research is required to evaluate the newly developed materials in educational setting.

Published
2025
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28. Production responses of multiparous dairy cattle with differing prepartum muscle reserves and supplementation of branched-chain volatile fatty acids

Author

K.M. Gouveia, L.M. Beckett, T.M. Casey, and J.P. Boerman

Subjects
longissimus dorsi muscle, branched-chain volatile fatty acids, transition period, Dairy processing. Dairy products, SF250.5-275, Dairying, SF221-250
Abstract

ABSTRACT: Periparturient dairy cattle undergo physiological adaptations to support fetal growth and colostrum synthesis in late gestation and milk production in early lactation. To support energy and protein demands, dairy cattle mobilize body tissue reserves. The objective of this study was to determine the effects of prepartum skeletal muscle reserves and supplementation of branched-chain volatile fatty acids (BCVFA) on body composition measurements, metabolic markers related to health, protein, and energy status, and subsequent milk yield in multiparous dairy cows. Skeletal muscle reserves were assessed by 3 ultrasounds of the longissimus dorsi muscle depth (LDD) measured 42 d before expected calving, and cows (n = 48) were assigned to either high muscle (HM; >4.6 cm) or low muscle (LM; ≤4.6 cm) groups. Cows were then randomly assigned to either control (CON) of soyhull pellets (80 g/d) or BCVFA treatment, which contained isobutyrate (40 g/d), isovalerate (20 g/d), and 2-methylbutyrate (20 g/d) calcium salt products. Treatments were top dressed from 42 d before expected calving until parturition, resulting in 4 combinations of muscle groups and treatments: HM-CON (n = 13), HM-BCVFA (n = 13), LM-CON (n = 11), and LM-BCVFA (n = 11). Measurements of the LDD, BW, and BCS were taken on the following days relative to calving: −42, −35, −21, −7, 0, 7, 14, 21, 28. Weekly blood samples were taken to measure glucose, BHB, and insulin concentrations, and 5 of the blood sample time points were used to determine 3-methylhistidine and creatinine blood concentrations. Milk yield was recorded daily for the first 28 d of lactation, and samples were taken from both milkings once a week for the first 4 wk to determine components. The statistical model included the fixed effects of treatment, group, time, and their interactions, and the random effect of cow nested within group and treatment. Prepartum muscle mobilization varied between muscle groups, as LM cows accreted muscle prepartum, and HM cows mobilized muscle. The HM cows had higher milk fat, protein, lactose, and energy-corrected milk yields. The BCVFA supplementation tended to increase blood glucose concentrations both prepartum and postpartum and decreased milk urea nitrogen concentrations. Greater prepartum skeletal muscle reserves improve productivity of early-lactation cows, likely due to differences in muscle mobilization, and BCVFA supplementation improves glucose dynamics during the transition period, which may improve the metabolic health of the periparturient dairy cow.

Published
2024
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29. Dyslexia: 'The Right Diagnosis … The Wrong Treatment'

Author

Jonathan Beckett

Abstract

The polarisation of attitudes towards dyslexia appears to be contingent upon the awareness of the implications of adopting a medical model to interpreting dyslexia (as a medical 'condition') or applying an educational overlay, based upon difficulties in certain areas, to interpreting and making provision for those with dyslexia. Specifically, it underscores the difficulties dyslexics have in reading and the comprehension of what has been read. Furthermore, it accentuates the approaches taken in the 1980s and the turn of the century to dyslexia was, for these interviewees, unfitting. However, it raises other questions about whether the current practice is suited to the needs of those with dyslexia, or whether a universal offer is made, regardless of specific need. In the wake of this research, three emergent themes occur, dyslexia and stigmatisation, the impact of stigmatisation and poorly suited provision upon self-esteem and the stress this generates. As key practitioner points, this disquisition underlines the need to tailor provision for inclusive education based upon the needs of the individual with dyslexia. It further illumines the stress of unsuitable provision, manifesting the imperative nature of adequate training and resourcing for dyslexia.

Published
2024
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32. Ancient Plasmodium genomes shed light on the history of human malaria

Author

Michel, Megan, Skourtanioti, Eirini, Pierini, Federica, Guevara, Evelyn K., Mötsch, Angela, Kocher, Arthur, Barquera, Rodrigo, Bianco, Raffaela A., Carlhoff, Selina, Coppola Bove, Lorenza, Freilich, Suzanne, Giffin, Karen, Hermes, Taylor, Hiß, Alina, Knolle, Florian, Nelson, Elizabeth A., Neumann, Gunnar U., Papac, Luka, Penske, Sandra, Rohrlach, Adam B., Salem, Nada, Semerau, Lena, Villalba-Mouco, Vanessa, Abadie, Isabelle, Aldenderfer, Mark, Beckett, Jessica F., Brown, Matthew, Campus, Franco G. R., Chenghwa, Tsang, Cruz Berrocal, María, Damašek, Ladislav, Duffett Carlson, Kellie Sara, Durand, Raphaël, Ernée, Michal, Fântăneanu, Cristinel, Frenzel, Hannah, García Atiénzar, Gabriel, Guillén, Sonia, Hsieh, Ellen, Karwowski, Maciej, Kelvin, David, Kelvin, Nikki, Khokhlov, Alexander, Kinaston, Rebecca L., Korolev, Arkadii, Krettek, Kim-Louise, Küßner, Mario, Lai, Luca, Look, Cory, Majander, Kerttu, Mandl, Kirsten, Mazzarello, Vittorio, McCormick, Michael, de Miguel Ibáñez, Patxuka, Murphy, Reg, Németh, Rita E., Nordqvist, Kerkko, Novotny, Friederike, Obenaus, Martin, Olmo-Enciso, Lauro, Onkamo, Päivi, Orschiedt, Jörg, Patrushev, Valerii, Peltola, Sanni, Romero, Alejandro, Rubino, Salvatore, Sajantila, Antti, Salazar-García, Domingo C., Serrano, Elena, Shaydullaev, Shapulat, Sias, Emanuela, Šlaus, Mario, Stančo, Ladislav, Swanston, Treena, Teschler-Nicola, Maria, Valentin, Frederique, Van de Vijver, Katrien, Varney, Tamara L., Vigil-Escalera Guirado, Alfonso, Waters, Christopher K., Weiss-Krejci, Estella, Winter, Eduard, Lamnidis, Thiseas C., Prüfer, Kay, Nägele, Kathrin, Spyrou, Maria, Schiffels, Stephan, Stockhammer, Philipp W., Haak, Wolfgang, Posth, Cosimo, Warinner, Christina, Bos, Kirsten I., Herbig, Alexander, and Krause, Johannes

