84,779 results on '"McCoy A"'
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2. Length-constrained, length-penalised and free elastic flows of planar curves inside cones
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Gazwani, Mashniah A. and McCoy, James A.
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Mathematics - Analysis of PDEs - Abstract
We study families of smooth, embedded, regular planar curves $ \alpha : \left [-1,1 \right ]\times \left [0,T \right )\to \mathbb{R}^{2}$ with generalised Neumann boundary conditions inside cones, satisfying three variants of the fourth-order nonlinear $L^2$- gradient flow for the elastic energy: (1) elastic flow with a length penalisation, (2) elastic flow with fixed length and (3) the unconstrained or `free' elastic flow. Assuming neither end of the evolving curve reaches the cone tip, existence of smooth solutions for all time given quite general initial data is well known, but classification of limiting shapes is generally not known. For cone angles not too large and with suitable smallness conditions on the $L^2$-norm of the first arc length derivative of curvature of the initial curve, we prove in cases (1) and (2) smooth exponential convergence of solutions in the $C^\infty$-topology to particular circular arcs, while in case (3), we show smooth convergence to an expanding self-similar arc., Comment: 26 pages, 1 figure
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- 2024
3. Shining Light on the Dark Sector: Search for Axion-like Particles and Other New Physics in Photonic Final States with FASER
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FASER collaboration, Abraham, Roshan Mammen, Ai, Xiaocong, Anders, John, Antel, Claire, Ariga, Akitaka, Ariga, Tomoko, Atkinson, Jeremy, Bernlochner, Florian U., Bianchi, Emma, Boeckh, Tobias, Boyd, Jamie, Brenner, Lydia, Burger, Angela, Cadoux, Franck, Cardella, Roberto, Casper, David W., Cavanagh, Charlotte, Chen, Xin, Cho, Eunhyung, Chouhan, Dhruv, Coccaro, Andrea, Débieux, Stephane, D'Onofrio, Monica, Desai, Ansh, Dmitrievsky, Sergey, Dobre, Radu, Eley, Sinead, Favre, Yannick, Fellers, Deion, Feng, Jonathan L., Fenoglio, Carlo Alberto, Ferrere, Didier, Fieg, Max, Filali, Wissal, Firu, Elena, Garabaglu, Ali, Gibson, Stephen, Gonzalez-Sevilla, Sergio, Gornushkin, Yuri, Gwilliam, Carl, Hayakawa, Daiki, Holzbock, Michael, Hsu, Shih-Chieh, Hu, Zhen, Iacobucci, Giuseppe, Inada, Tomohiro, Iodice, Luca, Jakobsen, Sune, Joos, Hans, Kajomovitz, Enrique, Kawahara, Hiroaki, Keyken, Alex, Kling, Felix, Köck, Daniela, Kontaxakis, Pantelis, Kose, Umut, Kotitsa, Rafaella, Kuehn, Susanne, Kugathasan, Thanushan, Levinson, Lorne, Li, Ke, Liu, Jinfeng, Liu, Yi, Lutz, Margaret S., MacDonald, Jack, Magliocca, Chiara, Mäkelä, Toni, McCoy, Lawson, McFayden, Josh, Medina, Andrea Pizarro, Milanesio, Matteo, Moretti, Théo, Nakamura, Mitsuhiro, Nakano, Toshiyuki, Nevay, Laurie, Ohashi, Ken, Otono, Hidetoshi, Paolozzi, Lorenzo, Petersen, Brian, Preda, Titi, Prim, Markus, Queitsch-Maitland, Michaela, Rokujo, Hiroki, Rubbia, André, Sabater-Iglesias, Jorge, Sato, Osamu, Scampoli, Paola, Schmieden, Kristof, Schott, Matthias, Sfyrla, Anna, Sgalaberna, Davide, Shamim, Mansoora, Shively, Savannah, Takubo, Yosuke, Tarannum, Noshin, Theiner, Ondrej, Torrence, Eric, Martinez, Oscar Ivan Valdes, Vasina, Svetlana, Vormwald, Benedikt, Wang, Di, Wang, Yuxiao, Welch, Eli, Xu, Yue, Zahorec, Samuel, Zambito, Stefano, and Zhang, Shunliang
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High Energy Physics - Experiment - Abstract
The first FASER search for a light, long-lived particle decaying into a pair of photons is reported. The search uses LHC proton-proton collision data at $\sqrt{s}=13.6~\text{TeV}$ collected in 2022 and 2023, corresponding to an integrated luminosity of $57.7\text{fb}^{-1}$. A model with axion-like particles (ALPs) dominantly coupled to weak gauge bosons is the primary target. Signal events are characterised by high-energy deposits in the electromagnetic calorimeter and no signal in the veto scintillators. One event is observed, compared to a background expectation of $0.44 \pm 0.39$ events, which is entirely dominated by neutrino interactions. World-leading constraints on ALPs are obtained for masses up to $300~\text{MeV}$ and couplings to the Standard Model W gauge boson, $g_{aWW}$, around $10^{-4}$ GeV$^{-1}$, testing a previously unexplored region of parameter space. Other new particle models that lead to the same experimental signature, including ALPs coupled to gluons or photons, U(1)$_B$ gauge bosons, up-philic scalars, and a Type-I two-Higgs doublet model, are also considered for interpretation, and new constraints on previously viable parameter space are presented in this paper., Comment: 37 pages, 22 figures
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- 2024
4. Cusp types of arithmetic hyperbolic manifolds
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McCoy, Duncan and Sell, Connor
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Mathematics - Geometric Topology - Abstract
We establish necessary and sufficient conditions for determining when a flat manifold can occur as a cusp cross-section within a given commensurability class of arithmetic hyperbolic manifolds of simplest type. This reduces the problem of identifying which commensurability classes of arithmetic hyperbolic manifolds can contain a specific flat manifold as a cusp cross-section to a question involving rational representations of the flat manifold's holonomy group. As applications, we prove that a flat manifold $M$ with a holonomy group of odd order appears as a cusp cross-section in every commensurability class of arithmetic hyperbolic manifolds if and only if $b_1(M)\geq 3$. We also provide examples of flat manifolds that arise as cusp cross-sections in a unique commensurability class of arithmetic hyperbolic manifolds and exhibit examples of pairs of flat manifolds that can never appear as cusp cross-sections within the same commensurability class.
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- 2024
5. Motivations for Early High-Profile FRIB Experiments
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Brown, B. Alex, Gade, Alexandra, Stroberg, S. Ragnar, Escher, Jutta, Fossez, Kevin, Giuliani, Pablo, Hoffman, Calem R., Nazarewicz, Witold, Seng, Chien-Yeah, Sorensen, Agnieszka, Vassh, Nicole, Bazin, Daniel, Brown, Kyle W., Capri, Mark A., Crawford, Heather, Danielewic, Pawel, Drischler, Christian, Ruiz, Ronald F. Garcia, Godbey, Kyle, Grzywacz, Robert, Holt, Jeremy W., Iwasaki, Hiro, Lee, Dean, Lenzi, Silvia M., Liddick, Sean, Lubna, Rebeka, Macchiavelli, Augusto O., Pinedo, Gabriel Martinez, McCoy, Anna, Mercenne, Alexis, Minamisono, Kei, Monteagudo, Belen, Navratil, Petr, Ringle, Ryan, Sargsyan, Grigor, Schatz, Hendrik, Spieker, Mark-Christoph, Volya, Alexander, Zegers, Remco G. T., Zelevinsky, Vladimir, and Zhang, Xilin
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Nuclear Theory - Abstract
This white paper is the result of a collaboration by those that attended a workshop at the Facility for Rare Isotope Beams (FRIB), organized by the FRIB Theory Alliance (FRIB-TA), on Theoretical Justifications and Motivations for Early High-Profile FRIB Experiments. It covers a wide range of topics related to the science that will be explored at FRIB. After a brief introduction, the sections address: (II) Overview of theoretical methods, (III) Experimental capabilities, (IV) Structure, (V) Near-threshold Physics, (VI) Reaction mechanisms, (VII) Nuclear equations of state, (VIII) Nuclear astrophysics, (IX) Fundamental symmetries, and (X) Experimental design and uncertainty quantification., Comment: 227 pages, 24 figures
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- 2024
6. When a language model is optimized for reasoning, does it still show embers of autoregression? An analysis of OpenAI o1
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McCoy, R. Thomas, Yao, Shunyu, Friedman, Dan, Hardy, Mathew D., and Griffiths, Thomas L.
