7,794 results on '"Nicholls P."'
Search Results
152. Author Correction: Optical coherence tomography in coronary atherosclerosis assessment and intervention
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Araki, Makoto, Park, Seung-Jung, Dauerman, Harold L., Uemura, Shiro, Kim, Jung-Sun, Di Mario, Carlo, Johnson, Thomas W., Guagliumi, Giulio, Kastrati, Adnan, Joner, Michael, Holm, Niels Ramsing, Alfonso, Fernando, Wijns, William, Adriaenssens, Tom, Nef, Holger, Rioufol, Gilles, Amabile, Nicolas, Souteyrand, Geraud, Meneveau, Nicolas, Gerbaud, Edouard, Opolski, Maksymilian P., Gonzalo, Nieves, Tearney, Guillermo J., Bouma, Brett, Aguirre, Aaron D., Mintz, Gary S., Stone, Gregg W., Bourantas, Christos V., Räber, Lorenz, Gili, Sebastiano, Mizuno, Kyoichi, Kimura, Shigeki, Shinke, Toshiro, Hong, Myeong-Ki, Jang, Yangsoo, Cho, Jin Man, Yan, Bryan P., Porto, Italo, Niccoli, Giampaolo, Montone, Rocco A., Thondapu, Vikas, Papafaklis, Michail I., Michalis, Lampros K., Reynolds, Harmony, Saw, Jacqueline, Libby, Peter, Weisz, Giora, Iannaccone, Mario, Gori, Tommaso, Toutouzas, Konstantinos, Yonetsu, Taishi, Minami, Yoshiyasu, Takano, Masamichi, Raffel, O. Christopher, Kurihara, Osamu, Soeda, Tsunenari, Sugiyama, Tomoyo, Kim, Hyung Oh, Lee, Tetsumin, Higuma, Takumi, Nakajima, Akihiro, Yamamoto, Erika, Bryniarski, Krzysztof L., Di Vito, Luca, Vergallo, Rocco, Fracassi, Francesco, Russo, Michele, Seegers, Lena M., McNulty, Iris, Park, Sangjoon, Feldman, Marc, Escaned, Javier, Prati, Francesco, Arbustini, Eloisa, Pinto, Fausto J., Waksman, Ron, Garcia-Garcia, Hector M., Maehara, Akiko, Ali, Ziad, Finn, Aloke V., Virmani, Renu, Kini, Annapoorna S., Daemen, Joost, Kume, Teruyoshi, Hibi, Kiyoshi, Tanaka, Atsushi, Akasaka, Takashi, Kubo, Takashi, Yasuda, Satoshi, Croce, Kevin, Granada, Juan F., Lerman, Amir, Prasad, Abhiram, Regar, Evelyn, Saito, Yoshihiko, Sankardas, Mullasari Ajit, Subban, Vijayakumar, Weissman, Neil J., Chen, Yundai, Yu, Bo, Nicholls, Stephen J., Barlis, Peter, West, Nick E. J., Arbab-Zadeh, Armin, Ye, Jong Chul, Dijkstra, Jouke, Lee, Hang, Narula, Jagat, Crea, Filippo, Nakamura, Sunao, Kakuta, Tsunekazu, Fujimoto, James, Fuster, Valentin, and Jang, Ik-Kyung
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- 2024
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153. Measuring diachronic sense change: new models and Monte Carlo methods for Bayesian inference
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Zafar, Schyan and Nicholls, Geoff
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Computer Science - Computation and Language ,Statistics - Methodology - Abstract
In a bag-of-words model, the senses of a word with multiple meanings, e.g. "bank" (used either in a river-bank or an institution sense), are represented as probability distributions over context words, and sense prevalence is represented as a probability distribution over senses. Both of these may change with time. Modelling and measuring this kind of sense change is challenging due to the typically high-dimensional parameter space and sparse datasets. A recently published corpus of ancient Greek texts contains expert-annotated sense labels for selected target words. Automatic sense-annotation for the word "kosmos" (meaning decoration, order or world) has been used as a test case in recent work with related generative models and Monte Carlo methods. We adapt an existing generative sense change model to develop a simpler model for the main effects of sense and time, and give MCMC methods for Bayesian inference on all these models that are more efficient than existing methods. We carry out automatic sense-annotation of snippets containing "kosmos" using our model, and measure the time-evolution of its three senses and their prevalence. As far as we are aware, ours is the first analysis of this data, within the class of generative models we consider, that quantifies uncertainty and returns credible sets for evolving sense prevalence in good agreement with those given by expert annotation., Comment: Additional results included in the appendix
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- 2021
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- View/download PDF
154. World Heart Federation Cholesterol Roadmap 2022
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Ray, Kausik K, Ference, Brian A, Séverin, Tania, Blom, Dirk, Nicholls, Stephen J, Shiba, Mariko H, Almahmeed, Wael, Alonso, Rodrigo, Daccord, Magdalena, Ezhov, Marat, Olmo, Rosa Fernández, Jankowski, Piotr, Lanas, Fernando, Mehta, Roopa, Puri, Raman, Wong, Nathan D, Wood, David, Zhao, Dong, Gidding, Samuel S, Virani, Salim S, Lloyd-Jones, Donald, Pinto, Fausto, Perel, Pablo, and Santos, Raul D
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Biomedical and Clinical Sciences ,Cardiovascular Medicine and Haematology ,Heart Disease ,Health Services ,Patient Safety ,Prevention ,Atherosclerosis ,Cardiovascular ,Clinical Research ,Heart Disease - Coronary Heart Disease ,Good Health and Well Being ,Humans ,Cholesterol ,Hydroxymethylglutaryl-CoA Reductase Inhibitors ,Dyslipidemias ,Lipoproteins ,Apolipoproteins B ,Cardiovascular Diseases ,cholesterol ,low-density lipoprotein cholesterol prevention ,ASCVD ,lipid lowering therapy ,familial hypercholesterolaemia ,Cardiorespiratory Medicine and Haematology ,Cardiovascular medicine and haematology - Abstract
BackgroundAtherosclerotic cardiovascular diseases (ASCVD) including myocardial infarction, stroke and peripheral arterial disease continue to be major causes of premature death, disability and healthcare expenditure globally. Preventing the accumulation of cholesterol-containing atherogenic lipoproteins in the vessel wall is central to any healthcare strategy to prevent ASCVD. Advances in current concepts about reducing cumulative exposure to apolipoprotein B (apo B) cholesterol-containing lipoproteins and the emergence of novel therapies provide new opportunities to better prevent ASCVD. The present update of the World Heart Federation Cholesterol Roadmap provides a conceptual framework for the development of national policies and health systems approaches, so that potential roadblocks to cholesterol management and thus ASCVD prevention can be overcome.MethodsThrough a review of published guidelines and research papers since 2017, and consultation with a committee composed of experts in clinical management of dyslipidaemias and health systems research in low-and-middle income countries (LMICs), this Roadmap identifies (1) key principles to effective ASCVD prevention (2) gaps in implementation of these interventions (knowledge-practice gaps); (3) health system roadblocks to treatment of elevated cholesterol in LMICs; and (4) potential strategies for overcoming these.ResultsReducing the future burden of ASCVD will require diverse approaches throughout the life-course. These include: a greater focus on primordial prevention; availability of affordable cholesterol testing; availability of universal cholesterol screening for inherited dyslipidaemias; risk stratification moving beyond 10-year risk to look at lifetime risk with adequate risk estimators; wider availability of affordable cholesterol-lowering therapies which should include statins as essential medications globally; use of adequate doses of potent statin regimens; and combination therapies with ezetimibe or other therapies in order to attain and maintain robust reductions in LDL-C in those at highest risk. Continuing efforts are needed on health literacy for both the public and healthcare providers, utilising multi-disciplinary teams in healthcare and applications that quantify both ASCVD risk and benefits of treatment as well as increased adherence to therapies.ConclusionsThe adverse effects of LDL-cholesterol and apo B containing lipoprotein exposure are cumulative and result in ASCVD. These are preventable by implementation of different strategies, aimed at efficiently tackling atherosclerosis at different stages throughout the human life-course. Preventive strategies should therefore be updated to implement health policy, lifestyle changes and when needed pharmacotherapies earlier with investment in, and a shift in focus towards, early preventive strategies that preserve cardiovascular health rather than treat the consequences of ASCVD.
