183,142 results on '"Carpenter, A."'
Search Results
2. Harnessing the Power of Gradient-Based Simulations for Multi-Objective Optimization in Particle Accelerators
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Rajput, Kishansingh, Schram, Malachi, Edelen, Auralee, Colen, Jonathan, Kasparian, Armen, Roussel, Ryan, Carpenter, Adam, Zhang, He, and Benesch, Jay
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Physics - Accelerator Physics ,Computer Science - Neural and Evolutionary Computing - Abstract
Particle accelerator operation requires simultaneous optimization of multiple objectives. Multi-Objective Optimization (MOO) is particularly challenging due to trade-offs between the objectives. Evolutionary algorithms, such as genetic algorithm (GA), have been leveraged for many optimization problems, however, they do not apply to complex control problems by design. This paper demonstrates the power of differentiability for solving MOO problems using a Deep Differentiable Reinforcement Learning (DDRL) algorithm in particle accelerators. We compare DDRL algorithm with Model Free Reinforcement Learning (MFRL), GA and Bayesian Optimization (BO) for simultaneous optimization of heat load and trip rates in the Continuous Electron Beam Accelerator Facility (CEBAF). The underlying problem enforces strict constraints on both individual states and actions as well as cumulative (global) constraint for energy requirements of the beam. A physics-based surrogate model based on real data is developed. This surrogate model is differentiable and allows back-propagation of gradients. The results are evaluated in the form of a Pareto-front for two objectives. We show that the DDRL outperforms MFRL, BO, and GA on high dimensional problems.
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- 2024
3. Audience Reach of Scientific Data Visualizations in Planetarium-Screened Films
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Borkiewicz, Kalina, Jensen, Eric, Miao, Yiwen, Levy, Stuart, Naiman, J. P., Carpenter, Jeff, and Isaacs, Katherine E.
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Physics - Popular Physics ,Astrophysics - Instrumentation and Methods for Astrophysics ,Computer Science - Computers and Society ,Computer Science - Graphics ,Computer Science - Human-Computer Interaction - Abstract
Quantifying the global reach of planetarium dome shows presents significant challenges due to the lack of standardized viewership tracking mechanisms across diverse planetarium venues. We present an analysis of the global impact of dome shows, presenting data regarding four documentary films from a single visualization lab. Specifically, we designed and administered a viewership survey of four long-running shows that contained cinematic scientific visualizations. Reported survey data shows that between 1.2 - 2.6 million people have viewed these four films across the 68 responding planetariums (mean: 1.9 million). When we include estimates and extrapolate for the 315 planetariums that licensed these shows, we arrive at an estimate of 16.5 - 24.1 million people having seen these films (mean: 20.3 million).
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- 2024
4. Extending the ALMA Census of Circumstellar Disks in the Upper Scorpius OB Association
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Carpenter, John M., Esplin, Taran L., Luhman, Kevin L., Mamajek, Eric E., and Andrews, Sean M.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Astrophysics of Galaxies - Abstract
We present ALMA Band 7 continuum (340 GHz) and CO J=3-2 observations for an extended sample of disks in the Upper Scorpius OB Association (Upper Sco, age ~ 10 Myr). The targets were selected from previous studies that identified new members of Upper Sco using photometry and astrometry from the Gaia mission, and the presence of a disk has been inferred from mid-infrared excess emission. The new ALMA observations are combined with previous ALMA data to define a sample of 202 Upper Sco members with disks that have spectral types between G0 and M5.5. Among these sources, 120 (59%) have been detected in the continuum with a signal-to-noise ratio >= 3, and 83 (41%) have been detected in CO J=3-2. Both the continuum and CO J=3-2 fluxes show a strong correlation with the spectral type of the central star and the type of disk inferred from the shape of the infrared spectral energy distribution, where disks around earlier type stars and full disks are more luminous than disks around later type stars and evolved and debris disks. The median dust continuum luminosity is lower for disks in Upper Sco than in younger regions, as found in previous studies, where the differences are more pronounced in later spectral types (M4-M5) than in earlier spectral types., Comment: Accepted for publication in ApJ; 53 pages, 13 figures
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- 2024
5. MultiVENT 2.0: A Massive Multilingual Benchmark for Event-Centric Video Retrieval
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Kriz, Reno, Sanders, Kate, Etter, David, Murray, Kenton, Carpenter, Cameron, Van Ochten, Kelly, Recknor, Hannah, Guallar-Blasco, Jimena, Martin, Alexander, Colaianni, Ronald, King, Nolan, Yang, Eugene, and Van Durme, Benjamin
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Computation and Language - Abstract
Efficiently retrieving and synthesizing information from large-scale multimodal collections has become a critical challenge. However, existing video retrieval datasets suffer from scope limitations, primarily focusing on matching descriptive but vague queries with small collections of professionally edited, English-centric videos. To address this gap, we introduce $\textbf{MultiVENT 2.0}$, a large-scale, multilingual event-centric video retrieval benchmark featuring a collection of more than 218,000 news videos and 3,906 queries targeting specific world events. These queries specifically target information found in the visual content, audio, embedded text, and text metadata of the videos, requiring systems leverage all these sources to succeed at the task. Preliminary results show that state-of-the-art vision-language models struggle significantly with this task, and while alternative approaches show promise, they are still insufficient to adequately address this problem. These findings underscore the need for more robust multimodal retrieval systems, as effective video retrieval is a crucial step towards multimodal content understanding and generation tasks.
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- 2024
6. Enhancing Peer Review in Astronomy: A Machine Learning and Optimization Approach to Reviewer Assignments for ALMA
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Carpenter, John M., Corvillón, Andrea, and Shah, Nihar B.
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Astrophysics - Instrumentation and Methods for Astrophysics ,Computer Science - Artificial Intelligence ,Computer Science - Digital Libraries - Abstract
The increasing volume of papers and proposals undergoing peer review emphasizes the pressing need for greater automation to effectively manage the growing scale. In this study, we present the deployment and evaluation of machine learning and optimization techniques for assigning proposals to reviewers that was developed for the Atacama Large Millimeter/submillimeter Array (ALMA) during the Cycle 10 Call for Proposals issued in 2023. By utilizing topic modeling algorithms, we identify the proposal topics and assess reviewers' expertise based on their historical ALMA proposal submissions. We then apply an adapted version of the assignment optimization algorithm from PeerReview4All (Stelmakh et al. 2021a) to maximize the alignment between proposal topics and reviewer expertise. Our evaluation shows a significant improvement in matching reviewer expertise: the median similarity score between the proposal topic and reviewer expertise increased by 51 percentage points compared to the previous cycle, and the percentage of reviewers reporting expertise in their assigned proposals rose by 20 percentage points. Furthermore, the assignment process proved highly effective in that no proposals required reassignment due to significant mismatches, resulting in a savings of 3 to 5 days of manual effort., Comment: 19 pages, 5 figures, submitted to PASP
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- 2024
7. Unusual portals to new exotics, the W-gluon portal
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Carpenter, Linda M. and Schwind, Katherine
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High Energy Physics - Phenomenology - Abstract
We explore models where new light exotic states interact with the Standard Model through an asymmetric di-boson portal with one gluon and one W boson. We consider the complete set of effective operators up to dimension 6 which couple a single light exotic (LEX) state to at least one W boson and 1 gluon. Other Standard Model particles may also be present in the interactions. We discover that the W-gluon portal allows us to access a large array of exotic states in non-trivial representations of SU(3) and SU(2). We discuss new single production collider modes and phenomenological signatures for these light exotic states at LHC and e-p colliders., Comment: 29 pages, 16 figures, 9 tables
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- 2024
8. Enabling Novel Mission Operations and Interactions with ROSA: The Robot Operating System Agent
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Royce, Rob, Kaufmann, Marcel, Becktor, Jonathan, Moon, Sangwoo, Carpenter, Kalind, Pak, Kai, Towler, Amanda, Thakker, Rohan, and Khattak, Shehryar
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Computer Science - Robotics ,Computer Science - Artificial Intelligence ,Computer Science - Human-Computer Interaction - Abstract
The advancement of robotic systems has revolutionized numerous industries, yet their operation often demands specialized technical knowledge, limiting accessibility for non-expert users. This paper introduces ROSA (Robot Operating System Agent), an AI-powered agent that bridges the gap between the Robot Operating System (ROS) and natural language interfaces. By leveraging state-of-the-art language models and integrating open-source frameworks, ROSA enables operators to interact with robots using natural language, translating commands into actions and interfacing with ROS through well-defined tools. ROSA's design is modular and extensible, offering seamless integration with both ROS1 and ROS2, along with safety mechanisms like parameter validation and constraint enforcement to ensure secure, reliable operations. While ROSA is originally designed for ROS, it can be extended to work with other robotics middle-wares to maximize compatibility across missions. ROSA enhances human-robot interaction by democratizing access to complex robotic systems, empowering users of all expertise levels with multi-modal capabilities such as speech integration and visual perception. Ethical considerations are thoroughly addressed, guided by foundational principles like Asimov's Three Laws of Robotics, ensuring that AI integration promotes safety, transparency, privacy, and accountability. By making robotic technology more user-friendly and accessible, ROSA not only improves operational efficiency but also sets a new standard for responsible AI use in robotics and potentially future mission operations. This paper introduces ROSA's architecture and showcases initial mock-up operations in JPL's Mars Yard, a laboratory, and a simulation using three different robots. The core ROSA library is available as open-source., Comment: Under review for IEEE Aerospace Conference, 20 pages, 20 figures
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- 2024
9. Grounding Partially-Defined Events in Multimodal Data
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Sanders, Kate, Kriz, Reno, Etter, David, Recknor, Hannah, Martin, Alexander, Carpenter, Cameron, Lin, Jingyang, and Van Durme, Benjamin
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Computer Science - Computation and Language ,Computer Science - Computer Vision and Pattern Recognition - Abstract
How are we able to learn about complex current events just from short snippets of video? While natural language enables straightforward ways to represent under-specified, partially observable events, visual data does not facilitate analogous methods and, consequently, introduces unique challenges in event understanding. With the growing prevalence of vision-capable AI agents, these systems must be able to model events from collections of unstructured video data. To tackle robust event modeling in multimodal settings, we introduce a multimodal formulation for partially-defined events and cast the extraction of these events as a three-stage span retrieval task. We propose a corresponding benchmark for this task, MultiVENT-G, that consists of 14.5 hours of densely annotated current event videos and 1,168 text documents, containing 22.8K labeled event-centric entities. We propose a collection of LLM-driven approaches to the task of multimodal event analysis, and evaluate them on MultiVENT-G. Results illustrate the challenges that abstract event understanding poses and demonstrates promise in event-centric video-language systems., Comment: Preprint; 9 pages; 2024 EMNLP Findings
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- 2024
10. Simulating binary black hole mergers using discontinuous Galerkin methods
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Lovelace, Geoffrey, Nelli, Kyle C., Deppe, Nils, Vu, Nils L., Throwe, William, Bonilla, Marceline S., Carpenter, Alexander, Kidder, Lawrence E., Macedo, Alexandra, Scheel, Mark A., Afram, Azer, Boyle, Michael, Ceja, Andrea, Giesler, Matthew, Habib, Sarah, Jones, Ken Z., Kumar, Prayush, Lara, Guillermo, Melchor, Denyz, Mendes, Iago B., Mitman, Keefe, Morales, Marlo, Moxon, Jordan, O'Shea, Eamonn, Pannone, Kyle, Pfeiffer, Harald P., Ramirez-Aguilar, Teresita, Sanchez, Jennifer, Tellez, Daniel, Teukolsky, Saul A., and Wittek, Nikolas A.