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
In "Embers of Autoregression" (McCoy et al., 2023), we showed that several large language models (LLMs) have some important limitations that are attributable to their origins in next-word prediction. Here we investigate whether these issues persist with o1, a new system from OpenAI that differs from previous LLMs in that it is optimized for reasoning. We find that o1 substantially outperforms previous LLMs in many cases, with particularly large improvements on rare variants of common tasks (e.g., forming acronyms from the second letter of each word in a list, rather than the first letter). Despite these quantitative improvements, however, o1 still displays the same qualitative trends that we observed in previous systems. Specifically, o1 -- like previous LLMs -- is sensitive to the probability of examples and tasks, performing better and requiring fewer "thinking tokens" in high-probability settings than in low-probability ones. These results show that optimizing a language model for reasoning can mitigate but might not fully overcome the language model's probability sensitivity., Comment: 6 pages; updated to fix typo in Fig 4 caption
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- 2024
7. Implementing New Technology in Educational Systems
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Allen, Scott, Bardach, Lisa, Jirout, Jamie, Mackey, Allyson, McCoy, Dana, Pesando, Luca Maria, and Kizilcec, René
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Physics - Physics Education - Abstract
Educators are more than workers within educational systems; they are stewards of educational systems. They must analyze student performance data, identify patterns that inform targeted interventions and personalized learning plans, continuously develop the curriculum, set ambitious learning goals and use up-to-date pedagogical theory to adapt instructional strategies, act as advocates for educational policies that promote inclusivity and equity, and much more. Most educators deeply care about the learning and wellbeing of their students and colleagues. Given the chance, they will do whatever they can to make improvements to these ends. In this role as architects of change, educators deal with conflicting definitions of success, multiple stakeholders, complex causal relationships, ambiguous data, and intricate human factors. Amid all this, most educators and the educational systems around them are strained to the capacity of what their time, training, and budgets allow. The problem is not merely that they must perform demanding tasks, but more so that they must constantly implement improvements and interventions amid the complex challenges of the organizations in which they work. These challenges can be especially difficult in implementation of related education technology, which is continuously developing at sometimes rapid pace. Whether the context is an individual classroom, a school district, or a postsecondary institution, implementing beneficial human-technology partnerships requires attending to the needs and constraints of these classrooms, districts, institutions, and so forth as organizations and engaging in this work as a partnership with educators. This chapter lays out the principles and processes of developing successful educator-technology partnerships including key considerations for each step and an example protocol for engaging in this endeavor., Comment: Book Chapter, 24 pages, 6 tables, 1 figure
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- 2024
8. The search for alternating surgeries
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Baker, Kenneth L., Kegel, Marc, and McCoy, Duncan
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Mathematics - Geometric Topology ,57M25, 57R65, 57M12 - Abstract
Surgery on a knot in $S^3$ is said to be an alternating surgery if it yields the double branched cover of an alternating link. The main theoretical contribution is to show that the set of alternating surgery slopes is algorithmically computable and to establish several structural results. Furthermore, we calculate the set of alternating surgery slopes for many examples of knots, including all hyperbolic knots in the SnapPy census. These examples exhibit several interesting phenomena including strongly invertible knots with a unique alternating surgery and asymmetric knots with two alternating surgery slopes. We also establish upper bounds on the set of alternating surgeries, showing that an alternating surgery slope on a hyperbolic knot satisfies $|p/q| \leq 3g(K)+4$. Notably, this bound applies to lens space surgeries, thereby strengthening the known genus bounds from the conjecture of Goda and Teragaito., Comment: 67 pages, 7 figures, 3 tables
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- 2024
9. Quasi-alternating surgeries
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Baker, Kenneth L., Kegel, Marc, and McCoy, Duncan
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Mathematics - Geometric Topology ,57K10, 57R65, 57R58, 57K16, 57K14, 57K32, 57M12 - Abstract
In this article, we explore phenomena relating to quasi-alternating surgeries on knots, where a quasi-alternating surgery on a knot is a Dehn surgery yielding the double branched cover of a quasi-alternating link. Since the double branched cover of a quasi-alternating link is an L-space, quasi-alternating surgeries are special examples of L-space surgeries. We show that all SnapPy census L-space knots admit quasi-alternating surgeries except for the knots t09847 and o9_30634 which both do not have any quasi-alternating surgeries. In particular, this finishes Dunfield's classification of the L-space knots among all SnapPy census knots. In addition, we show that all asymmetric census L-space knots have exactly two quasi-alternating slopes that are consecutive integers. Similar behavior is observed for some of the Baker-Luecke asymmetric L-space knots. We also classify the quasi-alternating surgeries on torus knots and explore briefly the notion of formal L-space surgeries. This allows us to give examples of asymmetric formal L-spaces., Comment: 28 pages, 4 figures, 6 tables
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- 2024
10. Two curious strongly invertible L-space knots
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Baker, Kenneth L., Kegel, Marc, and McCoy, Duncan
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Mathematics - Geometric Topology ,57K10, 57R65, 57R58, 57K16, 57K14, 57K32, 57M12 - Abstract
We present two examples of strongly invertible L-space knots whose surgeries are never the double branched cover of a Khovanov thin link in the 3-sphere. Consequently, these knots provide counterexamples to a conjectural characterization of strongly invertible L-space knots due to Watson. We also discuss other exceptional properties of these two knots, for example, these two L-space knots have formal semigroups that are actual semigroups., Comment: 12 pages, 4 figures, 2 tables
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- 2024
11. Diffraction Gratings for X-ray Spectroscopy
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Heilmann, Ralf K., Huenemoerder, David P., McCoy, Jake A., and McEntaffer, Randall L.
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Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
X-ray diffraction gratings play an essential role in high-resolution spectroscopy of astrophysical phenomena. We present some scientific highlights from the X-ray grating spectrometers (XGS) on board of the Chandra and XMM/Newton missions, XGS optical design, and the basic physics of grating diffraction geometry and efficiency. We review design, fabrication, and performance of the currently orbiting transmission and reflection grating elements, followed by descriptions of the state-of-the art of more advanced grating technologies that promise orders-of-magnitude improvements in XGS performance, especially in combination with advanced X-ray telescope mirrors. A few key science questions that require new grating technology are posed, and powerful future mission concepts and recent and approved missions are presented., Comment: 40 pages, 12 figures. To be submitted to Springer for publication in the ISSI Scientific Reports series
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- 2024
12. Engineering in Medicine: Bridging the Cognitive and Emotional Distance between Medical and Non-Medical Students
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Milan Toma, Faiz Sy, Lise McCoy, Michael Nizich, and William Blazey
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In the current study, we focused on measuring the development of important professional attitudes, such as "compassion satisfaction" and "burnout." Students from four different colleges worked in teams to conceptualize innovative engineering products. During the ideation phase of their project, participants completed a Professional Quality of Life survey to assess metrics related to "compassion satisfaction" and "burnout." On average, the combined "compassion satisfaction" score was high for both medical students (42/50) and non-medical students (43/50). In terms of "burnout," 77% of medical students and 81% of non-medical students reported low "burnout"; the average "burnout" score for medical students was 19/50, and for non-medical students 17/50. Only one statement produced a statistically significant difference between groups. For the statement, "I am a caring person," only 31% of medical students self-described as being a very caring person 'very often' as opposed to 62% of non-medical students. Through this innovative curriculum project, faculty were able to measure the level of student "compassion satisfaction," and "burnout" for the students involved. Surrounded by the rationality of science, students learned to communicate and contribute to projects that supported a positive sense of contribution and effort, and a low perception of "burnout."
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- 2024
13. The Developmental Consequences of Early Exposure to Climate Change-Related Risks
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Jorge Cuartas, Dana C. McCoy, Isabella Torres, Lindsey Burghardt, Jack P. Shonkoff, and Hirokazu Yoshikawa
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The climate crisis encompasses a constellation of risks that threaten human livelihoods, well-being, and survival globally. In this article, we present a new framework based on bioecological and dynamic systems perspectives, and on evidence for conceptualizing how the distinctive dual time frame of both acute (e.g., extreme weather events) and chronic (e.g., ecological degradation) climate change-related risks experienced prenatally and early in life across multiple ecological contexts can threaten human development. We conclude with a call to developmental researchers, practitioners, and policymakers to invest more efforts in understanding and addressing the climate crisis and its developmental consequences to ensure a sustainable future for all.
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- 2024
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14. Prevention of adverse HIV treatment outcomes: machine learning to enable proactive support of people at risk of HIV care disengagement in Tanzania.
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Xie, Zhongming, Hu, Huiyu, Kadota, Jillian, Packel, Laura, Mlowe, Matilda, Kwilasa, Sylvester, Maokola, Werner, Shabani, Siraji, Sabasaba, Amon, Njau, Prosper, Wang, Jingshen, and McCoy, Sandra
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HIV & AIDS ,electronic health records ,machine learning ,Humans ,HIV Infections ,Tanzania ,Machine Learning ,Female ,Adult ,Male ,Electronic Health Records ,Middle Aged ,Viral Load ,Anti-HIV Agents ,Young Adult ,Algorithms ,Adolescent ,Treatment Outcome - Abstract
OBJECTIVES: This study aimed to develop a machine learning (ML) model to predict disengagement from HIV care, high viral load or death among people living with HIV (PLHIV) with the goal of enabling proactive support interventions in Tanzania. The algorithm addressed common challenges when applying ML to electronic medical record (EMR) data: (1) imbalanced outcome distribution; (2) heterogeneity across multisite EMR data and (3) evolving virological suppression thresholds. DESIGN: Observational study using a national EMR database. SETTING: Conducted in two regions in Tanzania, using data from the National HIV Care database. PARTICIPANTS: The study included over 6 million HIV care visit records from 295 961 PLHIV in two regions in Tanzanias National HIV Care database from January 2015 to May 2023. RESULTS: Our ML model effectively identified PLHIV at increased risk of adverse outcomes. Key predictors included past disengagement from care, antiretroviral therapy (ART) status (which tracks a patients engagement with ART across visits), age and time on ART. The downsampling approach we implemented effectively managed imbalanced data to reduce prediction bias. Site-specific algorithms performed better compared with a universal approach, highlighting the importance of tailoring ML models to local contexts. A sensitivity analysis confirmed the models robustness to changes in viral load suppression thresholds. CONCLUSIONS: ML models leveraging large-scale databases of patient data offer significant potential to identify PLHIV for interventions to enhance engagement in HIV care in resource-limited settings. Tailoring algorithms to local contexts and flexibility towards evolving clinical guidelines are essential for maximising their impact.
