4,167 results on '"Atkinson, David"'
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2. Cerebral Squalls
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Atkinson, David
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- 2024
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3. Above and Beyond: Fashioning an Accessible Health Service for Aboriginal Youth in Remote Western Australia
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Warwick, Susannah, LeLievre, Matthew, Seear, Kimberley, Atkinson, David, and Marley, Julia V.
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- 2021
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4. Unsettled Law: Time to Generate New Approaches?
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Atkinson, David and Morrison, Jacob
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Computer Science - Computers and Society - Abstract
We identify several important and unsettled legal questions with profound ethical and societal implications arising from generative artificial intelligence (GenAI), focusing on its distinguishable characteristics from traditional software and earlier AI models. Our key contribution is formally identifying the issues that are unique to GenAI so scholars, practitioners, and others can conduct more useful investigations and discussions. While established legal frameworks, many originating from the pre-digital era, are currently employed in GenAI litigation, we question their adequacy. We argue that GenAI's unique attributes, including its general-purpose nature, reliance on massive datasets, and potential for both pervasive societal benefits and harms, necessitate a re-evaluation of existing legal paradigms. We explore potential areas for legal and regulatory adaptation, highlighting key issues around copyright, privacy, torts, contract law, criminal law, property law, and the First Amendment. Through an exploration of these multifaceted legal challenges, we aim to stimulate discourse and policy considerations surrounding GenAI, emphasizing a proactive approach to legal and ethical frameworks. While we refrain from advocating specific legal changes, we underscore the need for policymakers to carefully consider the issues raised. We conclude by summarizing key questions across these areas of law in a helpful table for easy reference., Comment: 14 pages
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- 2024
5. Token Erasure as a Footprint of Implicit Vocabulary Items in LLMs
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Feucht, Sheridan, Atkinson, David, Wallace, Byron, and Bau, David
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Computer Science - Computation and Language ,Computer Science - Machine Learning ,I.2.7 - Abstract
LLMs process text as sequences of tokens that roughly correspond to words, where less common words are represented by multiple tokens. However, individual tokens are often semantically unrelated to the meanings of the words/concepts they comprise. For example, Llama-2-7b's tokenizer splits the word "northeastern" into the tokens ['_n', 'ort', 'he', 'astern'], none of which correspond to semantically meaningful units like "north" or "east." Similarly, the overall meanings of named entities like "Neil Young" and multi-word expressions like "break a leg" cannot be directly inferred from their constituent tokens. Mechanistically, how do LLMs convert such arbitrary groups of tokens into useful higher-level representations? In this work, we find that last token representations of named entities and multi-token words exhibit a pronounced "erasure" effect, where information about previous and current tokens is rapidly forgotten in early layers. Using this observation, we propose a method to "read out" the implicit vocabulary of an autoregressive LLM by examining differences in token representations across layers, and present results of this method for Llama-2-7b and Llama-3-8B. To our knowledge, this is the first attempt to probe the implicit vocabulary of an LLM., Comment: 13 pages, 14 figures. Code and data at https://footprints.baulab.info/
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- 2024
6. Standing Type in Dicey/Marshall Issues of The Berkshire Tragedy
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Atkinson, David
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- 2020
7. Recipes for forming a carbon-rich giant planet
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Mousis, Olivier, Cavalié, Thibault, Lunine, Jonathan I., Mandt, Kathleen E., Hueso, Ricardo, Aguichine, Artyom, Schneeberger, Antoine, Couzinou, Tom Benest, Atkinson, David H., Hue, Vincent, Hofstadter, Mark, and Srisuchinwong, Udomlerd
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Astrophysics - Earth and Planetary Astrophysics - Abstract
The exploration of carbon-to-oxygen ratios has yielded intriguing insights into the composition of close-in giant exoplanets, giving rise to a distinct classification: carbon-rich planets, characterized by a carbon-to-oxygen ratio $\ge$ 1 in their atmospheres, as opposed to giant planets exhibiting carbon-to-oxygen ratios close to the protosolar value. In contrast, despite numerous space missions dispatched to the outer solar system and the proximity of Jupiter, Saturn, Uranus, and Neptune, our understanding of the carbon-to-oxygen ratio in these giants remains notably deficient. Determining this ratio is crucial as it serves as a marker linking a planet's volatile composition directly to its formation region within the disk. This article provides an overview of the current understanding of the carbon-to-oxygen ratio in the four gas giants of our solar system and explores why there is yet no definitive dismissal of the possibility that Jupiter, Saturn, Uranus, or Neptune could be considered carbon-rich planets. Additionally, we delve into the three primary formation scenarios proposed in existing literature to account for a bulk carbon-to-oxygen ratio $\ge$ 1 in a giant planet. A significant challenge lies in accurately inferring the bulk carbon-to-oxygen ratio of our solar system's gas giants. Retrieval methods involve integrating in situ measurements from entry probes equipped with mass spectrometers and remote sensing observations conducted at microwave wavelengths by orbiters. However, these methods fall short of fully discerning the deep carbon-to-oxygen abundance in the gas giants due to their limited probing depth, typically within the 10-100 bar range., Comment: Space Science Reviews, in press
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- 2024
8. The global landscape of academic guidelines for generative AI and Large Language Models
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Jiao, Junfeng, Afroogh, Saleh, Chen, Kevin, Atkinson, David, and Dhurandhar, Amit
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Computer Science - Computers and Society ,Computer Science - Artificial Intelligence ,Computer Science - Computation and Language - Abstract
The integration of Generative Artificial Intelligence (GAI) and Large Language Models (LLMs) in academia has spurred a global discourse on their potential pedagogical benefits and ethical considerations. Positive reactions highlight some potential, such as collaborative creativity, increased access to education, and empowerment of trainers and trainees. However, negative reactions raise concerns about ethical complexities, balancing innovation and academic integrity, unequal access, and misinformation risks. Through a systematic survey and text-mining-based analysis of global and national directives, insights from independent research, and eighty university-level guidelines, this study provides a nuanced understanding of the opportunities and challenges posed by GAI and LLMs in education. It emphasizes the importance of balanced approaches that harness the benefits of these technologies while addressing ethical considerations and ensuring equitable access and educational outcomes. The paper concludes with recommendations for fostering responsible innovation and ethical practices to guide the integration of GAI and LLMs in academia.