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General Relativity and Quantum Cosmology - Abstract
Binary black holes are the most abundant source of gravitational-wave observations. Gravitational-wave observatories in the next decade will require tremendous increases in the accuracy of numerical waveforms modeling binary black holes, compared to today's state of the art. One approach to achieving the required accuracy is using spectral-type methods that scale to many processors. Using the SpECTRE numerical-relativity code, we present the first simulations of a binary black hole inspiral, merger, and ringdown using discontinuous Galerkin methods. The efficiency of discontinuous Galerkin methods allows us to evolve the binary through ~18 orbits at reasonable computational cost. We then use SpECTRE's Cauchy Characteristic Evolution (CCE) code to extract the gravitational waves at future null infinity. The open-source nature of SpECTRE means this is the first time a spectral-type method for simulating binary black hole evolutions is available to the entire numerical-relativity community., Comment: 32 pages, 12 figures, 28 ancillary input files
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- 2024
11. Leveraging Large Language Models for Predicting Cost and Duration in Software Engineering Projects
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Carpenter, Justin, Wu, Chia-Ying, and Eisty, Nasir U.
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Computer Science - Software Engineering - Abstract
Accurate estimation of project costs and durations remains a pivotal challenge in software engineering, directly impacting budgeting and resource management. Traditional estimation techniques, although widely utilized, often fall short due to their complexity and the dynamic nature of software development projects. This study introduces an innovative approach using Large Language Models (LLMs) to enhance the accuracy and usability of project cost predictions. We explore the efficacy of LLMs against traditional methods and contemporary machine learning techniques, focusing on their potential to simplify the estimation process and provide higher accuracy. Our research is structured around critical inquiries into whether LLMs can outperform existing models, the ease of their integration into current practices, outperform traditional estimation, and why traditional methods still prevail in industry settings. By applying LLMs to a range of real-world datasets and comparing their performance to both state-of-the-art and conventional methods, this study aims to demonstrate that LLMs not only yield more accurate estimates but also offer a user-friendly alternative to complex predictive models, potentially transforming project management strategies within the software industry.
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- 2024
12. Predicting electrical conductivity in bi-metal composites
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Blaschke, Daniel N., Carpenter, John S., and Hunter, Abigail
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Condensed Matter - Materials Science - Abstract
Generating high magnetic fields requires materials with not only high electric conductivity, but also good strength properties in order to withstand the necessarily strong Lorentz forces. A number of bi-metal composites, most notably Cu/Nb, are considered to be good candidates for this purpose. Here, we generalize our previous work on Cu/Nb in order to predict, from theory, the dependence of electric conductivity on the microstructure and volume fraction of the less conductive component for a number of other bi-metal composites. Together with information on strength properties (taken from previous literature), the conductivity information we provide in this work can help to identify new promising candidate materials (such as Cu/Nb, Cu/Ag, Cu/W, ...) for magnet applications with the highest achievable field strengths., Comment: 11 pages, 4 figures; v2+v3 minor revision
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- 2024
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13. Fast and light-efficient wavefront shaping with a MEMS phase-only light modulator
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Rocha, José C. A., Wright, Terry, Būtaitė, Unė G, Carpenter, Joel, Gordon, George S. D., and Phillips, David B.
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Physics - Optics - Abstract
Over the last two decades, spatial light modulators (SLMs) have revolutionised our ability to shape optical fields. They grant independent dynamic control over thousands of degrees-of-freedom within a single light beam. In this work we test a new type of SLM, known as a phase-only light modulator (PLM), that blends the high efficiency of liquid crystal SLMs with the fast switching rates of binary digital micro-mirror devices (DMDs). A PLM has a 2D mega-pixel array of micro-mirrors. The vertical height of each micro-mirror can be independently adjusted with 4-bit precision. Here we provide a concise tutorial on the operation and calibration of a PLM. We demonstrate arbitrary pattern projection, aberration correction, and control of light transport through complex media. We show high-speed wavefront shaping through a multimode optical fibre -- scanning over 2000 points at 1.44 kHz. We make available our custom high-speed PLM control software library developed in C++. As PLMs are based upon micro-electromechanical system (MEMS) technology, they are polarisation agnostic, and possess fundamental switching rate limitations equivalent to that of DMDs -- with operation at up to 10 kHz anticipated in the near future. We expect PLMs will find high-speed light shaping applications across a range of fields including adaptive optics, microscopy, optogenetics and quantum optics., Comment: 15 pages, 5 figures
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- 2024
14. Fieldwork Educators' Perceptions of the Revised Fieldwork Performance Evaluation
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Todd Sanders and Amanda M. Carpenter
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The American Occupational Therapy Association's Fieldwork Performance Evaluation plays a vital role in occupational therapy education by guiding students and fieldwork educators in determining students' entry-level competence. This evaluation tool dates to 1953 and has undergone numerous revisions as the profession evolved and changes were made to the practice framework. Revisions have included changes to the stated purpose of the evaluation tool, items to be scored, scoring scale, and number of items on the tool. The purpose of this study was to survey Academic Fieldwork Coordinators (AFWCs) to examine their perceptions of the 2020 revision of the evaluation. We surveyed 68 AFWCs in occupational therapy and occupational therapy assistant programs. The majority had positive perceptions of the changes to the tool. The American Occupational Therapy Association, academic programs, and fieldwork sites should consider the findings of this study to help ensure effective and accurate evaluation of future students.
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- 2024
15. Science Students Develop Multiple Employability Literacies from Large, Early-Year Courses without Employability Modules
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Lauren Carpenter, Sophie Hubbard, N. Scout Basinski, and Susan Rowland
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Concerns have been raised about the employability of Science graduates, however undergraduate Science curricula rarely focus on building employability. Our goal is to harness existing Science-focused curricula to improve Science graduate employability. In this study we asked whether students could identify learning of employability literacies from their experiences in undergraduate Science courses that do not explicitly teach employability literacies. To address these questions, we employed a short reflective activity in three large first year courses; these courses focused on scientific content and processes, and did not include employability modules. We asked students to choose an employability literacy from a menu and describe how components of the course prompted them to develop this literacy. Students chose a wide variety of literacies and linked their development to multiple aspects of their course experience. They also consistently indicated they had achieved multiple literacies from their course. Course coordinators highlighted the strength-based quality of the reflections, which differed from the usual course evaluation comments given by students. Coordinators who used the reflection activity in the first year were eager to continue in subsequent semesters and years. This mechanism gives students and staff the opportunity to understand the wide and varied opportunities for employability skill development that already exist in undergraduate Science courses. The approach does not require course teaching amendments or student skill-building instruction. This study shows that students can achieve multiple employability literacies from early-year courses, and raises new possibilities around how we can boost students' understanding and development of their employability.
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- 2024
16. Automated Video Tracking of Autistic Children's Movement during Caregiver-Child Interaction: An Exploratory Study
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Alexandra L. Bey, Maura Sabatos-DeVito, Kimberly L. H. Carpenter, Lauren Franz, Jill Howard, Saritha Vermeer, Ryan Simmons, Jesse D. Troy, and Geraldine Dawson
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Objective, quantitative measures of caregiver-child interaction during play are needed to complement caregiver or examiner ratings for clinical assessment and tracking intervention responses. In this exploratory study, we examined the feasibility of using automated video tracking, Noldus EthoVision XT, to measure 159 2-to-7-year-old autistic children's patterns of movement during play-based, caregiver-child interactions and examined their associations with standard clinical measures and human observational coding of caregiver-child joint engagement. Results revealed that autistic children who exhibited higher durations and velocity of movement were, on average, younger, had lower cognitive abilities, greater autism-related features, spent less time attending to the caregiver, and showed lower levels of joint engagement. After adjusting for age and nonverbal cognitive abilities, we found that children who remained in close proximity to their caregiver were more likely to engage in joint engagement that required support from the caregiver. These findings suggest that video tracking offers promise as a scalable, quantitative, and relevant measure of autism-related behaviors.
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- 2024
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17. Adaptive Behavior in Young Autistic Children: Associations with Irritability and ADHD Symptoms
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Kimberly L. H. Carpenter, Naomi O. Davis, Marina Spanos, Maura Sabatos-DeVito, Rachel Aiello, Grace T. Baranek, Scott N. Compton, Helen L. Egger, Lauren Franz, Soo-Jeong Kim, Bryan H. King, Alexander Kolevzon, Christopher J. McDougle, Kevin Sanders, Jeremy Veenstra-VanderWeele, Linmarie Sikich, Scott H. Kollins, and Geraldine Dawson
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Attention-deficit/hyperactivity disorder (ADHD) symptoms affect 40-60% of autistic children and have been linked to differences in adaptive behavior. It is unclear whether adaptive behavior in autistic youth is directly impacted by co-occurring ADHD symptoms or by another associated feature of both autism and ADHD, such as increased irritability. The current study examined relationships between irritability, ADHD symptoms, and adaptive behavior in 3- to 7-year-old autistic children. Results suggest that, after adjusting for co-occurring ADHD symptoms, higher levels of irritability are associated with differences in social adaptive behavior specifically. Understanding relationships between irritability, ADHD, and adaptive behavior in autistic children is critical because measures of adaptive behavior, such as the Vineland Scales of Adaptive Functioning, are often used as a proxy for global functioning, as well as for developing intervention plans and measuring outcomes as primary endpoints in clinical trials.
