248,135 results on '"Thomson, A."'
Search Results
2. Statistical Quality Comparison of the Bitstrings Generated by a Physical Unclonable Function across Xilinx, Altera and Microsemi Devices
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Jao, Jenilee, Hoffman, Kristi, Reid, Cheryl, Thomson, Ryan, Thompson, Michael, and Plusquellic, Jim
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Computer Science - Cryptography and Security - Abstract
Entropy or randomness represents a foundational security property in security-related operations, such as key generation. Key generation in turn is central to security protocols such as authentication and encryption. Physical unclonable functions (PUF) are hardware-based primitives that can serve as key generation engines in modern microelectronic devices and applications. PUFs derive entropy from manufacturing variations that exist naturally within and across otherwise identical copies of a device. However, the levels of random variations that represent entropy, which are strongly correlated to the quality of the PUF-generated bitstrings, vary from one manufacturer to another. In this paper, we evaluate entropy across a set of devices manufactured by three mainstream FPGA vendors, Xilinx, Altera and Microsemi. The devices selected for evaluation are considered low-end commercial devices to make the analysis relevant to IoT applications. The SiRF PUF is used in the evaluation, and is constructed nearly identically across the three vendor devices, setting aside minor differences that exist in certain logic element primitives used within the PUF architecture, and which have only a minor impact on our comparative analysis. The SiRF PUF uses a high-resolution time-to-digital converter (TDC) crafted from high-speed carry-chain logic embedded within each device to measure path delays in an engineered netlist of logic gates as a source of entropy. Therefore, our analysis includes an evaluation of actual path delay variation as it exists across the three device classes, as well as a statistical evaluation of the PUF-generated bitstrings. A reliablity analysis is also provided using data collected in industrial-standard temperature experiments to round out the evaluation of important statistical properties of the PUF., Comment: 15 pages, 22 figures, IEEE journal
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- 2024
3. Probing the Magnetised Gas Distribution in Galaxy Groups and the Cosmic Web with POSSUM Faraday Rotation Measures
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Anderson, Craig S., McClure-Griffiths, N. M., Rudnick, L., Gaensler, B. M., O'Sullivan, S. P., Bradbury, S., Akahori, T., Baidoo, L., Bruggen, M., Carretti, E., Duchesne, S., Heald, G., Jung, S. L., Kaczmarek, J., Leahy, D., Loi, F., Ma, Y. K., Osinga, E., Seta, A., Stuardi, C., Thomson, A. J. M., Van Eck, C., Vernstrom, T., and West, J.
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Astrophysics - Astrophysics of Galaxies ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
We present initial results from the Polarisation Sky Survey of the Universe's Magnetism (POSSUM), analysing 22,817 Faraday Rotation Measures (RMs) with median uncertainties of 1.2 rad m^-2 across 1,520 square degrees to study magnetised gas associated with 55 nearby galaxy groups (z less than 0.025) with halo masses between 10^12.5 and 10^14.0 M_sun. We identify two distinct gas phases: the Intragroup Medium (IGrM) within 0-2 splashback radii and the Warm-Hot Intergalactic Medium (WHIM) extending from 2 to 7 splashback radii. These phases enhance the standard deviation of residual (i.e., Galactic foreground RM-subtracted) RMs by 6.9 +/- 1.8 rad m^-2 and 4.2 +/- 1.2 rad m^-2, respectively. Estimated magnetic field strengths are several microGauss within the IGrM and 0.1-1 microGauss in the WHIM. We estimate the plasma beta in both phases and show that magnetic pressure might be more dynamically important than in the ICM of more massive clusters or sparse cosmic web filaments. Our findings indicate that "missing baryons" in the WHIM likely extend beyond the gravitational radii of group-mass halos to Mpc scales, consistent with large-scale, outflow-driven "magnetised bubbles" seen in cosmological simulations. We demonstrate that RM grids are an effective method for detecting magnetised thermal gas at galaxy group interfaces and within the cosmic web. This approach complements X-ray and Sunyaev-Zel'dovich effect methods, and when combined with Fast Radio Burst Dispersion Measures, data from the full POSSUM survey, comprising approximately a million RMs, will allow direct magnetic field measurements to further our understanding of baryon circulation in these environments and the magnetised universe., Comment: 15 pages, 7 figures, 3 tables. Accepted for publication in MNRAS
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- 2024
4. A Brief Review of Quantum Machine Learning for Financial Services
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Doosti, Mina, Wallden, Petros, Hamill, Conor Brian, Hankache, Robert, Brown, Oliver Thomson, and Heunen, Chris
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Quantum Physics ,Computer Science - Computational Engineering, Finance, and Science - Abstract
This review paper examines state-of-the-art algorithms and techniques in quantum machine learning with potential applications in finance. We discuss QML techniques in supervised learning tasks, such as Quantum Variational Classifiers, Quantum Kernel Estimation, and Quantum Neural Networks (QNNs), along with quantum generative AI techniques like Quantum Transformers and Quantum Graph Neural Networks (QGNNs). The financial applications considered include risk management, credit scoring, fraud detection, and stock price prediction. We also provide an overview of the challenges, potential, and limitations of QML, both in these specific areas and more broadly across the field. We hope that this can serve as a quick guide for data scientists, professionals in the financial sector, and enthusiasts in this area to understand why quantum computing and QML in particular could be interesting to explore in their field of expertise., Comment: 19 pages
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- 2024
5. Symmetry-broken metallic orders in spin-orbit-coupled Bernal bilayer graphene
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Koh, Jin Ming, Thomson, Alex, Alicea, Jason, and Lantagne-Hurtubise, Étienne
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Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Strongly Correlated Electrons ,Condensed Matter - Superconductivity - Abstract
We explore Bernal bilayer graphene in the presence of long-range Coulomb interactions, short-range Hund's coupling, and proximity-induced Ising spin-orbit coupling using self-consistent Hartree-Fock simulations. We show that the interplay between these three ingredients produces an intricate phase diagram comprising a multitude of symmetry-broken metallic states tunable via doping and applied displacement field. In particular, we find intervalley coherent and spin-canted ground states that may hold the key to understanding spin-orbit-enabled superconductivity observed in this platform. We also investigate various phase transitions where a continuous $\mathrm{U}(1)$ symmetry is broken to ascertain the possible role of critical fluctuations on pairing., Comment: 10 pages and 7 figures in the main text + Supplementary materials
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- 2024
6. Design of a Health Monitoring System for a Planetary Exploration Rover
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Swinton, Sarah, McGookin, Euan, and Thomson, Douglas
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Computer Science - Robotics - Abstract
It is generally considered that a trustworthy autonomous planetary exploration rover must be able to operate safely and effectively within its environment. Central to trustworthy operation is the ability for the rover to recognise and diagnose abnormal behaviours during its operation. Failure to diagnose faulty behaviour could lead to degraded performance or an unplanned halt in operation. This work investigates a health monitoring method that can be used to improve the capabilities of a fault detection system for a planetary exploration rover. A suite of four metrics, named 'rover vitals', are evaluated as indicators of degradation in the rover's performance. These vitals are combined to give an overall estimate of the rover's 'health'. By comparing the behaviour of a faulty real system with a non-faulty observer, residuals are generated in terms of two high-level metrics: heading and velocity. Adaptive thresholds are applied to the residuals to enable the detection of faulty behaviour, where the adaptive thresholds are informed by the rover's perceived health. Simulation experiments carried out in MATLAB showed that the proposed health monitoring and fault detection methodology can detect high-risk faults in both the sensors and actuators of the rover., Comment: Presented at IEEE International Conference on Space Robotics (ISPARO) 2024
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- 2024
7. Active Healing of Microtubule-Motor Networks
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Yang, Fan, Liu, Shichen, Lee, Heun Jin, Phillips, Rob, and Thomson, Matt
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Condensed Matter - Soft Condensed Matter ,Physics - Biological Physics - Abstract
Cytoskeletal networks have a self-healing property where networks can repair defects to maintain structural integrity. However, both the mechanisms and dynamics of healing remain largely unknown. Here we report an unexplored healing mechanism in microtubule-motor networks by active crosslinking. We directly generate network cracks using a light-controlled microtubule-motor system, and observe that the cracks can self-heal. Combining theory and experiment, we find that the networks must overcome internal elastic resistance in order to heal cracks, giving rise to a bifurcation of dynamics dependent on the initial opening angle of the crack: the crack heals below a critical angle and opens up at larger angles. Simulation of a continuum model reproduces the bifurcation dynamics, revealing the importance of a boundary layer where free motors and microtubules can actively crosslink and thereby heal the crack. We also formulate a simple elastic-rod model that can qualitatively predict the critical angle, which is found to be tunable by two dimensionless geometric parameters, the ratio of the boundary layer and network width, and the aspect ratio of the network. Our results provide a new framework for understanding healing in cytoskeletal networks and designing self-healable biomaterials.
