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51. 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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52. 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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53. 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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54. 10 tips to help avoid wire fraud scams

Author

Ference, Sarah Beckett

Subjects
Money transfer -- Safety and security measures -- Laws, regulations and rules, Accountants -- Customer relations -- Information management -- Finance, Data security -- Management -- Laws, regulations and rules, Fraud -- Prevention -- Remedies -- Laws, regulations and rules, Accounting firms -- Information management -- Safety and security measures -- Customer relations, Government regulation, Company business management, Company systems management, Company financing, Data security issue, Banking, finance and accounting industries, Business, Law
Abstract

Wire transfer fraud, typically perpetrated via business email compromise, is a known risk to all types of businesses, including CPA firms. When a CPA firm handles client money, additional risk [...]

Published
2024

55. Overview of the distributed image processing infrastructure to produce the Legacy Survey of Space and Time

Author

Hernandez, Fabio, Beckett, George, Clark, Peter, Doidge, Matt, Jenness, Tim, Karavakis, Edward, Boulc'h, Quentin Le, Love, Peter, Mainetti, Gabriele, Noble, Timothy, White, Brandon, and Yang, Wei

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

The Vera C. Rubin Observatory is preparing to execute the most ambitious astronomical survey ever attempted, the Legacy Survey of Space and Time (LSST). Currently the final phase of construction is under way in the Chilean Andes, with the Observatory's ten-year science mission scheduled to begin in 2025. Rubin's 8.4-meter telescope will nightly scan the southern hemisphere collecting imagery in the wavelength range 320-1050 nm covering the entire observable sky every 4 nights using a 3.2 gigapixel camera, the largest imaging device ever built for astronomy. Automated detection and classification of celestial objects will be performed by sophisticated algorithms on high-resolution images to progressively produce an astronomical catalog eventually composed of 20 billion galaxies and 17 billion stars and their associated physical properties. In this article we present an overview of the system currently being constructed to perform data distribution as well as the annual campaigns which reprocess the entire image dataset collected since the beginning of the survey. These processing campaigns will utilize computing and storage resources provided by three Rubin data facilities (one in the US and two in Europe). Each year a Data Release will be produced and disseminated to science collaborations for use in studies comprising four main science pillars: probing dark matter and dark energy, taking inventory of solar system objects, exploring the transient optical sky and mapping the Milky Way. Also presented is the method by which we leverage some of the common tools and best practices used for management of large-scale distributed data processing projects in the high energy physics and astronomy communities. We also demonstrate how these tools and practices are utilized within the Rubin project in order to overcome the specific challenges faced by the Observatory., Comment: 8 pages, 2 figures, 26th International Conference on Computing in High Energy & Nuclear Physics

Published
2023

56. Finding Adversarial Inputs for Heuristics using Multi-level Optimization

Author

Namyar, Pooria, Arzani, Behnaz, Beckett, Ryan, Segarra, Santiago, Raj, Himanshu, Krishnaswamy, Umesh, Govindan, Ramesh, and Kandula, Srikanth

Subjects
Computer Science - Networking and Internet Architecture, Computer Science - Computer Science and Game Theory
Abstract

Production systems use heuristics because they are faster or scale better than their optimal counterparts. Yet, practitioners are often unaware of the performance gap between a heuristic and the optimum or between two heuristics in realistic scenarios. We present MetaOpt, a system that helps analyze heuristics. Users specify the heuristic and the optimal (or another heuristic) as input, and MetaOpt automatically encodes these efficiently for a solver to find performance gaps and their corresponding adversarial inputs. Its suite of built-in optimizations helps it scale its analysis to practical problem sizes. To show it is versatile, we used MetaOpt to analyze heuristics from three domains (traffic engineering, vector bin packing, and packet scheduling). We found a production traffic engineering heuristic can require 30% more capacity than the optimal to satisfy realistic demands. Based on the patterns in the adversarial inputs MetaOpt produced, we modified the heuristic to reduce its performance gap by 12.5$\times$. We examined adversarial inputs to a vector bin packing heuristic and proved a new lower bound on its performance.

Published
2023

57. Kivi: Verification for Cluster Management

Author

Liu, Bingzhe, Lim, Gangmuk, Beckett, Ryan, and Godfrey, P. Brighten

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

Modern cloud infrastructure is powered by cluster management systems such as Kubernetes and Docker Swarm. While these systems seek to minimize users' operational burden, the complex, dynamic, and non-deterministic nature of these systems makes them hard to reason about, potentially leading to failures ranging from performance degradation to outages. We present Kivi, the first system for verifying controllers and their configurations in cluster management systems. Kivi focuses on the popular system Kubernetes, and models its controllers and events into processes whereby their interleavings are exhaustively checked via model checking. Central to handling autoscaling and large-scale deployments is our design that seeks to find violations in a smaller and reduced topology. We also develop several model optimizations in Kivi to scale to large clusters. We show that Kivi is effective and accurate in finding issues in realistic and complex scenarios and showcase two new issues in Kubernetes controller source code., Comment: 18 pages

Published
2023

58. Intraperitoneal Focal Fat Infarction of the Falciform Ligament: A Report of Two Cases

Author

Chen, Michael Y, Pahwa, Anokh, and Beckett, Katrina R

Subjects
falciform ligament, epigastric pain, appendagitis, focal fat infarction, epiploic appendagitis
Abstract

Falciform ligament appendagitis (FLA) is a rare cause of intraperitoneal focal fat infarction (IFFI) characterized by the torsion of a fatty appendage related to the falciform ligament. FLA demonstrates characteristic features on computed tomography (CT), especially the hyperattenuating ring sign. Because of these characteristic features, a diagnosis of FLA can be achieved with CT alone. By recognizing the signs of FLA, radiologists can prevent unnecessary surgical intervention. We report two cases of FLA with associated images to assist radiologists in diagnosing this rare entity.

