169,006 results on '"Watkins A."'
Search Results
52. Remyelination protects neurons from DLK-mediated neurodegeneration.
- Author
-
Duncan, Greg, Ingram, Sam, Emberley, Katie, Hill, Jo, Cordano, Christian, Abdelhak, Ahmed, McCane, Michael, Jenks, Jennifer, Jabassini, Nora, Ananth, Kirtana, Ferrara, Skylar, Stedelin, Brittany, Sivyer, Benjamin, Aicher, Sue, Scanlan, Thomas, Watkins, Trent, Mishra, Anusha, Nelson, Jonathan, Green, Ari, and Emery, Ben
- Subjects
Animals ,Remyelination ,Neurons ,Mice ,Demyelinating Diseases ,Apoptosis ,MAP Kinase Kinase Kinases ,Phosphorylation ,Disease Models ,Animal ,Myelin Sheath ,Mice ,Inbred C57BL ,Male ,Oligodendroglia ,Axons ,Female ,Microglia - Abstract
Chronic demyelination and oligodendrocyte loss deprive neurons of crucial support. It is the degeneration of neurons and their connections that drives progressive disability in demyelinating disease. However, whether chronic demyelination triggers neurodegeneration and how it may do so remain unclear. We characterize two genetic mouse models of inducible demyelination, one distinguished by effective remyelination and the other by remyelination failure and chronic demyelination. While both demyelinating lines feature axonal damage, mice with blocked remyelination have elevated neuronal apoptosis and altered microglial inflammation, whereas mice with efficient remyelination do not feature neuronal apoptosis and have improved functional recovery. Remyelination incapable mice show increased activation of kinases downstream of dual leucine zipper kinase (DLK) and phosphorylation of c-Jun in neuronal nuclei. Pharmacological inhibition or genetic disruption of DLK block c-Jun phosphorylation and the apoptosis of demyelinated neurons. Together, we demonstrate that remyelination is associated with neuroprotection and identify DLK inhibition as protective strategy for chronically demyelinated neurons.
- Published
- 2024
53. AI-based automation of enrollment criteria and endpoint assessment in clinical trials in liver diseases
- Author
-
Iyer, Janani S, Juyal, Dinkar, Le, Quang, Shanis, Zahil, Pokkalla, Harsha, Pouryahya, Maryam, Pedawi, Aryan, Stanford-Moore, S Adam, Biddle-Snead, Charles, Carrasco-Zevallos, Oscar, Lin, Mary, Egger, Robert, Hoffman, Sara, Elliott, Hunter, Leidal, Kenneth, Myers, Robert P, Chung, Chuhan, Billin, Andrew N, Watkins, Timothy R, Patterson, Scott D, Resnick, Murray, Wack, Katy, Glickman, Jon, Burt, Alastair D, Loomba, Rohit, Sanyal, Arun J, Glass, Ben, Montalto, Michael C, Taylor-Weiner, Amaro, Wapinski, Ilan, and Beck, Andrew H
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Clinical Trials and Supportive Activities ,Clinical Research ,6.1 Pharmaceuticals ,Oral and gastrointestinal ,Humans ,Artificial Intelligence ,Clinical Trials as Topic ,Non-alcoholic Fatty Liver Disease ,Liver Cirrhosis ,Patient Selection ,Endpoint Determination ,Female ,Retrospective Studies ,Male ,Automation ,Liver Diseases ,Reproducibility of Results ,Medical and Health Sciences ,Immunology ,Biomedical and clinical sciences ,Health sciences - Abstract
Clinical trials in metabolic dysfunction-associated steatohepatitis (MASH, formerly known as nonalcoholic steatohepatitis) require histologic scoring for assessment of inclusion criteria and endpoints. However, variability in interpretation has impacted clinical trial outcomes. We developed an artificial intelligence-based measurement (AIM) tool for scoring MASH histology (AIM-MASH). AIM-MASH predictions for MASH Clinical Research Network necroinflammation grades and fibrosis stages were reproducible (κ = 1) and aligned with expert pathologist consensus scores (κ = 0.62-0.74). The AIM-MASH versus consensus agreements were comparable to average pathologists for MASH Clinical Research Network scores (82% versus 81%) and fibrosis (97% versus 96%). Continuous scores produced by AIM-MASH for key histological features of MASH correlated with mean pathologist scores and noninvasive biomarkers and strongly predicted progression-free survival in patients with stage 3 (P
- Published
- 2024
54. “I’m both smoking and vaping”: a longitudinal qualitative study of US young adults who tried to quit smoking cigarettes by using electronic cigarettes
- Author
-
Nguyen, Nhung, Koester, Kimberly A, Kim, Minji, Watkins, Shannon Lea, and Ling, Pamela M
- Subjects
Public Health ,Health Sciences ,Substance Misuse ,Clinical Research ,Prevention ,Tobacco ,Tobacco Smoke and Health ,Electronic Nicotine Delivery Systems ,3.1 Primary prevention interventions to modify behaviours or promote wellbeing ,Cancer ,Respiratory ,Cardiovascular ,Stroke ,Good Health and Well Being ,Humans ,Vaping ,Young Adult ,Longitudinal Studies ,Smoking Cessation ,Adult ,Male ,Female ,Adolescent ,California ,Qualitative Research ,Cigarette Smoking ,cessation ,electronic nicotine delivery devices ,nicotine ,priority ,special populations ,priority/special populations - Abstract
ObjectiveTo describe how young adults use electronic cigarettes (electronic nicotine delivery systems (ENDS)) for smoking cessation and reasons why they may or may not successfully quit smoking.MethodsLongitudinal qualitative data were collected annually from 2017 to 2019 for 25 young adult tobacco users (aged 18-29 years) in California (USA) who used ENDS to quit/reduce smoking. Thematic and trajectory analyses were used to identify key within-person and between-person changes in tobacco/nicotine use over time.ResultsFive types of tobacco use transition were identified among baseline dual users of cigarettes and ENDS: sustained dual use without reduced smoking (n=8), transition to exclusive daily ENDS use (n=6), sustained dual use with reduced smoking (n=5), transition back to exclusive smoking (n=4) and transition to neither smoking nor vaping (n=2). Participants' ENDS use behaviour varied over time in terms of vaping quantity and device characteristics (eg, changing nicotine concentrations/flavours, switching between multiple devices). Three themes that related to successfully replacing cigarettes with ENDS were perceived positive physical effects, perceived satisfaction and enjoyment and context changes. Four themes for unsuccessful replacement were perceived negative physical discomforts, perceived addictiveness and harm, unsatisfactory substitution for cigarettes and device malfunction.ConclusionsYoung adults' experiences with using ENDS as a smoking cessation aid were highly variable. Adequate nicotine delivery and perceived safety and benefits contributed to successfully reducing or quitting cigarettes. Providing behavioural counselling and standardising ENDS products may enhance cessation for young adults.