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- 2024
8. Towards shutdownable agents via stochastic choice
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Thornley, Elliott, Roman, Alexander, Ziakas, Christos, Ho, Leyton, and Thomson, Louis
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Computer Science - Artificial Intelligence - Abstract
Some worry that advanced artificial agents may resist being shut down. The Incomplete Preferences Proposal (IPP) is an idea for ensuring that doesn't happen. A key part of the IPP is using a novel 'Discounted REward for Same-Length Trajectories (DREST)' reward function to train agents to (1) pursue goals effectively conditional on each trajectory-length (be 'USEFUL'), and (2) choose stochastically between different trajectory-lengths (be 'NEUTRAL' about trajectory-lengths). In this paper, we propose evaluation metrics for USEFULNESS and NEUTRALITY. We use a DREST reward function to train simple agents to navigate gridworlds, and we find that these agents learn to be USEFUL and NEUTRAL. Our results thus suggest that DREST reward functions could also train advanced agents to be USEFUL and NEUTRAL, and thereby make these advanced agents useful and shutdownable.
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- 2024
9. Isotropy of cosmic rays beyond $10^{20}$ eV favors their heavy mass composition
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Telescope Array Collaboration, Abbasi, R. U., Abe, Y., Abu-Zayyad, T., Allen, M., Arai, Y., Arimura, R., Barcikowski, E., Belz, J. W., Bergman, D. R., Blake, S. A., Buckland, I., Cheon, B. G., Chikawa, M., Fujii, T., Fujisue, K., Fujita, K., Fujiwara, R., Fukushima, M., Furlich, G., Globus, N., Gonzalez, R., Hanlon, W., Hayashida, N., He, H., Hibi, R., Hibino, K., Higuchi, R., Honda, K., Ikeda, D., Inoue, N., Ishii, T., Ito, H., Ivanov, D., Iwasaki, A., Jeong, H. M., Jeong, S., Jui, C. C. H., Kadota, K., Kakimoto, F., Kalashev, O., Kasahara, K., Kasami, S., Kawakami, S., Kawata, K., Kharuk, I., Kido, E., Kim, H. B., Kim, J. H., Kim, S. W., Kimura, Y., Komae, I., Kuzmin, V., Kuznetsov, M., Kwon, Y. J., Lee, K. H., Lubsandorzhiev, B., Lundquist, J. P., Matsumiya, H., Matsuyama, T., Matthews, J. N., Mayta, R., Mizuno, K., Murakami, M., Myers, I., Nagataki, S., Nakai, K., Nakamura, T., Nishio, E., Nonaka, T., Oda, H., Ogio, S., Onishi, M., Ohoka, H., Okazaki, N., Oku, Y., Okuda, T., Omura, Y., Ono, M., Oshima, A., Oshima, H., Ozawa, S., Park, I. H., Park, K. Y., Potts, M., Pshirkov, M. S., Remington, J., Rodriguez, D. C., Rott, C., Rubtsov, G. I., Ryu, D., Sagawa, H., Saito, R., Sakaki, N., Sako, T., Sakurai, N., Sato, D., Sato, K., Sato, S., Sekino, K., Shah, P. D., Shibata, N., Shibata, T., Shikita, J., Shimodaira, H., Shin, B. K., Shin, H. S., Shinto, D., Smith, J. D., Sokolsky, P., Stokes, B. T., Stroman, T. A., Takagi, Y., Takahashi, K., Takamura, M., Takeda, M., Takeishi, R., Taketa, A., Takita, M., Tameda, Y., Tanaka, K., Tanaka, M., Tanoue, Y., Thomas, S. B., Thomson, G. B., Tinyakov, P., Tkachev, I., Tokuno, H., Tomida, T., Troitsky, S., Tsuda, R., Tsunesada, Y., Udo, S., Urban, F., Warren, D., Wong, T., Yamazaki, K., Yashiro, K., Yoshida, F., Zhezher, Y., and Zundel, Z.
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Astrophysics - High Energy Astrophysical Phenomena - Abstract
We report an estimation of the injected mass composition of ultra-high energy cosmic rays (UHECRs) at energies higher than 10 EeV. The composition is inferred from an energy-dependent sky distribution of UHECR events observed by the Telescope Array surface detector by comparing it to the Large Scale Structure of the local Universe. In the case of negligible extra-galactic magnetic fields the results are consistent with a relatively heavy injected composition at E ~ 10 EeV that becomes lighter up to E ~ 100 EeV, while the composition at E > 100 EeV is very heavy. The latter is true even in the presence of highest experimentally allowed extra-galactic magnetic fields, while the composition at lower energies can be light if a strong EGMF is present. The effect of the uncertainty in the galactic magnetic field on these results is subdominant., Comment: 8 pages, 3 figures, accepted for publication in PRL
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- 2024
10. Mass composition of ultra-high energy cosmic rays from distribution of their arrival directions with the Telescope Array
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Telescope Array Collaboration, Abbasi, R. U., Abe, Y., Abu-Zayyad, T., Allen, M., Arai, Y., Arimura, R., Barcikowski, E., Belz, J. W., Bergman, D. R., Blake, S. A., Buckland, I., Cheon, B. G., Chikawa, M., Fujii, T., Fujisue, K., Fujita, K., Fujiwara, R., Fukushima, M., Furlich, G., Globus, N., Gonzalez, R., Hanlon, W., Hayashida, N., He, H., Hibi, R., Hibino, K., Higuchi, R., Honda, K., Ikeda, D., Inoue, N., Ishii, T., Ito, H., Ivanov, D., Iwasaki, A., Jeong, H. M., Jeong, S., Jui, C. C. H., Kadota, K., Kakimoto, F., Kalashev, O., Kasahara, K., Kasami, S., Kawakami, S., Kawata, K., Kharuk, I., Kido, E., Kim, H. B., Kim, J. H., Kim, S. W., Kimura, Y., Komae, I., Kuzmin, V., Kuznetsov, M., Kwon, Y. J., Lee, K. H., Lubsandorzhiev, B., Lundquist, J. P., Matsumiya, H., Matsuyama, T., Matthews, J. N., Mayta, R., Mizuno, K., Murakami, M., Myers, I., Nagataki, S., Nakai, K., Nakamura, T., Nishio, E., Nonaka, T., Oda, H., Ogio, S., Onishi, M., Ohoka, H., Okazaki, N., Oku, Y., Okuda, T., Omura, Y., Ono, M., Oshima, A., Oshima, H., Ozawa, S., Park, I. H., Park, K. Y., Potts, M., Pshirkov, M. S., Remington, J., Rodriguez, D. C., Rott, C., Rubtsov, G. I., Ryu, D., Sagawa, H., Saito, R., Sakaki, N., Sako, T., Sakurai, N., Sato, D., Sato, K., Sato, S., Sekino, K., Shah, P. D., Shibata, N., Shibata, T., Shikita, J., Shimodaira, H., Shin, B. K., Shin, H. S., Shinto, D., Smith, J. D., Sokolsky, P., Stokes, B. T., Stroman, T. A., Takagi, Y., Takahashi, K., Takamura, M., Takeda, M., Takeishi, R., Taketa, A., Takita, M., Tameda, Y., Tanaka, K., Tanaka, M., Tanoue, Y., Thomas, S. B., Thomson, G. B., Tinyakov, P., Tkachev, I., Tokuno, H., Tomida, T., Troitsky, S., Tsuda, R., Tsunesada, Y., Udo, S., Urban, F., Warren, D., Wong, T., Yamazaki, K., Yashiro, K., Yoshida, F., Zhezher, Y., and Zundel, Z.