Published
2024

59. Next-generation MRI scanner designed for ultra-high-resolution human brain imaging at 7 Tesla.

Author

Feinberg, David, Beckett, Alexander, Vu, An, Stockmann, Jason, Huber, Laurentius, Ma, Samantha, Ahn, Sinyeob, Setsompop, Kawin, Cao, Xiaozhi, Park, Suhyung, Wald, Lawrence, Polimeni, Jonathan, Mareyam, Azma, Gruber, Bernhard, Stirnberg, Rüdiger, Liao, Congyu, Yacoub, Essa, Davids, Mathias, Bell, Paul, Rummert, Elmar, Koehler, Michael, Potthast, Andreas, Gonzalez-Insua, Ignacio, Stocker, Stefan, Gunamony, Shajan, Dietz, Peter, and Liu, Chunlei

Subjects
Humans, Brain, Magnetic Resonance Imaging, Head, Neuroimaging, Signal-To-Noise Ratio
Abstract

To increase granularity in human neuroimaging science, we designed and built a next-generation 7 Tesla magnetic resonance imaging scanner to reach ultra-high resolution by implementing several advances in hardware. To improve spatial encoding and increase the image signal-to-noise ratio, we developed a head-only asymmetric gradient coil (200 mT m-1, 900 T m-1s-1) with an additional third layer of windings. We integrated a 128-channel receiver system with 64- and 96-channel receiver coil arrays to boost signal in the cerebral cortex while reducing g-factor noise to enable higher accelerations. A 16-channel transmit system reduced power deposition and improved image uniformity. The scanner routinely performs functional imaging studies at 0.35-0.45 mm isotropic spatial resolution to reveal cortical layer functional activity, achieves high angular resolution in diffusion imaging and reduces acquisition time for both functional and structural imaging.

Published
2023

62. The Ruminant Telomere-to-Telomere (RT2T) Consortium

Author

Kalbfleisch, Theodore S., McKay, Stephanie D., Murdoch, Brenda M., Adelson, David L., Almansa-Villa, Diego, Becker, Gabrielle, Beckett, Linda M., Benítez-Galeano, María José, Biase, Fernando, Casey, Theresa, Chuong, Edward, Clark, Emily, Clarke, Shannon, Cockett, Noelle, Couldrey, Christine, Davis, Brian W., Elsik, Christine G., Faraut, Thomas, Gao, Yahui, Genet, Carine, Grady, Patrick, Green, Jonathan, Green, Richard, Guan, Dailu, Hagen, Darren, Hartley, Gabrielle A., Heaton, Mike, Hoyt, Savannah J., Huang, Wen, Jarvis, Erich, Kalleberg, Jenna, Khatib, Hasan, Koepfi, Klaus-Peter, Koltes, James, Koren, Sergey, Kuehn, Christa, Leeb, Tosso, Leonard, Alexander, Liu, George E., Low, Wai Yee, McConnell, Hunter, McRae, Kathryn, Miga, Karen, Mousel, Michelle, Neibergs, Holly, Olagunju, Temitayo, Pennell, Matt, Petry, Bruna, Pewsner, Mirjam, Phillippy, Adam M., Pickett, Brandon D., Pineda, Paulene, Potapova, Tamara, Rachagani, Satyanarayana, Rhie, Arang, Rijnkels, Monique, Robic, Annie, Rodriguez Osorio, Nelida, Safonova, Yana, Schettini, Gustavo, Schnabel, Robert D., Sirpu Natesh, Nagabhishek, Stegemiller, Morgan, Storer, Jessica, Stothard, Paul, Stull, Caleb, Tosser-Klopp, Gwenola, Traglia, Germán M., Tuggle, Christopher K., Van Tassell, Curtis P., Watson, Corey, Weikard, Rosemarie, Wimmers, Klaus, Xie, Shangqian, Yang, Liu, Smith, Timothy P. L., O’Neill, Rachel J., and Rosen, Benjamin D.

Published
2024
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65. 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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66. Flashpoints Signal Hidden Inherent Instabilities in Land-Use Planning

Author

Aliahmadi, Hazhir, Beckett, Maeve, Connolly, Sam, Chen, Dongmei, and van Anders, Greg

Subjects
Computer Science - Artificial Intelligence, Condensed Matter - Statistical Mechanics, Computer Science - Computational Engineering, Finance, and Science, Physics - Physics and Society
Abstract

Land-use decision-making processes have a long history of producing globally pervasive systemic equity and sustainability concerns. Quantitative, optimization-based planning approaches, e.g. Multi-Objective Land Allocation (MOLA), seemingly open the possibility to improve objectivity and transparency by explicitly evaluating planning priorities by the type, amount, and location of land uses. Here, we show that optimization-based planning approaches with generic planning criteria generate a series of unstable "flashpoints" whereby tiny changes in planning priorities produce large-scale changes in the amount of land use by type. We give quantitative arguments that the flashpoints we uncover in MOLA models are examples of a more general family of instabilities that occur whenever planning accounts for factors that coordinate use on- and between-sites, regardless of whether these planning factors are formulated explicitly or implicitly. We show that instabilities lead to regions of ambiguity in land-use type that we term "gray areas". By directly mapping gray areas between flashpoints, we show that quantitative methods retain utility by reducing combinatorially large spaces of possible land-use patterns to a small, characteristic set that can engage stakeholders to arrive at more efficient and just outcomes., Comment: 9 pages, 5 figures

Published
2023

67. Gender Inclusive Methods in Studies of STEM Practitioners

Author

Rasmussen, Kaitlin, Chen, Jocelyne, Colquhoun, Rebecca L., Frentz, Sophia, Hiatt, Laurel, Kosciesza, Aiden James, Olsen, Charlotte, O'Neill, Theo J., Zamloot, Vic, and Strauss, Beckett E.

Subjects
Statistics - Applications
Abstract

Gender inequity is one of the biggest challenges facing the STEM workforce. While there are many studies that look into gender disparities within STEM and academia, the majority of these have been designed and executed by those unfamiliar with research in sociology and gender studies. They adopt a normative view of gender as a binary choice of 'male' or 'female,' leaving individuals whose genders do not fit within that model out of such research entirely. This especially impacts those experiencing multiple axes of marginalization, such as race, disability, and socioeconomic status. For STEM fields to recruit and retain members of historically excluded groups, a new paradigm must be developed. Here, we collate a new dataset of the methods used in 119 past studies of gender equity, and recommend better survey practices and institutional policies based on a more complex and accurate approach to gender. We find that problematic approaches to gender in surveys can be classified into 5 main themes - treating gender as white, observable, discrete, as a statistic, and as inconsequential. We recommend allowing self-reporting of gender and never automating gender assignment within research. This work identifies the key areas of development for studies of gender-based inclusion within STEM, and provides recommended solutions to support the methodological uplift required for this work to be both scientifically sound and fully inclusive., Comment: 33 pages (15 pages plus references), 1 table. Follows work of arXiv:1907.04893 and arXiv:1907.04893