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- 2022
155. Evaluation of an artificial intelligence-based medical device for diagnosis of autism spectrum disorder
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Megerian, Jonathan T, Dey, Sangeeta, Melmed, Raun D, Coury, Daniel L, Lerner, Marc, Nicholls, Christopher J, Sohl, Kristin, Rouhbakhsh, Rambod, Narasimhan, Anandhi, Romain, Jonathan, Golla, Sailaja, Shareef, Safiullah, Ostrovsky, Andrey, Shannon, Jennifer, Kraft, Colleen, Liu-Mayo, Stuart, Abbas, Halim, Gal-Szabo, Diana E, Wall, Dennis P, and Taraman, Sharief
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Health Services and Systems ,Health Sciences ,Brain Disorders ,Mental Health ,Clinical Research ,Prevention ,Behavioral and Social Science ,Autism ,Intellectual and Developmental Disabilities (IDD) ,Health Services ,Bioengineering ,Clinical Trials and Supportive Activities ,4.2 Evaluation of markers and technologies ,Detection ,screening and diagnosis ,Health services and systems - Abstract
Autism spectrum disorder (ASD) can be reliably diagnosed at 18 months, yet significant diagnostic delays persist in the United States. This double-blinded, multi-site, prospective, active comparator cohort study tested the accuracy of an artificial intelligence-based Software as a Medical Device designed to aid primary care healthcare providers (HCPs) in diagnosing ASD. The Device combines behavioral features from three distinct inputs (a caregiver questionnaire, analysis of two short home videos, and an HCP questionnaire) in a gradient boosted decision tree machine learning algorithm to produce either an ASD positive, ASD negative, or indeterminate output. This study compared Device outputs to diagnostic agreement by two or more independent specialists in a cohort of 18-72-month-olds with developmental delay concerns (425 study completers, 36% female, 29% ASD prevalence). Device output PPV for all study completers was 80.8% (95% confidence intervals (CI), 70.3%-88.8%) and NPV was 98.3% (90.6%-100%). For the 31.8% of participants who received a determinate output (ASD positive or negative) Device sensitivity was 98.4% (91.6%-100%) and specificity was 78.9% (67.6%-87.7%). The Device's indeterminate output acts as a risk control measure when inputs are insufficiently granular to make a determinate recommendation with confidence. If this risk control measure were removed, the sensitivity for all study completers would fall to 51.6% (63/122) (95% CI 42.4%, 60.8%), and specificity would fall to 18.5% (56/303) (95% CI 14.3%, 23.3%). Among participants for whom the Device abstained from providing a result, specialists identified that 91% had one or more complex neurodevelopmental disorders. No significant differences in Device performance were found across participants' sex, race/ethnicity, income, or education level. For nearly a third of this primary care sample, the Device enabled timely diagnostic evaluation with a high degree of accuracy. The Device shows promise to significantly increase the number of children able to be diagnosed with ASD in a primary care setting, potentially facilitating earlier intervention and more efficient use of specialist resources.
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- 2022
156. Multi-century dynamics of the climate and carbon cycle under both high and net negative emissions scenarios
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Koven, Charles D, Arora, Vivek K, Cadule, Patricia, Fisher, Rosie A, Jones, Chris D, Lawrence, David M, Lewis, Jared, Lindsay, Keith, Mathesius, Sabine, Meinshausen, Malte, Mills, Michael, Nicholls, Zebedee, Sanderson, Benjamin M, Séférian, Roland, Swart, Neil C, Wieder, William R, and Zickfeld, Kirsten
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Earth Sciences ,Atmospheric Sciences ,Climate Action ,Oceanography ,Physical Geography and Environmental Geoscience ,Climate change science ,Geoinformatics - Abstract
Future climate projections from Earth system models (ESMs) typically focus on the timescale of this century. We use a set of five ESMs and one Earth system model of intermediate complexity (EMIC) to explore the dynamics of the Earth's climate and carbon cycles under contrasting emissions trajectories beyond this century to the year 2300. The trajectories include a very-high-emissions, unmitigated fossil-fuel-driven scenario, as well as a mitigation scenario that diverges from the first scenario after 2040 and features an "overshoot", followed by a decrease in atmospheric CO2 concentrations by means of large net negative CO2 emissions. In both scenarios and for all models considered here, the terrestrial system switches from being a net sink to either a neutral state or a net source of carbon, though for different reasons and centered in different geographic regions, depending on both the model and the scenario. The ocean carbon system remains a sink, albeit weakened by carbon cycle feedbacks, in all models under the high-emissions scenario and switches from sink to source in the overshoot scenario. The global mean temperature anomaly is generally proportional to cumulative carbon emissions, with a deviation from proportionality in the overshoot scenario that is governed by the zero emissions commitment. Additionally, 23rd century warming continues after the cessation of carbon emissions in several models in the high-emissions scenario and in one model in the overshoot scenario. While ocean carbon cycle responses qualitatively agree in both globally integrated and zonal mean dynamics in both scenarios, the land models qualitatively disagree in zonal mean dynamics, in the relative roles of vegetation and soil in driving C fluxes, in the response of the sink to CO2, and in the timing of the sink-source transition, particularly in the high-emissions scenario. The lack of agreement among land models on the mechanisms and geographic patterns of carbon cycle feedbacks, alongside the potential for lagged physical climate dynamics to cause warming long after CO2 concentrations have stabilized, points to the possibility of surprises in the climate system beyond the 21st century time horizon, even under relatively mitigated global warming scenarios, which should be taken into consideration when setting global climate policy. Copyright:
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- 2022
157. Genomic reconstruction of the SARS-CoV-2 epidemic in England
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Robson, Samuel C, Connor, Thomas R, Loman, Nicholas J, Golubchik, Tanya, Martinez Nunez, Rocio T, Bonsall, David, Rambaut, Andrew, Snell, Luke B, Ludden, Catherine, Corden, Sally, Nastouli, Eleni, Nebbia, Gaia, Lythgoe, Katrina, Torok, M Estee, Goodfellow, Ian G, Prieto, Jacqui A, Saeed, Kordo, Houlihan, Catherine, Frampton, Dan, Hamilton, William L, Witney, Adam A, Bucca, Giselda, Pope, Cassie F, Moore, Catherine, Thomson, Emma C, Harrison, Ewan M, Smith, Colin P, Rogan, Fiona, Beckwith, Shaun M, Murray, Abigail, Singleton, Dawn, Eastick, Kirstine, Sheridan, Liz A, Randell, Paul, Jackson, Leigh M, Gonçalves, Sónia, Fairley, Derek J, Loose, Matthew W, Watkins, Joanne, Moses, Samuel, Nicholls, Sam, Bull, Matthew, Smith, Darren L, Aanensen, David M, Aggarwal, Dinesh, Shepherd, James G, Curran, Martin D, Parmar, Surendra, Parker, Matthew D, Williams, Catryn, Glaysher, Sharon, Underwood, Anthony P, Bashton, Matthew, Pacchiarini, Nicole, Loveson, Katie F, Byott, Matthew, Carabelli, Alessandro M, Templeton, Kate E, de Silva, Thushan I, Wang, Dennis, Langford, Cordelia F, Gunson, Rory N, Cottrell, Simon, O’Grady, Justin, Kwiatkowski, Dominic, Lillie, Patrick J, Cortes, Nicholas, Moore, Nathan, Thomas, Claire, Burns, Phillipa J, Mahungu, Tabitha W, Liggett, Steven, Beckett, Angela H, Holden, Matthew TG, Levett, Lisa J, Osman, Husam, Hassan-Ibrahim, Mohammed O, Simpson, David A, Chand, Meera, Gupta, Ravi K, Darby, Alistair C, Paterson, Steve, Pybus, Oliver G, Volz, Erik, de Angelis, Daniela, Robertson, David L, Page, Andrew J, Bassett, Andrew R, Wong, Nick, Taha, Yusri, Erkiert, Michelle J, Spencer Chapman, Michael H, Dewar, Rebecca, McHugh, Martin P, Mookerjee, Siddharth, Aplin, Stephen, Harvey, Matthew, Sass, Thea, Umpleby, Helen, and Wheeler, Helen
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Genetics ,Prevention ,Emerging Infectious Diseases ,Infectious Diseases ,Lung ,Good Health and Well Being ,Amino Acid Substitution ,COVID-19 ,England ,Epidemiological Monitoring ,Genome ,Viral ,Genomics ,Humans ,Molecular Epidemiology ,Mutation ,Quarantine ,SARS-CoV-2 ,Spatio-Temporal Analysis ,Spike Glycoprotein ,Coronavirus ,Wellcome Sanger Institute COVID-19 Surveillance Team ,COVID-19 Genomics UK (COG-UK) Consortium* ,General Science & Technology - Abstract
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.