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- 2024
9. A Legal Risk Taxonomy for Generative Artificial Intelligence
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Atkinson, David and Morrison, Jacob
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Computer Science - Computers and Society - Abstract
For the first time, this paper presents a taxonomy of legal risks associated with generative AI (GenAI) by breaking down complex legal concepts to provide a common understanding of potential legal challenges for developing and deploying GenAI models. The methodology is based on (1) examining the legal claims that have been filed in existing lawsuits and (2) evaluating the reasonably foreseeable legal claims that may be filed in future lawsuits. First, we identified 29 lawsuits against prominent GenAI entities and tallied the claims of each lawsuit. From there, we identified seven claims that are cited at least four times across these lawsuits as the most likely claims for future GenAI lawsuits. For each of these seven claims, we describe the elements of the claim (what the plaintiff must prove to prevail) and provide an example of how it may apply to GenAI. Next, we identified 30 other potential claims that we consider to be more speculative, because they have been included in fewer than four lawsuits or have yet to be filed. We further separated those 30 claims into 19 that are most likely to be made in relation to pre-deployment of GenAI models and 11 that are more likely to be made in connection with post-deployment of GenAI models since the legal risks will vary between entities that create versus deploy them. For each of these claims, we describe the elements of the claim and the potential remedies that plaintiffs may seek to help entities determine their legal risks in developing or deploying GenAI. Lastly, we close the paper by noting the novelty of GenAI technology and propose some applications for the paper's taxonomy in driving further research., Comment: 29 pages, 2 tables, preprint
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- 2024
10. Locating and Editing Factual Associations in Mamba
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Sharma, Arnab Sen, Atkinson, David, and Bau, David
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Computer Science - Computation and Language - Abstract
We investigate the mechanisms of factual recall in the Mamba state space model. Our work is inspired by previous findings in autoregressive transformer language models suggesting that their knowledge recall is localized to particular modules at specific token locations; we therefore ask whether factual recall in Mamba can be similarly localized. To investigate this, we conduct four lines of experiments on Mamba. First, we apply causal tracing or interchange interventions to localize key components inside Mamba that are responsible for recalling facts, revealing that specific components within middle layers show strong causal effects at the last token of the subject, while the causal effect of intervening on later layers is most pronounced at the last token of the prompt, matching previous findings on autoregressive transformers. Second, we show that rank-one model editing methods can successfully insert facts at specific locations, again resembling findings on transformer LMs. Third, we examine the linearity of Mamba's representations of factual relations. Finally we adapt attention-knockout techniques to Mamba in order to dissect information flow during factual recall. We compare Mamba directly to a similar-sized autoregressive transformer LM and conclude that despite significant differences in architectural approach, when it comes to factual recall, the two architectures share many similarities., Comment: 18 pages, COLM-2024
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- 2024
11. Algorithmic progress in language models
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Ho, Anson, Besiroglu, Tamay, Erdil, Ege, Owen, David, Rahman, Robi, Guo, Zifan Carl, Atkinson, David, Thompson, Neil, and Sevilla, Jaime
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
We investigate the rate at which algorithms for pre-training language models have improved since the advent of deep learning. Using a dataset of over 200 language model evaluations on Wikitext and Penn Treebank spanning 2012-2023, we find that the compute required to reach a set performance threshold has halved approximately every 8 months, with a 95% confidence interval of around 5 to 14 months, substantially faster than hardware gains per Moore's Law. We estimate augmented scaling laws, which enable us to quantify algorithmic progress and determine the relative contributions of scaling models versus innovations in training algorithms. Despite the rapid pace of algorithmic progress and the development of new architectures such as the transformer, our analysis reveals that the increase in compute made an even larger contribution to overall performance improvements over this time period. Though limited by noisy benchmark data, our analysis quantifies the rapid progress in language modeling, shedding light on the relative contributions from compute and algorithms.
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- 2024
12. Young Aboriginal People's Perspective on Access to Health Care in Remote Australia: Hearing Their Voices
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Warwick, Susannah, Atkinson, David, Kitaura, Therese, LeLievre, Matthew, and Marley, Julia V
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- 2019
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13. OLMo: Accelerating the Science of Language Models
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Groeneveld, Dirk, Beltagy, Iz, Walsh, Pete, Bhagia, Akshita, Kinney, Rodney, Tafjord, Oyvind, Jha, Ananya Harsh, Ivison, Hamish, Magnusson, Ian, Wang, Yizhong, Arora, Shane, Atkinson, David, Authur, Russell, Chandu, Khyathi Raghavi, Cohan, Arman, Dumas, Jennifer, Elazar, Yanai, Gu, Yuling, Hessel, Jack, Khot, Tushar, Merrill, William, Morrison, Jacob, Muennighoff, Niklas, Naik, Aakanksha, Nam, Crystal, Peters, Matthew E., Pyatkin, Valentina, Ravichander, Abhilasha, Schwenk, Dustin, Shah, Saurabh, Smith, Will, Strubell, Emma, Subramani, Nishant, Wortsman, Mitchell, Dasigi, Pradeep, Lambert, Nathan, Richardson, Kyle, Zettlemoyer, Luke, Dodge, Jesse, Lo, Kyle, Soldaini, Luca, Smith, Noah A., and Hajishirzi, Hannaneh
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Computer Science - Computation and Language - Abstract
Language models (LMs) have become ubiquitous in both NLP research and in commercial product offerings. As their commercial importance has surged, the most powerful models have become closed off, gated behind proprietary interfaces, with important details of their training data, architectures, and development undisclosed. Given the importance of these details in scientifically studying these models, including their biases and potential risks, we believe it is essential for the research community to have access to powerful, truly open LMs. To this end, we have built OLMo, a competitive, truly Open Language Model, to enable the scientific study of language models. Unlike most prior efforts that have only released model weights and inference code, we release OLMo alongside open training data and training and evaluation code. We hope this release will empower the open research community and inspire a new wave of innovation.