- Published
- 2024
55. TESS Giants Transiting Giants. VI. Newly Discovered Hot Jupiters Provide Evidence for Efficient Obliquity Damping after the Main Sequence
- Author
-
Saunders, Nicholas, Grunblatt, Samuel K., Chontos, Ashley, Dai, Fei, Huber, Daniel, Zhang, Jingwen, Stefansson, Gudmundur, van Saders, Jennifer L., Winn, Joshua N., Hey, Daniel, Howard, Andrew W., Fulton, Benjamin, Isaacson, Howard, Beard, Corey, Giacalone, Steven, van Zandt, Judah, Murphey, Joseph M. Akana, Rice, Malena, Blunt, Sarah, Turtelboom, Emma, Dalba, Paul A., Lubin, Jack, Brinkman, Casey, Louden, Emma M., Page, Emma, Watkins, Cristilyn N., Collins, Karen A., Stockdale, Chris, Tan, Thiam-Guan, Schwarz, Richard P., Massey, Bob, Howell, Steve B., Vanderburg, Andrew, Ricker, George R., Jenkins, Jon M., Seager, Sara, Christiansen, Jessie L., Daylan, Tansu, Falk, Ben, Brodheim, Max, Gibson, Steven R., Hill, Grant M., Holden, Bradford, Householder, Aaron, Kaye, Stephen, Laher, Russ R., Lanclos, Kyle, Petigura, Erik A., Roy, Arpita, Rubenzahl, Ryan A., Schwab, Christian, Shaum, Abby P., Sirk, Martin M., Smith, Christopher L., Walawender, Josh, and Yeh, Sherry
- Subjects
Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Solar and Stellar Astrophysics - Abstract
The degree of alignment between a star's spin axis and the orbital plane of its planets (the stellar obliquity) is related to interesting and poorly understood processes that occur during planet formation and evolution. Hot Jupiters orbiting hot stars ($\gtrsim$6250 K) display a wide range of obliquities, while similar planets orbiting cool stars are preferentially aligned. Tidal dissipation is expected to be more rapid in stars with thick convective envelopes, potentially explaining this trend. Evolved stars provide an opportunity to test the damping hypothesis, particularly stars that were hot on the main sequence and have since cooled and developed deep convective envelopes. We present the first systematic study of the obliquities of hot Jupiters orbiting subgiants that recently developed convective envelopes using Rossiter-McLaughlin observations. Our sample includes two newly discovered systems in the Giants Transiting Giants Survey (TOI-6029 b, TOI-4379 b). We find that the orbits of hot Jupiters orbiting subgiants that have cooled below $\sim$6250 K are aligned or nearly aligned with the spin-axis of their host stars, indicating rapid tidal realignment after the emergence of a stellar convective envelope. We place an upper limit for the timescale of realignment for hot Jupiters orbiting subgiants at $\sim$500 Myr. Comparison with a simplified tidal evolution model shows that obliquity damping needs to be $\sim$4 orders of magnitude more efficient than orbital period decay to damp the obliquity without destroying the planet, which is consistent with recent predictions for tidal dissipation from inertial waves excited by hot Jupiters on misaligned orbits., Comment: 22 pages, 14 figures, 3 tables
- Published
- 2024
- Full Text
- View/download PDF
56. An Earth-sized Planet on the Verge of Tidal Disruption
- Author
-
Dai, Fei, Howard, Andrew W., Halverson, Samuel, Orell-Miquel, Jaume, Palle, Enric, Isaacson, Howard, Fulton, Benjamin, Price, Ellen M., Plotnykov, Mykhaylo, Rogers, Leslie A., Valencia, Diana, Paragas, Kimberly, Greklek-McKeon, Michael, Barrientos, Jonathan Gomez, Knutson, Heather A., Petigura, Erik A., Weiss, Lauren M., Lee, Rena, Brinkman, Casey L., Huber, Daniel, Steffansson, Gudmundur, Masuda, Kento, Giacalone, Steven, Lu, Cicero X., Kite, Edwin S., Hu, Renyu, Gaidos, Eric, Zhang, Michael, Rubenzahl, Ryan A., Winn, Joshua N., Han, Te, Beard, Corey, Holcomb, Rae, Householder, Aaron, Gilbert, Gregory J., Lubin, Jack, Ong, J. M. Joel, Polanski, Alex S., Saunders, Nicholas, Van Zandt, Judah, Yee, Samuel W., Zhang, Jingwen, Zink, Jon, Holden, Bradford, Baker, Ashley, Brodheim, Max, Crossfield, Ian J. M., Deich, William, Edelstein, Jerry, Gibson, Steven R., Hill, Grant M., Jelinsky, Sharon R, Kassis, Marc, Laher, Russ R., Lanclos, Kyle, Lilley, Scott, Payne, Joel N., Rider, Kodi, Robertson, Paul, Roy, Arpita, Schwab, Christian, Shaum, Abby P., Sirk, Martin M., Smith, Chris, Vandenberg, Adam, Walawender, Josh, Wang, Sharon X., Shin-Ywan, Wang, Wishnow, Edward, Wright, Jason T., Yeh, Sherry, Caballero, Jos. A., Morales, Juan C., Murgas, Felipe, Nagel, Evangelos, Reiners, Ansgar, Schweitzer, Andreas, Tabernero, Hugo M., Zechmeister, Mathias, Spencer, Alton, Ciardi, David R., Clark, Catherine A., Lund, Michael B., Caldwell, Douglas A., Collins, Karen A., Schwarz, Richard P., Barkaoui, Khalid, Watkins, Cristilyn N., Shporer, Avi, Narita, Norio, Fukui, Akihiko, Srdoc, Gregor, Latham, David W., Jenkins, Jon M., Ricker, George R., Seager, Sara, and Vanderspek, Roland
- Subjects
Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Solar and Stellar Astrophysics - Abstract
TOI-6255~b (GJ 4256) is an Earth-sized planet (1.079$\pm0.065$ $R_\oplus$) with an orbital period of only 5.7 hours. With the newly commissioned Keck Planet Finder (KPF) and CARMENES spectrographs, we determined the planet's mass to be 1.44$\pm$0.14 $M_{\oplus}$. The planet is just outside the Roche limit, with $P_{\rm orb}/P_{\rm Roche}$ = 1.13 $\pm0.10$. The strong tidal force likely deforms the planet into a triaxial ellipsoid with a long axis that is $\sim$10\% longer than the short axis. Assuming a reduced stellar tidal quality factor $Q_\star^\prime \approx10^7$, we predict that tidal orbital decay will cause TOI-6255 to reach the Roche limit in roughly 400 Myr. Such tidal disruptions may produce the possible signatures of planet engulfment that have been on stars with anomalously high refractory elemental abundances compared to its conatal binary companion. TOI-6255 b is also a favorable target for searching for star-planet magnetic interactions, which might cause interior melting and hasten orbital decay. TOI-6255 b is a top target (Emission Spectroscopy Metric of about 24) for phase curve observations with the James Webb Space Telescope., Comment: 18 pages, 7 figures, 5 tables, accepted to AAS Journals. The first RV mass measurement from the Keck Planet Finder
- Published
- 2024
57. Theia: Distilling Diverse Vision Foundation Models for Robot Learning
- Author
-
Shang, Jinghuan, Schmeckpeper, Karl, May, Brandon B., Minniti, Maria Vittoria, Kelestemur, Tarik, Watkins, David, and Herlant, Laura
- Subjects
Computer Science - Robotics ,Computer Science - Artificial Intelligence ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
Vision-based robot policy learning, which maps visual inputs to actions, necessitates a holistic understanding of diverse visual tasks beyond single-task needs like classification or segmentation. Inspired by this, we introduce Theia, a vision foundation model for robot learning that distills multiple off-the-shelf vision foundation models trained on varied vision tasks. Theia's rich visual representations encode diverse visual knowledge, enhancing downstream robot learning. Extensive experiments demonstrate that Theia outperforms its teacher models and prior robot learning models using less training data and smaller model sizes. Additionally, we quantify the quality of pre-trained visual representations and hypothesize that higher entropy in feature norm distributions leads to improved robot learning performance. Code, models, and demo are available at https://theia.theaiinstitute.com., Comment: CoRL 2024
- Published
- 2024
58. Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design
- Author
-
Tagasovska, Nataša, Park, Ji Won, Kirchmeyer, Matthieu, Frey, Nathan C., Watkins, Andrew Martin, Ismail, Aya Abdelsalam, Jamasb, Arian Rokkum, Lee, Edith, Bryson, Tyler, Ra, Stephen, and Cho, Kyunghyun
- Subjects
Quantitative Biology - Biomolecules ,Computer Science - Machine Learning - Abstract
Machine learning (ML) has demonstrated significant promise in accelerating drug design. Active ML-guided optimization of therapeutic molecules typically relies on a surrogate model predicting the target property of interest. The model predictions are used to determine which designs to evaluate in the lab, and the model is updated on the new measurements to inform the next cycle of decisions. A key challenge is that the experimental feedback from each cycle inspires changes in the candidate proposal or experimental protocol for the next cycle, which lead to distribution shifts. To promote robustness to these shifts, we must account for them explicitly in the model training. We apply domain generalization (DG) methods to classify the stability of interactions between an antibody and antigen across five domains defined by design cycles. Our results suggest that foundational models and ensembling improve predictive performance on out-of-distribution domains. We publicly release our codebase extending the DG benchmark ``DomainBed,'' and the associated dataset of antibody sequences and structures emulating distribution shifts across design cycles.
- Published
- 2024
59. HSTPROMO Internal Proper Motion Kinematics of Dwarf Spheroidal Galaxies: I. Velocity Anisotropy and Dark Matter Cusp Slope of Draco
- Author
-
Vitral, Eduardo, van der Marel, Roeland P., Sohn, Sangmo Tony, Libralato, Mattia, del Pino, Andrés, Watkins, Laura L., Bellini, Andrea, Walker, Matthew G., Besla, Gurtina, Pawlowski, Marcel S., and Mamon, Gary A.