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- 2024
15. fSCIG 10% in pediatric primary immunodeficiency diseases: a European post-authorization safety study.
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Čižnár, Peter, Roderick, Marion, Schneiderova, Helen, Jeseňák, Miloš, Kriván, Gergely, Brodszki, Nicholas, Jolles, Stephen, Atisso, Charles, Fielhauer, Katharina, Saeed-Khawaja, Shumyla, McCoy, Barbara, and Yel, Leman
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Hyaluronidase ,Immunoglobulins ,Inborn errors of immunity (IEI) ,Patient safety ,Pediatrics ,Primary immunodeficiency diseases ,Subcutaneous - Abstract
BACKGROUND: The safety, tolerability, and immunogenicity of hyaluronidase-facilitated subcutaneous immunoglobulin (fSCIG) 10% (dual-vial unit of human immunoglobulin 10% and recombinant human hyaluronidase [rHuPH20]) were assessed in children with primary immunodeficiency diseases (PIDs). METHODS: This phase 4, post-authorization, prospective, interventional, multicenter study (NCT03116347) conducted in the European Economic Area, enrolled patients aged 2 to < 18 years with a documented PID diagnosis who had received immunoglobulin therapy for ≥ 3 months before enrollment. New fSCIG 10% starters underwent fSCIG 10% dose ramp-up for ≤ 6 weeks (epoch 1) before receiving fSCIG 10% for ≤ 3 years (epoch 2); patients pretreated with fSCIG 10% entered epoch 2 directly. The primary outcome was the number and rate (per infusion) of all noninfectious treatment-related serious and severe adverse events (AEs). RESULTS: In total, 42 patients were enrolled and dosed (median [range] age: 11.5 [3-17] years; 81% male; 23 new starters; 19 pretreated). Overall, 49 related noninfectious, treatment-emergent AEs (TEAEs) were reported in 15 patients; most were mild in severity (87.8%). No treatment-related serious TEAEs were reported. Two TEAEs (infusion site pain and emotional distress) were reported as severe and treatment-related in a single new fSCIG 10% starter. The rate of local TEAEs was lower in pretreated patients (0.1 event/patient-year) versus new starters (1.3 events/patient-year). No patients tested positive for binding anti-rHuPH20 antibodies (titer of ≥ 1:160). CONCLUSIONS: No safety signals were identified, and the incidence of local AEs declined over the duration of fSCIG 10% treatment. This study supports fSCIG 10% long-term safety in children with PIDs. TRIAL REGISTRATION NUMBER (CLINICALTRIALS.GOV): NCT03116347.
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- 2024
16. The Interaction Between Climate Forcing and Feedbacks
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Gettelman, A, Eidhammer, T, Duffy, ML, McCoy, DT, Song, C, and Watson‐Parris, D
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Earth Sciences ,Atmospheric Sciences ,Climate Action ,Physical Geography and Environmental Geoscience ,Atmospheric sciences ,Climate change science - Abstract
Abstract: A Perturbed Parameter Ensemble (PPE) with the Community Atmosphere Model version 6 (CAM6) is used to better understand the sensitivity of aerosol forcing and cloud feedbacks to changes in model processes. Aerosol forcing through aerosol‐cloud interactions is mostly negative (a cooling) due to shortwave radiation, while feedbacks are positive or negative in different regions due to contrasting longwave and shortwave effects. Both forcing and feedbacks are related to the mean climate state. Higher magnitude cloud radiative effects generally mean larger magnitude net negative forcing and larger magnitude net positive feedback. Aerosol forcing is broadly related to the susceptibility of clouds to drop number. Feedbacks also related to susceptibility, but to a lesser extent and in different regions to aerosol forcing. Aerosol forcing and cloud feedbacks are anti‐correlated in the CAM6 PPE such that stronger negative forcing is associated with stronger positive feedbacks. Even the processes governing forcing and feedback sensitivity in the PPE are similar. These include the warm rain formation process, ice loss processes and deep convective intensity.
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- 2024
17. Buffering of Aerosol‐Cloud Adjustments by Coupling Between Radiative Susceptibility and Precipitation Efficiency
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Song, Ci, McCoy, Daniel T, Eidhammer, Trude, Gettelman, Andrew, McCoy, Isabel L, Watson‐Parris, Duncan, Wall, Casey J, Elsaesser, Gregory, and Wood, Robert
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Earth Sciences ,Atmospheric Sciences ,Climate Action ,aerosol-cloud interactions ,global climate models ,Meteorology & Atmospheric Sciences - Abstract
Abstract: Aerosol‐cloud interactions (ACI) in warm clouds are the primary source of uncertainty in effective radiative forcing (ERF) during the historical period and, by extension, inferred climate sensitivity. The ERF due to ACI (ERFaci) is composed of the radiative forcing due to changes in cloud microphysics and cloud adjustments to microphysics. Here, we examine the processes that drive ERFaci using a perturbed parameter ensemble (PPE) hosted in CAM6. Observational constraints on the PPE result in substantial constraints in the response of cloud microphysics and macrophysics to anthropogenic aerosol, but only minimal constraint on ERFaci. Examination of cloud and radiation processes in the PPE reveal buffering of ERFaci by the interaction of precipitation efficiency and radiative susceptibility.
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- 2024
18. Showing the Receipts: Understanding the Modern Ransomware Ecosystem
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Cable, Jack, Gray, Ian W., and McCoy, Damon
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Computer Science - Cryptography and Security - Abstract
Ransomware attacks continue to wreak havoc across the globe, with public reports of total ransomware payments topping billions of dollars annually. While the use of cryptocurrency presents an avenue to understand the tactics of ransomware actors, to date published research has been constrained by relatively limited public datasets of ransomware payments. We present novel techniques to identify ransomware payments with low false positives, classifying nearly \$700 million in previously-unreported ransomware payments. We publish the largest public dataset of over \$900 million in ransomware payments -- several times larger than any existing public dataset. We then leverage this expanded dataset to present an analysis focused on understanding the activities of ransomware groups over time. This provides unique insights into ransomware behavior and a corpus for future study of ransomware cybercriminal activity., Comment: To be published in 2024 APWG Symposium on Electronic Crime Research (eCrime)
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- 2024
19. Privacy or Transparency? Negotiated Smartphone Access as a Signifier of Trust in Romantic Relationships
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Doerfler, Periwinkle, Turk, Kieron Ivy, Geeng, Chris, McCoy, Damon, Ackerman, Jeffrey, and Dragiewicz, Molly
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Computer Science - Cryptography and Security - Abstract
In this work, we analyze two large-scale surveys to examine how individuals think about sharing smartphone access with romantic partners as a function of trust in relationships. We find that the majority of couples have access to each others' devices, but may have explicit or implicit boundaries on how this access is to be used. Investigating these boundaries and related social norms, we find that there is little consensus about the level of smartphone access (i.e., transparency), or lack thereof (i.e., privacy) that is desirable in romantic contexts. However, there is broad agreement that the level of access should be mutual and consensual. Most individuals understand trust to be the basis of their decisions about transparency and privacy. Furthermore, we find individuals have crossed these boundaries, violating their partners' privacy and betraying their trust. We examine how, when, why, and by whom these betrayals occur. We consider the ramifications of these boundary violations in the case of intimate partner violence. Finally, we provide recommendations for design changes to enable technological enforcement of boundaries currently enforced by trust, bringing access control in line with users' sharing preferences.
