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1. Insights into Lunar Mineralogy: An Unsupervised Approach for Clustering of the Moon Mineral Mapper (M3) spectral data

Author

Thoresen, Freja, Drozdovskiy, Igor, Cowley, Aidan, Laban, Magdelena, Besse, Sebastien, and Blunier, Sylvain

Subjects
Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Machine Learning
Abstract

This paper presents a novel method for mapping spectral features of the Moon using machine learning-based clustering of hyperspectral data from the Moon Mineral Mapper (M3) imaging spectrometer. The method uses a convolutional variational autoencoder to reduce the dimensionality of the spectral data and extract features of the spectra. Then, a k-means algorithm is applied to cluster the latent variables into five distinct groups, corresponding to dominant spectral features, which are related to the mineral composition of the Moon's surface. The resulting global spectral cluster map shows the distribution of the five clusters on the Moon, which consist of a mixture of, among others, plagioclase, pyroxene, olivine, and Fe-bearing minerals across the Moon's surface. The clusters are compared to the mineral maps from the Kaguya mission, which showed that the locations of the clusters overlap with the locations of high wt% of minerals such as plagioclase, clinopyroxene, and olivine. The paper demonstrates the usefulness of unbiased unsupervised learning for lunar mineral exploration and provides a comprehensive analysis of lunar mineralogy.

Published
2024

2. Breccia and basalt classification of thin sections of Apollo rocks with deep learning

Author

Thoresen, Freja, Cowley, Aidan, Haak, Romeo, Lewe, Jonas, Moriceau, Clara, Knapczyk, Piotr, and Engelschiøn, Victoria S.

Subjects
Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Machine Learning
Abstract

Human exploration of the moon is expected to resume in the next decade, following the last such activities in the Apollo programme time. One of the major objectives of returning to the Moon is to continue retrieving geological samples, with a focus on collecting high-quality specimens to maximize scientific return. Tools that assist astronauts in making informed decisions about sample collection activities can maximize the scientific value of future lunar missions. A lunar rock classifier is a tool that can potentially provide the necessary information for astronauts to analyze lunar rock samples, allowing them to augment in-situ value identification of samples. Towards demonstrating the value of such a tool, in this paper, we introduce a framework for classifying rock types in thin sections of lunar rocks. We leverage the vast collection of petrographic thin-section images from the Apollo missions, captured under plane-polarized light (PPL), cross-polarised light (XPL), and reflected light at varying magnifications. Advanced machine learning methods, including contrastive learning, are applied to analyze these images and extract meaningful features. The contrastive learning approach fine-tunes a pre-trained Inception-Resnet-v2 network with the SimCLR loss function. The fine-tuned Inception-Resnet-v2 network can then extract essential features effectively from the thin-section images of Apollo rocks. A simple binary classifier is trained using transfer learning from the fine-tuned Inception-ResNet-v2 to 98.44\% ($\pm$1.47) accuracy in separating breccias from basalts.

Published
2024

3. Decomposing Infrared Luminosity Functions into Star-Forming and AGN Components using CIGALE

Author

Lyon, Daniel J., Cowley, Michael J., Pye, Oliver, and Hopkins, Andrew M.

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

This study presents a comprehensive analysis of the infrared (IR) luminosity functions (LF) of star-forming (SF) galaxies and active galactic nuclei (AGN) using data from the ZFOURGE survey. We employ CIGALE to decompose the spectral energy distribution (SED) of galaxies into SF and AGN components to investigate the co-evolution of these processes at higher redshifts and fainter luminosities. Our CIGALE-derived SF and AGN LFs are generally consistent with previous studies, with an enhancement at the faint end of the AGN LFs. We attribute this to CIGALE's capability to recover low-luminosity AGN more accurately, which may be underrepresented in other works. As anticipated, the CIGALE SF LFs are best fit with a Schechter function, whereas the AGN LFs align more closely with a Saunders function. We find evidence for a significant evolutionary epoch for AGN activity at $z \approx 1$, comparable to the peak of cosmic star formation at $z \approx 2$, which we also recover well. Based on our results, the gas supply in the early universe favoured the formation of brighter star-forming galaxies until $z=2$, below which the gas for SF becomes increasingly exhausted. Conversely, AGN activity peaked earlier and declined more slowly until $z \approx 1$, suggesting a possible feedback scenario in which $2.5-3$ Gyrs offset the evolution of SF and AGN activity., Comment: 16 pages, 7 figures, 8 tables. Submitted for publication in PASA

Published
2024

4. Evolution of radiation profiles in a strongly baffled divertor on MAST Upgrade

Author

Federici, Fabio, Reinke, Matthew L., Lipschultz, Bruce, Lovell, Jack J., Verhaegh, Kevin, Cowley, Cyd, Kryjak, Mike, Ryan, Peter, Thornton, Andrew J., Harrison, James R., Peterson, Byron J., Lomanowski, Bartosz, Lore, Jeremy D., and Damizia, Yacopo

Subjects
Physics - Plasma Physics
Abstract

Plasma detachment involves interactions of the plasma with impurities and neutral particles, leading to significant losses of plasma power, momentum, and particles. Accurate mapping of plasma emissivity in the divertor and X-point region is essential for assessing the relationship between particle flux and radiative detachment. The recently validated InfraRed Video Bolometer (IRVB) diagnostic, in MAST-U enables this mapping with higher spatial resolution than more established methods like resistive bolometers. In previous preliminary work, the evolution of radiative detachment was characterised in L-mode (power entering the scrape-off layer, PSOL ~0.4MW). With a conventional divertor the inner leg consistently detached ahead of the outer leg, and radiative detachment preceded particle flux detachment. This work presents results also from the third MAST-U experimental campaign, fuelled from the low field side instead of the high field side, including Ohmic and beam heated L-mode shots (with a power exiting the core up to PSOL ~1-1.5MW). The radiation peak moves upstream from the target at lower upstream densities than the ion target flux roll-over (typically considered the detachment onset), while the inner leg detaches before the outer one. The movement of the radiation is in partial agreement with the expectations from the DLS model, predicting a sudden shift from the target to the X-point. The energy confinement is found to be related to detachment, but there seems to be some margin between the radiation on the inner leg reaching the X-point and confinement being affected, a beneficial characteristic if it could be extrapolated to future reactors. For increasing PSOL the particle flux roll over is almost unaffected, while radiative detachment occurs at higher density in both legs, but much higher on the outer, suggesting an uneven distribution of the power exiting the core., Comment: Submitted to Nuclear Materials and Energy

Published
2024

5. Comparison of On-Campus and Virtual Self-Assessment Outcomes for Incoming Appalachian STEM Undergraduates' First Research Experience

Author

Kristin Stover, Kimberly Cowley, Gillian Gaunt, Olivia George, Kristy Henson, Tuoen Liu, and Christopher L. Pankey

Abstract

The First2 Network is an alliance of higher education institutions across the State of West Virginia striving to improve science, technology, engineering, or math (STEM) education by supporting rural, first-generation, and underrepresented college students pursuing STEM majors. Over the summers of 2019 and 2020, the First2 Network delivered two-week summer research immersion experiences at various institutions throughout West Virginia, including our institutions. The 2019 program was delivered on-campus at four universities while the 2020 program was redesigned to be delivered virtually, due to the COVID-19 pandemic, across nine sites. Before and after the immersion experience, students who participated in the program completed a variety of survey questionnaires for the assessment of their interests, expectations, identity, and belonging in STEM. We found that the in-person research experience in 2019 had better outcomes compared to the virtual experience, suggesting that students conducting research directly under their faculty supervisors in-person and on-site will have a more positive impact on their STEM education and career. However, participation in the virtual research format with structured group activities still resulted in an improvement in belonging and STEM identity, indicating that connecting with students remotely is still worthwhile when it is the most viable option. The student population in West Virginia/Appalachia region faces a number of academic barriers, so there is much to gain by finding new ways to reach as many students as possible with early career development programs. Our virtually delivered program using citizen science projects, group discussions, and team building activities may be a useful template for other STEM programs to search for new ways to connect with a broader population of students offsite.

Published
2024

6. Galactic kinematics of various stellar types

Author

Cowley, Charles R. and Stencel, Robert E.

