3,805 results on '"Wilkinson, Mark"'
Search Results
2. Weyl Group Representation of Billiard Trajectories for One-dimensional Hard Sphere Dynamics
- Author
-
Wilkinson, Mark
- Subjects
Mathematical Physics ,Mathematics - Dynamical Systems ,82C23, 70Fxx, 37A15, 37C83, 28C10 - Abstract
We present an exact formula for the dynamics of $N$ hard spheres of radius $r>0$ on an infinite line which evolve under the assumption that total linear momentum and kinetic energy of the system is conserved for all times. This model is commonly known as the one-dimensional Tonks gas or the hard rod gas model. Our exact formula is expressed as a sum over the Weyl group associated to the root system $A_{N-1}$ and is valid for all initial data in a full-measure subset of the tangent bundle of the hard sphere table. As an application of our explicit formula, we produce a simple proof that the associated billiard flow admits the Liouville measure on the tangent bundle of the hard sphere table as an invariant measure., Comment: 1 figure
- Published
- 2023
3. Common conditions of use elements. Atomic concepts for consistent and effective information governance
- Author
-
Sanchez Gonzalez, Maria del Carmen, Kamerling, Pim, Iermito, Mariapia, Casati, Sara, Riaz, Umar, Veal, Colin D., Maini, Monika, Jeanson, Francis, Benhamed, Oussama Mohammed, van Enckevort, Esther, Landi, Annalisa, Mimouni, Yanis, Le Cornec, Clèmence, Coviello, Domenico A., Franchin, Tiziana, Fusco, Francesca, Ramírez García, Jose Antonio, van der Zanden, Loes F. M., Bernier, Alexander, Wilkinson, Mark D., Mueller, Heimo, Gibson, Spencer J., and Brookes, Anthony J.
- Published
- 2024
- Full Text
- View/download PDF
4. Getting your DUCs in a row - standardising the representation of Digital Use Conditions
- Author
-
Jeanson, Francis, Gibson, Spencer J., Alper, Pinar, Bernier, Alexander, Woolley, J. Patrick, Mietchen, Daniel, Strug, Andrzej, Becker, Regina, Kamerling, Pim, Sanchez Gonzalez, Maria del Carmen, Mah, Nancy, Novakowski, Ann, Wilkinson, Mark D., Benhamed, Oussama Mohammed, Landi, Annalisa, Krog, Georg Philip, Müller, Heimo, Riaz, Umar, Veal, Colin, Holub, Petr, van Enckevort, Esther, and Brookes, Anthony J.
- Published
- 2024
- Full Text
- View/download PDF
5. EURO-NMD registry: federated FAIR infrastructure, innovative technologies and concepts of a patient-centred registry for rare neuromuscular disorders
- Author
-
Atalaia, Antonio, Wandrei, Dagmar, Lalout, Nawel, Thompson, Rachel, Tassoni, Adrian, ’t Hoen, Peter A. C., Athanasiou, Dimitrios, Baker, Suzie-Ann, Sakellariou, Paraskevi, Paliouras, Georgios, D’Angelo, Carla, Horvath, Rita, Mancuso, Michelangelo, van der Beek, Nadine, Kornblum, Cornelia, Kirschner, Janbernd, Pareyson, Davide, Bassez, Guillaume, Blacas, Laura, Jacoupy, Maxime, Eng, Catherine, Lamy, François, Plançon, Jean-Philippe, Haberlova, Jana, Brusse, Esther, Hoeijmakers, Janneke G. J., de Visser, Marianne, Claeys, Kristl G., Paradas, Carmen, Toscano, Antonio, Silani, Vincenzo, Gyenge, Melinda, Reviers, Evy, Hamroun, Dalil, Vroom, Elisabeth, Wilkinson, Mark D., Lochmuller, Hanns, and Evangelista, Teresinha
- Published
- 2024
- Full Text
- View/download PDF
6. Maximal Codimension Collisions and Invariant Measures for Hard Spheres on a Line
- Author
-
Wilkinson, Mark
- Subjects
Mathematics - Dynamical Systems ,Mathematical Physics ,Mathematics - Analysis of PDEs ,37C83, 28C10 (Primary) 37A60, 70G55 (Secondary) - Abstract
For any $N\geq 3$, we study invariant measures of the dynamics of $N$ hard spheres whose centres are constrained to lie on a line. In particular, we study the invariant submanifold $\mathcal{M}$ of the tangent bundle of the hard sphere billiard table comprising initial data that lead to the simultaneous collision of all $N$ hard spheres. Firstly, we obtain a characterisation of those continuously-differentiable $N$-body scattering maps which generate a billiard dynamics on $\mathcal{M}$ admitting a canonical weighted Hausdorff measure on $\mathcal{M}$ (that we term the Liouville measure on $\mathcal{M}$) as an invariant measure. We do this by deriving a second boundary-value problem for a fully nonlinear PDE that all such scattering maps satisfy by necessity. Secondly, by solving a family of functional equations, we find sufficient conditions on measures which are absolutely continuous with respect to the Hausdorff measure in order that they be invariant for billiard flows that conserve momentum and energy. Finally, we show that the unique momentum- and energy-conserving linear $N$-body scattering map yields a billiard dynamics which admits the Liouville measure on $\mathcal{M}$ as an invariant measure., Comment: 44 pages, 1 figure
- Published
- 2023
7. Genomic and global gene expression profiling in pediatric and young adult acute leukemia with PICALM::MLLT10 Fusion
- Author
-
Ma, Jingqun, Liu, Yen-Chun, Voss, Rebecca K., Ma, Jing, Palagani, Ajay, Caldwell, Elizabeth, Rosikiewicz, Wojciech, Cardenas, Maria, Foy, Scott, Umeda, Masayuki, Wilkinson, Mark R., Inaba, Hiroto, Klco, Jeffery M., Rubnitz, Jeffrey E., and Wang, Lu
- Published
- 2024
- Full Text
- View/download PDF
8. London quantum-secured metro network
- Author
-
Lord, Andrew, Woodward, Robert, Murai, Shinya, Sato, Hideaki, Dynes, James, Wright, Paul, White, Catherine, Davey, Russell, Wilkinson, Mark, Clinton-Tarestad, Piers, Hawkins, Ian, Farrington, Kristopher, and Shields, Andrew
- Subjects
Quantum Physics - Abstract
We describe a London Quantum-Secured Metro Network using Quantum Key Distribution between three London nodes together with customer access tails. The commercially- eady solution is fully integrated into the BT network and on-boarded its first customer., Comment: https://opg.optica.org/abstract.cfm?uri=OFC-2023-W4K.4
- Published
- 2023
9. Maximal Codimension Collisions and Invariant Measures for Hard Spheres on a Line
- Author
-
Wilkinson, Mark
- Published
- 2024
- Full Text
- View/download PDF
10. Brassica rapa CURLY LEAF is a major H3K27 methyltransferase regulating flowering time
- Author
-
Poza-Viejo, Laura, Payá-Milans, Miriam, Wilkinson, Mark D., Piñeiro, Manuel, Jarillo, José A., and Crevillén, Pedro
- Published
- 2024
- Full Text
- View/download PDF
11. Wilson and China: A Revised History of the Shandong Question (review)
- Author
-
Wilkinson, Mark F
- Published
- 2003
- Full Text
- View/download PDF
12. The value of doctrine: Assessing British officers' perspectives
- Author
-
Harvey, Claudia and Wilkinson, Mark
- Subjects
DOCTRINE - Armed Forces - Great Britain - Study and Teaching ,STRATEGY - Great Britain - Study and Teaching ,AFGHANISTAN CRISIS, 2001- - Strategy - Study and Teaching ,ROLES AND MISSIONS - Armed Forces - Great Britain - Study and Teaching - Abstract
illus bibliog
- Published
- 2009
13. A new implementation of the geometric method for solving the Eady slice equations
- Author
-
Egan, Charlie P., Bourne, David P., Cotter, Colin J., Cullen, Mike J. P., Pelloni, Beatrice, Roper, Steven M., and Wilkinson, Mark
- Subjects
Mathematics - Numerical Analysis - Abstract
We present a new implementation of the geometric method of Cullen & Purser (1984) for solving the semi-geostrophic Eady slice equations which model large scale atmospheric flows and frontogenesis. The geometric method is a Lagrangian discretisation, where the PDE is approximated by a particle system. An important property of the discretisation is that it is energy conserving. We restate the geometric method in the language of semi-discrete optimal transport theory and exploit this to develop a fast implementation that combines the latest results from numerical optimal transport theory with a novel adaptive time-stepping scheme. Our results enable a controlled comparison between the Eady-Boussinesq vertical slice equations and their semi-geostrophic approximation. We provide further evidence that weak solutions of the Eady-Boussinesq vertical slice equations converge to weak solutions of the semi-geostrophic Eady slice equations as the Rossby number tends to zero., Comment: 43 pages, 9 figures