- Subjects
Astrophysics - Astrophysics of Galaxies ,Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We analyze four epochs of HST imaging over 18 years for the Draco dwarf spheroidal galaxy. We measure precise proper motions (PMs) for hundreds of stars and combine these with existing line-of-sight (LOS) velocities. This provides the first radially-resolved 3D velocity dispersion profiles for any dwarf galaxy. These constrain the intrinsic velocity anisotropy and resolve the mass-anisotropy degeneracy. We solve the Jeans equations in oblate axisymmetric geometry to infer the mass profile. We find the velocity dispersion to be radially anisotropic along the symmetry axis and tangentially anisotropic in the equatorial plane, with a globally-averaged value $\overline{\beta_{\mathrm B}}=-0.20^{+ 0.28}_{- 0.53}$, (where $1 - \beta_{\mathrm B} \equiv \langle v_{\mathrm{ tan}}^2 \rangle / \langle v_{\mathrm{ rad}}^2 \rangle$ in 3D). The logarithmic dark matter (DM) density slope over the observed radial range, $\Gamma_{\mathrm{ dark}}$, is $-0.83^{+ 0.32}_{- 0.37}$, consistent with the inner cusp predicted in $\Lambda$CDM cosmology. As expected given Draco's low mass and ancient star formation history, it does not appear to have been dissolved by baryonic processes. We rule out cores larger than 487, 717, 942 pc at respective 1-, 2-, 3-$\sigma$ confidence, thus imposing important constraints on the self-interacting DM cross-section. Spherical models yield biased estimates for both the velocity anisotropy and the inferred slope. The circular velocity at our outermost data point (900 pc) is $24.19^{+ 6.31}_{- 2.97} \ \mathrm{km~s^{-1}}s$. We infer a dynamical distance of $75.37^{+ 4.73}_{- 4.00}$ kpc, and show that Draco has a modest LOS rotation, with $\left
= 0.22 \pm 0.09$. Our results provide a new stringent test of the so-called `cusp-core' problem that can be readily extended to other dwarfs., Comment: 35 pages, 18 figures, 3 Tables. Accepted for publication in ApJ. Journal version has better readability. Data is available at Zenodo: https://zenodo.org/records/11111113 - Published
- 2024
- Full Text
- View/download PDF
60. Light Dark Matter Constraints from SuperCDMS HVeV Detectors Operated Underground with an Anticoincidence Event Selection
- Author
-
SuperCDMS Collaboration, Albakry, M. F., Alkhatib, I., Alonso-González, D., Amaral, D. W. P., Anczarski, J., Aralis, T., Aramaki, T., Arnquist, I. J., Langroudy, I. Ataee, Azadbakht, E., Bathurst, C., Bhattacharyya, R., Biffl, A. J., Brink, P. L., Buchanan, M., Bunker, R., Cabrera, B., Calkins, R., Cameron, R. A., Cartaro, C., Cerdeño, D. G., Chang, Y. -Y., Chaudhuri, M., Chen, J. -H., Chen, R., Chott, N., Cooley, J., Coombes, H., Cushman, P., Cyna, R., Das, S., De Brienne, F., Dharani, S., di Vacri, M. L., Diamond, M. D., Elwan, M., Fascione, E., Figueroa-Feliciano, E., Fouts, K., Fritts, M., Germond, R., Ghaith, M., Golwala, S. R., Hall, J., Harms, S. A. S., Harris, K., Hassan, N., Hong, Z., Hoppe, E. W., Hsu, L., Huber, M. E., Iyer, V., Jardin, D., Kashyap, V. K. S., Keller, S. T. D., Kelsey, M. H., Kennard, K. T., Kubik, A., Kurinsky, N. A., Lee, M., Leyva, J., Liu, J., Liu, Y., Loer, B., Asamar, E. Lopez, Lukens, P., MacFarlane, D. B., Mahapatra, R., Mammo, J. S., Mast, N., Mayer, A. J., Theenhausen, H. Meyer zu, Michaud, É., Michielin, E., Mirabolfathi, N., Mirzakhani, M., Mohanty, B., Monteiro, D., Nelson, J., Neog, H., Novati, V., Orrell, J. L., Osborne, M. D., Oser, S. M., Pandey, L., Pandey, S., Partridge, R., Pedreros, D. S., Peng, W., Perna, L., Perry, W. L., Podviianiuk, R., Poudel, S. S., Pradeep, A., Pyle, M., Rau, W., Reid, E., Ren, R., Reynolds, T., Rios, M., Roberts, A., Robinson, A. E., Ryan, J. L., Saab, T., Sadek, D., Sadoulet, B., Sahoo, S. P., Saikia, I., Sander, J., Sattari, A., Schmidt, B., Schnee, R. W., Scorza, S., Serfass, B., Simchony, A., Sincavage, D. J., Sinervo, P., Street, J., Sun, H., Tanner, E., Terry, G. D., Toback, D., Verma, S., Villano, A. N., von Krosigk, B., Watkins, S. L., Wen, O., Williams, Z., Wilson, M. J., Winchell, J., Wykoff, K., Yellin, S., Young, B. A., Yu, T. C., Zatschler, B., Zatschler, S., Zaytsev, A., Zhang, E., Zheng, L., Zuniga, A., and Zurowski, M. J.
- Subjects
High Energy Physics - Experiment ,Astrophysics - Cosmology and Nongalactic Astrophysics ,Physics - Instrumentation and Detectors - Abstract
This article presents constraints on dark-matter-electron interactions obtained from the first underground data-taking campaign with multiple SuperCDMS HVeV detectors operated in the same housing. An exposure of 7.63 g-days is used to set upper limits on the dark-matter-electron scattering cross section for dark matter masses between 0.5 and 1000 MeV/$c^2$, as well as upper limits on dark photon kinetic mixing and axion-like particle axioelectric coupling for masses between 1.2 and 23.3 eV/$c^2$. Compared to an earlier HVeV search, sensitivity was improved as a result of an increased overburden of 225 meters of water equivalent, an anticoincidence event selection, and better pile-up rejection. In the case of dark-matter-electron scattering via a heavy mediator, an improvement by up to a factor of 25 in cross-section sensitivity was achieved., Comment: 7 pages + title and references, 4 figures, and 1 table
- Published
- 2024
61. Surviving in the Hot Neptune Desert: The Discovery of the Ultra-Hot Neptune TOI-3261b
- Author
-
Nabbie, Emma, Huang, Chelsea X., Burt, Jennifer A., Armstrong, David J., Mamajek, Eric E., Adibekyan, Vardan, Sousa, Sérgio G., Lopez, Eric D., Thorngren, Daniel P., Fernández, Jorge, Li, Gongjie, Jenkins, James S., Vines, Jose I., da Silva, João Gomes, Wittenmyer, Robert A., Bayliss, Daniel, Briceño, César, Collins, Karen A., Dumusque, Xavier, Horne, Keith D., Keniger, Marcelo F., Law, Nicholas, Lillo-Box, Jorge, Liu, Shang-Fei, Mann, Andrew W., Nielsen, Louise Dyregaard, Osborn, Ares, Relles, Howard M., Rodrigues, José J., Bell, Juan, Srdoc, Gregor, Stockdale, Chris, Strøm, Paul A., Gardner-Watkins, Cristilyn N., Wheatley, Peter J., Wright, Duncan J., Zhou, George, Ziegler, Carl, Ricker, George R., Seager, Sara, Vanderspek, Roland, Winn, Joshua W., Jenkins, Jon M., Fausnaugh, Michael, Kunimoto, Michelle, Osborn, Hugh P., Quinn, Samuel N., and Wohler, Bill
- Subjects
Astrophysics - Earth and Planetary Astrophysics - Abstract
The recent discoveries of Neptune-sized ultra-short period planets (USPs) challenge existing planet formation theories. It is unclear whether these residents of the Hot Neptune Desert have similar origins to smaller, rocky USPs, or if this discrete population is evidence of a different formation pathway altogether. We report the discovery of TOI-3261b, an ultra-hot Neptune with an orbital period $P$ = 0.88 days. The host star is a $V = 13.2$ magnitude, slightly super-solar metallicity ([Fe/H] $\simeq$ 0.15), inactive K1.5 main sequence star at $d = 300$ pc. Using data from the Transiting Exoplanet Survey Satellite and the Las Cumbres Observatory Global Telescope, we find that TOI-3261b has a radius of $3.82_{-0.35}^{+0.42}$ $R_{\oplus}$. Moreover, radial velocities from ESPRESSO and HARPS reveal a mass of $30.3_{-2.4}^{+2.2}$ $M_{\oplus}$, more than twice the median mass of Neptune-sized planets on longer orbits. We investigate multiple mechanisms of mass loss that can reproduce the current-day properties of TOI-3261b, simulating the evolution of the planet via tidal stripping and photoevaporation. Thermal evolution models suggest that TOI-3261b should retain an envelope potentially enriched with volatiles constituting $\sim$5% of its total mass. This is the second highest envelope mass fraction among ultra-hot Neptunes discovered to date, making TOI-3261b an ideal candidate for atmospheric follow-up observations., Comment: 20 pages, 11 figures, accepted to AJ
- Published
- 2024
62. NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries
- Author
-
Nowara, Ewa M., Pinheiro, Pedro O., Mahajan, Sai Pooja, Mahmood, Omar, Watkins, Andrew Martin, Saremi, Saeed, and Maser, Michael
- Subjects
Computer Science - Machine Learning ,Quantitative Biology - Biomolecules - Abstract
We present NEBULA, the first latent 3D generative model for scalable generation of large molecular libraries around a seed compound of interest. Such libraries are crucial for scientific discovery, but it remains challenging to generate large numbers of high quality samples efficiently. 3D-voxel-based methods have recently shown great promise for generating high quality samples de novo from random noise (Pinheiro et al., 2023). However, sampling in 3D-voxel space is computationally expensive and use in library generation is prohibitively slow. Here, we instead perform neural empirical Bayes sampling (Saremi & Hyvarinen, 2019) in the learned latent space of a vector-quantized variational autoencoder. NEBULA generates large molecular libraries nearly an order of magnitude faster than existing methods without sacrificing sample quality. Moreover, NEBULA generalizes better to unseen drug-like molecules, as demonstrated on two public datasets and multiple recently released drugs. We expect the approach herein to be highly enabling for machine learning-based drug discovery. The code is available at https://github.com/prescient-design/nebula
- Published
- 2024
63. Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms
- Author
-
Stanton, Samuel, Alberstein, Robert, Frey, Nathan, Watkins, Andrew, and Cho, Kyunghyun
- Subjects
Computer Science - Machine Learning ,Computer Science - Neural and Evolutionary Computing - Abstract
There is a growing body of work seeking to replicate the success of machine learning (ML) on domains like computer vision (CV) and natural language processing (NLP) to applications involving biophysical data. One of the key ingredients of prior successes in CV and NLP was the broad acceptance of difficult benchmarks that distilled key subproblems into approachable tasks that any junior researcher could investigate, but good benchmarks for biophysical domains are rare. This scarcity is partially due to a narrow focus on benchmarks which simulate biophysical data; we propose instead to carefully abstract biophysical problems into simpler ones with key geometric similarities. In particular we propose a new class of closed-form test functions for biophysical sequence optimization, which we call Ehrlich functions. We provide empirical results demonstrating these functions are interesting objects of study and can be non-trivial to solve with a standard genetic optimization baseline.
