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Community science 2023年第2期2卷

作者： K. L. Akerlof K. M. F. Timm A. Chase E. T. Cloyd E. Heath B. A. McGhghy A. Bamzai-Dodson G. Bogard S. Carter J. Garron M. Gavazzi N. Kettle M. Labriole J. S. Littell M. Madajewicz J. Reyes L. Rivers III J. L. Sheats C. F. Simpson R. C. Toohey Department of Environmental Science & Policy George Mason University Fairfax VA USA Contribution: Conceptualization Funding acquisition Investigation Methodology Project administration Data curation Formal analysis Writing - original draft Writing - review & editing International Arctic Research Center University of Alaska Fairbanks Fairbanks AK USA Contribution: Conceptualization Funding acquisition Investigation Methodology Writing - original draft Writing - review & editing Contribution: Investigation Writing - original draft Writing - review & editing Department of Energy and Environment Government of the District of Columbia Washington DC USA Contribution: Conceptualization Funding acquisition Investigation Writing - original draft Writing - review & editing American Association for the Advancement of Science Washington DC USA American Geophysical Union Washington DC USA Contribution: Writing - original draft Writing - review & editing U.S. Geological Survey North Central Climate Adaptation Science Center Boulder CO USA U.S. Geological Survey National Climate Adaptation Science Center Reston VA USA U.S. Department of Agriculture Research Triangle Park NC USA New York Hall of Science Queens NY USA U.S. Geological Survey Alaska Climate Adaptation Science Center Anchorage AK USA Center for Climate Systems Research The Climate School Columbia University New York NY USA NOAA Climate Adaptation Partnerships (CAP) Consortium for Climate Risk in the Urban Northeast (CCRUN) New York NY USA U.S. Department of Agriculture Washington DC USA Environmental Protection Agency Office of Research and Development Research Triangle Park NC USA Department of Social Behavioral and Population Sciences Tulane University School of Public Health &Tropical Medicine New Orleans LA USA Aspen Institute Science & Society Program Washington DC USA National Oceanic and Atmospheric Administration Climate Adaptation Partnerships Silver Spring MD USA

Co-production practices are increasingly being adopted in research conducted for the purpose of societal impact. However, the ways in which co-production is conducted can perpetuate long-standing inequity and inequality. This study investigates which principles of co-production design are perceived to advance more equitable processes and outcomes based on the experiences of participants in three projects funded by U.S. federal programs that support decision-relevant climate science, along with others engaged in co-production efforts. We found three distinct perspectives: (a) Ways of Knowing and Power; (b) Participants and Interactions; and (c) science as Capacity Building. Each viewpoint differentially weights the salience of statements associated with five dimensions of co-production practices: (a) outcomes; (b) power; (c) place-based, community rights and respect; (d) audiences and participation; and (e) interactions. In the final stage of the study, we hosted a workshop of participants representing various roles in co-production efforts to vet and discuss each perspective. We found that the perspectives remained distinct after each of the groups selected core statements that reflect their views. The degree of variation across the three perspectives suggests that co-production processes would benefit from an initial discussion of, and decisions about, rules of engagement to ensure that participants view the process as equitable.

关键词： co-production equity climate change federal research programs

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The K2 & TESS Synergy III: search and rescue of the lost ephemeris for K2’s first planet

arXiv

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arXiv 2024年

作者： Thygesen, Erica Rodriguez, Joseph E. Beurs, Zoë L.D.E. Vanderburg, Andrew Livingston, John H. Irwin, Jonathon Venner, Alexander Cretignier, Michael Collins, Karen A. Bieryla, Allyson Charbonneau, David Crossfield, Ian J.M. Dumusque, Xavier Kielkopf, John Latham, David W. Werner, Michael Center for Data Intensive and Time Domain Astronomy Department of Physics and Astronomy Michigan State University East LansingMI48824 United States Department of Earth Atmospheric and Planetary Sciences Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics Kavli Institute for Astrophysics and Space Research Massachusetts Institute of Technology CambridgeMA02139 United States Astrobiology Center 2-21-1 Osawa Mitaka Tokyo181-8588 Japan National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Astronomical Science Program Graduate University for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Institute of Astronomy University of Cambridge Madingley Road CambridgeCB3 0HA United Kingdom Centre for Astrophysics University of Southern Queensland West Street ToowoombaQLD4350 Australia Department of Physics University of Oxford OxfordOX13RH United Kingdom Center for Astrophysics Harvard & Smithsonian 60 Garden St CambridgeMA02138 United States Department of Physics and Astronomy University of Kansas LawrenceKS66045 United States Geneva Observatory University of Geneva Chemin des Mailettes 51 Versoix1290 Switzerland Department of Physics and Astronomy University of Louisville LouisvilleKY40292 United States NASA Jet Propulsion Laboratory PasadenaCA United States