- Published
- 2022
- Full Text
- View/download PDF
14. The Emergent Discipline of Health Web Science
- Author
-
Luciano, Joanne S, Cumming, Grant P, Wilkinson, Mark D, and Kahana, Eva
- Subjects
Computer applications to medicine. Medical informatics ,R858-859.7 ,Public aspects of medicine ,RA1-1270 - Abstract
The transformative power of the Internet on all aspects of daily life, including health care, has been widely recognized both in the scientific literature and in public discourse. Viewed through the various lenses of diverse academic disciplines, these transformations reveal opportunities realized, the promise of future advances, and even potential problems created by the penetration of the World Wide Web for both individuals and for society at large. Discussions about the clinical and health research implications of the widespread adoption of information technologies, including the Internet, have been subsumed under the disciplinary label of Medicine 2.0. More recently, however, multi-disciplinary research has emerged that is focused on the achievement and promise of the Web itself, as it relates to healthcare issues. In this paper, we explore and interrogate the contributions of the burgeoning field of Web Science in relation to health maintenance, health care, and health policy. From this, we introduce Health Web Science as a subdiscipline of Web Science, distinct from but overlapping with Medicine 2.0. This paper builds on the presentations and subsequent interdisciplinary dialogue that developed among Web-oriented investigators present at the 2012 Medicine 2.0 Conference in Boston, Massachusetts.
- Published
- 2013
- Full Text
- View/download PDF
15. The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions
- Author
-
Vandervalk, Ben, McCarthy, E Luke, Cruz-Toledo, José, Klein, Artjom, Baker, Christopher J O, Dumontier, Michel, and Wilkinson, Mark D
- Subjects
Medicine ,Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
BackgroundThe Web provides widespread access to vast quantities of health-related information that can improve quality-of-life through better understanding of personal symptoms, medical conditions, and available treatments. Unfortunately, identifying a credible and personally relevant subset of information can be a time-consuming and challenging task for users without a medical background. ObjectiveThe objective of the Personal Health Lens system is to aid users when reading health-related webpages by providing warnings about personally relevant drug interactions. More broadly, we wish to present a prototype for a novel, generalizable approach to facilitating interactions between a patient, their practitioner(s), and the Web. MethodsWe utilized a distributed, Semantic Web-based architecture for recognizing personally dangerous drugs consisting of: (1) a private, local triple store of personal health information, (2) Semantic Web services, following the Semantic Automated Discovery and Integration (SADI) design pattern, for text mining and identifying substance interactions, (3) a bookmarklet to trigger analysis of a webpage and annotate it with personalized warnings, and (4) a semantic query that acts as an abstract template of the analytical workflow to be enacted by the system. ResultsA prototype implementation of the system is provided in the form of a Java standalone executable JAR file. The JAR file bundles all components of the system: the personal health database, locally-running versions of the SADI services, and a javascript bookmarklet that triggers analysis of a webpage. In addition, the demonstration includes a hypothetical personal health profile, allowing the system to be used immediately without configuration. Usage instructions are provided. ConclusionsThe main strength of the Personal Health Lens system is its ability to organize medical information and to present it to the user in a personalized and contextually relevant manner. While this prototype was limited to a single knowledge domain (drug/drug interactions), the proposed architecture is generalizable, and could act as the foundation for much richer personalized-health-Web clients, while importantly providing a novel and personalizable mechanism for clinical experts to inject their expertise into the browsing experience of their patients in the form of customized semantic queries and ontologies.
- Published
- 2013
- Full Text
- View/download PDF
16. A Lie Algebra-Theoretic Approach to Characterisation of Collision Invariants of the Boltzmann Equation for General Convex Particles
- Author
-
Wilkinson, Mark
- Subjects
Mathematical Physics ,Mathematics - Analysis of PDEs ,Physics - Classical Physics - Abstract
By studying scattering Lie groups and their associated Lie algebras, we introduce a new method for the characterisation of collision invariants for physical scattering families associated to smooth, convex hard particles in the particular case that the collision invariant is of class $\mathscr{C}^{1}$. This work extends that of Saint-Raymond and Wilkinson (Communications on Pure and Applied Mathematics (2018), 71(8), pp. 1494-1534), in which the authors characterise collision invariants only in the case of the so-called canonical physical scattering family. Indeed, our method extends to the case of non-canonical physical scattering, whose existence was reported in Wilkinson (Archive for Rational Mechanics and Analysis (2020), 235(3), pp. 2055-2083). Moreover, our new method improves upon the work in Saint-Raymond and Wilkinson as we place no symmetry hypotheses on the underlying non-spherical particles which make up the gas under consideration. The techniques established in this paper also yield a new proof of the result of Boltzmann for collision invariants of class $\mathscr{C}^{1}$ in the classical case of hard spheres., Comment: 30 pages
- Published
- 2021
17. Plug and play virus-like particles for the generation of anti-toxin antibodies
- Author
-
Edge, Rebecca J., Marriott, Amy E., Stars, Emma L., Patel, Rohit N., Wilkinson, Mark C., King, Lloyd D.W., Slagboom, Julien, Tan, Choo Hock, Ratanabanangkoon, Kavi, Draper, Simon J., and Ainsworth, Stuart
- Published
- 2024
- Full Text
- View/download PDF
18. Genomic SNPs resolve the phylogeny of an ancient amphibian island radiation from the Seychelles
- Author
-
Sherlock, Miranda B., Streicher, Jeffrey W., Gower, David J., Maddock, Simon T., Nussbaum, Ronald A., Oommen, Oommen V., Serra Silva, Ana, Day, Julia J., and Wilkinson, Mark
- Published
- 2024
- Full Text
- View/download PDF
19. A Retrospective Longitudinal Study of 460 Patients with ABCA4-Associated Retinal Disease
- Author
-
Fenner, Beau J., Whitmore, S. Scott, DeLuca, Adam P., Andorf, Jean L., Daggett, Heather T., Luse, Meagan A., Haefeli, Lorena M., Riley, Janet B., Critser, Douglas B., Wilkinson, Mark E., Dumitrescu, Alina V., Drack, Arlene V., Boyce, Timothy M., Russell, Jonathan F., Binkley, Elaine M., Sohn, Elliott H., Russell, Stephen R., Boldt, H. Culver, Mullins, Robert F., Tucker, Budd A., Scheetz, Todd E., Han, Ian C., and Stone, Edwin M.
