272,705 results on '"A. A. Cole"'
Search Results
102. Membrane curvature sensing and symmetry breaking of the M2 proton channel from Influenza A.
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Lincoff, James, Helsell, Cole, Marcoline, Frank, Natale, Andrew, and Grabe, Michael
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M2 channel ,elasticity theory ,influenza ,membrane curvature ,molecular biophysics ,negative Gaussian curvature ,simulation ,structural biology ,viruses ,Viral Matrix Proteins ,Molecular Dynamics Simulation ,Cell Membrane ,Influenza A virus ,Lipid Bilayers ,Protein Conformation ,Viroporin Proteins - Abstract
The M2 proton channel aids in the exit of mature influenza viral particles from the host plasma membrane through its ability to stabilize regions of high negative Gaussian curvature (NGC) that occur at the neck of budding virions. The channels are homo-tetramers that contain a cytoplasm-facing amphipathic helix (AH) that is necessary and sufficient for NGC generation; however, constructs containing the transmembrane spanning helix, which facilitates tetramerization, exhibit enhanced curvature generation. Here, we used all-atom molecular dynamics (MD) simulations to explore the conformational dynamics of M2 channels in lipid bilayers revealing that the AH is dynamic, quickly breaking the fourfold symmetry observed in most structures. Next, we carried out MD simulations with the protein restrained in four- and twofold symmetric conformations to determine the impact on the membrane shape. While each pattern was distinct, all configurations induced pronounced curvature in the outer leaflet, while conversely, the inner leaflets showed minimal curvature and significant lipid tilt around the AHs. The MD-generated profiles at the protein-membrane interface were then extracted and used as boundary conditions in a continuum elastic membrane model to calculate the membrane-bending energy of each conformation embedded in different membrane surfaces characteristic of a budding virus. The calculations show that all three M2 conformations are stabilized in inward-budding, concave spherical caps and destabilized in outward-budding, convex spherical caps, the latter reminiscent of a budding virus. One of the C2-broken symmetry conformations is stabilized by 4 kT in NGC surfaces with the minimum energy conformation occurring at a curvature corresponding to 33 nm radii. In total, our work provides atomistic insight into the curvature sensing capabilities of M2 channels and how enrichment in the nascent viral particle depends on protein shape and membrane geometry.
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- 2024
103. Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields.
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Behara, Pavan, Jang, Hyesu, Horton, Joshua, Gokey, Trevor, Dotson, David, Boothroyd, Simon, Bayly, Christopher, Cole, Daniel, Wang, Lee-Ping, and Mobley, David
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A wide range of density functional methods and basis sets are available to derive the electronic structure and properties of molecules. Quantum mechanical calculations are too computationally intensive for routine simulation of molecules in the condensed phase, prompting the development of computationally efficient force fields based on quantum mechanical data. Parametrizing general force fields, which cover a vast chemical space, necessitates the generation of sizable quantum mechanical data sets with optimized geometries and torsion scans. To achieve this efficiently, choosing a quantum mechanical method that balances computational cost and accuracy is crucial. In this study, we seek to assess the accuracy of quantum mechanical theory for specific properties such as conformer energies and torsion energetics. To comprehensively evaluate various methods, we focus on a representative set of 59 diverse small molecules, comparing approximately 25 combinations of functional and basis sets against the reference level coupled cluster calculations at the complete basis set limit.
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- 2024
104. The Early Data Release of the Dark Energy Spectroscopic Instrument
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Collaboration, DESI, Adame, AG, Aguilar, J, Ahlen, S, Alam, S, Aldering, G, Alexander, DM, Alfarsy, R, Prieto, C Allende, Alvarez, M, Alves, O, Anand, A, Andrade-Oliveira, F, Armengaud, E, Asorey, J, Avila, S, Aviles, A, Bailey, S, Balaguera-Antolínez, A, Ballester, O, Baltay, C, Bault, A, Bautista, J, Behera, J, Beltran, SF, BenZvi, S, Silva, L Beraldo E, Bermejo-Climent, JR, Berti, A, Besuner, R, Beutler, F, Bianchi, D, Blake, C, Blum, R, Bolton, AS, Brieden, S, Brodzeller, A, Brooks, D, Brown, Z, Buckley-Geer, E, Burtin, E, Cabayol-Garcia, L, Cai, Z, Canning, R, Cardiel-Sas, L, Rosell, A Carnero, Castander, FJ, Cervantes-Cota, JL, Chabanier, S, Chaussidon, E, Chaves-Montero, J, Chen, S, Chen, X, Chuang, C, Claybaugh, T, Cole, S, Cooper, AP, Cuceu, A, Davis, TM, Dawson, K, de Belsunce, R, de la Cruz, R, de la Macorra, A, Della Costa, J, de Mattia, A, Demina, R, Demirbozan, U, DeRose, J, Dey, A, Dey, B, Dhungana, G, Ding, J, Ding, Z, Doel, P, Doshi, R, Douglass, K, Edge, A, Eftekharzadeh, S, Eisenstein, DJ, Elliott, A, Ereza, J, Escoffier, S, Fagrelius, P, Fan, X, Fanning, K, Fawcett, VA, Ferraro, S, Flaugher, B, Font-Ribera, A, Forero-Romero, JE, Forero-Sánchez, D, Frenk, CS, Gänsicke, BT, García, LÁ, García-Bellido, J, Garcia-Quintero, C, Garrison, LH, Gil-Marín, H, Golden-Marx, J, and Gontcho, S Gontcho A
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Astronomical Sciences ,Physical Sciences ,Astronomical and Space Sciences ,Astronomy & Astrophysics ,Astronomical sciences ,Particle and high energy physics - Abstract
The Dark Energy Spectroscopic Instrument (DESI) completed its 5 month Survey Validation in 2021 May. Spectra of stellar and extragalactic targets from Survey Validation constitute the first major data sample from the DESI survey. This paper describes the public release of those spectra, the catalogs of derived properties, and the intermediate data products. In total, the public release includes good-quality spectral information from 466,447 objects targeted as part of the Milky Way Survey, 428,758 as part of the Bright Galaxy Survey, 227,318 as part of the Luminous Red Galaxy sample, 437,664 as part of the Emission Line Galaxy sample, and 76,079 as part of the Quasar sample. In addition, the release includes spectral information from 137,148 objects that expand the scope beyond the primary samples as part of a series of secondary programs. Here, we describe the spectral data, data quality, data products, Large-Scale Structure science catalogs, access to the data, and references that provide relevant background to using these spectra.