Published
2024
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33. Long-chain fatty acids mediate hepatic metabolic flux in preruminating dairy calves fed flaxseed oil, high oleic soybean oil, or milk fat

Author

Linda M. Beckett, Victor M.R. Malacco, Kyrstin M. Gouveia, Adrianna Mann, Chaylen J. Andolino, KaLynn Harlow, Nishanth E. Sunny, Rafael C. Neves, John R. Burgess, Jaquelyn P. Boerman, Theresa.M. Casey, and Shawn S. Donkin

Subjects
preruminating calf, flaxseed oil, metabolic flux, high oleic soybean oil, Dairy processing. Dairy products, SF250.5-275, Dairying, SF221-250
Abstract

ABSTRACT: Nutrition and physiological state affect hepatic metabolism. Our objective was to determine whether feeding flaxseed oil (∼50% C18:3n-3 cis), high oleic soybean oil (∼70% C18:1 cis-9), or milk fat (∼50% C16:0) alters hepatic expression of PC, PCK1, and PCK2 and the flow of carbons from propionate and pyruvate into the tricarboxylic acid (TCA) cycle in preruminating calves. Male Holstein calves (n = 40) were assigned to a diet of skim milk with either: 3% milk fat (MF; n = 8), 3% flaxseed oil (Flax; n = 8), 3% high oleic soybean oil (HOSO; n = 8), 1.5% MF + 1.5% high oleic soybean oil (MF-HOSO; n = 8), or 1.5% MF + 1.5% flaxseed oil (MF-Flax; n = 8) from d 14 to d 21 postnatal. At d 21 postnatal, a liver biopsy was taken for gene expression and metabolic flux analysis. Liver explants were incubated in [U-13C] propionate and [U-13C] pyruvate to trace carbon flux through TCA cycle intermediates or with [U-14C] lactate, [1-14C] palmitic acid, or [2-14C] propionate to quantify substrate oxidation to CO2 and acid-soluble products. Compared with other treatments, plasma C18:3n-3 cis was 10 times higher and C18:1 cis-9 was 3 times lower in both Flax (Flax and MF-Flax) treatments. PC, PCK1, and PCK2 expression and flux of [U-13C] pyruvate as well as [U-13C] propionate were not different among treatments. PC expression was negatively correlated with the enrichment of citrate M+5 and malate M+3, and PCK2 was negatively correlated with citrate M+5, suggesting that when expression of these enzymes is increased, carbon from pyruvate enters the TCA cycle via PC-mediated carboxylation, and then oxaloacetate is converted to phosphoenolpyruvate via PCK2. Acid-soluble product formation and PC expression were reduced in HOSO (MF-HOSO and HOSO) treatments compared with Flax (MF-Flax and Flax), indicating that fatty acids regulate PC expression and carbon flux, but that fatty acid flux control points are not connected to PC, PCK1, or PCK2. In conclusion, fatty acids regulate hepatic expression of PC, PCK1, and PCK2, and carbon flux, but the point of control is distinct.

Published
2024
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34. Geographically widespread and novel hemotropic mycoplasmas and bartonellae in Mexican free-tailed bats and sympatric North American bat species

Author

Daniel J. Becker, Kristin E. Dyer, Lauren R. Lock, Beckett L. Olbrys, Shawn A. Pladas, Anushka A. Sukhadia, Bret Demory, Juliana Maria Nunes Batista, Micaela Pineda, Nancy B. Simmons, Amanda M. Adams, Winifred F. Frick, M. Teague O'Mara, and Dmitriy V. Volokhov

Subjects
hemoplasmas, Tadarida brasiliensis, migration, One Health, Bartonella, Microbiology, QR1-502
Abstract

ABSTRACT Bacterial pathogens remain poorly characterized in bats, especially in North America. We describe novel (and in some cases panmictic) hemoplasmas (10.1% positivity) and bartonellae (25.6% positivity) across three colonies of Mexican free-tailed bats (Tadarida brasiliensis), a partially migratory species that can seasonally travel hundreds of kilometers. Molecular analyses identified three novel Candidatus hemoplasma species most similar to another novel Candidatus species in Neotropical molossid bats. We also detected novel hemoplasmas in sympatric cave myotis (Myotis velifer) and pallid bats (Antrozous pallidus), with sequences in the latter 96.5% related to Candidatus Mycoplasma haematohominis. We identified nine Bartonella genogroups, including those in cave myotis with 96.1% similarity to Candidatus Bartonella mayotimonensis. We also detected Bartonella rochalimae in migratory Mexican free-tailed bats, representing the first report of this human pathogen in the Chiroptera. Monthly sampling of migratory Mexican free-tailed bats during their North American occupancy period also revealed significant seasonality in infection for both bacterial pathogens, with prevalence increasing following spring migration, peaking in the maternity season, and declining into fall migration. The substantial diversity and seasonality of hemoplasmas and bartonellae observed here suggest that additional longitudinal, genomic, and immunological studies in bats are warranted to inform One Health approaches.IMPORTANCEBats have been intensively sampled for viruses but remain mostly understudied for bacterial pathogens. However, bacterial pathogens can have significant impacts on both human health and bat morbidity and even mortality. Hemoplasmas and bartonellae are facultative intracellular bacteria of special interest in bats, given their high prevalence and substantial genetic diversity. Surveys have also supported plausible zoonotic transmission of these bacteria from bats to humans, including Candidatus Mycoplasma haematohominis and Candidatus Bartonella mayotimonensis. Greater characterization of these bacteria across global bat diversity (over 1,480 species) is therefore warranted to inform infection risks for both bats and humans, although little surveillance has thus far been conducted in North American bats. We here describe novel (and in some cases panmictic) hemoplasmas and bartonellae across three colonies of Mexican free-tailed bats and sympatric bat species. We find high genetic diversity and seasonality of these pathogens, including lineages closely related to human pathogens, such as Bartonella rochalimae.