- Published
- 2024
- Full Text
- View/download PDF
20. Captives of Empire: The Japanese Internment of Allied Civilians in China, 1941–1945 (review)
- Author
-
Wilkinson, Mark
- Published
- 2008
- Full Text
- View/download PDF
21. Hyper acute stroke : the specialist nursing impact ; Exploring feelings of secondary traumatic stress : a qualitative enquiry
- Author
-
Wilkinson, Mark
- Abstract
Secondary Traumatic Stress (STS) has been defined as the natural consequent behaviours and emotions resulting from knowing about a traumatizing event experienced by a significant other- the stress resulting from helping or wanting to help a traumatized or suffering person (Figley, 1995). STS significantly impacts on nursing practice and performance, patient satisfaction and has organizational negative implications. Stroke specialist nurses are at risk of developing STS due to patients presenting with acute and often unpredictable illness. However, the emotional impact on their practice has not been investigated. This study aimed to perform a qualitative exploration of stroke specialist nurses' feelings of STS encountered in caring for patients with hyper acute presentations. Design: Narrative Methodology. Methods: Following university study ethical approval, stroke specialist nurses from across the UK were asked to participate and were asked to provide stories of their traumatic or stressful experiences related to hyper acute stroke. Data was collected electronically where participants contributed their narratives by email (n=10) and by audiotaped semi structured interviews (n=14). Results: Narrative analysis resulted in the emergence of four core themes: trigger situations, stress reactions, factors which exacerbate STS reactions and coping strategies. Conclusions: The data suggests that stroke specialist nurses are exposed to traumatic events occasioned during the hyper acute care episode. This subjection led to them describing feelings commensurate with STS. The physical and psychosocial effects have implications for nurses, patients and acute stroke services.
- Published
- 2022
22. Chemodynamics of metal-poor wide binaries in the Galactic halo: Association with the Sequoia event
- Author
-
Lim, Dongwook, Koch-Hansen, Andreas J., Hansen, Camilla Juul, Lépine, Sebastien, Marshall, Jennifer L., Wilkinson, Mark I., and Peñarrubia, Jorge
- Subjects
Astrophysics - Astrophysics of Galaxies - Abstract
Recently, an increasing number of wide binaries has been discovered. Their chemical and dynamical properties are studied through extensive surveys and pointed observations. However, the formation of these wide binaries is far from clear, although several scenarios have been suggested. In order to investigate the chemical compositions of these systems, we analysed high-resolution spectroscopy of three wide binary pairs belonging to the Galactic halo. In total, another three candidates from our original sample of 11 candidates observed at various resolutions with various instruments were refuted as co-moving pairs because their radial velocities are significantly different. Within our sample of wide binaries, we found homogeneity amongst the pair components in dynamical properties (proper motion and line-of-sight velocities) and also in chemical composition. Their metallicities are -1.16, -1.42, and -0.79 dex in [Fe/H] for each wide binary pair, which places these stars on the metal-poor side of wide binaries reported in the literature. In particular, the most metal-poor pair in our sample (WB2 = HD134439/HD134440) shows a lower [$\alpha$/Fe] abundance ratio than Milky Way field stars, which is a clear signature of an accreted object. We also confirmed that this wide binary shares remarkably similar orbital properties with stars and globular clusters associated with the Sequoia event. Thus, it appears that the WB2 pair was formed in a dwarf galaxy environment and subsequently dissolved into the Milky Way halo. Although the other two wide binaries appear to arise from a different formation mechanism, our results provide a novel opportunity for understanding the formation of wide binaries and the assembly process of the Milky Way., Comment: 13 pages, 7 figures, accepted for publication in A&A
- Published
- 2021
- Full Text
- View/download PDF
23. Soft mode anisotropy in negative thermal expansion material ReO$_3$
- Author
-
Bird, Tobias A., Wilkinson, Mark G. L., Keen, David A., Smith, Ronald I., Bristowe, Nicholas C., Dove, Martin T., Phillips, Anthony E., and Senn, Mark S.
- Subjects
Condensed Matter - Materials Science ,Condensed Matter - Disordered Systems and Neural Networks ,Condensed Matter - Other Condensed Matter - Abstract
We use a symmetry-motivated approach to analyse neutron pair distribution function data to investigate the mechanism of negative thermal expansion (NTE) in ReO$_3$. This analysis shows that the local structure of ReO$_3$ is dominated by an in-phase octahedral tilting mode and that the octahedral units are far less flexible to scissoring type deformations than the octahedra in the related compound ScF$_3$. These results support the idea that structural flexibility is an important factor in NTE materials, allowing the phonon modes that drive a volume contraction of the lattice to occupy a greater volume in reciprocal space. The lack of flexibility in ReO$_3$ restricts the NTE-driving phonons to a smaller region of reciprocal space, limiting the magnitude and temperature range of NTE. In addition, we investigate the thermal expansion properties of the material at high temperature and do not find the reported second NTE region. Finally, we show that the local fluctuations, even at elevated temperatures, respect the symmetry and order parameter direction of the observed $P4/mbm$ high pressure phase of ReO$_3$. The result indicates that the motions associated with rigid unit modes are highly anisotropic in these systems., Comment: 9 pages, 6 figures
- Published
- 2021
- Full Text
- View/download PDF
24. New data-based analysis tool for functioning of natural flood management measures reveals multi-site time-variable effectiveness
- Author
-
Roberts, Martyn T., Wilkinson, Mark E., Hallett, Paul D., and Geris, Josie
- Published
- 2024
- Full Text
- View/download PDF
25. A Fresh Look at FAIR for Research Software
- Author
-
Katz, Daniel S., Gruenpeter, Morane, Honeyman, Tom, Hwang, Lorraine, Wilkinson, Mark D., Sochat, Vanessa, Anzt, Hartwig, and Goble, Carole
- Subjects
Computer Science - Software Engineering - Abstract
This document captures the discussion and deliberation of the FAIR for Research Software (FAIR4RS) subgroup that took a fresh look at the applicability of the FAIR Guiding Principles for scientific data management and stewardship for research software. We discuss the vision of research software as ideally reproducible, open, usable, recognized, sustained and robust, and then review both the characteristic and practiced differences of research software and data. This vision and understanding of initial conditions serves as a backdrop for an attempt at translating and interpreting the guiding principles to more fully align with research software. We have found that many of the principles remained relatively intact as written, as long as considerable interpretation was provided. This was particularly the case for the "Findable" and "Accessible" foundational principles. We found that "Interoperability" and "Reusability" are particularly prone to a broad and sometimes opposing set of interpretations as written. We propose two new principles modeled on existing ones, and provide modified guiding text for these principles to help clarify our final interpretation. A series of gaps in translation were captured during this process, and these remain to be addressed. We finish with a consideration of where these translated principles fall short of the vision laid out in the opening.