- Published
- 2024
64. TOI-2374 b and TOI-3071 b: two metal-rich sub-Saturns well within the Neptunian desert
- Author
-
Hacker, Alejandro, Díaz, Rodrigo F., Armstrong, David J., Fernández, Jorge Fernández, Müller, Simon, Delgado-Mena, Elisa, Sousa, Sérgio G., Adibekyan, Vardan, Stassun, Keivan G., Collins, Karen A., Yee, Samuel W., Bayliss, Daniel, Bieryla, Allyson, Bouchy, François, Butler, R. Paul, Crane, Jeffrey D., Dumusque, Xavier, Hartman, Joel D., Helled, Ravit, Jenkins, Jon, Keniger, Marcelo Aron F., Lewis, Hannah, Lillo-Box, Jorge, Lund, Michael B., Nielsen, Louise D., Osborn, Ares, Osip, David, Paegert, Martin, Radford, Don J., Santos, Nuno C., Seager, Sara, Shectman, Stephen A., Srdoc, Gregor, Strøm, Paul A., Tan, Thiam-Guan, Teske, Johanna K., Vezie, Michael, Watanabe, David, Watkins, Cristilyn N., Wheatley, Peter J., Winn, Joshua N., Wohler, Bill, and Ziegler, Carl
- Subjects
Astrophysics - Earth and Planetary Astrophysics - Abstract
We report the discovery of two transiting planets detected by the Transiting Exoplanet Survey Satellite (TESS), TOI-2374 b and TOI-3071 b, orbiting a K5V and an F8V star, respectively, with periods of 4.31 and 1.27 days, respectively. We confirm and characterize these two planets with a variety of ground-based and follow-up observations, including photometry, precise radial velocity monitoring and high-resolution imaging. The planetary and orbital parameters were derived from a joint analysis of the radial velocities and photometric data. We found that the two planets have masses of $(57 \pm 4)$ $M_\oplus$ or $(0.18 \pm 0.01)$ $M_J$, and $(68 \pm 4)$ $M_\oplus$ or $(0.21 \pm 0.01)$ $M_J$, respectively, and they have radii of $(6.8 \pm 0.3)$ $R_\oplus$ or $(0.61 \pm 0.03)$ $R_J$ and $(7.2 \pm 0.5)$ $R_\oplus$ or $(0.64 \pm 0.05)$ $R_J$, respectively. These parameters correspond to sub-Saturns within the Neptunian desert, both planets being hot and highly irradiated, with $T_{\rm eq} \approx 745$ $K$ and $T_{\rm eq} \approx 1812$ $K$, respectively, assuming a Bond albedo of 0.5. TOI-3071 b has the hottest equilibrium temperature of all known planets with masses between $10$ and $300$ $M_\oplus$ and radii less than $1.5$ $R_J$. By applying gas giant evolution models we found that both planets, especially TOI-3071 b, are very metal-rich. This challenges standard formation models which generally predict lower heavy-element masses for planets with similar characteristics. We studied the evolution of the planets' atmospheres under photoevaporation and concluded that both are stable against evaporation due to their large masses and likely high metallicities in their gaseous envelopes., Comment: 24 pages, 22 figures, 10 tables, accepted for publication in MNRAS
- Published
- 2024
65. The properties of AGN in dwarf galaxies identified via SED fitting
- Author
-
Bichang'a, B., Kaviraj, S., Lazar, I., Jackson, R. A., Das, S., Smith, D. J. B., Watkins, A. E., and Martin, G.
- Subjects
Astrophysics - Astrophysics of Galaxies - Abstract
Given their dominance of the galaxy number density, dwarf galaxies are central to our understanding of galaxy formation. While the incidence of AGN and their impact on galaxy evolution has been extensively studied in massive galaxies, much less is known about the role of AGN in the evolution of dwarfs. We search for radiatively-efficient AGN in the nearby (0.1 < z < 0.3) dwarf (10^8 MSun < M < 10^10 MSun) population, using SED fitting (via Prospector) applied to deep ultraviolet to mid-infrared photometry of 508 dwarf galaxies. Around a third (32 +/- 2 per cent) of our dwarfs show signs of AGN activity. We compare the properties of our dwarf AGN to control samples, constructed from non-AGN, which have the same distributions of redshift and stellar mass as their AGN counterparts. KS tests between the AGN and control distributions indicates that the AGN do not show differences in their distances to nodes, filaments and nearby massive galaxies from their control counterparts. This indicates that AGN triggering in the dwarf regime is not strongly correlated with local environment. The fraction of AGN hosts with early-type morphology and those that are interacting are also indistinguishable from the controls within the uncertainties, suggesting that interactions do not play a significant role in inducing AGN activity in our sample. Finally, the star formation activity in dwarf AGN is only slightly lower than that in their control counterparts, suggesting that the presence of radiatively-efficient AGN does not lead to significant, prompt quenching of star formation in these systems., Comment: Accepted for publication in MNRAS
- Published
- 2024
66. Baryon number violation involving tau leptons
- Author
-
Heeck, Julian and Watkins, Dima
- Subjects
High Energy Physics - Phenomenology ,High Energy Physics - Experiment - Abstract
Baryon number violation is our most sensitive probe of physics beyond the Standard Model, especially through the study of nucleon decays. Angular momentum conservation requires a lepton in the final state of such decays, kinematically restricted to electrons, muons, or neutrinos. We show that operators involving taus, which are at first sight too heavy to play a role in nucleon decays, still lead to clean nucleon decay channels with tau neutrinos. While many of them are already constrained from existing two-body searches such as $p\to \pi^+\nu$, other operators induce many-body decays such as $p \to \eta \pi^{+} \bar\nu_\tau$ and $n\to K^+ \pi^-\nu_\tau$ that have never been searched for., Comment: 15 pages; matches JHEP version
- Published
- 2024
- Full Text
- View/download PDF
67. The Fraction of Dust Mass in the Form of PAHs on 10-50 pc Scales in Nearby Galaxies
- Author
-
Sutter, Jessica, Sandstrom, Karin, Chastenet, Jérémy, Leroy, Adam K., Koch, Eric W., Williams, Thomas G., Chown, Ryan, Belfiore, Francesco, Bigiel, Frank, Boquien, Médéric, Cao, Yixian, Chevance, Mélanie, Dale, Daniel A., Egorov, Oleg V., Glover, Simon C. O., Groves, Brent, Klessen, Ralf S., Kreckel, Kathryn, Larson, Kirsten L., Oakes, Elias K., Pathak, Debosmita, Ramambason, Lise, Rosolowsky, Erik, and Watkins, Elizabeth J.