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- 2024
14. Dolma: an Open Corpus of Three Trillion Tokens for Language Model Pretraining Research
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Soldaini, Luca, Kinney, Rodney, Bhagia, Akshita, Schwenk, Dustin, Atkinson, David, Authur, Russell, Bogin, Ben, Chandu, Khyathi, Dumas, Jennifer, Elazar, Yanai, Hofmann, Valentin, Jha, Ananya Harsh, Kumar, Sachin, Lucy, Li, Lyu, Xinxi, Lambert, Nathan, Magnusson, Ian, Morrison, Jacob, Muennighoff, Niklas, Naik, Aakanksha, Nam, Crystal, Peters, Matthew E., Ravichander, Abhilasha, Richardson, Kyle, Shen, Zejiang, Strubell, Emma, Subramani, Nishant, Tafjord, Oyvind, Walsh, Pete, Zettlemoyer, Luke, Smith, Noah A., Hajishirzi, Hannaneh, Beltagy, Iz, Groeneveld, Dirk, Dodge, Jesse, and Lo, Kyle
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Computer Science - Computation and Language - Abstract
Information about pretraining corpora used to train the current best-performing language models is seldom discussed: commercial models rarely detail their data, and even open models are often released without accompanying training data or recipes to reproduce them. As a result, it is challenging to conduct and advance scientific research on language modeling, such as understanding how training data impacts model capabilities and limitations. To facilitate scientific research on language model pretraining, we curate and release Dolma, a three-trillion-token English corpus, built from a diverse mixture of web content, scientific papers, code, public-domain books, social media, and encyclopedic materials. We extensively document Dolma, including its design principles, details about its construction, and a summary of its contents. We present analyses and experimental results on intermediate states of Dolma to share what we have learned about important data curation practices. Finally, we open-source our data curation toolkit to enable reproduction of our work as well as support further research in large-scale data curation., Comment: Accepted at ACL 2024; Dataset: https://hf.co/datasets/allenai/dolma; Code: https://github.com/allenai/dolma
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- 2024
15. Testing Language Model Agents Safely in the Wild
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Naihin, Silen, Atkinson, David, Green, Marc, Hamadi, Merwane, Swift, Craig, Schonholtz, Douglas, Kalai, Adam Tauman, and Bau, David
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Computer Science - Artificial Intelligence - Abstract
A prerequisite for safe autonomy-in-the-wild is safe testing-in-the-wild. Yet real-world autonomous tests face several unique safety challenges, both due to the possibility of causing harm during a test, as well as the risk of encountering new unsafe agent behavior through interactions with real-world and potentially malicious actors. We propose a framework for conducting safe autonomous agent tests on the open internet: agent actions are audited by a context-sensitive monitor that enforces a stringent safety boundary to stop an unsafe test, with suspect behavior ranked and logged to be examined by humans. We design a basic safety monitor (AgentMonitor) that is flexible enough to monitor existing LLM agents, and, using an adversarial simulated agent, we measure its ability to identify and stop unsafe situations. Then we apply the AgentMonitor on a battery of real-world tests of AutoGPT, and we identify several limitations and challenges that will face the creation of safe in-the-wild tests as autonomous agents grow more capable.
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- 2023
16. ssVERDICT: Self-Supervised VERDICT-MRI for Enhanced Prostate Tumour Characterisation
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Sen, Snigdha, Singh, Saurabh, Pye, Hayley, Moore, Caroline M., Whitaker, Hayley, Punwani, Shonit, Atkinson, David, Panagiotaki, Eleftheria, and Slator, Paddy J.
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Machine Learning - Abstract
Purpose: Demonstrating and assessing self-supervised machine learning fitting of the VERDICT (Vascular, Extracellular and Restricted DIffusion for Cytometry in Tumours) model for prostate. Methods: We derive a self-supervised neural network for fitting VERDICT (ssVERDICT) that estimates parameter maps without training data. We compare the performance of ssVERDICT to two established baseline methods for fitting diffusion MRI models: conventional nonlinear least squares (NLLS) and supervised deep learning. We do this quantitatively on simulated data, by comparing the Pearson's correlation coefficient, mean-squared error (MSE), bias, and variance with respect to the simulated ground truth. We also calculate in vivo parameter maps on a cohort of 20 prostate cancer patients and compare the methods' performance in discriminating benign from cancerous tissue via Wilcoxon's signed-rank test. Results: In simulations, ssVERDICT outperforms the baseline methods (NLLS and supervised DL) in estimating all the parameters from the VERDICT prostate model in terms of Pearson's correlation coefficient, bias, and MSE. In vivo, ssVERDICT shows stronger lesion conspicuity across all parameter maps, and improves discrimination between benign and cancerous tissue over the baseline methods. Conclusion: ssVERDICT significantly outperforms state-of-the-art methods for VERDICT model fitting, and shows for the first time, fitting of a complex three-compartment biophysical model with machine learning without the requirement of explicit training labels., Comment: 12 pages, 5 figures. Submitted to Magnetic Resonance in Medicine
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- 2023
17. Combiner and HyperCombiner Networks: Rules to Combine Multimodality MR Images for Prostate Cancer Localisation
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Yan, Wen, Chiu, Bernard, Shen, Ziyi, Yang, Qianye, Syer, Tom, Min, Zhe, Punwani, Shonit, Emberton, Mark, Atkinson, David, Barratt, Dean C., and Hu, Yipeng
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,68T07 - Abstract
One of the distinct characteristics in radiologists' reading of multiparametric prostate MR scans, using reporting systems such as PI-RADS v2.1, is to score individual types of MR modalities, T2-weighted, diffusion-weighted, and dynamic contrast-enhanced, and then combine these image-modality-specific scores using standardised decision rules to predict the likelihood of clinically significant cancer. This work aims to demonstrate that it is feasible for low-dimensional parametric models to model such decision rules in the proposed Combiner networks, without compromising the accuracy of predicting radiologic labels: First, it is shown that either a linear mixture model or a nonlinear stacking model is sufficient to model PI-RADS decision rules for localising prostate cancer. Second, parameters of these (generalised) linear models are proposed as hyperparameters, to weigh multiple networks that independently represent individual image modalities in the Combiner network training, as opposed to end-to-end modality ensemble. A HyperCombiner network is developed to train a single image segmentation network that can be conditioned on these hyperparameters during inference, for much improved efficiency. Experimental results based on data from 850 patients, for the application of automating radiologist labelling multi-parametric MR, compare the proposed combiner networks with other commonly-adopted end-to-end networks. Using the added advantages of obtaining and interpreting the modality combining rules, in terms of the linear weights or odds-ratios on individual image modalities, three clinical applications are presented for prostate cancer segmentation, including modality availability assessment, importance quantification and rule discovery., Comment: 30 pages, 6 figures