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- 2024
20. A survey on embeddings of 3-manifolds in definite 4-manifolds
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Aceto, Paolo, McCoy, Duncan, and Park, JungHwan
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Mathematics - Geometric Topology - Abstract
This article presents a survey on the topic of embedding 3-manifolds in definite 4-manifolds, emphasizing the latest progress in the field. We will focus on the significant role played by Donaldson's diagonalization theorem and the combinatorics of integral lattices in understanding these embeddings. Additionally, the article introduces a new result concerning the embedding of amphichiral lens spaces in negative-definite manifolds., Comment: 16 pages, 1 figure, final version
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- 2024
21. Deciphering the Factors Influencing the Efficacy of Chain-of-Thought: Probability, Memorization, and Noisy Reasoning
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Prabhakar, Akshara, Griffiths, Thomas L., and McCoy, R. Thomas
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
Chain-of-Thought (CoT) prompting has been shown to enhance the multi-step reasoning capabilities of Large Language Models (LLMs). However, debates persist about whether LLMs exhibit abstract generalization or rely on shallow heuristics when given CoT prompts. To understand the factors influencing CoT reasoning we provide a detailed case study of the symbolic reasoning task of decoding shift ciphers, where letters are shifted forward some number of steps in the alphabet. We analyze the pattern of results produced by three LLMs -- GPT-4, Claude 3, and Llama 3.1 -- performing this task using CoT prompting. By focusing on a single relatively simple task, we are able to identify three factors that systematically affect CoT performance: the probability of the task's expected output (probability), what the model has implicitly learned during pre-training (memorization), and the number of intermediate operations involved in reasoning (noisy reasoning). We show that these factors can drastically influence task accuracy across all three LLMs; e.g., when tested with GPT-4, varying the output's probability of occurrence shifts accuracy from 26% to 70%. Overall, we conclude that CoT prompting performance reflects both memorization and a probabilistic version of genuine reasoning. Code and data at this https://github.com/aksh555/deciphering_cot, Comment: EMNLP 2024 Findings; 9 pages plus references and appendices
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- 2024
22. Is In-Context Learning a Type of Gradient-Based Learning? Evidence from the Inverse Frequency Effect in Structural Priming
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Zhou, Zhenghao, Frank, Robert, and McCoy, R. Thomas
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Computer Science - Computation and Language - Abstract
Large language models (LLMs) have shown the emergent capability of in-context learning (ICL). One line of research has explained ICL as functionally performing gradient descent. In this paper, we introduce a new way of diagnosing whether ICL is functionally equivalent to gradient-based learning. Our approach is based on the inverse frequency effect (IFE) -- a phenomenon in which an error-driven learner is expected to show larger updates when trained on infrequent examples than frequent ones. The IFE has previously been studied in psycholinguistics because humans show this effect in the context of structural priming (the tendency for people to produce sentence structures they have encountered recently); the IFE has been used as evidence that human structural priming must involve error-driven learning mechanisms. In our experiments, we simulated structural priming within ICL and found that LLMs display the IFE, with the effect being stronger in larger models. We conclude that ICL is indeed a type of gradient-based learning, supporting the hypothesis that a gradient component is implicitly computed in the forward pass during ICL. Our results suggest that both humans and LLMs make use of gradient-based, error-driven processing mechanisms.
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- 2024
23. modeLing: A Novel Dataset for Testing Linguistic Reasoning in Language Models
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Chi, Nathan A., Malchev, Teodor, Kong, Riley, Chi, Ryan A., Huang, Lucas, Chi, Ethan A., McCoy, R. Thomas, and Radev, Dragomir
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Computer Science - Computation and Language - Abstract
We introduce modeLing, a novel benchmark of Linguistics Olympiad-style puzzles which tests few-shot reasoning in AI systems. Solving these puzzles necessitates inferring aspects of a language's grammatical structure from a small number of examples. Such puzzles provide a natural testbed for language models, as they require compositional generalization and few-shot inductive reasoning. Consisting solely of new puzzles written specifically for this work, modeLing has no risk of appearing in the training data of existing AI systems: this ameliorates the risk of data leakage, a potential confounder for many prior evaluations of reasoning. Evaluating several large open source language models and GPT on our benchmark, we observe non-negligible accuracy, demonstrating few-shot emergent reasoning ability which cannot merely be attributed to shallow memorization. However, imperfect model performance suggests that modeLing can be used to measure further progress in linguistic reasoning.
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- 2024
24. Probabilistic Programming with Programmable Variational Inference
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Becker, McCoy R., Lew, Alexander K., Wang, Xiaoyan, Ghavami, Matin, Huot, Mathieu, Rinard, Martin C., and Mansinghka, Vikash K.
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Computer Science - Programming Languages ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
Compared to the wide array of advanced Monte Carlo methods supported by modern probabilistic programming languages (PPLs), PPL support for variational inference (VI) is less developed: users are typically limited to a predefined selection of variational objectives and gradient estimators, which are implemented monolithically (and without formal correctness arguments) in PPL backends. In this paper, we propose a more modular approach to supporting variational inference in PPLs, based on compositional program transformation. In our approach, variational objectives are expressed as programs, that may employ first-class constructs for computing densities of and expected values under user-defined models and variational families. We then transform these programs systematically into unbiased gradient estimators for optimizing the objectives they define. Our design enables modular reasoning about many interacting concerns, including automatic differentiation, density accumulation, tracing, and the application of unbiased gradient estimation strategies. Additionally, relative to existing support for VI in PPLs, our design increases expressiveness along three axes: (1) it supports an open-ended set of user-defined variational objectives, rather than a fixed menu of options; (2) it supports a combinatorial space of gradient estimation strategies, many not automated by today's PPLs; and (3) it supports a broader class of models and variational families, because it supports constructs for approximate marginalization and normalization (previously introduced only for Monte Carlo inference). We implement our approach in an extension to the Gen probabilistic programming system (genjax.vi, implemented in JAX), and evaluate on several deep generative modeling tasks, showing minimal performance overhead vs. hand-coded implementations and performance competitive with well-established open-source PPLs.
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- 2024
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25. Data-Adaptive Identification of Subpopulations Vulnerable to Chemical Exposures using Stochastic Interventions
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McCoy, David, Zhang, Wenxin, Hubbard, Alan, van der Laan, Mark, and Schuler, Alejandro
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Statistics - Methodology - Abstract
In environmental epidemiology, identifying subpopulations vulnerable to chemical exposures and those who may benefit differently from exposure-reducing policies is essential. For instance, sex-specific vulnerabilities, age, and pregnancy are critical factors for policymakers when setting regulatory guidelines. However, current semi-parametric methods for heterogeneous treatment effects are often limited to binary exposures and function as black boxes, lacking clear, interpretable rules for subpopulation-specific policy interventions. This study introduces a novel method using cross-validated targeted minimum loss-based estimation (TMLE) paired with a data-adaptive target parameter strategy to identify subpopulations with the most significant differential impact from simulated policy interventions that reduce exposure. Our approach is assumption-lean, allowing for the integration of machine learning while still yielding valid confidence intervals. We demonstrate the robustness of our methodology through simulations and application to NHANES data. Our analysis of NHANES data for persistent organic pollutants on leukocyte telomere length (LTL) identified age as the maximum effect modifier. Specifically, we found that exposure to 3,3',4,4',5-pentachlorobiphenyl (pcnb) consistently had a differential impact on LTL, with a one standard deviation reduction in exposure leading to a more pronounced increase in LTL among younger populations compared to older ones. We offer our method as an open-source software package, \texttt{EffectXshift}, enabling researchers to investigate the effect modification of continuous exposures. The \texttt{EffectXshift} package provides clear and interpretable results, informing targeted public health interventions and policy decisions.
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- 2024
26. A Relevance Model for Threat-Centric Ranking of Cybersecurity Vulnerabilities
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McCoy, Corren, Gore, Ross, Nelson, Michael L., and Weigle, Michele C.
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Computer Science - Cryptography and Security ,K.6.5 - Abstract
The relentless process of tracking and remediating vulnerabilities is a top concern for cybersecurity professionals. The key challenge is trying to identify a remediation scheme specific to in-house, organizational objectives. Without a strategy, the result is a patchwork of fixes applied to a tide of vulnerabilities, any one of which could be the point of failure in an otherwise formidable defense. Given that few vulnerabilities are a focus of real-world attacks, a practical remediation strategy is to identify vulnerabilities likely to be exploited and focus efforts towards remediating those vulnerabilities first. The goal of this research is to demonstrate that aggregating and synthesizing readily accessible, public data sources to provide personalized, automated recommendations for organizations to prioritize their vulnerability management strategy will offer significant improvements over using the Common Vulnerability Scoring System (CVSS). We provide a framework for vulnerability management specifically focused on mitigating threats using adversary criteria derived from MITRE ATT&CK. We test our approach by identifying vulnerabilities in software associated with six universities and four government facilities. Ranking policy performance is measured using the Normalized Discounted Cumulative Gain (nDCG). Our results show an average 71.5% - 91.3% improvement towards the identification of vulnerabilities likely to be targeted and exploited by cyber threat actors. The return on investment (ROI) of patching using our policies results in a savings of 23.3% - 25.5% in annualized costs. Our results demonstrate the efficacy of creating knowledge graphs to link large data sets to facilitate semantic queries and create data-driven, flexible ranking policies., Comment: 24 pages, 8 figures, 14 tables
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- 2024
27. Reliability and Validity of the Responsive Care Tool for Children 0-3 Years Old in a Rural, South Asian Setting
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Elizabeth Hentschel, Saima Siyal, Dana C. McCoy, Henning Tiemeier, and Aisha K. Yousafzai
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Research has shown the importance of responsive caregiving for fostering positive development early in life; however, tools measuring these interactions are often impractical for larger scale intervention trials and in settings with resource constraints. The present study provides reliability and validity evidence from Sindh, Pakistan for a tool developed to quantify responsive caregiving. Data were collected from 200 randomly selected households on responsive caregiving, sociodemographic characteristics, early learning, and early child development. The results indicated that the responsive care tool can be feasibly administered in less than 5 min in a low-resource setting. An exploratory factor analysis found that the tool's indicators reliably loaded onto two distinct factors, responsive interactions and caregiver-initiated interactions, accounting for 96.01% of the underlying variation in scores. A confirmatory factor analysis reflecting input from modification indices showed satisfactory fit statistics and adequate factor loadings (all above 0.70). Internal consistencies of the two factors were also high, with alphas of 0.93 and 0.83, respectively. Convergent validity of the responsive interactions factor was demonstrated by a strong and positive correlation with measures of psychosocial stimulation, early learning, maternal education, and household wealth. Predictive validity of the responsive interactions factor was demonstrated by a strong and positive association with child development. The caregiver-initiated interactions factor was significantly and negatively associated with psychosocial stimulation and child development. The resulting evidence provides programs with an open access, observational, reliable, and valid measure to quantify responsive caregiving at the program level in low-resource settings.