Subjects
Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Astrophysics of Galaxies
Abstract

We compare and contrast the kinematics of various classes of stars, both normal (with M-K spectral types) and peculiar. Numerous plots show the differences in spatial and velocity distributions as well as distributions in kinetic energy vs. angular momentum (KE vs. LZ) space. In the latter plots, young, thin disk stars on nearly circular orbits cling to the left edge of a so-called solar parabola, while older objects on elliptical orbits fill the central parabolic region. Some of the young Wolf-Rayet stars violate this trend due to smaller semi-major axes than the Sun or orbital eccentricities. Deviation of the vertex of the velocity ellipsoid is discussed as an indication of population and youth, with an emphasis on Ap, Bp, Am, Fm, Herbig AeBe, and lambda Boo stars. Both the vertex deviation and phase space distribution provide useful insights., Comment: 11 pages, 7 figures

Published
2024

7. Simulating the Impact of Baffling on Divertor Performance Using SOLPS-ITER

Author

Cowley, Cyd, Moulton, David, and Lipschultz, Bruce

Subjects
Physics - Plasma Physics
Abstract

Strong divertor baffling is a feature expected to have a number of advantages for core-edge integration in tokamaks, yet one which requires much more detailed and extensive study. In this work, the impacts of baffling on a hydrogenic plasma are studied in isolation, through artificial fixed-fraction impurity SOLPS-ITER simulations. These simulations are of the connected double null Super-X divertor on the MAST-U tokamak, with extreme cases of a closed and open divertor. Simulations show a divertor with a tightly baffled entrance can lead to better access to detachment on the outer targets, likely caused by reduced convection upstream. Adding tight baffling at the throat also leads to two orders of magnitude increase in neutral compression, and an order of magnitude more efficient pumping, with more peaked core density profiles. Finally, in contrast to the localised radiation of the closed divertor, the open divertor shows radiation along the entire plasma edge which moves upstream and inward into the core as detachment evolves; leading to sub-10eV temperatures in the near SOL at x-point., Comment: 21 pages, 13 figures

Published
2024

8. Formation of the Supersonic Solar Wind: Parker's Theory Revisited

Author

Song, Paul, Tu, Jiannan, Cowley, Stanley W. H., Wang, Chi, and Li, Hui

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

We examine and propose to fundamentally modify the classical theory of solar wind formation. To form a supersonic solar wind, the classical theory requires that a subsonic flow speed must start at a specific initial speed from the coronal base, called eigenspeed, go along a continuous eigenfunction, and reach the sonic point, which is where the flow speed equals the sonic speed, while the critical condition, which is where the effective driving force is zero, is satisfied. Any mismatch between the sonic point and critical condition distances results in either subsonic winds when the initial speed is below the eigenspeed, or no solar wind when the initial speed is above the eigenspeed. Because the critical condition is determined by the solar wind temperature profile, which depends on ionization process at the top of the chromosphere and the heating process around the coronal base but not by the processes at the sonic point, the required match between the two is generally not met and hence the momentum equation in the conventional theory encounters difficulty when the initial speed is above the eigenspeed. To resolve the difficulty, we propose a discontinuity between the sonic point and the critical condition to reach supersonic solar wind solutions. As a result, supersonic solar winds can be produced when the initial speed in the coronal base is greater than the eigenspeed. The critical solution or eigen function provided by the conventional solar wind model describes the condition that separates the supersonic solar winds from subsonic ones., Comment: This manuscript has been withdrawn and is not published in any journals yet

Published
2024

9. Spectral approaches to stress relaxation in epithelial monolayers

Author

Cowley, Natasha, Revell, Christopher K., Johns, Emma, Woolner, Sarah, and Jensen, Oliver E.

Subjects
Physics - Biological Physics, Condensed Matter - Soft Condensed Matter
Abstract

We investigate the viscoelastic relaxation to equilibrium of a disordered planar epithelium described using the cell vertex model. In its standard form, the model is formulated as coupled evolution equations for the locations of vertices of confluent polygonal cells. Exploiting the model's gradient-flow structure, we use singular-value decomposition to project modes of deformation of vertices onto modes of deformation of cells. We show how eigenmodes of discrete Laplacian operators (specified by constitutive assumptions related to dissipation and mechanical energy) provide a spatial basis for evolving fields, and demonstrate how the operators can incorporate approximations of conventional spatial derivatives. We relate the spectrum of relaxation times to the eigenvalues of the Laplacians, modified by corrections that account for the fact that the cell network (and therefore the Laplacians) evolve during relaxation to an equilibrium prestressed state, providing the monolayer with geometric stiffness. While dilational modes of the Laplacians capture rapid relaxation in some circumstances, showing diffusive dynamics, geometric stiffness is typically a dominant source of monolayer rigidity, as we illustrate for monolayers exposed to unsteady stretching deformations., Comment: 8 figures

Published
2024

14. Applied User Research in Virtual Reality: Tools, Methods, and Challenges

Author

Bensch, Leonie, Casini, Andrea, Cowley, Aidan, Dufresne, Florian, Guerra, Enrico, de Medeiros, Paul, Nilsson, Tommy, Rometsch, Flavie, Treuer, Andreas, and Vock, Anna

Subjects
Computer Science - Human-Computer Interaction, Computer Science - Multimedia, 93B51, 97M50, H.1.2, I.3.8, J.4, J.m, K.8.2, J.6
Abstract

This chapter explores the practice of conducting user research studies and design assessments in virtual reality (VR). An overview of key VR hardware and software tools is provided, including game engines, such as Unity and Unreal Engine. Qualitative and quantitative research methods, along with their various synergies with VR, are likewise discussed, and some of the challenges associated with VR, such as limited sensory stimulation, are reflected upon. VR is proving particularly useful in the context of space systems development, where its utilisation offers a cost-effective and secure method for simulating extraterrestrial environments, allowing for rapid prototyping and evaluation of innovative concepts under representative operational conditions. To illustrate this, we present a case study detailing the application of VR to aid aerospace engineers testing their ideas with end-users and stakeholders during early design stages of the European Space Agency's (ESA) prospective Argonaut lunar lander. This case study demonstrates the effectiveness of VR simulations in gathering important feedback concerning the operability of the Argonaut lander in poor lighting conditions as well as surfacing relevant ergonomics considerations and constraints. The chapter concludes by discussing the strengths and weaknesses associated with VR-based user studies and proposes future research directions, emphasising the necessity for novel VR interfaces to overcome existing technical limitations.

Published
2024

15. Designing for Human Operations on the Moon: Challenges and Opportunities of Navigational HUD Interfaces

Author

Bensch, Leonie, Nilsson, Tommy, Wulkop, Jan, de Medeiros, Paul, Herzberger, Nicolas Daniel, Preutenborbeck, Michael, Gerndt, Andreas, Flemisch, Frank, Dufresne, Florian, Albuquerque, Georgia, and Cowley, Aidan

Subjects
Computer Science - Human-Computer Interaction, 93B51, 97M50, H.1.2, I.3.8, J.4, J.m, K.8.2
Abstract

Future crewed missions to the Moon will face significant environmental and operational challenges, posing risks to the safety and performance of astronauts navigating its inhospitable surface. Whilst head-up displays (HUDs) have proven effective in providing intuitive navigational support on Earth, the design of novel human-spaceflight solutions typically relies on costly and time-consuming analogue deployments, leaving the potential use of lunar HUDs largely under-explored. This paper explores an alternative approach by simulating navigational HUD concepts in a high-fidelity Virtual Reality (VR) representation of the lunar environment. In evaluating these concepts with astronauts and other aerospace experts (n=25), our mixed methods study demonstrates the efficacy of simulated analogues in facilitating rapid design assessments of early-stage HUD solutions. We illustrate this by elaborating key design challenges and guidelines for future lunar HUDs. In reflecting on the limitations of our approach, we propose directions for future design exploration of human-machine interfaces for the Moon.