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- 2021
158. Apabetalone and hospitalization for heart failure in patients following an acute coronary syndrome: a prespecified analysis of the BETonMACE study
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Nicholls, Stephen J, Schwartz, Gregory G, Buhr, Kevin A, Ginsberg, Henry N, Johansson, Jan O, Kalantar-Zadeh, Kamyar, Kulikowski, Ewelina, Toth, Peter P, Wong, Norman, Sweeney, Michael, and Ray, Kausik K
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Pharmacology and Pharmaceutical Sciences ,Biomedical and Clinical Sciences ,Clinical Research ,Clinical Trials and Supportive Activities ,Diabetes ,Heart Disease ,Heart Disease - Coronary Heart Disease ,Cardiovascular ,Atherosclerosis ,6.1 Pharmaceuticals ,Evaluation of treatments and therapeutic interventions ,Acute Coronary Syndrome ,Aged ,Cardiovascular Agents ,Diabetes Mellitus ,Type 2 ,Double-Blind Method ,Female ,Heart Failure ,Humans ,Male ,Middle Aged ,Patient Admission ,Patient Readmission ,Quinazolinones ,Time Factors ,Treatment Outcome ,BET inhibitors ,Acute coronary syndrome ,Heart failure ,Clinical trial ,Cardiovascular disease ,Epigenetics ,BETonMACE Investigators ,Cardiorespiratory Medicine and Haematology ,Cardiovascular System & Hematology ,Cardiovascular medicine and haematology - Abstract
BackgroundPatients with diabetes and acute coronary syndrome (ACS) are at high risk for subsequent heart failure. Apabetalone is a selective inhibitor of bromodomain and extra-terminal (BET) proteins, epigenetic regulators of gene expression. Preclinical data suggest that apabetalone exerts favorable effects on pathways related to myocardial structure and function and therefore could impact subsequent heart failure events. The effect of apabetalone on heart failure events after an ACS is not currently known.MethodsThe phase 3 BETonMACE trial was a double-blind, randomized comparison of apabetalone versus placebo on the incidence of major adverse cardiovascular events (MACE) in 2425 patients with a recent ACS and diabetes. This prespecified secondary analysis investigated the impact of apabetalone on hospitalization for congestive heart failure, not previously studied.ResultsPatients (age 62 years, 74.4% males, 90% high-intensity statin use, LDL-C 70.3 mg/dL, HDL-C 33.3 mg/dL and HbA1c 7.3%) were followed for an average 26 months. Apabetalone treated patients experienced the nominal finding of a lower rate of first hospitalization for heart failure (2.4% vs. 4.0%, HR 0.59 [95%CI 0.38-0.94], P = 0.03), total number of hospitalizations for heart failure (35 vs. 70, HR 0.47 [95%CI 0.27-0.83], P = 0.01) and the combination of cardiovascular death or hospitalization for heart failure (5.7% vs. 7.8%, HR 0.72 [95%CI 0.53-0.98], P = 0.04).ConclusionApabetalone treatment was associated with fewer hospitalizations for heart failure in patients with type 2 diabetes and recent ACS. Future studies are warranted to define the potential for BET inhibition with apabetalone to prevent heart failure in patients with diabetes and ACS.
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- 2021
159. Relation of insulin treatment for type 2 diabetes to the risk of major adverse cardiovascular events after acute coronary syndrome: an analysis of the BETonMACE randomized clinical trial
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Schwartz, Gregory G, Nicholls, Stephen J, Toth, Peter P, Sweeney, Michael, Halliday, Christopher, Johansson, Jan O, Wong, Norman CW, Kulikowski, Ewelina, Kalantar-Zadeh, Kamyar, Ginsberg, Henry N, and Ray, Kausik K
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Biomedical and Clinical Sciences ,Clinical Sciences ,Brain Disorders ,Heart Disease - Coronary Heart Disease ,Cardiovascular ,Prevention ,Diabetes ,Heart Disease ,Clinical Trials and Supportive Activities ,Clinical Research ,Atherosclerosis ,6.1 Pharmaceuticals ,Evaluation of treatments and therapeutic interventions ,Metabolic and endocrine ,Acute Coronary Syndrome ,Aged ,Diabetes Mellitus ,Type 2 ,Female ,Humans ,Hypoglycemic Agents ,Insulin ,Male ,Middle Aged ,Quinazolinones ,Recurrence ,Risk Assessment ,Risk Factors ,Time Factors ,Treatment Outcome ,Acute coronary syndrome ,Epigenetics ,BET proteins ,Cardiorespiratory Medicine and Haematology ,Cardiovascular System & Hematology ,Cardiovascular medicine and haematology - Abstract
BackgroundIn stable patients with type 2 diabetes (T2D), insulin treatment is associated with elevated risk for major adverse cardiovascular events (MACE). Patients with acute coronary syndrome (ACS) and T2D are at particularly high risk for recurrent MACE despite evidence-based therapies. It is uncertain to what extent this risk is further magnified in patients with recent ACS who are treated with insulin. We examined the relationship of insulin use to risk of MACE and modification of that risk by apabetalone, a bromodomain and extra-terminal (BET) protein inhibitor.MethodsThe analysis utilized data from the BETonMACE phase 3 trial that compared apabetalone to placebo in patients with T2D, low HDL cholesterol, andACS. The primary MACE outcome (cardiovascular death, myocardial infarction, or stroke) was examined according to insulin treatment and assigned study treatment. Multivariable Cox regression was used to determine whether insulin use was independently associated with the risk of MACE.ResultsAmong 2418 patients followed for median 26.5 months, 829 (34.2%) were treated with insulin. Despite high utilization of evidence-based treatments including coronary revascularization, intensive statin treatment, and dual antiplatelet therapy, the 3-year incidence of MACE in the placebo group was elevated among insulin-treated patients (20.4%) compared to those not-treated with insulin (12.8%, P = 0.0001). Insulin treatment remained strongly associated with the risk of MACE (HR 2.10, 95% CI 1.42-3.10, P = 0.0002) after adjustment for demographic, clinical, and treatment variables. Apabetalone had a consistent, favorable effect on MACE in insulin-treated and not insulin-treated patients.ConclusionInsulin-treated patients with T2D, low HDL cholesterol, and ACS are at high risk for recurrent MACE despite the use of evidence-based, contemporary therapies. A strong association of insulin treatment with risk of MACE persists after adjustment for other characteristics associated with MACE. There is unmet need for additional treatments to mitigate this risk. Trial registration ClinicalTrials.gov NCT02586155, registered October 26, 2015.
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- 2021
160. Supernova Model Discrimination with Hyper-Kamiokande
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Collaboration, Hyper-Kamiokande, Abe, K., Adrich, P., Aihara, H., Akutsu, R., Alekseev, I., Ali, A., Ameli, F., Anghel, I., Anthony, L. H. V., Antonova, M., Araya, A., Asaoka, Y., Ashida, Y., Aushev, V., Ballester, F., Bandac, I., Barbi, M., Barker, G. J., Barr, G., Batkiewicz-Kwasniak, M., Bellato, M., Berardi, V., Bergevin, M., Bernard, L., Bernardini, E., Berns, L., Bhadra, S., Bian, J., Blanchet, A., Blaszczyk, F. d. M., Blondel, A., Boiano, A., Bolognesi, S., Bonavera, L., Booth, N., Borjabad, S., Boschi, T., Bose, D., Boyd, S . B., Bozza, C., Bravar, A., Bravo-Berguño, D., Bronner, C., Brown, L., Bubak, A., Buchowicz, A., Avanzini, M. Buizza, Cafagna, F. S., Calabria, N. F., Calvo-Mozota, J. M., Cao, S., Cartwright, S. L., Carroll, A., Catanesi, M. G., Cebriàn, S., Chabera, M., Chakraborty, S., Checchia, C., Choi, J. H., Choubey, S., Cicerchia, M., Coleman, J., Collazuol, G., Cook, L., Cowan, G., Cuen-Rochin, S., Danilov, M., Lopez, G. Daz, De la Fuente, E., de Perio, P., De Rosa, G., Dealtry, T., Densham, C. J., Dergacheva, A., Deshmukh, N., Devi, M. M., Di Lodovico, F., Di Meo, P., Di