K2-2 b/HIP 116454 b, the first exoplanet discovery by K2 during its Two-Wheeled Concept Engineering Test, is a sub-Neptune (formula presented) orbiting a relatively bright (KS = 8.03) K-dwarf on a 9.1 day period. Unfortunately, due to a spurious follow-up transit detection and ephemeris degradation, the transit ephemeris for this planet was lost. In this work, we recover and refine the transit ephemeris for K2-2 b, showing a ∼40σ discrepancy from the discovery results. To accurately measure the transit ephemeris and update the parameters of the system, we jointly fit space-based photometric observations from NASA’s K2, TESS, and Spitzer missions with new photometric observations from the ground, as well as radial velocities from HARPS-N that are corrected for stellar activity using a new modeling technique. Ephemerides becoming lost or significantly degraded, as is the case for most transiting planets, highlights the importance of systematically updating transit ephemerides with upcoming large efforts expected to characterize hundreds of exoplanet atmospheres. K2-2 b sits at the high-mass peak of the known radius valley for sub-Neptunes, and is now well-suited for transmission spectroscopy with current and future facilities. Our updated transit ephemeris will ensure no more than a 13-minute uncertainty through 2030. Copyright © 2024, The Authors. All rights reserved.

关键词： NASA

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P59 Generation and characterization of a novel XMEA mouse model and pharmacological evaluation of autophagy antagonists

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Neuromuscular Disorders 2023年 33卷 S73-S73页

作者： Karuppasamy, M. English, K. Sanders, V. Lopez, M. Kaur, G. Worthey, L. Huang, L. Dowling, J. Alexander, M. Division of Neurology Dept Paediatrics Univ Alabama at Birmingham and Children's of Alabama Birmingham USA Dept Genetics Univ Alabama at Birmingham USA Center for Computational Genomics and Data Science at Children's of Alabama Birmingham USA Program for Genetics and Genome Biology Hosp for Sick Children Toronto Canada Div Neurology Hosp for Sick Children Toronto Canada Depts Molecular Genetics University of Toronto Canada Dept Paediatrics University of Toronto Canada UAB Center for Exercise Medicine University of Alabama at Birmingham USA Civitan International Research Center University of Alabama at Birmingham USA UAB Center for Neurodegeneration and Experimental Therapeutics (CNET)) Birmingham USA

X-linked myopathy with excessive autophagy (XMEA) is a rare autophagic vacuolar myopathy, characterized by progressive proximal weakness, internalization of capillaries, muscle fiber splitting, high levels of serum creatine kinase and accumulation of cytoplasmic autophagic vacuoles. VMA21 pathogenic mutations reduce the efficiency of autolysosome to acidify proteins resulting in the accumulation of vacuolar inclusions in XMEA patients. The VMA21 protein maintains the V-ATPase protein pump, which is responsible for the acidification of lysosomes, and is disrupted in XMEA. VMA21 mutations lead to elevated lysosomal pH and a defective cell debris degradation system. Consequently, elevated autophagolysosomes move to the surface of myofibers, combine with the sarcolemma and release the cell debris around myofibers. The muscles in the shoulders, thighs and hips are predominantly affected resulting in the eventual loss of ambulation. The consequence of VMA21 mutations on other systems including the cardiac, respiratory and central nervous systems is unknown. Currently, no animal model for XMEA exists, and the lack of a suitable XMEA animal model is a significant barrier towards any effective treatment. The main objective of this study is to characterize our novel XMEA patient-based Vma21 KI mice which contain a Vma21 c.164G>T insertion resulting in the retention of a splice sequence thereby disrupting the reading frame leading towards the degradation of the VMA21 protein. We identified selective autophagy antagonists as therapeutically beneficial in blocking XMEA pathologies in our XMEA model zebrafish and expanded therapeutic testing of our lead hits into our Vma21 KI/XMEA mice. One FDA-approved lead compound, edaravone, an oxidative stress and autophagy inhibitor in ALS, demonstrated significant therapeutic correction in our XMEA zebrafish and we have expanded these studies into our Vma21 KI/XMEA mice. Therapeutic and basic science knowledge gained from our studies could