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- 2023
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18. Fundamental Science Achieved with a Single Probe in Each Giant Planet Atmosphere
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Mandt, Kathleen E., Simon, Amy A., Mousis, Olivier, Atkinson, David H., and Hofstadter, Mark
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- 2024
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19. Planetary Exploration Horizon 2061 Report Chapter 5: Enabling technologies for planetary exploration
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Grande, Manuel, Guo, Linli, Blanc, Michel, Makaya, Advenit, Asmar, Sami, Atkinson, David, Bourdon, Anne, Chabert, Pascal, Chien, Steve, Day, John, Fairen, Alberto G., Freeman, Anthony, Genova, Antonio, Herique, Alain, Kofman, Wlodek, Lazio, Joseph, Mousis, Olivier, Ori, Gian Gabriele, Parro, Victor, Preston, Robert, Rodriguez-Manfredi, Jose A, Sterken, Veerle, Stephenson, Keith, Hook, Joshua Vander, Waite, Hunter, and Zine, Sonia
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Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Earth and Planetary Astrophysics ,Physics - Geophysics - Abstract
The main objective of this chapter is to present an overview of the different areas of key technologies that will be needed to fly the technically most challenging of the representative missions identified in chapter 4 (the Pillar 2 Horizon 2061 report). It starts with a description of the future scientific instruments which will address the key questions of Horizon 2061 described in chapter 3 (the Pillar 1 Horizon 2061 report) and the new technologies that the next generations of space instruments will require (section 2). From there, the chapter follows the line of logical development and implementation of a planetary mission: section 3 describes some of the novel mission architectures that will be needed and how they will articulate interplanetary spacecraft and science platforms; section 4 summarizes the system-level technologies needed: power, propulsion, navigation, communication, advanced autonomy on board planetary spacecraft; section 5 describes the diversity of specialized science platforms that will be needed to survive, operate and return scientific data from the extreme environments that future missions will target; section 6 describes the new technology developments that will be needed for long-duration missions and semi-permanent settlements; finally, section 7 attempts to anticipate on the disruptive technologies that should emerge and progressively prevail in the decades to come to meet the long-term needs of future planetary missions., Comment: 100 pages, 23 figures, Horizon 2061 is a science-driven, foresight exercise, for future scientific investigations
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- 2023
20. The James Madison Carpenter Collection of Traditional Song and Drama
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Bishop, Julia C., Atkinson, David, and Walser, Robert Young
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- 2014
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21. Child’s Unfinished Masterpiece: The English and Scottish Popular Ballads (review)
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Atkinson, David
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- 2012
22. The English Revival Canon: Child Ballads and the Invention of Tradition
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Atkinson, David, 1955 Feb. 23-
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- 2001
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23. Where is VALDO? VAscular Lesions Detection and segmentatiOn challenge at MICCAI 2021
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Sudre, Carole H., Van Wijnen, Kimberlin, Dubost, Florian, Adams, Hieab, Atkinson, David, Barkhof, Frederik, Birhanu, Mahlet A., Bron, Esther E., Camarasa, Robin, Chaturvedi, Nish, Chen, Yuan, Chen, Zihao, Chen, Shuai, Dou, Qi, Evans, Tavia, Ezhov, Ivan, Gao, Haojun, Sanguesa, Marta Girones, Gispert, Juan Domingo, Anson, Beatriz Gomez, Hughes, Alun D., Ikram, M. Arfan, Ingala, Silvia, Jaeger, H. Rolf, Kofler, Florian, Kuijf, Hugo J., Kutnar, Denis, Lee, Minho, Li, Bo, Lorenzini, Luigi, Menze, Bjoern, Molinuevo, Jose Luis, Pan, Yiwei, Puybareau, Elodie, Rehwald, Rafael, Su, Ruisheng, Shi, Pengcheng, Smith, Lorna, Tillin, Therese, Tochon, Guillaume, Urien, Helene, van der Velden, Bas H. M., van der Velpen, Isabelle F., Wiestler, Benedikt, Wolters, Frank J., Yilmaz, Pinar, de Groot, Marius, Vernooij, Meike W., and de Bruijne, Marleen
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence - Abstract
Imaging markers of cerebral small vessel disease provide valuable information on brain health, but their manual assessment is time-consuming and hampered by substantial intra- and interrater variability. Automated rating may benefit biomedical research, as well as clinical assessment, but diagnostic reliability of existing algorithms is unknown. Here, we present the results of the \textit{VAscular Lesions DetectiOn and Segmentation} (\textit{Where is VALDO?}) challenge that was run as a satellite event at the international conference on Medical Image Computing and Computer Aided Intervention (MICCAI) 2021. This challenge aimed to promote the development of methods for automated detection and segmentation of small and sparse imaging markers of cerebral small vessel disease, namely enlarged perivascular spaces (EPVS) (Task 1), cerebral microbleeds (Task 2) and lacunes of presumed vascular origin (Task 3) while leveraging weak and noisy labels. Overall, 12 teams participated in the challenge proposing solutions for one or more tasks (4 for Task 1 - EPVS, 9 for Task 2 - Microbleeds and 6 for Task 3 - Lacunes). Multi-cohort data was used in both training and evaluation. Results showed a large variability in performance both across teams and across tasks, with promising results notably for Task 1 - EPVS and Task 2 - Microbleeds and not practically useful results yet for Task 3 - Lacunes. It also highlighted the performance inconsistency across cases that may deter use at an individual level, while still proving useful at a population level.