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- 2024
105. Measuring the Conditional Luminosity and Stellar Mass Functions of Galaxies by Combining the Dark Energy Spectroscopic Instrument Legacy Imaging Surveys Data Release 9, Survey Validation 3, and Year 1 Data
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Wang, Yirong, Yang, Xiaohu, Gu, Yizhou, Xu, Xiaoju, Xu, Haojie, Wang, Yuyu, Katsianis, Antonios, Han, Jiaxin, He, Min, Zheng, Yunliang, Li, Qingyang, Wang, Yaru, Hong, Wensheng, Wang, Jiaqi, Tan, Zhenlin, Zou, Hu, Lange, Johannes Ulf, Hahn, ChangHoon, Behroozi, Peter, Aguilar, Jessica Nicole, Ahlen, Steven, Brooks, David, Claybaugh, Todd, Cole, Shaun, de la Macorra, Axel, Dey, Biprateep, Doel, Peter, Forero-Romero, Jaime E, Honscheid, Klaus, Kehoe, Robert, Kisner, Theodore, Lambert, Andrew, Manera, Marc, Meisner, Aaron, Miquel, Ramon, Moustakas, John, Nie, Jundan, Poppett, Claire, Rezaie, Mehdi, Rossi, Graziano, Sanchez, Eusebio, Schubnell, Michael, Tarlé, Gregory, Weaver, Benjamin Alan, and Zhou, Zhimin
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Astronomical Sciences ,Physical Sciences ,Astronomical and Space Sciences ,Atomic ,Molecular ,Nuclear ,Particle and Plasma Physics ,Physical Chemistry (incl. Structural) ,Astronomy & Astrophysics ,Astronomical sciences ,Particle and high energy physics ,Space sciences - Abstract
In this investigation, we leverage the combination of the Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Surveys Data Release 9, Survey Validation 3, and Year 1 data sets to estimate the conditional luminosity functions and conditional stellar mass functions (CLFs and CSMFs) of galaxies across various halo mass bins and redshift ranges. To support our analysis, we utilize a realistic DESI mock galaxy redshift survey (MGRS) generated from a high-resolution Jiutian simulation. An extended halo-based group finder is applied to both MGRS catalogs and DESI observation. By comparing the r- and z-band luminosity functions (LFs) and stellar mass functions (SMFs) derived using both photometric and spectroscopic data, we quantified the impact of photometric redshift (photo-z) errors on the galaxy LFs and SMFs, especially in the low-redshift bin at the low-luminosity/mass end. By conducting prior evaluations of the group finder using MGRS, we successfully obtain a set of CLF and CSMF measurements from observational data. We find that at low redshift, the faint-end slopes of CLFs and CSMFs below ∼109 h −2 L ⊙ (or h −2 M ⊙) evince a compelling concordance with the subhalo mass functions. After correcting the cosmic variance effect of our local Universe following Chen et al., the faint-end slopes of the LFs/SMFs turn out to also be in good agreement with the slope of the halo mass function.
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- 2024
106. Severe PTSD is marked by reduced oxytocin and elevated vasopressin.
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Horn, Alexander, Cole, Steve, Nazarloo, Hans, Parmida, Nazarloo, Davis, John, Carrier, David, Bryan, Craig, and Carter, Cameron
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Cortisol ,Oxytocin ,PTSD ,Stress ,Vasopressin - Abstract
Neuroendocrine analyses of posttraumatic stress disorder (PTSD) have generally focused on hypothalamic-pituitary-adrenal (HPA) axis alterations. In the present analyses, we examine two additional neuroendocrine factors that have been previously implicated in biological stress responses: oxytocin (OT) and arginine vasopressin (AVP). Here we examined basal neuropeptide status in military veterans clinically diagnosed with PTSD (n = 29) and in two non-traumatized comparison groups with previous stress exposure (n = 11 SWAT trainees and n = 21 ultramarathon runners). PTSD patients showed low levels of plasma OT and high levels of AVP. The ratio of AVP/OT robustly related to PTSD status, and emerged as a statistically plausible mediator of relationships between the number of personal traumatic experiences and subsequent PTSD symptom burden. Over the course of behavioral therapy for PTSD, measures of OT showed a significant but modest normalization. Plasma cortisol levels were not statistically different among the three groups. This study suggests that AVP/OT ratios may represent a neuroendocrine predictor of severe PTSD, as well as a potential treatment response biomarker.