- Subjects
Astrophysics - Astrophysics of Galaxies - Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a ubiquitous component of the interstellar medium (ISM) in z~0 massive, star-forming galaxies and play key roles in ISM energy balance, chemistry, and shielding. Wide field of view, high resolution mid-infrared (MIR) images from JWST provides the ability to map the fraction of dust in the form of PAHs and the properties of these key dust grains at 10-50 pc resolution in galaxies outside the Local Group. We use MIR JWST photometric observations of a sample of 19 nearby galaxies from the "Physics at High Angular Resolution in Nearby GalaxieS" (PHANGS) survey to investigate the variations of the PAH fraction. By comparison to lower resolution far-IR mapping, we show that a combination of the MIRI filters (R$_{\rm{PAH}}$ = [F770W+F1130W]/F2100W) traces the fraction of dust by mass in the form of PAHs (i.e., the PAH fraction, or q$_{\rm{PAH}}$). Mapping R$_{\rm{PAH}}$ across the 19 PHANGS galaxies, we find that the PAH fraction steeply decreases in HII regions, revealing the destruction of these small grains in regions of ionized gas. Outside HII regions, we find R$_{\rm{PAH}}$ is constant across the PHANGS sample with an average value of 3.43$\pm$0.98, which, for an illuminating radiation field of intensity 2-5 times that of the radiation field in the solar neighborhood, corresponds to q$_{\rm{PAH}}$ values of 3-6%., Comment: Accepted at ApJ, 39 pages, 25 figures
- Published
- 2024
68. A Survey of Robotic Language Grounding: Tradeoffs between Symbols and Embeddings
- Author
-
Cohen, Vanya, Liu, Jason Xinyu, Mooney, Raymond, Tellex, Stefanie, and Watkins, David
- Subjects
Computer Science - Robotics ,Computer Science - Artificial Intelligence ,Computer Science - Computation and Language - Abstract
With large language models, robots can understand language more flexibly and more capable than ever before. This survey reviews and situates recent literature into a spectrum with two poles: 1) mapping between language and some manually defined formal representation of meaning, and 2) mapping between language and high-dimensional vector spaces that translate directly to low-level robot policy. Using a formal representation allows the meaning of the language to be precisely represented, limits the size of the learning problem, and leads to a framework for interpretability and formal safety guarantees. Methods that embed language and perceptual data into high-dimensional spaces avoid this manually specified symbolic structure and thus have the potential to be more general when fed enough data but require more data and computing to train. We discuss the benefits and tradeoffs of each approach and finish by providing directions for future work that achieves the best of both worlds., Comment: IJCAI 2024 Survey Track
- Published
- 2024
69. Chemical control of self-assembly by the electrosolvation force
- Author
-
Wang, Sida, Walker-Gibbons, Rowan, Watkins, Bethany, Lin, Binghui, and Krishnan, Madhavi
- Subjects
Condensed Matter - Soft Condensed Matter - Abstract
Self-assembly of matter in solution generally relies on attractive interactions that overcome entropy and drive the formation of higher-order molecular and particulate structures. Such interactions play key roles in a variety of contexts, e.g., crystallisation, biomolecular folding and condensation, pathological protein aggregation, pharmaceuticals and fine chemicals. The electrosolvation force entails a new conceptual paradigm in the known palette of interactions that drive the spontaneous accretion and organisation of matter. However, an understanding of the underlying physical chemistry, and therefore the ability to exert control over and tune the interaction, remains incomplete. Here we demonstrate that this force arises from the structure of the interfacial electrolyte. Neutral molecules such as a different solvent, osmolytes or surfactants, can - even at very low concentrations in the medium - disrupt or reinforce pre-existing interfacial solvent structure, thereby furnishing unanticipated chemical tuning of the ability of matter to self-assemble. The observations further present unexpected mechanistic elements that may explain the impact of co-solvents and osmolytes on protein structure, stability and pathological protein condensation. Our findings shed new light on microscopic mechanisms that drive the emergence of order and structure from molecular to macroscopic scales in the solution phase.
- Published
- 2024
70. Early Results from the HUMDRUM Survey: A Small, Earth-mass Planet Orbits TOI-1450A
- Author
-
Brady, M., Bean, J., Seifahrt, A., Kasper, D., Luque, R., Stefánsson, G., Stürmer, J., Charbonneau, D., Collins, K., Doty, J., Essack, Z., Fukui, A., Horta, F. Grau, Hedges, C., Hellier, C., Jenkins, J., Narita, N., Quinn, S., Shporer, A., Schwarz, R., Seager, S., Stassun, K., Striegel, S., Watkins, C., Winn, J., and Zambelli, R.
- Subjects
Astrophysics - Earth and Planetary Astrophysics - Abstract
M dwarf stars provide us with an ideal opportunity to study nearby small planets. The HUMDRUM (HUnting for M Dwarf Rocky planets Using MAROON-X) survey uses the MAROON-X spectrograph, which is ideally suited to studying these stars, to measure precise masses of a volume-limited ($<\,30$ pc) sample of transiting M dwarf planets. TOI-1450 is a nearby (22.5 pc) binary system containing a M3 dwarf with a roughly 3000 K companion. Its primary star, TOI-1450A, was identified by $TESS$ to have a 2.04d transit signal, and is included in the HUMDRUM sample. In this paper, we present MAROON-X radial velocities which confirm the planetary nature of this signal and measure its mass at a nearly 10% precision. The 2.04d planet, TOI-1450Ab, has $R_b\,=\,1.13\,\pm\,0.04\,R_\oplus$ and $M_b\,=\,1.26\,\pm\,0.13\,M_\oplus$. It is the second-lowest-mass transiting planet with a high-precision RV mass measurement. With this mass and radius, the planet's mean density is compatible with an Earth-like composition. Given its short orbital period and slightly sub-Earth density, it may be amenable to $JWST$ follow-up to test whether the planet has retained an atmosphere despite extreme heating from the nearby star. We also discover a non-transiting planet in the system with a period of 5.07 days and a $M\mathrm{sin}i_c\,=\,1.53\,\pm\,0.18\,M_\oplus$. We also find a 2.01d signal present in the systems's $TESS$ photometry that likely corresponds to the rotation period of TOI-1450A's binary companion, TOI-1450B. TOI-1450A, meanwhile, appears to have a rotation period of approximately 40 days, which is in-line with our expectations for a mid-M dwarf., Comment: 31 pages, 17 figures, accepted in AJ
- Published
- 2024
71. Three short-period Earth-sized planets around M dwarfs discovered by TESS: TOI-5720b, TOI-6008b and TOI-6086b
- Author
-
Barkaoui, K., Schwarz, R. P., Narita, N., Mistry, P., Magliano, C., Hirano, T., Maity, M., Burgasser, A. J., Rackham, B. V., Murgas, F., Pozuelos, F. J., Stassun, K. G., Everett, M. E., Ciardi, D. R., Lamman, C., Pass, E. K., Bieryla, A., Aganze, C., Esparza-Borges, E., Collins, K. A., Covone, G., de Leon, J., D'evora-Pajares, M., de Wit, J., Fukuda, Izuru, Fukui, A., Gerasimov, R., Gillon, M., Hayashi, Y., Howell, S. B., Ikoma, M., Ikuta, K., Jenkins, J. M., Karpoor, P. R., Kawai, Y., Kimura, T., Kotani, T., Latham, D. W., Mori, M., Palle, E., Parviainen, H., Patel, Y. G., Ricker, G., Relles, H. M., Shporer, A., Seager, S., Softich, E., Srdoc, G., Tamura, M., Theissen, C. A., Twicken, J. D., Vanderspek, R., Watanabe, N., Watkins, C. N., Winn, J. N., and Wohler, B.
- Subjects
Astrophysics - Earth and Planetary Astrophysics - Abstract
One of the main goals of the NASA's TESS (Transiting Exoplanet Survey Satellite) mission is the discovery of Earth-like planets around nearby M-dwarf stars. Here, we present the discovery and validation of three new short-period Earth-sized planets orbiting nearby M-dwarfs: TOI- 5720b, TOI-6008b and TOI-6086b. We combined TESS data, ground-based multi-color light curves, ground-based optical and near-infrared spectroscopy, and Subaru/IRD RVs data to validate the planetary candidates and constrain the physical parameters of the systems. In addition, we used archival images, high-resolution imaging, and statistical validation techniques to support the planetary validation. TOI-5720b is a planet with a radius of Rp=1.09 Re orbiting a nearby (23 pc) M2.5 host, with an orbital period of P=1.43 days. It has an equilibrium temperature of Teq=708 K and an incident flux of Sp=41.7 Se. TOI-6008b has a period of P=0.86 day, a radius of Rp=1.03 Re, an equilibrium temperature of Teq=707 K and an incident flux of Sp=41.5 Se. The host star (TOI-6008) is a nearby (36 pc) M5 with an effective temperature of Teff=3075 K. Based on the RV measurements collected with Subaru/IRD, we set a 3-sigma upper limit of Mp<4 M_Earth, thus ruling out a star or brown dwarf as the transiting companion. TOI-6086b orbits its nearby (31 pc) M3 host star (Teff=3200 K) every 1.39 days, and has a radius of Rp=1.18 Re, an equilibrium temperature of Teq=634 K and an incident flux of Sp=26.8 Se. Additional high precision radial velocity measurements are needed to derive the planetary masses and bulk densities, and to search for additional planets in the systems. Moreover, short-period earth-sized planets orbiting around nearby M-dwarfs are suitable targets for atmospheric characterization with the James Webb Space Telescope (JWST) through transmission and emission spectroscopy, and phase curve photometry., Comment: Accepted for publication in Astronomy & Astrophysics
- Published
- 2024
72. RT-utils: A Minimal Python Library for RT-struct Manipulation
- Author
-
Shrestha, Asim, Watkins, Adam, Yousefirizi, Fereshteh, Rahmim, Arman, and Uribe, Carlos F.
- Subjects
Physics - Medical Physics - Abstract
Towards the need for automated and precise AI-based analysis of medical images, we present RT-utils, a specialized Python library tuned for the manipulation of radiotherapy (RT) structures stored in DICOM format. RT-utils excels in converting the polygon contours into binary masks, ensuring accuracy and efficiency. By converting DICOM RT structures into standardized formats such as NumPy arrays and SimpleITK Images, RT-utils optimizes inputs for computational solutions such as AI-based automated segmentation techniques or radiomics analysis. Since its inception in 2020, RT-utils has been used extensively with a focus on simplifying complex data processing tasks. RT-utils offers researchers a powerful solution to enhance workflows and drive significant advancements in medical imaging.
- Published
- 2024
73. Quantifying Smooth Muscles Regional Organization in the Rat Bladder Using Immunohistochemistry, Multiphoton Microscopy and Machine Learning
- Author
-
Asadbeygi, Alireza, Tobe, Yasutaka, Yoshimura, Naoki, Stocker, Sean D., Watkins, Simon, Watton, Paul, and Robertson, Anne M.