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- 2022
24. Cross-Modality Image Registration using a Training-Time Privileged Third Modality
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Yang, Qianye, Atkinson, David, Fu, Yunguan, Syer, Tom, Yan, Wen, Punwani, Shonit, Clarkson, Matthew J., Barratt, Dean C., Vercauteren, Tom, and Hu, Yipeng
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Computer Science - Computer Vision and Pattern Recognition ,Electrical Engineering and Systems Science - Image and Video Processing - Abstract
In this work, we consider the task of pairwise cross-modality image registration, which may benefit from exploiting additional images available only at training time from an additional modality that is different to those being registered. As an example, we focus on aligning intra-subject multiparametric Magnetic Resonance (mpMR) images, between T2-weighted (T2w) scans and diffusion-weighted scans with high b-value (DWI$_{high-b}$). For the application of localising tumours in mpMR images, diffusion scans with zero b-value (DWI$_{b=0}$) are considered easier to register to T2w due to the availability of corresponding features. We propose a learning from privileged modality algorithm, using a training-only imaging modality DWI$_{b=0}$, to support the challenging multi-modality registration problems. We present experimental results based on 369 sets of 3D multiparametric MRI images from 356 prostate cancer patients and report, with statistical significance, a lowered median target registration error of 4.34 mm, when registering the holdout DWI$_{high-b}$ and T2w image pairs, compared with that of 7.96 mm before registration. Results also show that the proposed learning-based registration networks enabled efficient registration with comparable or better accuracy, compared with a classical iterative algorithm and other tested learning-based methods with/without the additional modality. These compared algorithms also failed to produce any significantly improved alignment between DWI$_{high-b}$ and T2w in this challenging application., Comment: Accepted by IEEE Transactions on Medical Imaging (TMI, 2022)
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- 2022
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25. Revealing the Mysteries of Venus: The DAVINCI Mission
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Garvin, James B., Getty, Stephanie A., Arney, Giada N., Johnson, Natasha M., Kohler, Erika, Schwer, Kenneth O., Sekerak, Michael, Bartels, Arlin, Saylor, Richard S., Elliott, Vincent E., Goodloe, Colby S., Garrison, Matthew B., Cottini, Valeria, Izenberg, Noam, Lorenz, Ralph, Malespin, Charles A., Ravine, Michael, Webster, Christopher R., Atkinson, David H., Aslam, Shahid, Atreya, Sushil, Bos, Brent J., Brinckerhoff, William B., Campbell, Bruce, Crisp, David, Filiberto, Justin R., Forget, Francois, Gilmore, Martha, Gorius, Nicolas, Grinspoon, David, Hofmann, Amy E., Kane, Stephen R., Kiefer, Walter, Lebonnois, Sebastien, Mahaffy, Paul R., Pavlov, Alexander, Trainer, Melissa, Zahnle, Kevin J., and Zolotov, Mikhail
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
The Deep Atmosphere Venus Investigation of Noble gases, Chemistry, and Imaging (DAVINCI) mission described herein has been selected for flight to Venus as part of the NASA Discovery Program. DAVINCI will be the first mission to Venus to incorporate science-driven flybys and an instrumented descent sphere into a unified architecture. The anticipated scientific outcome will be a new understanding of the atmosphere, surface, and evolutionary path of Venus as a possibly once-habitable planet and analog to hot terrestrial exoplanets. The primary mission design for DAVINCI as selected features a preferred launch in summer/fall 2029, two flybys in 2030, and descent sphere atmospheric entry by the end of 2031. The in situ atmospheric descent phase subsequently delivers definitive chemical and isotopic composition of the Venus atmosphere during a cloud-top to surface transect above Alpha Regio. These in situ investigations of the atmosphere and near infrared descent imaging of the surface will complement remote flyby observations of the dynamic atmosphere, cloud deck, and surface near infrared emissivity. The overall mission yield will be at least 60 Gbits (compressed) new data about the atmosphere and near surface, as well as first unique characterization of the deep atmosphere environment and chemistry, including trace gases, key stable isotopes, oxygen fugacity, constraints on local rock compositions, and topography of a tessera., Comment: 41 pages, 14 figures, accepted for publication in the Planetary Science Journal
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- 2022
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26. Strong carers, strong communities: A cluster randomised controlled trial to improve wellbeing of family carers of older people in remote Aboriginal communities
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LoGiudice, Dina, Josif, Cathryn, Malay, Roslyn, Hyde, Zoe, Haswell, Melissa R, Lindeman, Melissa, Etherton-Beer, Christopher, Atkinson, David, Bessarab, Dawn, Flicker, Leon, and Smith, Kate
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- 2021
27. Parent perceptions of minimally invasive dental treatment of Australian Aboriginal pre-school children in rural and remote communities