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- 2024
107. The HEALthy Brain and Child Development Study (HBCD): NIH collaboration to understand the impacts of prenatal and early life experiences on brain development.
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Volkow, Nora, Gordon, Joshua, Bianchi, Diana, Chiang, Michael, Clayton, Janine, Klein, William, Koob, George, Koroshetz, Walter, Pérez-Stable, Eliseo, Simoni, Jane, Tromberg, Bruce, Woychik, Richard, Hommer, Rebecca, Spotts, Erica, Xu, Benjamin, Zehr, Julia, Cole, Katherine, Dowling, Gayathri, Freund, Michelle, Howlett, Katia, Jordan, Chloe, Murray, Traci, Pariyadath, Vani, Prabhakar, Janani, Rankin, Michele, Sarampote, Christopher, and Weiss, Susan
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Brain development ,HBCD ,Longitudinal ,Neuroimaging ,Prenatal substance use ,Social determinants of health - Abstract
The human brain undergoes rapid development during the first years of life. Beginning in utero, a wide array of biological, social, and environmental factors can have lasting impacts on brain structure and function. To understand how prenatal and early life experiences alter neurodevelopmental trajectories and shape health outcomes, several NIH Institutes, Centers, and Offices collaborated to support and launch the HEALthy Brain and Child Development (HBCD) Study. The HBCD Study is a multi-site prospective longitudinal cohort study, that will examine human brain, cognitive, behavioral, social, and emotional development beginning prenatally and planned through early childhood. Influenced by the success of the ongoing Adolescent Brain Cognitive DevelopmentSM Study (ABCD Study®) and in partnership with the NIH Helping to End Addiction Long-term® Initiative, or NIH HEAL Initiative®, the HBCD Study aims to establish a diverse cohort of over 7000 pregnant participants to understand how early life experiences, including prenatal exposure to addictive substances and adverse social environments as well as their interactions with an individuals genes, can affect neurodevelopmental trajectories and outcomes. Knowledge gained from the HBCD Study will help identify targets for early interventions and inform policies that promote resilience and mitigate the neurodevelopmental effects of adverse childhood experiences and environments.
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- 2024
108. Community case management to accelerate access to healthcare in Mali: A realist process evaluation nested within a cluster randomised trial
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Whidden, Caroline, Cissé, Amadou Beydi, Cole, Faith, Doumbia, Saibou, Guindo, Abdoulaye, Karambé, Youssouf, Treleaven, Emily, Liu, Jenny, Tolo, Oumar, Guindo, Lamine, Togola, Bréhima, Chiu, Calvin, Tembely, Aly, Keita, Youssouf, Greenwood, Brian, Chandramohan, Daniel, Johnson, Ari, Kayentao, Kassoum, and Webster, Jayne
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Public Health ,Health Sciences ,Clinical Research ,Clinical Trials and Supportive Activities ,Health Services ,Behavioral and Social Science ,8.1 Organisation and delivery of services ,Generic health relevance ,Good Health and Well Being ,Cluster randomized trials ,Community health workers ,Health services research ,Health systems evaluation ,Primary health care ,Process evaluation ,Realist evaluation ,Public Health and Health Services ,Policy and Administration ,Political Science ,Health Policy & Services ,Health services and systems ,Public health ,Policy and administration - Abstract
The Proactive Community Case Management (ProCCM) trial in Mali reinforced the health system across both arms with user fee removal, professional Community Health Workers (CHWs), and upgraded primary health centres (PHCs)-and randomized village-clusters to receive proactive home visits by CHWs (intervention) or fixed site-based services by passive CHWs (control). Across both arms, sick children's 24-hour treatment and pregnant women's four or more antenatal visits doubled, and under-five mortality halved, over three years compared to baseline. In the intervention arm, proactive CHW home visits had modest effects on children's curative and women's antenatal care utilization, but no effect on under-five mortality, compared to the control arm. We aimed to explain these results by examining implementation, mechanisms, and context in both arms. We conducted a process evaluation with a mixed method convergent design that included 79 in-depth interviews with providers and participants over two time-points, surveys with 195 providers, and secondary analyses of clinical data. We embedded realist approaches in novel ways to test, refine, and consolidate theories about how ProCCM worked, generating three context-intervention-actor-mechanism-outcome nodes that unfolded in a cascade. First, removing user fees and deploying professional CHWs in every cluster enabled participants to seek health sector care promptly and created a context of facilitated access. Second, health systems support to all CHWs and PHCs enabled equitable, respectful, quality healthcare, which motivated increased, rapid utilization. Third, proactive CHW home visits facilitated CHWs and participants to deliver and seek care, and build relationships, trust, and expectations, but these mechanisms were also activated in both arms. Addressing multiple structural barriers to care, user fee removal, professional CHWs, and upgraded clinics interacted with providers' and patients' agency to achieve rapid care and child survival in both arms. Proactive home visits expedited or compounded mechanisms that were activated and changed the context across arms.
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- 2024
109. The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling.
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Wang, Lily, Behara, Pavan, Thompson, Matthew, Gokey, Trevor, Wang, Yuanqing, Wagner, Jeffrey, Cole, Daniel, Gilson, Michael, Shirts, Michael, and Mobley, David
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Force fields are a key component of physics-based molecular modeling, describing the energies and forces in a molecular system as a function of the positions of the atoms and molecules involved. Here, we provide a review and scientific status report on the work of the Open Force Field (OpenFF) Initiative, which focuses on the science, infrastructure and data required to build the next generation of biomolecular force fields. We introduce the OpenFF Initiative and the related OpenFF Consortium, describe its approach to force field development and software, and discuss accomplishments to date as well as future plans. OpenFF releases both software and data under open and permissive licensing agreements to enable rapid application, validation, extension, and modification of its force fields and software tools. We discuss lessons learned to date in this new approach to force field development. We also highlight ways that other force field researchers can get involved, as well as some recent successes of outside researchers taking advantage of OpenFF tools and data.