- Published
- 2021
26. Linear dynamics of the semi-geostrophic equations in Eulerian coordinates on $\mathbb{R}^{3}$
- Author
-
Lisai, Stefania and Wilkinson, Mark
- Subjects
Mathematics - Analysis of PDEs ,Mathematical Physics ,35A01, 35B35, 35Q86 - Abstract
We consider a class of steady solutions of the semi-geostrophic equations on $\mathbb{R}^3$ and derive the linearised dynamics around those solutions. The linear PDE which governs perturbations around those steady states is a transport equation featuring a pseudo-differential operator of order 0. We study well-posedness of this equation in $L^2(\mathbb{R}^3;\mathbb{R}^3)$ introducing a representation formula for the solutions, and extend the result to the space of tempered distributions on $\mathbb{R}^{3}$. We investigate stability of the steady solutions by looking at plane wave solutions of the linearised problem, and discuss differences in the case of the quasi-geostrophic equations., Comment: 20 pages
- Published
- 2020
- Full Text
- View/download PDF
27. Semi-discrete optimal transport methods for the semi-geostrophic equations
- Author
-
Bourne, David P., Egan, Charlie P., Pelloni, Beatrice, and Wilkinson, Mark
- Subjects
Mathematics - Analysis of PDEs - Abstract
We give a new and constructive proof of the existence of global-in-time weak solutions of the 3-dimensional incompressible semi-geostrophic equations (SG) in geostrophic coordinates, for arbitrary initial measures with compact support. This new proof, based on semi-discrete optimal transport techniques, works by characterising discrete solutions of SG in geostrophic coordinates in terms of trajectories satisfying an ordinary differential equation. It is advantageous in its simplicity and its explicit relation to Eulerian coordinates through the use of Laguerre tessellations. Using our method, we obtain improved time-regularity for a large class of discrete initial measures, and we compute explicitly two discrete solutions. The method naturally gives rise to an efficient numerical method, which we illustrate by presenting simulations of a 2-dimensional semi-geostrophic flow in geostrophic coordinates generated using a numerical solver for the semi-discrete optimal transport problem coupled with an ordinary differential equation solver., Comment: 35 pages, 2 figures
- Published
- 2020
- Full Text
- View/download PDF
28. Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert
- Author
-
Mandakovic, Dinka, Aguado-Norese, Constanza, García-Jiménez, Beatriz, Hodar, Christian, Maldonado, Jonathan E., Gaete, Alexis, Latorre, Mauricio, Wilkinson, Mark D., Gutiérrez, Rodrigo A., Cavieres, Lohengrin A., Medina, Joaquín, Cambiazo, Verónica, and Gonzalez, Mauricio
- Published
- 2023
- Full Text
- View/download PDF
29. Towards complete and error-free genome assemblies of all vertebrate species
- Author
-
Rhie, Arang, McCarthy, Shane A, Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Ko, Byung June, Chaisson, Mark, Gedman, Gregory L, Cantin, Lindsey J, Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grutzner, Frank, Warren, Wesley C, Balakrishnan, Christopher N, Burt, Dave, George, Julia M, Biegler, Matthew T, Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F, Franchini, Paolo, Detrich, H William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin JP, Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T, Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B, Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E, Putnam, Nicholas H, Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Wood, Jonathan, Dagnew, Robel E, Guan, Dengfeng, London, Sarah E, Clayton, David F, Mello, Claudio V, Friedrich, Samantha R, Lovell, Peter V, Osipova, Ekaterina, Al-Ajli, Farooq O, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S, Makova, Kateryna D, Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P, Kwak, Woori, and Clawson, Hiram
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,Generic health relevance ,Animals ,Birds ,Gene Library ,Genome ,Genome Size ,Genome ,Mitochondrial ,Genomics ,Haplotypes ,High-Throughput Nucleotide Sequencing ,Molecular Sequence Annotation ,Sequence Alignment ,Sequence Analysis ,DNA ,Sex Chromosomes ,Vertebrates ,General Science & Technology - Abstract
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
- Published
- 2021
30. Comparing morphological and secretory aspects of cephalic glands among the New World coral snakes brings novel insights on their biological roles
- Author
-
Oliveira, Leonardo de, Nachtigall, Pedro Gabriel, Vialla, Vincent Louis, Campos, Pollyanna F., Costa-Neves, Adriana da, Zaher, Hussam, Silva Jr., Nelson Jorge da, Grazziotin, Felipe G., Wilkinson, Mark, and Junqueira-de-Azevedo, Inácio L.M.
- Published
- 2023
- Full Text
- View/download PDF
31. The TaCslA12 gene expressed in the wheat grain endosperm synthesizes wheat-like mannan when expressed in yeast and Arabidopsis.
- Author
-
Verhertbruggen, Yves, Bouder, Axelle, Vigouroux, Jacqueline, Alvarado, Camille, Geairon, Audrey, Guillon, Fabienne, Wilkinson, Mark D, Stritt, Fabian, Pauly, Markus, Lee, Mi Yeon, Mortimer, Jenny C, Scheller, Henrik V, Mitchell, Rowan AC, Voiniciuc, Cătălin, Saulnier, Luc, and Chateigner-Boutin, Anne-Laure
- Subjects
Saccharomyces cerevisiae ,Plants ,Genetically Modified ,Arabidopsis ,Triticum ,Tobacco ,Mannans ,Genes ,Plant ,Endosperm ,Edible Grain ,Cell walls ,Developing endosperm ,Heterologous expression ,Mannan ,Wheat grain ,Plant Biology ,Crop and Pasture Production ,Plant Biology & Botany - Abstract
Mannan is a class of cell wall polysaccharides widespread in the plant kingdom. Mannan structure and properties vary according to species and organ. The cell walls of cereal grains have been extensively studied due to their role in cereal processing and to their beneficial effect on human health as dietary fiber. Recently, we showed that mannan in wheat (Triticum aestivum) grain endosperm has a linear structure of β-1,4-linked mannose residues. The aim of this work was to study the biosynthesis and function of wheat grain mannan. We showed that mannan is deposited in the endosperm early during grain development, and we identified candidate mannan biosynthetic genes expressed in the endosperm. The functional study in wheat was unsuccessful therefore our best candidate genes were expressed in heterologous systems. The endosperm-specificTaCslA12 gene expressed in Pichia pastoris and in an Arabidopsis thaliana mutant depleted in glucomannan led to the production of wheat-like linear mannan lacking glucose residues and with moderate acetylation. Therefore, this gene encodes a mannan synthase and is likely responsible for the synthesis of wheat endosperm mannan.
- Published
- 2021
32. FAIR: Making Data AI-Ready
- Author
-
Sansone, Susanna-Assunta, primary, Rocca-Serra, Philippe, additional, Wilkinson, Mark, additional, and Harland, Lee, additional
- Published
- 2023
- Full Text
- View/download PDF
33. Targeting protein folding in the malaria parasite
- Author
-
Wilkinson, Mark Dale, Baum, Jake, and Willison, Keith
- Abstract
The protein folding machinery in Plasmodium falciparum, the main causative agent of malaria disease, has been directly linked to emerging parasite drug resistance. The Chaperonin Containing TCP-1 ring (CCT) complex is the most up-regulated chaperonin in these drug resistant parasites and is therefore an attractive target to antagonize resistance in the field. Whilst there is a wealth of information about the CCT complex in higher eukaryotes, there is a paucity of information about the complex in more divergent species, such as the malaria parasite. The work presented in this thesis explores the CCT complex in P. falciparum (PfCCT) and the folding of its substrates, including the essential and abundant protein actin. First, I present a technique for studying actin on a single molecule level. Using this system, I observe the dynamic changes in actin's macromolecular structure, its folding and drug-binding in real-time. To understand PfCCT, I biochemically char- acterise one of its essential cofactors, PhLP2, and isolate the complex from parasite lysate. I identify the PfCCT interactome and obtain a low-resolution structure of the complex, which has a highly conserved interactome and structure. Towards targeting the complex, I use a biosynthetic platform that expresses a puta- tive CCT-targeting compound, violacein, to conduct a high-throughput screen. I test the effect of violacein and biosynthetically-derived violacein derivatives on parasite growth. I show that violacein inhibits both wild type and drug-resistant parasite iso- lates from the field and identify a number of derivatives that are more potent than the parent compound. I show that violacein affects actin dynamics in vivo, resulting in an accumulation of actin signal indicative of incorrect protein folding, supporting the hypothesis that violacein targets the CCT complex. The work presented in this thesis provides a clear route for antimalarial drug development, ultimately towards targeting protein folding to stem the deadly disease.