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Piggott, Susan, Carter, Sheryl, Forrest, Helen, Atkinson, David, Mackean, Tamara, McPhee, Rob, and Arrow, Peter
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- 2021
28. CUBES Phase A design overview -- The Cassegrain U-Band Efficient Spectrograph for the Very Large Telescope
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Zanutta, Alessio, Cristiani, Stefano, Atkinson, David, Baldini, Veronica, Balestra, Andrea, Barbuy, Beatriz, Macanhan, Vanessa Bawden P., Calcines, Ariadna, Calderone, Giorgio, Case, Scott, Castilho, Bruno V., Cescutti, Gabriele, Cirami, Roberto, Coretti, Igor, Covino, Stefano, Cupani, Guido, De Caprio, Vincenzo, Dekker, Hans, Di Marcantonio, Paolo, D'Odorico, Valentina, Ernandes, Heitor, Evans, Chris, Feger, Tobias, Feiz, Carmen, Franchini, Mariagrazia, Genoni, Matteo, Gneiding, Clemens D., Kaluszynski, Mikolaj, Landoni, Marco, Lawrence, Jon, Lunney, David, Miller, Chris, Molaverdikhani, Karan, Opitom, Cyrielle, Pariani, Giorgio, Piranomonte, Silvia, Quirrenbach, Andreas, Redaelli, Edoardo Maria Alberto, Riva, Marco, Robertson, David, Rossi, Silvia, Rothmaier, Florian, Seifert, Walter, Smiljanic, Rodolfo, Sturmer, Julian, Stilz, Ingo, Trost, Andrea, Verducci, Orlando, Waring, Chris, Watson, Stephen, Wells, Martyn, Xu, Wenli, Zafar, Tayyaba, and Zorba, Sonia
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Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
We present the baseline conceptual design of the Cassegrain U-Band Efficient Spectrograph (CUBES) for the Very Large Telescope. CUBES will provide unprecedented sensitivity for spectroscopy on a 8 - 10 m class telescope in the ground ultraviolet (UV), spanning a bandwidth of > 100 nm that starts at 300 nm, the shortest wavelength accessible from the ground. The design has been optimized for end-to-end efficiency and provides a spectral resolving power of R > 20000, that will unlock a broad range of new topics across solar system, Galactic and extraglactic astronomy. The design also features a second, lower-resolution (R \sim 7000) mode and has the option of a fiberlink to the UVES instrument for simultaneous observations at longer wavelengths. Here we present the optical, mechanical and software design of the various subsystems of the instrument after the Phase A study of the project. We discuss the expected performances for the layout choices and highlight some of the performance trade-offs considered to best meet the instrument top-level requirements. We also introduce the model-based system engineering approach used to organize and manage the project activities and interfaces, in the context that it is increasingly necessary to integrate such tools in the development of complex astronomical projects., Comment: Accepted for publication in Experimental Astronomy
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- 2022
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29. Integrative Approaches to Understanding Organismal Responses to Aquatic Deoxygenation.
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Woods, H Arthur, Moran, Amy L, Atkinson, David, Audzijonyte, Asta, Berenbrink, Michael, Borges, Francisco O, Burnett, Karen G, Burnett, Louis E, Coates, Christopher J, Collin, Rachel, Costa-Paiva, Elisa M, Duncan, Murray I, Ern, Rasmus, Laetz, Elise MJ, Levin, Lisa A, Lindmark, Max, Lucey, Noelle M, McCormick, Lillian R, Pierson, James J, Rosa, Rui, Roman, Michael R, Sampaio, Eduardo, Schulte, Patricia M, Sperling, Erik A, Walczyńska, Aleksandra, and Verberk, Wilco CEP
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Biological Sciences ,Ecology ,Climate Action ,Animals ,Climate Change ,Aquatic Organisms ,Biological Evolution ,Oxygen ,Stress ,Physiological ,Ecosystem ,Biological sciences - Abstract
AbstractOxygen bioavailability is declining in aquatic systems worldwide as a result of climate change and other anthropogenic stressors. For aquatic organisms, the consequences are poorly known but are likely to reflect both direct effects of declining oxygen bioavailability and interactions between oxygen and other stressors, including two-warming and acidification-that have received substantial attention in recent decades and that typically accompany oxygen changes. Drawing on the collected papers in this symposium volume ("An Oxygen Perspective on Climate Change"), we outline the causes and consequences of declining oxygen bioavailability. First, we discuss the scope of natural and predicted anthropogenic changes in aquatic oxygen levels. Although modern organisms are the result of long evolutionary histories during which they were exposed to natural oxygen regimes, anthropogenic change is now exposing them to more extreme conditions and novel combinations of low oxygen with other stressors. Second, we identify behavioral and physiological mechanisms that underlie the interactive effects of oxygen with other stressors, and we assess the range of potential organismal responses to oxygen limitation that occur across levels of biological organization and over multiple timescales. We argue that metabolism and energetics provide a powerful and unifying framework for understanding organism-oxygen interactions. Third, we conclude by outlining a set of approaches for maximizing the effectiveness of future work, including focusing on long-term experiments using biologically realistic variation in experimental factors and taking truly cross-disciplinary and integrative approaches to understanding and predicting future effects.