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- 2024
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28. African American Language in Children's Literature
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Ramona T. Pittman, Rebekah E. Piper, Whitney McCoy, and Melody Alanis
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The purpose of this study was to determine the most prevalent African American Language (AAL) phonological and grammatical features in slavery- and Civil Rights-themed children's literature. Seventy-six books were initially selected to determine if they used AAL in dialogue or in narration. Of the 76 books, only 39 included AAL. The 39 books were analyzed further to categorize the specific AAL features used. The results revealed that the reduction of the final g (e.g., "thinkin'") was the most prevalent phonological feature. Moreover, phonological features were used more often in slavery-themed texts than in Civil Rights texts. Additionally, the most frequently used AAL grammatical features were negation tense markers (e.g., "didn't" and "neither") and subject-verb agreement ("he listen"). Grammatical features of AAL appeared more often in slavery-themed texts than Civil Rights themed texts. Implications for practice include suggestions for selecting, evaluating, and reading the books from this study with students. Implications for research include investigating other AAL features in slavery- and Civil Rights-themed books, authenticating the storylines of slavery- and Civil Rights-themed books, and analyzing other books with AAL that do not use these themes.
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- 2024
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29. Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References
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Taylor, Dylan J, Eizenga, Jordan M, Li, Qiuhui, Das, Arun, Jenike, Katharine M, Kenny, Eimear E, Miga, Karen H, Monlong, Jean, McCoy, Rajiv C, Paten, Benedict, and Schatz, Michael C
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Precision Medicine ,Human Genome ,Generic health relevance ,Good Health and Well Being ,Humans ,Genome ,Human ,Human Genome Project ,Genetic Variation ,Genomics ,Sequence Analysis ,DNA ,Telomere ,telomere-to-telomere ,pangenome ,reference genome sequence ,genetic diversity ,precision ,medicine ,precision medicine ,Evolutionary Biology ,Law ,Genetics & Heredity - Abstract
The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome reference sequence remained incomplete and lacked representation of human genetic diversity. Recently, two major advances have emerged to address these shortcomings: complete gap-free human genome sequences, such as the one developed by the Telomere-to-Telomere Consortium, and high-quality pangenomes, such as the one developed by the Human Pangenome Reference Consortium. Facilitated by advances in long-read DNA sequencing and genome assembly algorithms, complete human genome sequences resolve regions that have been historically difficult to sequence, including centromeres, telomeres, and segmental duplications. In parallel, pangenomes capture the extensive genetic diversity across populations worldwide. Together, these advances usher in a new era of genomics research, enhancing the accuracy of genomic analysis, paving the path for precision medicine, and contributing to deeper insights into human biology.
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- 2024
30. Effect of a digital school-based intervention on adolescent family planning and reproductive health in Rwanda: a cluster-randomized trial
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Hémono, Rebecca, Gatare, Emmyson, Kayitesi, Laetitia, Hunter, Lauren A, Packel, Laura, Ippoliti, Nicole, Cerecero-García, Diego, Contreras-Loya, David, Gadsden, Paola, Bautista-Arredondo, Sergio, Sayinzoga, Felix, Mugisha, Michael, Bertozzi, Stefano M, Hope, Rebecca, and McCoy, Sandra I
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Paediatrics ,Biomedical and Clinical Sciences ,Public Health ,Health Sciences ,Behavioral and Social Science ,Dissemination and Implementation Research ,Adolescent Sexual Activity ,Prevention ,Contraception/Reproduction ,Clinical Trials and Supportive Activities ,Pediatric ,Clinical Research ,Reproductive health and childbirth ,Good Health and Well Being ,Medical and Health Sciences ,Immunology ,Biomedical and clinical sciences ,Health sciences - Abstract
We conducted a cluster-randomized hybrid effectiveness-implementation study of CyberRwanda, a digital family planning and reproductive health intervention for Rwandan adolescents. Sixty schools were randomized 1:1:1 to control or to one of two implementation models-self-service (self-guided access on tablets) or facilitated (peer-led clubs plus tablet access) with no masking. Eligible participants were aged 12-19 years, in secondary school levels 1 or 2, and willing to provide consent or assent/parental consent and contact information for follow-up. In 2021, 6,078 randomly selected adolescents were enrolled. At 24 months, 91.3% of participants were retained and included in the primary intention-to-treat analyses (control, n = 1,845; self-service, n = 1,849 and facilitated, n = 1,858). There were no adverse events related to the study. CyberRwanda did not affect the primary outcomes of modern contraceptive use (prevalence ratio (PR) = 1.04; 95% confidence interval (CI) = 0.76, 1.42), childbearing (PR = 1.33; 95% CI = 0.71, 2.50) and HIV testing (PR = 1.00; 95% CI = 0.91, 1.11) in the full sample. Significantly higher modern contraceptive use observed in the CyberRwanda facilitated arm in a prespecified analysis of sexually active participants suggests that longer-term evaluation is needed to examine effects as more of the study population becomes sexually active and has increased demand for contraception. ClinicalTrials.gov registration: NCT04198272 .
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- 2024
31. Likelihood-based interactive local docking into cryo-EM maps in ChimeraX
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Read, Randy J, Pettersen, Eric F, McCoy, Airlie J, Croll, Tristan I, Terwilliger, Thomas C, Poon, Billy K, Meng, Elaine C, Liebschner, Dorothee, and Adams, Paul D
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Biological Sciences ,Chemical Sciences ,Physical Sciences ,Cryoelectron Microscopy ,Software ,Molecular Docking Simulation ,Protein Conformation ,cryo-EM ,docking ,likelihood ,ChimeraX ,emplace_local - Abstract
The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.