- Published
- 2020
- Full Text
- View/download PDF
34. Intra-professional specialist differentiation in the UK surgical profession
- Author
-
Wilkinson, Mark and Richards, Martin
- Subjects
617 ,Professionalisation ,Surgery ,Capital - Abstract
This thesis studies specialist differentiation in the surgical profession of the United Kingdom, seeking to clarify what the combinations of factors favour or hinder it. It draws on interviews with two hundred surgeons, general practitioners and hospital CEO’s, as well as on sociological literature, especially Bucher and Strauss’s (1961) ‘Process Model’, the concept of ‘profession’ developed by Freidson (1970), Larson’s (1977) model of the ‘Professional Project’ and Bourdieu’s (1981, 1984, 1986, 1988, 1990, 1991, 2005) seminal work on ‘Capital’ and ‘Power’ in ‘Social fields’. The thesis aims to interpret specialisation as a dynamic political process influenced by different groups’ deployment of accumulated specific types of ‘capital’, challenging the view, widespread in the profession itself and still present in functionalist sociological literature, that specialist differentiation is an inevitable consequence of advances in knowledge and technology. In addition to the introduction, conclusion and appendices, the thesis includes chapters on: (1) theoretical framework; (2) methodology; (3) the role of knowledge and technology in specialist differentiation; (4) the role of institutions before the establishment of the NHS; (5) the role of the relationship between the profession and the state in the period 1948-1990; (6) ditto in the period 1991-1997; (7) the current situation and how it might develop.
- Published
- 2020
- Full Text
- View/download PDF
35. Long-term daily stream temperature record for Scotland reveals spatio-temporal patterns in warming of rivers in the past and further warming in the future
- Author
-
Loerke, Eva, Pohle, Ina, Wilkinson, Mark E., Rivington, Mike, Wardell-Johnson, Douglas, and Geris, Josie
- Published
- 2023
- Full Text
- View/download PDF
36. Smooth Solutions of the Surface Semi-Geostrophic Equations
- Author
-
Lisai, Stefania and Wilkinson, Mark
- Subjects
Mathematics - Analysis of PDEs - Abstract
The semi-geostrophic equations have attracted the attention of the physical and mathematical communities since the work of Hoskins in the 1970s owing to their ability to model the formation of fronts in rotation-dominated flows, and also to their connection with optimal transport theory. In this paper, we study an active scalar equation, whose activity is determined by way of a Neumann-to-Dirichlet map associated to a fully nonlinear second-order Neumann boundary value problem on the infinite strip $\mathbb{R}^{2}\times(0,1)$, that models a semi-geostrophic flow in regime of constant potential vorticity. This system is an expression of an Eulerian semi-geostrophic flow in a co-ordinate system originally due to Hoskins, to which we shall refer as {\em Hoskins' coordinates}. We obtain results on the local-in-time existence and uniqueness of classical solutions of this active scalar equation in H\"older spaces., Comment: 27 pages. Typos corrected. To appear in Calc of Var & PDEs
- Published
- 2019
37. BioHackathon 2015: Semantics of data for life sciences and reproducible research
- Author
-
Vos, Rutger A, Katayama, Toshiaki, Mishima, Hiroyuki, Kawano, Shin, Kawashima, Shuichi, Kim, Jin-Dong, Moriya, Yuki, Tokimatsu, Toshiaki, Yamaguchi, Atsuko, Yamamoto, Yasunori, Wu, Hongyan, Amstutz, Peter, Antezana, Erick, Aoki, Nobuyuki P, Arakawa, Kazuharu, Bolleman, Jerven T, Bolton, Evan, Bonnal, Raoul JP, Bono, Hidemasa, Burger, Kees, Chiba, Hirokazu, Cohen, Kevin B, Deutsch, Eric W, Fernández-Breis, Jesualdo T, Fu, Gang, Fujisawa, Takatomo, Fukushima, Atsushi, García, Alexander, Goto, Naohisa, Groza, Tudor, Hercus, Colin, Hoehndorf, Robert, Itaya, Kotone, Juty, Nick, Kawashima, Takeshi, Kim, Jee-Hyub, Kinjo, Akira R, Kotera, Masaaki, Kozaki, Kouji, Kumagai, Sadahiro, Kushida, Tatsuya, Lütteke, Thomas, Matsubara, Masaaki, Miyamoto, Joe, Mohsen, Attayeb, Mori, Hiroshi, Naito, Yuki, Nakazato, Takeru, Nguyen-Xuan, Jeremy, Nishida, Kozo, Nishida, Naoki, Nishide, Hiroyo, Ogishima, Soichi, Ohta, Tazro, Okuda, Shujiro, Paten, Benedict, Perret, Jean-Luc, Prathipati, Philip, Prins, Pjotr, Queralt-Rosinach, Núria, Shinmachi, Daisuke, Suzuki, Shinya, Tabata, Tsuyosi, Takatsuki, Terue, Taylor, Kieron, Thompson, Mark, Uchiyama, Ikuo, Vieira, Bruno, Wei, Chih-Hsuan, Wilkinson, Mark, Yamada, Issaku, Yamanaka, Ryota, Yoshitake, Kazutoshi, Yoshizawa, Akiyasu C, Dumontier, Michel, Kosaki, Kenjiro, and Takagi, Toshihisa
- Subjects
Medical Biochemistry and Metabolomics ,Biological Sciences ,Bioinformatics and Computational Biology ,Biomedical and Clinical Sciences ,Networking and Information Technology R&D (NITRD) ,Genetics ,Biological Science Disciplines ,Computational Biology ,Data Mining ,Metadata ,Reproducibility of Results ,Semantic Web ,BioHackathon ,Bioinformatics ,Databases ,Linked Open Data ,Ontology ,Visualization ,Web Services ,Workflows ,Biochemistry and Cell Biology ,Clinical Sciences ,Oncology and Carcinogenesis - Abstract
We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.