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1650P Identification of potential targets in pancreatic adenocarcinoma: The KRAS Wild-Type subset

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Annals of Oncology 2023年 34卷 S910-S910页

作者： D.A. Acosta Eyzaguirre C. Fabregat-Franco F. Castet D.E. López Valbuena G. Castillo S. Vega S. Aguilar Izquierdo A. Sierra T. Tian A. Vivancos R. Dienstmann T. Macarulla Gastrointestinal Cancer Unit Vall d’Hebron University Hospital Barcelona Spain Medical Oncology Vall d’Hebron University Hospital Barcelona Spain VHIO Vall d’Hebron Institute of Oncology (VHIO) Barcelona Spain VHIOTECA & Prescreening Program Vall d’Hebron Institute of Oncology (VHIO) Barcelona Spain Upper GI Cancer Translational Research Group Vall d’Hebron Institute of Oncology (VHIO) Barcelona Spain Cancer Genomics Group Vall d’Hebron Institute of Oncology (VHIO) Barcelona Spain Oncology Data Science (ODysSey) Group Vall d’Hebron Institue of Oncology (VHIO) Barcelona Spain

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Hyper-molecules: On the representation and recovery of dynamical structures, with application to flexible macro-molecular structures in cryo-EM

arXiv

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arXiv 2019年

作者： Lederman, Roy R. Andén, Joakim Singer, Amit Department of Statistics and Data Science Yale University New HavenCT United States Center for Computational Mathematics Flatiron Institute New YorkNY United States Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States

Cryo-electron microscopy (cryo-EM), the subject of the 2017 Nobel Prize in Chemistry, is a technology for determining the 3-D structure of macromolecules from many noisy 2-D projections of instances of these macromolecules, whose orientations and positions are unknown. The molecular structures are not rigid objects, but flexible objects involved in dynamical processes. The different conformations are exhibited by different instances of the macromolecule observed in a cryo-EM experiment, each of which is recorded as a particle image. The range of conformations and the conformation of each particle are not known a priori;one of the great promises of cryo-EM is to map this conformation space. Remarkable progress has been made in determining rigid structures from homogeneous samples of molecules in spite of the unknown orientation of each particle image and significant progress has been made in recovering a few distinct states from mixtures of rather distinct conformations, but more complex heterogeneous samples remain a major challenge. We introduce the "hyper-molecule" framework for modeling structures across different states of heterogeneous molecules, including continuums of states. The key idea behind this framework is representing heterogeneous macromolecules as high-dimensional objects, with the additional dimensions representing the conformation space. This idea is then refined to model properties such as localized heterogeneity. In addition, we introduce an algorithmic framework for recovering such maps of heterogeneous objects from experimental data using a Bayesian formulation of the problem and Markov chain Monte Carlo (MCMC) algorithms to address the computational challenges in recovering these high dimensional hyper-molecules. We demonstrate these ideas in a prototype applied to synthetic data. Copyright © 2019, The Authors. All rights reserved.

关键词： Medical imaging

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Visualizing the PHATE of neural networks

arXiv

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arXiv 2019年

作者： Gigante, Scott Krishnaswamy, Smita Charles, Adam S. Mishne, Gal Comp. Biol. Bioinf. Program Yale University New HavenCT06511 Depts. of Genetics and Computer Science Yale University New HavenCT06520 Princeton Neuroscience Institute Princeton University PrincetonNJ08544 Halıcıoglu Data Science Institute University of California San Diego San DiegoCA92093

Understanding why and how certain neural networks outperform others is key to guiding future development of network architectures and optimization methods. To this end, we introduce a novel visualization algorithm that reveals the internal geometry of such networks: Multislice PHATE (M-PHATE), the first method designed explicitly to visualize how a neural network's hidden representations of data evolve throughout the course of training. We demonstrate that our visualization provides intuitive, detailed summaries of the learning dynamics beyond simple global measures (i.e., validation loss and accuracy), without the need to access validation data. Furthermore, M-PHATE better captures both the dynamics and community structure of the hidden units as compared to visualization based on standard dimensionality reduction methods (e.g., ISOMAP, t-SNE). We demonstrate M-PHATE with two vignettes: continual learning and generalization. In the former, the M-PHATE visualizations display the mechanism of "catastrophic forgetting" which is a major challenge for learning in task-switching contexts. In the latter, our visualizations reveal how increased heterogeneity among hidden units correlates with improved generalization performance. An implementation of M-PHATE, along with scripts to reproduce the figures in this paper, is available at https://***/scottgigante/M-PHATE. Copyright © 2019, The Authors. All rights reserved.