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Astrophysics - High Energy Astrophysical Phenomena - Abstract
We use a new method to estimate the injected mass composition of ultrahigh cosmic rays (UHECRs) at energies higher than 10 EeV. The method is based on comparison of the energy-dependent distribution of cosmic ray arrival directions as measured by the Telescope Array experiment (TA) with that calculated in a given putative model of UHECR under the assumption that sources trace the large-scale structure (LSS) of the Universe. As we report in the companion letter, the TA data show large deflections with respect to the LSS which can be explained, assuming small extra-galactic magnetic fields (EGMF), by an intermediate composition changing to a heavy one (iron) in the highest energy bin. Here we show that these results are robust to uncertainties in UHECR injection spectra, the energy scale of the experiment and galactic magnetic fields (GMF). The assumption of weak EGMF, however, strongly affects this interpretation at all but the highest energies E > 100 EeV, where the remarkable isotropy of the data implies a heavy injected composition even in the case of strong EGMF. This result also holds if UHECR sources are as rare as $2 \times 10^{-5}$ Mpc$^{-3}$, that is the conservative lower limit for the source number density., Comment: 18 pages, 11 figures, accepted for publication in PRD
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- 2024
11. Magnetism in LAMOST CP stars observed by TESS
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Thomson-Paressant, Keegan, Neiner, Coralie, and Labadie-Bartz, Jonathan
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Astrophysics - Solar and Stellar Astrophysics - Abstract
Context. A thousand new magnetic candidate CP stars have been identified with LAMOST, among which about 700 prime targets have rotational modulation determined from TESS. Aims. We aim to check for the presence of a magnetic field in a subsample of these LAMOST CP stars, test the viability of the 5200 A depression used to select the mCP candidates in the LAMOST survey as a reliable indicator of magnetism, and expand on the limited database of known magnetic hot stars. The sample includes some pulsators that would be valuable targets for magneto-asteroseismology. Methods. We selected approx. 100 magnetic candidate LAMOST CP stars, presenting a depression at 5200 A in their spectrum and that also display rotational modulation in their TESS photometric lightcurves. We obtained spectropolarimetric observations of 39 targets from this sample with ESPaDOnS at CFHT. We utilise the Least Squares Deconvolution method to generate the mean profile of the Stokes V and I parameters, from which the longitudinal magnetic field strength for each target can be determined. For HD 49198, we performed more in-depth analysis to determine the polar magnetic field strength and configuration. Results. We detect fields in at least 36 of our sample of 39 targets. This success rate in detecting magnetic field (above 92%) is very high compared to the occurrence of magnetic fields in hot stars (about 10%). Four of these newly discovered magnetic stars are magnetic pulsators. In particular, we detect the strongest field around a delta Scuti star discovered to date: a 12 kG dipolar field in HD 49198. Conclusions. From our analysis, we conclude that using the 5200 A depression displayed in the spectra in combination with rotational modulation in photometric data is a very reliable method for identifying magnetic candidates in this population of stars., Comment: 18 pages, 13 figures, 2 tables
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- 2024
12. Observation of Declination Dependence in the Cosmic Ray Energy Spectrum
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The Telescope Array Collaboration, Abbasi, R. U., Abu-Zayyad, T., Allen, M., Belz, J. W., Bergman, D. R., Buckland, I., Campbell, W., Cheon, B. G., Endo, K., Fedynitch, A., Fujii, T., Fujisue, K., Fujita, K., Fukushima, M., Furlich, G., Gerber, Z., Globus, N., Hanlon, W., Hayashida, N., He, H., Hibino, K., Higuchi, R., Ikeda, D., Ishii, T., Ivanov, D., Jeong, S., Jui, C. C. H., Kadota, K., Kakimoto, F., Kalashev, O., Kasahara, K., Kawachi, Y., Kawata, K., Kharuk, I., Kido, E., Kim, H. B., Kim, J. H., Kim, S. W., Kobo, R., Komae, I., Komatsu, K., Komori, K., Koyama, C., Kudenko, M., Kuroiwa, M., Kusumori, Y., Kuznetsov, M., Kwon, Y. J., Lee, K. H., Lee, M. J., Lubsandorzhiev, B., Lundquist, J. P., Matsuzawa, A., Matthews, J. A., Matthews, J. N., Mizuno, K., Mori, M., Murakami, M., Nagataki, S., Nakahara, M., Nakamura, T., Nakayama, T., Nakayama, Y., Nonaka, T., Ogio, S., Ohoka, H., Okazaki, N., Onishi, M., Oshima, A., Oshima, H., Ozawa, S., Park, I. H., Park, K. Y., Potts, M., Przybylak, M., Pshirkov, M. S., Remington, J., Rott, C., Rubtsov, G. I., Ryu, D., Sagawa, H., Sakaki, N., Sakamoto, R., Sako, T., Sakurai, N., Sakurai, S., Sato, D., Sato, S., Sekino, K., Shibata, T., Shikita, J., Shimodaira, H., Shin, B. K., Shin, H. S., Shinozaki, K., Smith, J. D., Sokolsky, P., Stokes, B. T., Stroman, T. A., Takagi, Y., Takahashi, K., Takeda, M., Takeishi, R., Taketa, A., Takita, M., Tameda, Y., Tanaka, K., Tanaka, M., Thomas, S. B., Thomson, G. B., Tinyakov, P., Tkachev, I., Tomida, T., Troitsky, S., Tsunesada, Y., Udo, S., Urban, F., Vaiman, I. A., Vrábel, M., Warren, D., Yamazaki, K., Zhezher, Y., Zundel, Z., and Zvirzdin, J.
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Astrophysics - High Energy Astrophysical Phenomena - Abstract
We report on an observation of the difference between northern and southern skies of the ultrahigh energy cosmic ray energy spectrum with a significance of ${\sim}8\sigma$. We use measurements from the two largest experiments$\unicode{x2014}$the Telescope Array observing the northern hemisphere and the Pierre Auger Observatory viewing the southern hemisphere. Since the comparison of two measurements from different observatories introduces the issue of possible systematic differences between detectors and analyses, we validate the methodology of the comparison by examining the region of the sky where the apertures of the two observatories overlap. Although the spectra differ in this region, we find that there is only a $1.8\sigma$ difference between the spectrum measurements when anisotropic regions are removed and a fiducial cut in the aperture is applied., Comment: 8 pages, 6 figures
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- 2024
13. Materials for Quantum Technologies: a Roadmap for Spin and Topology
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Banerjee, N., Bell, C., Ciccarelli, C., Hesjedal, T., Johnson, F., Kurebayashi, H., Moore, T. A., Moutafis, C., Stern, H. L., Vera-Marun, I. J., Wade, J., Barton, C., Connolly, M. R., Curson, N. J., Fallon, K., Fisher, A. J., Gangloff, D. A., Griggs, W., Linfield, E., Marrows, C. H., Rossi, A., Schindler, F., Smith, J., Thomson, T., and Kazakova, O.
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Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Materials Science - Abstract
This Roadmap provides an overview of the critical role of materials in exploiting spin and topology for next-generation quantum technologies including computing, sensing, information storage and networking devices. We explore the key materials systems that support spin and topological phenomena and discuss their figures of merit. Spin and topology-based quantum technologies have several advantages over their classical, charged-based counterparts, including non-volatility, faster data processing speeds, higher integration densities and lower power consumption. We discuss the main challenges facing the field, identify strategies to overcome them, and provide a realistic outlook on future possibilities of spin-based and topological materials in quantum technology applications., Comment: Roadmap of the UKRI EPSRC Materials for Quantum Network (M4QN) Spin & Topology group. 25 pages, 5 figures, includes supplement. Comments welcome!
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- 2024
14. Redemption by the spiritual purity of nakedness : d’Indy’s Istar and an ancient Assyrian legend
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THOMSON, ANDREW
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- 2024
15. Engineering programmable material-to-cell pathways via synthetic notch receptors to spatially control differentiation in multicellular constructs.
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Garibyan, Mher, Hoffman, Tyler, Makaske, Thijs, Do, Stephanie, Wu, Yifan, Williams, Brian, March, Alexander, Cho, Nathan, Pedroncelli, Nicolas, Lima, Ricardo, Soto, Jennifer, Jackson, Brooke, Santoso, Jeffrey, Khademhosseini, Ali, Thomson, Matt, Li, Song, McCain, Megan, and Morsut, Leonardo
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Receptors ,Notch ,Cell Differentiation ,Tissue Engineering ,Animals ,Humans ,Signal Transduction ,Mice ,Extracellular Matrix ,Fibroblasts ,Extracellular Matrix Proteins ,Ligands ,Tissue Scaffolds ,Muscle ,Skeletal ,Endothelial Cells ,HEK293 Cells - Abstract
Synthetic Notch (synNotch) receptors are genetically encoded, modular synthetic receptors that enable mammalian cells to detect environmental signals and respond by activating user-prescribed transcriptional programs. Although some materials have been modified to present synNotch ligands with coarse spatial control, applications in tissue engineering generally require extracellular matrix (ECM)-derived scaffolds and/or finer spatial positioning of multiple ligands. Thus, we develop here a suite of materials that activate synNotch receptors for generalizable engineering of material-to-cell signaling. We genetically and chemically fuse functional synNotch ligands to ECM proteins and ECM-derived materials. We also generate tissues with microscale precision over four distinct reporter phenotypes by culturing cells with two orthogonal synNotch programs on surfaces microcontact-printed with two synNotch ligands. Finally, we showcase applications in tissue engineering by co-transdifferentiating fibroblasts into skeletal muscle or endothelial cell precursors in user-defined micropatterns. These technologies provide avenues for spatially controlling cellular phenotypes in mammalian tissues.