- Published
- 2020
38. EURO-NMD registry: federated FAIR infrastructure, innovative technologies and concepts of a patient-centred registry for rare neuromuscular disorders
- Author
-
European Commission, Atalaia, Antonio [0000-0002-9345-0953], Wandrei, Dagmar [0000-0002-8144-162X], Lalout, Nawel [0000-0003-3707-8373], Tassoni, Adrian [0000-0001-5392-4125], t Hoen, Peter A.C. [0000-0003-4450-3112], Sakellariou, Paraskevi [0000-0002-9091-0053], Horvàth, Rita [0000-0002-9841-170X], Mancuso, Michelangelo [0000-0003-2738-8562], van der Beek, Nadine [0000-0001-9161-3301], Kornblum, Cornelia [0000-0002-0111-7281], Kirschner, Janbernd [0000-0003-1618-7386], Pareyson, Davide [0000-0001-6854-765X], Bassez, Guillaume [0000-0002-2044-1052], Jacoupy, Maxime [0000-0003-1841-7747], Eng, Catherine [0000-0003-4318-2345], Lamy, François [0000-0001-6542-1381], Haberlova, Jana [0000-0003-2734-9715], Brusse, Esther [0000-0002-1452-2219], Hoeijmakers, Janneke [0000-0001-6940-0027], de Visser, Marianne [0000-0002-5591-7452], Claeys, Kristl [0000-0001-9937-443X], Paradas, Carmen [0000-0002-6917-2236], Silani, Vincenzo [0000-0002-7698-3854], Reviers, Evy [0000-0002-6044-5234], Hamroun, Dalil [0000-0002-4853-8227], Vroom, Elisabeth [0000-0002-3422-2782], Wilkinson, Mark D. [0000-0001-6960-357X], Lochmuller, Hanns [0000-0003-2324-8001], Evangelista, Teresinha [0000-0002-1329-9131], Atalaia, Antonio, Wandrei, Dagmar, Lalout, Nawel, Thompson, Rachel, Tassoni, Adrian, t Hoen, Peter A.C., Athanasiou, Dimitrios, Baker, Suzie-Ann, Sakellariou, Paraskevi, Paliouras, Georgios, D'Angelo, Carla, Horvàth, Rita, Mancuso, Michelangelo, van der Beek, Nadine, Kornblum, Cornelia, Kirschner, Janbernd, Pareyson, Davide, Bassez, Guillaume, Blacas, Laura, Jacoupy, Maxime, Eng, Catherine, Lamy, François, Plançon, Jean-Philippe, Haberlova, Jana, Brusse, Esther, Hoeijmakers, Janneke, de Visser, Marianne, Claeys, Kristl, Paradas, Carmen, Toscano, Antonio, Silani, Vincenzo, Gyenge, Melinda, Reviers, Evy, Hamroun, Dalil, Vroom, Elisabeth, Wilkinson, Mark D., Lochmuller, Hanns, Evangelista, Teresinha, European Commission, Atalaia, Antonio [0000-0002-9345-0953], Wandrei, Dagmar [0000-0002-8144-162X], Lalout, Nawel [0000-0003-3707-8373], Tassoni, Adrian [0000-0001-5392-4125], t Hoen, Peter A.C. [0000-0003-4450-3112], Sakellariou, Paraskevi [0000-0002-9091-0053], Horvàth, Rita [0000-0002-9841-170X], Mancuso, Michelangelo [0000-0003-2738-8562], van der Beek, Nadine [0000-0001-9161-3301], Kornblum, Cornelia [0000-0002-0111-7281], Kirschner, Janbernd [0000-0003-1618-7386], Pareyson, Davide [0000-0001-6854-765X], Bassez, Guillaume [0000-0002-2044-1052], Jacoupy, Maxime [0000-0003-1841-7747], Eng, Catherine [0000-0003-4318-2345], Lamy, François [0000-0001-6542-1381], Haberlova, Jana [0000-0003-2734-9715], Brusse, Esther [0000-0002-1452-2219], Hoeijmakers, Janneke [0000-0001-6940-0027], de Visser, Marianne [0000-0002-5591-7452], Claeys, Kristl [0000-0001-9937-443X], Paradas, Carmen [0000-0002-6917-2236], Silani, Vincenzo [0000-0002-7698-3854], Reviers, Evy [0000-0002-6044-5234], Hamroun, Dalil [0000-0002-4853-8227], Vroom, Elisabeth [0000-0002-3422-2782], Wilkinson, Mark D. [0000-0001-6960-357X], Lochmuller, Hanns [0000-0003-2324-8001], Evangelista, Teresinha [0000-0002-1329-9131], Atalaia, Antonio, Wandrei, Dagmar, Lalout, Nawel, Thompson, Rachel, Tassoni, Adrian, t Hoen, Peter A.C., Athanasiou, Dimitrios, Baker, Suzie-Ann, Sakellariou, Paraskevi, Paliouras, Georgios, D'Angelo, Carla, Horvàth, Rita, Mancuso, Michelangelo, van der Beek, Nadine, Kornblum, Cornelia, Kirschner, Janbernd, Pareyson, Davide, Bassez, Guillaume, Blacas, Laura, Jacoupy, Maxime, Eng, Catherine, Lamy, François, Plançon, Jean-Philippe, Haberlova, Jana, Brusse, Esther, Hoeijmakers, Janneke, de Visser, Marianne, Claeys, Kristl, Paradas, Carmen, Toscano, Antonio, Silani, Vincenzo, Gyenge, Melinda, Reviers, Evy, Hamroun, Dalil, Vroom, Elisabeth, Wilkinson, Mark D., Lochmuller, Hanns, and Evangelista, Teresinha
- Abstract
The EURO-NMD Registry collects data from all neuromuscular patients seen at EURO-NMD's expert centres. In-kind contributions from three patient organisations have ensured that the registry is patient-centred, meaningful, and impactful. The consenting process covers other uses, such as research, cohort finding and trial readiness.
- Published
- 2024
39. Common conditions of use elements. Atomic concepts for consistent and effective information governance
- Author
-
European Commission, Sanchez Gonzalez, Maria Del Carmen [0000-0002-8523-9218], Kamerling, Pim [0009-0007-3897-0466], Casati, Sara [0000-0002-5049-7321], Riaz, Umar [0009-0002-2265-8770], Veal, Colin [0000-0002-9840-2512], Jeanson, Francis [0000-0001-6085-2967], Benhamed, M. [0000-0002-2567-1914], van Enckevort, Esther [0000-0002-2440-3993], Landi, Annalisa [0000-0001-9368-6424], Mimouni, Yanis [0000-0002-7527-524X], Coviello, Domenico [0000-0001-8440-865X], Franchin, Tiziana [0000-0003-2745-0733], Fusco, Francesca [0000-0002-7578-6058], van der Zanden, Loes [0000-0003-3914-7491], Wilkinson, Mark D. [0000-0001-6960-357X], Mueller, Heimo [0000-0002-9691-4872], Gibson, Spencer [0000-0003-0768-1542], Brookes, Anthony [0000-0001-8686-0017], Sanchez Gonzalez, Maria Del Carmen, Kamerling, Pim, Iermito, Mariapia, Casati, Sara, Riaz, Umar, Veal, Colin, Maini, Monika, Jeanson, Francis, Benhamed, M., van Enckevort, Esther, Landi, Annalisa, Mimouni, Yanis, Le Cornec, Clémence M. A., Coviello, Domenico, Franchin, Tiziana, Fusco, Francesca, Ramírez García, Jose Antonio, van der Zanden, Loes, Bernier, Alexander, Wilkinson, Mark D., Mueller, Heimo, Gibson, Spencer, Brookes, Anthony, European Commission, Sanchez Gonzalez, Maria Del Carmen [0000-0002-8523-9218], Kamerling, Pim [0009-0007-3897-0466], Casati, Sara [0000-0002-5049-7321], Riaz, Umar [0009-0002-2265-8770], Veal, Colin [0000-0002-9840-2512], Jeanson, Francis [0000-0001-6085-2967], Benhamed, M. [0000-0002-2567-1914], van Enckevort, Esther [0000-0002-2440-3993], Landi, Annalisa [0000-0001-9368-6424], Mimouni, Yanis [0000-0002-7527-524X], Coviello, Domenico [0000-0001-8440-865X], Franchin, Tiziana [0000-0003-2745-0733], Fusco, Francesca [0000-0002-7578-6058], van der Zanden, Loes [0000-0003-3914-7491], Wilkinson, Mark D. [0000-0001-6960-357X], Mueller, Heimo [0000-0002-9691-4872], Gibson, Spencer [0000-0003-0768-1542], Brookes, Anthony [0000-0001-8686-0017], Sanchez Gonzalez, Maria Del Carmen, Kamerling, Pim, Iermito, Mariapia, Casati, Sara, Riaz, Umar, Veal, Colin, Maini, Monika, Jeanson, Francis, Benhamed, M., van Enckevort, Esther, Landi, Annalisa, Mimouni, Yanis, Le Cornec, Clémence M. A., Coviello, Domenico, Franchin, Tiziana, Fusco, Francesca, Ramírez García, Jose Antonio, van der Zanden, Loes, Bernier, Alexander, Wilkinson, Mark D., Mueller, Heimo, Gibson, Spencer, and Brookes, Anthony
- Abstract
Myriad policy, ethical and legal considerations underpin the sharing of biological resources, implying the need for standardised and yet flexible ways to digitally represent diverse 'use conditions'. We report a core lexicon of terms that are atomic, non-directional 'concepts of use', called Common Conditions of use Elements. This work engaged biobanks and registries relevant to the European Joint Programme for Rare Diseases and aimed to produce a lexicon that would have generalised utility. Seventy-six concepts were initially identified from diverse real-world settings, and via iterative rounds of deliberation and user-testing these were optimised and condensed down to 20 items. To validate utility, support software and training information was provided to biobanks and registries who were asked to create Sharing Policy Profiles. This succeeded and involved adding standardised directionality and scope annotations to the employed terms. The addition of free-text parameters was also explored. The approach is now being adopted by several real-world projects, enabling this standard to evolve progressively into a universal basis for representing and managing conditions of use.