Published
2023

68. What do LLMs need to Synthesize Correct Router Configurations?

Author

Mondal, Rajdeep, Tang, Alan, Beckett, Ryan, Millstein, Todd, and Varghese, George

Subjects
Computer Science - Networking and Internet Architecture, Computer Science - Programming Languages
Abstract

We investigate whether Large Language Models (e.g., GPT-4) can synthesize correct router configurations with reduced manual effort. We find GPT-4 works very badly by itself, producing promising draft configurations but with egregious errors in topology, syntax, and semantics. Our strategy, that we call Verified Prompt Programming, is to combine GPT-4 with verifiers, and use localized feedback from the verifier to automatically correct errors. Verification requires a specification and actionable localized feedback to be effective. We show results for two use cases: translating from Cisco to Juniper configurations on a single router, and implementing no-transit policy on multiple routers. While human input is still required, if we define the leverage as the number of automated prompts to the number of human prompts, our experiments show a leverage of 10X for Juniper translation, and 6X for implementing no-transit policy, ending with verified configurations.

Published
2023

69. Thermochemical Stability of Low-Iron, Manganese-Enriched Olivine in Astrophysical Environments

Author

Ebel, Denton S., Weisberg, Michael K., and Beckett, John R.

Subjects
Astrophysics - Earth and Planetary Astrophysics, Condensed Matter - Materials Science, Physics - Geophysics
Abstract

Low-iron, manganese-enriched (LIME) olivine grains are found in cometary samples returned by the Stardust mission to comet 81P/Wild 2. Similar grains are found in primitive meteoritic clasts and unequilibrated meteorite matrix. LIME olivine is thermodynamically stable in a vapor of solar composition at high temperature at total pressures of a millibar to a microbar, but enrichment of solar composition vapor in a dust of chondritic composition causes the FeO/MnO ratio of olivine to increase. The compositions of LIME olivines in primitive materials indicate oxygen fugacities close to that of a very reducing vapor of solar composition. The compositional zoning of LIME olivines in amoeboid olivine aggregates is consistent with equilibration with nebular vapor in the stability field of olivine, without reequilibration at lower temperatures. A similar history is likely for LIME olivines found in comet samples and in interplanetary dust particles. LIME olivine is not likely to persist in nebular conditions in which silicate liquids are stable., Comment: 15 pages, 5 figures

Published
2023
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70. Whole blood and freeze-dried plasma in Canadian trauma care

Author

Dion, Pierre-Marc, Mack, Johnathan, Alam, Asim, Vuong, Sebastian, Scott, Jeff, Miller, Damien, and Beckett, Andrew

Subjects
Usage, History, Storage, Safety and security measures, Blood plasma -- Storage -- Usage, Whole blood exchange transfusion -- History -- Usage -- Safety and security measures, Exchange transfusion, Whole blood -- History -- Usage -- Safety and security measures
Abstract

EARLY USE OF WHOLE BLOOD AND FREEZE-DRIED PLASMA Blood transfusions have evolved dramatically over the past 4 centuries, from the earliest experiments in the 17th century to the sophisticated transfusions [...], This article highlights the crucial role of blood transfusion in trauma care and explores the historical and contemporary use of whole blood and freeze-dried plasma in Canadian health care. Early use of whole blood and freeze-dried plasma during global conflicts led to advancements in transfusion medicine. The transition to blood component therapy improved transfusion safety and precision. However, there is an increasing interest in using whole blood and freeze-dried plasma, supported by recent evidence suggesting potential benefits over blood component therapy, particularly in trauma cases. Canadian initiatives, such as leukoreduced whole blood production for the military, indicate efforts to address logistical challenges in delivering trauma care, especially in remote areas. Challenges remain, including logistical issues and regulatory complexities, requiring coordinated efforts for effective implementation. Overall, there's growing support for integrating whole blood and freeze-dried plasma into trauma care across Canada.

Published
2024
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71. 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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72. The Sporadic Early‐onset Alzheimer's Disease Signature Of Atrophy: Preliminary Findings From The Longitudinal Early‐onset Alzheimer's Disease Study (LEADS) Cohort

Author

Touroutoglou, Alexandra, Katsumi, Yuta, Brickhouse, Michael, Zaitsev, Alexander, Eckbo, Ryan, Aisen, Paul, Beckett, Laurel, Dage, Jeffrey L, Eloyan, Ani, Foroud, Tatiana, Ghetti, Bernardino, Griffin, Percy, Hammers, Dustin, Jack, Clifford R, Kramer, Joel H, Iaccarino, Leonardo, La Joie, Renaud, Mundada, Nidhi S, Koeppe, Robert, Kukull, Walter A, Murray, Melissa E, Nudelman, Kelly, Polsinelli, Angelina J, Rumbaugh, Malia, Soleimani‐Meigooni, David N, Toga, Arthur, Vemuri, Prashanthi, Atri, Alireza, Day, Gregory S, Duara, Ranjan, Graff‐Radford, Neill R, Honig, Lawrence S, Jones, David T, Masdeu, Joseph C, Mendez, Mario F, Musiek, Erik, Onyike, Chiadi U, Riddle, Meghan, Rogalski, Emily, Salloway, Stephen, Sha, Sharon, Turner, R Scott, Wingo, Thomas S, Wolk, David A, Womack, Kyle, Carrillo, Maria C, Rabinovici, Gil D, Apostolova, Liana G, Dickerson, Bradford C, and Consortium, the LEADS

Subjects
Biological Psychology, Psychology, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Dementia, Brain Disorders, Aging, Alzheimer's Disease, Neurosciences, Acquired Cognitive Impairment, Neurodegenerative, Biomedical Imaging, 4.1 Discovery and preclinical testing of markers and technologies, 4.2 Evaluation of markers and technologies, Neurological, Humans, Alzheimer Disease, Reproducibility of Results, Temporal Lobe, Magnetic Resonance Imaging, Atrophy, Biomarkers, disease signature, early-onset Alzheimer's disease, magnetic resonance imaging, LEADS Consortium, Clinical Sciences, Geriatrics, Clinical sciences, Biological psychology
Abstract