Published
2024
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16. Touching the Moon: Leveraging Passive Haptics, Embodiment and Presence for Operational Assessments in Virtual Reality

Author

Dufresne, Florian, Nilsson, Tommy, Gorisse, Geoffrey, Guerra, Enrico, Zenner, André, Christmann, Olivier, Bensch, Leonie, Callus, Nikolai Anton, and Cowley, Aidan

Subjects
Computer Science - Human-Computer Interaction, 93B51, 97M50, H.1.2, I.3.8, J.4, J.m, K.8.2, J.6
Abstract

Space agencies are in the process of drawing up carefully thought-out Concepts of Operations (ConOps) for future human missions on the Moon. These are typically assessed and validated through costly and logistically demanding analogue field studies. While interactive simulations in Virtual Reality (VR) offer a comparatively cost-effective alternative, they have faced criticism for lacking the fidelity of real-world deployments. This paper explores the applicability of passive haptic interfaces in bridging the gap between simulated and real-world ConOps assessments. Leveraging passive haptic props (equipment mockup and astronaut gloves), we virtually recreated the Apollo 12 mission procedure and assessed it with experienced astronauts and other space experts. Quantitative and qualitative findings indicate that haptics increased presence and embodiment, thus improving perceived simulation fidelity and validity of user reflections. We conclude by discussing the potential role of passive haptic modalities in facilitating early-stage ConOps assessments for human endeavours on the Moon and beyond., Comment: CHI'24, May 11-16, 2024, Honolulu, HI, USA

Published
2024
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17. Room-temperature optically detected coherent control of molecular spins

Author

Mena, Adrian, Mann, Sarah K., Cowley-Semple, Angus, Bryan, Emma, Heutz, Sandrine, McCamey, Dane R., Attwood, Max, and Bayliss, Sam L.

Subjects
Quantum Physics, Physics - Chemical Physics
Abstract

Benefiting from both molecular tunability and versatile methods for deployment, optically interfaced molecular spins are a promising platform for quantum technologies such as sensing and imaging. Room-temperature optically detected coherent spin control is a key enabler for many applications, combining sensitive readout, versatile spin manipulation, and ambient operation. Here we demonstrate such functionality in a molecular spin system. Using the photoexcited triplet state of organic chromophores (pentacene doped in a para-terphenyl host), we optically detect coherent spin manipulation with photoluminescence contrasts exceeding 10% and microsecond coherence times at room temperature. We further demonstrate how coherent control of multiple triplet sublevels can significantly enhance optical spin contrast, and extend optically detected coherent control to a thermally evaporated thin film, retaining high photoluminescence contrast and coherence times of order one microsecond. These results open opportunities for room-temperature quantum technologies that can be systematically tailored through synthetic chemistry., Comment: 9 pages, 4 figures

Published
2024
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18. Metastability of stratified magnetohydrostatic equilibria and their relaxation

Author

Hosking, David N., Wasserman, David, and Cowley, Steven C.

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Physics - Fluid Dynamics, Physics - Plasma Physics
Abstract

Motivated by explosive releases of energy in fusion, space and astrophysical plasmas, we consider the nonlinear stability of stratified magnetohydrodynamic (MHD) equilibria against interchanges of straight magnetic-flux tubes. We demonstrate that in MHD (unlike in hydrodynamics) linear stability does not guarantee nonlinear stability, even in this simple case. We show that the minimum-energy configurations attainable by metastable equilibria under non-diffusive 2D dynamics can be determined by solving a combinatorial optimization problem. These minimum-energy states are, to good approximation, the final states reached by simulations of destabilized metastable equilibria where turbulent mixing is suppressed by viscosity. For the case of fully turbulent relaxation, we construct a statistical mechanical theory based on the maximization of Boltzmann's mixing entropy. This theory is analogous to the Lynden-Bell statistical mechanics of stellar systems and collisionless plasmas and to the Robert-Sommeria-Miller (RSM) theory of 2D vortex turbulence. Our theory reproduces well the results of our numerical simulations for sufficiently large perturbations to the metastable equilibrium., Comment: 40 pages, 36 figures

Published
2024

19. ROAD MAP TO SUCCESS: Navigating School Library Web Content Creation and Management: Together, we continue to inspire, educate, and advocate, knowing that our collective efforts enhance the library experience for every student we serve

Author

Cowley, Sarah

Subjects
Library use studies -- Forecasts and trends, School libraries -- Services -- Technology application, Market trend/market analysis, Technology application, Computers, Library and information science
Abstract

Imagine a group of librarians having the power to impact nearly 100,000 students--that's the incredible role of school librarians in Jefferson County Public Schools in Louisville, Ky. Our district stands [...]

Published
2024

21. Cold Chain Management of Fruits and Vegetables at Manama Central Market in Bahrain

Author

Fu, Lianning, Li, Zhen, Cowley, Lorraine, di Prisco, Marco, Series Editor, Chen, Sheng-Hong, Series Editor, Vayas, Ioannis, Series Editor, Kumar Shukla, Sanjay, Series Editor, Sharma, Anuj, Series Editor, Kumar, Nagesh, Series Editor, Wang, Chien Ming, Series Editor, Cui, Zhen-Dong, Series Editor, Lu, Xinzheng, Series Editor, Meng, Lingyun, editor, Qian, Yongsheng, editor, Bai, Yun, editor, Lv, Bin, editor, and Tang, Yuanjie, editor

Published
2025
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22. Resubmission Assistance: Understanding Current Practices and Perspectives

Author

Polasky, Sarah, Wilson, Jeannie, Carsen, JulieAnna, Stover, Lillian, Cowley, Shelby, and Nielsen, Ann

Abstract

The impact of resubmission assistance on grant proposal success is relatively unknown. Given that a significant proportion of proposals, up to 90%, are rejected by the sponsor, this lack of information makes it difficult for Research Development (RD) professionals to decide whether to invest resources in this service. This study responded to New Opportunities for Research Development (NORD)/InfoReady's request for proposals specifically focused on resubmission assistance. The study used a combination of artifact review, interview, and survey methodologies to identify the most common types of resubmission assistance and identify areas in which RD professionals would like to offer services. This study helped identify the field's strengths and weaknesses within the area of resubmission assistance, and sets the stage for future research to clearly define the core components of research assistance.

Published
2023

23. Tau depletion in human neurons mitigates Aβ-driven toxicity

Author

Ng, Bryan, Vowles, Jane, Bertherat, Féodora, Abey, Ajantha, Kilfeather, Peter, Beccano-Kelly, Dayne, Stefana, M. Irina, O’Brien, Darragh P., Bengoa-Vergniory, Nora, Carling, Phillippa J., Todd, John A., Caffrey, Tara M., Connor-Robson, Natalie, Cowley, Sally A., and Wade-Martins, Richard

Published
2024
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24. Systematic identification of structure-specific protein–protein interactions

Author

Holfeld, Aleš, Schuster, Dina, Sesterhenn, Fabian, Gillingham, Alison K, Stalder, Patrick, Haenseler, Walther, Barrio-Hernandez, Inigo, Ghosh, Dhiman, Vowles, Jane, Cowley, Sally A, Nagel, Luise, Khanppnavar, Basavraj, Serdiuk, Tetiana, Beltrao, Pedro, Korkhov, Volodymyr M, Munro, Sean, Riek, Roland, de Souza, Natalie, and Picotti, Paola

Published
2024
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27. Divertor shaping with neutral baffling as a solution to the tokamak power exhaust challenge

Author

Verhaegh, K., Harrison, J. R., Moulton, D., Lipschultz, B., Lonigro, N., Osborne, N., Ryan, P., Theiler, C., Wijkamp, T., Brida, D., Cowley, C., Derks, G., Doyle, R., Federici, F., Kool, B., Février, O., Hakola, A., Henderson, S., Reimerdes, H., Thornton, A. J., Vianello, N., Wischmeier, M., and Xiang, L.

Subjects
Physics - Plasma Physics
Abstract

Exhausting power from the hot fusion core to the plasma-facing components is one of the biggest challenges in fusion energy. The MAST Upgrade tokamak uniquely integrates strong containment of neutrals within the exhaust area (divertor) with extreme divertor shaping capability. By systematically altering the divertor shape, this study shows the strongest evidence to date that long-legged divertors with a high magnetic field gradient (total flux expansion) deliver key power exhaust benefits without adversely impacting the hot fusion core. These benefits are already achieved with relatively modest geometry adjustments that are more feasible to integrate in reactor designs. Benefits include reduced target heat loads and improved access to, and stability of, a neutral gas buffer that 'shields' the target and enhances power exhaust (detachment). Analysis and model comparisons shows these benefits are obtained by combining multiple shaping aspects: long-legged divertors have expanded plasma-neutral interaction volume that drive reductions in particle and power loads, while total flux expansion enhances detachment access and stability. Containing the neutrals in the exhaust area with physical structures further augments these shaping benefits. These results demonstrate strategic variation in the divertor geometry and magnetic topology is a potential solution to one of fusion's biggest challenges: power exhaust.