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- 2024
110. CEERS: 7.7 μm PAH Star Formation Rate Calibration with JWST MIRI
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Ronayne, Kaila, Papovich, Casey, Yang, Guang, Shen, Lu, Dickinson, Mark, Kennicutt, Robert, Alavi, Anahita, Haro, Pablo Arrabal, Bagley, Micaela B, Burgarella, Denis, Le Bail, Aurélien, Bell, Eric F, Cleri, Nikko J, Cole, Justin, Costantin, Luca, de la Vega, Alexander, Daddi, Emanuele, Elbaz, David, Finkelstein, Steven L, Grogin, Norman A, Holwerda, Benne W, Kartaltepe, Jeyhan S, Kirkpatrick, Allison, Koekemoer, Anton M, Lucas, Ray A, Magnelli, Benjamin, Mobasher, Bahram, Pérez-González, Pablo G, Prichard, Laura, Rafelski, Marc, Rodighiero, Giulia, Sunnquist, Ben, Teplitz, Harry I, Wang, Xin, Windhorst, Rogier A, and Yung, LY Aaron
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Space Sciences ,Physical Sciences ,Astronomical and Space Sciences ,Atomic ,Molecular ,Nuclear ,Particle and Plasma Physics ,Physical Chemistry (incl. Structural) ,Astronomy & Astrophysics ,Astronomical sciences ,Particle and high energy physics ,Space sciences - Abstract
We test the relationship between UV-derived star formation rates (SFRs) and the 7.7 μm polycyclic aromatic hydrocarbon luminosities from the integrated emission of galaxies at z ∼ 0-2. We utilize multiband photometry covering 0.2-160 μm from the Hubble Space Telescope, CFHT, JWST, Spitzer, and Herschel for galaxies in the Cosmic Evolution Early Release Science (CEERS) Survey. We perform spectral energy distribution (SED) modeling of these data to measure dust-corrected far-UV (FUV) luminosities, L FUV, and UV-derived SFRs. We then fit SED models to the JWST/MIRI 7.7-21 μm CEERS data to derive rest-frame 7.7 μm luminosities, L 770, using the average flux density in the rest-frame MIRI F770W bandpass. We observe a correlation between L 770 and L FUV, where log L 770 ∝ ( 1.27 ± 0.04 ) log L FUV . L 770 diverges from this relation for galaxies at lower metallicities, lower dust obscuration, and for galaxies dominated by evolved stellar populations. We derive a “single-wavelength” SFR calibration for L 770 that has a scatter from model estimated SFRs (σ ΔSFR) of 0.24 dex. We derive a “multiwavelength” calibration for the linear combination of the observed FUV luminosity (uncorrected for dust) and the rest-frame 7.7 μm luminosity, which has a scatter of σ ΔSFR = 0.21 dex. The relatively small decrease in σ suggests this is near the systematic accuracy of the total SFRs using either calibration. These results demonstrate that the rest-frame 7.7 μm emission constrained by JWST/MIRI is a tracer of the SFR for distant galaxies to this accuracy, provided the galaxies are dominated by star formation with moderate-to-high levels of attenuation and metallicity.
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- 2024
111. A dyadic longitudinal analysis of parent-adolescent inflammation trends and the role of shared socioeconomic characteristics on family inflammation.
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Rocha, Sarah, Bower, Julienne, Chiang, Jessica, Cole, Steve, Irwin, Michael, Seeman, Teresa, and Fuligni, Andrew
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C-reactive protein ,Dyadic modeling ,Family dependency ,Inflammation ,Socioeconomic status - Abstract
The objective of the present study was to evaluate the interdependency of parent-adolescent inflammation trends across time and to examine whether shared family socioeconomic characteristics explained between-family differences in parents and adolescents risk for inflammation. A total of N = 348 families, consisting of one parent and one adolescent child, were followed every two years in a three-wave longitudinal study. Sociodemographic questionnaires were used to determine parental educational attainment and family income-to-needs ratio (INR). At each time point, parents and adolescents collected dried blood spot (DBS) samples that were assayed for circulating CRP and log-transformed prior to analysis by longitudinal dyadic models. Models revealed significant differences in parents and adolescents inflammation trends over time (bint = - 0.13, p
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- 2024
112. The present and future of QCD