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- 2024
32. Impact of financial incentives on viral suppression among adults initiating HIV treatment in Tanzania: a hybrid effectiveness–implementation trial
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Njau, Prosper F, Katabaro, Emmanuel, Winters, Solis, Sabasaba, Amon, Hassan, Kassim, Joseph, Babuu, Maila, Hamza, Msasa, Janeth, Fahey, Carolyn A, Packel, Laura, Dow, William H, Jewell, Nicholas P, Ulenga, Nzovu, Mwenda, Natalino, and McCoy, Sandra I
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Health Services and Systems ,Biomedical and Clinical Sciences ,Health Sciences ,Dissemination and Implementation Research ,Mental Health ,Clinical Research ,Behavioral and Social Science ,Cost Effectiveness Research ,Sexually Transmitted Infections ,HIV/AIDS ,Clinical Trials and Supportive Activities ,Prevention ,Comparative Effectiveness Research ,Women's Health ,Social Determinants of Health ,Health Services ,Infectious Diseases ,3.1 Primary prevention interventions to modify behaviours or promote wellbeing ,Infection ,Good Health and Well Being ,Medical and Health Sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
BackgroundSmall incentives could improve engagement in HIV care. We evaluated the short-term and longer-term effects of financial incentives for visit attendance on viral suppression among adults initiating antiretroviral therapy (ART) in Tanzania.MethodsIn a type 1 hybrid effectiveness-implementation study, we randomised (1:1) 32 primary care HIV clinics in four Tanzanian regions to usual care (control group) or the intervention (usual care plus ≤6 monthly incentives [22 500 Tanzanian Shillings, about US$10, each], conditional on visit attendance). Adults (aged ≥18 years) initiating ART (
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- 2024
33. Supporting young women’s health through girl-friendly drug vendors in Lake Zone, Tanzania: protocol for the AmbassADDOrs for Health cluster-randomised controlled trial
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Mnyippembe, Agatha, Sheira, Lila A, McCoy, Sandra I, Njau, Prosper F, Packel, Laura J, Hassan, Kassim, Solorzano-Barrera, Camila, Maokola, Werner, Dufour, Mi-Suk Kang, Sabasaba, Amon, and Liu, Jenny
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Biomedical and Clinical Sciences ,Public Health ,Health Sciences ,Sexually Transmitted Infections ,Teenage Pregnancy ,Clinical Research ,Behavioral and Social Science ,Clinical Trials and Supportive Activities ,Pediatric ,Women's Health ,Prevention ,Adolescent Sexual Activity ,HIV/AIDS ,Pediatric AIDS ,Contraception/Reproduction ,Infectious Diseases ,3.1 Primary prevention interventions to modify behaviours or promote wellbeing ,Reproductive health and childbirth ,Infection ,Good Health and Well Being ,Humans ,Tanzania ,Female ,Adolescent ,Young Adult ,HIV Infections ,Pregnancy ,Randomized Controlled Trials as Topic ,Commerce ,Clinical Trial ,Epidemiology ,HIV & AIDS ,Public health ,Clinical Sciences ,Public Health and Health Services ,Other Medical and Health Sciences ,Biomedical and clinical sciences ,Health sciences ,Psychology - Abstract
IntroductionAdverse sexual and reproductive health (SRH) outcomes, such as unplanned pregnancies and HIV infection, disproportionately affect adolescent girls and young women (AGYW; aged 15-24 years) in east Africa. Increasing uptake of preventive SRH services via innovative, youth-centred interventions is imperative to addressing disparities in SRH outcomes.Methods and analysisFrom 2018 to 2019, we used human-centred design to co-develop a theoretically driven HIV and pregnancy prevention intervention for AGYW at private drug shops called Accredited Drug Dispensing Outlets (ADDOs) in Tanzania. The result, Malkia Klabu (Queen Club), was a customer loyalty programme designed to strengthen ADDOs' role as SRH providers while encouraging uptake of critical SRH prevention products among AGYW. Malkia Klabu members had access to free contraceptives and oral HIV self-test (HIVST) kits and earned punches on a loyalty card for other shop purchases; punches were redeemable for small prizes. Our pilot among 40 shops showed that intervention ADDOs had higher AGYW patronage and distributed more HIVST kits and contraceptives to AGYW relative to business-as-usual (ie, client purchasing) comparison shops. We will conduct a cluster-randomised controlled trial (c-RCT) among 120-140 ADDOs in 40 health catchment areas in Shinyanga and Mwanza Regions (Lake Zone), Tanzania. ADDO shop recruitment includes a 1-month run-in with a tablet-based electronic inventory management system for tracking shop transactions, followed by enrolment, randomisation and a 24-month trial period. Our c-RCT evaluating the human-centred design-derived intervention will assess population impact on the primary outcomes of HIV diagnoses and antenatal care registrations, measured with routine health facility data. We will also assess secondary outcomes focusing on mechanisms of action, evaluate programme exposure and AGYW behaviour change in interviews with AGYW, and assess shop-level implementation strategies and fidelity.Ethics and disseminationEthical approval was granted from both the University of California, San Francisco and the Tanzanian National Institute for Medical Research. Study progress and final outcomes will be posted annually to the National Clinical Trials website; study dissemination will occur at conferences, peer-reviewed manuscripts and local convenings of stakeholders.Trial registration numberNCT05357144.
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- 2024
34. A Systematic Review of HIV Pre-exposure Prophylaxis (PrEP) Implementation in U.S. Emergency Departments: Patient Screening, Prescribing, and Linkage to Care.
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Chitle, Pooja, McCoy, Sandra, White, Douglas, and Jackson, Kristopher
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Differentiated service delivery ,Emergency department ,Emergency medicine ,HIV ,PrEP ,Pre-exposure prophylaxis ,Humans ,HIV Infections ,Pre-Exposure Prophylaxis ,Aftercare ,Anti-HIV Agents ,Patient Discharge ,Emergency Service ,Hospital - Abstract
In the pursuit of ending the HIV epidemic, U.S. emergency departments (EDs) have emerged as a valuable setting to increase HIV testing and linkage to care. There is limited data available, however, describing the incorporation of HIV prevention initiatives in U.S. EDs. Over the last decade, HIV pre-exposure prophylaxis (PrEP) has significantly changed the HIV prevention landscape globally and very little is known about the provision of PrEP in U.S. EDs. To address this gap in the literature, we conducted a systematic review of peer-reviewed quantitative studies and conference abstracts spanning July 2012 - October 2022. Of 433 citations, 11 articles and 13 abstracts meet our inclusion criteria, representing 18 unique studies addressing PrEP screening, prescribing, and/or linkage to PrEP care.Most studies describe screening processes to identify PrEP-eligible patients (n = 17); most studies leveraged a patients STI history as initial PrEP eligibility screening criteria. Fewer studies describe PrEP prescribing (n = 2) and/or linkage to PrEP care (n = 8).Findings from this systematic review highlight the potential for U.S. EDs to increase PrEP uptake among individuals at risk for HIV infection. Despite a growing number of studies exploring processes for incorporating PrEP into the ED setting, such studies are small-scale and time limited. Models providing prescribing PrEP in the ED show higher initiation rates than post-discharge engagement models. Electronic health record (EHR)-based HIV screening is valuable, but post-ED linkage rates are low. Our findings emphasize the need to establish best practices for initiating and supporting prevention effective PrEP use in the ED setting.
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- 2024
35. “De novo replication repair deficient glioblastoma, IDH-wildtype” is a distinct glioblastoma subtype in adults that may benefit from immune checkpoint blockade
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Hadad, Sara, Gupta, Rohit, Oberheim Bush, Nancy Ann, Taylor, Jennie W, Villanueva-Meyer, Javier E, Young, Jacob S, Wu, Jasper, Ravindranathan, Ajay, Zhang, Yalan, Warrier, Gayathri, McCoy, Lucie, Shai, Anny, Pekmezci, Melike, Perry, Arie, Bollen, Andrew W, Phillips, Joanna J, Braunstein, Steve E, Raleigh, David R, Theodosopoulos, Philip, Aghi, Manish K, Chang, Edward F, Hervey-Jumper, Shawn L, Costello, Joseph F, de Groot, John, Butowski, Nicholas A, Clarke, Jennifer L, Chang, Susan M, Berger, Mitchel S, Molinaro, Annette M, and Solomon, David A
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Biomedical and Clinical Sciences ,Clinical Sciences ,Oncology and Carcinogenesis ,Brain Cancer ,Cancer ,Precision Medicine ,Brain Disorders ,Genetics ,Human Genome ,Clinical Research ,Cancer Genomics ,Neurosciences ,Immunotherapy ,Orphan Drug ,Rare Diseases ,2.1 Biological and endogenous factors ,Good Health and Well Being ,Adult ,Humans ,Child ,Middle Aged ,Aged ,Glioblastoma ,Immune Checkpoint Inhibitors ,Homozygote ,Prospective Studies ,Brain Neoplasms ,Sequence Deletion ,Mutation ,Isocitrate Dehydrogenase ,Giant cell glioblastoma ,Hypermutation ,Ultrahypermutation ,Mismatch repair deficiency ,POLE ,Lynch syndrome ,Immune checkpoint blockade ,Molecular neuropathology ,Molecular neuro-oncology ,Neurology & Neurosurgery - Abstract
Glioblastoma is a clinically and molecularly heterogeneous disease, and new predictive biomarkers are needed to identify those patients most likely to respond to specific treatments. Through prospective genomic profiling of 459 consecutive primary treatment-naïve IDH-wildtype glioblastomas in adults, we identified a unique subgroup (2%, 9/459) defined by somatic hypermutation and DNA replication repair deficiency due to biallelic inactivation of a canonical mismatch repair gene. The deleterious mutations in mismatch repair genes were often present in the germline in the heterozygous state with somatic inactivation of the remaining allele, consistent with glioblastomas arising due to underlying Lynch syndrome. A subset of tumors had accompanying proofreading domain mutations in the DNA polymerase POLE and resultant "ultrahypermutation". The median age at diagnosis was 50 years (range 27-78), compared with 63 years for the other 450 patients with conventional glioblastoma (p
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- 2024
36. Characterizing Novel Indium Phosphide Pad Detectors with Focused X-ray Beams and Laboratory Tests
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Almazan, Earl, Affolder, Anthony, Dyckes, Ian, Fadeyev, Vitaliy, Hance, Michael, Jadhav, Manoj, Kim, Sungjoon, McCoy, Thomas, Metcalfe, Jessica, Nielsen, Jason, Ott, Jennifer, Poley, Luise, Shin, Taylor, Sperlich, Dennis, and Sumant, Anirudha V.