Published
2023

28. Kinetic stability of Chapman-Enskog plasmas

Author

Bott, Archie F. A., Cowley, Steven C., and Schekochihin, Alexander A.

Subjects
Physics - Plasma Physics, Astrophysics - High Energy Astrophysical Phenomena
Abstract

In this paper, we investigate the kinetic stability of classical, collisional plasma - that is, plasma in which the mean-free-path $\lambda$ of constituent particles is short compared to the length scale $L$ over which fields and bulk motions in the plasma vary macroscopically, and the collision time is short compared to the evolution time. Fluid equations are typically used to describe such plasmas, since their distribution functions are close to being Maxwellian. The small deviations from the Maxwellian distribution are calculated via the Chapman-Enskog (CE) expansion in $\lambda/L \ll 1$, and determine macroscopic momentum and heat fluxes in the plasma. Such a calculation is only valid if the underlying CE distribution function is stable at collisionless length scales and/or time scales. We find that at sufficiently high plasma $\beta$, the CE distribution function can be subject to numerous microinstabilities across a wide range of scales. For a particular form of the CE distribution function arising in magnetised plasma, we provide a detailed analytic characterisation of all significant microinstabilities, including peak growth rates and their associated wavenumbers. Of specific note is the discovery of several new microinstabilities, including one at sub-electron-Larmor scales (the 'whisper instability') whose growth rate in some parameter regimes is large compared to other instabilities. Our approach enables us to construct the kinetic stability maps of classical, two-species collisional plasma in terms of $\lambda$, the electron inertial scale $d_e$ and $\beta$. This work is of general consequence in emphasising the fact that high-$\beta$ collisional plasmas can be kinetically unstable; for strongly magnetised CE plasmas, the condition for instability is $\beta > L/\lambda$. In this situation, the determination of transport coefficients via the standard CE approach is not valid., Comment: 182 pages total (99 main text, remaining appendices), 31 figures

Published
2023

29. Evolved galaxies in high-density environments across $2.0\leq z<4.2$ using the ZFOURGE survey

Author

Hartzenberg, Georgia R., Cowley, Michael J., Hopkins, Andrew M., and Allen, Rebecca J.

Subjects
Astrophysics - Astrophysics of Galaxies
Abstract

To explore the role environment plays in influencing galaxy evolution at high redshifts, we study $2.0\leq z<4.2$ environments using the FourStar Galaxy Evolution (ZFOURGE) survey. Using galaxies from the COSMOS legacy field with ${\rm log(M_{*}/M_{\odot})}\geq9.5$, we use a seventh nearest neighbour density estimator to quantify galaxy environment, dividing this into bins of low, intermediate and high density. We discover new high density environment candidates across $2.0\leq z<2.4$ and $3.1\leq z<4.2$. We analyse the quiescent fraction, stellar mass and specific star formation rate (sSFR) of our galaxies to understand how these vary with redshift and environment. Our results reveal that, across $2.0\leq z<2.4$, the high density environments are the most significant regions, which consist of elevated quiescent fractions, ${\rm log(M_{*}/M_{\odot})}\geq10.2$ massive galaxies and suppressed star formation activity. At $3.1\leq z<4.2$, we find that high density regions consist of elevated stellar masses but require more complete samples of quiescent and sSFR data to study the effects of environment in more detail at these higher redshifts. Overall, our results suggest that well-evolved, passive galaxies are already in place in high density environments at $z\sim2.4$, and that the Butcher-Oemler effect and SFR-density relation may not reverse towards higher redshifts as previously thought., Comment: 11 pages, 5 figures, final version published in PASA

Published
2023
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30. Resonant excitation of plasma waves in a plasma channel

Author

Ross, Aimee J., Chappell, James, van de Wetering, Johannes J., Cowley, James, Archer, Emily, Bourgeois, Nicolas, Corner, Laura, Emerson, David R., Feder, Linus, Gu, Xiao J., Jakobsson, Oscar, Jones, Harry, Picksley, Alexander, Reid, Linus, Wang, Wei-Ting, Walczak, Roman, and Hooker, Simon M.

Subjects
Physics - Accelerator Physics, Physics - Plasma Physics
Abstract

We demonstrate resonant excitation of a plasma wave by a train of short laser pulses guided in a pre-formed plasma channel, for parameters relevant to a plasma-modulated plasma accelerator (P-MoPA). We show experimentally that a train of $N \approx 10$ short pulses, of total energy $\sim 1$ J, can be guided through $110$ mm long plasma channels with on-axis densities in the range $10^{17} - 10^{18}$ cm$^{-3}$. The spectrum of the transmitted train is found to be strongly red-shifted when the plasma period is tuned to the intra-train pulse spacing. Numerical simulations are found to be in excellent agreement with the measurements and indicate that the resonantly excited plasma waves have an amplitude in the range $3$ - $10$ GV m$^{-1}$, corresponding to an accelerator stage energy gain of order $1$ GeV., Comment: 13 pages, 14 figures (including Supplemental Material)

Published
2023
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31. Bayesian parameter estimation for characterising mobile ion vacancies in perovskite solar cells

Author

McCallum, Samuel G., Nicholls, Oliver, Jensen, Kjeld O., Cowley, Matthew V., Lerpinière, James E., and Walker, Alison B.

Subjects
Condensed Matter - Materials Science, Physics - Applied Physics
Abstract

To overcome the challenges associated with poor temporal stability of perovskite solar cells, methods are required that allow for fast iteration of fabrication and characterisation, such that optimal device performance and stability may be actively pursued. Currently, establishing the causes of underperformance is both complex and time-consuming, and optimisation of device fabrication thus inherently slow. Here, we present a means of computational device characterisation of mobile halide ion parameters from room temperature current-voltage (J-V) measurements only, requiring $\sim 2$ hours of computation on basic computing resources. With our approach, the physical parameters of the device may be reverse modelled from experimental J-V measurements. In a drift-diffusion model, the set of coupled drift-diffusion partial differential equations cannot be inverted explicitly, so a method for inverting the drift-diffusion simulation is required. We show how Bayesian Parameter Estimation (BPE) coupled with a drift-diffusion perovskite solar cell model can determine the extent to which device parameters affect performance measured by J-V characteristics. Our method is demonstrated by investigating the extent to which device performance is influenced by mobile halide ions for a specific fabricated device. The ion vacancy density $N_0$ and diffusion coefficient $D_I$ were found to be precisely characterised for both simulated and fabricated devices. This result opens up the possibility of pinpointing origins of degradation by finding which parameters most influence device J-V curves as the cell degrades.

Published
2023

32. Attention in high-performance cognition is goal-directed, selective, focused, and sustained

Author

Cowley, Benjamin and Kirjanen, Aila

Subjects
Cognitive Neuroscience, Psychology, Attention, Intelligent agents, Learning, Skill acquisition and learning, Survey
Abstract

We introduce the concept of high-performance cognition as a domain-general function of acquiring and performing cognitively demanding skills to a high level. We conduct a survey among academic experts to identify key attention categories of high-performance cognition: by independent consensus they highlight the importance of goal-directed attention. Selective, focused, and sustained attention are strongly associated at slightly less complete consensus. They qualify their ratings with free-text reflections. Our work offers a new framing for skilled performance and its underlying cognitive processes.