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Achenbach, P, Adhikari, D, Afanasev, A, Afzal, F, Aidala, CA, Al-bataineh, A, Almaalol, DK, Amaryan, M, Androić, D, Armstrong, WR, Arratia, M, Arrington, J, Asaturyan, A, Aschenauer, EC, Atac, H, Avakian, H, Averett, T, Gayoso, C Ayerbe, Bai, X, Barish, KN, Barnea, N, Basar, G, Battaglieri, M, Baty, AA, Bautista, I, Bazilevsky, A, Beattie, C, Behera, SC, Bellini, V, Bellwied, R, Benesch, JF, Benmokhtar, F, Bernardes, CA, Bernauer, JC, Bhatt, H, Bhatta, S, Boer, M, Boettcher, TJ, Bogacz, SA, Bossi, HJ, Brandenburg, JD, Brash, EJ, Briceño, RA, Briscoe, WJ, Brodsky, SJ, Brown, DA, Burkert, VD, Caines, H, Cali, IA, Camsonne, A, Carman, DS, Caylor, J, Cerci, DS, Cerci, S, Llatas, M Chamizo, Chatterjee, S, Chen, JP, Chen, Y, Chen, Y-C, Chien, Y-T, Chou, P-C, Chu, X, Chudakov, E, Cline, E, Cloët, IC, Cole, PL, Connors, ME, Constantinou, M, Cosyn, W, Dusa, S Covrig, Cruz-Torres, R, D'Alesio, U, da Silva, C, Davoudi, Z, Dean, CT, Dean, DJ, Demarteau, M, Deshpande, A, Detmold, W, Deur, A, Devkota, BR, Dhital, S, Diefenthaler, M, Dobbs, S, Döring, M, Dong, X, Dotel, R, Dow, KA, Downie, EJ, Drachenberg, JL, Dumitru, A, Dunlop, JC, Dupre, R, Durham, JM, Dutta, D, Edwards, RG, Ehlers, RJ, Fassi, L El, Elaasar, M, and Elouadrhiri, L
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Nuclear and Plasma Physics ,Physical Sciences ,Astronomical and Space Sciences ,Atomic ,Molecular ,Nuclear ,Particle and Plasma Physics ,Quantum Physics ,Nuclear & Particles Physics ,Astronomical sciences ,Nuclear and plasma physics ,Particle and high energy physics - Abstract
This White Paper presents an overview of the current status and future perspective of QCD research, based on the community inputs and scientific conclusions from the 2022 Hot and Cold QCD Town Meeting. We present the progress made in the last decade toward a deep understanding of both the fundamental structure of the sub-atomic matter of nucleon and nucleus in cold QCD, and the hot QCD matter in heavy ion collisions. We identify key questions of QCD research and plausible paths to obtaining answers to those questions in the near future, hence defining priorities of our research over the coming decades.
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- 2024
113. Generating mock galaxy catalogues for flux-limited samples like the DESI Bright Galaxy Survey
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Smith, A, Grove, C, Cole, S, Norberg, P, Zarrouk, P, Yuan, S, Aguilar, J, Ahlen, S, Brooks, D, Claybaugh, T, de la Macorra, A, Doel, P, Forero-Romero, JE, Gaztañaga, E, Gontcho, S Gontcho A, Hahn, C, Kehoe, R, Kremin, A, Levi, ME, Manera, M, Meisner, A, Miquel, R, Moustakas, J, Nie, J, Percival, WJ, Rezaie, M, Rossi, G, Sanchez, E, Seo, H, Tarlé, G, and Zhou, Z
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Astronomical Sciences ,Physical Sciences ,Bioengineering ,Astronomical and Space Sciences ,Astronomy & Astrophysics ,Astronomical sciences ,Particle and high energy physics ,Space sciences - Abstract
Accurate mock galaxy catalogues are crucial to validate analysis pipelines used to constrain dark energy models. We present a fast HOD-fitting method which we apply to the AbacusSummit simulations to create a set of mock catalogues for the DESI Bright Galaxy Survey, which contain r-band magnitudes and colours (g - r) The halo tabulation method fits HODs for different absolute magnitude threshold samples simultaneously, preventing unphysical HOD crossing between samples. We validate the HOD fitting procedure by fitting to real-space clustering measurements and galaxy number densities from the MXXL BGS mock, which was tuned to the SDSS and GAMA surveys. The best-fitting clustering measurements and number densities are mostly within the assumed errors, but the clustering for the faint samples is low on large scales. The best-fitting HOD parameters are robust when fitting to simulations with different realizations of the initial conditions. When varying the cosmology, trends are seen as a function of each cosmological parameter. We use the best-fitting HOD parameters to create cubic box and cut sky mocks from the AbacusSummit simulations, in a range of cosmologies. As an illustration, we compare the sample of galaxies in the mock with BGS measurements from the DESI one-percent survey. We find good agreement in the number densities, and the projected correlation function is reasonable, with differences that can be improved in the future by fitting directly to BGS clustering measurements. The cubic box and cut-sky mocks in different cosmologies are made publicly available.