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Physics - Instrumentation and Detectors ,High Energy Physics - Experiment - Abstract
Future tracking systems in High Energy Physics experiments will require large instrumented areas with low radiation length. Crystalline silicon sensors have been used in tracking systems for decades, but are difficult to manufacture and costly to produce for large areas. We are exploring alternative sensor materials that are amenable to fast fabrication techniques used for thin film devices. Indium Phosphide pad sensors were fabricated at Argonne National Lab using commercially available InP:Fe 2-inch mono-crystal substrates. Current-voltage and capacitance-voltage characterizations were performed to study the basic operating characteristics of a group of sensors. Micro-focused X-ray beams at Canadian Light Source and Diamond Light Source were used to study the response to ionizing radiation, and characterize the uniformity of the response for several devices. The results show a high degree of performance uniformity in our evaluations, both within a device and between the 48 tested devices. This motivates further studies into thin film devices for future tracking detectors., Comment: 30 pages, 27 figures
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- 2024
37. Adaptive Quotient Filters
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Wen, Richard, McCoy, Hunter, Tench, David, Tagliavini, Guido, Bender, Michael A., Conway, Alex, Farach-Colton, Martin, Johnson, Rob, and Pandey, Prashant
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Computer Science - Data Structures and Algorithms - Abstract
Adaptive filters, such as telescoping and adaptive cuckoo filters, update their representation upon detecting a false positive to avoid repeating the same error in the future. Adaptive filters require an auxiliary structure, typically much larger than the main filter and often residing on slow storage, to facilitate adaptation. However, existing adaptive filters are not practical and have seen no adoption in real-world systems due to two main reasons. Firstly, they offer weak adaptivity guarantees, meaning that fixing a new false positive can cause a previously fixed false positive to come back. Secondly, the sub-optimal design of the auxiliary structure results in adaptivity overheads so substantial that they can actually diminish the overall system performance compared to a traditional filter. In this paper, we design and implement AdaptiveQF, the first practical adaptive filter with minimal adaptivity overhead and strong adaptivity guarantees, which means that the performance and false-positive guarantees continue to hold even for adversarial workloads. The AdaptiveQF is based on the state-of-the-art quotient filter design and preserves all the critical features of the quotient filter such as cache efficiency and mergeability. Furthermore, we employ a new auxiliary structure design which results in considerably low adaptivity overhead and makes the AdaptiveQF practical in real systems.
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- 2024
38. Dominion: A New Frontier for AI Research
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Halawi, Danny, Sarmasi, Aron, Saltzen, Siena, and McCoy, Joshua
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Computer Science - Artificial Intelligence - Abstract
In recent years, machine learning approaches have made dramatic advances, reaching superhuman performance in Go, Atari, and poker variants. These games, and others before them, have served not only as a testbed but have also helped to push the boundaries of AI research. Continuing this tradition, we examine the tabletop game Dominion and discuss the properties that make it well-suited to serve as a benchmark for the next generation of reinforcement learning (RL) algorithms. We also present the Dominion Online Dataset, a collection of over 2,000,000 games of Dominion played by experienced players on the Dominion Online webserver. Finally, we introduce an RL baseline bot that uses existing techniques to beat common heuristic-based bots, and shows competitive performance against the previously strongest bot, Provincial.
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- 2024
39. Seeds of Stereotypes: A Large-Scale Textual Analysis of Race and Gender Associations with Diseases in Online Sources
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Hansen, Lasse Hyldig, Andersen, Nikolaj, Gallifant, Jack, McCoy, Liam G., Stone, James K, Izath, Nura, Aguirre-Jerez, Marcela, Bitterman, Danielle S, Gichoya, Judy, and Celi, Leo Anthony
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Computer Science - Computation and Language - Abstract
Background Advancements in Large Language Models (LLMs) hold transformative potential in healthcare, however, recent work has raised concern about the tendency of these models to produce outputs that display racial or gender biases. Although training data is a likely source of such biases, exploration of disease and demographic associations in text data at scale has been limited. Methods We conducted a large-scale textual analysis using a dataset comprising diverse web sources, including Arxiv, Wikipedia, and Common Crawl. The study analyzed the context in which various diseases are discussed alongside markers of race and gender. Given that LLMs are pre-trained on similar datasets, this approach allowed us to examine the potential biases that LLMs may learn and internalize. We compared these findings with actual demographic disease prevalence as well as GPT-4 outputs in order to evaluate the extent of bias representation. Results Our findings indicate that demographic terms are disproportionately associated with specific disease concepts in online texts. gender terms are prominently associated with disease concepts, while racial terms are much less frequently associated. We find widespread disparities in the associations of specific racial and gender terms with the 18 diseases analyzed. Most prominently, we see an overall significant overrepresentation of Black race mentions in comparison to population proportions. Conclusions Our results highlight the need for critical examination and transparent reporting of biases in LLM pretraining datasets. Our study suggests the need to develop mitigation strategies to counteract the influence of biased training data in LLMs, particularly in sensitive domains such as healthcare.
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- 2024
40. Asteroid (101955) Bennu in the Laboratory: Properties of the Sample Collected by OSIRIS-REx
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Lauretta, Dante S., Connolly, Jr., Harold C., Aebersold, Joseph E., Alexander, Conel M. O. D., Ballouz, Ronald-L., Barnes, Jessica J., Bates, Helena C., Bennett, Carina A., Blanche, Laurinne, Blumenfeld, Erika H., Clemett, Simon J., Cody, George D., DellaGiustina, Daniella N., Dworkin, Jason P., Eckley, Scott A., Foustoukos, Dionysis I., Franchi, Ian A., Glavin, Daniel P., Greenwood, Richard C., Haenecour, Pierre, Hamilton, Victoria E., Hill, Dolores H., Hiroi, Takahiro, Ishimaru, Kana, Jourdan, Fred, Kaplan, Hannah H., Keller, Lindsay P., King, Ashley J., Koefoed, Piers, Kontogiannis, Melissa K., Le, Loan, Macke, Robert J., McCoy, Timothy J., Milliken, Ralph E., Najorka, Jens, Nguyen, Ann N., Pajola, Maurizio, Polit, Anjani T., Roper, Heather L., Russell, Sara S., Ryan, Andrew J., Sandford, Scott A., Schofield, Paul F., Schultz, Cody D., Tachibana, Shogo, Thomas-Keprta, Kathie L., Thompson, Michelle S., Tu, Valerie, Tusberti, Filippo, Wang, Kun, Zega, Thomas J., Wolner, C. W. V., and Team, the OSIRIS-REx Sample Analysis
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
On 24 September 2023, the NASA OSIRIS-REx mission dropped a capsule to Earth containing approximately 120 g of pristine carbonaceous regolith from Bennu. We describe the delivery and initial allocation of this asteroid sample and introduce its bulk physical, chemical, and mineralogical properties from early analyses. The regolith is very dark overall, with higher-reflectance inclusions and particles interspersed. Particle sizes range from sub-micron dust to a stone about 3.5 cm long. Millimeter-scale and larger stones typically have hummocky or angular morphologies. A subset of the stones appears mottled by brighter material that occurs as veins and crusts. Hummocky stones have the lowest densities and mottled stones have the highest. Remote sensing of the surface of Bennu detected hydrated phyllosilicates, magnetite, organic compounds, carbonates, and scarce anhydrous silicates, all of which the sample confirms. We also find sulfides, presolar grains, and, less expectedly, Na-rich phosphates, as well as other trace phases. The sample composition and mineralogy indicate substantial aqueous alteration and resemble those of Ryugu and the most chemically primitive, low-petrologic-type carbonaceous chondrites. Nevertheless, we find distinct hydrogen, nitrogen, and oxygen isotopic compositions, and some of the material we analyzed is enriched in fluid-mobile elements. Our findings underscore the value of sample return, especially for low-density material that may not readily survive atmospheric entry, and lay the groundwork for more comprehensive analyses., Comment: 73 pages, 22 figures
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- 2024
41. First Measurement of the $\nu_e$ and $\nu_\mu$ Interaction Cross Sections at the LHC with FASER's Emulsion Detector