关键词： Visualization

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Association of COVID19-induced anosmia and ageusia with depression and suicidal ideation

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Journal of Affective Disorders Reports 2021年 5卷 100156-100156页

作者： Yom-Tov, Elad Lekkas, Damien Jacobson, Nicholas C. Faculty of Industrial Engineering and Management Technion - Israel Institute of Technology Haifa 3200003 Israel Center for Technology and Behavioral Health Geisel School of Medicine Dartmouth College 46 Centerra Parkway EverGreen Center Suite 315 Lebanon 03756 NH United States Quantitative Biomedical Sciences Program Dartmouth College NH United States Department of Biomedical Data Science Geisel School of Medicine Dartmouth College Williamson Building 3rd Floor 1 Medical Center Drive Lebanon 03756 NH United States Department of Psychiatry Geisel School of Medicine Dartmouth College 1 Medical Center Drive Lebanon 03756 NH United States

Background: Clinical reports from patients suffering from the novel coronavirus (COVID-19) reflect a high prevalence of sensory deprivation or loss pertaining to smell (dysosmia/anosmia) and/or taste (dysgeusia/ageusia). Given the importance of the senses to daily functioning and personal experience, the mental health consequences of these symptoms warrant further attention. Methods: A cohort of Reddit users posting within the /r/covid19positive subforum (N = 15,821) was leveraged to analyze instantaneous risk of transition to a state of suicidal ideation or depression using Cox proportional-hazards models. Risk transition was defined by posts made in suicide- or depression-related forums, or mentions of relevant phrases with and without mention of anosmia/ageusia in /r/covid19positive. Self-diagnosis of COVID-19 was also modeled as a separate and simultaneous predictor of mental health risk. Results: Mention of anosmia/ageusia was significantly associated with transition to a risk state. Users with a history of anosmia/ageusia-related posts and who self-identified as COVID-19 positive had 30% higher instantaneous risk relative to others. The highest increase in instantaneous risk of suicidal ideation or depression occurred more than 100 days after first posting in /r/covid19positive. Limitations: Use of self-diagnosed disease as well as a broad array of anosmia/ageusia-related terminology may entail both information bias and overestimates of symptom incidence. Conclusions: The specific effects of COVID-19 on the senses may have long-term implications for patient mental health well-being beyond the primary recovery period. Future work is needed to investigate the longitudinal mental health burden of residual COVID-19 symptom presentation. © 2021

关键词： Ageusia Anosmia Coronavirus (COVID-19) Depression Social network Suicidal ideation

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The EB-correlation in Resolved Polarized Images: Connections to Astrophysics of Black Holes

arXiv

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arXiv 2023年

作者： Emami, Razieh Doeleman, Sheperd S. Wielgus, MacIek Chang, Dominic Chatterjee, Koushik Smith, Randall Liska, Matthew Steiner, James F. Ricarte, Angelo Narayan, Ramesh Tremblay, Grant Finkbeiner, Douglas Hernquist, Lars Chan, Chi-Kwan Blackburn, Lindy Prather, Ben S. Tiede, Paul Broderick, Avery E. Vogelsberger, Mark Alcock, Charles Roelofs, Freek Center for Astrophysics Harvard & Smithsonian 60 Garden Street CambridgeMA02138 United States Black Hole Initiative Harvard University 20 Garden Street CambridgeMA02138 United States Max-Planck-Institut für Radioastronomie Auf dem Hügel 69 BonnD-53121 Germany Steward Observatory Department of Astronomy University of Arizona 933 N. Cherry Ave. TucsonAZ85721 United States Data Science Institute University of Arizona 1230 N. Cherry Ave. TucsonAZ85721 United States Program in Applied Mathematics University of Arizona 617 N. Santa Rita TucsonAZ85721 United States CCS-2 Los Alamos National Laboratory P.O. Box 1663 Los AlamosNM87545 United States Perimeter Institute for Theoretical Physics 31 Caroline Street North WaterlooONN2L 2Y5 Canada Department of Physics and Astronomy University of Waterloo 200 University Avenue West WaterlooONN2L 3G1 Canada Department of Physics Kavli Institute for Astrophysics and Space Research Massachusetts Institute of Technology CambridgeMA02139 United States