- Published
- 2024
40. Getting your DUCs in a row - standardising the representation of Digital Use Conditions
- Author
-
European Commission, Jeanson, Francis [0000-0001-6085-2967], Gibson, Spencer [0000-0003-0768-1542], Alper, Pinar [0000-0002-2224-0780], Woolley, J. Patrick [0000-0002-2829-8756], Mietchen, Daniel [0000-0001-9488-1870], Strug, Andrzej [0000-0003-1948-4597], Becker, Regina [0000-0002-6711-8375], Kamerling, Pim [0009-0007-3897-0466], Sánchez-González, M. [0000-0002-8523-9218], Mah, Nancy [0000-0002-1240-8076], Novakowski, Ann [0000-0002-1309-8356], Wilkinson, Mark D. [0000-0001-6960-357X], Benhamed, M. [0000-0002-2567-1914], Landi, Annalisa [0000-0001-9368-6424], Müller, Heimo [0000-0002-9691-4872], Riaz, Umar [0009-0002-2265-8770], Veal, Colin [0000-0002-9840-2512], Holub, Petr [0000-0002-5358-616X], van Enckevort, Esther [0000-0002-2440-3993], Brookes, Anthony [0000-0001-8686-0017], Jeanson, Francis, Gibson, Spencer, Alper, Pinar, Bernier, Alexander, Woolley, J. Patrick, Mietchen, Daniel, Strug, Andrzej, Becker, Regina, Kamerling, Pim, Sánchez-González, M., Mah, Nancy, Novakowski, Ann, Wilkinson, Mark D., Benhamed, M., Landi, Annalisa, Krog, Georg Philip, Müller, Heimo, Riaz, Umar, Veal, Colin, Holub, Petr, van Enckevort, Esther, Brookes, Anthony, European Commission, Jeanson, Francis [0000-0001-6085-2967], Gibson, Spencer [0000-0003-0768-1542], Alper, Pinar [0000-0002-2224-0780], Woolley, J. Patrick [0000-0002-2829-8756], Mietchen, Daniel [0000-0001-9488-1870], Strug, Andrzej [0000-0003-1948-4597], Becker, Regina [0000-0002-6711-8375], Kamerling, Pim [0009-0007-3897-0466], Sánchez-González, M. [0000-0002-8523-9218], Mah, Nancy [0000-0002-1240-8076], Novakowski, Ann [0000-0002-1309-8356], Wilkinson, Mark D. [0000-0001-6960-357X], Benhamed, M. [0000-0002-2567-1914], Landi, Annalisa [0000-0001-9368-6424], Müller, Heimo [0000-0002-9691-4872], Riaz, Umar [0009-0002-2265-8770], Veal, Colin [0000-0002-9840-2512], Holub, Petr [0000-0002-5358-616X], van Enckevort, Esther [0000-0002-2440-3993], Brookes, Anthony [0000-0001-8686-0017], Jeanson, Francis, Gibson, Spencer, Alper, Pinar, Bernier, Alexander, Woolley, J. Patrick, Mietchen, Daniel, Strug, Andrzej, Becker, Regina, Kamerling, Pim, Sánchez-González, M., Mah, Nancy, Novakowski, Ann, Wilkinson, Mark D., Benhamed, M., Landi, Annalisa, Krog, Georg Philip, Müller, Heimo, Riaz, Umar, Veal, Colin, Holub, Petr, van Enckevort, Esther, and Brookes, Anthony
- Abstract
Improving patient care and advancing scientific discovery requires responsible sharing of research data, healthcare records, biosamples, and biomedical resources that must also respect applicable use conditions. Defining a standard to structure and manage these use conditions is a complex and challenging task. This is exemplified by a near unlimited range of asset types, a high variability of applicable conditions, and differing applications at the individual or collective level. Furthermore, the specifics and granularity required are likely to vary depending on the ultimate contexts of use. All these factors confound alignment of institutional missions, funding objectives, regulatory and technical requirements to facilitate effective sharing. The presented work highlights the complexity and diversity of the problem, reviews the current state of the art, and emphasises the need for a flexible and adaptable approach. We propose Digital Use Conditions (DUC) as a framework that addresses these needs by leveraging existing standards, striking a balance between expressiveness versus ambiguity, and considering the breadth of applicable information with their context of use.
- Published
- 2024
41. The genomic landscape of pediatric acute lymphoblastic leukemia
- Author
-
Brady, Samuel W., Roberts, Kathryn G., Gu, Zhaohui, Shi, Lei, Pounds, Stanley, Pei, Deqing, Cheng, Cheng, Dai, Yunfeng, Devidas, Meenakshi, Qu, Chunxu, Hill, Ashley N., Payne-Turner, Debbie, Ma, Xiaotu, Iacobucci, Ilaria, Baviskar, Pradyuamna, Wei, Lei, Arunachalam, Sasi, Hagiwara, Kohei, Liu, Yanling, Flasch, Diane A., Liu, Yu, Parker, Matthew, Chen, Xiaolong, Elsayed, Abdelrahman H., Pathak, Omkar, Li, Yongjin, Fan, Yiping, Michael, J. Robert, Rusch, Michael, Wilkinson, Mark R., Foy, Scott, Hedges, Dale J., Newman, Scott, Zhou, Xin, Wang, Jian, Reilly, Colleen, Sioson, Edgar, Rice, Stephen V., Pastor Loyola, Victor, Wu, Gang, Rampersaud, Evadnie, Reshmi, Shalini C., Gastier-Foster, Julie, Guidry Auvil, Jaime M., Gesuwan, Patee, Smith, Malcolm A., Winick, Naomi, Carroll, Andrew J., Heerema, Nyla A., Harvey, Richard C., Willman, Cheryl L., Larsen, Eric, Raetz, Elizabeth A., Borowitz, Michael J., Wood, Brent L., Carroll, William L., Zweidler-McKay, Patrick A., Rabin, Karen R., Mattano, Leonard A., Maloney, Kelly W., Winter, Stuart S., Burke, Michael J., Salzer, Wanda, Dunsmore, Kimberly P., Angiolillo, Anne L., Crews, Kristine R., Downing, James R., Jeha, Sima, Pui, Ching-Hon, Evans, William E., Yang, Jun J., Relling, Mary V., Gerhard, Daniela S., Loh, Mignon L., Hunger, Stephen P., Zhang, Jinghui, and Mullighan, Charles G.