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- 2024
16. SWOG S1820: A pilot randomized trial of the Altering Intake, Managing Bowel Symptoms Intervention in Survivors of Rectal Cancer
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Sun, Virginia, Guthrie, Katherine A, Crane, Tracy E, Arnold, Kathryn B, Colby, Sarah, Freylersythe, Sarah G, Braun‐Inglis, Christa, Topacio, Roxanne, Messick, Craig A, Carmichael, Joseph C, Muskovitz, Andrew A, Nashawaty, Mohammed, Bajaj, Madhuri, Cohen, Stacey A, Flaherty, Devin C, O’Rourke, Mark A, Jones, Lee, Krouse, Robert S, and Thomson, Cynthia A
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Health Services and Systems ,Nursing ,Health Sciences ,Rare Diseases ,Clinical Trials and Supportive Activities ,Behavioral and Social Science ,Colo-Rectal Cancer ,Clinical Research ,Cancer ,Digestive Diseases ,Health Disparities ,Women's Health ,Nutrition ,Prevention ,Management of diseases and conditions ,7.1 Individual care needs ,Oral and gastrointestinal ,Humans ,Rectal Neoplasms ,Middle Aged ,Female ,Male ,Pilot Projects ,Cancer Survivors ,Quality of Life ,Aged ,Adult ,bowel dysfunction ,low anterior resection syndrome ,quality of life ,rectal cancer ,Oncology and Carcinogenesis ,Public Health and Health Services ,Oncology & Carcinogenesis ,Oncology and carcinogenesis ,Public health - Abstract
BackgroundSurvivors of rectal cancer experience persistent bowel dysfunction after treatments. Dietary interventions may be an effective approach for symptom management and posttreatment diet quality. SWOG S1820 was a pilot randomized trial of the Altering Intake, Managing Symptoms in Rectal Cancer (AIMS-RC) intervention for bowel dysfunction in survivors of rectal cancer.MethodsNinety-three posttreatment survivors were randomized to the AIMS-RC group (N = 47) or the Healthy Living Education attention control group (N = 46) after informed consent and completion of a prerandomization run-in. Outcome measures were completed at baseline and at 18 and 26 weeks postrandomization. The primary end point was total bowel function score, and exploratory end points included low anterior resection syndrome (LARS) score, quality of life, dietary quality, motivation, self-efficacy, and positive/negative affect.ResultsMost participants were White and college educated, with a mean age of 55.2 years and median time since surgery of 13.1 months. There were no statistically significant differences in total bowel function score by group, with the AIMS-RC group demonstrating statistically significant improvements in the exploratory end points of LARS (p = .01) and the frequency subscale of the bowel function index (p = .03). The AIMS-RC group reported significantly higher acceptability of the study.ConclusionsSWOG S1820 did not provide evidence of benefit from the AIMS-RC intervention relative to the attention control. Select secondary end points did demonstrate improvements. The study was highly feasible and acceptable for participants in the National Cancer Institute Community Oncology Research Program. Findings provide strong support for further refinement and effectiveness testing of the AIMS-RC intervention.
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- 2024
17. Baseline characteristics and recruitment for SWOG S1820: altering intake, managing bowel symptoms in survivors of rectal cancer (AIMS-RC)
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Sun, Virginia, Thomson, Cynthia A, Crane, Tracy E, Arnold, Kathryn B, Guthrie, Katherine A, Freylersythe, Sarah G, Braun-Inglis, Christa, Jones, Lee, Carmichael, Joseph C, Messick, Craig, Flaherty, Devin, Ambrale, Samir, Cohen, Stacey A, and Krouse, Robert S
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Health Services and Systems ,Nursing ,Health Sciences ,Behavioral and Social Science ,Clinical Trials and Supportive Activities ,Cancer ,Colo-Rectal Cancer ,Prevention ,Clinical Research ,Nutrition ,Digestive Diseases ,Rare Diseases ,Oral and gastrointestinal ,Good Health and Well Being ,Humans ,Rectal Neoplasms ,Male ,Female ,Middle Aged ,Cancer Survivors ,Aged ,Quality of Life ,Adult ,Patient Selection ,Self Efficacy ,Feasibility Studies ,Bowel dysfunction ,Diet modification ,Intervention ,Quality of life ,Self-management ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Oncology & Carcinogenesis ,Biomedical and clinical sciences ,Health sciences ,Psychology - Abstract
PurposeMany survivors of rectal cancer experience persistent bowel dysfunction. There are few evidence-based symptom management interventions to improve bowel control. The purpose of this study is to describe recruitment and pre-randomization baseline sociodemographic, health status, and clinical characteristics for SWOG S1820, a trial of the Altering Intake, Managing Symptoms in Rectal Cancer (AIMS-RC) intervention.MethodsSWOG S1820 aimed to determine the preliminary efficacy, feasibility, and acceptability of AIMS-RC, a symptom management intervention for bowel health, comparing intervention to attention control. Survivors with a history of cancers of the rectosigmoid colon or rectum, within 6-24 months of primary treatment completion, with a post-surgical permanent ostomy or anastomosis, and over 18 years of age were enrolled. Outcomes included total bowel function, low anterior resection syndrome, quality of life, motivation for managing bowel health, self-efficacy for managing symptoms, positive and negative affect, and study feasibility and acceptability.ResultsThe trial completed accrual over a 29-month period and enrolled 117 participants from 34 institutions across 17 states and one US Pacific territory. At baseline, most enrolled participants reported self-imposed diet adjustments after surgery, persistent dietary intolerances, and bowel discomfort post-treatment, with high levels of constipation and diarrhea (grades 1-4).ConclusionsSWOG S1820 was able to recruit, in a timely manner, a study cohort that is demographically representative of US survivors of rectal cancer. Baseline characteristics illustrate the connection between diet/eating and bowel symptoms post-treatment, with many participants reporting diet adjustments and persistent inability to be comfortable with dietary intake.ClinicaltrialsGov registration date12/19/2019.ClinicaltrialsGov identifierNCT#04205955.
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- 2024
18. Oblique spin injection to graphene via geometry controlled magnetic nanowires
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Toscano-Figueroa, Jesus C., Burrow, Daniel, Guarochico-Moreira, Victor H., Xie, Chengkun, Thomson, Thomas, Grigorieva, Irina V., and Vera-Marun, Ivan J.
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Condensed Matter - Mesoscale and Nanoscale Physics - Abstract
We exploit the geometry of magnetic nanowires, which define 1D contacts to an encapsulated graphene channel, to introduce an out-of-plane component in the polarisation of spin carriers. By design, the magnetic nanowires traverse the angled sides of the 2D material heterostructure. Consequently, the easy axis of the nanowires is inclined, and so the local magnetisation is oblique at the injection point. As a result, when performing non-local spin valve measurements we simultaneously observe both switching and spin precession phenomena, implying the spin population possesses both in-plane and out-of-plane polarisation components. By comparing the relative magnitudes of these components, we quantify the angle of the total spin polarisation vector. The extracted angle is consistent with the angle of the nanowire at the graphene interface, evidencing that the effect is a consequence of the device geometry. This simple method of spin-based vector magnetometry provides an alternative technique to define the spin polarisation in 2D spintronic devices.
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- 2024
19. Leveraging Open-Source Large Language Models for encoding Social Determinants of Health using an Intelligent Router
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Goel, Akul, Hari, Surya Narayanan, Waltman, Belinda, and Thomson, Matt
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Computer Science - Artificial Intelligence - Abstract
Social Determinants of Health (SDOH) play a significant role in patient health outcomes. The Center of Disease Control (CDC) introduced a subset of ICD-10 codes called Z-codes in an attempt to officially recognize and measure SDOH in the health care system. However, these codes are rarely annotated in a patient's Electronic Health Record (EHR), and instead, in many cases, need to be inferred from clinical notes. Previous research has shown that large language models (LLMs) show promise on extracting unstructured data from EHRs. However, with thousands of models to choose from with unique architectures and training sets, it's difficult to choose one model that performs the best on coding tasks. Further, clinical notes contain trusted health information making the use of closed-source language models from commercial vendors difficult, so the identification of open source LLMs that can be run within health organizations and exhibits high performance on SDOH tasks is an urgent problem. Here, we introduce an intelligent routing system for SDOH coding that uses a language model router to direct medical record data to open source LLMs that demonstrate optimal performance on specific SDOH codes. The intelligent routing system exhibits state of the art performance of 97.4% accuracy averaged across 5 codes, including homelessness and food insecurity, on par with closed models such as GPT-4o. In order to train the routing system and validate models, we also introduce a synthetic data generation and validation paradigm to increase the scale of training data without needing privacy protected medical records. Together, we demonstrate an architecture for intelligent routing of inputs to task-optimal language models to achieve high performance across a set of medical coding sub-tasks.