Published
2025
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35. Robust, fully-automated assessment of cerebral perivascular spaces and white matter lesions: a multicentre MRI longitudinal study of their evolution and association with risk of dementia and accelerated brain atrophyResearch in context

Author

Giuseppe Barisano, Michael Iv, Jeiran Choupan, Melanie Hayden-Gephart, Michael Weiner, Paul Aisen, Ronald Petersen, Clifford R. Jack, William Jagust, John Q. Trojanowki, Arthur W. Toga, Laurel Beckett, Robert C. Green, Andrew J. Saykin, John Morris, Leslie M. Shaw, Enchi Liu, Tom Montine, Ronald G. Thomas, Michael Donohue, Sarah Walter, Devon Gessert, Tamie Sather, Gus Jiminez, Danielle Harvey, Matthew Bernstein, Nick Fox, Paul Thompson, Norbert Schuff, Charles DeCarli, Bret Borowski, Jeff Gunter, Matt Senjem, Prashanthi Vemuri, David Jones, Kejal Kantarci, Chad Ward, Robert A. Koeppe, Norm Foster, Eric M. Reiman, Kewei Chen, Chet Mathis, Susan Landau, Nigel J. Cairns, Erin Householder, Lisa Taylor Reinwald, Virginia Lee, Magdalena Korecka, Michal Figurski, Karen Crawford, Scott Neu, Tatiana M. Foroud, Steven Potkin, Li Shen, Faber Kelley, Sungeun Kim, Kwangsik Nho, Zaven Kachaturian, Richard Frank, Peter J. Snyder, Susan Molchan, Jeffrey Kaye, Joseph Quinn, Betty Lind, Raina Carter, Sara Dolen, Lon S. Schneider, Sonia Pawluczyk, Mauricio Beccera, Liberty Teodoro, Bryan M. Spann, James Brewer, Helen Vanderswag, Adam Fleisher, Judith L. Heidebrink, Joanne L. Lord, Sara S. Mason, Colleen S. Albers, David Knopman, Kris Johnson, Rachelle S. Doody, Javier Villanueva Meyer, Munir Chowdhury, Susan Rountree, Mimi Dang, Yaakov Stern, Lawrence S. Honig, Karen L. Bell, Beau Ances, John C. Morris, Maria Carroll, Sue Leon, Mark A. Mintun, Stacy Schneider, Angela Oliver, Daniel Marson, Randall Griffith, David Clark, David Geld-macher, John Brockington, Erik Roberson, Hillel Grossman, Effie Mitsis, Leyla deToledo-Morrell, Raj C. Shah, Ranjan Duara, Daniel Varon, Maria T. Greig, Peggy Roberts, Marilyn Albert, Chiadi Onyike, Daniel D’Agostino, Stephanie Kielb, James E. Galvin, Dana M. Pogorelec, Brittany Cerbone, Christina A. Michel, Henry Rusinek, Mony J. de Leon, Lidia Glodzik, Susan De Santi, P. Murali Doraiswamy, Jeffrey R. Petrella, Terence Z. Wong, Steven E. Arnold, Jason H. Karlawish, David Wolk, Charles D. Smith, Greg Jicha, Peter Hardy, Partha Sinha, Elizabeth Oates, Gary Conrad, Oscar L. Lopez, MaryAnn Oakley, Donna M. Simpson, Anton P. Porsteinsson, Bonnie S. Goldstein, Kim Martin, Kelly M. Makino, M. Saleem Ismail, Connie Brand, Ruth A. Mulnard, Gaby Thai, Catherine Mc Adams Ortiz, Kyle Womack, Dana Mathews, Mary Quiceno, Ramon Diaz Arrastia, Richard King, Myron Weiner, Kristen Martin Cook, Michael DeVous, Allan I. Levey, James J. Lah, Janet S. Cellar, Jeffrey M. Burns, Heather S. Anderson, Russell H. Swerdlow, Liana Apostolova, Kathleen Tingus, Ellen Woo, Daniel H.S. Silverman, Po H. Lu, George Bartzokis, Neill R. Graff Radford, Francine Parfitt, Tracy Kendall, Heather Johnson, Martin R. Farlow, AnnMarie Hake, Brandy R. Matthews, Scott Herring, Cynthia Hunt, Christopher H. van Dyck, Richard E. Carson, Martha G. MacAvoy, Howard Chertkow, Howard Bergman, Chris Hosein, Sandra Black, Bojana Stefanovic, Curtis Caldwell, Ging-Yuek Robin Hsiung, Howard Feldman, Benita Mudge, Michele Assaly, Andrew Kertesz, John Rogers, Dick Trost, Charles Bernick, Donna Munic, Diana Kerwin, Marek Marsel Mesulam, Kristine Lipowski, Chuang Kuo Wu, Nancy Johnson, Carl Sadowsky, Walter Martinez, Teresa Villena, Raymond Scott Turner, Kathleen Johnson, Brigid Reynolds, Reisa A. Sperling, Keith A. Johnson, Gad Marshall, Meghan Frey, Jerome Yesavage, Joy L. Taylor, Barton Lane, Allyson Rosen, Jared Tinklenberg, Marwan N. Sabbagh, Christine M. Belden, Sandra A. Jacobson, Sherye A. Sirrel, Neil Kowall, Ronald Killiany, Andrew E. Budson, Alexander Norbash, Patricia Lynn Johnson, Thomas O. Obisesan, Saba Wolday, Joanne Allard, Alan Lerner, Paula Ogrocki, Leon Hudson, Evan Fletcher, Owen Carmichael, John Olichney, Smita Kittur, Michael Borrie, T.Y. Lee, Rob Bartha, Sterling Johnson, Sanjay Asthana, Cynthia M. Carlsson, Steven G. Potkin, Adrian Preda, Dana Nguyen, Pierre Tariot, Stephanie Reeder, Vernice Bates, Horacio Capote, Michelle Rainka, Douglas W. Scharre, Maria Kataki, Anahita Adeli, Earl A. Zimmerman, Dzintra Celmins, Alice D. Brown, Godfrey D. Pearlson, Karen Blank, Karen Anderson, Robert B. Santulli, Tamar J. Kitzmiller, Eben S. Schwartz, Kaycee M. Sink, Jeff D. Williamson, Pradeep Garg, Franklin Watkins, Brian R. Ott, Henry Querfurth, Geoffrey Tremont, Stephen Salloway, Paul Malloy, Stephen Correia, Howard J. Rosen, Bruce L. Miller, Jacobo Mintzer, Kenneth Spicer, David Bachman, Elizabeth Finger, Stephen Pasternak, Irina Rachinsky, Dick Drost, Nunzio Pomara, Raymundo Hernando, Antero Sarrael, Susan K. Schultz, Laura L. Boles Ponto, Hyungsub Shim, Karen Elizabeth Smith, Norman Relkin, Gloria Chaing, Lisa Raudin, Amanda Smith, Kristin Fargher, and Balebail Ashok Raj