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- 2022
30. Joint estimation of relaxation and diffusion tissue parameters for prostate cancer with relaxation-VERDICT MRI
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Palombo, Marco, Valindria, Vanya, Singh, Saurabh, Chiou, Eleni, Giganti, Francesco, Pye, Hayley, Whitaker, Hayley C., Atkinson, David, Punwani, Shonit, Alexander, Daniel C., and Panagiotaki, Eleftheria
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- 2023
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31. 2. Charles and Sarah Bates and the Transition from Black-Letter
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Atkinson, David, primary
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- 2023
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32. 1. Introduction
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Atkinson, David, primary and Roud, Steve, additional
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- 2023
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33. 11. Street Literature and Cheap Fiction
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Atkinson, David, primary
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- 2023
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34. 6. Chapmen’s Books Printed for Henry Woodgate and Samuel Brooks (1757–61)
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Atkinson, David, primary
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- 2023
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35. 12. Afterword
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Atkinson, David, primary and Roud, Steve, additional
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- 2023
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36. Rivaroxaban for stroke patients with antiphospholipid syndrome (RISAPS): protocol for a randomized controlled, phase IIb proof-of-principle trial
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Mittal, Prabal, Gafoor, Rafael, Sayar, Zara, Efthymiou, Maria, Tohidi-Esfahani, Ibrahim, Appiah-Cubi, Stella, Arachchillage, Deepa J., Atkinson, David, Bordea, Ekaterina, Cardoso, M. Jorge, Caverly, Emilia, Chandratheva, Arvind, Chau, Marisa, Freemantle, Nick, Gates, Carolyn, Ja¨ger, H. Rolf, Kaul, Arvind, Mitchell, Chris, Nguyen, Hanh, Packham, Bunis, Paskell, Jaye, Patel, Jignesh P., Round, Chris, Sanna, Giovanni, Zaidi, Abbas, Werring, David J., Isenberg, David, and Cohen, Hannah
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- 2024
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37. Not Hipsters
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Atkinson, David S.
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- 2013
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38. Health service delivery and workforce in northern Australia: A scoping review
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Edelman, Alexandra, Grundy, John, Larkins, Sarah, Topp, Stephanie M, Atkinson, David, Patel, Bhavini, Strivens, Edward, Moodley, Nishila, and Whittaker, Maxine
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- 2020
39. Immigration Restriction in the Anglo-American Settler World, 1830s–1930s
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Atkinson, David C., primary
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- 2023
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40. The English and Scottish Popular Ballads (review)
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Atkinson, David, 1955 Feb. 23-
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- 2005
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41. Combiner and HyperCombiner networks: Rules to combine multimodality MR images for prostate cancer localisation
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Yan, Wen, Chiu, Bernard, Shen, Ziyi, Yang, Qianye, Syer, Tom, Min, Zhe, Punwani, Shonit, Emberton, Mark, Atkinson, David, Barratt, Dean C., and Hu, Yipeng
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- 2024
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42. Where is VALDO? VAscular Lesions Detection and segmentatiOn challenge at MICCAI 2021
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Sudre, Carole H., Van Wijnen, Kimberlin, Dubost, Florian, Adams, Hieab, Atkinson, David, Barkhof, Frederik, Birhanu, Mahlet A., Bron, Esther E., Camarasa, Robin, Chaturvedi, Nish, Chen, Yuan, Chen, Zihao, Chen, Shuai, Dou, Qi, Evans, Tavia, Ezhov, Ivan, Gao, Haojun, Girones Sanguesa, Marta, Gispert, Juan Domingo, Gomez Anson, Beatriz, Hughes, Alun D., Ikram, M. Arfan, Ingala, Silvia, Jaeger, H. Rolf, Kofler, Florian, Kuijf, Hugo J., Kutnar, Denis, Lee, Minho, Li, Bo, Lorenzini, Luigi, Menze, Bjoern, Molinuevo, Jose Luis, Pan, Yiwei, Puybareau, Elodie, Rehwald, Rafael, Su, Ruisheng, Shi, Pengcheng, Smith, Lorna, Tillin, Therese, Tochon, Guillaume, Urien, Hélène, van der Velden, Bas H.M., van der Velpen, Isabelle F., Wiestler, Benedikt, Wolters, Frank J., Yilmaz, Pinar, de Groot, Marius, Vernooij, Meike W., and de Bruijne, Marleen
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- 2024
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43. MARVEL, a four-telescope array for high-precision radial-velocity monitoring
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Raskin, Gert, Schwab, Christian, Vandenbussche, Bart, De Ridder, Joris, Lanthermann, Cyprien, Padilla, Jesus Pérez, Tkachenko, Andrew, Sana, Hugues, Royer, Pierre, Prins, Saskia, Decin, Leen, Defrère, Denis, Pember, Jacob, Atkinson, David, Glasse, Alistair, Pollacco, Don, Tinetti, Giovanna, Güdel, Manuel, Stürmer, Julian, Ribas, Ignasi, Brandeker, Alexis, Buchhave, Lars, Halverson, Samuel, Avila, Gerardo, Morren, Johan, and Van Winckel, Hand
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Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
Since the first discovery of a planet outside of our Solar System in 1995, exoplanet research has shifted from detecting to characterizing worlds around other stars. The TESS (NASA, launched 2019) and PLATO mission (ESA, planned launch 2026) will find and constrain the size of thousands of exoplanets around bright stars all over the sky. Radial velocity measurements are needed to characterize the orbit and mass, and complete the picture of densities and composition of the exoplanet systems found. The Ariel mission (ESA, planned launch 2028) will characterize exoplanet atmospheres with infrared spectroscopy. Characterization of stellar activity using optical spectroscopy from the ground is key to retrieve the spectral footprint of the planetary atmosphere in Ariel's spectra. To enable the scientific harvest of the TESS, PLATO and Ariel space missions, we plan to install MARVEL as an extension of the existing Mercator Telescope at the Roque De Los Muchachos Observatory on La Palma (SPAIN). MARVEL consists of an array of four 80 cm telescopes linked through optical fibers to a single high-resolution echelle spectrograph, optimized for extreme-precision radial velocity measurements. It can observe the radial velocities of four different stars simultaneously or, alternatively, combine the flux from four telescopes pointing to a single faint target in one spectrum. MARVEL is constructed by a KU Leuven (Belgium) led collaboration, with contributions from the UK, Austria, Australia, Sweden, Denmark and Spain. In this paper, we present the MARVEL instrument with special focus on the optical design and expected performance of the spectrograph, and report on the status of the project., Comment: SPIE Astronomical Telescopes + Instrumentation 2020, Ground-based and Airborne Instrumentation for Astronomy VIII