IntroductionMagnetic resonance imaging (MRI) research has advanced our understanding of neurodegeneration in sporadic early-onset Alzheimer's disease (EOAD) but studies include small samples, mostly amnestic EOAD, and have not focused on developing an MRI biomarker.MethodsWe analyzed MRI scans to define the sporadic EOAD-signature atrophy in a small sample (n = 25) of Massachusetts General Hospital (MGH) EOAD patients, investigated its reproducibility in the large longitudinal early-onset Alzheimer's disease study (LEADS) sample (n = 211), and investigated the relationship of the magnitude of atrophy with cognitive impairment.ResultsThe EOAD-signature atrophy was replicated across the two cohorts, with prominent atrophy in the caudal lateral temporal cortex, inferior parietal lobule, and posterior cingulate and precuneus cortices, and with relative sparing of the medial temporal lobe. The magnitude of EOAD-signature atrophy was associated with the severity of cognitive impairment.DiscussionThe EOAD-signature atrophy is a reliable and clinically valid biomarker of AD-related neurodegeneration that could be used in clinical trials for EOAD.HighlightsWe developed an early-onset Alzheimer's disease (EOAD)-signature of atrophy based on magnetic resonance imaging (MRI) scans. EOAD signature was robustly reproducible across two independent patient cohorts. EOAD signature included prominent atrophy in parietal and posterior temporal cortex. The EOAD-signature atrophy was associated with the severity of cognitive impairment. EOAD signature is a reliable and clinically valid biomarker of neurodegeneration.

Published
2023

73. Cerebrospinal fluid biomarkers in the Longitudinal Early‐onset Alzheimer's Disease Study

Author

Dage, Jeffrey L, Eloyan, Ani, Thangarajah, Maryanne, Hammers, Dustin B, Fagan, Anne M, Gray, Julia D, Schindler, Suzanne E, Snoddy, Casey, Nudelman, Kelly NH, Faber, Kelley M, Foroud, Tatiana, Aisen, Paul, Griffin, Percy, Grinberg, Lea T, Iaccarino, Leonardo, Kirby, Kala, Kramer, Joel, Koeppe, Robert, Kukull, Walter A, La Joie, Renaud, Mundada, Nidhi S, Murray, Melissa E, Rumbaugh, Malia, Soleimani‐Meigooni, David N, Toga, Arthur W, Touroutoglou, Alexandra, Vemuri, Prashanthi, Atri, Alireza, Beckett, Laurel A, Day, Gregory S, Graff‐Radford, Neill R, Duara, Ranjan, Honig, Lawrence S, Jones, David T, Masdeu, Joseph C, Mendez, Mario F, Musiek, Erik, Onyike, Chiadi U, Riddle, Meghan, Rogalski, Emily, Salloway, Stephen, Sha, Sharon J, Turner, Raymond S, Wingo, Thomas S, Wolk, David A, Womack, Kyle B, Carrillo, Maria C, Dickerson, Bradford C, Rabinovici, Gil D, Apostolova, Liana G, and Consortium, LEADS

Subjects
Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Clinical Research, Neurodegenerative, Aging, Alzheimer's Disease, Brain Disorders, Acquired Cognitive Impairment, Dementia, Prevention, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), 4.1 Discovery and preclinical testing of markers and technologies, 2.1 Biological and endogenous factors, 4.2 Evaluation of markers and technologies, Neurological, Humans, Alzheimer Disease, Chitinase-3-Like Protein 1, Amyloid beta-Peptides, tau Proteins, Longitudinal Studies, Biomarkers, Neurogranin, Alzheimer's disease, amyloid, astrogliosis, A1342/40, biomarkers, CSF, dementia, neurogranin, NfL, pTau181, SNAP-25, tau, tTau, VILIP-1, YKL-40, LEADS Consortium, Aβ42/40, Geriatrics, Clinical sciences, Biological psychology
Abstract

IntroductionOne goal of the Longitudinal Early Onset Alzheimer's Disease Study (LEADS) is to define the fluid biomarker characteristics of early-onset Alzheimer's disease (EOAD).MethodsCerebrospinal fluid (CSF) concentrations of Aβ1-40, Aβ1-42, total tau (tTau), pTau181, VILIP-1, SNAP-25, neurogranin (Ng), neurofilament light chain (NfL), and YKL-40 were measured by immunoassay in 165 LEADS participants. The associations of biomarker concentrations with diagnostic group and standard cognitive tests were evaluated.ResultsBiomarkers were correlated with one another. Levels of CSF Aβ42/40, pTau181, tTau, SNAP-25, and Ng in EOAD differed significantly from cognitively normal and early-onset non-AD dementia; NfL, YKL-40, and VILIP-1 did not. Across groups, all biomarkers except SNAP-25 were correlated with cognition. Within the EOAD group, Aβ42/40, NfL, Ng, and SNAP-25 were correlated with at least one cognitive measure.DiscussionThis study provides a comprehensive analysis of CSF biomarkers in sporadic EOAD that can inform EOAD clinical trial design.

Published
2023

74. Baseline neuropsychiatric symptoms and psychotropic medication use midway through data collection of the Longitudinal Early‐Onset Alzheimer's Disease Study (LEADS) cohort

Author

Polsinelli, Angelina J, Wonderlin, Ryan J, Hammers, Dustin B, Garcia, Alex Pena, Eloyan, Ani, Taurone, Alexander, Thangarajah, Maryanne, Beckett, Laurel, Gao, Sujuan, Wang, Sophia, Kirby, Kala, Logan, Paige E, Aisen, Paul, Dage, Jeffrey L, Foroud, Tatiana, Griffin, Percy, Iaccarino, Leonardo, Kramer, Joel H, Koeppe, Robert, Kukull, Walter A, La Joie, Renaud, Mundada, Nidhi S, Murray, Melissa E, Nudelman, Kelly, Soleimani‐Meigooni, David N, Rumbaugh, Malia, Toga, Arthur W, Touroutoglou, Alexandra, Vemuri, Prashanthi, Atri, Alireza, Day, Gregory S, Duara, Ranjan, Graff‐Radford, Neill R, Honig, Lawrence S, Jones, David T, Masdeu, Joseph, Mendez, Mario F, Womack, Kyle, Musiek, Erik, Onyike, Chiadi U, Riddle, Meghan, Rogalski, Emily, Salloway, Steven, Sha, Sharon J, Turner, Raymond S, Wingo, Thomas S, Wolk, David A, Carrillo, Maria C, Dickerson, Bradford C, Rabinovici, Gil D, Apostolova, Liana G, and Consortium, LEADS