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- 2024
114. Higher expression of denervation‐responsive genes is negatively associated with muscle volume and performance traits in the study of muscle, mobility, and aging (SOMMA)
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Lukasiewicz, Cole J, Tranah, Gregory J, Evans, Daniel S, Coen, Paul M, Barnes, Haley N, Huo, Zhiguang, Esser, Karyn A, Zhang, Xiping, Wolff, Christopher, Wu, Kevin, Lane, Nancy E, Kritchevsky, Steven B, Newman, Anne B, Cummings, Steven R, Cawthon, Peggy M, and Hepple, Russell T
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Medical Physiology ,Biomedical and Clinical Sciences ,Aging ,Genetics ,Underpinning research ,1.1 Normal biological development and functioning ,Musculoskeletal ,gene expression profiling ,muscle ,skeletal ,neuromuscular junction ,denervation ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
With aging skeletal muscle fibers undergo repeating cycles of denervation and reinnervation. In approximately the 8th decade of life reinnervation no longer keeps pace, resulting in the accumulation of persistently denervated muscle fibers that in turn cause an acceleration of muscle dysfunction. The significance of denervation in important clinical outcomes with aging is poorly studied. The Study of Muscle, Mobility, and Aging (SOMMA) is a large cohort study with the primary objective to assess how aging muscle biology impacts clinically important traits. Using transcriptomics data from vastus lateralis muscle biopsies in 575 participants we have selected 49 denervation-responsive genes to provide insights to the burden of denervation in SOMMA, to test the hypothesis that greater expression of denervation-responsive genes negatively associates with SOMMA participant traits that included time to walk 400 meters, fitness (VO2peak), maximal mitochondrial respiration, muscle mass and volume, and leg muscle strength and power. Consistent with our hypothesis, increased transcript levels of: a calciumdependent intercellular adhesion glycoprotein (CDH15), acetylcholine receptor subunits (CHRNA1, CHRND, CHRNE), a glycoprotein promoting reinnervation (NCAM1), a transcription factor regulating aspects of muscle organization (RUNX1), and a sodium channel (SCN5A) were each negatively associated with at least 3 of these traits. VO2peak and maximal respiration had the strongest negative associations with 15 and 19 denervation-responsive genes, respectively. In conclusion, the abundance of denervationresponsive gene transcripts is a significant determinant of muscle and mobility outcomes in aging humans, supporting the imperative to identify new treatment strategies to restore innervation in advanced age.
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- 2024
115. Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters
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Lalanne, Jean-Benoît, Regalado, Samuel G, Domcke, Silvia, Calderon, Diego, Martin, Beth K, Li, Xiaoyi, Li, Tony, Suiter, Chase C, Lee, Choli, Trapnell, Cole, and Shendure, Jay
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Biochemistry and Cell Biology ,Bioinformatics and Computational Biology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,Bioengineering ,1.1 Normal biological development and functioning ,Generic health relevance ,Single-Cell Analysis ,Animals ,Mice ,Gene Expression Regulation ,Developmental ,Genes ,Reporter ,Regulatory Sequences ,Nucleic Acid ,Humans ,Transcription Factors ,Chromatin ,Regulatory Elements ,Transcriptional ,Gene Expression Profiling ,Technology ,Medical and Health Sciences ,Developmental Biology ,Biological sciences - Abstract
The inability to scalably and precisely measure the activity of developmental cis-regulatory elements (CREs) in multicellular systems is a bottleneck in genomics. Here we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode stabilization via circularization, these scalable single-cell quantitative expression reporters provide high-contrast readouts, analogous to classic in situ assays but entirely from sequencing. Screening >200 regions of accessible chromatin in a multicellular in vitro model of early mammalian development, we identify 13 (8 previously uncharacterized) autonomous and cell-type-specific developmental CREs. We further demonstrate that chimeric CRE pairs generate cognate two-cell-type activity profiles and assess gain- and loss-of-function multicellular expression phenotypes from CRE variants with perturbed transcription factor binding sites. Single-cell quantitative expression reporters can be applied in developmental and multicellular systems to quantitatively characterize native, perturbed and synthetic CREs at scale, with high sensitivity and at single-cell resolution.
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- 2024
116. Blinding scheme for the scale-dependence bias signature of local primordial non-Gaussianity for DESI 2024
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Chaussidon, E., de Mattia, A., Yèche, C., Aguilar, J., Ahlen, S., Brooks, D., Claybaugh, T., Cole, S., de la Macorra, A., Doel, P., Fanning, K., Gaztañaga, E., Gontcho, S. Gontcho A, Howlett, C., Kisner, T., Lambert, A., Guillou, L. Le, Manera, M., Meisner, A., Miquel, R., Niz, G., Palanque-Delabrouille, N., Percival, W. J., Prada, F., Ross, A. J., Rossi, G., Sanchez, E., Schlegel, D., Schubnell, M., Seo, H., Sprayberry, D., Tarlé, G., Vargas-Magaña, M., Weaver, B. A., and Zou, H.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
The next generation of spectroscopic surveys is expected to achieve an unprecedented level of accuracy in the measurement of cosmological parameters. To avoid confirmation bias and thereby improve the reliability of these results, blinding procedures become a standard practice in the cosmological analyses of such surveys. Blinding is especially crucial when the impact of observational systematics is important relative to the cosmological signal, and a detection of that signal would have significant implications. This is the case for local primordial non-gaussianity, as probed by the scale-dependent bias of the galaxy power spectrum at large scales that are heavily sensitive to the dependence of the target selection on the imaging quality, known as imaging systematics. We propose a blinding method for the scale-dependent bias signature of local primordial non-gaussianity at the density field level which consists in generating a set of weights for the data that replicate the scale-dependent bias. The applied blinding is predictable, and can be straightforwardly combined with other catalog-level blinding procedures that have been designed for the baryon acoustic oscillation and redshift space distortion signals. The procedure is validated through simulations that replicate data from the first year of observation of the Dark Energy Spectroscopic Instrument, but may find applications to other upcoming spectroscopic surveys.