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- 2020
44. Accidental subcutaneous copper salt injection : toxic effects and management
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Atkinson, David, Beasley, Michael, and Dryburgh, Peter
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- 2004
45. CUBES phase a design overview: The Cassegrain U-Band efficient spectrograph for the very large telescope
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Zanutta, Alessio, Cristiani, Stefano, Atkinson, David, Baldini, Veronica, Balestra, Andrea, Barbuy, Beatriz, Macanhan, Vanessa Bawden P., Calcines, Ariadna, Calderone, Giorgio, Case, Scott, Castilho, Bruno V., Cescutti, Gabriele, Cirami, Roberto, Coretti, Igor, Covino, Stefano, Cupani, Guido, De Caprio, Vincenzo, Dekker, Hans, Di Marcantonio, Paolo, D’Odorico, Valentina, Ernandes, Heitor, Evans, Chris, Feger, Tobias, Feiz, Carmen, Franchini, Mariagrazia, Genoni, Matteo, Gneiding, Clemens D., Kałuszyński, Mikołaj, Landoni, Marco, Lawrence, Jon, Lunney, David, Miller, Chris, Molaverdikhani, Karan, Opitom, Cyrielle, Pariani, Giorgio, Piranomonte, Silvia, Quirrenbach, Andreas, Redaelli, Edoardo Maria Alberto, Riva, Marco, Robertson, David, Rossi, Silvia, Rothmaier, Florian, Seifert, Walter, Smiljanic, Rodolfo, Stürmer, Julian, Stilz, Ingo, Trost, Andrea, Verducci, Orlando, Waring, Chris, Watson, Stephen, Wells, Martyn, Xu, Wenli, Zafar, Tayyaba, and Zorba, Sonia
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- 2023
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46. A New Condition for Transitivity of Probabilistic Support
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Atkinson, David and Peijnenburg, Jeanne
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- 2023
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47. The Saturn Ring Skimmer Mission Concept: The next step to explore Saturn's rings, atmosphere, interior, and inner magnetosphere
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Tiscareno, Matthew S., Vaquero, Mar, Hedman, Matthew M., Cao, Hao, Estrada, Paul R., Ingersoll, Andrew P., Miller, Kelly E., Parisi, Marzia, Atkinson, David. H., Brooks, Shawn M., Cuzzi, Jeffrey N., Fuller, James, Hendrix, Amanda R., Johnson, Robert E., Koskinen, Tommi, Kurth, William S., Lunine, Jonathan I., Nicholson, Philip D., Paty, Carol S., Schindhelm, Rebecca, Showalter, Mark R., Spilker, Linda J., Strange, Nathan J., and Tseng, Wendy
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Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Earth and Planetary Astrophysics - Abstract
The innovative Saturn Ring Skimmer mission concept enables a wide range of investigations that address fundamental questions about Saturn and its rings, as well as giant planets and astrophysical disk systems in general. This mission would provide new insights into the dynamical processes that operate in astrophysical disk systems by observing individual particles in Saturn's rings for the first time. The Ring Skimmer would also constrain the origin, history, and fate of Saturn's rings by determining their compositional evolution and material transport rates. In addition, the Ring Skimmer would reveal how the rings, magnetosphere, and planet operate as an inter-connected system by making direct measurements of the ring's atmosphere, Saturn's inner magnetosphere and the material owing from the rings into the planet. At the same time, this mission would clarify the dynamical processes operating in the planet's visible atmosphere and deep interior by making extensive high-resolution observations of cloud features and repeated measurements of the planet's extremely dynamic gravitational field. Given the scientific potential of this basic mission concept, we advocate that it be studied in depth as a potential option for the New Frontiers program., Comment: White paper submitted to the Planetary Science and Astrobiology Decadal Survey (submission #420)
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- 2020
48. What Gets Echoed? Understanding the 'Pointers' in Explanations of Persuasive Arguments
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Atkinson, David, Srinivasan, Kumar Bhargav, and Tan, Chenhao
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence ,Computer Science - Computers and Society ,Computer Science - Human-Computer Interaction ,Computer Science - Machine Learning - Abstract
Explanations are central to everyday life, and are a topic of growing interest in the AI community. To investigate the process of providing natural language explanations, we leverage the dynamics of the /r/ChangeMyView subreddit to build a dataset with 36K naturally occurring explanations of why an argument is persuasive. We propose a novel word-level prediction task to investigate how explanations selectively reuse, or echo, information from what is being explained (henceforth, explanandum). We develop features to capture the properties of a word in the explanandum, and show that our proposed features not only have relatively strong predictive power on the echoing of a word in an explanation, but also enhance neural methods of generating explanations. In particular, while the non-contextual properties of a word itself are more valuable for stopwords, the interaction between the constituent parts of an explanandum is crucial in predicting the echoing of content words. We also find intriguing patterns of a word being echoed. For example, although nouns are generally less likely to be echoed, subjects and objects can, depending on their source, be more likely to be echoed in the explanations., Comment: 19 pages, 3 figures, EMNLP 2019, the code and dataset are available at https://chenhaot.com/papers/explanation-pointers.html
- Published
- 2019
49. Use of super resolution reconstruction MRI for surgical planning in Placenta accreta spectrum disorder: Case series
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Mufti, Nada, Chappell, Joanna, O'Brien, Patrick, Attilakos, George, Irzan, Hassna, Sokolska, Magda, Narayanan, Priya, Gaunt, Trevor, Humphries, Paul D., Patel, Premal, Whitby, Elspeth, Jauniaux, Eric, Hutchinson, J. Ciaran, Sebire, Neil J., Atkinson, David, Kendall, Giles, Ourselin, Sebastien, Vercauteren, Tom, David, Anna L., and Melbourne, Andrew
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- 2023
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50. Guest editorial: The future of universities: view from the top
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Atkinson, David
- Published
- 2023
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