Subjects
Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Neurodegenerative, Depression, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Mental Health, Acquired Cognitive Impairment, Alzheimer's Disease, Dementia, Aging, Brain Disorders, Clinical Research, Mental Illness, 2.1 Biological and endogenous factors, 2.4 Surveillance and distribution, Neurological, Mental health, Humans, Aged, Alzheimer Disease, Longitudinal Studies, Data Collection, early-onset Alzheimer's disease, early-onset dementia, mild cognitive impairment, neuropharmacology, neuropsychiatric symptoms, psychotropic medications, LEADS Consortium, Geriatrics, Clinical sciences, Biological psychology
Abstract

IntroductionWe examined neuropsychiatric symptoms (NPS) and psychotropic medication use in a large sample of individuals with early-onset Alzheimer's disease (EOAD; onset 40-64 years) at the midway point of data collection for the Longitudinal Early-onset Alzheimer's Disease Study (LEADS).MethodsBaseline NPS (Neuropsychiatric Inventory - Questionnaire; Geriatric Depression Scale) and psychotropic medication use from 282 participants enrolled in LEADS were compared across diagnostic groups - amyloid-positive EOAD (n = 212) and amyloid negative early-onset non-Alzheimer's disease (EOnonAD; n = 70).ResultsAffective behaviors were the most common NPS in EOAD at similar frequencies to EOnonAD. Tension and impulse control behaviors were more common in EOnonAD. A minority of participants were using psychotropic medications, and use was higher in EOnonAD.DiscussionOverall NPS burden and psychotropic medication use were higher in EOnonAD than EOAD participants. Future research will investigate moderators and etiological drivers of NPS, and NPS differences in EOAD versus late-onset AD.

Published
2023

75. Profiling baseline performance on the Longitudinal Early‐Onset Alzheimer's Disease Study (LEADS) cohort near the midpoint of data collection

Author

Hammers, Dustin B, Eloyan, Ani, Taurone, Alexander, Thangarajah, Maryanne, Beckett, Laurel, Gao, Sujuan, Kirby, Kala, Aisen, Paul, Dage, Jeffrey L, Foroud, Tatiana, Griffin, Percy, Grinberg, Lea T, Jack, Clifford R, Kramer, Joel, Koeppe, Robert, Kukull, Walter A, Mundada, Nidhi S, La Joie, Renaud, Soleimani‐Meigooni, David N, Iaccarino, Leonardo, Murray, Melissa E, Nudelman, Kelly, Polsinelli, Angelina J, Rumbaugh, Malia, Toga, Arthur, Touroutoglou, Alexandra, Vemuri, Prashanthi, Atri, Alireza, Day, Gregory S, Duara, Ranjan, Graff‐Radford, Neill R, Honig, Lawrence S, Jones, David T, Masdeu, Joseph, Mendez, Mario F, Womack, Kyle, Musiek, Erik, Onyike, Chiadi U, Riddle, Meghan, Rogalski, Emily, Salloway, Steven, Sha, Sharon J, Turner, Raymond Scott, Wingo, Thomas S, Wolk, David A, Carrillo, Maria C, Dickerson, Bradford C, Rabinovici, Gil D, Apostolova, Liana G, and Consortium, the LEADS

Subjects
Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Clinical Research, Neurodegenerative, Genetics, Aging, Alzheimer's Disease, Brain Disorders, Acquired Cognitive Impairment, Dementia, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), 2.1 Biological and endogenous factors, 2.4 Surveillance and distribution, Neurological, Humans, Alzheimer Disease, Apolipoproteins E, Longitudinal Studies, Apolipoprotein E4, Data Collection, Alzheimer's disease, atypical variant, amnestic, early-onset, memory, LEADS Consortium, Geriatrics, Clinical sciences, Biological psychology
Abstract

ObjectiveThe Longitudinal Early-Onset Alzheimer's Disease Study (LEADS) seeks to provide comprehensive understanding of early-onset Alzheimer's disease (EOAD; onset

Published
2023

76. Pathogenic variants in the Longitudinal Early‐onset Alzheimer's Disease Study cohort

Author

Nudelman, Kelly NH, Jackson, Trever, Rumbaugh, Malia, Eloyan, Ani, Abreu, Marco, Dage, Jeffrey L, Snoddy, Casey, Faber, Kelley M, Foroud, Tatiana, Hammers, Dustin B, Committee, DIAN DIAN‐TU Clinical Genetics, Taurone, Alexander, Thangarajah, Maryanne, Aisen, Paul, Beckett, Laurel, Kramer, Joel, Koeppe, Robert, Kukull, Walter A, Murray, Melissa E, Toga, Arthur W, Vemuri, Prashanthi, Atri, Alireza, Day, Gregory S, Duara, Ranjan, Graff‐Radford, Neill R, Honig, Lawrence S, Jones, David T, Masdeu, Joseph C, Mendez, Mario, Musiek, Erik, Onyike, Chiadi U, Riddle, Meghan, Rogalski, Emily, Salloway, Stephen, Sha, Sharon J, Turner, R Scott, Wingo, Thomas S, Wolk, David A, Carrillo, Maria C, Dickerson, Bradford C, Rabinovici, Gil D, Apostolova, Liana G, and Consortium, the LEADS

Subjects
Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Dementia, Alzheimer's Disease, Clinical Research, Acquired Cognitive Impairment, Neurodegenerative, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Genetics, Aging, Brain Disorders, 2.1 Biological and endogenous factors, Neurological, Humans, Alzheimer Disease, Amyloid beta-Protein Precursor, C9orf72 Protein, Genetic Testing, Longitudinal Studies, Mutation, Presenilin-1, Presenilin-2, Alzheimer's disease, APP, C9ORF7, dementia, early onset, genetics, GRN, MAPT, PSEN1, PSEN2, sequencing, DIAN/DIAN-TU Clinical/Genetics Committee, LEADS Consortium, Geriatrics, Clinical sciences, Biological psychology
Abstract