Palma, I., Doyle, T. A., Drakopoulou, E., Drapier, O., Dumarchez, J., Dunne, P., Dziewiecki, M., Eklund, L., Hedri, S. El, Ellis, J., Emery, S., Esmaili, A., Esteve, R., Evangelisti, A., Feely, M., Fedotov, S., Feng, J., Fernandez, P., Fernández-Martinez, E., Ferrario, P., Ferrazzi, B., Feusels, T., Finch, A., Finley, C., Fiorentini, A., Fiorillo, G., Fitton, M., Frankiewicz, K., Friend, M., Fujii, Y., Fukuda, Y., Galinski, G., Gao, J., Garde, C., Garfagnini, A., Garode, S., Gialanella, L., Giganti, C., Gomez-Cadenas, J. J., Gonin, M., González-Nuevo, J., Gorin, A., Gornea, R., Gousy-Leblanc, V., Gramegna, F., Grassi, M., Grella, G., Guigue, M., Gumplinger, P., Hadley, D. R., Harada, M., Hartfiel, B., Hartz, M., Hassani, S., Hastings, N. C., Hayato, Y., Hernando-Morata, J. A., Herrero, V., Hill, J., Hiraide, K., Hirota, S., Holin, A., Horiuchi, S., Hoshina, K., Hultqvist, K., Iacob, F., Ichikawa, A. K., Ibnsalih, W. Idrissi, Iijima, T., Ikeda, M., Inomoto, M., Inoue, K., Insler, J., Ioannisian, A., Ishida, T., Ishidoshiro, K., Ishino, H., Ishitsuka, M., Ito, H., Ito, S., Itow, Y., Iwamoto, K., Izmaylov, A., Izumi, N., Izumiyama, S., Jakkapu, M., Jamieson, B., Jang, H. I., Jang, J. S., Jenkins, S. J., Jeon, S. H., Jiang, M., Jo, H. S., Jonsson, P., Joo, K. K., Kajita, T., Kakuno, H., Kameda, J., Kano, Y., Kalaczynski, P., Karlen, D., Kasperek, J., Kataoka, Y., Kato, A., Katori, T., Kazarian, N., Kearns, E., Khabibullin, M., Khotjantsev, A., Kikawa, T., Kikec, M., Kim, J. H., Kim, J. Y., Kim, S. B., Kim, S. Y., King, S., Kinoshita, T., Kisiel, J., Klekotko, A., Kobayashi, T., Koch, L., Koga, M., Koerich, L., Kolev, N., Konaka, A., Kormos, L. L., Koshio, Y., Korzenev, A., Kotsar, Y., Kouzakov, K. A., Kowalik, K. L., Kravchuk, L., Kryukov, A. P., Kudenko, Y., Kumita, T., Kurjata, R., Kutter, T., Kuze, M., Kwak, K., La Commara, M., Labarga, L., Lagoda, J., James, M. Lamers, Lamoureux, M., Laveder, M., Lavitola, L., Lawe, M., Learned, J. G., Lee, J., Leitner, R., Lezaun, V., Lim, I. T., Lindner, T., Litchfield, R. P., Long, K. R., Longhin, A., Loverre, P., Lu, X., Ludovici, L., Maekawa, Y., Magaletti, L., Magar, K., Mahn, K., Makida, Y., Malek, M., Malinský, M., Marchi, T., Maret, L., Mariani, C., Marinelli, A., Martens, K., Marti, Ll., Martin, J. F., Martin, D., Marzec, J., Matsubara, T., Matsumoto, R., Matsuno, S., Matusiak, M., Mazzucato, E., McCarthy, M., McCauley, N., McElwee, J., McGrew, C., Mefodiev, A., Medhi, A., Mehta, P., Mellet, L., Menjo, H., Mermod, P., Metelko, C., Mezzetto, M., Migenda, J., Migliozzi, P., Mijakowski, P., Miki, S., Miller, E. W., Minakata, H., Minamino, A., Mine, S., Mineev, O., Mitra, A., Miura, M., Moharana, R., Mollo, C. M., Mondal, T., Mongelli, M., Monrabal, F., Moon, D. H., Moon, C. S., Mora, F. J., Moriyama, S., Mueller, Th. A., Munteanu, L., Murase, K., Nagao, Y., Nakadaira, T., Nakagiri, K., Nakahata, M., Nakai, S., Nakajima, Y., Nakamura, K., Nakamura, KI., Nakamura, H., Nakano, Y., Nakaya, T., Nakayama, S., Nakayoshi, K., Machado, L. Nascimento, Naseby, C. E. R., Navarro-Garcia, B., Needham, M., Nicholls, T., Niewczas, K., Nishimura, Y., Noah, E., Nova, F., Nugent, J. C., Nunokawa, H., Obrebski, W., Ochoa-Ricoux, J. P., O'Connor, E., Ogawa, N., Ogitsu, T., Ohta, K., Okamoto, K., O'Keeffe, H. M., Okumura, K., Onishchuk, Y., Orozco-Luna, F., Oshlianskyi, A., Ospina, N., Ostrowski, M., O'Sullivan, E., O'Sullivan, L., Ovsiannikova, T., Oyama, Y., Ozaki, H., Pac, M. Y., Paganini, P., Palladino, V., Paolone, V., Pari, M., Parsa, S., Pasternak, J., Pastore, C., Pastuszak, G., Patel, D. A., Pavin, M., Payne, D., Peña-Garay, C., Pidcott, C., Guerra, E. Pinzon, Playfer, S., Pointon, B. W., Popov, A., Popov, B., Porwit, K., Posiadala-Zezula, M., Poutissou, J. -M., Pozimski, J., Pronost, G., Prouse, N. W., Przewlocki, P., Quilain, B., Quiroga, A. A., Radicioni, E., Radics, B., Rajda, P. J., Renner, J., Rescigno, M., Retiere, F., Ricciardi, G., Riccio, C., Richards, B., Rondio, E., Rose, H. J., Roskovec, B., Roth, S., Rott, C., Rountree, S. D., Rubbia, A., Ruggeri, A. C., Ruggles, C., Russo, S., Rychter, A., Ryu, D., Sakashita, K., Samani, S., Sánchez, F., Sánchez, M. L., Sanchez, M. C., Sano, S., Santos, J. D., Santucci, G., Sarmah, P., Sashima, I., Sato, K., Scott, M., Seiya, Y., Sekiguchi, T., Sekiya, H., Seo, J. W., Seo, S. H., Sgalaberna, D., Shaikhiev, A., Shan, Z., Shaykina, A., Shimizu, I., Shin, C. D., Shinoki, M., Shiozawa, M., Sinnis, G., Skrobova, N., Skwarczynski, K., Smy, M. B., Sobczyk, J., Sobel, H. W., Soler, F. J. P., Sonoda, Y., Spina, R., Spisso, B., Spradlin, P., Stankevich, K. L., Stawarz, L., Stellacci, S. M., Stopa, K., Studenikin, A. I., Gómez, S. L. Suárez, Suganuma, T., Suvorov, S., Suwa, Y., Suzuki, A. T., Suzuki, S. Y., Suzuki, Y., Svirida, D., Svoboda, R., Taani, M., Tada, M., Takeda, A., Takemoto, Y., Takenaka, A., Taketa, A., Takeuchi, Y., Takhistov, V., Tanaka, H., Tanaka, H. A., Tanaka, H. I., Tanaka, M., Tashiro, T., Thiesse, M., Thompson, L. F., Toledo, J., Tomatani-Sánchez, A. K., Tortone, G., Tsui, K. M., Tsukamoto, T., Tzanov, M., Uchida, Y., Vagins, M. R., Valder, S., Valentino, V., Vasseur, G., Vijayvargi, A., Vilela, C., Vinning, W. G. S., Vivolo, D., Vladisavljevic, T., Vogelaar, R. B., Vyalkov, M. M., Wachala, T., Walker, J., Wark, D., Wascko, M. O., Wendell, R. A., Wilkes, R. J., Wilking, M. J., Wilson, J. R., Wronka, S., Xia, J., Xie, Z., Xin, T., Yamaguchi, Y., Yamamoto, K., Yanagisawa, C., Yano, T., Yen, S., Yershov, N., Yeum, D. N., Yokoyama, M., Yonenaga, M., Yoo, J., Yu, I., Yu, M., Zakrzewski, T., Zaldivar, B., Zalipska, J., Zaremba, K., Zarnecki, G., Ziembicki, M., Zietara, K., Zito, M., and Zsoldos, S.
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Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - High Energy Astrophysical Phenomena ,High Energy Physics - Experiment ,Physics - Instrumentation and Detectors - Abstract
Core-collapse supernovae are among the most magnificent events in the observable universe. They produce many of the chemical elements necessary for life to exist and their remnants -- neutron stars and black holes -- are interesting astrophysical objects in their own right. However, despite millennia of observations and almost a century of astrophysical study, the explosion mechanism of core-collapse supernovae is not yet well understood. Hyper-Kamiokande is a next-generation neutrino detector that will be able to observe the neutrino flux from the next galactic core-collapse supernova in unprecedented detail. We focus on the first 500 ms of the neutrino burst, corresponding to the accretion phase, and use a newly-developed, high-precision supernova event generator to simulate Hyper-Kamiokande's response to five different supernova models. We show that Hyper-Kamiokande will be able to distinguish between these models with high accuracy for a supernova at a distance of up to 100 kpc. Once the next galactic supernova happens, this ability will be a powerful tool for guiding simulations towards a precise reproduction of the explosion mechanism observed in nature., Comment: 21 pages, 7 figures. Article based on thesis published as arXiv:2002.01649. v2: added references and some explanations in response to reviewer comments
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- 2021
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161. Long-Term Durability of Certolizumab Pegol in Patients with Rheumatoid Arthritis Over 5 Years: An Analysis of Pooled Clinical Trial Data
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Bykerk, Vivian P., Nash, Peter, Nicholls, David, Tanaka, Yoshiya, Winthrop, Kevin, Popova, Christina, Tilt, Nicola, and Haaland, Derek
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- 2023
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162. Immuno-PET Monitoring of CD8+ T Cell Infiltration Post ICOS Agonist Antibody Treatment Alone and in Combination with PD-1 Blocking Antibody Using a 89Zr Anti-CD8+ Mouse Minibody in EMT6 Syngeneic Tumor Mouse
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Alsaid, Hasan, Cheng, Shih-Hsun, Bi, Meixia, Xie, Fang, Rambo, Mary, Skedzielewski, Tinamarie, Hoang, Bao, Mohanan, Sunish, Comroe, Debra, Gehman, Andrew, Hsu, Chih-Yang, Farhangi, Kamyar, Tran, Hoang, Sherina, Valeriia, Doan, Minh, Groseclose, M. Reid, Hopson, Christopher B., Brett, Sara, Wilson, Ian A., Nicholls, Andrew, Ballas, Marc, Waight, Jeremy D., and Jucker, Beat M.
