17,729 results on '"O'Connell, P."'
Search Results
2. OpenAI o1 System Card
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OpenAI, Jaech, Aaron, Kalai, Adam, Lerer, Adam, Richardson, Adam, El-Kishky, Ahmed, Low, Aiden, Helyar, Alec, Madry, Aleksander, Beutel, Alex, Carney, Alex, Iftimie, Alex, Karpenko, Alex, Passos, Alex Tachard, Neitz, Alexander, Prokofiev, Alexander, Wei, Alexander, Tam, Allison, Bennett, Ally, Kumar, Ananya, Saraiva, Andre, Vallone, Andrea, Duberstein, Andrew, Kondrich, Andrew, Mishchenko, Andrey, Applebaum, Andy, Jiang, Angela, Nair, Ashvin, Zoph, Barret, Ghorbani, Behrooz, Rossen, Ben, Sokolowsky, Benjamin, Barak, Boaz, McGrew, Bob, Minaiev, Borys, Hao, Botao, Baker, Bowen, Houghton, Brandon, McKinzie, Brandon, Eastman, Brydon, Lugaresi, Camillo, Bassin, Cary, Hudson, Cary, Li, Chak Ming, de Bourcy, Charles, Voss, Chelsea, Shen, Chen, Zhang, Chong, Koch, Chris, Orsinger, Chris, Hesse, Christopher, Fischer, Claudia, Chan, Clive, Roberts, Dan, Kappler, Daniel, Levy, Daniel, Selsam, Daniel, Dohan, David, Farhi, David, Mely, David, Robinson, David, Tsipras, Dimitris, Li, Doug, Oprica, Dragos, Freeman, Eben, Zhang, Eddie, Wong, Edmund, Proehl, Elizabeth, Cheung, Enoch, Mitchell, Eric, Wallace, Eric, Ritter, Erik, Mays, Evan, Wang, Fan, Such, Felipe Petroski, Raso, Filippo, Leoni, Florencia, Tsimpourlas, Foivos, Song, Francis, von Lohmann, Fred, Sulit, Freddie, Salmon, Geoff, Parascandolo, Giambattista, Chabot, Gildas, Zhao, Grace, Brockman, Greg, Leclerc, Guillaume, Salman, Hadi, Bao, Haiming, Sheng, Hao, Andrin, Hart, Bagherinezhad, Hessam, Ren, Hongyu, Lightman, Hunter, Chung, Hyung Won, Kivlichan, Ian, O'Connell, Ian, Osband, Ian, Gilaberte, Ignasi Clavera, Akkaya, Ilge, Kostrikov, Ilya, Sutskever, Ilya, Kofman, Irina, Pachocki, Jakub, Lennon, James, Wei, Jason, Harb, Jean, Twore, Jerry, Feng, Jiacheng, Yu, Jiahui, Weng, Jiayi, Tang, Jie, Yu, Jieqi, Candela, Joaquin Quiñonero, Palermo, Joe, Parish, Joel, Heidecke, Johannes, Hallman, John, Rizzo, John, Gordon, Jonathan, Uesato, Jonathan, Ward, Jonathan, Huizinga, Joost, Wang, Julie, Chen, Kai, Xiao, Kai, Singhal, Karan, Nguyen, Karina, Cobbe, Karl, Shi, Katy, Wood, Kayla, Rimbach, Kendra, Gu-Lemberg, Keren, Liu, Kevin, Lu, Kevin, Stone, Kevin, Yu, Kevin, Ahmad, Lama, Yang, Lauren, Liu, Leo, Maksin, Leon, Ho, Leyton, Fedus, Liam, Weng, Lilian, Li, Linden, McCallum, Lindsay, Held, Lindsey, Kuhn, Lorenz, Kondraciuk, Lukas, Kaiser, Lukasz, Metz, Luke, Boyd, Madelaine, Trebacz, Maja, Joglekar, Manas, Chen, Mark, Tintor, Marko, Meyer, Mason, Jones, Matt, Kaufer, Matt, Schwarzer, Max, Shah, Meghan, Yatbaz, Mehmet, Guan, Melody Y., Xu, Mengyuan, Yan, Mengyuan, Glaese, Mia, Chen, Mianna, Lampe, Michael, Malek, Michael, Wang, Michele, Fradin, Michelle, McClay, Mike, Pavlov, Mikhail, Wang, Miles, Wang, Mingxuan, Murati, Mira, Bavarian, Mo, Rohaninejad, Mostafa, McAleese, Nat, Chowdhury, Neil, Ryder, Nick, Tezak, Nikolas, Brown, Noam, Nachum, Ofir, Boiko, Oleg, Murk, Oleg, Watkins, Olivia, Chao, Patrick, Ashbourne, Paul, Izmailov, Pavel, Zhokhov, Peter, Dias, Rachel, Arora, Rahul, Lin, Randall, Lopes, Rapha Gontijo, Gaon, Raz, Miyara, Reah, Leike, Reimar, Hwang, Renny, Garg, Rhythm, Brown, Robin, James, Roshan, Shu, Rui, Cheu, Ryan, Greene, Ryan, Jain, Saachi, Altman, Sam, Toizer, Sam, Toyer, Sam, Miserendino, Samuel, Agarwal, Sandhini, Hernandez, Santiago, Baker, Sasha, McKinney, Scott, Yan, Scottie, Zhao, Shengjia, Hu, Shengli, Santurkar, Shibani, Chaudhuri, Shraman Ray, Zhang, Shuyuan, Fu, Siyuan, Papay, Spencer, Lin, Steph, Balaji, Suchir, Sanjeev, Suvansh, Sidor, Szymon, Broda, Tal, Clark, Aidan, Wang, Tao, Gordon, Taylor, Sanders, Ted, Patwardhan, Tejal, Sottiaux, Thibault, Degry, Thomas, Dimson, Thomas, Zheng, Tianhao, Garipov, Timur, Stasi, Tom, Bansal, Trapit, Creech, Trevor, Peterson, Troy, Eloundou, Tyna, Qi, Valerie, Kosaraju, Vineet, Monaco, Vinnie, Pong, Vitchyr, Fomenko, Vlad, Zheng, Weiyi, Zhou, Wenda, McCabe, Wes, Zaremba, Wojciech, Dubois, Yann, Lu, Yinghai, Chen, Yining, Cha, Young, Bai, Yu, He, Yuchen, Zhang, Yuchen, Wang, Yunyun, Shao, Zheng, and Li, Zhuohan
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Computer Science - Artificial Intelligence - Abstract
The o1 model series is trained with large-scale reinforcement learning to reason using chain of thought. These advanced reasoning capabilities provide new avenues for improving the safety and robustness of our models. In particular, our models can reason about our safety policies in context when responding to potentially unsafe prompts, through deliberative alignment. This leads to state-of-the-art performance on certain benchmarks for risks such as generating illicit advice, choosing stereotyped responses, and succumbing to known jailbreaks. Training models to incorporate a chain of thought before answering has the potential to unlock substantial benefits, while also increasing potential risks that stem from heightened intelligence. Our results underscore the need for building robust alignment methods, extensively stress-testing their efficacy, and maintaining meticulous risk management protocols. This report outlines the safety work carried out for the OpenAI o1 and OpenAI o1-mini models, including safety evaluations, external red teaming, and Preparedness Framework evaluations.
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- 2024
3. Single-exposure X-ray dark-field imaging via a dual-energy propagation-based setup
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Ahlers, Jannis N., Pavlov, Konstantin M., Kitchen, Marcus J., Harker, Stephanie A., Pryor, Emily J., Pollock, James A., Croughan, Michelle K., How, Ying Ying, Zdora, Marie-Christine, Costello, Lucy F., O'Connell, Dylan W., Hall, Christopher, and Morgan, Kaye S.
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Physics - Optics ,Physics - Medical Physics - Abstract
X-ray dark-field imaging visualises scattering from sample microstructure, and has found application in medical and security contexts. While most X-ray dark-field imaging techniques rely on masks, gratings, or crystals, recent work on the Fokker--Planck model of diffusive imaging has enabled dark-field imaging in the propagation-based geometry. Images captured at multiple propagation distances or X-ray energies can be used to reconstruct dark-field from propagation-based images but have previously required multiple exposures. Here, we show single-exposure dark-field imaging by exploiting the harmonic content in a monochromatised synchrotron beam and utilising an energy-discriminating photon-counting detector to capture dual-energy propagation-based images. The method is validated by filming time-varying samples, showing the advantage of the dark-field contrast in analysing dynamic evolution. We measure and adjust for the impact of detector charge-sharing on the images. This work opens the way for low-dose and dynamic dark-field X-ray imaging without the need for a high-stability set-up and precision optics., Comment: 9 pages, 7 figures
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- 2024
4. Managing Project Teams in an Online Class of 1000+ Students
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Anaraki, Nazanin Tabatabaei, Ng, Taneisha, Verma, Gaurav, Fu, Yu, O'Connell, Martin, Hull, Matthew, Routray, Susanta, Roozbahani, Max Mahdi, and Chau, Duen Horng
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Computer Science - Computers and Society ,Computer Science - Human-Computer Interaction - Abstract
Team projects in Computer Science (CS) help students build collaboration skills, apply theory, and prepare for real-world software development. Online classes present unique opportunities to transform the accessibility of CS education at scale. Still, the geographical distribution of students and staff adds complexity to forming effective teams, providing consistent feedback, and facilitating peer interactions. We discuss our approach of managing, evaluating, and providing constructive feedback to over 200 project teams, comprising 1000+ graduate students distributed globally, two professors, and 25+ teaching assistants. We deployed and iteratively refined this approach over 10 years while offering the Data and Visual Analytics course (CSE 6242) at Georgia Institute of Technology. Our approach and insights can help others striving to make CS education accessible, especially in online and large-scale settings., Comment: Poster at Technical Symposium on Computer Science Education (SIGCSE TS 2025), 2 pages
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- 2024
5. Assessing Personalized AI Mentoring with Large Language Models in the Computing Field
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Luo, Xiao, O'Connell, Sean, and Mithun, Shamima
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
This paper provides an in-depth evaluation of three state-of-the-art Large Language Models (LLMs) for personalized career mentoring in the computing field, using three distinct student profiles that consider gender, race, and professional levels. We evaluated the performance of GPT-4, LLaMA 3, and Palm 2 using a zero-shot learning approach without human intervention. A quantitative evaluation was conducted through a custom natural language processing analytics pipeline to highlight the uniqueness of the responses and to identify words reflecting each student's profile, including race, gender, or professional level. The analysis of frequently used words in the responses indicates that GPT-4 offers more personalized mentoring compared to the other two LLMs. Additionally, a qualitative evaluation was performed to see if human experts reached similar conclusions. The analysis of survey responses shows that GPT-4 outperformed the other two LLMs in delivering more accurate and useful mentoring while addressing specific challenges with encouragement languages. Our work establishes a foundation for developing personalized mentoring tools based on LLMs, incorporating human mentors in the process to deliver a more impactful and tailored mentoring experience.