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- 2024
20. Improving Harmonic Analysis using Multitapering: Precise frequency estimation of stellar oscillations using the harmonic F-test
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Patil, Aarya A., Eadie, Gwendolyn M., Speagle, Joshua S., and Thomson, David J.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics ,Statistics - Applications - Abstract
In Patil et. al 2024a, we developed a multitaper power spectrum estimation method, mtNUFFT, for analyzing time-series with quasi-regular spacing, and showed that it not only improves upon the statistical issues of the Lomb-Scargle periodogram, but also provides a factor of three speed up in some applications. In this paper, we combine mtNUFFT with the harmonic F-test to test the hypothesis that a strictly periodic signal or its harmonic (as opposed to e.g. a quasi-periodic signal) is present at a given frequency. This mtNUFFT/F-test combination shows that multitapering allows detection of periodic signals and precise estimation of their frequencies, thereby improving both power spectrum estimation and harmonic analysis. Using asteroseismic time-series data for the Kepler-91 red giant, we show that the F-test automatically picks up the harmonics of its transiting exoplanet as well as certain dipole ($l=1$) mixed modes. We use this example to highlight that we can distinguish between different types of stellar oscillations, e.g., transient (damped, stochastically-excited) and strictly periodic (undamped, heat-driven). We also illustrate the technique of dividing a time-series into chunks to further examine the transient versus periodic nature of stellar oscillations. The harmonic F-test combined with mtNUFFT is implemented in the public Python package tapify (https://github.com/aaryapatil/tapify), which opens opportunities to perform detailed investigations of periodic signals in time-domain astronomy., Comment: 15 pages, 6 figures, Submitted to AJ as a companion paper to arXiv:2209.15027
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- 2024
21. Faraday tomography with CHIME: the `tadpole' feature G137+7
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Mohammed, Nasser, Ordog, Anna, Booth, Rebecca A., Bracco, Andrea, Brown, Jo-Anne C., Carretti, Ettore, Dickey, John M., Foreman, Simon, Halpern, Mark, Haverkorn, Marijke, Hill, Alex S., Hinshaw, Gary, Kania, Joseph W, Kothes, Roland, Landecker, T. L., MacEachern, Joshua, Masui, Kiyoshi W., Menard, Aimee, Ransom, Ryan R., Reich, Wolfgang, Reich, Patricia, Shaw, J. Richard, Siegel, Seth R., Tahani, Mehrnoosh, Thomson, Alec J. M., Pinsonneault-Marotte, Tristan, Wang, Haochen, West, Jennifer L., Wolleben, Maik, and Wulf, Dallas
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Astrophysics - Astrophysics of Galaxies - Abstract
A direct consequence of Faraday rotation is that the polarized radio sky does not resemble the total intensity sky at long wavelengths. We analyze G137+7, which is undetectable in total intensity but appears as a depolarization feature. We use the first polarization maps from the Canadian Hydrogen Intensity Mapping Experiment. Our $400-729$ MHz bandwidth and angular resolution, $17'$ to $30'$, allow us to use Faraday synthesis to analyze the polarization structure. In polarized intensity and polarization angle maps, we find a "tail" extending $10^\circ$ from the "head" and designate the combined object the "tadpole". Similar polarization angles, distinct from the background, indicate that the head and tail are physically associated. The head appears as a depolarized ring in single channels, but wideband observations show that it is a Faraday rotation feature. Our investigations of H I and H$\alpha$ find no connections to the tadpole. The tail suggests motion of either the gas or an ionizing star through the ISM; the B2(e) star HD 20336 is a candidate. While the head features a coherent, $\sim -8$ rad m$^2$ Faraday depth, Faraday synthesis also identifies multiple components in both the head and tail. We verify the locations of the components in the spectra using QU fitting. Our results show that $\sim$octave-bandwidth Faraday rotation observations at $\sim 600$ MHz are sensitive to low-density ionized or partially-ionized gas which is undetectable in other tracers., Comment: ApJ in press. Replacement corrects typographical error in equation 6
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- 2024
22. Deep Reinforcement Learning for Time-Critical Wilderness Search And Rescue Using Drones
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Ewers, Jan-Hendrik, Anderson, David, and Thomson, Douglas
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Computer Science - Robotics ,Computer Science - Machine Learning ,Electrical Engineering and Systems Science - Systems and Control - Abstract
Traditional search and rescue methods in wilderness areas can be time-consuming and have limited coverage. Drones offer a faster and more flexible solution, but optimizing their search paths is crucial. This paper explores the use of deep reinforcement learning to create efficient search missions for drones in wilderness environments. Our approach leverages a priori data about the search area and the missing person in the form of a probability distribution map. This allows the deep reinforcement learning agent to learn optimal flight paths that maximize the probability of finding the missing person quickly. Experimental results show that our method achieves a significant improvement in search times compared to traditional coverage planning and search planning algorithms. In one comparison, deep reinforcement learning is found to outperform other algorithms by over $160\%$, a difference that can mean life or death in real-world search operations. Additionally, unlike previous work, our approach incorporates a continuous action space enabled by cubature, allowing for more nuanced flight patterns., Comment: 16 pages, 19 figures. Submitted
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- 2024
23. A Novel Methodology for Autonomous Planetary Exploration Using Multi-Robot Teams
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Swinton, Sarah, Ewers, Jan-Hendrik, McGookin, Euan, Anderson, David, and Thomson, Douglas
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Computer Science - Robotics - Abstract
One of the fundamental limiting factors in planetary exploration is the autonomous capabilities of planetary exploration rovers. This study proposes a novel methodology for trustworthy autonomous multi-robot teams which incorporates data from multiple sources (HiRISE orbiter imaging, probability distribution maps, and on-board rover sensors) to find efficient exploration routes in Jezero crater. A map is generated, consisting of a 3D terrain model, traversability analysis, and probability distribution map of points of scientific interest. A three-stage mission planner generates an efficient route, which maximises the accumulated probability of identifying points of interest. A 4D RRT* algorithm is used to determine smooth, flat paths, and prioritised planning is used to coordinate a safe set of paths. The above methodology is shown to coordinate safe and efficient rover paths, which ensure the rovers remain within their nominal pitch and roll limits throughout operation., Comment: 6 pages. 10 figures. This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible
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- 2024
24. Enhancing Reinforcement Learning in Sensor Fusion: A Comparative Analysis of Cubature and Sampling-based Integration Methods for Rover Search Planning
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Ewers, Jan-Hendrik, Swinton, Sarah, Anderson, David, McGookin, Euan, and Thomson, Douglas
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Computer Science - Robotics ,Electrical Engineering and Systems Science - Systems and Control - Abstract
This study investigates the computational speed and accuracy of two numerical integration methods, cubature and sampling-based, for integrating an integrand over a 2D polygon. Using a group of rovers searching the Martian surface with a limited sensor footprint as a test bed, the relative error and computational time are compared as the area was subdivided to improve accuracy in the sampling-based approach. The results show that the sampling-based approach exhibits a $14.75\%$ deviation in relative error compared to cubature when it matches the computational performance at $100\%$. Furthermore, achieving a relative error below $1\%$ necessitates a $10000\%$ increase in relative time to calculate due to the $\mathcal{O}(N^2)$ complexity of the sampling-based method. It is concluded that for enhancing reinforcement learning capabilities and other high iteration algorithms, the cubature method is preferred over the sampling-based method., Comment: Submitted to IROS 2024
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- 2024
25. BenthicNet: A global compilation of seafloor images for deep learning applications
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Lowe, Scott C., Misiuk, Benjamin, Xu, Isaac, Abdulazizov, Shakhboz, Baroi, Amit R., Bastos, Alex C., Best, Merlin, Ferrini, Vicki, Friedman, Ariell, Hart, Deborah, Hoegh-Guldberg, Ove, Ierodiaconou, Daniel, Mackin-McLaughlin, Julia, Markey, Kathryn, Menandro, Pedro S., Monk, Jacquomo, Nemani, Shreya, O'Brien, John, Oh, Elizabeth, Reshitnyk, Luba Y., Robert, Katleen, Roelfsema, Chris M., Sameoto, Jessica A., Schimel, Alexandre C. G., Thomson, Jordan A., Wilson, Brittany R., Wong, Melisa C., Brown, Craig J., and Trappenberg, Thomas
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
Advances in underwater imaging enable the collection of extensive seafloor image datasets that are necessary for monitoring important benthic ecosystems. The ability to collect seafloor imagery has outpaced our capacity to analyze it, hindering expedient mobilization of this crucial environmental information. Recent machine learning approaches provide opportunities to increase the efficiency with which seafloor image datasets are analyzed, yet large and consistent datasets necessary to support development of such approaches are scarce. Here we present BenthicNet: a global compilation of seafloor imagery designed to support the training and evaluation of large-scale image recognition models. An initial set of over 11.4 million images was collected and curated to represent a diversity of seafloor environments using a representative subset of 1.3 million images. These are accompanied by 2.6 million annotations translated to the CATAMI scheme, which span 190,000 of the images. A large deep learning model was trained on this compilation and preliminary results suggest it has utility for automating large and small-scale image analysis tasks. The compilation and model are made openly available for use by the scientific community at https://doi.org/10.20383/103.0614.