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FASER Collaboration, Abraham, Roshan Mammen, Anders, John, Antel, Claire, Ariga, Akitaka, Ariga, Tomoko, Atkinson, Jeremy, Bernlochner, Florian U., Boeckh, Tobias, Boyd, Jamie, Brenner, Lydia, Burger, Angela, Cadoux, Franck, Cardella, Roberto, Casper, David W., Cavanagh, Charlotte, Chen, Xin, Coccaro, Andrea, Debieux, Stephane, D'Onofrio, Monica, Desai, Ansh, Dmitrievsky, Sergey, Eley, Sinead, Favre, Yannick, Fellers, Deion, Feng, Jonathan L., Fenoglio, Carlo Alberto, Ferrere, Didier, Fieg, Max, Filali, Wissal, Fujimori, Haruhi, Garabaglu, Ali, Gibson, Stephen, Gonzalez-Sevilla, Sergio, Gornushkin, Yuri, Gwilliam, Carl, Hayakawa, Daiki, Hsu, Shih-Chieh, Hu, Zhen, Iacobucci, Giuseppe, Inada, Tomohiro, Iodice, Luca, Jakobsen, Sune, Joos, Hans, Kajomovitz, Enrique, Kanai, Takumi, Kawahara, Hiroaki, Keyken, Alex, Kling, Felix, Kock, Daniela, Kontaxakis, Pantelis, Kose, Umut, Kotitsa, Rafaella, Kuehn, Susanne, Kugathasan, Thanushan, Lefebvre, Helena, Levinson, Lorne, Li, Ke, Liu, Jinfeng, Lutz, Margaret S., MacDonald, Jack, Magliocca, Chiara, Martinelli, Fulvio, McCoy, Lawson, McFayden, Josh, Medina, Andrea Pizarro, Milanesio, Matteo, Moretti, Theo, Munker, Magdalena, Nakamura, Mitsuhiro, Nakano, Toshiyuki, Neuhaus, Friedemann, Nevay, Laurie, Nonaka, Motoya, Okui, Kazuaki, Ohashi, Ken, Otono, Hidetoshi, Pang, Hao, Paolozzi, Lorenzo, Petersen, Brian, Prim, Markus, Queitsch-Maitland, Michaela, Rokujo, Hiroki, Ruiz-Choliz, Elisa, Rubbia, André, Sabater-Iglesias, Jorge, Sato, Osamu, Scampoli, Paola, Schmieden, Kristof, Schott, Matthias, Sfyrla, Anna, Shamim, Mansoora, Shively, Savannah, Takubo, Yosuke, Tarannum, Noshin, Theiner, Ondrej, Torrence, Eric, Vasina, Svetlana, Vormwald, Benedikt, Wang, Di, Wang, Yuxiao, Welch, Eli, Zahorec, Samuel, Zambito, Stefano, and Zhang, Shunliang
- Subjects
High Energy Physics - Experiment ,High Energy Physics - Phenomenology ,Physics - Instrumentation and Detectors - Abstract
This paper presents the first results of the study of high-energy electron and muon neutrino charged-current interactions in the FASER$\nu$ emulsion/tungsten detector of the FASER experiment at the LHC. A subset of the FASER$\nu$ volume, which corresponds to a target mass of 128.6~kg, was exposed to neutrinos from the LHC $pp$ collisions with a centre-of-mass energy of 13.6~TeV and an integrated luminosity of 9.5 fb$^{-1}$. Applying stringent selections requiring electrons with reconstructed energy above 200~GeV, four electron neutrino interaction candidate events are observed with an expected background of $0.025^{+0.015}_{-0.010}$, leading to a statistical significance of 5.2$\sigma$. This is the first direct observation of electron neutrino interactions at a particle collider. Eight muon neutrino interaction candidate events are also detected, with an expected background of $0.22^{+0.09}_{-0.07}$, leading to a statistical significance of 5.7$\sigma$. The signal events include neutrinos with energies in the TeV range, the highest-energy electron and muon neutrinos ever detected from an artificial source. The energy-independent part of the interaction cross section per nucleon is measured over an energy range of 560--1740 GeV (520--1760 GeV) for $\nu_e$ ($\nu_{\mu}$) to be $(1.2_{-0.7}^{+0.8}) \times 10^{-38}~\mathrm{cm}^{2}\,\mathrm{GeV}^{-1}$ ($(0.5\pm0.2) \times 10^{-38}~\mathrm{cm}^{2}\,\mathrm{GeV}^{-1}$), consistent with Standard Model predictions. These are the first measurements of neutrino interaction cross sections in those energy ranges.
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- 2024
- Full Text
- View/download PDF
42. A Toolbox for Surfacing Health Equity Harms and Biases in Large Language Models
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Pfohl, Stephen R., Cole-Lewis, Heather, Sayres, Rory, Neal, Darlene, Asiedu, Mercy, Dieng, Awa, Tomasev, Nenad, Rashid, Qazi Mamunur, Azizi, Shekoofeh, Rostamzadeh, Negar, McCoy, Liam G., Celi, Leo Anthony, Liu, Yun, Schaekermann, Mike, Walton, Alanna, Parrish, Alicia, Nagpal, Chirag, Singh, Preeti, Dewitt, Akeiylah, Mansfield, Philip, Prakash, Sushant, Heller, Katherine, Karthikesalingam, Alan, Semturs, Christopher, Barral, Joelle, Corrado, Greg, Matias, Yossi, Smith-Loud, Jamila, Horn, Ivor, and Singhal, Karan
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Computer Science - Computers and Society ,Computer Science - Computation and Language ,Computer Science - Machine Learning - Abstract
Large language models (LLMs) hold promise to serve complex health information needs but also have the potential to introduce harm and exacerbate health disparities. Reliably evaluating equity-related model failures is a critical step toward developing systems that promote health equity. We present resources and methodologies for surfacing biases with potential to precipitate equity-related harms in long-form, LLM-generated answers to medical questions and conduct a large-scale empirical case study with the Med-PaLM 2 LLM. Our contributions include a multifactorial framework for human assessment of LLM-generated answers for biases, and EquityMedQA, a collection of seven datasets enriched for adversarial queries. Both our human assessment framework and dataset design process are grounded in an iterative participatory approach and review of Med-PaLM 2 answers. Through our empirical study, we find that our approach surfaces biases that may be missed via narrower evaluation approaches. Our experience underscores the importance of using diverse assessment methodologies and involving raters of varying backgrounds and expertise. While our approach is not sufficient to holistically assess whether the deployment of an AI system promotes equitable health outcomes, we hope that it can be leveraged and built upon towards a shared goal of LLMs that promote accessible and equitable healthcare.
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- 2024
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43. Studies in Teaching: 2023 Research Digest. Action Research Projects Presented at Annual Research Forum (Winston-Salem, North Carolina, June 29, 2023)
- Author
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Wake Forest University, Department of Education and McCoy, Leah P.
- Abstract
This document presents the proceedings of the 27th Annual Research Forum held June 29, 2023, at Wake Forest University in Winston-Salem, North Carolina. Included are the following fifteen action research papers: (1) The Effects of Real-World Mathematics Activities on High School Students' Attitudes (Alexa Altizer); (2) An Investigation of the Effect of Explicit Spatial Reasoning Instruction on Student Self-Efficacy in High School Chemistry (Emma Armstrong); (3) The Influence of Goal Setting on Student Motivation for English Learners (Anna Bush); (4) Having Fun & Learning Deeply: Constructivist Assessments in a Social Studies Classroom (Molly Dwyer); (5) "Why Is There a Cage in Central Park?": The Impact of Political Art on Engagement and Understanding in Civics (Elena Ecelbarger); (6) The Privilege of Wonder (Courtney C. Fadley); (7) Have You Heard?: The Impact of Auditory Sources on Student Engagement and Achievement in Secondary Social Studies (Connor Flaherty); (8) Influence of Creative Portfolios on Students' Engagement with Grammar (Bailey Inama); (9) Arts Integration in the Elementary Math Classroom (Ashlyn John); (10) The Influence of the CRAAP Test and the SIFT Method on University Students' Understanding of Credibility of Information Online (Amanda Kaufman); (11) The Effect of Music Integration on Student Engagement with Novels (Caroline Pope); (12) Dedicated Social Studies Instruction in Elementary Schools: A Case Study (Kathleen Rainey); (13) The Impact of Reflection Activities on High School Student's Math Identity (Allie Rice); (14) The Influence of Humor on Student Engagement with Nonfiction Texts (Lily Richards); and (15) The Influence of Authentic Letter Writing on Students' Attitudes toward Writing in the Secondary English Classroom (Luke Tatum). Individual papers contain references, tables, and figures. [For the 2022 Research Digest, see ED621431.]
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- 2023
44. IAMSE Artificial Intelligence Meeting Survey: AI’s Impact on Medical Education Faculty
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McKell, Douglas, McCoy, Lise, and Niño, Diego F.
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- 2024
- Full Text
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45. Co-transcriptional production of programmable RNA condensates and synthetic organelles
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Fabrini, Giacomo, Farag, Nada, Nuccio, Sabrina Pia, Li, Shiyi, Stewart, Jaimie Marie, Tang, Anli A., McCoy, Reece, Owens, Róisín M., Rothemund, Paul W. K., Franco, Elisa, Di Antonio, Marco, and Di Michele, Lorenzo
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- 2024
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46. Simulation of asteroid deflection with a megajoule-class X-ray pulse
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Moore, Nathan W., Mesh, Mikhail, Sanchez, Jason J., Schaeuble, Marc-Andre, McCoy, Chad A., Aragon, Carlos R., Cochrane, Kyle R., Powell, Michael J., and Root, Seth
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- 2024
- Full Text
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47. Physical Restraint Use in Hospitalized Patients: A Study of Routinely Collected Health Records Data
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Luccarelli, James, Gan, Tsu K., Golas, Sara B., Sriraman, Poorvi, Snydeman, Colleen K., Sacks, Chana A., and McCoy, Jr, Thomas H.
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- 2024
- Full Text
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48. Demographics, management and outcomes of major trauma in older patients at an Irish trauma unit
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Haines, Madeline, Measey, Molly Maeve, Whitty, Ailbhe, McCoy, Nigel, and McCabe, Aileen
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- 2024
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49. Associations Between Infant Formula Exposure, Housing Instability and Postneonatal Mortality Among Participants in the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC)
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Castillo, Nichole and McCoy, Marcia
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- 2024
- Full Text
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50. Rapid Screening of Colorado Potato Beetle Resistance Derived from Solanum okadae
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McCoy, Hanna J., Fenstemaker, Sean, MacKinley, Pamela, Vickruck, Jess, Bamberg, John, Calhoun, Larry A., and Tai, Helen H.
- Published
- 2024
- Full Text
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