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- 2024
6. Amplitudes for Hawking Radiation
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Aoude, Rafael, O'Connell, Donal, and Sergola, Matteo
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High Energy Physics - Theory ,General Relativity and Quantum Cosmology - Abstract
We obtain the Hawking spectrum by exponentiating a series of Feynman diagrams describing a scalar field scattering through a collapse background. Our approach is rooted in semiclassical methods of scattering amplitudes which have recently been developed for application to gravitational-wave physics. The diagrams we encounter do not compute a standard amplitude, but rather an in-in generalisation of an amplitude which is closely connected to the Bogoliubov coefficients. We also compute the subdominant one-loop correction in our perturbative approach, analogous to the triangle correction to Schwarzschild scattering. This term can be interpreted as a finite-size correction sensitive to the radius of the black hole., Comment: 35 pages + appendices
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- 2024
7. Scoping review of methodology for aiding generalisability and transportability of clinical prediction models
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Ploddi, Kritchavat, Sperrin, Matthew, Martin, Glen P., and O'Connell, Maurice M.
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Statistics - Methodology - Abstract
Generalisability and transportability of clinical prediction models (CPMs) refer to their ability to maintain predictive performance when applied to new populations. While CPMs may show good generalisability or transportability to a specific new population, it is rare for a CPM to be developed using methods that prioritise good generalisability or transportability. There is an emerging literature of such techniques; therefore, this scoping review aims to summarise the main methodological approaches, assumptions, advantages, disadvantages and future development of methodology aiding the generalisability/transportability. Relevant articles were systematically searched from MEDLINE, Embase, medRxiv, arxiv databases until September 2023 using a predefined set of search terms. Extracted information included methodology description, assumptions, applied examples, advantages and disadvantages. The searches found 1,761 articles; 172 were retained for full text screening; 18 were finally included. We categorised the methodologies according to whether they were data-driven or knowledge-driven, and whether are specifically tailored for target population. Data-driven approaches range from data augmentation to ensemble methods and density ratio weighting, while knowledge-driven strategies rely on causal methodology. Future research could focus on comparison of such methodologies on simulated and real datasets to identify their strengths specific applicability, as well as synthesising these approaches for enhancing their practical usefulness.
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- 2024
8. Cardiac Computed Tomography Measurements in Pulmonary Embolism Associated with Clinical Deterioration
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Weekes, Anthony J., Pikus, Angela M., Hambright, Parker L., and O’Connell, Nathaniel
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pulmonary embolism ,Outcomes ,adverse outcomes ,computed tomography ,Artificial Intelligence ,Prognosis ,right ventricular dysfunction ,risk stratification ,intermediate risk - Abstract
Introduction: Most pulmonary embolism response teams (PERT) use a radiologist-determined right ventricle to left ventricle ratio (RV:LV) cut-off of 1.0 to risk-stratify pulmonary embolism (PE) patients. Continuous measurements from computed tomography pulmonary angiograms (CTPAs) may improve risk stratification. We assessed associations of CTPA cardiac measurements with acute clinical deterioration and use of advanced PE interventions.Methods: This was a retrospective study of a PE registry used by eight affiliated emergency departments. We used an artificial intelligence (AI) algorithm to measure RV:LV on anonymized CTPAs from registry patients for whom the PERT was activated (2018–2023) by institutional guidelines. Primary outcome was in-hospital PE-related clinical deterioration defined as cardiac arrest, vasoactive medication use for hypotension, or rescue respiratory interventions. Secondary outcome was advanced intervention use. We used bivariable and multivariable analyses. For the latter, we used least absolute shrinkage and selection operator (LASSO) and random forest (RF) to determine associations of all candidate variables with the primary outcome (clinical deterioration), and the Youden index to determine RV:LV optimal cut-offs for primary outcome.Results: Artificial intelligence analyzed 1,467 CTPAs, with 88% agreement on RV:LV categorization with radiologist reports (kappa 0.36, 95% confidence interval [CI] 0.28–0.43). Of 1,639 patients, 190 (11.6%) had PE-related clinical deterioration, and 314 (19.2%) had advanced interventions. Mean RV:LV were 1.50 (0.39) vs 1.30 (0.32) for those with and without clinical deterioration and 1.62 (0.33) vs 1.35 (0.32) for those with and without advanced intervention use. The RV:LV cut-off of 1.0 by AI and radiologists had 0.02 and 0.53 P-values for clinical deterioration, respectively. With adjusted LASSO, top clinical deterioration predictors were cardiac arrest at presentation, lowest systolic blood pressure, and intensive care unit admission. The RV:LV measurement was a top 10 predictor of clinical deterioration by RF. Optimal cut-off for RV:LV was 1.54 with odds ratio of 2.50 (1.85, 3.45) and area under the curve 0.6 (0.66, 0.70).Conclusion: Artifical intelligence-derived RV:LV measurements ≥1.5 on initial CTPA had strong associations with in-hospital clinical deterioration and advanced interventions in a large PERT database. This study points to the potential of capitalizing on immediately available CTPA RV:LV measurements for gauging PE severity and risk stratification.
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- 2025
9. Identification of novel genomic loci for anxiety symptoms and extensive genetic overlap with psychiatric disorders
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Tesfaye, Markos, Jaholkowski, Piotr, Shadrin, Alexey A, van der Meer, Dennis, Hindley, Guy FL, Holen, Børge, Parker, Nadine, Parekh, Pravesh, Birkenæs, Viktoria, Rahman, Zillur, Bahrami, Shahram, Kutrolli, Gleda, Frei, Oleksandr, Djurovic, Srdjan, Dale, Anders M, Smeland, Olav B, O'Connell, Kevin S, and Andreassen, Ole A
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Biological Psychology ,Biomedical and Clinical Sciences ,Psychology ,Behavioral and Social Science ,Pediatric ,Mental Illness ,Human Genome ,Genetics ,Schizophrenia ,Biotechnology ,Serious Mental Illness ,Mental Health ,Brain Disorders ,2.1 Biological and endogenous factors ,Mental health ,Good Health and Well Being ,Humans ,Genome-Wide Association Study ,Bipolar Disorder ,Autism Spectrum Disorder ,Depressive Disorder ,Major ,Attention Deficit Disorder with Hyperactivity ,Female ,Anxiety Disorders ,Male ,Multifactorial Inheritance ,Adult ,Genetic Loci ,Anxiety ,Comorbidity ,Middle Aged ,Mental Disorders ,anxiety ,genetic loci ,genetic overlap ,psychiatric disorder ,Clinical Sciences ,Neurosciences ,Cognitive Sciences ,Clinical sciences ,Biological psychology - Abstract
AimsAnxiety disorders are prevalent and anxiety symptoms (ANX) co-occur with many psychiatric disorders. We aimed to identify genomic loci associated with ANX, characterize its genetic architecture, and genetic overlap with psychiatric disorders.MethodsWe included a genome-wide association study of ANX (meta-analysis of UK Biobank and Million Veterans Program, n = 301,732), schizophrenia (SCZ), bipolar disorder (BIP), major depression (MD), attention-deficit/hyperactivity disorder (ADHD), and autism spectrum disorder (ASD), and validated the findings in the Norwegian Mother, Father, and Child Cohort (n = 95,841). We employed the bivariate causal mixture model and local analysis of covariant association to characterize the genetic architecture including overlap between the phenotypes. Conditional and conjunctional false discovery rate analyses were performed to boost the identification of loci associated with anxiety and shared with psychiatric disorders.ResultsAnxiety was polygenic with 12.9k genetic variants and overlapped extensively with psychiatric disorders (4.1k-11.4k variants) with predominantly positive genetic correlations between anxiety and psychiatric disorders. We identified 119 novel loci for anxiety by conditioning on the psychiatric disorders, and loci shared between anxiety and MD n=47 , BIP n=33 , SCZ n=71 , ADHD n=20 , and ASD n=5 . Genes annotated to anxiety loci exhibit enrichment for a broader range of biological pathways including cell adhesion and neurofibrillary tangle compared with genes annotated to the shared loci.ConclusionsAnxiety is highly polygenic phenotype with extensive genetic overlap with psychiatric disorders, and we identified novel loci for anxiety implicating new molecular pathways. The shared genetic architecture may underlie the extensive cross-disorder comorbidity of anxiety, and the identified molecular underpinnings may lead to potential drug targets.