- Subjects
Quantitative Biology - Tissues and Organs ,Electrical Engineering and Systems Science - Image and Video Processing - Abstract
The smooth muscle bundles (SMBs) in the bladder act as contractile elements which enable the bladder to void effectively. In contrast to skeletal muscles, these bundles are not highly aligned, rather they are oriented more heterogeneously throughout the bladder wall. In this work, for the first time, this regional orientation of the SMBs is quantified across the whole bladder, without the need for optical clearing or cryosectioning. Immunohistochemistry staining was utilized to visualize smooth muscle cell actin in multiphoton microscopy (MPM) images of bladder smooth muscle bundles (SMBs). Feature vectors for each pixel were generated using a range of filters, including Gaussian blur, Gaussian gradient magnitude, Laplacian of Gaussian, Hessian eigenvalues, structure tensor eigenvalues, Gabor, and Sobel gradients. A Random Forest classifier was subsequently trained to automate the segmentation of SMBs in the MPM images. Finally, the orientation of SMBs in each bladder region was quantified using the CT-FIRE package. This information is essential for biomechanical models of the bladder that include contractile elements.
- Published
- 2024
74. The SDSS-V Local Volume Mapper (LVM): Scientific Motivation and Project Overview
- Author
-
Drory, Niv, Blanc, Guillermo A., Kreckel, Kathryn, Sanchez, Sebastian F., Mejia-Narvaez, Alfredo, Johnston, Evelyn J., Jones, Amy M., Pellegrini, Eric W., Konidaris, Nicholas P., Herbst, Tom, Sanchez-Gallego, Jose, Kollmeier, Juna A., de Almeida, Florence, Barrera-Ballesteros, Jorge K., Bizyaev, Dmitry, Brownstein, Joel R., Saguer, Mar Canal i, Cherinka, Brian, Cioni, Maria-Rosa L., Congiu, Enrico, Cosens, Maren, Dias, Bruno, Donor, John, Egorov, Oleg, Egorova, Evgeniia, Froning, Cynthia S., Garcia, Pablo, Glover, Simon C. O., Greve, Hannah, Haeberle, Maximilian, Hoy, Kevin, Ibarra, Hector, Li, Jing, Klessen, Ralf S., Krishnarao, Dhanesh, Kumari, Nimisha, Long, Knox S., Mendez-Delgado, Jose Eduardo, Popa, Silvia Anastasia, Ramirez, Solange, Rix, Hans-Walter, Sanchez, Aurora Mata, Sankrit, Ravi, Sattler, Natascha, Sayres, Conor, Singh, Amrita, Stringfellow, Guy, Wachter, Stefanie, Watkins, Elizabeth Jayne, Wong, Tony, and Wofford, Aida
- Subjects
Astrophysics - Astrophysics of Galaxies - Abstract
We present the Sloan Digital Sky Survey V (SDSS-V) Local Volume Mapper (LVM). The LVM is an integral-field spectroscopic survey of the Milky Way, Magellanic Clouds, and of a sample of local volume galaxies, connecting resolved pc-scale individual sources of feedback to kpc-scale ionized interstellar medium (ISM) properties. The 4-year survey covers the southern Milky Way disk at spatial resolutions of 0.05 to 1 pc, the Magellanic Clouds at 10 pc resolution, and nearby large galaxies at larger scales totaling $>4300$ square degrees of sky, and more than 55M spectra. It utilizes a new facility of alt-alt mounted siderostats feeding 16 cm refractive telescopes, lenslet-coupled fiber-optics, and spectrographs covering 3600-9800A at R ~ 4000. The ultra-wide field IFU has a diameter of 0.5 degrees with 1801 hexagonally packed fibers of 35.3 arcsec apertures. The siderostats allow for a completely stationary fiber system, avoiding instability of the line spread function seen in traditional fiber feeds. Scientifically, LVM resolves the regions where energy, momentum, and chemical elements are injected into the ISM at the scale of gas clouds, while simultaneously charting where energy is being dissipated (via cooling, shocks, turbulence, bulk flows, etc.) to global scales. This combined local and global view enables us to constrain physical processes regulating how stellar feedback operates and couples to galactic kinematics and disk-scale structures, such as the bar and spiral arms, as well as gas in- and out-flows., Comment: 29 pages, 12 figures, accepted for publication in The Astronomical Journal
- Published
- 2024
75. The Quest for Educational Equity in Schools in Multicultural Australia
- Author
-
Noble, Greg and Watkins, Megan
- Published
- 2024
76. Discourses of Distrust : How Lack of Trust in the U.S. Health-Care System Shaped COVID-19 Vaccine Hesitancy
- Author
-
CASSELMAN-HONTALAS, AMY, ADAMS-SANTOS, DOMINIQUE, and WATKINS-HAYES, CELESTE
- Published
- 2024
77. Acting, Charting, and Fluency: Using a Modified SAFMEDS Procedure to Increase Recall in a Stage Actor and Non-Actor
- Author
-
Fragale, Demitria, Ruiz, Salvador, Newsome, Kendra Brooks, Day-Watkins, Jessica, and Verdun, Victoria
- Published
- 2025
- Full Text
- View/download PDF
78. The Impact of Vaccination on COVID-19, Influenza, and Respiratory Syncytial Virus-Related Outcomes: A Narrative Review
- Author
-
Debbag, Roberto, Rudin, Deborah, Ceddia, Francesca, and Watkins, John
- Published
- 2025
- Full Text
- View/download PDF
79. Making General Education Meaningful
- Author
-
James G. Martin Center for Academic Renewal and Watkins, Shannon
- Abstract
Higher education serves many purposes. One purpose dominates, however: to students, their parents, future employers, government officials, and many academic administrators, higher education is all about preparing students for the professional workforce. Other requirements, such as general education programs, are considered to be of lesser importance. In many cases, they are designed solely to support the primary goal of training professionals, providing generalized skills that can be translated to many professions. Yet treating general education programs as secondary constitutes a great loss of opportunity, as well-designed programs have the potential to help students become better citizens, deeper thinkers, and more moral people. In this report, the author explores actual learning processes at a primary level and shows why a tightly crafted general education that deliberately connects various types of knowledge and learning is vastly superior to one that that allows students wide latitude to choose among unconnected courses that may appear to be interesting at the time but offer little long-term insight. And is also preferable to one that attempts to teach skills without bothering with the content involved. This report should be read--and acted upon--by all policymakers, administrators, and academics who are truly concerned with the quality of education that colleges and universities provide.
- Published
- 2023
80. Bilateral femoral neck fractures in pregnancy suggestive of transient osteoporosis of the hip in a patient with hyperparathyroidism: a case report
- Author
-
Blake, Ryan J., Melemai, Vincent K., Fitzpatrick, Brody M., Hubbard, David F., Dietz, Matthew J., and Watkins, Colleen M.
- Published
- 2024
- Full Text
- View/download PDF
81. The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion
- Author
-
Nash, Will J., Man, Angela, McTaggart, Seanna, Baker, Kendall, Barker, Tom, Catchpole, Leah, Durrant, Alex, Gharbi, Karim, Irish, Naomi, Kaithakottil, Gemy, Ku, Debby, Providence, Aaliyah, Shaw, Felix, Swarbreck, David, Watkins, Chris, McCartney, Ann M., Formenti, Giulio, Mouton, Alice, Vella, Noel, von Reumont, Björn M., Vella, Adriana, and Haerty, Wilfried
- Published
- 2024
- Full Text
- View/download PDF
82. A STAT3–STING–IFN axis controls the metastatic spread of small cell lung cancer
- Author
-
Guanizo, Aleks C., Luong, Quinton, Jayasekara, W. Samantha N., de Geus, Eveline D., Inampudi, Chaitanya, Xue, Vincent Senyang, Chen, Jasmine, de Weerd, Nicole A., Matthews, Antony Y., Gantier, Michael P., Balic, Jesse J., Arulananda, Surein, Garama, Daniel J., Hertzog, Paul J., Ganju, Vinod, Watkins, D. Neil, Cain, Jason E., and Gough, Daniel J.
- Published
- 2024
- Full Text
- View/download PDF
83. Posttraumatic Stress Disorder and Substance Use Disorder Screening, Assessment, and Treatment
- Author
-
Patton, Samantha C., Watkins, Laura E., Killeen, Therese K., and Hien, Denise A.
- Published
- 2024
- Full Text
- View/download PDF
84. Implicit motor sequence learning using three-dimensional reaching movements with the non-dominant left arm
- Author
-
Smith, Charles R., Baird, Jessica F., Buitendorp, Joelle, Horton, Hannah, Watkins, Macie, and Stewart, Jill C.
- Published
- 2024
- Full Text
- View/download PDF
85. Trends in inpatient versus outpatient upper extremity fracture surgery from 2008 to 2021 and their implications for equitable access: a retrospective cohort study
- Author
-
Beagles, Clay B., Watkins, Ian T., Lechtig, Aron, Blazar, Philip, Chen, Neal C., and Lans, Jonathan
- Published
- 2024
- Full Text
- View/download PDF
86. Trends in pancreatic cancer mortality in the United States 1999–2020: a CDC database population-based study
- Author
-
Didier, Alexander J., Nandwani, Swamroop, Fahoury, Alan M., Craig, Daniel J., Watkins, Dean, Campbell, Andrew, Spencer, Caleb T., Batten, Macelyn, Vijendra, Divya, and Sutton, Jeffrey M.