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- 2023
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163. The UK Fens Climate Change Risk Assessment : Big challenges and strategic solutions
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Jenkins, Katie, Nicholls, Robert J., Sayers, Paul, Redhead, John, Price, Jeff, Pywell, Richard, He, Yi, Minns, Asher, Tozer, Noah, Carr, Sam, Jenkins, Katie, Nicholls, Robert J., Sayers, Paul, Redhead, John, Price, Jeff, Pywell, Richard, He, Yi, Minns, Asher, Tozer, Noah, and Carr, Sam
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- 2024
164. Tree based credible set estimation
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Lee, Jeong Eun. and Nicholls, Geoff K.
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Statistics - Methodology - Abstract
Estimating a joint Highest Posterior Density credible set for a multivariate posterior density is challenging as dimension gets larger. Credible intervals for univariate marginals are usually presented for ease of computation and visualisation. There are often two layers of approximation, as we may need to compute a credible set for a target density which is itself only an approximation to the true posterior density. We obtain joint Highest Posterior Density credible sets for density estimation trees given by Li et al. (2016) approximating a density truncated to a compact subset of R^d as this is preferred to a copula construction. These trees approximate a joint posterior distribution from posterior samples using a piecewise constant function defined by sequential binary splits. We use a consistent estimator to measure of the symmetric difference between our credible set estimate and the true HPD set of the target density samples. This quality measure can be computed without the need to know the true set. We show how the true-posterior-coverage of an approximate credible set estimated for an approximate target density may be estimated in doubly intractable cases where posterior samples are not available. We illustrate our methods with simulation studies and find that our estimator is competitive with existing methods.
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- 2020
165. A Simplistic Machine Learning Approach to Contact Tracing
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Gómez, Carlos, Belton, Niamh, Quach, Boi, Nicholls, Jack, and Anand, Devanshu
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
This report is based on the modified NIST challenge, Too Close For Too Long, provided by the SFI Centre for Machine Learning (ML-Labs). The modified challenge excludes the time calculation (too long) aspect. By handcrafting features from phone instrumental data we develop two machine learning models, a GBM and an MLP, to estimate distance between two phones. Our method is able to outperform the leading NIST challenge result by the Hong Kong University of Science and Technology (HKUST) by a significant margin., Comment: 6 pages, 7 tables, 2 figures
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- 2020
166. Benchmarking Resource Usage of Underlying Datatypes of Apache Spark
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Nicholls, Brittany, Adangwa, Mariama, Estes, Rachel, Iradukunda, Hugues Nelson, Zhang, Qingquan, and Zhu, Ting
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Electrical Engineering and Systems Science - Systems and Control - Abstract
The purpose of this paper is to examine how resource usage of an analytic is affected by the different underlying datatypes of Spark analytics - Resilient Distributed Datasets (RDDs), Datasets, and DataFrames. The resource usage of an analytic is explored as a viable and preferred alternative of benchmarking big data analytics instead of the current common benchmarking performed using execution time. The run time of an analytic is shown to not be guaranteed to be a reproducible metric since many external factors to the job can affect the execution time. Instead, metrics readily available through Spark including peak execution memory are used to benchmark the resource usage of these different datatypes in common applications of Spark analytics, such as counting, caching, repartitioning, and KMeans.
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- 2020
167. Spatially resolved direct method metallicity in a high-redshift analogue local galaxy: temperature structure impact on metallicity gradients
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Cameron, Alex J., Yuan, Tiantian, Trenti, Michele, Nicholls, David C., and Kewley, Lisa J.
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Astrophysics - Astrophysics of Galaxies - Abstract
We investigate how HII region temperature structure assumptions affect "direct-method" spatially-resolved metallicity observations using multispecies auroral lines in a galaxy from the SAMI Galaxy Survey. SAMI609396B, at redshift $z=0.018$, is a low-mass galaxy in a minor merger with intense star formation, analogous to conditions at high redshifts. We use three methods to derive direct metallicities and compare with strong-line diagnostics. The spatial metallicity trends show significant differences among the three direct methods. Our first method is based on the commonly used electron temperature $T_e$([OIII]) from the [OIII]$\lambda$4363 auroral line and a traditional $T_e$([OII]) -- $T_e$([OIII]) calibration. The second method applies a recent empirical correction to the O$^+$ abundance from the [OIII]/[OII] strong-line ratio. The third method infers the $T_e$([OII]) from the [SII]$\lambda\lambda$4069,76 auroral lines. The first method favours a positive metallicity gradient along SAMI609396B, whereas the second and third methods yield flattened gradients. Strong-line diagnostics produce mostly flat gradients, albeit with unquantified contamination from shocked regions. We conclude that overlooked assumptions about the internal temperature structure of HII regions in the direct method can lead to large discrepancies in metallicity gradient studies. Our detailed analysis of SAMI609396B underlines that high-accuracy metallicity gradient measurements require a wide array of emission lines and improved spatial resolutions in order to properly constrain excitation sources, physical conditions, and temperature structures of the emitting gas. Integral-field spectroscopic studies with future facilities such as JWST/NIRSpec and ground-based ELTs will be crucial in minimising systematic effects on measured gradients in distant galaxies., Comment: 21 pages, 14 figures, Accepted for Publication in MNRAS
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- 2020
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168. Challenges in constructing genetic instruments for pharmacologic therapies
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Ference, B. A., Smith, G. Davey, Holmes, M. V., Catapano, A. L., Ray, K. K., and Nicholls, S. J.
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Quantitative Biology - Quantitative Methods - Abstract
The genes that encode the targets of most therapies do not have rare variants with large-effect or common variants with moderate effects on the biomarker reflecting the pharmacologic action of the corresponding therapy. Therefore, providing genetic target validation for most therapies is challenging. Novel methods are being developed to combine multiple variants in the gene encoding the target of a therapy that are weakly associated with the biomarker reflecting the pharmacologic action of that therapy into a genetic score that can be used as an adequate instrumental variable. We describe one approach to solve this important problem.
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- 2020
169. Extended nonergodic regime and spin subdiffusion in disordered SU(2)-symmetric Floquet systems
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Yang, Zhi-Cheng, Nicholls, Stuart, and Cheng, Meng
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Condensed Matter - Disordered Systems and Neural Networks ,Condensed Matter - Statistical Mechanics ,Condensed Matter - Strongly Correlated Electrons ,Quantum Physics - Abstract
We explore thermalization and quantum dynamics in a one-dimensional disordered SU(2)-symmetric Floquet model, where a many-body localized phase is prohibited by the non-abelian symmetry. Despite the absence of localization, we find an extended nonergodic regime at strong disorder where the system exhibits nonthermal behaviors. In the strong disorder regime, the level spacing statistics exhibit neither a Wigner-Dyson nor a Poisson distribution, and the spectral form factor does not show a linear-in-time growth at early times characteristic of random matrix theory. The average entanglement entropy of the Floquet eigenstates is subthermal, although violating an area-law scaling with system sizes. We further compute the expectation value of local observables and find strong deviations from the eigenstate thermalization hypothesis. The infinite temperature spin autocorrelation function decays at long times as $t^{-\beta}$ with $\beta < 0.5$, indicating subdiffusive transport at strong disorders., Comment: updated to accepted version
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- 2020
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170. Spatial Variation in Strong Line Ratios and Physical Conditions in Two Strongly-Lensed Galaxies at z~1.4
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Florian, Michael K., Rigby, Jane R., Acharyya, Ayan, Sharon, Keren, Gladders, Michael D., Kewley, Lisa, Khullar, Gourav, Gozman, Katya, Brammer, Gabriel, Momcheva, Ivelina, Nicholls, David, LaMassa, Stephanie, Dahle, Hakon, Bayliss, Matthew B., Wuyts, Eva, Johnson, Traci, and Whitaker, Katherine
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Astrophysics - Astrophysics of Galaxies - Abstract
For studies of galaxy formation and evolution, one of the major benefits of the James Webb Space Telescope is that space-based IFUs like those on its NIRSpec and MIRI instruments will enable spatially resolved spectroscopy of distant galaxies, including spectroscopy at the scale of individual star-forming regions in galaxies that have been gravitationally lensed. In the meantime, there is only a very small subset of lensed sources where work like this is possible even with the Hubble Space Telescope's Wide Field Camera 3 infrared channel grisms. We examine two of these sources, SDSS J1723+3411 and SDSS J2340+2947, using HST WFC3/IR grism data and supporting spatially-unresolved spectroscopy from several ground-based instruments to explore the size of spatial variations in observed strong emission line ratios like O32, R23, which are sensitive to ionization parameter and metallicity, and the Balmer decrement as an indicator of reddening. We find significant spatial variation in the reddening and the reddening-corrected O32 and R23 values which correspond to spreads of a few tenths of a dex in ionization parameter and metallicity. We also find clear evidence of a negative radial gradient in star formation in SDSS J2340+2947 and tentative evidence of one in SDSS J1723+3411, though its star formation is quite asymmetric. Finally, we find that reddening can vary enough spatially to make spatially-resolved reddening corrections necessary in order to characterize gradients in line ratios and the physical conditions inferred from them, necessitating the use of space-based IFUs for future work on larger, more statistically robust samples., Comment: 24 pages, including references, 6 tables, 17 figures, and appendix. Submitted to ApJ June 19, 2020
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- 2020
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171. Distortion estimates for approximate Bayesian inference
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Xing, Hanwen, Nicholls, Geoff K., and Lee, Jeong Eun
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Statistics - Computation - Abstract
Current literature on posterior approximation for Bayesian inference offers many alternative methods. Does our chosen approximation scheme work well on the observed data? The best existing generic diagnostic tools treating this kind of question by looking at performance averaged over data space, or otherwise lack diagnostic detail. However, if the approximation is bad for most data, but good at the observed data, then we may discard a useful approximation. We give graphical diagnostics for posterior approximation at the observed data. We estimate a "distortion map" that acts on univariate marginals of the approximate posterior to move them closer to the exact posterior, without recourse to the exact posterior.