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- 2024
10. GPT-4o System Card
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OpenAI, Hurst, Aaron, Lerer, Adam, Goucher, Adam P., Perelman, Adam, Ramesh, Aditya, Clark, Aidan, Ostrow, AJ, Welihinda, Akila, Hayes, Alan, Radford, Alec, Mądry, Aleksander, Baker-Whitcomb, Alex, Beutel, Alex, Borzunov, Alex, Carney, Alex, Chow, Alex, Kirillov, Alex, Nichol, Alex, Paino, Alex, Renzin, Alex, Passos, Alex Tachard, Kirillov, Alexander, Christakis, Alexi, Conneau, Alexis, Kamali, Ali, Jabri, Allan, Moyer, Allison, Tam, Allison, Crookes, Amadou, Tootoochian, Amin, Tootoonchian, Amin, Kumar, Ananya, Vallone, Andrea, Karpathy, Andrej, Braunstein, Andrew, Cann, Andrew, Codispoti, Andrew, Galu, Andrew, Kondrich, Andrew, Tulloch, Andrew, Mishchenko, Andrey, Baek, Angela, Jiang, Angela, Pelisse, Antoine, Woodford, Antonia, Gosalia, Anuj, Dhar, Arka, Pantuliano, Ashley, Nayak, Avi, Oliver, Avital, Zoph, Barret, Ghorbani, Behrooz, Leimberger, Ben, Rossen, Ben, Sokolowsky, Ben, Wang, Ben, Zweig, Benjamin, Hoover, Beth, Samic, Blake, McGrew, Bob, Spero, Bobby, Giertler, Bogo, Cheng, Bowen, Lightcap, Brad, Walkin, Brandon, Quinn, Brendan, Guarraci, Brian, Hsu, Brian, Kellogg, Bright, Eastman, Brydon, Lugaresi, Camillo, Wainwright, Carroll, Bassin, Cary, Hudson, Cary, Chu, Casey, Nelson, Chad, Li, Chak, Shern, Chan Jun, Conger, Channing, Barette, Charlotte, Voss, Chelsea, Ding, Chen, Lu, Cheng, Zhang, Chong, Beaumont, Chris, Hallacy, Chris, Koch, Chris, Gibson, Christian, Kim, Christina, Choi, Christine, McLeavey, Christine, Hesse, Christopher, Fischer, Claudia, Winter, Clemens, Czarnecki, Coley, Jarvis, Colin, Wei, Colin, Koumouzelis, Constantin, Sherburn, Dane, Kappler, Daniel, Levin, Daniel, Levy, Daniel, Carr, David, Farhi, David, Mely, David, Robinson, David, Sasaki, David, Jin, Denny, Valladares, Dev, Tsipras, Dimitris, Li, Doug, Nguyen, Duc Phong, Findlay, Duncan, Oiwoh, Edede, Wong, Edmund, Asdar, Ehsan, Proehl, Elizabeth, Yang, Elizabeth, Antonow, Eric, Kramer, Eric, Peterson, Eric, Sigler, Eric, Wallace, Eric, Brevdo, Eugene, Mays, Evan, Khorasani, Farzad, Such, Felipe Petroski, Raso, Filippo, Zhang, Francis, von Lohmann, Fred, Sulit, Freddie, Goh, Gabriel, Oden, Gene, Salmon, Geoff, Starace, Giulio, Brockman, Greg, Salman, Hadi, Bao, Haiming, Hu, Haitang, Wong, Hannah, Wang, Haoyu, Schmidt, Heather, Whitney, Heather, Jun, Heewoo, Kirchner, Hendrik, Pinto, Henrique Ponde de Oliveira, Ren, Hongyu, Chang, Huiwen, Chung, Hyung Won, Kivlichan, Ian, O'Connell, Ian, Osband, Ian, Silber, Ian, Sohl, Ian, Okuyucu, Ibrahim, Lan, Ikai, Kostrikov, Ilya, Sutskever, Ilya, Kanitscheider, Ingmar, Gulrajani, Ishaan, Coxon, Jacob, Menick, Jacob, Pachocki, Jakub, Aung, James, Betker, James, Crooks, James, Lennon, James, Kiros, Jamie, Leike, Jan, Park, Jane, Kwon, Jason, Phang, Jason, Teplitz, Jason, Wei, Jason, Wolfe, Jason, Chen, Jay, Harris, Jeff, Varavva, Jenia, Lee, Jessica Gan, Shieh, Jessica, Lin, Ji, Yu, Jiahui, Weng, Jiayi, Tang, Jie, Yu, Jieqi, Jang, Joanne, Candela, Joaquin Quinonero, Beutler, Joe, Landers, Joe, Parish, Joel, Heidecke, Johannes, Schulman, John, Lachman, Jonathan, McKay, Jonathan, Uesato, Jonathan, Ward, Jonathan, Kim, Jong Wook, Huizinga, Joost, Sitkin, Jordan, Kraaijeveld, Jos, Gross, Josh, Kaplan, Josh, Snyder, Josh, Achiam, Joshua, Jiao, Joy, Lee, Joyce, Zhuang, Juntang, Harriman, Justyn, Fricke, Kai, Hayashi, Kai, Singhal, Karan, Shi, Katy, Karthik, Kavin, Wood, Kayla, Rimbach, Kendra, Hsu, Kenny, Nguyen, Kenny, Gu-Lemberg, Keren, Button, Kevin, Liu, Kevin, Howe, Kiel, Muthukumar, Krithika, Luther, Kyle, Ahmad, Lama, Kai, Larry, Itow, Lauren, Workman, Lauren, Pathak, Leher, Chen, Leo, Jing, Li, Guy, Lia, Fedus, Liam, Zhou, Liang, Mamitsuka, Lien, Weng, Lilian, McCallum, Lindsay, Held, Lindsey, Ouyang, Long, Feuvrier, Louis, Zhang, Lu, Kondraciuk, Lukas, Kaiser, Lukasz, Hewitt, Luke, Metz, Luke, Doshi, Lyric, Aflak, Mada, Simens, Maddie, Boyd, Madelaine, Thompson, Madeleine, Dukhan, Marat, Chen, Mark, Gray, Mark, Hudnall, Mark, Zhang, Marvin, Aljubeh, Marwan, Litwin, Mateusz, Zeng, Matthew, Johnson, Max, Shetty, Maya, Gupta, Mayank, Shah, Meghan, Yatbaz, Mehmet, Yang, Meng Jia, Zhong, Mengchao, Glaese, Mia, Chen, Mianna, Janner, Michael, Lampe, Michael, Petrov, Michael, Wu, Michael, Wang, Michele, Fradin, Michelle, Pokrass, Michelle, Castro, Miguel, de Castro, Miguel Oom Temudo, Pavlov, Mikhail, Brundage, Miles, Wang, Miles, Khan, Minal, Murati, Mira, Bavarian, Mo, Lin, Molly, Yesildal, Murat, Soto, Nacho, Gimelshein, Natalia, Cone, Natalie, Staudacher, Natalie, Summers, Natalie, LaFontaine, Natan, Chowdhury, Neil, Ryder, Nick, Stathas, Nick, Turley, Nick, Tezak, Nik, Felix, Niko, Kudige, Nithanth, Keskar, Nitish, Deutsch, Noah, Bundick, Noel, Puckett, Nora, Nachum, Ofir, Okelola, Ola, Boiko, Oleg, Murk, Oleg, Jaffe, Oliver, Watkins, Olivia, Godement, Olivier, Campbell-Moore, Owen, Chao, Patrick, McMillan, Paul, Belov, Pavel, Su, Peng, Bak, Peter, Bakkum, Peter, Deng, Peter, Dolan, Peter, Hoeschele, Peter, Welinder, Peter, Tillet, Phil, Pronin, Philip, Tillet, Philippe, Dhariwal, Prafulla, Yuan, Qiming, Dias, Rachel, Lim, Rachel, Arora, Rahul, Troll, Rajan, Lin, Randall, Lopes, Rapha Gontijo, Puri, Raul, Miyara, Reah, Leike, Reimar, Gaubert, Renaud, Zamani, Reza, Wang, Ricky, Donnelly, Rob, Honsby, Rob, Smith, Rocky, Sahai, Rohan, Ramchandani, Rohit, Huet, Romain, Carmichael, Rory, Zellers, Rowan, Chen, Roy, Chen, Ruby, Nigmatullin, Ruslan, Cheu, Ryan, Jain, Saachi, Altman, Sam, Schoenholz, Sam, Toizer, Sam, Miserendino, Samuel, Agarwal, Sandhini, Culver, Sara, Ethersmith, Scott, Gray, Scott, Grove, Sean, Metzger, Sean, Hermani, Shamez, Jain, Shantanu, Zhao, Shengjia, Wu, Sherwin, Jomoto, Shino, Wu, Shirong, Shuaiqi, Xia, Phene, Sonia, Papay, Spencer, Narayanan, Srinivas, Coffey, Steve, Lee, Steve, Hall, Stewart, Balaji, Suchir, Broda, Tal, Stramer, Tal, Xu, Tao, Gogineni, Tarun, Christianson, Taya, Sanders, Ted, Patwardhan, Tejal, Cunninghman, Thomas, Degry, Thomas, Dimson, Thomas, Raoux, Thomas, Shadwell, Thomas, Zheng, Tianhao, Underwood, Todd, Markov, Todor, Sherbakov, Toki, Rubin, Tom, Stasi, Tom, Kaftan, Tomer, Heywood, Tristan, Peterson, Troy, Walters, Tyce, Eloundou, Tyna, Qi, Valerie, Moeller, Veit, Monaco, Vinnie, Kuo, Vishal, Fomenko, Vlad, Chang, Wayne, Zheng, Weiyi, Zhou, Wenda, Manassra, Wesam, Sheu, Will, Zaremba, Wojciech, Patil, Yash, Qian, Yilei, Kim, Yongjik, Cheng, Youlong, Zhang, Yu, He, Yuchen, Zhang, Yuchen, Jin, Yujia, Dai, Yunxing, and Malkov, Yury
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Computers and Society ,Computer Science - Machine Learning ,Computer Science - Sound ,Electrical Engineering and Systems Science - Audio and Speech Processing - Abstract
GPT-4o is an autoregressive omni model that accepts as input any combination of text, audio, image, and video, and generates any combination of text, audio, and image outputs. It's trained end-to-end across text, vision, and audio, meaning all inputs and outputs are processed by the same neural network. GPT-4o can respond to audio inputs in as little as 232 milliseconds, with an average of 320 milliseconds, which is similar to human response time in conversation. It matches GPT-4 Turbo performance on text in English and code, with significant improvement on text in non-English languages, while also being much faster and 50\% cheaper in the API. GPT-4o is especially better at vision and audio understanding compared to existing models. In line with our commitment to building AI safely and consistent with our voluntary commitments to the White House, we are sharing the GPT-4o System Card, which includes our Preparedness Framework evaluations. In this System Card, we provide a detailed look at GPT-4o's capabilities, limitations, and safety evaluations across multiple categories, focusing on speech-to-speech while also evaluating text and image capabilities, and measures we've implemented to ensure the model is safe and aligned. We also include third-party assessments on dangerous capabilities, as well as discussion of potential societal impacts of GPT-4o's text and vision capabilities.