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- 2024
117. Love-C relations for elastic hybrid stars
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Dong, Zoey Zhiyuan, Faggert, Joshua Cole, Lau, Shu Yan, and Yagi, Kent
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General Relativity and Quantum Cosmology ,Astrophysics - High Energy Astrophysical Phenomena ,Nuclear Theory - Abstract
Neutron stars (NSs) provide a unique laboratory to study matter under extreme densities. Recent observations from gravitational and electromagnetic waves have enabled constraints on NS properties, such as tidal deformability (related to the tidal Love number) and stellar compactness. Although each of these two NS observables depends strongly on the stellar internal structure, the relation between them (called the Love-C relation) is known to be equation-of-state insensitive. In this study, we investigate the effects of a possible crystalline phase in the core of hybrid stars (HSs) on the mass-radius and Love-C relations, where HSs are a subclass of NS models with a quark matter core and a nuclear matter envelope with a sharp phase transition in between. We find that both the maximum mass and the corresponding radius increase as one increases the stiffness of the quark matter core controlled by the speed of sound, while the density discontinuity at the nuclear-quark matter transition effectively softens the equations of state. Deviations of the Love-C relation for elastic HSs from that of fluid NSs become more pronounced with a larger shear modulus, lower transition pressure, and larger density gap and can be as large as 60%. These findings suggest a potential method for testing the existence of distinct phases within HSs, though deviations are not large enough to be detected with current measurements of the tidal deformability and compactness., Comment: 29 pages, 12 figures, Accepted for publication in General Relativity and Gravitation
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- 2024
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118. Interdisciplinary Expertise to Advance Equitable Explainable AI
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Bennett, Chloe R., Cole-Lewis, Heather, Farquhar, Stephanie, Haamel, Naama, Babenko, Boris, Lang, Oran, Fleck, Mat, Traynis, Ilana, Lau, Charles, Horn, Ivor, and Lyles, Courtney
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Computer Science - Computers and Society ,Computer Science - Artificial Intelligence ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
The field of artificial intelligence (AI) is rapidly influencing health and healthcare, but bias and poor performance persists for populations who face widespread structural oppression. Previous work has clearly outlined the need for more rigorous attention to data representativeness and model performance to advance equity and reduce bias. However, there is an opportunity to also improve the explainability of AI by leveraging best practices of social epidemiology and health equity to help us develop hypotheses for associations found. In this paper, we focus on explainable AI (XAI) and describe a framework for interdisciplinary expert panel review to discuss and critically assess AI model explanations from multiple perspectives and identify areas of bias and directions for future research. We emphasize the importance of the interdisciplinary expert panel to produce more accurate, equitable interpretations which are historically and contextually informed. Interdisciplinary panel discussions can help reduce bias, identify potential confounders, and identify opportunities for additional research where there are gaps in the literature. In turn, these insights can suggest opportunities for AI model improvement.
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- 2024
119. Gone but Not Forgotten: Improved Benchmarks for Machine Unlearning
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Grimes, Keltin, Abidi, Collin, Frank, Cole, and Gallagher, Shannon
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Computer Science - Machine Learning - Abstract
Machine learning models are vulnerable to adversarial attacks, including attacks that leak information about the model's training data. There has recently been an increase in interest about how to best address privacy concerns, especially in the presence of data-removal requests. Machine unlearning algorithms aim to efficiently update trained models to comply with data deletion requests while maintaining performance and without having to resort to retraining the model from scratch, a costly endeavor. Several algorithms in the machine unlearning literature demonstrate some level of privacy gains, but they are often evaluated only on rudimentary membership inference attacks, which do not represent realistic threats. In this paper we describe and propose alternative evaluation methods for three key shortcomings in the current evaluation of unlearning algorithms. We show the utility of our alternative evaluations via a series of experiments of state-of-the-art unlearning algorithms on different computer vision datasets, presenting a more detailed picture of the state of the field.
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- 2024
120. Computing hydration free energies of small molecules with first principles accuracy
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Moore, J. Harry, Cole, Daniel J., and Csanyi, Gabor
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Physics - Chemical Physics - Abstract
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. The free energy of hydration in particular is a well-studied physicochemical property of drug-like molecules and is commonly used to assess and optimise the accuracy of nonbonded parameters in empirical forcefields, and as a fast-to-compute surrogate of performance for protein-ligand binding free energy estimation. Machine learned potentials (MLPs) show great promise as more accurate alternatives to empirical forcefields, but are not readily decomposed into physically motivated functional forms, which has thus far rendered them incompatible with standard alchemical free energy methods that manipulate individual pairwise interaction terms. However, since the accuracy of free energy calculations is highly sensitive to the forcefield, this is a key area in which MLPs have the potential to address the shortcomings of empirical forcefields. In this work, we introduce an efficient alchemical free energy method compatible with MLPs, enabling, for the first time, calculations of biomolecular free energy with \textit{ab initio} accuracy. Using a pretrained, transferrable, alchemically equipped MACE model, we demonstrate sub-chemical accuracy for the hydration free energies of organic molecules.
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- 2024
121. The JWST Resolved Stellar Populations Early Release Science Program VII. Stress Testing the NIRCam Exposure Time Calculator
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Savino, A., Gennaro, M., Dolphin, A. E., Weisz, D. R., Correnti, M., Anderson, J., Beaton, R., Boyer, M. L., Cohen, R. E., Cole, A. A., Durbin, M. J., Garling, C. T., Geha, M. C., Gilbert, K. M., Kalirai, J., Kallivayalil, N., McQuinn, K. B. W., Newman, M. J. B., Richstein, H., Skillman, E. D., Warfield, J. T., and Williams, B. F.