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- 2024
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18. Per- and polyfluoroalkyl substances (PFAS) in drinking water in Southeast Los Angeles: Industrial legacy and environmental justice
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Von Behren, Julie, Reynolds, Peggy, Bradley, Paul M, Gray, James L, Kolpin, Dana W, Romanok, Kristin M, Smalling, Kelly L, Carpenter, Catherine, Avila, Wendy, Ventura, Andria, English, Paul B, Jones, Rena R, and Solomon, Gina M
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Environmental Sciences ,Pollution and Contamination ,Foodborne Illness ,Health Disparities ,Social Determinants of Health ,2.2 Factors relating to the physical environment ,Los Angeles ,Water Pollutants ,Chemical ,Drinking Water ,Fluorocarbons ,Environmental Monitoring ,Alkanesulfonic Acids ,Caprylates ,Water Supply ,PFAS ,Drinking water ,California ,Environmental justice - Abstract
Per- and polyfluoroalkyl substances (PFAS) are persistent chemicals of increasing concern to human health. PFAS contamination in water systems has been linked to a variety of sources including hydrocarbon fire suppression activities, industrial and military land uses, agricultural applications of biosolids, and consumer products. To assess PFAS in California tap water, we collected 60 water samples from inside homes in four different geographic regions, both urban and rural. We selected mostly small water systems with known history of industrial chemical or pesticide contamination and that served socioeconomically disadvantaged communities. Thirty percent of the tap water samples (18) had a detection of at least one of the 32 targeted PFAS and most detections (89 %) occurred in heavily industrialized Southeast Los Angeles (SELA). The residents of SELA are predominately Latino and low-income. Concentrations of perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) ranged from 6.8 to 13.6 ng/L and 9.4-17.8 ng/L, respectively in SELA and were higher than State (PFOA: 0.007 ng/L; PFOS: 1.0 ng/L) and national health-based goals (zero). To look for geographic patterns, we mapped potential sources of PFAS contamination, such as chrome plating facilities, airports, landfills, and refineries, located near the SELA water systems; consistent with the multiple potential sources in the area, no clear spatial associations were observed. The results indicate the importance of systematic testing of PFAS in tap water, continued development of PFAS regulatory standards and advisories for a greater number of compounds, improved drinking-water treatments to mitigate potential health threats to communities, especially in socioeconomically disadvantaged and industrialized areas.
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- 2024
19. Integrating the Memory Support Intervention into the Transdiagnostic Intervention for Sleep and Circadian Dysfunction (TranS-C): can improving memory for treatment in midlife and older adults improve patient outcomes? Study protocol for a randomized controlled trial.
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Milner, Anne, Hache, Rafael, Oliver, Sophia, Sarfan, Laurel, Spencer, Julia, Cogan, Ashby, Jiang, Yimei, Agnew, Emma, Zieve, Garret, Martin, Jennifer, Zeidler, Michelle, Dong, Lu, Carpenter, Joseph, Varghese, Joshua, Bol, Kiely, Bajwa, Zia, Tighe, Caitlan, and Harvey, Allison
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Circadian ,Memory support ,Sleep ,Transdiagnostic ,Humans ,Middle Aged ,Randomized Controlled Trials as Topic ,Treatment Outcome ,Memory ,Sleep ,Aged ,Female ,Sleep Wake Disorders ,Male ,Circadian Rhythm ,Memory Disorders ,Chronobiology Disorders ,Sleep Quality ,Age Factors - Abstract
BACKGROUND: Poor memory for treatment is associated with poorer treatment adherence and poorer patient outcomes. The memory support intervention (MSI) was developed to improve patient memory for treatment with the goal of improving patient outcomes. The aim of this study protocol is to conduct a confirmatory efficacy trial to test whether a new, streamlined, and potent version of the MSI improves outcomes for midlife and older adults. This streamlined MSI is comprised of constructive memory supports that will be applied to a broader range of treatment content. The platform for this study is the Transdiagnostic Intervention for Sleep and Circadian Dysfunction (TranS-C). We will focus on midlife and older adults who are low income and experiencing mobility impairments. METHODS: Participants (N = 178) will be randomly allocated to TranS-C + MSI or TranS-C alone. Both intervention arms include eight 50-min weekly sessions. Assessments will be conducted at pre-treatment, post-treatment, 6-, and 12-month follow-up (6FU and 12FU). Aim 1 will compare the effects of TranS-C + MSI versus TranS-C alone on sleep and circadian functioning, daytime functioning, well-being, and patient memory. Aim 2 will test whether patient memory for treatment mediates the relationship between treatment condition and patient outcomes. Aim 3 will evaluate if previously reported poor treatment response subgroups will moderate the relationship between treatment condition and (a) patient memory for treatment and (b) treatment outcome. Exploratory analyses will compare treatment condition on (a) patient adherence, patient-rated treatment credibility, and patient utilization of treatment contents, and (b) provider-rated acceptability, appropriateness, and feasibility. DISCUSSION: This study has the potential to provide evidence for (a) the efficacy of a new simplified version of the MSI for maintaining health, well-being, and functioning, (b) the wider application of the MSI for midlife and older adults and to the treatment of sleep and circadian problems, and (c) the efficacy of the MSI for sub-groups who are likely to benefit from the intervention. TRIAL REGISTRATION: ClinicalTrials.gov NCT05986604. Registered on 2 August 2023.
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- 2024
20. Quantifying brain development in the HEALthy Brain and Child Development (HBCD) Study: The magnetic resonance imaging and spectroscopy protocol.
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Dean, Douglas, Tisdall, M, Wisnowski, Jessica, Feczko, Eric, Gagoski, Borjan, Alexander, Andrew, Edden, Richard, Gao, Wei, Hendrickson, Timothy, Howell, Brittany, Huang, Hao, Humphreys, Kathryn, Riggins, Tracy, Sylvester, Chad, Weldon, Kimberly, Yacoub, Essa, Ahtam, Banu, Beck, Natacha, Banerjee, Suchandrima, Boroday, Sergiy, Caprihan, Arvind, Caron, Bryan, Carpenter, Samuel, Chang, Yulin, Chung, Ai, Cieslak, Matthew, Clarke, William, Dale, Anders, Das, Samir, Davies-Jenkins, Christopher, Dufford, Alexander, Evans, Alan, Fesselier, Laetitia, Ganji, Sandeep, Gilbert, Guillaume, Graham, Alice, Gudmundson, Aaron, Macgregor-Hannah, Maren, Harms, Michael, Hilbert, Tom, Hui, Steve, Irfanoglu, M, Kecskemeti, Steven, Kober, Tobias, Kuperman, Joshua, Lamichhane, Bidhan, Landman, Bennett, Lecour-Bourcher, Xavier, Lee, Erik, Li, Xu, MacIntyre, Leigh, Madjar, Cecile, Manhard, Mary, Mayer, Andrew, Mehta, Kahini, Moore, Lucille, Murali-Manohar, Saipavitra, Navarro, Cristian, Nebel, Mary, Newman, Sharlene, Newton, Allen, Noeske, Ralph, Norton, Elizabeth, Oeltzschner, Georg, Ongaro-Carcy, Regis, Ou, Xiawei, Ouyang, Minhui, Parrish, Todd, Pekar, James, Pengo, Thomas, Pierpaoli, Carlo, Poldrack, Russell, Rajagopalan, Vidya, Rettmann, Dan, Rioux, Pierre, Rosenberg, Jens, Salo, Taylor, Satterthwaite, Theodore, Scott, Lisa, Shin, Eunkyung, Simegn, Gizeaddis, Simmons, W, Song, Yulu, Tikalsky, Barry, Tkach, Jean, van Zijl, Peter, Vannest, Jennifer, Versluis, Maarten, Zhao, Yansong, Zöllner, Helge, Fair, Damien, Smyser, Christopher, and Elison, Jed
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Development ,HBCD ,Infant ,MRI ,MRS ,Protocol - Abstract
The HEALthy Brain and Child Development (HBCD) Study, a multi-site prospective longitudinal cohort study, will examine human brain, cognitive, behavioral, social, and emotional development beginning prenatally and planned through early childhood. The acquisition of multimodal magnetic resonance-based brain development data is central to the studys core protocol. However, application of Magnetic Resonance Imaging (MRI) methods in this population is complicated by technical challenges and difficulties of imaging in early life. Overcoming these challenges requires an innovative and harmonized approach, combining age-appropriate acquisition protocols together with specialized pediatric neuroimaging strategies. The HBCD MRI Working Group aimed to establish a core acquisition protocol for all 27 HBCD Study recruitment sites to measure brain structure, function, microstructure, and metabolites. Acquisition parameters of individual modalities have been matched across MRI scanner platforms for harmonized acquisitions and state-of-the-art technologies are employed to enable faster and motion-robust imaging. Here, we provide an overview of the HBCD MRI protocol, including decisions of individual modalities and preliminary data. The result will be an unparalleled resource for examining early neurodevelopment which enables the larger scientific community to assess normative trajectories from birth through childhood and to examine the genetic, biological, and environmental factors that help shape the developing brain.
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- 2024
21. Systematic identification of post-transcriptional regulatory modules.
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Khoroshkin, Matvei, Buyan, Andrey, Dodel, Martin, Navickas, Albertas, Yu, Johnny, Trejo, Fathima, Doty, Anthony, Baratam, Rithvik, Zhou, Shaopu, Lee, Sean, Joshi, Tanvi, Garcia, Kristle, Choi, Benedict, Miglani, Sohit, Subramanyam, Vishvak, Modi, Hailey, Carpenter, Christopher, Markett, Daniel, Corces, M, Mardakheh, Faraz, Kulakovskiy, Ivan, and Goodarzi, Hani
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Humans ,RNA-Binding Proteins ,RNA ,Messenger ,Transcriptome ,RNA Processing ,Post-Transcriptional ,Gene Expression Regulation ,HEK293 Cells ,Single-Cell Analysis ,Gene Regulatory Networks ,Regulon - Abstract
In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, the landscape of RBP combinatorial interactions remains poorly explored. Here, we perform a systematic annotation of RBP combinatorial interactions via multimodal data integration. We build a large-scale map of RBP protein neighborhoods by generating in vivo proximity-dependent biotinylation datasets of 50 human RBPs. In parallel, we use CRISPR interference with single-cell readout to capture transcriptomic changes upon RBP knockdowns. By combining these physical and functional interaction readouts, along with the atlas of RBP mRNA targets from eCLIP assays, we generate an integrated map of functional RBP interactions. We then use this map to match RBPs to their context-specific functions and validate the predicted functions biochemically for four RBPs. This study provides a detailed map of RBP interactions and deconvolves them into distinct regulatory modules with annotated functions and target regulons. This multimodal and integrative framework provides a principled approach for studying post-transcriptional regulatory processes and enriches our understanding of their underlying mechanisms.