IntroductionOne goal of the Longitudinal Early-onset Alzheimer's Disease Study (LEADS) is to investigate the genetic etiology of early onset (40-64 years) cognitive impairment. Toward this goal, LEADS participants are screened for known pathogenic variants.MethodsLEADS amyloid-positive early-onset Alzheimer's disease (EOAD) or negative early-onset non-AD (EOnonAD) cases were whole exome sequenced (N = 299). Pathogenic variant frequency in APP, PSEN1, PSEN2, GRN, MAPT, and C9ORF72 was assessed for EOAD and EOnonAD. Gene burden testing was performed in cases compared to similar-age cognitively normal controls in the Parkinson's Progression Markers Initiative (PPMI) study.ResultsPreviously reported pathogenic variants in the six genes were identified in 1.35% of EOAD (3/223) and 6.58% of EOnonAD (5/76). No genes showed enrichment for carriers of rare functional variants in LEADS cases.DiscussionResults suggest that LEADS is enriched for novel genetic causative variants, as previously reported variants are not observed in most cases.HighlightsSequencing identified eight cognitively impaired pathogenic variant carriers. Pathogenic variants were identified in PSEN1, GRN, MAPT, and C9ORF72. Rare variants were not enriched in APP, PSEN1/2, GRN, and MAPT. The Longitudinal Early-onset Alzheimer's Disease Study (LEADS) is a key resource for early-onset Alzheimer's genetic research.

Published
2023

77. White matter hyperintensities are higher among early‐onset Alzheimer's disease participants than their cognitively normal and early‐onset nonAD peers: Longitudinal Early‐onset Alzheimer's Disease Study (LEADS)

Author

Eloyan, Ani, Thangarajah, Maryanne, An, Na, Borowski, Bret J, Reddy, Ashritha L, Aisen, Paul, Dage, Jeffrey L, Foroud, Tatiana, Ghetti, Bernardino, Griffin, Percy, Hammers, Dustin, Iaccarino, Leonardo, Jack, Clifford R, Kirby, Kala, Kramer, Joel, Koeppe, Robert, Kukull, Walter A, La Joie, Renaud, Mundada, Nidhi S, Murray, Melissa E, Nudelman, Kelly, Rumbaugh, Malia, Soleimani‐Meigooni, David N, Toga, Arthur, Touroutoglou, Alexandra, Atri, Alireza, Day, Gregory S, Duara, Ranjan, Graff‐Radford, Neill R, Honig, Lawrence S, Jones, David T, Masdeu, Joseph, Mendez, Mario F, Musiek, Erik, Onyike, Chiadi U, Rogalski, Emily, Salloway, Stephen, Sha, Sharon, Turner, Raymond S, Wingo, Thomas S, Wolk, David A, Womack, Kyle, Beckett, Laurel, Gao, Sujuan, Carrillo, Maria C, Rabinovici, Gil, Apostolova, Liana G, Dickerson, Brad, Vemuri, Prashanthi, and Consortium, and the LEADS

Subjects
Biological Psychology, Psychology, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Neurodegenerative, Behavioral and Social Science, Aging, Alzheimer's Disease, Neurosciences, Cerebrovascular, Brain Disorders, Acquired Cognitive Impairment, Dementia, Alzheimer's Disease Related Dementias (ADRD), Vascular Cognitive Impairment/Dementia, 2.1 Biological and endogenous factors, Neurological, Humans, Alzheimer Disease, White Matter, Amyloid beta-Peptides, tau Proteins, Magnetic Resonance Imaging, Cognitive Dysfunction, Amyloidogenic Proteins, Amyloid, Alzheimer's disease, amyloid, EOAD, tau PET, tau positron emission tomography, white matter hyperintensities, WMH, LEADS Consortium, Clinical Sciences, Geriatrics, Clinical sciences, Biological psychology
Abstract

IntroductionWe compared white matter hyperintensities (WMHs) in early-onset Alzheimer's disease (EOAD) with cognitively normal (CN) and early-onset amyloid-negative cognitively impaired (EOnonAD) groups in the Longitudinal Early-Onset Alzheimer's Disease Study.MethodsWe investigated the role of increased WMH in cognition and amyloid and tau burden. We compared WMH burden of 205 EOAD, 68 EOnonAD, and 89 CN participants in lobar regions using t-tests and analyses of covariance. Linear regression analyses were used to investigate the association between WMH and cognitive impairment and that between amyloid and tau burden.ResultsEOAD showed greater WMHs compared with CN and EOnonAD participants across all regions with no significant differences between CN and EOnonAD groups. Greater WMHs were associated with worse cognition. Tau burden was positively associated with WMH burden in the EOAD group.DiscussionEOAD consistently showed higher WMH volumes. Overall, greater WMHs were associated with worse cognition and higher tau burden in EOAD.HighlightsThis study represents a comprehensive characterization of WMHs in sporadic EOAD. WMH volumes are associated with tau burden from positron emission tomography (PET) in EOAD, suggesting WMHs are correlated with increasing burden of AD. Greater WMH volumes are associated with worse performance on global cognitive tests. EOAD participants have higher WMH volumes compared with CN and early-onset amyloid-negative cognitively impaired (EOnonAD) groups across all brain regions.

Published
2023

78. Circular-SWAT for deep learning based diagnostic classification of Alzheimer's disease: application to metabolome data

Author

Jo, Taeho, Kim, Junpyo, Bice, Paula, Huynh, Kevin, Wang, Tingting, Arnold, Matthias, Meikle, Peter J, Giles, Corey, Kaddurah-Daouk, Rima, Saykin, Andrew J, Nho, Kwangsik, Kueider-Paisley, Alexandra, Doraiswamy, P Murali, Blach, Colette, Moseley, Arthur, Thompson, Will, St John-Williams, Lisa, Mahmoudiandehkhordi, Siamak, Tenenbaum, Jessica, Welsh-Balmer, Kathleen, Plassman, Brenda, Risacher, Shannon L, Kastenmüller, Gabi, Han, Xianlin, Baillie, Rebecca, Knight, Rob, Dorrestein, Pieter, Brewer, James, Mayer, Emeran, Labus, Jennifer, Baldi, Pierre, Gupta, Arpana, Fiehn, Oliver, Barupal, Dinesh, Meikle, Peter, Mazmanian, Sarkis, Rader, Dan, Kling, Mitchel, Shaw, Leslie, Trojanowski, John, van Duijin, Cornelia, Nevado-Holgado, Alejo, Bennett, David, Krishnan, Ranga, Keshavarzian, Ali, Vogt, Robin, Ikram, Arfan, Hankemeier, Thomas, Thiele, Ines, Price, Nathan, Funk, Cory, Baloni, Priyanka, Jia, Wei, Wishart, David, Brinton, Roberta, Chang, Rui, Farrer, Lindsay, Au, Rhoda, Qiu, Wendy, Würtz, Peter, Koal, Therese, Mangravite, Lara, Krumsiek, Jan, Suhre, Karsten, Newman, John, Moreno, Herman, Foroud, Tatania, Sacks, Frank, Jansson, Janet, Weiner, Michael W, Aisen, Paul, Petersen, Ronald, Jack, Clifford R, Jagust, William, Trojanowki, John Q, Toga, Arthur W, Beckett, Laurel, Green, Robert C, Morris, John C, Perrin, Richard J, Shaw, Leslie M, Khachaturian, Zaven, Carrillo, Maria, Potter, William, Barnes, Lisa, Bernard, Marie, Gonzalez, Hector, Ho, Carole, Hsiao, John K, Jackson, Jonathan, Masliah, Eliezer, Masterman, Donna, Okonkwo, Ozioma, Perrin, Richard, and Ryan, Laurie