- Published
- 2024
- Full Text
- View/download PDF
87. Assessment of arterial supply to the stomach after bariatric surgery using multidetector CT arteriography
- Author
-
Khalil, Adham, Gomez, Erin, Gowda, Prateek C., Weinstein, Robert M., Eberly, Hänel Watkins, Prologo, Frank J., Birkholz, James H., Sarwani, Nabeel E., Friedberg, Eric, Rogers, Ann M., and Weiss, Clifford R.
- Published
- 2024
- Full Text
- View/download PDF
88. “Let Us Begin Well Together”: A Preparation-Positivity-Purpose Checklist for Helping Beginning Supervisors Optimize the Start of Supervision
- Author
-
Watkins Jr., C. Edward, Cădariu, Ioana-Eva, and Vîşcu, Loredana-Ileana
- Published
- 2024
- Full Text
- View/download PDF
89. People with Intellectual Disabilities, Dysphagia and Post-Covid Syndrome
- Author
-
Watkins, Lance, Kulkarni, Amit, Webber, Emma, Bassett, Paul, Lamb, Kirsten, Sawhney, Indermeet, Laugharne, Richard, Heslop, Pauline, Jones, Angela, Napier, Geraldine, Crocker, Angela, Sivan, Manoj, and Shankar, Rohit
- Published
- 2024
- Full Text
- View/download PDF
90. Origins and impact of extrachromosomal DNA
- Author
-
Bailey, Chris, Pich, Oriol, Thol, Kerstin, Watkins, Thomas B. K., Luebeck, Jens, Rowan, Andrew, Stavrou, Georgia, Weiser, Natasha E., Dameracharla, Bhargavi, Bentham, Robert, Lu, Wei-Ting, Kittel, Jeanette, Yang, S. Y. Cindy, Howitt, Brooke E., Sharma, Natasha, Litovchenko, Maria, Salgado, Roberto, Hung, King L., Cornish, Alex J., Moore, David A., Houlston, Richard S., Bafna, Vineet, Chang, Howard Y., Nik-Zainal, Serena, Kanu, Nnennaya, McGranahan, Nicholas, Flanagan, Adrienne M., Mischel, Paul S., Jamal-Hanjani, Mariam, and Swanton, Charles
- Published
- 2024
- Full Text
- View/download PDF
91. Guidance for researchers and peer-reviewers on the ethical use of Large Language Models (LLMs) in scientific research workflows
- Author
-
Watkins, Ryan
- Published
- 2024
- Full Text
- View/download PDF
92. Love and Hate: The Flâneur and the Tourist
- Author
-
Nuvolati, Giampaolo, Watkins, Translated by Jamie, Translated by, Aguiar, Marian, Series Editor, Mathieson, Charlotte, Series Editor, Pearce, Lynne, Series Editor, Merriman, Peter, Editorial Board Member, Bissell, David, Editorial Board Member, Seiler, Cotten, Editorial Board Member, Livesey, Ruth, Editorial Board Member, Adey, Peter, Editorial Board Member, Daly, Nicholas, Editorial Board Member, Green-Simms, Lindsey, Editorial Board Member, Cresswell, Tim, Editorial Board Member, Grossman, Jonathan, Editorial Board Member, Frenay, Adrien, editor, Iacoli, Giulio, editor, and Quaquarelli, Lucia, editor
- Published
- 2025
- Full Text
- View/download PDF
93. The 'Tangential' Geographies of Ring Roads: Mobile Stories from the Margins of Contemporary Italian Cities
- Author
-
Peterle, Giada, Watkins, Translated by Jamie, Translated by, Aguiar, Marian, Series Editor, Mathieson, Charlotte, Series Editor, Pearce, Lynne, Series Editor, Merriman, Peter, Editorial Board Member, Bissell, David, Editorial Board Member, Seiler, Cotten, Editorial Board Member, Livesey, Ruth, Editorial Board Member, Adey, Peter, Editorial Board Member, Daly, Nicholas, Editorial Board Member, Green-Simms, Lindsey, Editorial Board Member, Cresswell, Tim, Editorial Board Member, Grossman, Jonathan, Editorial Board Member, Frenay, Adrien, editor, Iacoli, Giulio, editor, and Quaquarelli, Lucia, editor
- Published
- 2025
- Full Text
- View/download PDF
94. Maps and Walking: The Cartographic Representation of the Urban Environment in My Two Worlds by Sergio Chejfec
- Author
-
Papotti, Davide, Watkins, Translated by Jamie, Translated by, Aguiar, Marian, Series Editor, Mathieson, Charlotte, Series Editor, Pearce, Lynne, Series Editor, Merriman, Peter, Editorial Board Member, Bissell, David, Editorial Board Member, Seiler, Cotten, Editorial Board Member, Livesey, Ruth, Editorial Board Member, Adey, Peter, Editorial Board Member, Daly, Nicholas, Editorial Board Member, Green-Simms, Lindsey, Editorial Board Member, Cresswell, Tim, Editorial Board Member, Grossman, Jonathan, Editorial Board Member, Frenay, Adrien, editor, Iacoli, Giulio, editor, and Quaquarelli, Lucia, editor
- Published
- 2025
- Full Text
- View/download PDF
95. Implications on star-formation-rate indicators from HII regions and diffuse ionised gas in the M101 Group
- Author
-
Watkins, A. E., Mihos, J. C., Harding, P., and Garner III, R.
- Subjects
Astrophysics - Astrophysics of Galaxies - Abstract
We examine the connection between diffuse ionised gas (DIG), HII regions, and field O and B stars in the nearby spiral M101 and its dwarf companion NGC 5474 using ultra-deep H$\alpha$ narrow-band imaging and archival GALEX UV imaging. We find a strong correlation between DIG H$\alpha$ surface brightness and the incident ionising flux leaked from the nearby HII regions, which we reproduce well using simple Cloudy simulations. While we also find a strong correlation between H$\alpha$ and co-spatial FUV surface brightness in DIG, the extinction-corrected integrated UV colours in these regions imply stellar populations too old to produce the necessary ionising photon flux. Combined, this suggests that HII region leakage, not field OB stars, is the primary source of DIG in the M101 Group. Corroborating this interpretation, we find systematic disagreement between the H$\alpha$- and FUV-derived star formation rates (SFRs) in the DIG, with SFR$_{{\rm H}\alpha} < $SFR$_{\rm FUV}$ everywhere. Within HII regions, we find a constant SFR ratio of 0.44 to a limit of $\sim10^{-5}$ M$_{\odot}$~yr$^{-1}$. This result is in tension with other studies of star formation in spiral galaxies, which typically show a declining SFR$_{{\rm H}\alpha}/$SFR$_{\rm FUV}$ ratio at low SFR. We reproduce such trends only when considering spatially averaged photometry that mixes HII regions, DIG, and regions lacking H$\alpha$ entirely, suggesting that the declining trends found in other galaxies may result purely from the relative fraction of diffuse flux, leaky compact HII regions, and non-ionising FUV-emitting stellar populations in different regions within the galaxy., Comment: 17 pages, 12 figures, accepted for publication in MNRAS
- Published
- 2024
96. Introducing v0.5 of the AI Safety Benchmark from MLCommons
- Author
-
Vidgen, Bertie, Agrawal, Adarsh, Ahmed, Ahmed M., Akinwande, Victor, Al-Nuaimi, Namir, Alfaraj, Najla, Alhajjar, Elie, Aroyo, Lora, Bavalatti, Trupti, Bartolo, Max, Blili-Hamelin, Borhane, Bollacker, Kurt, Bomassani, Rishi, Boston, Marisa Ferrara, Campos, Siméon, Chakra, Kal, Chen, Canyu, Coleman, Cody, Coudert, Zacharie Delpierre, Derczynski, Leon, Dutta, Debojyoti, Eisenberg, Ian, Ezick, James, Frase, Heather, Fuller, Brian, Gandikota, Ram, Gangavarapu, Agasthya, Gangavarapu, Ananya, Gealy, James, Ghosh, Rajat, Goel, James, Gohar, Usman, Goswami, Sujata, Hale, Scott A., Hutiri, Wiebke, Imperial, Joseph Marvin, Jandial, Surgan, Judd, Nick, Juefei-Xu, Felix, Khomh, Foutse, Kailkhura, Bhavya, Kirk, Hannah Rose, Klyman, Kevin, Knotz, Chris, Kuchnik, Michael, Kumar, Shachi H., Kumar, Srijan, Lengerich, Chris, Li, Bo, Liao, Zeyi, Long, Eileen Peters, Lu, Victor, Luger, Sarah, Mai, Yifan, Mammen, Priyanka Mary, Manyeki, Kelvin, McGregor, Sean, Mehta, Virendra, Mohammed, Shafee, Moss, Emanuel, Nachman, Lama, Naganna, Dinesh Jinenhally, Nikanjam, Amin, Nushi, Besmira, Oala, Luis, Orr, Iftach, Parrish, Alicia, Patlak, Cigdem, Pietri, William, Poursabzi-Sangdeh, Forough, Presani, Eleonora, Puletti, Fabrizio, Röttger, Paul, Sahay, Saurav, Santos, Tim, Scherrer, Nino, Sebag, Alice Schoenauer, Schramowski, Patrick, Shahbazi, Abolfazl, Sharma, Vin, Shen, Xudong, Sistla, Vamsi, Tang, Leonard, Testuggine, Davide, Thangarasa, Vithursan, Watkins, Elizabeth Anne, Weiss, Rebecca, Welty, Chris, Wilbers, Tyler, Williams, Adina, Wu, Carole-Jean, Yadav, Poonam, Yang, Xianjun, Zeng, Yi, Zhang, Wenhui, Zhdanov, Fedor, Zhu, Jiacheng, Liang, Percy, Mattson, Peter, and Vanschoren, Joaquin
- Subjects
Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
This paper introduces v0.5 of the AI Safety Benchmark, which has been created by the MLCommons AI Safety Working Group. The AI Safety Benchmark has been designed to assess the safety risks of AI systems that use chat-tuned language models. We introduce a principled approach to specifying and constructing the benchmark, which for v0.5 covers only a single use case (an adult chatting to a general-purpose assistant in English), and a limited set of personas (i.e., typical users, malicious users, and vulnerable users). We created a new taxonomy of 13 hazard categories, of which 7 have tests in the v0.5 benchmark. We plan to release version 1.0 of the AI Safety Benchmark by the end of 2024. The v1.0 benchmark will provide meaningful insights into the safety of AI systems. However, the v0.5 benchmark should not be used to assess the safety of AI systems. We have sought to fully document the limitations, flaws, and challenges of v0.5. This release of v0.5 of the AI Safety Benchmark includes (1) a principled approach to specifying and constructing the benchmark, which comprises use cases, types of systems under test (SUTs), language and context, personas, tests, and test items; (2) a taxonomy of 13 hazard categories with definitions and subcategories; (3) tests for seven of the hazard categories, each comprising a unique set of test items, i.e., prompts. There are 43,090 test items in total, which we created with templates; (4) a grading system for AI systems against the benchmark; (5) an openly available platform, and downloadable tool, called ModelBench that can be used to evaluate the safety of AI systems on the benchmark; (6) an example evaluation report which benchmarks the performance of over a dozen openly available chat-tuned language models; (7) a test specification for the benchmark.