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- 2024
22. A systematic search for RNA structural switches across the human transcriptome
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Khoroshkin, Matvei, Asarnow, Daniel, Zhou, Shaopu, Navickas, Albertas, Winters, Aidan, Goudreau, Jackson, Zhou, Simon K, Yu, Johnny, Palka, Christina, Fish, Lisa, Borah, Ashir, Yousefi, Kian, Carpenter, Christopher, Ansel, K Mark, Cheng, Yifan, Gilbert, Luke A, and Goodarzi, Hani
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,1.1 Normal biological development and functioning ,Humans ,Transcriptome ,Nucleic Acid Conformation ,3' Untranslated Regions ,RNA ,Sulfuric Acid Esters ,Nonsense Mediated mRNA Decay ,Cryoelectron Microscopy ,Computational Biology ,Technology ,Medical and Health Sciences ,Developmental Biology ,Biological sciences - Abstract
RNA structural switches are key regulators of gene expression in bacteria, but their characterization in Metazoa remains limited. Here, we present SwitchSeeker, a comprehensive computational and experimental approach for systematic identification of functional RNA structural switches. We applied SwitchSeeker to the human transcriptome and identified 245 putative RNA switches. To validate our approach, we characterized a previously unknown RNA switch in the 3' untranslated region of the RORC (RAR-related orphan receptor C) transcript. In vivo dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), coupled with cryogenic electron microscopy, confirmed its existence as two alternative structural conformations. Furthermore, we used genome-scale CRISPR screens to identify trans factors that regulate gene expression through this RNA structural switch. We found that nonsense-mediated messenger RNA decay acts on this element in a conformation-specific manner. SwitchSeeker provides an unbiased, experimentally driven method for discovering RNA structural switches that shape the eukaryotic gene expression landscape.
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- 2024
23. Constraints on the physical origin of large cavities in transition disks from multi-wavelength dust continuum emission
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Sierra, Anibal, Pérez, Laura M., Sotomayor, Benjamín, Benisty, Myriam, Chandler, Claire J., Andrews, Sean, Carpenter, John, Henning, Thomas, Testi, Leonardo, Ricci, Luca, and Wilner, David
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Solar and Stellar Astrophysics - Abstract
The physical origin of the large cavities observed in transition disks is to date still unclear. Different physical mechanisms (e.g., a companion, dead zones, enhanced grain growth) produce disk cavities of different depth, and the expected spatial distribution of gas and solids in each mechanism is not the same. In this work, we analyze the multi-wavelength interferometric visibilities of dust continuum observations obtained with ALMA and VLA for six transition disks: CQTau, UXTau A, LkCa15, RXJ1615, SR24S, and DMTau, and calculate brightness radial profiles, where diverse emission morphology is revealed at different wavelengths. The multi-wavelength data is used to model the spectral energy distribution and compute constraints on the radial profile of the dust surface density, maximum grain size, and dust temperature in each disk. They are compared with the observational signatures expected from various physical mechanisms responsible for disk cavities. The observational signatures suggest that the cavities observed in the disks around UXTau A, LkCa15, and RXJ1615 could potentially originate from a dust trap created by a companion. Conversely, in the disks around CQTau, SR24S, DMTau, the origin of the cavity remains unclear, although it is compatible with a pressure bump and grain growth within the cavity.
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- 2024
24. Detailed Study of Stars and Gas in a z = 8.3 Massive Merger with Extreme Dust Conditions
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Harshan, Anishya, Tripodi, Roberta, Martis, Nicholas S., Rihtaršič, Gregor, Bradač, Maruša, Asada, Yoshihisa, Brammer, Gabe, Desprez, Guillaume, Estrada-Carpenter, Vince, Matharu, Jasleen, Markov, Vladan, Muzzin, Adam, Mowla, Lamiya, Noirot, Gaël, Sarrouh, Ghassan T. E., Sawicki, Marcin, Strait, Victoria, and Willot, Chris
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Astrophysics - Astrophysics of Galaxies - Abstract
We present galaxy MACS0416-Y1 at z$_{\rm{spec}} = 8.312$ as observed by the CAnadian NIRISS Unbiased Cluster Survey (CANUCS). MACS0416-Y1 has been shown to have extreme dust properties, thus, we study the physical properties and star formation histories of its resolved components. Overall, we find that MACS0416-Y1 is undergoing a star formation burst in three resolved clumps. The central clump is less massive compared to the other clumps and possibly formed in the merging process of the two larger clumps. Although the star formation history indicates an ongoing star formation burst, this gas-rich galaxy shows comparable star formation efficiency to cosmic noon galaxies. Using NIRSpec prism spectroscopy, we measure metallicity, $12 +\log\rm{(O/H)} = 7.76\pm0.03$ , ionisation parameter, $\log U = -2.48\pm0.03$, and electron temperature $\rm{T}_e = 18000\pm 4000 K $. The emission line ratios of the galaxy indicate an evolved Interstellar medium (ISM) similar to $z\sim2$ star-forming galaxies. Further, we find possible presence of ionisation from an active galactic nuclei (AGN) using emission line diagnostics, however, we do not detect broad line component in H$\beta$ emission line. As this gas-rich galaxy is undergoing a major merger, we hypothesise that the high dust temperature in MACS0416-Y1 is caused by the star formation burst or a possible narrow-line AGN., Comment: Submitted to ApJL
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- 2024
25. Incorporating Local Step-Size Adaptivity into the No-U-Turn Sampler using Gibbs Self Tuning
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Bou-Rabee, Nawaf, Carpenter, Bob, Kleppe, Tore Selland, and Marsden, Milo
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Statistics - Methodology ,Mathematics - Probability ,Statistics - Computation - Abstract
Adapting the step size locally in the no-U-turn sampler (NUTS) is challenging because the step-size and path-length tuning parameters are interdependent. The determination of an optimal path length requires a predefined step size, while the ideal step size must account for errors along the selected path. Ensuring reversibility further complicates this tuning problem. In this paper, we present a method for locally adapting the step size in NUTS that is an instance of the Gibbs self-tuning (GIST) framework. Our approach guarantees reversibility with an acceptance probability that depends exclusively on the conditional distribution of the step size. We validate our step-size-adaptive NUTS method on Neal's funnel density and a high-dimensional normal distribution, demonstrating its effectiveness in challenging scenarios., Comment: for companion code, see https://github.com/bob-carpenter/adaptive-hmc
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- 2024
26. Imagen 3
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Imagen-Team-Google, Baldridge, Jason, Bauer, Jakob, Bhutani, Mukul, Brichtova, Nicole, Bunner, Andrew, Chan, Kelvin, Chen, Yichang, Dieleman, Sander, Du, Yuqing, Eaton-Rosen, Zach, Fei, Hongliang, de Freitas, Nando, Gao, Yilin, Gladchenko, Evgeny, Colmenarejo, Sergio Gómez, Guo, Mandy, Haig, Alex, Hawkins, Will, Hu, Hexiang, Huang, Huilian, Igwe, Tobenna Peter, Kaplanis, Christos, Khodadadeh, Siavash, Kim, Yelin, Konyushkova, Ksenia, Langner, Karol, Lau, Eric, Luo, Shixin, Mokrá, Soňa, Nandwani, Henna, Onoe, Yasumasa, Oord, Aäron van den, Parekh, Zarana, Pont-Tuset, Jordi, Qi, Hang, Qian, Rui, Ramachandran, Deepak, Rane, Poorva, Rashwan, Abdullah, Razavi, Ali, Riachi, Robert, Srinivasan, Hansa, Srinivasan, Srivatsan, Strudel, Robin, Uria, Benigno, Wang, Oliver, Wang, Su, Waters, Austin, Wolff, Chris, Wright, Auriel, Xiao, Zhisheng, Xiong, Hao, Xu, Keyang, van Zee, Marc, Zhang, Junlin, Zhang, Katie, Zhou, Wenlei, Zolna, Konrad, Aboubakar, Ola, Akbulut, Canfer, Akerlund, Oscar, Albuquerque, Isabela, Anderson, Nina, Andreetto, Marco, Aroyo, Lora, Bariach, Ben, Barker, David, Ben, Sherry, Berman, Dana, Biles, Courtney, Blok, Irina, Botadra, Pankil, Brennan, Jenny, Brown, Karla, Buckley, John, Bunel, Rudy, Bursztein, Elie, Butterfield, Christina, Caine, Ben, Carpenter, Viral, Casagrande, Norman, Chang, Ming-Wei, Chang, Solomon, Chaudhuri, Shamik, Chen, Tony, Choi, John, Churbanau, Dmitry, Clement, Nathan, Cohen, Matan, Cole, Forrester, Dektiarev, Mikhail, Du, Vincent, Dutta, Praneet, Eccles, Tom, Elue, Ndidi, Feden, Ashley, Fruchter, Shlomi, Garcia, Frankie, Garg, Roopal, Ge, Weina, Ghazy, Ahmed, Gipson, Bryant, Goodman, Andrew, Górny, Dawid, Gowal, Sven, Gupta, Khyatti, Halpern, Yoni, Han, Yena, Hao, Susan, Hayes, Jamie, Hertz, Amir, Hirst, Ed, Hou, Tingbo, Howard, Heidi, Ibrahim, Mohamed, Ike-Njoku, Dirichi, Iljazi, Joana, Ionescu, Vlad, Isaac, William, Jana, Reena, Jennings, Gemma, Jenson, Donovon, Jia, Xuhui, Jones, Kerry, Ju, Xiaoen, Kajic, Ivana, Ayan, Burcu Karagol, Kelly, Jacob, Kothawade, Suraj, Kouridi, Christina, Ktena, Ira, Kumakaw, Jolanda, Kurniawan, Dana, Lagun, Dmitry, Lavitas, Lily, Lee, Jason, Li, Tao, Liang, Marco, Li-Calis, Maggie, Liu, Yuchi, Alberca, Javier Lopez, Lu, Peggy, Lum, Kristian, Ma, Yukun, Malik, Chase, Mellor, John, Mosseri, Inbar, Murray, Tom, Nematzadeh, Aida, Nicholas, Paul, Oliveira, João Gabriel, Ortiz-Jimenez, Guillermo, Paganini, Michela, Paine, Tom Le, Paiss, Roni, Parrish, Alicia, Peckham, Anne, Peswani, Vikas, Petrovski, Igor, Pfaff, Tobias, Pirozhenko, Alex, Poplin, Ryan, Prabhu, Utsav, Qi, Yuan, Rahtz, Matthew, Rashtchian, Cyrus, Rastogi, Charvi, Raul, Amit, Rebuffi, Sylvestre-Alvise, Ricco, Susanna, Riedel, Felix, Robinson, Dirk, Rohatgi, Pankaj, Rosgen, Bill, Rumbley, Sarah, Ryu, Moonkyung, Salgado, Anthony, Singla, Sahil, Schroff, Florian, Schumann, Candice, Shah, Tanmay, Shillingford, Brendan, Shivakumar, Kaushik, Shtatnov, Dennis, Singer, Zach, Sluzhaev, Evgeny, Sokolov, Valerii, Sottiaux, Thibault, Stimberg, Florian, Stone, Brad, Stutz, David, Su, Yu-Chuan, Tabellion, Eric, Tang, Shuai, Tao, David, Thomas, Kurt, Thornton, Gregory, Toor, Andeep, Udrescu, Cristian, Upadhyay, Aayush, Vasconcelos, Cristina, Vasiloff, Alex, Voynov, Andrey, Walker, Amanda, Wang, Luyu, Wang, Miaosen, Wang, Simon, Wang, Stanley, Wang, Qifei, Wang, Yuxiao, Weisz, Ágoston, Wiles, Olivia, Wu, Chenxia, Xu, Xingyu Federico, Xue, Andrew, Yang, Jianbo, Yu, Luo, Yurtoglu, Mete, Zand, Ali, Zhang, Han, Zhang, Jiageng, Zhao, Catherine, Zhaxybay, Adilet, Zhou, Miao, Zhu, Shengqi, Zhu, Zhenkai, Bloxwich, Dawn, Bordbar, Mahyar, Cobo, Luis C., Collins, Eli, Dai, Shengyang, Doshi, Tulsee, Dragan, Anca, Eck, Douglas, Hassabis, Demis, Hsiao, Sissie, Hume, Tom, Kavukcuoglu, Koray, King, Helen, Krawczyk, Jack, Li, Yeqing, Meier-Hellstern, Kathy, Orban, Andras, Pinsky, Yury, Subramanya, Amar, Vinyals, Oriol, Yu, Ting, and Zwols, Yori
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Computer Science - Computer Vision and Pattern Recognition - Abstract
We introduce Imagen 3, a latent diffusion model that generates high quality images from text prompts. We describe our quality and responsibility evaluations. Imagen 3 is preferred over other state-of-the-art (SOTA) models at the time of evaluation. In addition, we discuss issues around safety and representation, as well as methods we used to minimize the potential harm of our models.