Subjects
Medical Biochemistry and Metabolomics, Biomedical and Clinical Sciences, Neurodegenerative, Dementia, Aging, Acquired Cognitive Impairment, Alzheimer's Disease, Brain Disorders, Machine Learning and Artificial Intelligence, Networking and Information Technology R&D (NITRD), Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Neurosciences, Neurological, Humans, Aged, Magnetic Resonance Imaging, Deep Learning, Alzheimer Disease, Neuroimaging, Metabolome, Lipids, Cognitive Dysfunction, Alzheimer's Disease Metabolomics Consortium, Alzheimer's Disease Neuroimaging Initiative, Alzheimer's disease, Deep learning, Lipidomics, Machine learning, Metabolomics, Clinical Sciences, Public Health and Health Services, Clinical sciences, Epidemiology
Abstract

BackgroundDeep learning has shown potential in various scientific domains but faces challenges when applied to complex, high-dimensional multi-omics data. Alzheimer's Disease (AD) is a neurodegenerative disorder that lacks targeted therapeutic options. This study introduces the Circular-Sliding Window Association Test (c-SWAT) to improve the classification accuracy in predicting AD using serum-based metabolomics data, specifically lipidomics.MethodsThe c-SWAT methodology builds upon the existing Sliding Window Association Test (SWAT) and utilizes a three-step approach: feature correlation analysis, feature selection, and classification. Data from 997 participants from the Alzheimer's Disease Neuroimaging Initiative (ADNI) served as the basis for model training and validation. Feature correlations were analyzed using Weighted Gene Co-expression Network Analysis (WGCNA), and Convolutional Neural Networks (CNN) were employed for feature selection. Random Forest was used for the final classification.FindingsThe application of c-SWAT resulted in a classification accuracy of up to 80.8% and an AUC of 0.808 for distinguishing AD from cognitively normal older adults. This marks a 9.4% improvement in accuracy and a 0.169 increase in AUC compared to methods without c-SWAT. These results were statistically significant, with a p-value of 1.04 × 10ˆ-4. The approach also identified key lipids associated with AD, such as Cer(d16:1/22:0) and PI(37:6).InterpretationOur results indicate that c-SWAT is effective in improving classification accuracy and in identifying potential lipid biomarkers for AD. These identified lipids offer new avenues for understanding AD and warrant further investigation.FundingThe specific funding of this article is provided in the acknowledgements section.

Published
2023

79. Determinants of cognitive and brain resilience to tau pathology: a longitudinal analysis

Author

Bocancea, Diana I, Svenningsson, Anna L, van Loenhoud, Anna C, Groot, Colin, Barkhof, Frederik, Strandberg, Olof, Smith, Ruben, Weiner, Michael W, Aisen, Paul, Petersen, Ronald, Jack, Clifford R, Jagust, William, Trojanowki, John Q, Toga, Arthur W, Beckett, Laurel, Green, Robert C, Saykin, Andrew J, Morris, John C, Perrin, Richard J, Shaw, Leslie M, Khachaturian, Zaven, Carrillo, Maria, Potter, William, Barnes, Lisa, Bernard, Marie, González, Hector, Ho, Carole, Hsiao, John K, Jackson, Jonathan, Masliah, Eliezer, Masterman, Donna, Okonkwo, Ozioma, Ryan, Laurie, Silverberg, Nina, Fleisher, Adam, Sacrey, Diana Truran, Fockler, Juliet, Conti, Cat, Veitch, Dallas, Neuhaus, John, Jin, Chengshi, Nosheny, Rachel, Ashford, Miriam, Flenniken, Derek, Kormo, Adrienne, Montine, Tom, Conti, Cat B, Rafii, Michael, Raman, Rema, Jimenez, Gustavo, Donohue, Michael, Gessert, Devon, Salazar, Jennifer, Zimmerman, Caileigh, Cabrera, Yuliana, Walter, Sarah, Miller, Garrett, Coker, Godfrey, Clanton, Taylor, Hergesheimer, Lindsey, Smith, Stephanie, Adegoke, Olusegun, Mahboubi, Payam, Moore, Shelley, Pizzola, Jeremy, Shaffer, Elizabeth, Harvey, Danielle, Forghanian-Arani, Arvin, Borowski, Bret, Ward, Chad, Schwarz, Christopher, Jones, David, Gunter, Jeff, Kantarci, Kejal, Senjem, Matthew, Vemuri, Prashanthi, Reid, Robert, Fox, Nick C, Malone, Ian, Thompson, Paul, Thomopoulos, Sophia I, Nir, Talia M, Jahanshad, Neda, DeCarli, Charles, Knaack, Alexander, Fletcher, Evan, Tosun-Turgut, Duygu, Chen, Stephanie Rossi, Choe, Mark, and Crawfor, Karen

Subjects
Health Sciences, Dementia, Brain Disorders, Cerebrovascular, Aging, Neurosciences, Alzheimer's Disease Related Dementias (ADRD), Neurodegenerative, Biomedical Imaging, Vascular Cognitive Impairment/Dementia, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Alzheimer's Disease, Behavioral and Social Science, Clinical Research, Acquired Cognitive Impairment, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Mental health, Neurological, Humans, Alzheimer Disease, Longitudinal Studies, tau Proteins, Cross-Sectional Studies, Cerebral Cortical Thinning, Positron-Emission Tomography, Brain, Cognition, Apolipoproteins E, Alzheimer's disease, tau, resilience, cognition, PET, MRI, Alzheimer’s Disease Neuroimaging Initiative, Alzheimer’s disease, Medical and Health Sciences, Psychology and Cognitive Sciences, Neurology & Neurosurgery, Biomedical and clinical sciences, Health sciences, Psychology
Abstract