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- 2024
11. UVCANDELS: Catalogs of photometric redshifts and galaxy physical properties
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Mehta, Vihang, Rafelski, Marc, Sunnquist, Ben, Teplitz, Harry I., Scarlata, Claudia, Wang, Xin, Fontana, Adriano, Hathi, Nimish P., Iyer, Kartheik G., Alavi, Anahita, Colbert, James, Grogin, Norman, Koekemoer, Anton, Nedkova, Kalina V., Hayes, Matthew, Prichard, Laura, Siana, Brian, Smith, Brent M., Windhorst, Rogier, Ashcraft, Teresa, Bagley, Micaela, Baronchelli, Ivano, Barro, Guillermo, Blanche, Alex, Broussard, Adam, Carleton, Timothy, Chartab, Nima, Codoreanu, Alex, Cohen, Seth, Conselice, Christopher, Dai, Y. Sophia, Darvish, Behnam, Dave, Romeel, DeGroot, Laura, De Mello, Duilia, Dickinson, Mark, Emami, Najmeh, Ferguson, Henry, Ferreira, Leonardo, Finkelstein, Keely, Finkelstein, Steven, Gardner, Jonathan P., Gawiser, Eric, Gburek, Timothy, Giavalisco, Mauro, Grazian, Andrea, Gronwall, Caryl, Guo, Yicheng, Haro, Pablo Arrabal, Hemmati, Shoubaneh, Howell, Justin, Jansen, Rolf A., Ji, Zhiyuan, Kaviraj, Sugata, Kim, Keunho J., Kurczynski, Peter, Lazar, Ilin, Lucas, Ray A., MacKenty, John, Mantha, Kameswara Bharadwaj, Martin, Alec, Martin, Garreth, McCabe, Tyler, Mobasher, Bahram, Morales, Alexa M., O'Connell, Robert, Olsen, Charlotte, Otteson, Lillian, Ravindranath, Swara, Redshaw, Caleb, Rutkowski, Michael, Robertson, Brant, Sattari, Zahra, Soto, Emmaris, Sun, Lei, Taamoli, Sina, Vanzella, Eros, Yung, L. Y. Aaron, and Zabelle, Bonnabelle
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Astrophysics - Astrophysics of Galaxies - Abstract
The UltraViolet imaging of the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey Fields (UVCANDELS) program provides deep HST F275W and F435W imaging over four CANDELS fields (GOODS-N, GOODS-S, COSMOS, and EGS). We combine this newly acquired UV imaging with existing HST imaging from CANDELS as well as existing ancillary data to obtain robust photometric redshifts and reliable estimates for galaxy physical properties for over 150,000 galaxies in the $\sim$430 arcmin$^2$ UVCANDELS area. Here, we leverage the power of the new UV photometry to not only improve the photometric redshift measurements in these fields, but also constrain the full redshift probability distribution combining multiple redshift fitting tools. Furthermore, using the full UV-to-IR photometric dataset, we measure the galaxy physical properties by fitting templates from population synthesis models with two different parameterizations (flexible and fixed-form) of the star-formation histories (SFHs). Compared to the flexible SFH parametrization, we find that the fixed-form SFHs systematically underestimate the galaxy stellar masses, both at the low- ($\lesssim10^9 M_\odot$) and high- ($\gtrsim10^{10} M_\odot$) mass end, by as much as $\sim0.5$ dex. This underestimation is primarily due the limited ability of fixed-form SFH parameterization to simultaneously capture the chaotic nature of star-formation in these galaxies., Comment: 22 pages, 6 figures; accepted to ApJS; catalogs available via MAST
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- 2024
12. Computational Pathology for Accurate Prediction of Breast Cancer Recurrence: Development and Validation of a Deep Learning-based Tool
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Su, Ziyu, Guo, Yongxin, Wesolowski, Robert, Tozbikian, Gary, O'Connell, Nathaniel S., Niazi, M. Khalid Khan, and Gurcan, Metin N.
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Artificial Intelligence ,Quantitative Biology - Quantitative Methods - Abstract
Accurate recurrence risk stratification is crucial for optimizing treatment plans for breast cancer patients. Current prognostic tools like Oncotype DX (ODX) offer valuable genomic insights for HR+/HER2- patients but are limited by cost and accessibility, particularly in underserved populations. In this study, we present Deep-BCR-Auto, a deep learning-based computational pathology approach that predicts breast cancer recurrence risk from routine H&E-stained whole slide images (WSIs). Our methodology was validated on two independent cohorts: the TCGA-BRCA dataset and an in-house dataset from The Ohio State University (OSU). Deep-BCR-Auto demonstrated robust performance in stratifying patients into low- and high-recurrence risk categories. On the TCGA-BRCA dataset, the model achieved an area under the receiver operating characteristic curve (AUROC) of 0.827, significantly outperforming existing weakly supervised models (p=0.041). In the independent OSU dataset, Deep-BCR-Auto maintained strong generalizability, achieving an AUROC of 0.832, along with 82.0% accuracy, 85.0% specificity, and 67.7% sensitivity. These findings highlight the potential of computational pathology as a cost-effective alternative for recurrence risk assessment, broadening access to personalized treatment strategies. This study underscores the clinical utility of integrating deep learning-based computational pathology into routine pathological assessment for breast cancer prognosis across diverse clinical settings.
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- 2024
13. Can I Pet Your Robot? Incorporating Capacitive Touch Sensing into a Soft Socially Assistive Robot Platform
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O'Connell, Amy, Cislowski, Bailey, Culbertson, Heather, and Matarić, Maja
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Computer Science - Robotics ,Computer Science - Human-Computer Interaction - Abstract
This work presents a method of incorporating low-cost capacitive tactile sensors on a soft socially assistive robot platform. By embedding conductive thread into the robot's crocheted exterior, we formed a set of low-cost, flexible capacitive tactile sensors that do not disrupt the robot's soft, zoomorphic embodiment. We evaluated the sensors' performance through a user study (N=20) and found that the sensors reliably detected user touch events and localized touch inputs to one of three regions on the robot's exterior., Comment: Accepted as a Work-In-Progress submission at the 2024 IEEE Haptics Symposium
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- 2024
14. Evaluating Multiview Object Consistency in Humans and Image Models
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Bonnen, Tyler, Fu, Stephanie, Bai, Yutong, O'Connell, Thomas, Friedman, Yoni, Kanwisher, Nancy, Tenenbaum, Joshua B., and Efros, Alexei A.
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Computer Science - Computer Vision and Pattern Recognition - Abstract
We introduce a benchmark to directly evaluate the alignment between human observers and vision models on a 3D shape inference task. We leverage an experimental design from the cognitive sciences which requires zero-shot visual inferences about object shape: given a set of images, participants identify which contain the same/different objects, despite considerable viewpoint variation. We draw from a diverse range of images that include common objects (e.g., chairs) as well as abstract shapes (i.e., procedurally generated `nonsense' objects). After constructing over 2000 unique image sets, we administer these tasks to human participants, collecting 35K trials of behavioral data from over 500 participants. This includes explicit choice behaviors as well as intermediate measures, such as reaction time and gaze data. We then evaluate the performance of common vision models (e.g., DINOv2, MAE, CLIP). We find that humans outperform all models by a wide margin. Using a multi-scale evaluation approach, we identify underlying similarities and differences between models and humans: while human-model performance is correlated, humans allocate more time/processing on challenging trials. All images, data, and code can be accessed via our project page., Comment: Project page: https://tzler.github.io/MOCHI/ Code: https://github.com/tzler/mochi_code Huggingface dataset: https://huggingface.co/datasets/tzler/MOCHI
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- 2024
15. Mechanistic Origins of Yielding in Hybrid Double Network Hydrogels
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Kopnar, Vinay, O'Connell, Adam, Shirshova, Natasha, and Aufderhorst-Roberts, Anders
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Condensed Matter - Soft Condensed Matter - Abstract
Hybrid double-network hydrogels are a class of material that comprise transiently and permanently crosslinked polymer networks and exhibit an enhanced toughness that is believed to be governed by the yielding of the transient polymer network. The precise role of the two polymer networks in this yielding transition and their interplay remains an open question that we address here through constructing a series of hydrogel designs in which the interaction within and between the two polymer networks are systematically inhibited or enhanced. We characterise each of the hydrogel designs using large amplitude oscillatory shear rheology (LAOS). Inspecting yielding through elastic stress across hydrogel designs, we elucidate that the hybrid double-network hydrogel exhibits a two-step yielding behaviour that originates from to the presence of transient crosslinks. Examining the rheological response within each oscillatory cycle and across the hydrogel designs, we show that the micro-structural changes in the transient network are crucial in the second stage of this yielding. We surmise that the first step of yielding is determined by the intermolecular interactions between the two polymer networks by systematically altering the strength of the interactions. These interactions also influence the second step of yielding, which we show is governed by the transient intermolecular interactions within the polymer networks. Our study therefore reveals that the interactions between the polymer networks are as crucial as within the polymer networks and therefore provides insights into how the yielding mechanisms in soft composite materials can be identified, adjusted, and controlled.
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- 2024
16. The Emergence of Academic Capitalism at a Teaching University
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Derek R. O'Connell
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This case study uses the theory of academic capitalism (TAC) to explore how a public university known primarily for undergraduate education is incorporating market-oriented practices and structures, and how those changes could impact its curriculum and enrollment profile. Through initiatives to establish an engineering college, expand graduate education, and expand international student recruitment, the university's initiatives bring it closer to its research-oriented sister institution, one with a much different curriculum and enrollment profile. The findings extend the scope of TAC beyond the limited set of institutional types and issues explored in most existing research. The findings also provide insight for policymakers and higher education administrators into how public institutions oriented toward undergraduate education may change in the face of declining state financing and increasing reliance on tuition revenue.
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- 2024
17. Addressing the Ethnicity Degree Awarding Gap through Writing Retreats: A Case Study and Reflection
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Julia O’Connell and Alison Daniell
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The awarding gap between UK-domiciled full-time Black and white students is a significant problem at HE institutions across the country. This paper examines a case study of a dissertation writing retreat programme which sought to address this awarding gap at a university in the south of England. The programme was based on an innovative 'three Cs' framework which focused on three core areas: Community, Culture, and Curriculum. Inspired by the community-building and curriculum elements of the framework, the programme built trust and collaboration between specialists and students, aiming to empower Black students to excel in one of the most important and impactful aspects of their degree, whilst also providing them with a space to engage positively with their peers and the wider university community.
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- 2024
18. Does Religious Education in Catholic Schools in the Republic of Ireland Have a Future?
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Amalee Meehan and Daniel O'Connell
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Most European countries accept the necessity of school based Religious Education (RE). In Ireland, where almost 89% of primary and 47% of second level schools have a Catholic patron, the Catholic Bishops recognise the importance of RE in holistic education and uphold RE as an expression of school ethos. However, in an increasingly diverse society with rapidly falling numbers of people who identify and practice as Catholic, can the provision of RE in Catholic schools be sustained into the future? This paper examines the results of the first large scale, mixed methods empirical study into Catholic school (primary and secondary) ethos in the Republic of Ireland, of which Religious Education is an essential dimension. Through an examination of survey and semi-structured interview data from teachers and leaders, it analyses their views and experiences of RE and highlights the role and reality of RE in Catholic schools in Ireland today. Findings demonstrate a level of commitment and professionalism among stakeholders, and much in the way of good practice and commitment to the subject. However, they also indicate that support for RE as a subject, and for RE teachers and leaders, is urgently needed. Without ongoing, high-quality support for teachers, and systematic evaluation of the teaching and learning of RE, the future of RE in Catholic schools in Ireland looks bleak. While the study is carried out in Ireland, it is also of interest to other jurisdictions where schools are faced with similar challenges and to Catholic education systems looking to the future of Religious Education.