- Published
- 2022
- Full Text
- View/download PDF
42. Organ donation in principle and in practice: tensions and healthcare professionals’ troubled consciences
- Author
-
Machin, Laura L., Cooper, Jessie, Dixon, Heather, and Wilkinson, Mark
- Published
- 2022
- Full Text
- View/download PDF
43. Cullen's Stability Principle and Weak Solutions of the Free-surface Semi-geostrophic Equations
- Author
-
Cullen, Mike J. P., Kuna, Tobias, Pelloni, Beatrice, and Wilkinson, Mark
- Subjects
Mathematics - Analysis of PDEs ,Physics - Atmospheric and Oceanic Physics - Abstract
The semi-geostrophic equations are used widely in the modelling of large-scale atmospheric flows. In this note, we prove the global existence of weak solutions of the incompressible semi-geostrophic equations, in geostrophic coordinates, in a three-dimensional domain with a free upper boundary. The proof, based on an energy minimisation argument originally inspired by Cullen's Stability Principle, uses optimal transport results as well as the analysis of Hamiltonian ODEs in spaces of probability measures as studied by Ambrosio and Gangbo. We also give a general formulation of Cullen's Stability Principle in a rigorous mathematical framework.
- Published
- 2018
44. Reliable mass calculation in spherical gravitating systems
- Author
-
Diakogiannis, Foivos I., Lewis, Geraint F., Ibata, Rodrigo A., Guglielmo, Magda, Wilkinson, Mark I., and Power, Chris
- Subjects
Astrophysics - Astrophysics of Galaxies - Abstract
We present an innovative approach to the methodology of dynamical modelling, allowing practical reconstruction of the underlying dark matter mass without assuming both the density and anisotropy functions. With this, the mass-anisotropy degeneracy is reduced to simple model inference, incorporating the uncertainties inherent with observational data, statistically circumventing the mass-anisotropy degeneracy in spherical collisionless systems. We also tackle the inadequacy that the Jeans method of moments has on small datasets, with the aid of Generative Adversarial Networks: we leverage the power of artificial intelligence to reconstruct non-parametrically the projected line-of-sight velocity distribution. We show with realistic numerical simulations of dwarf spheroidal galaxies that we can distinguish between competing dark matter distributions and recover the anisotropy and mass profile of the system., Comment: 19 pages, 13 figures, accepted for publication in MNRAS
- Published
- 2018
- Full Text
- View/download PDF
45. On Global-in-time Chaotic Weak Solutions of the Liouville Equation for Hard Spheres
- Author
-
Wilkinson, Mark
- Subjects
Mathematics - Analysis of PDEs ,Condensed Matter - Statistical Mechanics - Abstract
We outline a new method of construction of global-in-time weak solutions of the Liouville equation - and also of the associated BBGKY hierarchy - corresponding to the hard sphere singular Hamiltonian. Our method makes use only of geometric reflection arguments on phase space. As a consequence of our method, in the case of $N=2$ hard spheres, we show for any chaotic initial data, the unique global-in-time weak solution $F$ of the Liouville equation is realised as $F=\mathsf{R}(f\otimes f)$ in the sense of tempered distributions on $T\mathbb{R}^{6}\times (-\infty, \infty)$, where $\mathsf{R}$ is a 'reflection-type' operator on Schwartz space, and $f$ is a global-in-time classical solution of the 1-particle free transport Liouville equation on $T\mathbb{R}^{3}$., Comment: 31 pages
- Published
- 2018
46. Local-in-time Physical Solutions of the Incompressible Semi-Geostrophic Equations in Eulerian Coordinates
- Author
-
Wilkinson, Mark
- Subjects
Mathematics - Analysis of PDEs ,Physics - Atmospheric and Oceanic Physics - Abstract
We prove the existence of local-in-time smooth solutions of the incompressible semi-geostrophic equations expressed in Eulerian co-ordinates in 3-dimensional smooth bounded simply-connected domains. Our solutions adhere to Cullen's Stability Principle in that the geopotential is guaranteed to be a convex map for all times of its existence. We achieve our results by appealing to the theory of so-called div-curl systems (or Hodge systems), making use of recent results of Wang, which yield useful estimates on the ageostrophic velocity field. To our knowledge, this work constitutes the first time that any notion of bounded solution of the semi-geostrophic equations in Eulerian co-ordinates has been constructed on a bounded domain. Indeed, our work solves an open problem as highlighted by, among others, A. Figalli in his CIME lectures on the semi-geostrophic equations. Our methods are largely elementary. We discuss the application of the novel ideas in this work to the case of variable Coriolis force in the final section of the article., Comment: 17 pages; some typos corrected; statement of main result modified; more details on proof of main result provided
- Published
- 2018
47. Dynamical modelling of dwarf-spheroidal galaxies using Gaussian-process emulation
- Author
-
Gration, Amery and Wilkinson, Mark I.
- Subjects
Astrophysics - Astrophysics of Galaxies - Abstract
We present a novel and efficient method for fitting dynamical models of stellar kinematic data in dwarf spheroidal galaxies (dSph). Our approach is based on Gaussian-process emulation (GPE), which is a sophisticated form of curve fitting that requires fewer training data than alternative methods. We use a set of validation tests and diagnostic criteria to assess the performance of the emulation procedure. We have implemented an algorithm in which both the GPE procedure and its validation are fully automated. Applying this method to synthetic data, with fewer than 100 model evaluations we are able to recover a robust confidence region for the three-dimensional parameter vector of a toy model of the phase-space distribution function of a dSph. Although the dynamical model presented in this paper is low-dimensional and static, we emphasize that the algorithm is applicable to any scheme that involves the evaluation of computationally expensive models. It therefore has the potential to render tractable previously intractable problems, for example, the modelling of individual dSphs using high-dimensional, time-dependent N-body simulations., Comment: 14 pages 11 figures
- Published
- 2018
- Full Text
- View/download PDF
48. On the Initial Boundary-Value Problem in the Kinetic Theory of Hard Particles II: Non-uniqueness
- Author
-
Wilkinson, Mark
- Subjects
Mathematical Physics ,Mathematics - Classical Analysis and ODEs ,Physics - Classical Physics - Abstract
We prove that to each initial datum in a set of positive measure in phase space, there exist uncountably-many associated weak solutions of Newton's equations of motion which govern the dynamics of two non-spherical sets with real-analytic boundaries subject to the conservation of linear momentum, angular momentum and kinetic energy. We prove this result by first exhibiting non-uniqueness of classical solution to a constrained Monge-Amp\`ere equation posed on Euclidean space, and then applying the deep existence theory of Ballard for hard particle dynamics. In the final section of the article, we discuss the relevance of this observation to the kinetic theory of hard particle systems.
- Published
- 2018
49. On the Initial Boundary-Value Problem in the Kinetic Theory of Hard Particles I: Non-existence
- Author
-
Wilkinson, Mark
- Subjects
Mathematics - Classical Analysis and ODEs ,Physics - Classical Physics - Abstract
In the first of two papers, we study the initial boundary-value problem that underlies the theory of the Boltzmann equation for general non-spherical hard particles. In this work, for two congruent ellipses and for a large class of associated boundary conditions, we identify initial conditions for which there do not exist local-in-time weak solutions of Newton's equations of motion. To our knowledge, this is the first time the necessity of rolling in the energy-conserving dynamics of strictly-convex rigid bodies has been demonstrated. This study was, in part, motivated by a recent observation of Palffy-Muhoray, Virga, Wilkinson and Zheng on the interpenetration of strictly-convex rigid bodies.
- Published
- 2018
50. The Mechano-Ubiquitinome of Articular Cartilage: Differential Ubiquitination and Activation of a Group of ER-Associated DUBs and ER Stress Regulators
- Author
-
Kaokhum, Nitchakarn, Pinto-Fernández, Adán, Wilkinson, Mark, Kessler, Benedikt M., and Ismail, Heba M.
- Published
- 2022
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.