Mechanisms of resilience against tau pathology in individuals across the Alzheimer's disease spectrum are insufficiently understood. Longitudinal data are necessary to reveal which factors relate to preserved cognition (i.e. cognitive resilience) and brain structure (i.e. brain resilience) despite abundant tau pathology, and to clarify whether these associations are cross-sectional or longitudinal. We used a longitudinal study design to investigate the role of several demographic, biological and brain structural factors in yielding cognitive and brain resilience to tau pathology as measured with PET. In this multicentre study, we included 366 amyloid-β-positive individuals with mild cognitive impairment or Alzheimer's disease dementia with baseline 18F-flortaucipir-PET and longitudinal cognitive assessments. A subset (n = 200) additionally underwent longitudinal structural MRI. We used linear mixed-effects models with global cognition and cortical thickness as dependent variables to investigate determinants of cognitive resilience and brain resilience, respectively. Models assessed whether age, sex, years of education, APOE-ε4 status, intracranial volume (and cortical thickness for cognitive resilience models) modified the association of tau pathology with cognitive decline or cortical thinning. We found that the association between higher baseline tau-PET levels (quantified in a temporal meta-region of interest) and rate of cognitive decline (measured with repeated Mini-Mental State Examination) was adversely modified by older age (Stβinteraction = -0.062, P = 0.032), higher education level (Stβinteraction = -0.072, P = 0.011) and higher intracranial volume (Stβinteraction = -0.07, P = 0.016). Younger age, higher education and greater cortical thickness were associated with better cognitive performance at baseline. Greater cortical thickness was furthermore associated with slower cognitive decline independent of tau burden. Higher education also modified the negative impact of tau-PET on cortical thinning, while older age was associated with higher baseline cortical thickness and slower rate of cortical thinning independent of tau. Our analyses revealed no (cross-sectional or longitudinal) associations for sex and APOE-ε4 status on cognition and cortical thickness. In this longitudinal study of clinically impaired individuals with underlying Alzheimer's disease neuropathological changes, we identified education as the most robust determinant of both cognitive and brain resilience against tau pathology. The observed interaction with tau burden on cognitive decline suggests that education may be protective against cognitive decline and brain atrophy at lower levels of tau pathology, with a potential depletion of resilience resources with advancing pathology. Finally, we did not find major contributions of sex to brain nor cognitive resilience, suggesting that previous links between sex and resilience might be mainly driven by cross-sectional differences.

Published
2023

80. Challenges with the Application of Cyber Security for Airworthiness (CSA) in Real-World Contexts

Author

LeClair, Beckett, McLeod, James, Ramsay, Lee, and Warren, Mick

Subjects
Computer Science - Cryptography and Security, Computer Science - Computers and Society
Abstract

The ever increasing push towards reliance upon computerised technology in commercial, general, and military aerospace brings with it an increasing amount of potential cyber hazards and attacks. Consequently, the variety of attack vectors is greater than ever. Recognized Good Practice standards such as DO 326A and ED 202A attempt to address this by providing guidelines for cyber security on in-service aircraft, though implementation work for such initiatives is still in early stages. From previous work on in service aircraft, the authors have determined that one of the key challenges is that of the retrospective application of new regulations to existing designs. This can present significant requirements for time, money, and Suitably Qualified and Experienced Personnel resource, things which are often in already limited supply in military environments. The authors have previously explored efficient ways of approaching compliance, with promising results. There is still the need to consider this retroactivity challenge in tandem with other key factors affecting the application of CSA, in order to determine any more potential mitigating actions that could lower the barrier to effective and efficient implementation of secure approaches in the air domain. This work explores the interrelated challenges surrounding real-world applications of CSA and the beginnings of how these may be overcome., Comment: Preprint for CTIC 2023

Published
2023

81. A Novel Dataset Towards Extracting Virus-Host Interactions

Author

Alshawi, Rasha, Sen, Atriya, Upham, Nathan S., and Sterner, Beckett

Subjects
Computer Science - Computation and Language
Abstract

We describe a novel dataset for the automated recognition of named taxonomic and other entities relevant to the association of viruses with their hosts. We further describe some initial results using pre-trained models on the named-entity recognition (NER) task on this novel dataset. We propose that our dataset of manually annotated abstracts now offers a Gold Standard Corpus for training future NER models in the automated extraction of host-pathogen detection methods from scientific publications, and further explain how our work makes first steps towards predicting the important human health-related concept of viral spillover risk automatically from the scientific literature., Comment: for associated dataset, see https://1drv.ms/u/s!AjanaqjkM2-ShN9rMT1BqrpAQRpakQ?e=TPkFgh

Published
2023

82. Assessing Trustworthiness of Autonomous Systems

Author

Chance, Gregory, Abeywickrama, Dhaminda B., LeClair, Beckett, Kerr, Owen, and Eder, Kerstin

Subjects
Computer Science - Artificial Intelligence, Computer Science - Computers and Society, Computer Science - Software Engineering
Abstract

As Autonomous Systems (AS) become more ubiquitous in society, more responsible for our safety and our interaction with them more frequent, it is essential that they are trustworthy. Assessing the trustworthiness of AS is a mandatory challenge for the verification and development community. This will require appropriate standards and suitable metrics that may serve to objectively and comparatively judge trustworthiness of AS across the broad range of current and future applications. The meta-expression `trustworthiness' is examined in the context of AS capturing the relevant qualities that comprise this term in the literature. Recent developments in standards and frameworks that support assurance of autonomous systems are reviewed. A list of key challenges are identified for the community and we present an outline of a process that can be used as a trustworthiness assessment framework for AS., Comment: 13 pages, 5 figures, 1 table

Published
2023

83. 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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84. 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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85. 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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86. 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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99. RILEM Contribution to Earthen Building

Author

Faria, Paulina, Beckett, Christopher T. S., Fabbri, Antonin, Keita, Emmanuel, Morel, Jean-Claude, Perlot, Céline, Perrot, Arnaud, Beckett, Christopher, editor, Bras, Ana, editor, Fabbri, Antonin, editor, Keita, Emmanuel, editor, Perlot, Céline, editor, and Perrot, Arnaud, editor

Published
2024
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