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- 2024
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19. Unraveling the shared genetics of common epilepsies and general cognitive ability
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Karadag, Naz, Hagen, Espen, Shadrin, Alexey A, van der Meer, Dennis, O'Connell, Kevin S, Rahman, Zillur, Kutrolli, Gleda, Parker, Nadine, Bahrami, Shahram, Fominykh, Vera, Heuser, Kjell, Taubøll, Erik, Ueland, Torill, Steen, Nils Eiel, Djurovic, Srdjan, Dale, Anders M, Frei, Oleksandr, Andreassen, Ole A, and Smeland, Olav B
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Biomedical and Clinical Sciences ,Biological Psychology ,Clinical Sciences ,Neurosciences ,Psychology ,Epilepsy ,Genetics ,Pediatric ,Neurodegenerative ,Human Genome ,Brain Disorders ,2.1 Biological and endogenous factors ,Neurological ,Humans ,Genome-Wide Association Study ,Cognition ,Cognitive Dysfunction ,Female ,Male ,Linkage Disequilibrium ,Polymorphism ,Single Nucleotide ,Phenotype ,Polygenic overlap ,Linkage disequilibrium score regression ,LDSC ,Gaussian causal mixture models ,MiXeR ,Conjunctional False Discovery Rate ,ConjFDR ,Neurology & Neurosurgery ,Clinical sciences ,Biological psychology - Abstract
PurposeCognitive impairment is prevalent among individuals with epilepsy, and increasing evidence indicates that genetic factors can underlie this relationship. However, the extent to which epilepsy subtypes differ in their genetic relationship with cognitive function, and information about the specific genetic variants involved remain largely unknown.MethodsWe investigated the genetic relationship between epilepsies and general cognitive ability (COG) using complementary statistical tools, including linkage disequilibrium score (LDSC) regression, MiXeR and conjunctional false discovery rate (conjFDR). We analyzed genome-wide association study data on COG (n = 269,867) and common epilepsies (n = 27,559 cases, 42,436 controls), including the broad phenotypes 'all epilepsy', focal epilepsies and genetic generalized epilepsies (GGE), as well as specific subtypes. We functionally annotated the identified loci using several biological resources and validated the results in independent samples.ResultsUsing MiXeR, COG (11.2k variants) was estimated to be almost four times more polygenic than 'all epilepsy', GGE, juvenile myoclonic epilepsy (JME), and childhood absence epilepsy (CAE) (2.5k - 2.9k variants). The other epilepsy phenotypes were insufficiently powered for MiXeR analysis. We quantified extensive genetic overlap between COG and epilepsy types, but with varying negative genetic correlations (-0.23 to -0.04). COG was estimated to share 2.9k variants with both GGE and 'all epilepsy', and 2.3k variants with both JME and CAE. Using conjFDR, we identified 66 distinct loci shared between COG and epilepsies, including novel associations for GGE (27), 'all epilepsy' (5), JME (5) and CAE (5). The implicated genes were significantly expressed in multiple brain regions. The results were validated in independent samples (COG: p = 3.62 × 10-7; 'all epilepsy': p = 2.58 × 10-3).ConclusionOur study further dissects the substantial genetic basis shared between epilepsies and COG and identifies novel shared loci. An improved understanding of the genetic relationship between epilepsies and COG may lead to the development of novel comorbidity-targeted epilepsy treatments.
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- 2024
20. Customer enrollment and participation in building demand management programs: A review of key factors
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Langevin, Jared, Cetin, Kristen, Willems, Sara, Kang, Jeonga, Mahmud, Roohany, Christensen, Toke Haunstrup, Li, Rongling, Knotzer, Armin, Olawale, Opeoluwa Wonuola, Saelens, Dirk, and O'Connell, Sarah
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Engineering ,Built Environment and Design ,Affordable and Clean Energy ,Building & Construction ,Built environment and design - Abstract
Increasing the efficiency and flexibility of electricity demand is necessary for ensuring a cost-effective and reliable transition to zero-carbon electricity systems. Such demand-side management (DSM) resources have been procured by utilities for decades via energy efficiency and demand response programs; however, the key drivers of program enrollment and customer participation levels remain poorly understood — even as governments and grid planners seek to scale up the deployment of DSM assets to meet climate targets. Here we systematically review the evidence on multiple factors that may influence customer enrollment and participation in building DSM programs, focusing primarily on residential and commercial buildings. We examine the contexts in which relationships between DSM factors and outcomes are most often explored and with which methods; we also score the strength, direction, and internal consistency of each factor's reported impact on the enrollment and participation outcomes. We find that studies most commonly assess the effects of economic incentives for load flexibility on program participation levels, often using simulation-based methods in lieu of measured data. Few studies focus on program enrollment outcomes or regulatory drivers of either enrollment or participation, and gaps are also evident in the coverage of emerging DSM opportunities like load electrification. Removal of structural barriers (e.g., the lack of controls infrastructure) and the use of third party services (e.g., load aggregators) are the factors with the largest positive impacts on DSM outcomes, but no single factor emerges as clearly most impactful. For a given factor, the range of reported impacts typically varies widely across the relevant studies reviewed. Our findings provide a snapshot of the state of knowledge about building DSM and customer decision-making, and they expose key gaps in understanding that must be filled if building DSM is to expand as a critical resource for operating clean power grids.
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- 2024
21. Supertranslations from Scattering Amplitudes
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Elkhidir, Asaad, O'Connell, Donal, and Roiban, Radu
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High Energy Physics - Theory ,General Relativity and Quantum Cosmology - Abstract
On-shell methods have found a new application to local observables such as asymptotic radiation fields and gravitational waveforms. While these observables are invariant under small gauge transformations, they are known to depend on a choice of asymptotic gauge; in gravity on asymptotically Minkowski spacetimes, this is a choice of BMS frame. In this letter, we provide a method for capturing these supertranslations, to all orders in perturbation theory, using the on-shell framework of scattering amplitudes., Comment: 9 pages. v2: improved discussion of the hard charge
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- 2024
22. A new perspective on Bayesian Operational Modal Analysis
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O'Connell, Brandon J., Champneys, Max D., and Rogers, Timothy J.
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Statistics - Machine Learning ,Computer Science - Machine Learning ,Electrical Engineering and Systems Science - Systems and Control - Abstract
In the field of operational modal analysis (OMA), obtained modal information is frequently used to assess the current state of aerospace, mechanical, offshore and civil structures. However, the stochasticity of operational systems and the lack of forcing information can lead to inconsistent results. Quantifying the uncertainty of the recovered modal parameters through OMA is therefore of significant value. In this article, a new perspective on Bayesian OMA is proposed: a Bayesian stochastic subspace identification (SSI) algorithm. Distinct from existing approaches to Bayesian OMA, a hierarchical probabilistic model is embedded at the core of covariance-driven SSI. Through substitution of canonical correlation analysis with a Bayesian equivalent, posterior distributions over the modal properties are obtained. Two inference schemes are presented for the proposed Bayesian formulation: Markov Chain Monte Carlo and variational Bayes. Two case studies are then explored. The first is benchmark study using data from a simulated, multi degree-of-freedom, linear system. Following application of Bayesian SSI, it is shown that the same posterior is targeted and recovered by both inference schemes, with good agreement between the posterior mean and the conventional SSI result. The second study applies the variational form to data obtained from an in-service structure: The Z24 bridge. The results of this study are presented at single model orders, and then using a stabilisation diagram. The recovered posterior uncertainty is presented and compared to the classic SSI result. It is observed that the posterior distributions with mean values coinciding with the natural frequencies exhibit lower variance than values situated away from the natural frequencies.
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- 2024
23. An Interactive Augmented Reality Interface for Personalized Proxemics Modeling
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Nigro, Massimiliano, O'Connell, Amy, Groechel, Thomas, Velentza, Anna-Maria, and Matarić, Maja
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Computer Science - Robotics - Abstract
Understanding and respecting personal space preferences is essential for socially assistive robots designed for older adult users. This work introduces and evaluates a novel personalized context-aware method for modeling users' proxemics preferences during human-robot interactions. Using an interactive augmented reality interface, we collected a set of user-preferred distances from the robot and employed an active transfer learning approach to fine-tune a specialized deep learning model. We evaluated this approach through two user studies: 1) a convenience population study (N = 24) to validate the efficacy of the active transfer learning approach; and 2) a user study involving older adults (N = 15) to assess the system's usability. We compared the data collected with the augmented reality interface and with the physical robot to examine the relationship between proxemics preferences for a virtual robot versus a physically embodied robot. We found that fine-tuning significantly improved model performance: on average, the error in testing decreased by 26.97% after fine-tuning. The system was well-received by older adult participants, who provided valuable feedback and suggestions for future work., Comment: M. Nigro, A. O'Connell, T. Groechel, A.M. Velentza and M. Matari\'c, "An Interactive Augmented Reality Interface for Personalized Proxemics Modeling: Comfort and Human-Robot Interactions," in IEEE Robotics & Automation Magazine, doi: 10.1109/MRA.2024.3415108
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- 2024
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24. Miniature fluorescence sensor for quantitative detection of brain tumour
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Ndabakuranye, Jean Pierre, Belcourt, James, Sharma, Deepak, O'Connell, Cathal D., Mondal, Victor, Srivastava, Sanjay K., Stacey, Alastair, Long, Sam, Fleiss, Bobbi, and Ahnood, Arman
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Electrical Engineering and Systems Science - Systems and Control ,Physics - Medical Physics - Abstract
Fluorescence-guided surgery has emerged as a vital tool for tumour resection procedures. As well as intraoperative tumour visualisation, 5-ALA-induced PpIX provides an avenue for quantitative tumour identification based on ratiometric fluorescence measurement. To this end, fluorescence imaging and fibre-based probes have enabled more precise demarcation between the cancerous and healthy tissues. These sensing approaches, which rely on collecting the fluorescence light from the tumour resection site and its remote spectral sensing, introduce challenges associated with optical losses. In this work, we demonstrate the viability of tumour detection at the resection site using a miniature fluorescence measurement system. Unlike the current bulky systems, which necessitate remote measurement, we have adopted a millimetre-sized spectral sensor chip for quantitative fluorescence measurements. A reliable measurement at the resection site requires a stable optical window between the tissue and the optoelectronic system. This is achieved using an antifouling diamond window, which provides stable optical transparency. The system achieved a sensitivity of 92.3% and specificity of 98.3% in detecting a surrogate tumour at a resolution of 1 x 1 mm2. As well as addressing losses associated with collecting and coupling fluorescence light in the current remote sensing approaches, the small size of the system introduced in this work paves the way for its direct integration with the tumour resection tools with the aim of more accurate interoperative tumour identification.