We present an in-depth analysis of a newly proposed correlation function in visibility space, between the E and B modes of the linear polarization, hereafter the EB-correlation, for a set of time-averaged GRMHD simulations compared with the phase map from different semi-analytic models as well as the Event Horizon Telescope (EHT) 2017 data for M87∗source. We demonstrate that the phase map of the time-averaged EB-correlation contains novel information that might be linked to the BH spin, accretion state and the electron temperature. A detailed comparison with a semi-analytic approach with different azimuthal expansion modes shows that to recover the morphology of the real/imaginary part of the correlation function and its phase, we require higher orders of these azimuthal modes. To extract the phase features, we propose to use the Zernike polynomial reconstruction developing an empirical metric to break degeneracies between models with different BH spins that are qualitatively similar. We use a set of different geometrical ring models with various magnetic and velocity field morphologies and show that both the image space and visibility based EB-correlation morphologies in MAD simulations can be explained with simple fluid and magnetic field geometries as used in ring models. SANEs by contrast are harder to model, demonstrating that the simple fluid and magnetic field geometries of ring models are not sufficient to describe them owing to higher Faraday Rotation depths. A qualitative comparison with the EHT data demonstrates that some of the features in the phase of EB-correlation might be well explained by the current models for BH spins as well as electron temperatures, while others may require a larger theoretical surveys. © 2023, CC BY.

关键词： Polarization

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Recurrence quantification analysis of dynamic brain networks

arXiv

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arXiv 2020年

作者： Lopes, Marinho A. Zhang, Jiaxiang Krzemiński, Dominik Hamandi, Khalid Chen, Qi Livi, Lorenzo Masuda, Naoki Department of Engineering Mathematics University of Bristol BS8 1UB United Kingdom Cardiff University Brain Research Imaging Centre School of Psychology Cardiff University CardiffCF24 4HQ United Kingdom Center for Studies of Psychological Application School of Psychology South China Normal University Guangzhou510631 China Departments of Computer Science and Mathematics University of Manitoba WinnipegMBR3T 2N2 Canada Department of Computer Science College of Engineering Mathematics and Physical Sciences University of Exeter ExeterEX4 4QF United Kingdom Department of Mathematics University at Buffalo State University of New York United States Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York United States

Evidence suggests that brain network dynamics is a key determinant of brain function and dysfunction. Here we propose a new framework to assess the dynamics of brain networks based on recurrence analysis. Our framework uses recurrence plots and recurrence quantification analysis to characterize dynamic networks. For resting-state magnetoencephalographic dynamic functional networks (dFNs), we have found that functional networks recur more quickly in people with epilepsy than healthy controls. This suggests that recurrence of dFNs may be used as a biomarker of epilepsy. For stereo electroencephalography data, we have found that dFNs involved in epileptic seizures emerge before seizure onset, and recurrence analysis allows us to detect seizures. We further observe distinct dFNs before and after seizures, which may inform neurostimulation strategies to prevent seizures. Our framework can also be used for understanding dFNs in brain function in health and other neurological disorders. Copyright © 2020, The Authors. All rights reserved.

关键词： Electroencephalography

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Skater’s dilemma

arXiv

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arXiv 2020年

作者： Ichinose, Genki Miyagawa, Daiki Ito, Junji Masuda, Naoki Department of Mathematical and Systems Engineering Shizuoka University 3-5-1 Johoku Naka-ku Hamamatsu432-8561 Japan Skating Club Yamanashi Gakuin University 2-4-5 Sakaori Kofu Yamanashi400-8575 Japan Department of Mathematics University at Buffalo State University of New York BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York BuffaloNY14260-5030 United States

In some athletic races, such as cycling and types of speed skating races, athletes have to complete a relatively long distance at a high speed in the presence of direct opponents. To win such a race, athletes are motivated to hide behind others to suppress energy consumption before a final moment of the race. This situation seems to produce a social dilemma: players want to hide behind others, whereas if a group of players attempts to do so, they may all lose to other players that overtake them. To support that speed skaters are involved in such a social dilemma, we analyzed video footage data for 14 mass start skating races to find that skaters that hid behind others to avoid air resistance for a long time before the final lap tended to win. Furthermore, the finish rank of the skaters in mass start races was independent of the record of the same skaters in time-trial races measured in the absence of direct opponents. The results suggest that how to strategically cope with a skater’s dilemma may be a key determinant for winning long-distance and high-speed races with direct *** Codes 91A80 Copyright © 2020, The Authors. All rights reserved.

关键词： Game theory

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