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- 2020
172. The moduli space of gradient flow lines and Morse homology
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Frauenfelder, Urs and Nicholls, Robert
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Mathematics - Algebraic Topology ,Mathematics - Geometric Topology ,Mathematics - Symplectic Geometry - Abstract
We present a set of notes on Morse Homology, which grew out of lectures the first named autor gave at Ludwig-Maximilian University in Munich, Seoul National University, and the University of Augsburg. Although we do not discuss Floer homology in these notes, they are written having Floer homology in mind. Therefore, we use concepts which can be generalized to the semi-infinite dimensional case. In the finite dimensional case, they might not always be the most efficient ones but on the other hand, the finite dimensional case has the advantage that these concepts can be visualized much more easily than in the semi-infinite dimensional one, giving the reader the right intuition how Floer homology works., Comment: 114 pages, 22 figures
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- 2020
173. Machine learning -- based diffractive imaging with subwavelength resolution
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Ghosh, Abantika, Roth, Diane J., Nicholls, Luke H., Wardley, William P., Zayats, Anatoly V., and Podolskiy, Viktor A.
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Physics - Optics ,Condensed Matter - Materials Science ,Electrical Engineering and Systems Science - Image and Video Processing - Abstract
Far-field characterization of small objects is severely constrained by the diffraction limit. Existing tools achieving sub-diffraction resolution often utilize point-by-point image reconstruction via scanning or labelling. Here, we present a new imaging technique capable of fast and accurate characterization of two-dimensional structures with at least wavelength/25 resolution, based on a single far-field intensity measurement. Experimentally, we realized this technique resolving the smallest-available to us 180-nm-scale features with 532-nm laser light. A comprehensive analysis of machine learning algorithms was performed to gain insight into the learning process and to understand the flow of subwavelength information through the system. Image parameterization, suitable for diffractive configurations and highly tolerant to random noise was developed. The proposed technique can be applied to new characterization tools with high spatial resolution, fast data acquisition, and artificial intelligence, such as high-speed nanoscale metrology and quality control, and can be further developed to high-resolution spectroscopy
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- 2020
174. Closed-Loop Control of a Piezo-Fluidic Amplifier
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Nicholls, Chris and Bacic, Marko
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Electrical Engineering and Systems Science - Systems and Control ,Physics - Fluid Dynamics - Abstract
Fluidic valves based on the Coand\u{a} effect are increasingly being considered for use in aerodynamic flow control applications. A limiting factor is their variation in switching time, which often precludes their use. The purpose of this paper is to demonstrate the closed-loop control of a recently developed, novel piezo-fluidic valve that reduces response time uncertainty at the expense of operating bandwidth. Use is made of the fact that a fluidic jet responds to a piezo tone by deflecting away from its steady state position. A control signal used to vary this deflection is amplitude modulated onto the piezo tone. Using only a pressure measurement from one of the device output channels, an output-based LQG regulator was designed to follow a desired reference deflection, achieving control of a 90 m/s jet. Finally, the controller's performance in terms of disturbance rejection and response time predictability is demonstrated., Comment: 31 pages, 23 figures. Published in AIAA Journal, 4th May 2020
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- 2020
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175. Transverse spinning of unpolarized light
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Eismann, J. S., Nicholls, L. H., Roth, D. J., Alonso, M. A., Banzer, P., Rodríguez-Fortuño, F. J., Zayats, A. V., Nori, F., and Bliokh, K. Y.
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Physics - Optics - Abstract
It is well known that spin angular momentum of light, and therefore that of photons, is directly related to their circular polarization. Naturally, for totally unpolarized light, polarization is undefined and the spin vanishes. However, for nonparaxial light, the recently discovered transverse spin component, orthogonal to the main propagation direction, is largely independent of the polarization state of the wave. Here we demonstrate, both theoretically and experimentally, that this transverse spin survives even in nonparaxial fields (e.g., tightly focused or evanescent) generated from a totally unpolarized light source. This counterintuitive phenomenon is closely related to the fundamental difference between the degrees of polarization for 2D paraxial and 3D nonparaxial fields. Our results open an avenue for studies of spin-related phenomena and optical manipulation using unpolarized light., Comment: 11 pages, 3 figures
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- 2020
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176. Semi-Modular Inference: enhanced learning in multi-modular models by tempering the influence of components
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Carmona, Chris U. and Nicholls, Geoff K.
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Statistics - Methodology ,Mathematics - Statistics Theory ,Statistics - Machine Learning - Abstract
Bayesian statistical inference loses predictive optimality when generative models are misspecified. Working within an existing coherent loss-based generalisation of Bayesian inference, we show existing Modular/Cut-model inference is coherent, and write down a new family of Semi-Modular Inference (SMI) schemes, indexed by an influence parameter, with Bayesian inference and Cut-models as special cases. We give a meta-learning criterion and estimation procedure to choose the inference scheme. This returns Bayesian inference when there is no misspecification. The framework applies naturally to Multi-modular models. Cut-model inference allows directed information flow from well-specified modules to misspecified modules, but not vice versa. An existing alternative power posterior method gives tunable but undirected control of information flow, improving prediction in some settings. In contrast, SMI allows tunable and directed information flow between modules. We illustrate our methods on two standard test cases from the literature and a motivating archaeological data set., Comment: for associated R package to reproduce results, see https://github.com/christianu7/aistats2020smi
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- 2020
177. Large Scale Tensor Regression using Kernels and Variational Inference
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Hu, Robert, Nicholls, Geoff K., and Sejdinovic, Dino
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Statistics - Machine Learning ,Computer Science - Machine Learning ,Statistics - Computation - Abstract
We outline an inherent weakness of tensor factorization models when latent factors are expressed as a function of side information and propose a novel method to mitigate this weakness. We coin our method \textit{Kernel Fried Tensor}(KFT) and present it as a large scale forecasting tool for high dimensional data. Our results show superior performance against \textit{LightGBM} and \textit{Field Aware Factorization Machines}(FFM), two algorithms with proven track records widely used in industrial forecasting. We also develop a variational inference framework for KFT and associate our forecasts with calibrated uncertainty estimates on three large scale datasets. Furthermore, KFT is empirically shown to be robust against uninformative side information in terms of constants and Gaussian noise.
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- 2020
178. This needs to be a journey that we’re actually on together’—the introduction of integrated care systems for children and young people in England: a qualitative study of the views of local system stakeholders during winter 2021/22
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Hope, Steven, Stepanova, Evgenia, Lloyd-Houldey, Oliver, Hillier-Brown, Frances, Hargreaves, Dougal, Nicholls, Dasha, Summerbell, Carolyn, Viner, Russell M., Dedat, Zainab, Owen, Emily C., and Scott, Stephanie
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- 2023
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179. Author Correction: Global survey shows planners use widely varying sea-level rise projections for coastal adaptation
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Hirschfeld, Daniella, Behar, David, Nicholls, Robert J., Cahill, Niamh, James, Thomas, Horton, Benjamin P., Portman, Michelle E., Bell, Rob, Campo, Matthew, Esteban, Miguel, Goble, Bronwyn, Rahman, Munsur, Addo, Kwasi Appeaning, Chundeli, Faiz Ahmed, Aunger, Monique, Babitsky, Orly, Beal, Anders, Boyle, Ray, Fang, Jiayi, Gohar, Amir, Hanson, Susan, Karamesines, Saul, Kim, M. J., Lohmann, Hilary, McInnes, Kathy, Mimura, Nobuo, Ramsay, Doug, Wenger, Landis, and Yokoki, Hiromune
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- 2023
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180. ‘Helper’ or ‘punisher’? A qualitative study exploring staff experiences of treating severe and complex eating disorder presentations in inpatient settings
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Bommen, Sienna, Nicholls, Helen, and Billings, Jo
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- 2023
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181. Recurrent connectivity supports higher-level visual and semantic object representations in the brain
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von Seth, Jacqueline, Nicholls, Victoria I., Tyler, Lorraine K., and Clarke, Alex
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- 2023
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182. Systemic perturbations in amino acids/amino acid derivatives and tryptophan pathway metabolites associated with murine influenza A virus infection
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Al-Shalan, Huda A. M., Zhou, Lu, Dong, Zhifan, Wang, Penghao, Nicholls, Philip K., Boughton, Berin, Stumbles, Philip A., Greene, Wayne K., and Ma, Bin
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- 2023
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183. Recognizing patient partner contributions to health research: a systematic review of reported practices
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Fox, Grace, Lalu, Manoj M., Sabloff, Tara, Nicholls, Stuart G., Smith, Maureen, Stacey, Dawn, Almoli, Faris, and Fergusson, Dean A.