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- 2024
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25. Genomics yields biological and phenotypic insights into bipolar disorder
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O’Connell, Kevin S., Koromina, Maria, van der Veen, Tracey, Boltz, Toni, David, Friederike S., Yang, Jessica Mei Kay, Lin, Keng-Han, Wang, Xin, Coleman, Jonathan R. I., Mitchell, Brittany L., McGrouther, Caroline C., Rangan, Aaditya V., Lind, Penelope A., Koch, Elise, Harder, Arvid, Parker, Nadine, Bendl, Jaroslav, Adorjan, Kristina, Agerbo, Esben, Albani, Diego, Alemany, Silvia, Alliey-Rodriguez, Ney, Als, Thomas D., Andlauer, Till F. M., Antoniou, Anastasia, Ask, Helga, Bass, Nicholas, Bauer, Michael, Beins, Eva C., Bigdeli, Tim B., Pedersen, Carsten Bøcker, Boks, Marco P., Børte, Sigrid, Bosch, Rosa, Brum, Murielle, Brumpton, Ben M., Brunkhorst-Kanaan, Nathalie, Budde, Monika, Bybjerg-Grauholm, Jonas, Byerley, William, Cabana-Domínguez, Judit, Cairns, Murray J., Carpiniello, Bernardo, Casas, Miquel, Cervantes, Pablo, Chatzinakos, Chris, Chen, Hsi-Chung, Clarence, Tereza, Clarke, Toni-Kim, Claus, Isabelle, Coombes, Brandon, Corfield, Elizabeth C., Cruceanu, Cristiana, Cuellar-Barboza, Alfredo, Czerski, Piotr M., Dafnas, Konstantinos, Dale, Anders M., Dalkner, Nina, Degenhardt, Franziska, DePaulo, J. Raymond, Djurovic, Srdjan, Drange, Ole Kristian, Escott-Price, Valentina, Fanous, Ayman H., Fellendorf, Frederike T., Ferrier, I. Nicol, Forty, Liz, Frank, Josef, Frei, Oleksandr, Freimer, Nelson B., Fullard, John F., Garnham, Julie, Gizer, Ian R., Gordon, Scott D., Gordon-Smith, Katherine, Greenwood, Tiffany A., Grove, Jakob, Guzman-Parra, José, Ha, Tae Hyon, Hahn, Tim, Haraldsson, Magnus, Hautzinger, Martin, Havdahl, Alexandra, Heilbronner, Urs, Hellgren, Dennis, Herms, Stefan, Hickie, Ian B., Hoffmann, Per, Holmans, Peter A., Huang, Ming-Chyi, Ikeda, Masashi, Jamain, Stéphane, Johnson, Jessica S., Jonsson, Lina, Kalman, Janos L., Kamatani, Yoichiro, Kennedy, James L., Kim, Euitae, Kim, Jaeyoung, Kittel-Schneider, Sarah, Knowles, James A., Kogevinas, Manolis, Kranz, Thorsten M., Krebs, Kristi, Kushner, Steven A., Lavebratt, Catharina, Lawrence, Jacob, Leber, Markus, Lee, Heon-Jeong, Liao, Calwing, Lucae, Susanne, Lundberg, Martin, MacIntyre, Donald J., Maier, Wolfgang, Maihofer, Adam X., Malaspina, Dolores, Manchia, Mirko, Maratou, Eirini, Martinsson, Lina, Mattheisen, Manuel, McGregor, Nathaniel W., McInnis, Melvin G., McKay, James D., Medeiros, Helena, Meyer-Lindenberg, Andreas, Millischer, Vincent, Morris, Derek W., Moutsatsou, Paraskevi, Mühleisen, Thomas W., O’Donovan, Claire, Olsen, Catherine M., Panagiotaropoulou, Georgia, Papiol, Sergi, Pardiñas, Antonio F., Park, Hye Youn, Perry, Amy, Pfennig, Andrea, Pisanu, Claudia, Potash, James B., Quested, Digby, Rapaport, Mark H., Regeer, Eline J., Rice, John P., Rivera, Margarita, Schulte, Eva C., Senner, Fanny, Shadrin, Alexey, Shilling, Paul D., Sigurdsson, Engilbert, Sindermann, Lisa, Sirignano, Lea, Siskind, Dan, Slaney, Claire, Sloofman, Laura G., Smeland, Olav B., Smith, Daniel J., Sobell, Janet L., Soler Artigas, Maria, Stein, Dan J., Stein, Frederike, Su, Mei-Hsin, Sung, Heejong, Świątkowska, Beata, Terao, Chikashi, Tesfaye, Markos, Tesli, Martin, Thorgeirsson, Thorgeir E., Thorp, Jackson G., Toma, Claudio, Tondo, Leonardo, Tooney, Paul A., Tsai, Shih-Jen, Tsermpini, Evangelia Eirini, Vawter, Marquis P., Vedder, Helmut, Vreeker, Annabel, Walters, James T. R., Winsvold, Bendik S., Witt, Stephanie H., Won, Hong-Hee, Ye, Robert, Young, Allan H., Zandi, Peter P., Zillich, Lea, Adolfsson, Rolf, Alda, Martin, Alfredsson, Lars, Backlund, Lena, Baune, Bernhard T., Bellivier, Frank, Bengesser, Susanne, Berrettini, Wade H., Biernacka, Joanna M., Boehnke, Michael, Børglum, Anders D., Breen, Gerome, Carr, Vaughan J., Catts, Stanley, Cichon, Sven, Corvin, Aiden, Craddock, Nicholas, Dannlowski, Udo, Dikeos, Dimitris, Etain, Bruno, Ferentinos, Panagiotis, Frye, Mark, Fullerton, Janice M., Gawlik, Micha, Gershon, Elliot S., Goes, Fernando S., Green, Melissa J., Grigoroiu-Serbanescu, Maria, Hauser, Joanna, Henskens, Frans A., Hjerling-Leffler, Jens, Hougaard, David M., Hveem, Kristian, Iwata, Nakao, Jones, Ian, Jones, Lisa A., Kahn, René S., Kelsoe, John R., Kircher, Tilo, Kirov, George, Kuo, Po-Hsiu, Landén, Mikael, Leboyer, Marion, Li, Qingqin S., Lissowska, Jolanta, Lochner, Christine, Loughland, Carmel, Luykx, Jurjen J., Martin, Nicholas G., Mathews, Carol A., Mayoral, Fermin, McElroy, Susan L., McIntosh, Andrew M., McMahon, Francis J., Medland, Sarah E., Melle, Ingrid, Milani, Lili, Mitchell, Philip B., Morken, Gunnar, Mors, Ole, Mortensen, Preben Bo, Müller-Myhsok, Bertram, Myers, Richard M., Myung, Woojae, Neale, Benjamin M., Nievergelt, Caroline M., Nordentoft, Merete, Nöthen, Markus M., Nurnberger, John I., O’Donovan, Michael C., Oedegaard, Ketil J., Olsson, Tomas, Owen, Michael J., Paciga, Sara A., Pantelis, Christos, Pato, Carlos N., Pato, Michele T., Patrinos, George P., Pawlak, Joanna M., Ramos-Quiroga, Josep Antoni, Reif, Andreas, Reininghaus, Eva Z., Ribasés, Marta, Rietschel, Marcella, Ripke, Stephan, Rouleau, Guy A., Roussos, Panos, Saito, Takeo, Schall, Ulrich, Schalling, Martin, Schofield, Peter R., Schulze, Thomas G., Scott, Laura J., Scott, Rodney J., Serretti, Alessandro, Smoller, Jordan W., Squassina, Alessio, Stahl, Eli A., Stefansson, Hreinn, Stefansson, Kari, Stordal, Eystein, Streit, Fabian, Sullivan, Patrick F., Turecki, Gustavo, Vaaler, Arne E., Vieta, Eduard, Vincent, John B., Waldman, Irwin D., Weickert, Cynthia S., Weickert, Thomas W., Werge, Thomas, Whiteman, David C., Zwart, John-Anker, Edenberg, Howard J., McQuillin, Andrew, Forstner, Andreas J., Mullins, Niamh, Di Florio, Arianna, Ophoff, Roel A., and Andreassen, Ole A.
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- 2025
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26. Opioid Prescriptions for Low Back Pain among Military-Connected Older Adults Across Multiple Care Systems: Opioid Prescriptions for Low Back Pain
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Taylor, Janiece L., Carreño, Patricia K., Alsobrooks, Shannon, Velosky, Alexander G., Herrera, Germaine F., Amoako, Maxwell, O’Connell, Megan, Costantino, Ryan C., and Highland, Krista B.
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- 2025
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27. Trophy fish heads are a source of body size information for historical and contemporary ecology
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O’Connell, Matthew, Humphries, Paul, Kopf, R. Keller, Bond, Jennifer, Spennemann, Dirk H. R., and McCasker, Nicole
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- 2025
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28. Identification of risk variants and cross-disorder pleiotropy through multi-ancestry genome-wide analysis of alcohol use disorder
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Icick, Romain, Shadrin, Alexey, Holen, Børge, Karadag, Naz, Parker, Nadine, O’Connell, Kevin S., Frei, Oleksandr, Bahrami, Shahram, Høegh, Margrethe Collier, Lagerberg, Trine Vik, Cheng, Weiqiu, Seibert, Tyler M., Djurovic, Srdjan, Dale, Anders M., Zhou, Hang, Edenberg, Howard J., Gelernter, Joel, Smeland, Olav B., Hindley, Guy, and Andreassen, Ole A.
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- 2025
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29. Case Study Analysis of a Decision Coaching Intervention for Young Adults with Early Psychosis
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Thomas, Elizabeth C., Lucksted, Alicia, Siminoff, Laura A., Hurford, Irene, O’Connell, Maria, Penn, David L., Casey, Irene, Smith, Margaret, Suarez, John, and Salzer, Mark S.
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- 2025
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30. Holocene vegetation and flora dynamics of the west Cork/Kerry region, south-western Ireland
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O’Connell, Michael and Overland, Anette
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- 2025
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31. A Cylindrical Surface Dielectric Resonator with Substantially High Sensitivity for Deep-Tissue EPR Oximetry: Cylindrical surface dielectric resonator for EPR oximetry
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Petryakov, Sergey V., Kmiec, Maciej M., O’Connell, Ryan C., Ubert, Conner S., Kassey, Victor B., Schaner, Philip E., and Kuppusamy, Periannan
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- 2024
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32. Established and emerging roles for pharmacy in operating theatres: a scoping review
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McGowan, Aisling, Deasy, Evelyn, Coyle, Mary, and O’Connell, Juliette
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- 2024
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33. Stable isotope evidence for pre-colonial maize agriculture and animal management in the Bolivian Amazon
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Hermenegildo, Tiago, Prümers, Heiko, Jaimes Betancourt, Carla, Roberts, Patrick, and O’Connell, Tamsin C.