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- 2024
27. Artemis-enabled Stellar Imager (AeSI): A Lunar Long-Baseline UV/Optical Imaging Interferometer
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Rau, Gioia, Carpenter, Kenneth G., Boyajian, Tabetha, Creech-Eakman, Michelle, Foster, Julianne, Karovska, Margarita, Leisawitz, David, Morse, Jon A., Mozurkewich, David, Peacock, Sarah, Petro, Noah, Scowen, Paul, Sitarski, Breann, van Belle, Gerard, and Wilkinson, Erik
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Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Earth and Planetary Astrophysics - Abstract
NASA's return to the Moon presents unparalleled opportunities to advance high-impact scientific capabilities. At the cutting edge of these possibilities are extremely high-resolution interferometric observations at visible and ultraviolet wavelengths. Such technology can resolve the surfaces of stars, explore the inner accretion disks of nascent stars and black holes, and eventually enable us to observe surface features and weather patterns on nearby exoplanets. We have been awarded Phase 1 support from NASA's Innovative Advanced Concepts (NIAC) program to explore the feasibility of constructing a high-resolution, long-baseline UV/optical imaging interferometer on the lunar surface, in conjunction with the Artemis Program. A 1996 study comparing interferometers on the Moon versus free-flyers in space concluded that, without pre-existing lunar infrastructure, free-flyers were preferable. However, with the advent of the Artemis Program, it is now crucial to revisit the potential of building lunar interferometers. Our objective is to conduct a study with the same level of rigor applied to large baseline, free-flying interferometers during the 2003-2005 NASA Vision Missions Studies. This preparation is essential for timely and effective utilization of the forthcoming lunar infrastructure. In this paper, we highlight the groundbreaking potential of a lunar surface-based interferometer. This concept study will be a huge step forward to larger arrays on both the moon and free-flying in space, over a wide variety of wavelengths and science topics. Our Phase 1 study began in April 2024, and here we present a concise overview of our vision and the progress made so far., Comment: 6 pages, 3 figures, SPIE Astronomical Telescopes + Instrumentation 2024 (Invited Paper)
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- 2024
28. MoonLITE: a CLPS-delivered NASA Astrophysics Pioneers lunar optical interferometer for sensitive, milliarcsecond observing
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van Belle, Gerard T., Ciardi, David, Hillsberry, Daniel, Jorgensen, Anders, Monnier, John, Smith, Krista Lynne, Boyajian, Tabetha, Carpenter, Kenneth, Clark, Catherine, Rau, Gioia, and Schaefer, Gail
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Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
MoonLITE (Lunar InTerferometry Explorer) is an Astrophysics Pioneers proposal to develop, build, fly, and operate the first separated-aperture optical interferometer in space, delivering sub-mas science results. MoonLITE will leverage the Pioneers opportunity for utilizing NASA's Commercial Lunar Payload Services (CLPS) to deliver an optical interferometer to the lunar surface, enabling unprecedented discovery power by combining high spatial resolution from optical interferometry with deep sensitivity from the stability of the lunar surface. Following landing, the CLPS-provided rover will deploy the pre-loaded MoonLITE outboard optical telescope 100 meters from the lander's inboard telescope, establishing a two-element interferometric observatory with a single deployment. MoonLITE will observe targets as faint as 17th magnitude in the visible, exceeding ground-based interferometric sensitivity by many magnitudes, and surpassing space-based optical systems resolution by a factor of 50 times. The capabilities of MoonLITE open a unique discovery space that includes direct size measurements of the smallest, coolest stars and substellar brown dwarfs; searches for close-in stellar companions orbiting exoplanet-hosting stars that could confound our understanding and characterization of the frequency of Earth-like planets; direct size measurements of young stellar objects and characterization of the terrestrial planet-forming regions of these young stars; measurements of the inner regions and binary fraction of active galactic nuclei; and a probe of the very nature of spacetime foam itself. A portion of the observing time will also be made available to the broader community via a guest observer program. MoonLITE takes advantage of the CLPS opportunity and delivers an unprecedented combination of sensitivity and angular resolution at the remarkably affordable cost point of Pioneers., Comment: 13 pages, 8 figures, SPIE Astronomical Telescopes + Instrumentation 2024
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- 2024
29. An FDA for AI? Pitfalls and Plausibility of Approval Regulation for Frontier Artificial Intelligence
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Carpenter, Daniel and Ezell, Carson
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Computer Science - Computers and Society - Abstract
Observers and practitioners of artificial intelligence (AI) have proposed an FDA-style licensing regime for the most advanced AI models, or 'frontier' models. In this paper, we explore the applicability of approval regulation -- that is, regulation of a product that combines experimental minima with government licensure conditioned partially or fully upon that experimentation -- to the regulation of frontier AI. There are a number of reasons to believe that approval regulation, simplistically applied, would be inapposite for frontier AI risks. Domains of weak fit include the difficulty of defining the regulated product, the presence of Knightian uncertainty or deep ambiguity about harms from AI, the potentially transmissible nature of risks, and distributed activities among actors involved in the AI lifecycle. We conclude by highlighting the role of policy learning and experimentation in regulatory development, describing how learning from other forms of AI regulation and improvements in evaluation and testing methods can help to overcome some of the challenges we identify., Comment: Accepted to Seventh AAAI/ACM Conference on AI, Ethics, and Society (2024)
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- 2024
30. The Class 0 protostars in Orion: Characterizing the properties of their magnetized envelopes
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Huang, B., Girart, J. M., Stephens, I. W., Fernandez-Lopez, M., Tobin, J. J., Cortes, P., Murillo, N. M., Myers, P. C., Sadavoy, S., Zhang, Q., Arce, H. G., Carpenter, J. M., Kwon, W., Gouellec, V. J. M. Le, Li, Z. -Y., Looney, L. W., Megeath, T., Cox, E. G., Karnath, N., and Segura-Cox, D.
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Astrophysics - Astrophysics of Galaxies - Abstract
We present a study connecting the physical properties of protostellar envelopes to the morphology of the envelope-scale magnetic field. We use the ALMA polarization observations of 55 young prtostars at 0.87 mm on $\sim400-3000$ au scales from the {\em B}-field Orion Protostellar Survey (BOPS) to infer the envelope-scale magnetic field and both dust and gas emission on comparable scales to measure the envelope properties. We find that the protostellar envelopes with compact polarized dust emission tend to have lower envelope masses, than the sources with more extended envelopes. We also find that protostars showing hourglass-field morphologies tend to have lower velocity dispersions in their envelopes, whereas systems with spiral-field morphologies have higher velocity dispersion. Combining with the disk properties taken from the Orion VLA/ALMA Nascent Disk and Multiplicity (VANDAM) survey, we connect envelope properties to fragmentation. Our results suggest that envelope mass may not correlate with fragmentation, whereas turbulence appears to promote fragmentation. On the other hand, we find that fragmentation is suppressed in systems with pinched magnetic fields, suggesting that the magnetic field play a role on providing additional support against gravitational collapse, and the formation of an hourglass-like field may coincide with enhanced magnetic braking that removes angular momentum and hinders the formation of embedded disks. Nevertheless, significant misalignment between magnetic field and outflow axes tends to reduce magnetic braking, leading to the formation of larger disks., Comment: 18 pages, 6 figures, submitted to ApJ
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- 2024
31. Hints of planet formation signatures in a large-cavity disk studied in the AGE-PRO ALMA Large Program
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Sierra, Anibal, Pérez, Laura M., Agurto-Gangas, Carolina, Miley, James, Zhang, Ke, Pinilla, Paola, Pascucci, Ilaria, Trapman, Leon, Kurtovic, Nicolas, Vioque, Miguel, Deng, Dingshan, Anania, Rossella, Carpenter, John, Cieza, Lucas A., González-Ruilova, Camilo, Hogerheijde, Michiel, Kuznetsova, Aleksandra, Rosotti, Giovanni P., Ruiz-Rodriguez, Dary A., Schwarz, Kamber, Tabone, Benoît, and TorresVillanueva, Estephani E.