Subjects
Perivascular spaces, White matter lesions, Small vessel disease, Dementia, Alzheimer’s disease, Glymphatic system, Medicine, Medicine (General), R5-920
Abstract

Summary: Background: Perivascular spaces (PVS) on brain MRI are surrogates for small parenchymal blood vessels and their perivascular compartment, and may relate to brain health. However, it is unknown whether PVS can predict dementia risk and brain atrophy trajectories in participants without dementia, as longitudinal studies on PVS are scarce and current methods for PVS assessment lack robustness and inter-scanner reproducibility. Methods: We developed a robust algorithm to automatically assess PVS count and size on clinical MRI, and investigated 1) their relationship with dementia risk and brain atrophy in participants without dementia, 2) their longitudinal evolution, and 3) their potential use as a screening tool in simulated clinical trials. We analysed 46,478 clinical measurements of cognitive functioning and 20,845 brain MRI scans from 10,004 participants (71.1 ± 9.7 years-old, 56.6% women) from three publicly available observational studies on ageing and dementia (the Alzheimer’s Disease Neuroimaging Initiative, the National Alzheimer’s Coordinating Centre database, and the Open Access Series of Imaging Studies). Clinical and MRI data collected between 2004 and 2022 were analysed with consistent methods, controlling for confounding factors, and combined using mixed-effects models. Findings: Our fully-automated method for PVS assessment showed excellent inter-scanner reproducibility (intraclass correlation coefficients >0.8). Fewer PVS and larger PVS diameter at baseline predicted higher dementia risk and accelerated brain atrophy. Longitudinal trajectories of PVS markers differed significantly in participants without dementia who converted to dementia compared with non-converters. In simulated placebo-controlled trials for treatments targeting cognitive decline, screening out participants at low risk of dementia based on our PVS markers enhanced the power of the trial independently of Alzheimer’s disease biomarkers. Interpretation: These robust cerebrovascular markers predict dementia risk and brain atrophy and may improve risk-stratification of patients, potentially reducing cost and increasing throughput of clinical trials to combat dementia. Funding: US National Institutes of Health.

Published
2025
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36. Long term health outcomes in people with diabetes 12 months after hospitalisation with COVID-19 in the UK: a prospective cohort studyResearch in context