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- 2024
26. A Deep Dive into Effects of Structural Bias on CMA-ES Performance along Affine Trajectories
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van Stein, Niki, Thomson, Sarah L., and Kononova, Anna V.
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Computer Science - Neural and Evolutionary Computing ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
To guide the design of better iterative optimisation heuristics, it is imperative to understand how inherent structural biases within algorithm components affect the performance on a wide variety of search landscapes. This study explores the impact of structural bias in the modular Covariance Matrix Adaptation Evolution Strategy (modCMA), focusing on the roles of various modulars within the algorithm. Through an extensive investigation involving 435,456 configurations of modCMA, we identified key modules that significantly influence structural bias of various classes. Our analysis utilized the Deep-BIAS toolbox for structural bias detection and classification, complemented by SHAP analysis for quantifying module contributions. The performance of these configurations was tested on a sequence of affine-recombined functions, maintaining fixed optimum locations while gradually varying the landscape features. Our results demonstrate an interplay between module-induced structural bias and algorithm performance across different landscape characteristics., Comment: 15 pages, 5 figures, submitted to PPSN 2024
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- 2024
27. Temporal True and Surrogate Fitness Landscape Analysis for Expensive Bi-Objective Optimisation
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Rodriguez, C. J., Thomson, S. L., Alderliesten, T., and Bosman, P. A. N.
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Computer Science - Neural and Evolutionary Computing - Abstract
Many real-world problems have expensive-to-compute fitness functions and are multi-objective in nature. Surrogate-assisted evolutionary algorithms are often used to tackle such problems. Despite this, literature about analysing the fitness landscapes induced by surrogate models is limited, and even non-existent for multi-objective problems. This study addresses this critical gap by comparing landscapes of the true fitness function with those of surrogate models for multi-objective functions. Moreover, it does so temporally by examining landscape features at different points in time during optimisation, in the vicinity of the population at that point in time. We consider the BBOB bi-objective benchmark functions in our experiments. The results of the fitness landscape analysis reveals significant differences between true and surrogate features at different time points during optimisation. Despite these differences, the true and surrogate landscape features still show high correlations between each other. Furthermore, this study identifies which landscape features are related to search and demonstrates that both surrogate and true landscape features are capable of predicting algorithm performance. These findings indicate that temporal analysis of the landscape features may help to facilitate the design of surrogate switching approaches to improve performance in multi-objective optimisation.
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- 2024
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28. Prototype Faraday rotation measure catalogs from the Polarisation Sky Survey of the Universe's Magnetism (POSSUM) pilot observations
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Vanderwoude, S., West, J. L., Gaensler, B. M., Rudnick, L., Van Eck, C. L., Thomson, A. J. M., Andernach, H., Anderson, C. S., Carretti, E., Heald, G. H., Leahy, J. P., McClure-Griffiths, N. M., O'Sullivan, S. P., Tahani, M., and Willis, A. G.
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Astrophysics - Astrophysics of Galaxies - Abstract
The Polarisation Sky Survey of the Universe's Magnetism (POSSUM) will conduct a sensitive $\sim$1 GHz radio polarization survey covering 20 000 square degrees of the Southern sky with the Australian Square Kilometre Array Pathfinder (ASKAP). In anticipation of the full survey, we analyze pilot observations of low-band (800-1087 MHz), mid-band (1316-1439 MHz), and combined-band observations for an extragalactic field and a Galactic-plane field (low-band only). Using the POSSUM processing pipeline, we produce prototype RM catalogs that are filtered to construct prototype RM grids. We assess typical RM grid densities and RM uncertainties and their dependence on frequency, bandwidth, and Galactic latitude. We present a median filter method for separating foreground diffuse emission from background components, and find that after application of the filter, 99.5% of measured RMs of simulated sources are within 3$\sigma$ of their true RM, with a typical loss of polarized intensity of 5% $\pm$ 5%. We find RM grid densities of 35.1, 30.6, 37.2, and 13.5 RMs per square degree and median uncertainties on RM measurements of 1.55, 12.82, 1.06, and 1.89 rad m$^{-2}$ for the median-filtered low-band, mid-band, combined-band, and Galactic observations, respectively. We estimate that the full POSSUM survey will produce an RM catalog of $\sim$775 000 RMs with median-filtered low-band observations and $\sim$877 000 RMs with median-filtered combined-band observations. We construct a structure function from the Galactic RM catalog, which shows a break at $0.7^{\circ}$, corresponding to a physical scale of 12-24 pc for the nearest spiral arm., Comment: 51 pages, 19 figures, 5 tables
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- 2024
29. Tunable ultrastrong magnon magnon coupling and spin Hall magnetoresistance in a van der Waals antiferromagnet
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Freeman, C. W. F., Xue, Z., Budniak, A. K., De Libero, H., Thomson, T., Bosman, M., Eda, G., Kurebayashi, H., and Cubukcu, M.
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Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Materials Science - Abstract
Antiferromagnetic (AFM) magnons and the manipulation of magnetisation via spin currents in van der Waals (vdW) materials offer substantial potential for applications in magnonics and spintronics. In this study, we demonstrate ultrastrong magnon-magnon coupling in the GHz regime within a vdW AFM, achieving a remarkable maximum normalised coupling strength of 0.47. Our investigation unveils the tunability of coupling strength through temperature-dependent magnetic anisotropies. Additionally, we show the prospect for further enhancement to the deep-strong magnon-magnon coupling regime by manipulating the anisotropy. Furthermore, we report spin Hall magnetoresistance in a vdW AFM-based device and study the field and temperature dependence. These findings highlight the transformative potential of vdW AFMs in advancing the field of spin-based technologies.
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- 2024
30. Assessing the Spurious Impacts of Ice-Constraining Methods on the Climate Response to Sea-Ice Loss using an Idealised Aquaplanet GCM
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Lewis, Neil T., England, Mark R., Screen, James A., Geen, Ruth, Mudhar, Regan, Seviour, William J. M., and Thomson, Stephen I.
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Physics - Atmospheric and Oceanic Physics - Abstract
Coupled climate model simulations designed to isolate the effects of Arctic sea-ice loss often apply artificial heating, either directly to the ice or through modification of the surface albedo, to constrain sea-ice in the absence of other forcings. Recent work has shown that this approach may lead to an overestimation of the climate response to sea-ice loss. In this study, we assess the spurious impacts of ice-constraining methods on the climate of an idealised aquaplanet general circulation model (GCM) with thermodynamic sea-ice. The true effect of sea-ice loss in this model is isolated by inducing ice loss through reduction of the freezing point of water, which does not require additional energy input. We compare results from freezing point modification experiments with experiments where sea-ice loss is induced using traditional ice-constraining methods, and confirm the result of previous work that traditional methods induce spurious additional warming. Furthermore, additional warming leads to an overestimation of the circulation response to sea-ice loss, which involves a weakening of the zonal wind and storm track activity in midlatitudes. Our results suggest that coupled model simulations with constrained sea-ice should be treated with caution, especially in boreal summer, where the true effect of sea-ice loss is weakest but we find the largest spurious response. Given that our results may be sensitive to the simplicity of the model we use, we suggest that devising methods to quantify the spurious effects of ice-constraining methods in more sophisticated models should be an urgent priority for future work., Comment: Submitted to Journal of Climate
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- 2024
31. DID:RING: Ring Signatures using Decentralised Identifiers For Privacy-Aware Identity
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Kasimatis, Dimitrios, Grierson, Sam, Buchanan, William J., Eckl, Chris, Papadopoulos, Pavlos, Pitropakis, Nikolaos, Thomson, Craig, and Ghaleb, Baraq
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Computer Science - Cryptography and Security - Abstract
Decentralised identifiers have become a standardised element of digital identity architecture, with supra-national organisations such as the European Union adopting them as a key component for a unified European digital identity ledger. This paper delves into enhancing security and privacy features within decentralised identifiers by integrating ring signatures as an alternative verification method. This allows users to identify themselves through digital signatures without revealing which public key they used. To this end, the study proposed a novel decentralised identity method showcased in a decentralised identifier-based architectural framework. Additionally, the investigation assesses the repercussions of employing this new method in the verification process, focusing specifically on privacy and security aspects. Although ring signatures are an established asset of cryptographic protocols, this paper seeks to leverage their capabilities in the evolving domain of digital identities.