Published
2024

33. Information foraging in human-ChatGPT interactions: factors of computational thinking dissociate exploration and exploitation

Author

Flores, Pablo, Cowley, Benjamin, and Rong, Guang

Subjects
Psychology, Behavioral Science, Decision making, Human-computer interaction, Interactive behavior
Abstract

LLMs can interact as though they understand language, yet they remain algorithms and can be used as such. This study explores a novel guided interaction design for modeling users' information foraging behavior when navigating GPT-generated content and the role of Computational Thinking skills in shaping such behavior. Conducted with nine educational researchers in a doctoral-level AIEd course, our research used editable prompt templates and keywords to structure the prompt crafting process. We modeled and analyzed participants' behaviors in terms of \textit{exploration} (to generate and explore various information landscapes) and \textit{exploitation} (to delve deeper in a specific landscape). Our data, including responses from the Computational Thinking Scale, suggests that Algorithmic Thinking and Creativity might encourage exploitation behavior, leaning more on AI-generated information rather than pre-defined design elements.

Published
2024

34. Neurotypical Adults employ Distinct Cognitive Mechanisms compared to Adults with ADHD during a Sustained Attention Task with Gestalt Stimuli

Author

Kuznetsova, Elizaveta, Tammi, Tuisku, Postnova, Natalia, Palomäki, Jussi, and Cowley, Benjamin

Subjects
Cognitive Neuroscience, Attention, Perception, Skill acquisition and learning, Clinical methods, Electroencephalography (EEG)
Abstract

Sustained attention is a fundamental cognitive ability that influences various aspects of human functioning. Studies of the neural correlates of attention commonly treat sustained attention as an isolated construct, however in any ecological context, sustained attention interacts with other executive functions such as inhibition of interference and processing of complex hierarchical stimuli. We have thus constructed a protocol to probe the interplay between these cognitive processes during visual attention task. We contrast putative typical vs atypical attention by comparing 18 healthy participants with 53 adults with Attention-Deficit/Hyperactivity Disorder, for whom difficulties with sustained attention are a core symptom and thus constitute a natural experiment condition. Our behavioural and brain-imaging analyses demonstrate distinct neural patterns in bottom-up visual processing and attention allocation mechanisms in ADHD and Control groups, highlighting different cognitive strategies utilised by adults with ADHD and healthy participants in tasks requiring sustained attention.

Published
2024

35. Towards objective, temporally resolved neurobehavioral predictors of emotional state

Author

Katherine E. Kabotyanski, Han G. Yi, Rahul Hingorani, Brian S. Robinson, Hannah P. Cowley, Matthew S. Fifer, Brock A. Wester, Bishal Lamichhane, Ashutosh Sabharwal, Anusha B. Allawala, Sameer V. Rajesh, Nabeel Diab, Raissa K. Mathura, Victoria Pirtle, Joshua Adkinson, Andrew J. Watrous, Eleonora Bartoli, Jiayang Xiao, Garrett P. Banks, Sanjay J. Mathew, Wayne K. Goodman, Xaq Pitkow, Nader Pouratian, Benjamin Y. Hayden, Nicole R. Provenza, and Sameer A. Sheth

Subjects
Naturalistic, Behavior, Emotion, Mood, Intracranial EEG, Deep brain stimulation, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Published
2024
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36. Novel paediatric case of a spinal high-grade astrocytoma with piloid features in a patient with Noonan Syndrome

Author

Jordan Staunton, Pamela Ajuyah, Angela Harris, Chelsea Mayoh, Marie Wong, Megan Rumford, Patricia J. Sullivan, Paul G. Ekert, Noemi Fuentes-Bolanos, Mark J. Cowley, Loretta M. S. Lau, David S. Ziegler, Paulette Barahona, and Neevika Manoharan

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Noonan Syndrome (NS) is associated with an increased risk of low-grade central nervous system tumours in children but only very rarely associated with high-grade gliomas. Here we describe the first reported case of a spinal high-grade astrocytoma with piloid features (HGAP) in a child with NS. This case was a diagnostic and treatment dilemma, prior to whole-genome germline and tumour sequencing, tumour transcriptome sequencing and DNA methylation analysis. The methylation profile matched strongly with HGAP and sequencing identified somatic FGFR1 and NF1 variants and a PTPN11 germline pathogenic variant. Therapeutic targets were identified but also alterations novel to HGAP such as differential expression of VEGFA and PD-L1. The germline PTPN11 finding has not been previously described in individuals with HGAP. This case underscores the power of precision medicine from a diagnostic, therapeutic and clinical management perspective, and describes an association between HGAP and NS which has not previously been reported.

Published
2024
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37. Optical genome mapping of structural variants in Parkinson’s disease-related induced pluripotent stem cells

Author

Joanne Trinh, Susen Schaake, Carolin Gabbert, Theresa Lüth, Sally A. Cowley, André Fienemann, Kristian K. Ullrich, Christine Klein, and Philip Seibler

Subjects
Optical genome mapping, iPSCs, Parkinson’s disease, Structural variants, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Certain structural variants (SVs) including large-scale genetic copy number variants, as well as copy number-neutral inversions and translocations may not all be resolved by chromosome karyotype studies. The identification of genetic risk factors for Parkinson’s disease (PD) has been primarily focused on the gene-disruptive single nucleotide variants. In contrast, larger SVs, which may significantly influence human phenotypes, have been largely underexplored. Optical genomic mapping (OGM) represents a novel approach that offers greater sensitivity and resolution for detecting SVs. In this study, we used induced pluripotent stem cell (iPSC) lines of patients with PD-linked SNCA and PRKN variants as a proof of concept to (i) show the detection of pathogenic SVs in PD with OGM and (ii) provide a comprehensive screening of genetic abnormalities in iPSCs. Results OGM detected SNCA gene triplication and duplication in patient-derived iPSC lines, which were not identified by long-read sequencing. Additionally, various exon deletions were confirmed by OGM in the PRKN gene of iPSCs, of which exon 3–5 and exon 2 deletions were unable to phase with conventional multiplex-ligation-dependent probe amplification. In terms of chromosomal abnormalities in iPSCs, no gene fusions, no aneuploidy but two balanced inter-chromosomal translocations were detected in one line that were absent in the parental fibroblasts and not identified by routine single nucleotide variant karyotyping. Conclusions In summary, OGM can detect pathogenic SVs in PD-linked genes as well as reveal genomic abnormalities for iPSCs that were not identified by other techniques, which is supportive for OGM’s future use in gene discovery and iPSC line screening.

Published
2024
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38. Tapasin assembly surveillance by the RNF185/Membralin ubiquitin ligase complex regulates MHC-I surface expression

Author

Michael L. van de Weijer, Krishna Samanta, Nikita Sergejevs, LuLin Jiang, Maria Emilia Dueñas, Tiaan Heunis, Timothy Y. Huang, Randal J. Kaufman, Matthias Trost, Sumana Sanyal, Sally A. Cowley, and Pedro Carvalho

Subjects
Science
Abstract

Abstract Immune surveillance by cytotoxic T cells eliminates tumor cells and cells infected by intracellular pathogens. This process relies on the presentation of antigenic peptides by Major Histocompatibility Complex class I (MHC-I) at the cell surface. The loading of these peptides onto MHC-I depends on the peptide loading complex (PLC) at the endoplasmic reticulum (ER). Here, we uncovered that MHC-I antigen presentation is regulated by ER-associated degradation (ERAD), a protein quality control process essential to clear misfolded and unassembled proteins. An unbiased proteomics screen identified the PLC component Tapasin, essential for peptide loading onto MHC-I, as a substrate of the RNF185/Membralin ERAD complex. Loss of RNF185/Membralin resulted in elevated Tapasin steady state levels and increased MHC-I at the surface of professional antigen presenting cells. We further show that RNF185/Membralin ERAD complex recognizes unassembled Tapasin and limits its incorporation into PLC. These findings establish a novel mechanism controlling antigen presentation and suggest RNF185/Membralin as a potential therapeutic target to modulate immune surveillance.