Author

Safoora Gharibzadeh, Ash Routen, Cameron Razieh, Francesco Zaccardi, Claire Lawson, Clare Gillies, Simon Heller, Melanie Davies, Helen Atkins, Stephen C. Bain, Nazir L. Lone, Krisnah Poinasamy, Tunde Peto, Elizabeth Robertson, Bob Young, Desmond Johnston, Jennifer Quint, Jonathan Valabhji, Khalida Ismail, Michael Marks, Alex Horsley, Annemarie Docherty, Ewen Harrison, James Chalmers, Ling-Pei Ho, Betty Raman, Chris Brightling, Omer Elneima, Rachel Evans, Neil Greening, Victoria C. Harris, Linzy Houchen-Wolloff, Marco Sereno, Aarti Shikotra, Amisha Singapuri, Louise Wain, Claudia Langenberg, John Dennis, John Petrie, Naveed Sattar, Olivia Leavy, Mattew Richardson, Ruth M. Saunders, Anne McArdle, Hamish McASuley, Tom Yates, Kamlesh Khunti, C.E. Brightling, R.A. Evans, L.V. Wain, J.D. Chalmers, V.C. Harris, L.P. Ho, A. Horsley, M. Marks, K. Poinasamy, B. Raman, A. Shikotra, A. Singapuri, R. Dowling, C. Edwardson, O. Elneima, S. Finney, N.J. Greening, B. Hargadon, L. Houchen--Wolloff, O.C. Leavy, H.J.C. McAuley, C. Overton, T. Plekhanova, R.M. Saunders, M. Sereno, C. Taylor, S. Terry, C. Tong, B. Zhao, D. Lomas, E. Sapey, C. Berry, C.E. Bolton, N. Brunskill, E.R. Chilvers, R. Djukanovic, Y. Ellis, D. Forton, N. French, J. George, N.A. Hanley, N. Hart, L. McGarvey, N. Maskell, H. McShane, M. Parkes, D. Peckham, P. Pfeffer, A. Sayer, A. Sheikh, A.A.R. Thompson, N. Williams, W. Greenhalf, M.G. Semple, M. Ashworth, H.E. Hardwick, L. Lavelle-Langham, W. Reynolds, V. Shaw, B. Venson, A.B. Docherty, E.M. Harrison, J.K. Baillie, L. Daines, R. Free, S. Kerr, N.I. Lone, D. Lozano-Rojas, K. Ntotsis, R. Pius, J. Quint, M. Richardson, M. Thorpe, M. Halling-Brown, F. Gleeson, J. Jacob, S. Neubauer, S. Siddiqui, J.M. Wild, S. Aslani, G. Baxter, M. Beggs, C. Bloomfield, M.P. Cassar, A. Chiribiri, E. Cox, D.J. Cuthbertson, V.M. Ferreira, L. Finnigan, S. Francis, P. Jezzard, G.J. Kemp, H. Lamlum, E. Lukaschuk, C. Manisty, G.P. McCann, C. McCracken, K. McGlynn, R. Menke, C.A. Miller, A.J. Moss, T.E. Nichols, C. Nikolaidou, C. O'Brien, G. Ogbole, B. Rangelov, D.P. O'Regan, A. Pakzad, S. Piechnik, S. Plein, I. Propescu, A.A. Samat, L. Saunders, Z.B. Sanders, R. Steeds, T. Treibel, E.M. Tunnicliffe, M. Webster, J. Willoughby, J. Weir McCall, C. Xie, M. Xu, H. Baxendale, M. Brown, B. Gooptu, R.G. Jenkins, D. Jones, I. Koychev, C. Langenberg, A. Lawrie, P.L. Molyneaux, J. Pearl, M. Ralser, N. Sattar, J.T. Scott, T. Shaw, D. Thomas, D. Wilkinson, L.G. Heaney, A. De Soyza, D. Adeloye, J.S. Brown, J. Busby, C. Echevarria, J. Hurst, P. Novotny, C. Nicolaou, I. Rudan, M. Shankar-Hari, S. Walker, B. Zheng, J.R. Geddes, M. Hotopf, K. Abel, R. Ahmed, L. Allan, C. Armour, D. Baguley, D. Baldwin, C. Ballard, K. Bhui, G. Breen, K. Breeze, M. Broome, T. Brugha, E. Bullmore, D. Burn, F. Callard, J. Cavanagh, T. Chalder, D. Clark, A. David, B. Deakin, H. Dobson, B. Elliott, J. Evans, R. Francis, E. Guthrie, P. Harrison, M. Henderson, A. Hosseini, N. Huneke, M. Husain, T. Jackson, I. Jones, T. Kabir, P. Kitterick, A. Korszun, J. Kwan, A. Lingford-Hughes, P. Mansoori, H. McAllister-Williams, K. McIvor, B. Michael, L. Milligan, R. Morriss, E. Mukaetova-Ladinska, K. Munro, A. Nevado-Holgado, T. Nicholson, S. Paddick, C. Pariante, J. Pimm, K. Saunders, M. Sharpe, G. Simons, J.P. Taylor, R. Upthegrove, S. Wessely, S. Amoils, C. Antoniades, A. Banerjee, A. Bularga, P. Chowienczyk, J.P. Greenwood, A.D. Hughes, K. Khunti, C. Lawson, N.L. Mills, A.N. Sattar, C.L. Sudlow, M. Toshner, P.J.M. Openshaw, D. Altmann, R. Batterham, N. Bishop, P.C. Calder, C.M. Efstathiou, J.L. Heeney, T. Hussell, P. Klenerman, F. Liew, J.M. Lord, P. Moss, S.L. Rowland-Jones, W. Schwaeble, R.S. Thwaites, L. Turtle, S. Walmsley, D. Wraith, M.J. Rowland, A. Rostron, B. Connolly, D.F. McAuley, D. Parekh, J. Simpson, C. Summers, J. Porter, R.J. Allen, R. Aul, S. Barratt, P. Beirne, J. Blaikley, R.C. Chambers, N. Chaudhuri, C. Coleman, E. Denneny, L. Fabbri, P.M. George, M. Gibbons, B. Guillen Guio, I. Hall, E. Hufton, I. Jarrold, G. Jenkins, S. Johnson, M.G. Jones, S. Jones, F. Khan, P. Mehta, J. Mitchell, J.E. Pearl, K. Piper Hanley, P. Rivera-Ortega, L.C. Saunders, D. Smith, M. Spears, L.G. Spencer, S. Stanel, I. Stewart, D. Thickett, R. Thwaites, S. Walsh, D.G. Wootton, L. Wright, S. Heller, M.J. Davies, H. Atkins, S. Bain, J. Dennis, K. Ismail, D. Johnston, P. Kar, P. McArdle, A. McGovern, T. Peto, J. Petrie, E. Robertson, K. Shah, J. Valabhji, B. Young, L.S. Howard, Mark Toshner, J. Newman, L. Price, A. Reddy, J. Rossdale, C. Sudlow, M. Wilkins, S.J. Singh, W.D.