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- 2024
32. Where the Really Hard Quadratic Assignment Problems Are: the QAP-SAT instances
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Verel, Sébastien, Thomson, Sarah, and Rifki, Omar
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Computer Science - Artificial Intelligence - Abstract
The Quadratic Assignment Problem (QAP) is one of the major domains in the field of evolutionary computation, and more widely in combinatorial optimization. This paper studies the phase transition of the QAP, which can be described as a dramatic change in the problem's computational complexity and satisfiability, within a narrow range of the problem parameters. To approach this phenomenon, we introduce a new QAP-SAT design of the initial problem based on submodularity to capture its difficulty with new features. This decomposition is studied experimentally using branch-and-bound and tabu search solvers. A phase transition parameter is then proposed. The critical parameter of phase transition satisfaction and that of the solving effort are shown to be highly correlated for tabu search, thus allowing the prediction of difficult instances.
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- 2024
33. Screening for Body Dysmorphic Disorder in Plastic Surgery Patients
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Thomson, David R., Thomson, Natasha E. V., and Southwick, Graeme
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- 2024
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34. Durable multimodal and holistic response for physiologic closed-loop spinal cord stimulation supported by objective evidence from the EVOKE double-blind randomized controlled trial.
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Kapural, Leonardo, Mekhail, Nagy, Costandi, Shrif, Gilmore, Christopher, Pope, Jason, Li, Sean, Hunter, Corey, Poree, Lawrence, Staats, Peter, Taylor, Rod, Eldabe, Sam, Kallewaard, Jan, Thomson, Simon, Petersen, Erika, Sayed, Dawood, Deer, Timothy, Antony, Ajay, Budwany, Ryan, Leitner, Angela, Soliday, Nicole, Duarte, Rui, and Levy, Robert
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chronic pain ,spinal cord stimulation ,treatment outcome ,Humans ,Chronic Pain ,Spinal Cord Stimulation ,Quality of Life ,Double-Blind Method ,Pain Measurement ,Treatment Outcome ,Spinal Cord - Abstract
INTRODUCTION: Chronic pain patients may experience impairments in multiple health-related domains. The design and interpretation of clinical trials of chronic pain interventions, however, remains primarily focused on treatment effects on pain intensity. This study investigates a novel, multidimensional holistic treatment response to evoked compound action potential-controlled closed-loop versus open-loop spinal cord stimulation as well as the degree of neural activation that produced that treatment response. METHODS: Outcome data for pain intensity, physical function, health-related quality of life, sleep quality and emotional function were derived from individual patient level data from the EVOKE multicenter, participant, investigator, and outcome assessor-blinded, parallel-arm randomized controlled trial with 24 month follow-up. Evaluation of holistic treatment response considered whether the baseline score was worse than normative values and whether minimal clinical important differences were reached in each of the domains that were impaired at baseline. A cumulative responder score was calculated to reflect the total minimal clinical important differences accumulated across all domains. Objective neurophysiological data, including spinal cord activation were measured. RESULTS: Patients were randomized to closed-loop (n=67) or open-loop (n=67). A greater proportion of patients with closed-loop spinal cord stimulation (49.3% vs 26.9%) were holistic responders at 24-month follow-up, with at least one minimal clinical important difference in all impaired domains (absolute risk difference: 22.4%, 95% CI 6.4% to 38.4%, p=0.012). The cumulative responder score was significantly greater for closed-loop patients at all time points and resulted in the achievement of more than three additional minimal clinical important differences at 24-month follow-up (mean difference 3.4, 95% CI 1.3 to 5.5, p=0.002). Neural activation was three times more accurate in closed-loop spinal cord stimulation (p
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- 2024
35. Modelling Political Coalition Negotiations Using LLM-based Agents
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Moghimifar, Farhad, Li, Yuan-Fang, Thomson, Robert, and Haffari, Gholamreza
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Computer Science - Computation and Language - Abstract
Coalition negotiations are a cornerstone of parliamentary democracies, characterised by complex interactions and strategic communications among political parties. Despite its significance, the modelling of these negotiations has remained unexplored with the domain of Natural Language Processing (NLP), mostly due to lack of proper data. In this paper, we introduce coalition negotiations as a novel NLP task, and model it as a negotiation between large language model-based agents. We introduce a multilingual dataset, POLCA, comprising manifestos of European political parties and coalition agreements over a number of elections in these countries. This dataset addresses the challenge of the current scope limitations in political negotiation modelling by providing a diverse, real-world basis for simulation. Additionally, we propose a hierarchical Markov decision process designed to simulate the process of coalition negotiation between political parties and predict the outcomes. We evaluate the performance of state-of-the-art large language models (LLMs) as agents in handling coalition negotiations, offering insights into their capabilities and paving the way for future advancements in political modelling.
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- 2024
36. Understanding fitness landscapes in morpho-evolution via local optima networks
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Thomson, Sarah L., Goff, Léni K. Le, Hart, Emma, and Buchanan, Edgar
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Computer Science - Artificial Intelligence - Abstract
Morpho-evolution (ME) refers to the simultaneous optimisation of a robot's design and controller to maximise performance given a task and environment. Many genetic encodings have been proposed which are capable of representing design and control. Previous research has provided empirical comparisons between encodings in terms of their performance with respect to an objective function and the diversity of designs that are evaluated, however there has been no attempt to explain the observed findings. We address this by applying Local Optima Network (LON) analysis to investigate the structure of the fitness landscapes induced by three different encodings when evolving a robot for a locomotion task, shedding new light on the ease by which different fitness landscapes can be traversed by a search process. This is the first time LON analysis has been applied in the field of ME despite its popularity in combinatorial optimisation domains; the findings will facilitate design of new algorithms or operators that are customised to ME landscapes in the future., Comment: Submitted to GECCO-2024
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- 2024
37. The VLBA CANDELS GOODS-North Survey. II -- Wide-field source catalogue comparison between the VLBA, EVN, e-MERLIN and VLA
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Njeri, Ann, Deane, Roger. P., Radcliffe, J. F., Beswick, R. J., Thomson, A. P., Muxlow, T. W. B., Garrett, M. A., and Harrison, C. M.
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Astrophysics - Astrophysics of Galaxies - Abstract
Deep radio surveys of extragalactic legacy fields trace a large range of spatial and brightness temperature sensitivity scales, and therefore have differing biases to radio-emitting physical components within galaxies. This is particularly true of radio surveys performed at less than 1 arcsec angular resolutions, and so robust comparisons are necessary to better understand the biases present in each survey. We present a multi-resolution and multi-wavelength analysis of the sources detected in a new Very Long Baseline Array (VLBA) survey of the CANDELS GOODS-North field. For the 24 VLBA-selected sources described in Paper I, we augment the VLBA data with EVN data, ~0.1-1 arcsecond angular resolution data provided by VLA and e-MERLIN. This sample includes new AGN detected in this field, thanks to a new source extraction technique that adopts priors from ancillary multi-wavelength data. The high brightness temperatures of these sources (Tb > 10^6 K) confirm AGN cores, that would often be missed or ambiguous in lower-resolution radio data of the same sources. Furthermore, only 15 sources are identified as 'radiative' AGN based on available X-ray and infrared constraints. By combining VLA and VLBA measurements, we find evidence that the majority of the extended radio emission is also AGN dominated, with only 3 sources with evidence for extended potentially star-formation dominated radio emission. We demonstrate the importance of wide-field multi-resolution (arcsecond-milliarcsecond) coverage of the faint radio source population, for a complete picture of the multi-scale processes within these galaxies., Comment: 20 pages, 11 figures
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- 2024
38. AI in Energy Digital Twining: A Reinforcement Learning-based Adaptive Digital Twin Model for Green Cities
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Cakir, Lal Verda, Duran, Kubra, Thomson, Craig, Broadbent, Matthew, and Canberk, Berk
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Computer Science - Machine Learning - Abstract
Digital Twins (DT) have become crucial to achieve sustainable and effective smart urban solutions. However, current DT modelling techniques cannot support the dynamicity of these smart city environments. This is caused by the lack of right-time data capturing in traditional approaches, resulting in inaccurate modelling and high resource and energy consumption challenges. To fill this gap, we explore spatiotemporal graphs and propose the Reinforcement Learning-based Adaptive Twining (RL-AT) mechanism with Deep Q Networks (DQN). By doing so, our study contributes to advancing Green Cities and showcases tangible benefits in accuracy, synchronisation, resource optimization, and energy efficiency. As a result, we note the spatiotemporal graphs are able to offer a consistent accuracy and 55% higher querying performance when implemented using graph databases. In addition, our model demonstrates right-time data capturing with 20% lower overhead and 25% lower energy consumption.