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Astrophysics - Earth and Planetary Astrophysics - Abstract
Detecting planet signatures in protoplanetary disks is fundamental to understanding how and where planets form. In this work, we report dust and gas observational hints of planet formation in the disk around 2MASS-J16120668-301027, as part of the ALMA Large Program "AGE-PRO: ALMA survey of Gas Evolution in Protoplanetary disks". The disk was imaged with the Atacama Large Millimeter/submillimeter Array (ALMA) at Band 6 (1.3 mm) in dust continuum emission and four molecular lines: $^{12}$CO(J=2-1), $^{13}$CO(J=2-1), C$^{18}$O(J=2-1), and H$_2$CO(J=3$_{(3,0)}$-2$_{(2,0)}$). Resolved observations of the dust continuum emission (angular resolution of $\sim 150$ mas, 20 au) show a ring-like structure with a peak at $0.57 ^{\prime \prime}$ (75 au), a deep gap with a minimum at 0.24$^{\prime \prime}$ (31 au), an inner disk, a bridge connecting the inner disk and the outer ring, along with a spiral arm structure, and a tentative detection (to $3\sigma$) of a compact emission at the center of the disk gap, with an estimated dust mass of $\sim 2.7-12.9$ Lunar masses. We also detected a kinematic kink (not coincident with any dust substructure) through several $^{12}$CO channel maps (angular resolution $\sim$ 200 mas, 30 au), located at a radius of $\sim 0.875^{\prime \prime}$ (115.6 au). After modeling the $^{12}$CO velocity rotation around the protostar, we identified a tentative rotating-like structure at the kink location with a geometry similar to that of the disk. We discuss potential explanations for the dust and gas substructures observed in the disk, and their potential connection to signatures of planet formation., Comment: 24 pages, 15 figures
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- 2024
32. DRAM Errors and Cosmic Rays: Space Invaders or Science Fiction?
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Boixaderas, Isaac, Amaya, Jorge, Moré, Sergi, Bartolome, Javier, Vicente, David, Unsal, Osman, Gizopoulos, Dimitris, Carpenter, Paul M., Radojković, Petar, and Ayguadé, Eduard
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
It is widely accepted that cosmic rays are a plausible cause of DRAM errors in high-performance computing (HPC) systems, and various studies suggest that they could explain some aspects of the observed DRAM error behavior. However, this phenomenon is insufficiently studied in production environments. We analyze the correlations between cosmic rays and DRAM errors on two HPC clusters: a production supercomputer with server-class DDR3-1600 and a prototype with LPDDR3-1600 and no hardware error correction. Our error logs cover 2000 billion MB-hours for the MareNostrum 3 supercomputer and 135 million MB-hours for the Mont-Blanc prototype. Our analysis combines quantitative analysis, formal statistical methods and machine learning. We detect no indications that cosmic rays have any influence on the DRAM errors. To understand whether the findings are specific to systems under study, located at 100 meters above the sea level, the analysis should be repeated on other HPC clusters, especially the ones located on higher altitudes. Also, analysis can (and should) be applied to revisit and extend numerous previous studies which use cosmic rays as a hypothetical explanation for some aspects of the observed DRAM error behaviors., Comment: Accepted for publication in SBAC-PAD'24
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- 2024
33. Reinforcement Learning-based Adaptive Mitigation of Uncorrected DRAM Errors in the Field
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Boixaderas, Isaac, Moré, Sergi, Bartolome, Javier, Vicente, David, Radojković, Petar, Carpenter, Paul M., and Ayguadé, Eduard
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Computer Science - Distributed, Parallel, and Cluster Computing ,Computer Science - Machine Learning - Abstract
Scaling to larger systems, with current levels of reliability, requires cost-effective methods to mitigate hardware failures. One of the main causes of hardware failure is an uncorrected error in memory, which terminates the current job and wastes all computation since the last checkpoint. This paper presents the first adaptive method for triggering uncorrected error mitigation. It uses a prediction approach that considers the likelihood of an uncorrected error and its current potential cost. The method is based on reinforcement learning, and the only user-defined parameters are the mitigation cost and whether the job can be restarted from a mitigation point. We evaluate our method using classical machine learning metrics together with a cost-benefit analysis, which compares the cost of mitigation actions with the benefits from mitigating some of the errors. On two years of production logs from the MareNostrum supercomputer, our method reduces lost compute time by 54% compared with no mitigation and is just 6% below the optimal Oracle method. All source code is open source., Comment: Published in HPDC'24
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- 2024
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34. posteriordb: Testing, Benchmarking and Developing Bayesian Inference Algorithms
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Magnusson, Måns, Torgander, Jakob, Bürkner, Paul-Christian, Zhang, Lu, Carpenter, Bob, and Vehtari, Aki
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Statistics - Computation - Abstract
The generality and robustness of inference algorithms is critical to the success of widely used probabilistic programming languages such as Stan, PyMC, Pyro, and Turing.jl. When designing a new general-purpose inference algorithm, whether it involves Monte Carlo sampling or variational approximation, the fundamental problem arises in evaluating its accuracy and efficiency across a range of representative target models. To solve this problem, we propose posteriordb, a database of models and data sets defining target densities along with reference Monte Carlo draws. We further provide a guide to the best practices in using posteriordb for model evaluation and comparison. To provide a wide range of realistic target densities, posteriordb currently comprises 120 representative models and has been instrumental in developing several general inference algorithms.
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- 2024
35. When, Where, and How Star Formation Happens in a Galaxy Pair at Cosmic Noon Using CANUCS JWST/NIRISS Grism Spectroscopy
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Estrada-Carpenter, Vicente, Sawicki, Marcin, Brammer, Gabe, Desprez, Guillaume, Abraham, Roberto, Asada, Yoshihisa, Bradač, Maruša, Iyer, Kartheik G., Martis, Nicholas S., Matharu, Jasleen, Mowla, Lamiya, Muzzin, Adam, Noirot, Gaël, Sarrouh, Ghassan T. E., Strait, Victoria, and Willott, Chris J.
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Astrophysics - Astrophysics of Galaxies - Abstract
Spatially resolved studies are key to understanding when, where, and how stars form within galaxies. Using slitless grism spectra and broadband imaging from the CAnadian NIRISS Unbiased Cluster Survey (CANUCS) we study the spatially resolved properties of a strongly lensed ($\mu$ = 5.4$\pm$1.8) z = 0.8718 galaxy pair consisting of a blue face-on galaxy (10.2 $\pm$ 0.2 log($M/M_\odot$)) with multiple star-forming clumps and a dusty red edge-on galaxy (9.9 $\pm$ 0.3 log($M/M_\odot$)). We produce accurate H$\alpha$ maps from JWST/NIRISS grism data using a new methodology that accurately models spatially varying continuum and emission line strengths. With spatially resolved indicators, we probe star formation on timescales of $\sim$ 10 Myr (NIRISS H$\alpha$ emission line maps) and $\sim$ 100 Myr (UV imaging and broadband SED fits). Taking the ratio of the H$\alpha$ to UV flux ($\eta$), we measure spatially resolved star formation burstiness. We find that in the face-on galaxy both H$\alpha$ and broadband star formation rates (SFRs) drop at large galactocentric radii by a factor of $\sim$ 4.7 and 3.8 respectively, while SFR over the last $\sim$ 100 Myrs has increased by a factor of 1.6. Additionally, of the 20 clumps identified in the galaxy pair we find that 7 are experiencing bursty star formation, while 10 clumps are quenching and 3 are in equilibrium (either being in a state of steady star formation or post-burst). Our analysis reveals that the blue face-on galaxy disk is predominantly in a quenching or equilibrium phase. However, the most intense quenching within the galaxy is seen in the quenching clumps. This pilot study demonstrates what JWST/NIRISS data can reveal about spatially varying star formation in galaxies at Cosmic Noon., Comment: MNRAS Accepted, 15 pages, 12 figures
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- 2024
36. Oralytics Reinforcement Learning Algorithm
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Trella, Anna L., Zhang, Kelly W., Carpenter, Stephanie M., Elashoff, David, Greer, Zara M., Nahum-Shani, Inbal, Ruenger, Dennis, Shetty, Vivek, and Murphy, Susan A.
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Computer Science - Artificial Intelligence - Abstract
Dental disease is still one of the most common chronic diseases in the United States. While dental disease is preventable through healthy oral self-care behaviors (OSCB), this basic behavior is not consistently practiced. We have developed Oralytics, an online, reinforcement learning (RL) algorithm that optimizes the delivery of personalized intervention prompts to improve OSCB. In this paper, we offer a full overview of algorithm design decisions made using prior data, domain expertise, and experiments in a simulation test bed. The finalized RL algorithm was deployed in the Oralytics clinical trial, conducted from fall 2023 to summer 2024.
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- 2024
37. A Dust-Trapping Ring in the Planet-Hosting Disk of Elias 2-24
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Carvalho, Adolfo S., Perez, Laura M., Sierra, Anibal, Mellado, Maria Jesus, Hillenbrand, Lynne A., Andrews, Sean, Benisty, Myriam, Birnstiel, Tilman, Carpenter, John M., Guzman, Viviana V., Huang, Jane, Isella, Andrea, Kurtovic, Nicolas, Ricci, Luca, and Wilner, David J.