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- 2024
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34. 50 Years of EPR Oximetry: from Capillary to Clinic
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O’Connell, Ryan C., Ubert, Conner S., Kmiec, Maciej M., Petryakov, Sergey V., Kassey, Victor B., Schaner, Philip E., and Kuppusamy, Periannan
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- 2024
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35. A Review of Studies Using Machine Learning to Detect Voice Biomarkers for Depression
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Donaghy, Philip, Ennis, Edel, Mulvenna, Maurice, Bond, Raymond, Kennedy, Niamh, McTear, Mike, O’Connell, Henry, Blaylock, Nate, and Brueckner, Raymond
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- 2024
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36. An evaluation of the knowledge, attitudes and treatment approaches of general dental practitioners in Ireland in the management of traumatic dental injuries
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Maloney, B., O’Connell, A. C., and Leith, R.
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- 2024
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37. Decoding the hallmarks of allograft dysfunction with a comprehensive pan-organ transcriptomic atlas
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Robertson, Harry, Kim, Hani Jieun, Li, Jennifer, Robertson, Nicholas, Robertson, Paul, Jimenez-Vera, Elvira, Ameen, Farhan, Tran, Andy, Trinh, Katie, O’Connell, Philip J., Yang, Jean Y. H., Rogers, Natasha M., and Patrick, Ellis
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- 2024
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38. Ophthalmology inpatient consultations: an Irish tertiary hospital experience
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McGrath, Robert, Ahern, Edward, James, Mark, Idrees, Zubair, and O’Connell, Eamonn
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- 2024
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39. Prevalence and population attributable fractions of potentially modifiable risk factors for dementia in Canada: A cross-sectional analysis of the Canadian Longitudinal Study on Aging
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Dolatshahi, Yasaman, Mayhew, Alexandra, O’Connell, Megan E., Liu-Ambrose, Teresa, Taler, Vanessa, Smith, Eric E., Hogan, David B., Kirkland, Susan, Costa, Andrew P., Wolfson, Christina, Raina, Parminder, Griffith, Lauren, and Jones, Aaron
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- 2024
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40. UVCANDELS: The role of dust on the stellar mass-size relation of disk galaxies at 0.5 $\leq z \leq$ 3.0
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Nedkova, Kalina V., Rafelski, Marc, Teplitz, Harry I., Mehta, Vihang, DeGroot, Laura, Ravindranath, Swara, Alavi, Anahita, Beckett, Alexander, Grogin, Norman A., Häußler, Boris, Koekemoer, Anton M., Oyarzún, Grecco A., Prichard, Laura, Revalski, Mitchell, Snyder, Gregory F., Sunnquist, Ben, Wang, Xin, Windhorst, Rogier A., Chartab, Nima, Conselice, Christopher J., Guo, Yicheng, Hathi, Nimish, Hayes, Matthew J., Ji, Zhiyuan, Kim, Keunho J., Lucas, Ray A., Mobasher, Bahram, O'Connell, Robert W., Sattari, Zahra, Smith, Brent M., Taamoli, Sina, Yung, L. Y. Aaron, and Team, the UVCANDELS
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Astrophysics - Astrophysics of Galaxies - Abstract
We use the Ultraviolet Imaging of the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey fields (UVCANDELS) to measure half-light radii in the rest-frame far-UV for $\sim$16,000 disk-like galaxies over $0.5\leq z \leq 3$. We compare these results to rest-frame optical sizes that we measure in a self-consistent way and find that the stellar mass-size relation of disk galaxies is steeper in the rest-frame UV than in the optical across our entire redshift range. We show that this is mainly driven by massive galaxies ($\gtrsim10^{10}$M$_\odot$), which we find to also be among the most dusty. Our results are consistent with the literature and have commonly been interpreted as evidence of inside-out growth wherein galaxies form their central structures first. However, they could also suggest that the centers of massive galaxies are more heavily attenuated than their outskirts. We distinguish between these scenarios by modeling and selecting galaxies at $z=2$ from the VELA simulation suite in a way that is consistent with UVCANDELS. We show that the effects of dust alone can account for the size differences we measure at $z=2$. This indicates that, at different wavelengths, size differences and the different slopes of the stellar mass-size relation do not constitute evidence for inside-out growth., Comment: Accepted for publication in ApJ. 22 pages, 12 figures, and 4 tables
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- 2024
41. Topology Change from Pointlike Sources
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Neiman, Yasha and O'Connell, David
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General Relativity and Quantum Cosmology ,High Energy Physics - Theory - Abstract
In this paper we study topology-changing spacetimes occurring from pointlike sources. Following an old idea of Penrose, we will opt for a non-Hausdorff model of topology change in which an initial pointlike source is ``doubled" and allowed to propagate along null rays into an eventual cobordism. By appealing to recent developments in non-Hausdorff differential geometry, we will describe and evaluate gravitational actions on these topology-changing spacetimes. Motivated by analogous results for the Trousers space, we describe a sign convention for Lorentzian angles that will ensure the dampening of our non-Hausdorff topology-changing spacetimes within a two-dimensional path integral for gravity., Comment: 43 pages, 9 figures. Ver 2: fixed typos and elaborated on certain points
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- 2024
42. PI3Kγ inhibition circumvents inflammation and vascular leak in SARS-CoV-2 and other infections
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Shepard, Ryan M, Ghebremedhin, Anghesom, Pratumchai, Isaraphorn, Robinson, Sally R, Betts, Courtney, Hu, Jingjing, Sasik, Roman, Fisch, Kathleen M, Zak, Jaroslav, Chen, Hui, Paradise, Marc, Rivera, Jason, Amjad, Mohammad, Uchiyama, Satoshi, Seo, Hideya, Campos, Alejandro D, Dayao, Denise Ann, Tzipori, Saul, Piedra-Mora, Cesar, Das, Soumita, Hasteh, Farnaz, Russo, Hana, Sun, Xin, Xu, Le, Crotty Alexander, Laura E, Duran, Jason M, Odish, Mazen, Pretorius, Victor, Kirchberger, Nell C, Chin, Shao-Ming, Von Schalscha, Tami, Cheresh, David, Morrey, John D, Alargova, Rossitza, O'Connell, Brenda, Martinot, Theodore A, Patel, Sandip P, Nizet, Victor, Martinot, Amanda J, Coussens, Lisa M, Teijaro, John R, and Varner, Judith A
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Biomedical and Clinical Sciences ,Clinical Sciences ,Infectious Diseases ,Lung ,Biodefense ,Coronaviruses ,Emerging Infectious Diseases ,2.1 Biological and endogenous factors ,Infection ,Good Health and Well Being ,Animals ,Humans ,Mice ,Capillary Permeability ,Class Ib Phosphatidylinositol 3-Kinase ,COVID-19 ,COVID-19 Drug Treatment ,Cytokine Release Syndrome ,Inflammation ,Methicillin-Resistant Staphylococcus aureus ,Mice ,Inbred C57BL ,Phosphoinositide-3 Kinase Inhibitors ,SARS-CoV-2 ,Staphylococcal Infections ,Biological Sciences ,Medical and Health Sciences ,Medical biotechnology ,Biomedical engineering - Abstract
Virulent infectious agents such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and methicillin-resistant Staphylococcus aureus (MRSA) induce tissue damage that recruits neutrophils, monocyte, and macrophages, leading to T cell exhaustion, fibrosis, vascular leak, epithelial cell depletion, and fatal organ damage. Neutrophils, monocytes, and macrophages recruited to pathogen-infected lungs, including SARS-CoV-2-infected lungs, express phosphatidylinositol 3-kinase gamma (PI3Kγ), a signaling protein that coordinates both granulocyte and monocyte trafficking to diseased tissues and immune-suppressive, profibrotic transcription in myeloid cells. PI3Kγ deletion and inhibition with the clinical PI3Kγ inhibitor eganelisib promoted survival in models of infectious diseases, including SARS-CoV-2 and MRSA, by suppressing inflammation, vascular leak, organ damage, and cytokine storm. These results demonstrate essential roles for PI3Kγ in inflammatory lung disease and support the potential use of PI3Kγ inhibitors to suppress inflammation in severe infectious diseases.
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- 2024
43. Low Stroke Volume Predicts Deterioration in Intermediate-Risk Pulmonary Embolism: Prospective Study
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Weekes, Anthony J., Hambright, Parker, Trautmann, Ariana, Ali, Shane, Pikus, Angela, Wellinsky, Nicole, Shah, Sanjeev, and O'Connell, Nathaniel
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pulmonary embolism ,Risk ,Outcome ,Prognosis ,Stroke Volume ,Echocardiography - Abstract
Introduction: Prognosis and management of patients with intermediate-risk pulmonary embolism (PE) is challenging. We investigated whether stroke volume may be used to identify the subset of this population at increased risk of clinical deterioration or PE-related death. Our secondary objective was to compare echocardiographic measurements of patients who received escalated interventions vs anticoagulation monotherapy.Methods: We selected patients with intermediate-risk PE, who had comprehensive echocardiography within 18 hours of PE diagnosis and before any escalated interventions, from a PE registry populated by 11 emergency departments. Echocardiographers measured right ventricle (RV) size, tricuspid annular plane systolic excursion (TAPSE), and stroke volume (SV) using velocity time integral (VTI) by left ventricular (LV) outflow tract Doppler or two-dimensional method of discs (MOD). The primary outcome was a composite of PE-related death, cardiac arrest, catecholamine administration for sustained hypotension, or emergency respiratory intervention during the index hospitalization. Secondary outcome was escalated intervention with reperfusion or extracorporeal membrane oxygenation therapy.Results: Of 370 intermediate-risk PE patients (mean age 64.0 ± 15.5 years, 38.1% male), 39 (10.5%) had the primary outcome. These 39 patients had lower mean SV regardless of measurement method than those without the primary outcome: SV MOD 36.2 vs 49.9 milliliters (mL), P < 0.001; SV Doppler 41.7 vs 57.2 mL, P = 0.003; VTI 13.6 vs 17.9 centimeters [cm], P = 0.003. Patients with primary outcome also had lower mean TAPSE than those without (1.54 vs 1.81 cm, P = 0.003). Multivariable models, selecting SV as predictor, had area under the receiver operating curve of 0.8 and Brier score 0.08. The best echocardiographic predictor of our primary outcome was SV MOD (odds ratio 0.72 [0.53, 0.94], P = 0.02). Patients who received escalated interventions had significantly lower SV or surrogate measurements, greater RV dilatation, and lower RV systolic function than patients who received anticoagulation monotherapy.Conclusion: Low stroke volume was a predictor of clinical deterioration and PE-related death. Low SV may be used to identify a subset of intermediate-risk PE patients, who are higher risk (intermediate-high risk), and for whom escalated interventions should be considered.