Published
2024
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39. High-throughput drug screening identifies novel therapeutics for Low Grade Serous Ovarian Carcinoma

Author

Kathleen I. Pishas, Karla J. Cowley, Marta Llaurado-Fernandez, Hannah Kim, Jennii Luu, Robert Vary, Nikola A. Bowden, Ian G. Campbell, Mark S. Carey, Kaylene J. Simpson, and Dane Cheasley

Subjects
Science
Abstract

Abstract Low grade serous carcinoma (LGSOC) is a rare epithelial ovarian cancer with unique molecular characteristics compared to the more common tubo-ovarian high-grade serous ovarian carcinoma. Pivotal clinical trials guiding the management of epithelial ovarian cancer lack sufficient cases of LGSOC for meaningful subgroup analysis, hence overall findings cannot be extrapolated to rarer chemo-resistant subtypes such as LGSOC. Furthermore, there is a need for more effective therapies for the treatment of relapsed disease, as treatment options are limited. To address this, we conducted the largest quantitative high-throughput drug screening effort (n = 3436 compounds) in 12 patient-derived LGSOC cell lines and one normal ovary cell line to identify unexplored therapeutic avenues. Using a combination of high-throughput robotics, high-content imaging and novel data analysis pipelines, our data set identified 60 high and 19 moderate confidence hits which induced cancer cell specific cytotoxicity at the lowest compound dose assessed (0.1 µM). We also revealed a series of known (mTOR/PI3K/AKT) and novel (EGFR and MDM2-p53) drug classes in which LGSOC cell lines showed demonstrable susceptibility to.

Published
2024
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40. Grb7, Grb10 and Grb14, encoding the growth factor receptor-bound 7 family of signalling adaptor proteins have overlapping functions in the regulation of fetal growth and post-natal glucose metabolism

Author

Kim Moorwood, Florentia M. Smith, Alastair S. Garfield, Michael Cowley, Lowenna J. Holt, Roger J. Daly, and Andrew Ward

Subjects
Cell signalling, Developmental biology, Epistasis, Fetal growth, Genomic imprinting, Insulin, Biology (General), QH301-705.5
Abstract

Abstract Background The growth factor receptor bound protein 7 (Grb7) family of signalling adaptor proteins comprises Grb7, Grb10 and Grb14. Each can interact with the insulin receptor and other receptor tyrosine kinases, where Grb10 and Grb14 inhibit insulin receptor activity. In cell culture studies they mediate functions including cell survival, proliferation, and migration. Mouse knockout (KO) studies have revealed physiological roles for Grb10 and Grb14 in glucose-regulated energy homeostasis. Both Grb10 KO and Grb14 KO mice exhibit increased insulin signalling in peripheral tissues, with increased glucose and insulin sensitivity and a modestly increased ability to clear a glucose load. In addition, Grb10 strongly inhibits fetal growth such that at birth Grb10 KO mice are 30% larger by weight than wild type littermates. Results Here, we generate a Grb7 KO mouse model. We show that during fetal development the expression patterns of Grb7 and Grb14 each overlap with that of Grb10. Despite this, Grb7 and Grb14 did not have a major role in influencing fetal growth, either alone or in combination with Grb10. At birth, in most respects both Grb7 KO and Grb14 KO single mutants were indistinguishable from wild type, while Grb7:Grb10 double knockout (DKO) were near identical to Grb10 KO single mutants and Grb10:Grb14 DKO mutants were slightly smaller than Grb10 KO single mutants. In the developing kidney Grb7 had a subtle positive influence on growth. An initial characterisation of Grb7 KO adult mice revealed sexually dimorphic effects on energy homeostasis, with females having a significantly smaller renal white adipose tissue depot and an enhanced ability to clear glucose from the circulation, compared to wild type littermates. Males had elevated fasted glucose levels with a trend towards smaller white adipose depots, without improved glucose clearance. Conclusions Grb7 and Grb14 do not have significant roles as inhibitors of fetal growth, unlike Grb10, and instead Grb7 may promote growth of the developing kidney. In adulthood, Grb7 contributes subtly to glucose mediated energy homeostasis, raising the possibility of redundancy between all three adaptors in physiological regulation of insulin signalling and glucose handling.

Published
2024
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41. Girl, Let Me Tell You: Exploring the Narratives of Black Women Professional Staff in Higher Education and How They Engage in Acts of Everyday Resistance

Author

Fredrika A. Cowley

Abstract

Black women have existed on the margins of higher education for many years. Our voices, perspectives, stories, struggles, and even our successes have been largely ignored by the dominant sociocultural group. Additionally, most of the literature on Black women in higher education either lumps us all together regardless of role or focuses on faculty or student affairs professionals. There is a lack of literature that focuses exclusively on the experiences of Black women professional staff in higher education. This study was an attempt to address this gap in the literature by describing the narratives of Black women professional staff in higher education and foregrounding their experiences of working as professional staff in higher education at a Historically White Institution (HWI) in the Mid-South region of the United States. The present study consisted of two research questions, and they were: (1) What are the narratives of Black women professional staff about their experiences in higher education? (2) How do Black women professional staff in higher education engage in acts of everyday resistance? This endarkened narrative drew on Black feminist theory and professional counterspaces to analyze the data gleaned from interviewing six Black women professional staff in higher education at a HWI in the Mid-South. The findings from the cocreators' narratives bring to light the following: (1) Black women are a diverse and non-homogenous group despite the shared identity of Black and female. (2) Black women professional staff often endure racism and microaggressions in their workplace. (3) Black women professional staff are intentional about how they present themselves in these spaces. (4) Black women professional staff also employ their own methods to carry out acts of everyday resistance. It is recommended that institutions acknowledge the problem and implement more inclusive, actionable, and sustainable DEI policies/initiatives. Other recommendations include Black women professional staff should actively seek to build relationships with each other, and there needs to be a complete revamping of the organization for Black faculty and staff for it to be a more impactful organization. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Published
2024

42. Print Exposure and Its Relationship to Spoken Language

Author

September Hope Cowley

Abstract

All communication systems rely on sets of rules that must generally be followed for successful communication to be possible; in the case of human language, these rules are given by the grammar. However, despite these rules, there is considerable variation that has been noted across the grammar. In this dissertation, I explore one understudied factor that may contribute to this variability, namely print exposure, and argue that print exposure is related to spoken language at multiple levels of the grammar. In Chapter 1, I present evidence that individuals with higher levels of print exposure provide more polarized ratings on a standard syntactic acceptability judgment task and argue that this is due to greater evidence for licit syntactic structures because of additional input due to exposure to print. In Chapter 2, I provide further evidence for this argument by examining the relationship between print exposure and participants' resolution preferences when confronted with sentences exhibiting quantifier scope ambiguity. I find that individuals with higher print exposure give lower ratings to sentences exhibiting quantifier scope ambiguity and have significantly longer reaction times for inverse items in particular, than lower print exposure participants. From this, I conclude that high print exposure may strengthen expectations for the dominant surface scope interpretation, again because of greater evidence for the more common or preferred structure. Finally, in Chapter 3, I explore the phenomenon of variability in scalar implicature, specifically with respect to the accessibility of stronger alternatives. I suggest two novel methods: one for generating scales for use in tasks on scalar implicature, and one for testing whether an implicature has occurred. I find some evidence that accessibility is an important factor in the computation of scalar implicature, but also note various improvements that should be considered with respect to the task design for the two new methods introduced in this study. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Published
2024

43. England in pieces

Author

Cowley, Jason

Subjects
Prime ministers -- Powers and duties, Emigration and immigration -- Political aspects, Populism -- Forecasts and trends, Riots -- Political aspects, Market trend/market analysis, Literature/writing, Political science
Abstract

The riots revealed hatred and division throughout the country. Keir Starmer has imposed order--but now he must reach out to the excluded of peripheral England and show how he will [...]

Published
2024

44. 'I've done more than anyone else to defeat the far right in Britain': Nigel Farage calls himself the 'Billy Graham of politics' and believes his style of radical right English populism can destroy the Conservative Party

Author

Cowley, Jason

Subjects
Legislators -- Interviews, Populism, Literature/writing, Political science
Abstract

The left, liberals and mainstream Conservatives loathe Nigel Farage. The feeling is mutual. Rishi Sunak fears him and his destructive potential and must understand now that the process of Brexit [...]

Published
2024

46. All-optical GeV electron bunch generation in a laser-plasma accelerator via truncated-channel injection

Author

Picksley, A., Chappell, J., Archer, E., Bourgeois, N., Cowley, J., Emerson, D. R., Feder, L., Gu, X. J., Jakobsson, O., Ross, A. J., Wang, W., Walczak, R., and Hooker, S. M.