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Solar and Stellar Astrophysics - Abstract
Rings and gaps are among the most widely observed forms of substructure in protoplanetary disks. A gap-ring pair may be formed when a planet carves a gap in the disk, which produces a local pressure maximum following the gap that traps inwardly drifting dust grains and appears as a bright ring due to the enhanced dust density. A dust-trapping ring would provide a promising environment for solid growth and possibly planetesimal production via the streaming instability. We present evidence of dust trapping in the bright ring of the planet-hosting disk Elias 2-24, from the analysis of 1.3 mm and 3 mm ALMA observations at high spatial resolution (0.029 arcsec, 4.0 au). We leverage the high spatial resolution to demonstrate that larger grains are more efficiently trapped and place constraints on the local turbulence ($8 \times 10^{-4} < \alpha_\mathrm{turb} < 0.03$) and the gas-to-dust ratio ($\Sigma_g / \Sigma_d < 30$) in the ring. Using a scattering-included marginal probability analysis we measure a total dust disk mass of $M_\mathrm{dust} = 13.8^{+0.7}_{-0.5} \times 10^{-4} \ M_\odot$. We also show that at the orbital radius of the proposed perturber, the gap is cleared of material down to a flux contrast of 10$^{-3}$ of the peak flux in the disk., Comment: 18 pages, 12 figures, accepted to ApJ
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- 2024
38. Learning Molecular Representation in a Cell
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Liu, Gang, Seal, Srijit, Arevalo, John, Liang, Zhenwen, Carpenter, Anne E., Jiang, Meng, and Singh, Shantanu
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Computer Science - Machine Learning ,Quantitative Biology - Quantitative Methods - Abstract
Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream applications: molecular property prediction against up to 27 baseline methods across four datasets, plus zero-shot molecule-morphology matching., Comment: 20 pages, 5 tables, 7 figures
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- 2024
39. CANUCS: Constraining the MACS J0416.1-2403 Strong Lensing Model with JWST NIRISS, NIRSpec and NIRCam
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Rihtaršič, Gregor, Bradač, Maruša, Desprez, Guillaume, Harshan, Anishya, Noirot, Gaël, Estrada-Carpenter, Vicente, Martis, Nicholas S., Abraham, Roberto G., Asada, Yoshihisa, Brammer, Gabriel, Iyer, Kartheik G., Matharu, Jasleen, Mowla, Lamiya, Muzzin, Adam, Sarrouh, Ghassan T. E., Sawicki, Marcin, Strait, Victoria, Willott, Chris J., Gledhill, Rachel, Markov, Vladan, and Tripodi, Roberta
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Astrophysics - Cosmology and Nongalactic Astrophysics ,Astrophysics - Astrophysics of Galaxies - Abstract
Strong gravitational lensing in galaxy clusters has become an essential tool in astrophysics, allowing us to directly probe the dark matter distribution and study magnified background sources. The precision and reliability of strong lensing models rely heavily on the number and quality of multiple images of background sources with spectroscopic redshifts. We present an updated strong lensing model of the galaxy cluster MACS J0416.1-2403 with the largest sample of multiple images with spectroscopic redshifts in a galaxy cluster field to date. Furthermore, we aim to demonstrate the effectiveness of JWST particularly its NIRISS camera, for strong lensing studies. We use the JWST 's NIRCam imaging and NIRSpec and NIRISS spectroscopy from the CAnadian NIRISS Unbiased Cluster Survey (CANUCS). The cluster mass model is constrained using Lenstool software. Our new dataset, used for constraining the lens model, comprises 303 secure multiple images from 111 background sources and includes systems with previously known MUSE redshift and systems for which we obtained spectroscopic redshift for the first time using NIRISS and NIRSpec spectroscopy. The total number of secure spectroscopic systems is >20% higher than in the previous strong lensing studies of this cluster. The derived strong lensing model can reproduce multiple images with the root-mean-square distance of 0.53''. We also provide a full catalogue with 415 multiple images, including less reliable candidates. We furthermore demonstrate the effectiveness of JWST particularly NIRISS, for strong lensing studies. As NIRISS F115W, F150W, and F200W grism spectroscopy captures at least two of the [OII] {\lambda}3727, [OIII] {\lambda}{\lambda}4959, 5007, and H{\alpha} lines at 1
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- 2024
40. MOTIVE: A Drug-Target Interaction Graph For Inductive Link Prediction
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Arevalo, John, Su, Ellen, Carpenter, Anne E, and Singh, Shantanu
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Computer Science - Machine Learning - Abstract
Drug-target interaction (DTI) prediction is crucial for identifying new therapeutics and detecting mechanisms of action. While structure-based methods accurately model physical interactions between a drug and its protein target, cell-based assays such as Cell Painting can better capture complex DTI interactions. This paper introduces MOTIVE, a Morphological cOmpound Target Interaction Graph dataset comprising Cell Painting features for 11,000 genes and 3,600 compounds, along with their relationships extracted from seven publicly available databases. We provide random, cold-source (new drugs), and cold-target (new genes) data splits to enable rigorous evaluation under realistic use cases. Our benchmark results show that graph neural networks that use Cell Painting features consistently outperform those that learn from graph structure alone, feature-based models, and topological heuristics. MOTIVE accelerates both graph ML research and drug discovery by promoting the development of more reliable DTI prediction models. MOTIVE resources are available at https://github.com/carpenter-singh-lab/motive.
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- 2024
41. Decay Energy Spectrometry for Improved Nuclear Material Analysis at the IAEA NML
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Kim, G. B., Kavner, A. R. L., Parsons-Davis, T., Friedrich, S., Drury, O. B., Lee, D., Zhang, X., Hines, N., Boyd, S. T. P., Weidenbenner, S., Schreiber, K., Martinson, S., Smith, C., McNeel, D., Salazar, S., Koehler, K., Carpenter, M., Croce, M., Schmidt, D., and Ullom, J.
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Physics - Instrumentation and Detectors ,Nuclear Experiment - Abstract
Decay energy spectrometry (DES) is a novel radiometric technique for high-precision analysis of nuclear materials. DES employs the unique thermal detection physics of cryogenic microcalorimeters with ultra-high energy resolution and 100$\%$ detection efficiency to accomplish high precision decay energy measurements. Low-activity nuclear samples of 1 Bq or less, and without chemical separation, are used to provide elemental and isotopic compositions in a single measurement. Isotopic ratio precisions of 1 ppm - 1,000 ppm (isotope dependent), which is close to that of the mass spectrometry, have been demonstrated in 12-hour DES measurements of ~5 Bq samples of certified reference materials of uranium (U) and plutonium (Pu). DES has very different systematic biases and uncertainties, as well as different sensitivities to nuclides, compared to mass-spectrometry techniques. Therefore, the accuracy and confidence of nuclear material assays can be improved by combining this new technique with existing mass-spectrometry techniques. Commercial-level DES techniques and equipment are being developed for the implementation of DES at the Nuclear Material Laboratory (NML) of International Atomic Energy Agency (IAEA) to provide complementary measurements to the existing technologies. The paper describes details of DES measurement methods, as well as DES precision and accuracy to U and Pu standard sources to discuss its capability in analysis of nuclear safeguards samples., Comment: This was submitted to 2022 IAEA symposium on nuclear safeguards (https://www.iaea.org/events/sg-2022), and posted at https://media.superevent.com/documents/20221027/668fdac0ee8d895ec6bcf293b1c42e6a/id-145.pdf
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- 2024
42. Sampling From Multiscale Densities With Delayed Rejection Generalized Hamiltonian Monte Carlo
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Turok, Gilad, Modi, Chirag, and Carpenter, Bob
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Statistics - Computation - Abstract
With the increasing prevalence of probabilistic programming languages, Hamiltonian Monte Carlo (HMC) has become the mainstay of applied Bayesian inference. However HMC still struggles to sample from densities with multiscale geometry: a large step size is needed to efficiently explore low curvature regions while a small step size is needed to accurately explore high curvature regions. We introduce the delayed rejection generalized HMC (DR-G-HMC) sampler that overcomes this challenge by employing dynamic step size selection, inspired by differential equation solvers. In a single sampling iteration, DR-G-HMC sequentially makes proposals with geometrically decreasing step sizes if necessary. This simulates Hamiltonian dynamics with increasing fidelity that, in high curvature regions, generates proposals with a higher chance of acceptance. DR-G-HMC also makes generalized HMC competitive by decreasing the number of rejections which otherwise cause inefficient backtracking and prevents directed movement. We present experiments to demonstrate that DR-G-HMC (1) correctly samples from multiscale densities, (2) makes generalized HMC methods competitive with the state of the art No-U-Turn sampler, and (3) is robust to tuning parameters., Comment: 9 pages, 5 figures
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- 2024
43. LncRNAs, nuclear architecture and the immune response
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Montano, Christy, Flores-Arenas, Cristina, and Carpenter, Susan
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Nuclear and Plasma Physics ,Biological Sciences ,Physical Sciences ,Genetics ,RNA ,Long Noncoding ,Humans ,Cell Nucleus ,Animals ,Immunity ,Innate ,Gene Expression Regulation ,Chromatin ,innate immunity ,long noncoding RNAs ,macrophages ,nucleus - Abstract
Long noncoding RNAs (LncRNAs) are key regulators of gene expression and can mediate their effects in both the nucleus and cytoplasm. Some of the best-characterized lncRNAs are localized within the nucleus, where they modulate the nuclear architecture and influence gene expression. In this review, we discuss the role of lncRNAs in nuclear architecture in the context of their gene regulatory functions in innate immunity. Here, we discuss various approaches to functionally characterize nuclear-localized lncRNAs and the challenges faced in the field.
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- 2024
44. A Comparison of Three Popular Methods for Handling Missing Data: Complete-Case Analysis, Inverse Probability Weighting, and Multiple Imputation
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Roderick J. Little, James R. Carpenter, and Katherine J. Lee
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Missing data are a pervasive problem in data analysis. Three common methods for addressing the problem are (a) complete-case analysis, where only units that are complete on the variables in an analysis are included; (b) weighting, where the complete cases are weighted by the inverse of an estimate of the probability of being complete; and (c) multiple imputation (MI), where missing values of the variables in the analysis are imputed as draws from their predictive distribution under an implicit or explicit statistical model, the imputation process is repeated to create multiple filled-in data sets, and analysis is carried out using simple MI combining rules. This article provides a non-technical discussion of the strengths and weakness of these approaches, and when each of the methods might be adopted over the others. The methods are illustrated on data from the Youth Cohort (Time) Series (YCS) for England, Wales and Scotland, 1984-2002.
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- 2024
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45. Computer Vision Analysis of Caregiver-Child Interactions in Children with Neurodevelopmental Disorders: A Preliminary Report
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Dmitry Yu. Isaev, Maura Sabatos-DeVito, J. Matias Di Martino, Kimberly Carpenter, Rachel Aiello, Scott Compton, Naomi Davis, Lauren Franz, Connor Sullivan, Geraldine Dawson, and Guillermo Sapiro
- Abstract
We report preliminary results of computer vision analysis of caregiver-child interactions during free play with children diagnosed with autism (N = 29, 41-91 months), attention-deficit/hyperactivity disorder (ADHD, N = 22, 48-100 months), or combined autism + ADHD (N = 20, 56-98 months), and neurotypical children (NT, N = 7, 55-95 months). We conducted micro-analytic analysis of 'reaching to a toy,' as a proxy for initiating or responding to a toy play bout. Dyadic analysis revealed two clusters of interaction patterns, which differed in frequency of 'reaching to a toy' and caregivers' contingent responding to the child's reach for a toy by also reaching for a toy. Children in dyads with higher caregiver responsiveness had less developed language, communication, and socialization skills. Clusters were not associated with diagnostic groups. These results hold promise for automated methods of characterizing caregiver responsiveness in dyadic interactions for assessment and outcome monitoring in clinical trials.