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- 2024
39. Force Propagation in Active Cytoskeletal Networks
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Liu, Shichen, Pan, Rosalind Wenshan, Lee, Heun Jin, Shadkhoo, Shahriar, Yang, Fan, Li, Chunhe, Qu, Zijie, Phillips, Rob, and Thomson, Matt
- Subjects
Condensed Matter - Soft Condensed Matter - Abstract
In biological systems, molecular-scale forces and motions are pivotal for enabling processes like motility, shape change, and replication. These forces and motions are organized, amplified, and transmitted across macroscopic scales by active materials such as the cytoskeleton, which drives micron-scale cellular movement and re-organization. Despite the integral role of active materials, understanding how molecular-scale interactions alter macroscopic structure and force propagation remains elusive. This knowledge gap presents challenges to the harnessing and regulation of such dynamics across diverse length scales. Here, we demonstrate how mediating the bundling of microtubules can shift active matter between a global force-transmitting phase and a local force-dissipating phase. A fivefold increase in microtubule effective length results in the transition from local to global phase with a hundredfold increase in velocity autocorrelation. Through theory and simulation, we identify signatures of a percolation-driven transition between the two phases. This provides evidence for how force propagation can be generated when local molecular interactions reach a sufficient length scale. We show that force propagation in the active matter system enables material transport. Consequently, we demonstrate that the global phase is capable of facilitating millimeter-scale human cell transport and manipulation, as well as powering the movement of aqueous droplets. These findings underscore the potential for designing active materials capable of force organization and transmission. Our results lay the foundation for further exploration into the organization and propagation of forces/stresses in biological systems, thereby paving the way for the engineering of active materials in synthetic biology and soft robotics., Comment: 15 pages, 4 figrues
- Published
- 2024
40. Hubble Asteroid Hunter III. Physical properties of newly found asteroids
- Author
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García-Martín, Pablo, Kruk, Sandor, Popescu, Marcel, Merín, Bruno, Stapelfeldt, Karl R., Evans, Robin W., Carry, Benoit, and Thomson, Ross
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Astrophysics - Earth and Planetary Astrophysics - Abstract
Determining the size distribution of asteroids is key for understanding the collisional history and evolution of the inner Solar System. We aim at improving our knowledge on the size distribution of small asteroids in the Main Belt by determining the parallaxes of newly detected asteroids in the Hubble Space Telescope (HST) Archive and hence their absolute magnitudes and sizes. Asteroids appear as curved trails in HST images due to the parallax induced by the fast orbital motion of the spacecraft. The parallax effect can be computed to obtain the distance to the asteroids by fitting simulated trajectories to the observed trails. Using distance, we can obtain the object's absolute magnitude and size estimation assuming an albedo value, along with some boundaries for its orbital parameters. In this work we analyse a set of 632 serendipitously imaged asteroids found in the ESA HST Archive. An object-detection machine learning algorithm was used to perform this task during previous work. Our raw data consists of 1,031 asteroids trails from unknown objects (not matching any entries in the MPC database). We also found 670 trails from known objects (objects featuring matching entries in the MPC). After an accuracy assessment and filtering process, our analysed HST set consists of 454 unknown objects and 178 known objects. We obtain a sample dominated by potential Main Belt objects featuring absolute magnitudes (H) mostly between 15 and 22 mag. The absolute magnitude cumulative distribution confirms the previously reported slope change for 15 < H < 18, from 0.56 to 0.26, maintained in our case down to absolute magnitudes around H = 20, hence expanding the previous results by approximately two magnitudes. HST archival observations can be used as an asteroid survey since the telescope pointings are statistically randomly oriented in the sky and they cover long periods of time., Comment: Accepted for publication in A&A. 10 pages, 2 tables, 17 figures
- Published
- 2024
41. Neural BSSRDF: Object Appearance Representation Including Heterogeneous Subsurface Scattering
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TG, Thomson, Frisvad, Jeppe Revall, Ramamoorthi, Ravi, and Jensen, Henrik Wann
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Computer Science - Graphics - Abstract
Monte Carlo rendering of translucent objects with heterogeneous scattering properties is often expensive both in terms of memory and computation. If we do path tracing and use a high dynamic range lighting environment, the rendering becomes computationally heavy. We propose a compact and efficient neural method for representing and rendering the appearance of heterogeneous translucent objects. The neural representation function resembles a bidirectional scattering-surface reflectance distribution function (BSSRDF). However, conventional BSSRDF models assume a planar half-space medium and only surface variation of the material, which is often not a good representation of the appearance of real-world objects. Our method represents the BSSRDF of a full object taking its geometry and heterogeneities into account. This is similar to a neural radiance field, but our representation works for an arbitrary distant lighting environment. In a sense, we present a version of neural precomputed radiance transfer that captures all-frequency relighting of heterogeneous translucent objects. We use a multi-layer perceptron (MLP) with skip connections to represent the appearance of an object as a function of spatial position, direction of observation, and direction of incidence. The latter is considered a directional light incident across the entire non-self-shadowed part of the object. We demonstrate the ability of our method to store highly complex materials while having high accuracy when comparing to reference images of the represented object in unseen lighting environments. As compared with path tracing of a heterogeneous light scattering volume behind a refractive interface, our method more easily enables importance sampling of the directions of incidence and can be integrated into existing rendering frameworks while achieving interactive frame rates.
- Published
- 2023
42. Away days
- Author
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THOMSON, ANDREW
- Published
- 2024
43. The Trichoptera of Panama XXVII. The third benchmark-a waypoint to the future
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Armitage, Brian J., Harris, Steven C., Ríos González, Tomás A., Aguirre, Yusseff P., Blahnik, Roger J., Thomson, Robin E., and Arefina-Armitage, Tatiana I.
- Published
- 2024
- Full Text
- View/download PDF
44. Identifying studies examining the validity of instruments for use as outcome measures in child and adolescent forensic mental health services: a systematic review
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Walker, Graham, Wilson, Naomi, Allely, Clare S., Thomson, Allan, Smith, Helen, and Lang, Jason
- Published
- 2024
- Full Text
- View/download PDF
45. A shifting role of thalamocortical connectivity in the emergence of cortical functional organization
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Park, Shinwon, Haak, Koen V., Oldham, Stuart, Cho, Hanbyul, Byeon, Kyoungseob, Park, Bo-yong, Thomson, Phoebe, Chen, Haitao, Gao, Wei, Xu, Ting, Valk, Sofie, Milham, Michael P., Bernhardt, Boris, Di Martino, Adriana, and Hong, Seok-Jun
- Published
- 2024
- Full Text
- View/download PDF
46. First-in-man study of the PSMA Minibody IR800-IAB2M for molecularly targeted intraoperative fluorescence guidance during radical prostatectomy
- Author
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Hamdy, Freddie C., Lamb, Alastair D., Tullis, Iain D. C., Verrill, Clare, Rombach, Ines, Rao, Srinivasa R., Colling, Richard, Barber, Paul R., Volpi, Davide, Barbera-Martin, Luis, Lopez, J Francisco, Omer, Altan, Hewitt, Aimi, Lovell, Shelagh, Niederer, Jane, Lambert, Adam, Snoeck, Joke, Thomson, Claire, Leslie, Tom, Bryant, Richard J., Mascioni, Alessandro, Jia, Fang, Torgov, Michael, Wilson, Ian, Gudas, Jean, Wu, Anna M., Olafsen, Tove, and Vojnovic, Borivoj
- Published
- 2024
- Full Text
- View/download PDF
47. Partial-implementation invariance and claims problems
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Dietzenbacher, Bas, Tamura, Yuki, and Thomson, William
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- 2024
- Full Text
- View/download PDF
48. Evaluating the impact of vocabulary instruction on oral vocabulary, phonemic awareness and nonword reading
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Brooks, Rose, Warmington, Meesha, and Thomson, Jenny
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- 2024
- Full Text
- View/download PDF
49. Meso—Cenozoic Exhumation of the Altai-Sayan Region: Constrained by Available Low-Temperature Thermochronology
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Wang, Yamei, Yin, Jiyuan, Thomson, Stuart N., Chen, Wen, Cai, Keda, Dong, Zengchan, and Tan, Fucheng
- Published
- 2024
- Full Text
- View/download PDF
50. Why bother with arts education in schools?
- Author
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Thomson, Pat
- Published
- 2024
- Full Text
- View/download PDF
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