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- 2023
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184. Safety and efficacy of pegunigalsidase alfa in patients with Fabry disease who were previously treated with agalsidase alfa: results from BRIDGE, a phase 3 open-label study
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Linhart, Aleš, Dostálová, Gabriela, Nicholls, Kathy, West, Michael L., Tøndel, Camilla, Jovanovic, Ana, Giraldo, Pilar, Vujkovac, Bojan, Geberhiwot, Tarekegn, Brill-Almon, Einat, Alon, Sari, Chertkoff, Raul, Rocco, Rossana, and Hughes, Derralynn
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- 2023
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185. Pericoronary adipose tissue attenuation on coronary computed tomography angiography associates with male sex and Indigenous Australian status
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Yuvaraj, Jeremy, Lim, Egynne, Vo, Tony, Huynh, David, Rocco, Cheniqua, Nerlekar, Nitesh, Cheng, Kevin, Lin, Andrew, Dey, Damini, Nicholls, Stephen J., Kangaharan, Nadarajah, and Wong, Dennis T.L.
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- 2023
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186. GATA2 mitotic bookmarking is required for definitive haematopoiesis
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Silvério-Alves, Rita, Kurochkin, Ilia, Rydström, Anna, Vazquez Echegaray, Camila, Haider, Jakob, Nicholls, Matthew, Rode, Christina, Thelaus, Louise, Lindgren, Aida Yifter, Ferreira, Alexandra Gabriela, Brandão, Rafael, Larsson, Jonas, de Bruijn, Marella F. T. R., Martin-Gonzalez, Javier, and Pereira, Carlos-Filipe
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- 2023
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187. Smoking and secondary ACL rupture are detrimental to knee health post ACL injury—a Bayesian analysis
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Nicholls, Micah, Ingvarsson, Thorvaldur, Filbay, Stephanie, Lohmander, Stefan, and Briem, Kristin
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- 2023
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188. The evolving landscape of sea-level rise science from 1990 to 2021
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Khojasteh, Danial, Haghani, Milad, Nicholls, Robert J., Moftakhari, Hamed, Sadat-Noori, Mahmood, Mach, Katharine J., Fagherazzi, Sergio, Vafeidis, Athanasios T., Barbier, Edward, Shamsipour, Abbas, and Glamore, William
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- 2023
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189. A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer
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Mayoh, Chelsea, Gifford, Andrew J., Terry, Rachael, Lau, Loretta M. S., Wong, Marie, Rao, Padmashree, Shai-Hee, Tyler, Saletta, Federica, Khuong-Quang, Dong-Anh, Qin, Vicky, Mateos, Marion K., Meyran, Deborah, Miller, Katherine E., Yuksel, Aysen, Mould, Emily V. A., Bowen-James, Rachel, Govender, Dinisha, Senapati, Akanksha, Zhukova, Nataliya, Omer, Natacha, Dholaria, Hetal, Alvaro, Frank, Tapp, Heather, Diamond, Yonatan, Pozza, Luciano Dalla, Moore, Andrew S., Nicholls, Wayne, Gottardo, Nicholas G., McCowage, Geoffrey, Hansford, Jordan R., Khaw, Seong-Lin, Wood, Paul J., Catchpoole, Daniel, Cottrell, Catherine E., Mardis, Elaine R., Marshall, Glenn M., Tyrrell, Vanessa, Haber, Michelle, Ziegler, David S., Vittorio, Orazio, Trapani, Joseph A., Cowley, Mark J., Neeson, Paul J., and Ekert, Paul G.
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- 2023
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190. Improving social justice in observational studies: protocol for the development of a global and Indigenous STROBE-equity reporting guideline
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Funnell, Sarah, Jull, Janet, Mbuagbaw, Lawrence, Welch, Vivian, Dewidar, Omar, Wang, Xiaoqin, Lesperance, Miranda, Ghogomu, Elizabeth, Rizvi, Anita, Akl, Elie A., Avey, Marc T., Antequera, Alba, Bhutta, Zulfiqar A., Chamberlain, Catherine, Craig, Peter, Cuervo, Luis Gabriel, Dicko, Alassane, Ellingwood, Holly, Feng, Cindy, Francis, Damian, Greer-Smith, Regina, Hardy, Billie-Jo, Harwood, Matire, Hatcher-Roberts, Janet, Horsley, Tanya, Juando-Prats, Clara, Kasonde, Mwenya, Kennedy, Michelle, Kredo, Tamara, Krentel, Alison, Kristjansson, Elizabeth, Langer, Laurenz, Little, Julian, Loder, Elizabeth, Magwood, Olivia, Mahande, Michael Johnson, Melendez-Torres, G. J., Moore, Ainsley, Niba, Loveline Lum, Nicholls, Stuart G., Nkangu, Miriam Nguilefem, Lawson, Daeria O., Obuku, Ekwaro, Okwen, Patrick, Pantoja, Tomas, Petkovic, Jennifer, Petticrew, Mark, Pottie, Kevin, Rader, Tamara, Ramke, Jacqueline, Riddle, Alison, Shamseer, Larissa, Sharp, Melissa, Shea, Bev, Tanuseputro, Peter, Tugwell, Peter, Tufte, Janice, Von Elm, Erik, Waddington, Hugh Sharma, Wang, Harry, Weeks, Laura, Wells, George, White, Howard, Wiysonge, Charles Shey, Wolfenden, Luke, and Young, Taryn
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- 2023
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191. SARS-CoV-2 infection aggravates cigarette smoke-exposed cell damage in primary human airway epithelia
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Chen, Rui, Hui, Kenrie Pui-Yan, Liang, Yingmin, Ng, Ka-Chun, Nicholls, John Malcolm, Ip, Mary Sau-Man, Peiris, Malik, Chan, Michael Chi-Wai, and Mak, Judith Choi-Wo
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- 2023
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192. On the stability & phase locking to a system reference of an optoelectronic oscillator with large delay
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Hasan, Mehedi, Nicholls, Charles, and Hall, Trevor
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- 2023
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193. Viral subversion of selective autophagy is critical for biogenesis of virus replication organelles
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Lan, Yun, van Leur, Sophie Wilhelmina, Fernando, Julia Ayano, Wong, Ho Him, Kampmann, Martin, Siu, Lewis, Zhang, Jingshu, Li, Mingyuan, Nicholls, John M., and Sanyal, Sumana
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- 2023
- Full Text
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194. Observational evidence for on-shelf heat transport driven by dense water export in the Weddell Sea
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Darelius, Elin, Daae, Kjersti, Dundas, Vår, Fer, Ilker, Hellmer, Hartmut H., Janout, Markus, Nicholls, Keith W., Sallée, Jean-Baptiste, and Østerhus, Svein
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- 2023
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195. Histone H3-wild type diffuse midline gliomas with H3K27me3 loss are a distinct entity with exclusive EGFR or ACVR1 mutation and differential methylation of homeobox genes
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Ajuyah, Pamela, Mayoh, Chelsea, Lau, Loretta M. S., Barahona, Paulette, Wong, Marie, Chambers, Hazel, Valdes-Mora, Fatima, Senapati, Akanksha, Gifford, Andrew J., D’Arcy, Colleen, Hansford, Jordan R., Manoharan, Neevika, Nicholls, Wayne, Williams, Molly M., Wood, Paul J., Cowley, Mark J., Tyrrell, Vanessa, Haber, Michelle, Ekert, Paul G., Ziegler, David S., and Khuong-Quang, Dong-Anh
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- 2023
- Full Text
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196. Risk factors of persistent adolescent thinness: findings from the UK Millennium Cohort Study
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Whitfield, H., Hargreaves, D., Nicholls, D., Watt, H. C., and Creese, H.