-C. Man, N. Armstrong, E. Baldry, M. Baldwin, N. Basu, M. Beadsworth, L. Bishop, A. Briggs, M. Buch, G. Carson, H. Chinoy, C. Dawson, E. Daynes, S. Defres, L. Gardiner, P. Greenhaff, S. Greenwood, M. Harvie, L. HOuchen-Wolloff, S. MacDonald, A. McArdle, A. McMahon, M. McNarry, G. Mills, C. Nolan, K. O'Donnell, Pimm, J. Sargent, L. Sigfrid, M. Steiner, D. Stensel, A.L. Tan, I. Vogiatzis, J. Whitney, D. Wilson, M. Witham, T. Yates, C. Laing, K. Bramham, P. Chowdhury, A. Frankel, L. Lightstone, S. McAdoo, K. McCafferty, M. Ostermann, N. Selby, C. Sharpe, M. Willicombe, L. Houchen-Wolloff, J. Bunker, R. Gill, C. Hastie, R. Nathu, N. Rogers, N. Smith, A. Shaw, L. Armstrong, B. Hairsine, H. Henson, C. Kurasz, L. Shenton, S. Fairbairn, A. Dell, N. Hawkings, J. Haworth, M. Hoare, A. Lucey, V. Lewis, G. Mallison, H. Nassa, C. Pennington, A. Price, C. Price, A. Storrie, G. Willis, S. Young, K. Chong-James, C. David, W.Y. James, A. Martineau, O. Zongo, A. Sanderson, V. Brown, T. Craig, S. Drain, B. King, N. Magee, D. McAulay, E. Major, J. McGinness, R. Stone, A. Haggar, A. Bolger, F. Davies, J. Lewis, A. Lloyd, R. Manley, E. McIvor, D. Menzies, K. Roberts, W. Saxon, D. Southern, C. Subbe, V. Whitehead, H. El-Taweel, J. Dawson, L. Robinson, D. Saralaya, L. Brear, K. Regan, K. Storton, J. Fuld, A. Bermperi, I. Cruz, K. Dempsey, A. Elmer, H. Jones, S. Jose, S. Marciniak, C. Ribeiro, J. Taylor, L. Watson, J. Worsley, R. Sabit, L. Broad, A. Buttress, T. Evans, M. Haynes, L. Jones, L. Knibbs, A. McQueen, C. Oliver, K. Paradowski, J. Williams, E. Harris, C. Sampson, C. Lynch, E. Davies, C. Evenden, A. Hancock, K. Hancock, M. Rees, L. Roche, N. Stroud, T. Thomas-Woods, M. Babores, J. Bradley-Potts, M. Holland, N. Keenan, S. Shashaa, H. Wassall, E. Beranova, H. Weston, T. Cosier, L. Austin, J. Deery, T. Hazelton, H. Ramos, R. Solly, S. Turney, L. Pearce, W. McCormick, S. Pugmire, W. Stoker, A. Wilson, L.A. Aguilar Jimenez, G. Arbane, S. Betts, K. Bisnauthsing, A. Dewar, G. Kaltsakas, H. Kerslake, M.M. Magtoto, P. Marino, L.M. Martinez, T.S. Solano, E. Wynn, W. Storrar, M. Alvarez Corral, A. Arias, E. Bevan, D. Griffin, J. Martin, J. Owen, S. Payne, A. Prabhu, A. Reed, C. Wrey Brown, T. Burdett, J. Featherstone, A. Layton, C. Mills, L. Stephenson, N. Easom, P. Atkin, K. Brindle, M.G. Crooks, K. Drury, R. Flockton, L. Holdsworth, A. Richards, D.L. Sykes, S. Thackray-Nocera, C. Wright, K.E. Lewis, A. Mohamed, G. Ross, S. Coetzee, K. Davies, R. Hughes, R. Loosley, L. O'Brien, Z. Omar, H. McGuinness, E. Perkins, J. Phipps, A. Taylor, H. Tench, R. Wolf-Roberts, O. Kon, D.C. Thomas, S. Anifowose, L. Burden, E. Calvelo, B. Card, C. Carr, D. Copeland, P. Cullinan, P. Daly, L. Evison, T. Fayzan, H. Gordon, S. Haq, C. King, K. March, M. Mariveles, L. McLeavey, N. Mohamed, S. Moriera, U. Munawar, J. Nunag, U. Nwanguma, L. Orriss-Dib, A. Ross, M. Roy, E. Russell, K. Samuel, J. Schronce, N. Simpson, L. Tarusan, C. Wood, N. Yasmin, R. Reddy, A.-M. Guerdette, M. Hewitt, K. Warwick, S. White, A.M. Shah, C.J. Jolley, O. Adeyemi, R. Adrego, H. Assefa-Kebede, J. Breeze, S. Byrne, P. Dulawan, A. Hayday, A. Hoare, A. Knighton, M. Malim, S. Patale, I. Peralta, N. Powell, A. Ramos, K. Shevket, F. Speranza, A. Te, A. Ashworth, J. Clarke, C. Coupland, M. Dalton, E. Wade, C. Favager, J. Greenwood, J. Glossop, L. Hall, T. Hardy, A. Humphries, J. Murira, J. Rangeley, G. Saalmink, B. Whittam, N. Window, J. Woods, G. Coakley, L. Allerton, A. Berridge, J. Brown, S. Cooper, A. Cross, S.L. Dobson, J. Earley, K. Hainey, J. Hawkes, V. Highett, S. Kaprowska, A.L. Key, S. Koprowska, N. Lewis-Burke, G. Madzamba, F. Malein, S. Marsh, C. Mears, L. Melling, M.J. Noonan, L. Poll, J. Pratt, E. Richardson, A. Rowe, K.A. Tripp, B. Vinson, L.O. Wajero, S.A. Williams-Howard, J. Wyles, S.N. Diwanji, P. Papineni, S. Gurram, S. Quaid, G.F. Tiongson, E. Watson, B. Al-Sheklly, C. Avram, P. Barran, J. Blaikely, N. Choudhury, D. Faluyi, T. Felton, T. Gorsuch, Z. Kausar, N. Odell, R. Osbourne, K. Radhakrishnan, S. Stockdale, D. Trivedi, A. Ayoub, G. Burns, G. Davies, H. Fisher, C. Francis, A. Greenhalgh, P. Hogarth, J. Hughes, K. Jiwa, G. Jones, G. MacGowan, D. Price, H. Tedd, S. Thomas, S. West, S. Wright, A. Young, M.J. McMahon, P. Neill, D. Anderson, H. Bayes, D. Grieve, I.B. McInnes, A. Brown, A. Dougherty, K. Fallon, L. Gilmour, K. Mangion, A. Morrow, K. Scott, R. Sykes, R. Touyz, E.K. Sage, F. Barrett, A. Donaldson, M. Patel, D. Bell, R. Hamil, K. Leitch, L. Macliver, J. Quigley, A. Smith, B. Welsh, G. Choudhury, S. Clohisey, A. Deans, J. Furniss, S. Kelly, D.E. Newby, D. Connell, A. Elliott, C. Deas, S. Mohammed, J. Rowland, A.R. Solstice, D. Sutherland, C.J. Tee, D. Arnold, S. Barrett, H. Adamali, A. Dipper, S. Dunn, A. Morley, L. Morrison, L. Stadon, S. Waterson, H. Welch, B. Jayaraman, T. Light, P. Almeida, J. Bonnington, M. Chrystal, C. Dupont, A. Gupta, L. Howard, W. Jang, S. Linford, L. Matthews, R. Needham, A. Nikolaidis, S. Prosper, K. Shaw, A.K. Thomas, N.M. Rahman, M. Ainsworth, A. Alamoudi, A. Bates, A. Bloss, A. Burns, P. Carter, M. Cassar, K.M. Channon, J. Chen, F. Conneh, T. Dong, R.I. Evans, E. Fraser, X. Fu, M. Havinden-Williams, N. Kanellakis, P. Kurupati, X. Li, C. Megson, K. Motohashi, D. Nicoll, G. Ogg, E. Pacpaco, M. Pavlides, Y. Peng, N. Petousi, J. Propescu, N. Rahman, N. Talbot, E. Tunnicliffe, B. Patel, R.E. Barker, D. Cristiano, N. Dormand, M. Gummadi, S. Kon, K. Liyanage, C.M. Nolan, S. Patel, O. Polgar, P. Shah, J.A. Walsh, H. Jarvis, S. Mandal, S. Ahmad, S. Brill, L. Lim, D. Matila, O. Olaosebikan, C. Singh, L. Garner, C. Johnson, J. Mackie, A. Michael, J. Pack, K. Paques, H. Parfrey, J. Parmar, N. Diar Bakerly, P. Dark, D. Evans, E. Hardy, A. Harvey, D. Holgate, S. Knight, N. Mairs, N. Majeed, L. McMorrow, J. Oxton, J. Pendlebury, C. Summersgill, R. Ugwuoke, S. Whittaker, W. Matimba-Mupaya, S. Strong-Sheldrake, J. Bagshaw, M. Begum, K. Birchall, R. Butcher, H. Carborn, F. Chan, K. Chapman, Y. Cheng, L. Chetham, C. Clark, Z. Coburn, J. Cole, M. Dixon, A. Fairman, J. Finnigan, H. Foot, D. Foote, A. Ford, R. Gregory, K. Harrington, L. Haslam, L. Hesselden, J. Hockridge, A. Holbourn, B. Holroyd-Hind, L. Holt, A. Howell, E. Hurditch, F. Ilyas, C. Jarman, E. Lee, J.-H. Lee, R. Lenagh, A. Lye, I. Macharia, M. Marshall, A. Mbuyisa, J. McNeill, S. Megson, J. Meiring, L. Milner, S. Misra, H. Newell, T. Newman, C. Norman, L. Nwafor, D. Pattenadk, M. Plowright, P. Ravencroft, C. Roddis, J. Rodger, P. Saunders, J. Sidebottom, J. Smith, L. Smith, N. Steele, G. Stephens, R. Stimpson, B. Thamu, N. Tinker, K. Turner, H. Turton, P. Wade, J. Watson, I. Wilson, A. Zawia, M. Ali, A. Dunleavy, N. Msimanga, M. Mencias, T. Samakomva, S. Siddique, J. Teixeira, V. Tavoukjian, J. Hutchinson, L. Allsop, K. Bennett, P. Buckley, M. Flynn, M. Gill, C. Goodwin, M. Greatorex, H. Gregory, C. Heeley, L. Holloway, M. Holmes, J. Kirk, W. Lovegrove, T.A. Sewell, S. Shelton, D. Sissons, K. Slack, S. Smith, D. Sowter, S. Turner, V. Whitworth, I. Wynter, L. Warburton, S. Painter, J. Tomlinson, C. Vickers, T. Wainwright, D. Redwood, J. Tilley, S. Palmer, G.A. Davies, L. Connor, A. Cook, T. Rees, F. Thaivalappil, C. Thomas, A. Butt, M. Coulding, S. Kilroy, J. McCormick, J. McIntosh, H. Savill, V. Turner, J. Vere, E. Fraile, J. Ugoji, S.S. Kon, H. Lota, G. Landers, M. Nasseri, S. Portukhay, A. Hormis, A. Daniels, J. Ingham, L. Zeidan, M. Chablani, L. Osborne, N. Ahwireng, B. Bang, D. Basire, A. Checkley, R. Evans, M. Heightman, T. Hillman, S. Janes, R. Jastrub, M. Lipman, S. Logan, M. Merida Morillas, H. Plant, J.C. Porter, K. Roy, E. Wall, B. Williams, N. Ahmad Haider, C. Atkin, R. Baggott, M. Bates, A. Botkai, A. Casey, B. Cooper, J. Dasgin, K. Draxlbauer, N. Gautam, J. Hazeldine, T. Hiwot, S. Holden, K. Isaacs, V. Kamwa, D. Lewis, S. Madathil, C. McGhee, K. Mcgee, A. Neal, A. Newton Cox, J. Nyaboko, Z. Peterkin, H. Qureshi, L. Ratcliffe, J. Short, T. Soulsby, J. Stockley, Z. Suleiman, T. Thompson, M. Ventura, S. Walder, C. Welch, S. Yasmin, K.P. Yip, P. Beckett, C. Dickens, U. Nanda, M. Aljaroof, H. Arnold, H. Aung, M. Bakali, M. Bakau, M. Bingham, M. Bourne, C. Bourne, P. Cairns, L. Carr, A. Charalambou, C. Christie, S. Diver, S. Edwards, H. Evans, J. Finch, S. Glover, N. Goodman, B. Gootpu, K. Hadley, P. Haldar, W. Ibrahim, L. Ingram, A. Lea, D. Lee, P. McCourt, T. Mcnally, A. Moss, W. Monteiro, M. Pareek, S. Parker, A. Rowland, A. Prickett, I.N. Qureshi, R. Russell, N. Samani, M. Sharma, J. Skeemer, M. Soares, E. Stringer, T. Thornton, M. Tobin, E. Turner, T.J.C. Ward, F. Woodhead, J. Wormleighton, A. Yousuf, C. Childs, S. Fletcher, M. Harvey, E. Marouzet, B. Marshall, R. Samuel, T. Sass, T. Wallis, H. Wheeler, R. Dharmagunawardena, E. Bright, P. Crisp, M. Stern, A. Wight, L. Bailey, A. Reddington, A. Ashish, J. Cooper, E. Robinson, A. Broadley, K. Howard, L. Barman, C. Brookes, K. Elliott, L. Griffiths, Z. Guy, D. Ionita, H. Redfearn, C. Sarginson, A. Turnbull, K. Holmes, and K. Lewis