Subjects
Physics - Accelerator Physics, Physics - Plasma Physics
Abstract

We describe a simple scheme, truncated-channel injection, to inject electrons directly into the wakefield driven by a drive pulse guided by an all-optical plasma channel. We use this approach to generate dark-current-free 1.2 GeV, 4.5 % relative energy spread electron bunches with 120 TW laser pulses guided in a 110-mm-long hydrodynamic optical-field-ionized (HOFI) plasma channel. Our experiments and particle-in-cell simulations show that high-quality electron bunches were only obtained when the drive pulse was closely aligned with the channel axis, and was focused close to the density down-ramp formed at the channel entrance. Start-to-end simulations of the channel formation, and electron injection and acceleration show that increasing the channel length to 410 mm would yield 3.65 GeV bunches, with a slice energy spread $\sim 5 \times 10^{-4}$.

Published
2023
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48. Stratified analyses refine association between TLR7 rare variants and severe COVID-19

Author

Jannik Boos, Caspar I. van der Made, Gayatri Ramakrishnan, Eamon Coughlan, Rosanna Asselta, Britt-Sabina Löscher, Luca V.C. Valenti, Rafael de Cid, Luis Bujanda, Antonio Julià, Erola Pairo-Castineira, J. Kenneth Baillie, Sandra May, Berina Zametica, Julia Heggemann, Agustín Albillos, Jesus M. Banales, Jordi Barretina, Natalia Blay, Paolo Bonfanti, Maria Buti, Javier Fernandez, Sara Marsal, Daniele Prati, Luisa Ronzoni, Nicoletta Sacchi, Joachim L. Schultze, Olaf Riess, Andre Franke, Konrad Rawlik, David Ellinghaus, Alexander Hoischen, Axel Schmidt, Kerstin U. Ludwig, Valeria Rimoldi, Elvezia M. Paraboschi, Alessandra Bandera, Flora Peyvandi, Giacomo Grasselli, Francesco Blasi, Francesco Malvestiti, Serena Pelusi, Cristiana Bianco, Lorenzo Miano, Angela Lombardi, Pietro Invernizzi, Alessio Gerussi, Giuseppe Citerio, Andrea Biondi, Maria Grazia Valsecchi, Marina Elena Cazzaniga, Giuseppe Foti, Ilaria Beretta, Mariella D'Angiò, Laura Rachele Bettini, Xavier Farré, Susana Iraola-Guzmán, Manolis Kogevinas, Gemma Castaño-Vinyals, Koldo Garcia-Etxebarria, Beatriz Nafria, Mauro D'Amato, Adriana Palom, Colin Begg, Sara Clohisey, Charles Hinds, Peter Horby, Julian Knight, Lowell Ling, David Maslove, Danny McAuley, Johnny Millar, Hugh Montgomery, Alistair Nichol, Peter J.M. Openshaw, Alexandre C. Pereira, Chris P. Ponting, Kathy Rowan, Malcolm G. Semple, Manu Shankar-Hari, Charlotte Summers, Timothy Walsh, Latha Aravindan, Ruth Armstrong, Heather Biggs, Ceilia Boz, Adam Brown, Richard Clark, Audrey Coutts, Judy Coyle, Louise Cullum, Sukamal Das, Nicky Day, Lorna Donnelly, Esther Duncan, Angie Fawkes, Paul Fineran, Max Head Fourman, Anita Furlong, James Furniss, Bernadette Gallagher, Tammy Gilchrist, Ailsa Golightly, Fiona Griffiths, Katarzyna Hafezi, Debbie Hamilton, Ross Hendry, Andy Law, Dawn Law, Rachel Law, Sarah Law, Rebecca Lidstone-Scott, Louise Macgillivray, Alan Maclean, Hanning Mal, Sarah McCafferty, Ellie Mcmaster, Jen Meikle, Shona C. Moore, Kirstie Morrice, Lee Murphy, Sheena Murphy, Mybaya Hellen, Wilna Oosthuyzen, Chenqing Zheng, Jiantao Chen, Nick Parkinson, Trevor Paterson, Katherine Schon, Andrew Stenhouse, Mihaela Das, Maaike Swets, Helen Szoor-McElhinney, Filip Taneski, Lance Turtle, Tony Wackett, Mairi Ward, Jane Weaver, Nicola Wrobel, Marie Zechner, Gill Arbane, Aneta Bociek, Sara Campos, Neus Grau, Tim Owen Jones, Rosario Lim, Martina Marotti, Marlies Ostermann, Christopher Whitton, Zoe Alldis, Raine Astin-Chamberlain, Fatima Bibi, Jack Biddle, Sarah Blow, Matthew Bolton, Catherine Borra, Ruth Bowles, Maudrian Burton, Yasmin Choudhury, David Collier, Amber Cox, Amy Easthope, Patrizia Ebano, Stavros Fotiadis, Jana Gurasashvili, Rosslyn Halls, Pippa Hartridge, Delordson Kallon, Jamila Kassam, Ivone Lancoma-Malcolm, Maninderpal Matharu, Peter May, Oliver Mitchelmore, Tabitha Newman, Mital Patel, Jane Pheby, Irene Pinzuti, Zoe Prime, Oleksandra Prysyazhna, Julian Shiel, Melanie Taylor, Carey Tierney, Suzanne Wood, Anne Zak, Olivier Zongo, Stephen Bonner, Keith Hugill, Jessica Jones, Steven Liggett, Evie Headlam, Nageswar Bandla, Minnie Gellamucho, Michelle Davies, Christopher Thompson, Marwa Abdelrazik, Dhanalakshmi Bakthavatsalam, Munzir Elhassan, Arunkumar Ganesan, Anne Haldeos, Jeronimo Moreno-Cuesta, Dharam Purohit, Rachel Vincent, Kugan Xavier, Kumar Rohit, Frater Alasdair, Malik Saleem, Carter David, Jenkins Samuel, Zoe Lamond, Wall Alanna, Jaime Fernandez-Roman, David O. Hamilton, Emily Johnson, Brian Johnston, Maria Lopez Martinez, Suleman Mulla, David Shaw, Alicia A.C. Waite, Victoria Waugh, Ingeborg D. Welters, Karen Williams, Anna Cavazza, Maeve Cockrell, Eleanor Corcoran, Maria Depante, Clare Finney, Ellen Jerome, Mark McPhail, Monalisa Nayak, Harriet Noble, Kevin O'Reilly, Evita Pappa, Rohit Saha, Sian Saha, John Smith, Abigail Knighton, David Antcliffe, Dorota Banach, Stephen Brett, Phoebe Coghlan, Ziortza Fernandez, Anthony Gordon, Roceld Rojo, Sonia Sousa Arias, Maie Templeton, Megan Meredith, Lucy Morris, Lucy Ryan, Amy Clark, Julia Sampson, Cecilia Peters, Martin Dent, Margaret Langley, Saima Ashraf, Shuying Wei, Angela Andrew, Archana Bashyal, Neil Davidson, Paula Hutton, Stuart McKechnie, Jean Wilson, David Baptista, Rebecca Crowe, Rita Fernandes, Rosaleen Herdman-Grant, Anna Joseph, Denise O'Connor, Meryem Allen, Adam Loveridge, India McKenley, Eriko Morino, Andres Naranjo, Richard Simms, Kathryn Sollesta, Andrew Swain, Harish Venkatesh, Jacyntha Khera, Jonathan Fox, Gillian Andrew, Lucy Barclay, Marie Callaghan, Rachael Campbell, Sarah Clark, Dave Hope, Lucy Marshall, Corrienne McCulloch, Kate Briton, Jo Singleton, Sohphie Birch, Lutece Brimfield, Zoe Daly, David Pogson, Steve Rose, Ceri Battle, Elaine Brinkworth, Rachel Harford, Carl Murphy, Luke Newey, Tabitha Rees, Marie Williams, Sophie Arnold, Petra Polgarova, Katerina Stroud, Eoghan Meaney, Megan Jones, Anthony Ng, Shruti Agrawal, Nazima Pathan, Deborah White, Esther Daubney, Kay Elston, Lina Grauslyte, Musarat Hussain, Mandeep Phull, Tatiana