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- 2023
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197. Global survey shows planners use widely varying sea-level rise projections for coastal adaptation
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Hirschfeld, Daniella, Behar, David, Nicholls, Robert J., Cahill, Niamh, James, Thomas, Horton, Benjamin P., Portman, Michelle E., Bell, Rob, Campo, Matthew, Esteban, Miguel, Goble, Bronwyn, Rahman, Munsur, Addo, Kwasi Appeaning, Chundeli, Faiz Ahmed, Aunger, Monique, Babitsky, Orly, Beal, Anders, Boyle, Ray, Fang, Jiayi, Gohar, Amir, Hanson, Susan, Karamesines, Saul, Kim, M. J., Lohmann, Hilary, McInnes, Kathy, Mimura, Nobuo, Ramsay, Doug, Wenger, Landis, and Yokoki, Hiromune
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- 2023
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198. Reduction in the risk of MACE with apabetalone in patients with recent acute coronary syndrome and diabetes according to NAFLD fibrosis score: exploratory analysis of the BETonMACE trial
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Toth, PP, Schwartz, GG, Nicholls, SJ, Halliday, C, Ginsberg, HN, Johansson, JO, Kalantar-Zadeh, K, Kulikowski, E, Lebioda, K, Wong, N, Sweeney, M, Ray, KK, and Investigators, BETonMACE
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Heart Disease ,Clinical Research ,Diabetes ,Clinical Trials and Supportive Activities ,Cardiovascular ,Cardiorespiratory Medicine and Haematology ,Clinical Sciences ,Cardiovascular System & Hematology - Abstract
Abstract Background/Introduction Both major adverse cardiovascular events (MACE) and non-alcoholic fatty-liver disease (NAFLD) are highly prevalent in patients with high BMI and long-standing type 2 diabetes (T2DM). NAFLD is characterized by an augmented hepatic inflammation and fat deposition and is strongly associated with metabolic syndrome. Patients with NAFLD are at an increased risk of cardiovascular (CV) events, and MACE is the leading cause of death for patients with NAFLD. Apabetalone (APB) is a novel selective inhibitor of bromodomain and extra-terminal (BET) proteins, epigenetic regulators of gene expression. In the Phase 3 BETonMACE trial treatment of 2,425 T2DM patients post ACS with APB, resulted in hazard ratios (HR) of 0.82 (p=0.11) for the primary endpoint of ischemic MACE (CV death, non-fatal MI or stroke) and 0.59 (p=0.03) for the secondary endpoint of heart failure hospitalization (HFH) vs placebo (PBO). Transient elevations of alanine aminotransferase greater than 5xULN occurred in 3.3% of APB treated patients. Purpose In this exploratory post hoc analysis of BETonMACE we evaluated risk modification for a composite of MACE+HFH by APB based on the Angulo NAFLD fibrosis score (FS) using 6 variables (age, BMI, hyperglycemia/diabetes, AST/ALT ratio, platelet count, and albumin). The NAFLD FS categorizes individuals into groups that correlate with differing levels of fibrosis in biopsy studies: (FS F0-F2, no significant fibrosis; FS ID, indeterminant; and FS F3-F4, significant fibrosis). Methods Baseline characteristics and blood measurements were used to determine NAFLD FS at baseline. The incidence of MACE+HHF was compared between treatment groups. Results Based on FS, there were 618 pts were classified as FS F0-F2 (n=328 APB, n=290 PBO), 1,440 pts were classified as FS ID (n=708 APB, n=732 PBO) and 289 pts were classified as FS F3-F4 (n=144 APB, n=145). MACE+HHF in the PBO group was higher in FS ID and FS F3-F4 compared to FS F0-F2 (17.2% vs 15.0% vs 9.7%) and therefore the former two groups were combined into an elevated risk FS+ group. FS+ pts were older (63 vs 56), had longer duration of T2DM (9.0 vs 7.3 yrs), and higher BMI (30.8 vs 28.6) compared to FS- pts. Overall, APB was associated with fewer MACE+HHF (HR 0.78, 95% CI 0.60–1.01, p=0.06) compared to PBO in the FS+ pts with adjustment for age, duration of T2DM and BMI. Conclusions Patients with T2DM and ACS may share common risk factors with patients with NAFLD. Apabetalone appears to exert a favorable effect on MACE in patients with risk factors for NAFLD. Whether apabetalone has a modulatory effect on the development and progression of NAFLD is an important question requiring further investigation. Funding Acknowledgement Type of funding sources: Private company. Main funding source(s): Resverlogix Corp.
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- 2021
199. Student Preparedness and Success in Introductory Psychology
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Altman, William S., Pena-Shaff, Judith B., Nicholls, Craig, and Domingo, Cassandra
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Background: Reading comprehension and writing ability are critical to students' success in introductory psychology. However, these generally are not prerequisites. There is conflicting evidence with regard to the effectiveness of remedial reading and writing classes for students with low placement exam scores. Objectives: To explore whether ACCUPLACER® test scores help predict performance in introductory psychology, and the effectiveness of reading and writing remediation classes in helping students, particularly those with low ACCUPLACER® scores. Method: Logistic regression analyses were used, to explore whether ACCUPLACER® test scores helped predict performance, and whether completing remediation classes helped students pass, controlling for ACCUPLACER® and WritePlacer® scores, at an upstate New York community college, between the years 2010 and 2015. Results: Placement test scores did help to predict successful course completion. There was not a statistically significant difference in successful course completion between students who passed the remedial courses and those who did not take them. Conclusions: Success in introductory psychology requires college-level reading and writing. Remedial courses' value in students' success in this class appears relatively small or non-significant. Teaching Implications: We propose solutions that may be more effective, involving embedding the remediation in the course, or in closely linked ancillary sections.
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- 2022
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200. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
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Meng, Bo, Kemp, Steven A, Papa, Guido, Datir, Rawlings, Ferreira, Isabella ATM, Marelli, Sara, Harvey, William T, Lytras, Spyros, Mohamed, Ahmed, Gallo, Giulia, Thakur, Nazia, Collier, Dami A, Mlcochova, Petra, Consortium, The COVID-19 Genomics UK, Robson, Samuel C, Loman, Nicholas J, Connor, Thomas R, Golubchik, Tanya, Nunez, Rocio T Martinez, Ludden, Catherine, Corden, Sally, Johnston, Ian, Bonsall, David, Smith, Colin P, Awan, Ali R, Bucca, Giselda, Torok, M Estee, Saeed, Kordo, Prieto, Jacqui A, Jackson, David K, Hamilton, William L, Snell, Luke B, Moore, Catherine, Harrison, Ewan M, Goncalves, Sonia, Fairley, Derek J, Loose, Matthew W, Watkins, Joanne, Livett, Rich, Moses, Samuel, Amato, Roberto, Nicholls, Sam, Bull, Matthew, Smith, Darren L, Barrett, Jeff, Aanensen, David M, Curran, Martin D, Parmar, Surendra, Aggarwal, Dinesh, Shepherd, James G, Parker, Matthew D, Glaysher, Sharon, Bashton, Matthew, Underwood, Anthony P, Pacchiarini, Nicole, Loveson, Katie F, Templeton, Kate E, Langford, Cordelia F, Sillitoe, John, de Silva, Thushan I, Wang, Dennis, Kwiatkowski, Dominic, Rambaut, Andrew, O’Grady, Justin, Cottrell, Simon, Holden, Matthew TG, Thomson, Emma C, Osman, Husam, Andersson, Monique, Chauhan, Anoop J, Hassan-Ibrahim, Mohammed O, Lawniczak, Mara, Alderton, Alex, Chand, Meera, Constantinidou, Chrystala, Unnikrishnan, Meera, Darby, Alistair C, Hiscox, Julian A, Paterson, Steve, Martincorena, Inigo, Volz, Erik M, Page, Andrew J, Pybus, Oliver G, Bassett, Andrew R, Ariani, Cristina V, Chapman, Michael H Spencer, Li, Kathy K, Shah, Rajiv N, Jesudason, Natasha G, Taha, Yusri, McHugh, Martin P, Dewar, Rebecca, Jahun, Aminu S, McMurray, Claire, Pandey, Sarojini, McKenna, James P, Nelson, Andrew, Young, Gregory R, McCann, Clare M, and Elliott, Scott
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Emerging Infectious Diseases ,Infectious Diseases ,Lung ,Pneumonia ,Good Health and Well Being ,Animals ,Antibodies ,Neutralizing ,Antibodies ,Viral ,COVID-19 ,Cell Line ,Chlorocebus aethiops ,HEK293 Cells ,Humans ,Immune Evasion ,Mutation ,Pandemics ,Phylogeny ,Protein Binding ,Recurrence ,SARS-CoV-2 ,Spike Glycoprotein ,Coronavirus ,Vero Cells ,COVID-19 Genomics UK (COG-UK) Consortium ,Alpha variant ,B.1.1.7 ,antibody escape ,deletion ,infectivity ,neutralizing antibodies ,resistance ,spike mutation ,Biochemistry and Cell Biology ,Medical Physiology - Abstract
We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.
- Published
- 2021
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