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- 2024
44. Epigenetic and proteomic signatures associate with clonal hematopoiesis expansion rate
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Mack, Taralynn M, Raddatz, Michael A, Pershad, Yash, Nachun, Daniel C, Taylor, Kent D, Guo, Xiuqing, Shuldiner, Alan R, O’Connell, Jeffrey R, Kenny, Eimear E, Loos, Ruth JF, Redline, Susan, Cade, Brian E, Psaty, Bruce M, Bis, Joshua C, Brody, Jennifer A, Silverman, Edwin K, Yun, Jeong H, Cho, Michael H, DeMeo, Dawn L, Levy, Daniel, Johnson, Andrew D, Mathias, Rasika A, Yanek, Lisa R, Heckbert, Susan R, Smith, Nicholas L, Wiggins, Kerri L, Raffield, Laura M, Carson, April P, Rotter, Jerome I, Rich, Stephen S, Manichaikul, Ani W, Gu, C Charles, Chen, Yii-Der Ida, Lee, Wen-Jane, Shoemaker, M Benjamin, Roden, Dan M, Kooperberg, Charles, Auer, Paul L, Desai, Pinkal, Blackwell, Thomas W, Smith, Albert V, Reiner, Alexander P, Jaiswal, Siddhartha, Weinstock, Joshua S, and Bick, Alexander G
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Biomedical and Clinical Sciences ,Clinical Sciences ,Hematology ,Genetics ,Biotechnology ,Aging ,Human Genome ,Stem Cell Research ,Precision Medicine ,Aetiology ,2.1 Biological and endogenous factors ,Cancer ,Good Health and Well Being ,Clinical sciences - Abstract
Clonal hematopoiesis of indeterminate potential (CHIP), whereby somatic mutations in hematopoietic stem cells confer a selective advantage and drive clonal expansion, not only correlates with age but also confers increased risk of morbidity and mortality. Here, we leverage genetically predicted traits to identify factors that determine CHIP clonal expansion rate. We used the passenger-approximated clonal expansion rate method to quantify the clonal expansion rate for 4,370 individuals in the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) cohort and calculated polygenic risk scores for DNA methylation aging, inflammation-related measures and circulating protein levels. Clonal expansion rate was significantly associated with both genetically predicted and measured epigenetic clocks. No associations were identified with inflammation-related lab values or diseases and CHIP expansion rate overall. A proteome-wide search identified predicted circulating levels of myeloid zinc finger 1 and anti-Müllerian hormone as associated with an increased CHIP clonal expansion rate and tissue inhibitor of metalloproteinase 1 and glycine N-methyltransferase as associated with decreased CHIP clonal expansion rate. Together, our findings identify epigenetic and proteomic patterns associated with the rate of hematopoietic clonal expansion.
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- 2024
45. Amyloid precursor protein induces reactive astrogliosis
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Jauregui, Gretsen Velezmoro, Vukić, Dragana, Onyango, Isaac G, Arias, Carlos, Novotný, Jan S, Texlová, Kateřina, Wang, Shanshan, Kovačovicova, Kristina Locker, Polakova, Natalie, Zelinkova, Jana, Čarna, Maria, Lacovich, Valentina, Head, Brian P, Havas, Daniel, Mistrik, Martin, Zorec, Robert, Verkhratsky, Alexei, Keegan, Liam, O'Connell, Mary A, Rissman, Robert, and Stokin, Gorazd B
- Subjects
Medical Physiology ,Biomedical and Clinical Sciences ,Physical Injury - Accidents and Adverse Effects ,Traumatic Brain Injury (TBI) ,Brain Disorders ,Neurodegenerative ,Traumatic Head and Spine Injury ,Neurosciences ,1.1 Normal biological development and functioning ,Aetiology ,Underpinning research ,2.1 Biological and endogenous factors ,Neurological ,Animals ,Gliosis ,Amyloid beta-Protein Precursor ,Astrocytes ,Mice ,Cells ,Cultured ,Mice ,Inbred C57BL ,Brain Injuries ,Traumatic ,Mice ,Knockout ,amyloid precursor protein ,astrocytes ,interferon pathway ,lipopolysaccharide ,reactive astrogliosis ,traumatic brain injury ,Human Movement and Sports Sciences ,Physiology ,Medical physiology - Abstract
AimAstrocytes respond to stressors by acquiring a reactive state characterized by changes in their morphology and function. Molecules underlying reactive astrogliosis, however, remain largely unknown. Given that several studies observed increase in the Amyloid Precursor Protein (APP) in reactive astrocytes, we here test whether APP plays a role in reactive astrogliosis.MethodsWe investigated whether APP instigates reactive astroglios by examining in vitro and in vivo the morphology and function of naive and APP-deficient astrocytes in response to APP and well-established stressors.ResultsOverexpression of APP in cultured astrocytes led to remodeling of the intermediate filament network, enhancement of cytokine production, and activation of cellular programs centered around the interferon (IFN) pathway, all signs of reactive astrogliosis. Conversely, APP deletion abrogated remodeling of the intermediate filament network and blunted expression of IFN-stimulated gene products in response to lipopolysaccharide. Following traumatic brain injury (TBI), mouse reactive astrocytes also exhibited an association between APP and IFN, while APP deletion curbed the increase in glial fibrillary acidic protein observed canonically in astrocytes in response to TBI.ConclusionsThe APP thus represents a candidate molecular inducer and regulator of reactive astrogliosis. This finding has implications for understanding pathophysiology of neurodegenerative and other diseases of the nervous system characterized by reactive astrogliosis and opens potential new therapeutic avenues targeting APP and its pathways to modulate reactive astrogliosis.
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- 2024
46. Student Achievement Is Much More about Cognitive Ability and Genetics than SES: A Response to Debouwere
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Gary N. Marks and Michael O'Connell
- Abstract
The first section of this paper sets the record straight regarding many of Debouwere's (2024, "Review of Education," 12, e3445) specific criticisms. The second section discusses the magnitude of the SES-achievement relationship, specifically Debouwere's (2024) contention that the correlation is strong around 0.5 or 0.6 compared to observed correlations mostly between 0.2 and 0.3. The third section deals with five issues that Debouwere (2024) raises in his paper: (1) the stability of SES vis-à-vis cognitive ability; (2) the accuracy of children's reports of parents' socioeconomic characteristics; (3) whether teachers discriminate by students' SES; (4) the importance of cognitive ability for educational differentiation (i.e., tracking and streaming); and (5) SES effects on student achievement, controlling for prior achievement. The fourth section discusses the role of genetics in student achievement. Meta-analyses and other studies indicate that about 50%-70% of the variance in student achievement is attributable to genetics (i.e., the heritability). The high heritability of student achievement accounts for its high stability, its strong correlations with cognitive ability and the weak effects of SES, net of prior achievement or cognitive ability.
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- 2024
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47. 'My Favourite Self:' A Retrospective Analysis of an Outdoor Orientation Program
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Timothy S. O'Connell, Anna H. Lathrop, and Kelly A. Pilato
- Abstract
Background: The short-term impacts of outdoor orientation programs (OOPs) have been documented in the literature for close to 40 years. While there is a fair amount of research examining the immediate effects of OOPs, there are relatively few studies exploring long-term impacts. Purpose: This study examined the important longitudinal "lessons learned" from participating in an OOP. Methodology/Approach: This study utilized a retrospective qualitative approach and employed the Most Significant Change technique to understand meaningful lessons learned. Alumni from an OOP participated in semi-structured interviews. Thematic analyses included open coding, focused coding, and axial coding. Findings/Conclusions: Primary themes that emerged from the coding process included community and social connections, mental health and well-being and environmental appreciation and value of nature. Participants reported learning valuable lessons related to community building, coping, stress relief, resiliency and thriving, and connection with nature. Implications: Results provide evidence supporting positive long-term effects of OOPs. A particular highlight is how participants noted the OOP helped shape their "favourite self" years after their university experience. Researchers and practitioners can use these results to inform OOP curricula and to include in program marketing and lobbying efforts.
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- 2024
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48. Graduate Student Perceptions of Nursing Faculty Immediacy: Caring Actions for Accelerated Online Courses
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Huber, Teresa H., Zajac, Lynne, O'Connell, Karen, Robinson, Denise, and Lane, Adrianne
- Abstract
This mixed method study utilized the Online Faculty Caring, Presence, and Immediacy Behaviors Survey and explored 142 graduate nursing students' perceptions of faculty immediacy in accelerated online courses. Students ranked online faculty immediacy characteristics and determined level of agreement with faculty actions. The quantitative findings were compared to determine differences between students who perceived that online faculty utilized immediacy behaviors versus students who perceived that faculty did not use immediacy behaviors. Five themes emerged from the qualitative results that reflect faculty presence, communication, support, and feedback, which emerged from the open-ended survey questions and support the quantitative results. The study findings informed the creation of specific strategies for online faculty who teach accelerated courses.
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- 2023
49. Math Corps' Tutoring Program: Math Knowledge Impacts and Participant Math Perceptions. Middle Years Math Grantee Report Series
- Author
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Mathematica, Robles, Silvia, O'Connell, Krista, Gothro, Andrew, and Place, Kate
- Abstract
Math Corps is an evidence-based tutoring program serving students in grades 4 through 8 that increases opportunities to learn and practice fundamental math skills related to understanding whole and rational numbers. Its intent is that all students, in particular students who are Black, Latino, and/or experiencing poverty, will reach grade-level proficiency in math. AmeriCorps tutors are matched with a school and provide support to approximately 24 students, in pairs or groups of three, for 90 minutes each week in 30- to 45-minute, in-person sessions. The success of the program is built on the collective value of three core features: (1) tutors who share backgrounds or lived experiences with the students they serve; (2) personalized tutoring using evidence-based curriculum; and (3) tutor training and coaching. This study aims to provide evidence of the impact of the Math Corps tutoring program on student math achievement through a regression-adjusted matched comparison design, as well as descriptive evidence about program attendance and participants' math confidence, sense of belonging in Math Corps, and student-tutor relationship quality and focus group data. This report is one in a series of six reports on math tutoring programs. The goal of this report series is to inform the tutoring field more broadly and support the provision of high-quality tutoring to as many students in the priority communities as possible. [This report was prepared with Math Corps.]
- Published
- 2023
50. Implementation of Cognitive (Neuropsychological) Interventions for Older Adults in Clinical or Community Settings: A Scoping Review
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Pike, Kerryn E., Li, Lily, Naismith, Sharon L., Bahar-Fuchs, Alex, Lee, Alessandra, Mehrani, Inga, Bentvelzen, Adam, Lautenschlager, Nicola T., O’Connell, Megan E., Blackberry, Irene, and Mowszowski, Loren
- Published
- 2024
- Full Text
- View/download PDF
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