- Published
- 2024
97. Bright Star Subtraction Pipeline for LSST: Progress Review
- Author
-
Bazkiaei, Amir E., Kelvin, Lee S., Brough, Sarah, O'Toole, Simon J., Watkins, Aaron, and Schmitz, Morgen A.
- Subjects
Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
We present the Bright Star Subtraction (BSS) pipeline for the Vera C. Rubin Observatory's Legacy Survey of Space and Time (LSST). This pipeline generates an extended PSF model using observed stars and subtracts the model from the bright stars in LSST data. When testing the pipeline on Hyper Suprime-Cam (HSC) data, we find that the shape of the extended PSF model depends on the location of the detector on the camera's focal plane. The closer a detector is to the edge of the focal plane, the less the extended PSF model is circularly symmetric. We introduce an algorithm that allows the user to consider the location dependency of the model., Comment: 4 pages, 1 figure; Astronomical Data Analysis Software & Systems XXXIII proceeding
- Published
- 2024
98. Real-time Geoinformation Systems to Improve the Quality, Scalability, and Cost of Internet of Things for Agri-environment Research
- Author
-
Runck, Bryan C., Schulz, Bobby, Bishop, Jeff, Carlson, Nathan, Chantigian, Bryan, Deters, Gary, Erdmann, Jesse, Ewing, Patrick M., Felzan, Michael, Fu, Xiao, Greyling, Jan, Hogan, Christopher J., Hollman, Andrew, Joglekar, Ali, Junker, Kris, Kantar, Michael, Kaunda, Lumbani, Krishna, Mohana, Lynch, Benjamin, Marchetto, Peter, Marsolek, Megan, McKay, Troy, Morris, Brad, Niaghi, Ali Rashid, Pamulaparthy, Keerthi, Pardey, Philip, Piotrowski, Ann, Poudyal, Christina, Prather, Tom, Raghavan, Barath, Reiter, Maggie, Rosen, Lucas, Salazar, Benjamin, Scobbie, Andrew, Sharma, Vasudha, Silverstein, Kevin A. T., Singh, Gurparteet, Strock, Jeff, Subedi, Samikshya, Tang, Evan, Turturillo, Gianna, Watkins, Eric, Webster, Blake, and Wilgenbusch, James
- Subjects
Quantitative Biology - Quantitative Methods - Abstract
With the increasing emphasis on machine learning and artificial intelligence to drive knowledge discovery in the agricultural sciences, spatial internet of things (IoT) technologies have become increasingly important for collecting real-time, high resolution data for these models. However, managing large fleets of devices while maintaining high data quality remains an ongoing challenge as scientists iterate from prototype to mature end-to-end applications. Here, we provide a set of case studies using the framework of technology readiness levels for an open source spatial IoT system. The spatial IoT systems underwent 3 major and 14 minor system versions, had over 2,727 devices manufactured both in academic and commercial contexts, and are either in active or planned deployment across four continents. Our results show the evolution of a generalizable, open source spatial IoT system designed for agricultural scientists, and provide a model for academic researchers to overcome the challenges that exist in going from one-off prototypes to thousands of internet-connected devices., Comment: 20 pages, 5 figures, 1 table
- Published
- 2024
99. Encoding of lexical tone in self-supervised models of spoken language
- Author
-
Shen, Gaofei, Watkins, Michaela, Alishahi, Afra, Bisazza, Arianna, and Chrupała, Grzegorz
- Subjects
Computer Science - Computation and Language ,Electrical Engineering and Systems Science - Audio and Speech Processing - Abstract
Interpretability research has shown that self-supervised Spoken Language Models (SLMs) encode a wide variety of features in human speech from the acoustic, phonetic, phonological, syntactic and semantic levels, to speaker characteristics. The bulk of prior research on representations of phonology has focused on segmental features such as phonemes; the encoding of suprasegmental phonology (such as tone and stress patterns) in SLMs is not yet well understood. Tone is a suprasegmental feature that is present in more than half of the world's languages. This paper aims to analyze the tone encoding capabilities of SLMs, using Mandarin and Vietnamese as case studies. We show that SLMs encode lexical tone to a significant degree even when they are trained on data from non-tonal languages. We further find that SLMs behave similarly to native and non-native human participants in tone and consonant perception studies, but they do not follow the same developmental trajectory., Comment: Accepted to NAACL 2024
- Published
- 2024
100. Shapes of dark matter haloes with discrete globular cluster dynamics: The example of NGC 5128 (Centaurus A)
- Author
-
Veršič, Tadeja, Rejkuba, Marina, Arnaboldi, Magda, Gerhard, Ortwin, Pulsoni, Claudia, Valenzuela, Lucas M., Hartke, Johanna, Watkins, Laura L., van de Ven, Glenn, and Thater, Sabine
- Subjects
Astrophysics - Astrophysics of Galaxies - Abstract
Within the $\Lambda$CDM cosmology, dark matter haloes are expected to deviate from spherical symmetry. Constraining the halo shapes at large galactocentric distances is challenging due to the low density of luminous tracers. The well-studied early-type galaxy NGC 5128 (Centaurus A - CenA), has a large number of radial velocities for globular clusters (GCs) and planetary nebulae (PNe) of its extended stellar halo. In this work, we aim to determine the deviation from spherical symmetry of the dark matter halo of CenA at 5 $R_{\rm e}$ using its GCs as kinematic tracers. We used the largest photometric catalogue of GC candidates to accurately characterise the spatial distribution of the relaxed population and investigated the presence of non-relaxed structures in the kinematic catalogue of GCs using the relaxed point-symmetric velocity field as determined by the host's PNe population. We used anisotropic Jeans modelling under axisymmetric assumptions together with the Gaussian likelihood and GCs as discrete tracers. The gravitational potential is generated by flattened stellar and dark matter distributions. We leveraged different orbital properties of the blue and red GCs to model them separately. We find that discrete kinematics of the GCs are consistent with being drawn from an underlying relaxed velocity field determined from PNe. The best-fit parameters of the gravitational potential recovered from the blue and red GCs separately agree well and the joint results are: $M_{200} = 1.86^{1.61}_{-0.69}\times 10^{12}$ M$_\odot$, $M_\star/L_{\rm B} = 2.98^{+0.96}_{-0.78}$ and the flattening $q_{\rm DM} = 1.45^{+0.78}_{-0.53}$. Both GC populations show mild rotation, with red having a slightly stronger rotational signature and radially biased orbits, and blue GCs preferring negative velocity anisotropy. An oblate or a spherical dark matter halo of CenA is strongly disfavoured by our modelling., Comment: 22 pages, 17 figures, 8 tables, accepted for publication in A&A
- Published
- 2024
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.