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- 2024
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46. Circulating KRAS G12D but not G12V is associated with survival in metastatic pancreatic ductal adenocarcinoma.
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Till, Jacob, McDaniel, Lee, Chang, Changgee, Long, Qi, Pfeiffer, Shannon, Lyman, Jaclyn, Padrón, Lacey, Maurer, Deena, Yu, Jia, Spencer, Christine, Gherardini, Pier, Da Silva, Diane, LaVallee, Theresa, Abbott, Charles, Chen, Richard, Boyle, Sean, Bhagwat, Neha, Cannas, Samuele, Sagreiya, Hersh, Li, Wenrui, Yee, Stephanie, Abdalla, Aseel, Wang, Zhuoyang, Yin, Melinda, Ballinger, Dominique, Wissel, Paul, Eads, Jennifer, Karasic, Thomas, Schneider, Charles, ODwyer, Peter, Teitelbaum, Ursina, Reiss, Kim, Rahma, Osama, Fisher, George, Ko, Andrew, Wainberg, Zev, Wolff, Robert, OReilly, Eileen, OHara, Mark, Cabanski, Christopher, Vonderheide, Robert, and Carpenter, Erica
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Humans ,Carcinoma ,Pancreatic Ductal ,Proto-Oncogene Proteins p21(ras) ,Pancreatic Neoplasms ,Female ,Male ,Circulating Tumor DNA ,Middle Aged ,Aged ,Biomarkers ,Tumor ,Prognosis ,Antineoplastic Combined Chemotherapy Protocols ,Mutation ,Progression-Free Survival ,Neoplasm Metastasis - Abstract
While high circulating tumor DNA (ctDNA) levels are associated with poor survival for multiple cancers, variant-specific differences in the association of ctDNA levels and survival have not been examined. Here we investigate KRAS ctDNA (ctKRAS) variant-specific associations with overall and progression-free survival (OS/PFS) in first-line metastatic pancreatic ductal adenocarcinoma (mPDAC) for patients receiving chemoimmunotherapy (PRINCE, NCT03214250), and an independent cohort receiving standard of care (SOC) chemotherapy. For PRINCE, higher baseline plasma levels are associated with worse OS for ctKRAS G12D (log-rank p = 0.0010) but not G12V (p = 0.7101), even with adjustment for clinical covariates. Early, on-therapy clearance of G12D (p = 0.0002), but not G12V (p = 0.4058), strongly associates with OS for PRINCE. Similar results are obtained for the SOC cohort, and for PFS in both cohorts. These results suggest ctKRAS G12D but not G12V as a promising prognostic biomarker for mPDAC and that G12D clearance could also serve as an early biomarker of response.
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- 2024
47. Compartment Syndrome Following Snake Envenomation in the United States: A Scoping Review of the Clinical Literature
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Newman, John, Therriault, Colin, White, Mia S., Nogee, Daniel, and Carpenter, Joseph E.
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antivenom ,Snakes ,Crotalinae ,Compartment Syndromes - Abstract
Introduction: Local tissue destruction following envenomation from North American snakes, particularly those within the Crotalinae subfamily, has the potential to progress to compartment syndrome. The pathophysiology of venom-induced compartment syndrome (VICS) is a debated topic and is distinct from trauma/reperfusion-induced compartment syndrome. Heterogeneity exists in the treatment practices of VICS, particularly regarding the decision to progress to fasciotomy. Associations with functional outcomes and evolution in clinical practice since the introduction of Crotalidae polyvalent immune Fab (FabAV) have not been well defined. Our goal was to identify the potential gaps in the literature regarding this phenomenon, as well as illuminate salient themes in the clinical characteristics and treatment practices of VICS.Methods: We conducted this systematic scoping-style review using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Records were included if they contained data surrounding the envenomation and hospital course of one or more patients who were envenomated by a snake species native to North America and were diagnosed with compartment syndromefrom 1980–2020.Results: We included 19 papers: 10 single- or two-patient case reports encompassing 12 patients, and nine chart reviews providing summary statistics of the included patients. In case reports, the median compartment pressure when reported was 60 millimeters of mercury (interquartile range 55–68), 66% underwent fasciotomy, and functional outcomes varied. Use of antivenom appeared to be more liberal with FabAV than the earlier antivenin Crotalidae polyvalent. Rapid progression of swelling was the most commonly reported symptom. Among the included retrospective chart reviews, important data such as compartment pressures, consistent laboratory values, and snake species was inconsistently reported.Conclusions: Venom-induced compartment syndrome is relatively rare. Existing papers generally describe good outcomes even in the absence of surgical management. Significant gaps in the literature regarding antivenom dosing practices, serial compartment pressure measurements, and functional outcomes highlight the need for prospective studies and consistent standardized reporting.
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- 2024
48. Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.
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Carpenter, Sara CD, Bogdanove, Adam J, Abbot, Bhuwan, Stajich, Jason E, Uehling, Jessie K, Lovett, Brian, Kasson, Matt T, and Carter, Morgan E
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Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Infectious Diseases ,Genetics ,2.2 Factors relating to the physical environment ,Generic health relevance ,Infection ,Symbiosis ,Rhizopus ,Burkholderia ,Bacterial Proteins ,Phylogeny ,Fungal Proteins ,Transcription Factors ,Genetic Variation ,effectors ,endofungal bacteria ,long- read sequencing ,meta- assembled genomes ,Mycetohabitans ,long-read sequencing ,meta-assembled genomes - Abstract
Endofungal Mycetohabitans (formerly Burkholderia) spp. rely on a type III secretion system to deliver mostly unidentified effector proteins when colonizing their host fungus, Rhizopus microsporus. The one known secreted effector family from Mycetohabitans consists of homologues of transcription activator-like (TAL) effectors, which are used by plant pathogenic Xanthomonas and Ralstonia spp. to activate host genes that promote disease. These 'Burkholderia TAL-like (Btl)' proteins bind corresponding specific DNA sequences in a predictable manner, but their genomic target(s) and impact on transcription in the fungus are unknown. Recent phenotyping of Btl mutants of two Mycetohabitans strains revealed that the single Btl in one Mycetohabitans endofungorum strain enhances fungal membrane stress tolerance, while others in a Mycetohabitans rhizoxinica strain promote bacterial colonization of the fungus. The phenotypic diversity underscores the need to assess the sequence diversity and, given that sequence diversity translates to DNA targeting specificity, the functional diversity of Btl proteins. Using a dual approach to maximize capture of Btl protein sequences for our analysis, we sequenced and assembled nine Mycetohabitans spp. genomes using long-read PacBio technology and also mined available short-read Illumina fungal-bacterial metagenomes. We show that btl genes are present across diverse Mycetohabitans strains from Mucoromycota fungal hosts yet vary in sequences and predicted DNA binding specificity. Phylogenetic analysis revealed distinct clades of Btl proteins and suggested that Mycetohabitans might contain more species than previously recognized. Within our data set, Btl proteins were more conserved across M. rhizoxinica strains than across M. endofungorum, but there was also evidence of greater overall strain diversity within the latter clade. Overall, the results suggest that Btl proteins contribute to bacterial-fungal symbioses in myriad ways.
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- 2024
49. Determinants of Symptomatic Intracranial Progression After an Initial Stereotactic Radiosurgery Course.
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Leng, Jim, Carpenter, David, Huang, Christina, Qazi, Jamiluddin, Arshad, Muzamil, Mullikin, Trey, Reitman, Zachary, Kirkpatrick, John, Floyd, Scott, Fecci, Peter, Chmura, Steven, Hong, Julian, and Salama, Joseph
- Abstract
PURPOSE: Clinical and imaging surveillance of patients with brain metastases is important after stereotactic radiosurgery (SRS) because many will experience intracranial progression (ITCP) requiring multidisciplinary management. The prognostic significance of neurologic symptoms at the time of ITCP is poorly understood. METHODS AND MATERIALS: This was a multi-institutional, retrospective cohort study from 2015 to 2020, including all patients with brain metastases completing an initial course of SRS. The primary outcome was overall survival (OS) by presence of neurologic symptoms at ITCP. OS, freedom from ITCP (FF-ITCP), and freedom from symptomatic ITCP (FF-SITCP) were assessed via Kaplan-Meier method. Cox proportional hazard models tested parameters impacting FF-ITCP and FF-SITCP. RESULTS: Among 1383 patients, median age was 63.4 years, 55% were female, and common primaries were non-small cell lung (49%), breast (15%), and melanoma (9%). At a median follow-up of 8.72 months, asymptomatic and symptomatic ITCP were observed in 504 (36%) and 194 (14%) patients, respectively. The majority of ITCP were distant ITCP (79.5%). OS was worse with SITCP (median, 10.2 vs 17.9 months, P < .001). SITCP was associated with clinical factors including total treatment volume (P = .012), melanoma histology (P = .001), prior whole brain radiation therapy (P = .003), number of brain metastases (P < .001), interval of 1 to 2 years from primary and brain metastasis diagnosis (P = .012), controlled extracranial disease (P = .042), and receipt of pre-SRS chemotherapy (P = .015). Patients who were younger and received post-SRS chemotherapy (P = .001), immunotherapy (P < .001), and targeted or small-molecule inhibitor therapy (P < .026) had better FF-SITCP. CONCLUSIONS: In this cohort study of patients with brain metastases completing SRS, neurologic symptoms at ITCP is prognostic for OS. This data informs post-SRS surveillance in clinical practice as well as future prospective studies needed in the modern management of brain metastases.
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- 2024
50. Crowdsourcing with Difficulty: A Bayesian Rating Model for Heterogeneous Items
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Han, Seong Woo, Adıgüzel, Ozan, and Carpenter, Bob
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
In applied statistics and machine learning, the "gold standards" used for training are often biased and almost always noisy. Dawid and Skene's justifiably popular crowdsourcing model adjusts for rater (coder, annotator) sensitivity and specificity, but fails to capture distributional properties of rating data gathered for training, which in turn biases training. In this study, we introduce a general purpose measurement-error model with which we can infer consensus categories by adding item-level effects for difficulty, discriminativeness, and guessability. We further show how to constrain the bimodal posterior of these models to avoid (or if necessary, allow) adversarial raters. We validate our model's goodness of fit with posterior predictive checks, the Bayesian analogue of $\chi^2$ tests. Dawid and Skene's model is rejected by goodness of fit tests, whereas our new model, which adjusts for item heterogeneity, is not rejected. We illustrate our new model with two well-studied data sets, binary rating data for caries in dental X-rays and implication in natural language.
- Published
- 2024
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