Pogreban, Lace Rosaroso, Erika Salciute, George Franke, Joanna Wong, Aparna George, Laura Ortiz-Ruiz de Gordoa, Emily Peasgood, Claire Phillips, Michelle Bates, Jo Dasgin, Jaspret Gill, Annette Nilsson, James Scriven, Carlos Castro Delgado, Deborah Dawson, Lijun Ding, Georgia Durrant, Obiageri Ezeobu, Sarah Farnell-Ward, Abiola Harrison, Rebecca Kanu, Susannah Leaver, Elena Maccacari, Soumendu Manna, Romina Pepermans Saluzzio, Joana Queiroz, Tinashe Samakomva, Christine Sicat, Joana Texeira, Edna Fernandes Da Gloria, Ana Lisboa, John Rawlins, Jisha Mathew, Ashley Kinch, William James Hurt, Nirav Shah, Victoria Clark, Maria Thanasi, Nikki Yun, Kamal Patel, Sara Bennett, Emma Goodwin, Matthew Jackson, Alissa Kent, Clare Tibke, Wiesia Woodyatt, Ahmed Zaki, Azmerelda Abraheem, Peter Bamford, Kathryn Cawley, Charlie Dunmore, Maria Faulkner, Rumanah Girach, Helen Jeffrey, Rhianna Jones, Emily London, Imrun Nagra, Farah Nasir, Hannah Sainsbury, Clare Smedley, Tahera Patel, Matthew Smith, Srikanth Chukkambotla, Aayesha Kazi, Janice Hartley, Joseph Dykes, Muhammad Hijazi, Sarah Keith, Meherunnisa Khan, Janet Ryan-Smith, Philippa Springle, Jacqueline Thomas, Nick Truman, Samuel Saad, Dabheoc Coleman, Christopher Fine, Roseanna Matt, Bethan Gay, Jack Dalziel, Syamlan Ali, Drew Goodchild, Rhiannan Harling, Ravi Bhatterjee, Wendy Goddard, Chloe Davison, Stephen Duberly, Jeanette Hargreaves, Rachel Bolton, Miriam Davey, David Golden, Rebecca Seaman, Shiney Cherian, Sean Cutler, Anne Emma Heron, Anna Roynon-Reed, Tamas Szakmany, Gemma Williams, Owen Richards, Yusuf Cheema, Hollie Brooke, Sarah Buckley, Jose Cebrian Suarez, Ruth Charlesworth, Karen Hansson, John Norris, Alice Poole, Alastair Rose, Rajdeep Sandhu, Brendan Sloan, Elizabeth Smithson, Muthu Thirumaran, Veronica Wagstaff, Alexandra Metcalfe, Mark Brunton, Jess Caterson, Holly Coles, Matthew Frise, Sabi Gurung Rai, Nicola Jacques, Liza Keating, Emma Tilney, Shauna Bartley, Parminder Bhuie, Sian Gibson, Amanda Lyle, Fiona McNeela, Jayachandran Radhakrishnan, Alistair Hughes, Bryan Yates, Jessica Reynolds, Helen Campbell, Maria Thompsom, Steve Dodds, Stacey Duffy, Sandra Greer, Karen Shuker, Ascanio Tridente, Reena Khade, Ashok Sundar, George Tsinaslanidis, Isobel Birkinshaw, Joseph Carter, Kate Howard, Joanne Ingham, Rosie Joy, Harriet Pearson, Samantha Roche, Zoe Scott, Hollie Bancroft, Mary Bellamy, Margaret Carmody, Jacqueline Daglish, Faye Moore, Joanne Rhodes, Mirriam Sangombe, Salma Kadiri, Maria Croft, Ian White, Victoria Frost, Maia Aquino, Rajeev Jha, Vinodh Krishnamurthy, Lai Lim, Li Lim, Edward Combes, Teishel Joefield, Sonja Monnery, Valerie Beech, Sallyanne Trotman, Christine Almaden-Boyle, Pauline Austin, Louise Cabrelli, Stephen Cole, Matt Casey, Susan Chapman, Clare Whyte, Yolanda Baird, Aaron Butler, Indra Chadbourn, Linda Folkes, Heather Fox, Amy Gardner, Raquel Gomez, Gillian Hobden, Luke Hodgson, Kirsten King, Michael Margarson, Tim Martindale, Emma Meadows, Dana Raynard, Yvette Thirlwall, David Helm, Jordi Margalef, Kristine Criste, Rebecca Cusack, Kim Golder, Hannah Golding, Oliver Jones, Samantha Leggett, Michelle Male, Martyna Marani, Kirsty Prager, Toran Williams, Belinda Roberts, Karen Salmon, Peter Anderson, Katie Archer, Karen Austin, Caroline Davis, Alison Durie, Olivia Kelsall, Jessica Thrush, Charlie Vigurs, Laura Wild, Hannah-Louise Wood, Helen Tranter, Alison Harrison, Nicholas Cowley, Michael McAlindon, Andrew Burtenshaw, Stephen Digby, Emma Low, Aled Morgan, Naiara Cother, Tobias Rankin, Sarah Clayton, Alex McCurdy, Cecilia Ahmed, Balvinder Baines, Sarah Clamp, Julie Colley, Risna Haq, Anne Hayes, Jonathan Hulme, Samia Hussain, Sibet Joseph, Rita Kumar, Zahira Maqsood, Manjit Purewal, Leonie Benham, Zena Bradshaw, Joanna Brown, Melanie Caswell, Jason Cupitt, Sarah Melling, Stephen Preston, Nicola Slawson, Emma Stoddard, Scott Warden, Bethan Deacon, Ceri Lynch, Carla Pothecary, Lisa Roche, Gwenllian Sera Howe, Jayaprakash Singh, Keri Turner, Hannah Ellis, Natalie Stroud, Jodie Hunt, Joy Dearden, Emma Dobson, Andy Drummond, Michelle Mulcahy, Sheila Munt, Grainne O'Connor, Jennifer Philbin, Chloe Rishton, Redmond Tully, Sarah Winnard, Susanne Cathcart, Katharine Duffy, Alex Puxty, Kathryn Puxty, Lynne Turner, Jane Ireland, Gary Semple, Kate Long, Simon Whiteley, Elizabeth Wilby, Bethan Ogg, Amanda Cowton, Andrea Kay, Melanie Kent, Kathryn Potts, Ami Wilkinson, Suzanne Campbell, Ellen Brown, Julie Melville, Jay Naisbitt, Rosane Joseph, Maria Lazo, Olivia Walton, Alan Neal, Peter Alexander, Schvearn Allen, Joanne Bradley-Potts, Craig Brantwood, Jasmine Egan, Timothy Felton, Grace Padden, Luke Ward, Stuart Moss, Susannah Glasgow, Lynn Abel, Michael Brett, Brian Digby, Lisa Gemmell, James Hornsby, Patrick MacGoey, Pauline O'Neil, Richard Price, Natalie Rodden, Kevin Rooney, Radha Sundaram, Nicola Thomson, Bridget Hopkins, Laura Thrasyvoulou, Heather Willis, Martyn Clark, Martina Coulding, Edward Jude, Jacqueline McCormick, Oliver Mercer, Darsh Potla, Hafiz Rehman, Heather Savill, Victoria Turner, Charlotte Downes, Kathleen Holding, Katie Riches, Mary Hilton, Mel Hayman, Deepak Subramanian, Priya Daniel, Oluronke Adanini, Nikhil Bhatia, Maines Msiska, Rebecca Collins, Ian Clement, Bijal Patel, A. Gulati, Carole Hays, K. 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Subjects
SARS-CoV-2, host genetics, toll-like receptor 7, targeted sequencing, rare variants, variant collapsing analysis, Genetics, QH426-470
Abstract

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

Published
2024
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49. The limerick declaration on rural health care 2022

Author

Glynn, Liam, Murphy, Andrew W, Scully, Robert, Strasser, Roger, Quinlan, Diarmuid, Cowley, Jerry, Hayes, Peter, O'Donnell, Patrick, O'Regan, Andrew, Tuli, Shagun, Santana, Marcela Araujo de Oliveira, Sparrow-Downes, Victoria M, Petrazzuoli, Ferdinando, Nowlan, Shelley, Collins, Claire, Fogarty, Frank, MacFarlane, Anne, Wynn-Jones, John, and Chater, Alan Bruce

Published
2023

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