Subjects
Diabetes, Covid-19, Long Covid, Medicine (General), R5-920
Abstract

Summary: Background: People with diabetes are at increased risk of hospitalisation, morbidity, and mortality following SARS-CoV-2 infection. Long-term outcomes for people with diabetes previously hospitalised with COVID-19 are, however, unknown. This study aimed to determine the longer-term physical and mental health effects of COVID-19 in people with and without diabetes. Methods: The PHOSP-COVID study is a multicentre, long-term follow-up study of adults discharged from hospital between 1 February 2020 and 31 March 2021 in the UK following COVID-19, involving detailed assessment at 5 and 12 months after discharge. The association between diabetes status and outcomes were explored using multivariable linear and logistic regressions. Findings: People with diabetes who survived hospital admission with COVID-19 display worse physical outcomes compared to those without diabetes at 5- and 12-month follow-up. People with diabetes displayed higher fatigue (only at 5 months), frailty, lower physical performance, and health-related quality of life and poorer cognitive function. Differences in outcomes between diabetes status groups were largely consistent from 5 to 12-months. In regression models, differences at 5 and 12 months were attenuated after adjustment for BMI and presence of other long-term conditions. Interpretation: People with diabetes reported worse physical outcomes up to 12 months after hospital discharge with COVID-19 compared to those without diabetes. These data support the need to reduce inequalities in long-term physical and mental health effects of SARS-CoV-2 infection in people with diabetes. Funding: UK Research and Innovation and National Institute for Health Research. The study was approved by the Leeds West Research Ethics Committee (20/YH/0225) and is registered on the ISRCTN Registry (ISRCTN10980107).

Published
2025
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37. NutriBase – management system for the integration and interoperability of food- and nutrition-related data and knowledge

Author

Eva Valenčič, Emma Beckett, Tamara Bucher, Clare E. Collins, and Barbara Koroušić Seljak

Subjects
database management system, food data compilation, food composition data, food composition database, knowledge base, Nutrition. Foods and food supply, TX341-641
Abstract

IntroductionContemporary data and knowledge management and exploration are challenging due to regular releases, updates, and different types and formats. In the food and nutrition domain, solutions for integrating such data and knowledge with respect to the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles are still lacking.MethodsTo address this issue, we have developed a data and knowledge management system called NutriBase, which supports the compilation of a food composition database and its integration with evidence-based knowledge. This research is a novel contribution because it allows for the interconnection and complementation of food composition data with knowledge and takes what has been done in the past a step further by enabling the integration of knowledge. NutriBase focuses on two important challenges; data (semantic) harmonization by using the existing ontologies, and reducing missing data by semi-automatic data imputation made from conflating with existing databases.Results and discussionThe developed web-based tool is highly modifiable and can be further customized to meet national or international requirements. It can help create and maintain the quality management system needed to assure data quality. Newly generated data and knowledge can continuously be added, as interoperability with other systems is enabled. The tool is intended for use by domain experts, food compilers, and researchers who can add and edit food-relevant data and knowledge. However, the tool is also accessible to food manufacturers, who can regularly update information about their products and thus give consumers access to current data. Moreover, the traceability of the data and knowledge provenance allows the compilation of a trustworthy management system. The system is designed to allow easy integration of data from different sources, which enables data borrowing and reduction of missing data. In this paper, the feasibility of NutriBase is demonstrated on Slovenian food-related data and knowledge, which is further linked with international resources. Outputs such as matched food components and food classifications have been integrated into semantic resources that are currently under development in various international projects.

Published
2025
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42. MPAT: Modular Petri Net Assembly Toolkit

Author

Stefano Chiaradonna, Petar Jevtić, and Beckett Sterner

Subjects
Petri Nets, Discrete event simulation, Spatial modeling, Spike, Snoopy, Computer software, QA76.75-76.765
Abstract

We present a Python package called Modular Petri Net Assembly Toolkit (MPAT) that empowers users to easily create large-scale, modular Petri Nets for various spatial configurations, including extensive spatial grids or those derived from shapefiles, augmented with heterogeneous information layers. Petri Nets are powerful discrete event system modeling tools in computational biology and engineering. However, their utility for automated construction of large-scale spatial models has been limited by gaps in existing modeling software packages. MPAT addresses this gap by supporting the development of modular Petri Net models with flexible spatial geometries.

Published
2024
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45. The possible influence of third-order shim coils on gradient–magnet interactions: an inter-field and inter-site study

Author

Boulant, Nicolas, Le Ster, Caroline, Amadon, Alexis, Aubert, Guy, Beckett, Alexander, Belorgey, Jean, Bonnelye, Cédric, Bosch, Dario, Brunner, David Otto, Dilasser, Guillaume, Dubois, Olivier, Ehses, Philipp, Feinberg, David, Feizollah, Sajjad, Gras, Vincent, Gross, Simon, Guihard, Quentin, Lannou, Hervé, Le Bihan, Denis, Mauconduit, Franck, Molinié, Frédéric, Nunio, François, Pruessmann, Klaas, Quettier, Lionel, Scheffler, Klaus, Stöcker, Tony, Tardif, Christine, Ugurbil, Kamil, Vignaud, Alexandre, Vu, An, and Wu, Xiaoping

Published
2024
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46. Advancing insights into microgravity induced muscle changes using Caenorhabditis elegans as a model organism

Author

Laura J. Beckett, Philip M. Williams, Li Shean Toh, Volker Hessel, Lukas Gerstweiler, Ian Fisk, Luis Toronjo-Urquiza, and Veeren M. Chauhan

Subjects
Biotechnology, TP248.13-248.65, Physiology, QP1-981
Abstract

Abstract Spaceflight presents significant challenges to the physiological state of living organisms. This can be due to the microgravity environment experienced during long-term space missions, resulting in alterations in muscle structure and function, such as atrophy. However, a comprehensive understanding of the adaptive mechanisms of biological systems is required to devise potential solutions and therapeutic approaches for adapting to spaceflight conditions. This review examines the current understanding of the challenges posed by spaceflight on physiological changes, alterations in metabolism, dysregulation of pathways and the suitability and advantages of using the model organism Caenorhabditis elegans nematodes to study the effects of spaceflight. Research has shown that changes in the gene and protein composition of nematodes significantly occur across various larval stages and rearing environments, including both microgravity and Earth gravity settings, often mirroring changes observed in astronauts. Additionally, the review explores significant insights into the fundamental metabolic changes associated with muscle atrophy and growth, which could lead to the development of diagnostic biomarkers and innovative techniques to prevent and counteract muscle atrophy. These insights not only advance our understanding of microgravity-induced muscle atrophy but also lay the groundwork for the development of targeted interventions to mitigate its effects in the future.

Published
2024
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