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Astrophysics - Astrophysics of Galaxies ,Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Solar and Stellar Astrophysics - Abstract
We empirically assess estimates from v3.0 of the JWST NIRCam Exposure Time Calculator (ETC) using observations of resolved stars in Local Group targets taken as part of the Resolved Stellar Populations Early Release Science (ERS) Program. For bright stars, we find that: (i) purely Poissonian estimates of the signal-to-noise ratio (SNR) are in good agreement between the ETC and observations, but non-ideal effects (e.g., flat field uncertainties) are the current limiting factor in the photometric precision that can be achieved; (ii) source position offsets, relative to the detector pixels, have a large impact on the ETC saturation predictions and introducing sub-pixel dithers in the observation design can improve the saturation limits by up to ~1 mag. For faint stars, for which the sky dominates the error budget, we find that the choice in ETC extraction strategy (e.g., aperture size relative to point spread function size) can affect the exposure time estimates by up to a factor of 5. We provide guidelines for configuring the ETC aperture photometry to produce SNR predictions in line with the ERS data. Finally, we quantify the effects of crowding on the SNRs over a large dynamic range in stellar density and provide guidelines for approximating the effects of crowding on SNRs predicted by the ETC., Comment: Accepted for publication in ApJ. 18 pages, 9 Figures, 2 Tables
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- 2024
122. A joint model for (un)bounded longitudinal markers, competing risks, and recurrent events using patient registry data
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Afonso, Pedro Miranda, Rizopoulos, Dimitris, Palipana, Anushka K., Gecili, Emrah, Brokamp, Cole, Clancy, John P., Szczesniak, Rhonda D., and Andrinopoulou, Eleni-Rosalina
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Statistics - Methodology - Abstract
Joint models for longitudinal and survival data have become a popular framework for studying the association between repeatedly measured biomarkers and clinical events. Nevertheless, addressing complex survival data structures, especially handling both recurrent and competing event times within a single model, remains a challenge. This causes important information to be disregarded. Moreover, existing frameworks rely on a Gaussian distribution for continuous markers, which may be unsuitable for bounded biomarkers, resulting in biased estimates of associations. To address these limitations, we propose a Bayesian shared-parameter joint model that simultaneously accommodates multiple (possibly bounded) longitudinal markers, a recurrent event process, and competing risks. We use the beta distribution to model responses bounded within any interval (a,b) without sacrificing the interpretability of the association. The model offers various forms of association, discontinuous risk intervals, and both gap and calendar timescales. A simulation study shows that it outperforms simpler joint models. We utilize the US Cystic Fibrosis Foundation Patient Registry to study the associations between changes in lung function and body mass index, and the risk of recurrent pulmonary exacerbations, while accounting for the competing risks of death and lung transplantation. Our efficient implementation allows fast fitting of the model despite its complexity and the large sample size from this patient registry. Our comprehensive approach provides new insights into cystic fibrosis disease progression by quantifying the relationship between the most important clinical markers and events more precisely than has been possible before. The model implementation is available in the R package JMbayes2.
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- 2024
123. The Construction of Large-scale Structure Catalogs for the Dark Energy Spectroscopic Instrument
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Ross, A. J., Aguilar, J., Ahlen, S., Alam, S., Anand, A., Bailey, S., Bianchi, D., Brieden, S., Brooks, D., Burtin, E., Rosell, A. Carnero, Chaussidon, E., Claybaugh, T., Cole, S., Dawson, K., de la Macorra, A., de Mattia, A., Dey, Arjun, Dey, Biprateep, Doel, P., Fanning, K., Ferraro, S., Ereza, J., Font-Ribera, A., Forero-Romero, J. E., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Guy, J., Hahn, C., Heydenreich, S., Honscheid, K., Howlett, C., Ishak, M., Karim, T., Kirkby, D., Kisner, T., Kong, H., Kremin, A., Krolewski, A., Lambert, A., Landriau, M., Lasker, J., Guillou, L. Le, Levi, M. E., Manera, M., Martini, P., McDonald, P., Meisner, A., Miquel, R., Moon, J., Moustakas, J., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Newman, J. A., Nie, J., Niz, G., Palanque-Delabrouille, N., Percival, W. J., Poppett, C., Prada, F., Raichoor, A., Ravoux, C., Rezaie, M., Rosado-Marin, A., Rossi, G., Samushia, L., Sanchez, E., Schlafly, E. F., Schlegel, D., Seo, H., Smith, A., Sprayberry, D., Tarlé, G., Valcin, D., Vargas-Magaña, M., Weaver, B. A., Wilson, M., Yu, J., Zarrouk, P., Zhao, C., Zhou, R., and Zou, H.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We present the technical details on how large-scale structure (LSS) catalogs are constructed from redshifts measured from spectra observed by the Dark Energy Spectroscopic Instrument (DESI). The LSS catalogs provide the information needed to determine the relative number density of DESI tracers as a function of redshift and celestial coordinates and, e.g., determine clustering statistics. We produce catalogs that are weighted subsamples of the observed data, each matched to a weighted `random' catalog that forms an unclustered sampling of the probability density that DESI could have observed those data at each location. Precise knowledge of the DESI observing history and associated hardware performance allows for a determination of the DESI footprint and the number of times DESI has covered it at sub-arcsecond level precision. This enables the completeness of any DESI sample to be modeled at this same resolution. The pipeline developed to create LSS catalogs has been designed to easily allow robustness tests and enable future improvements. We describe how it allows ongoing work improving the match between galaxy and random catalogs, such as including further information when assigning redshifts to randoms, accounting for fluctuations in target density, accounting for variation in the redshift success rate, and accommodating blinding schemes., Comment: Accepted (by JCAP) version of supporting publication of DESI 2024II: Sample definitions, characteristics, and two-point clustering statistics
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- 2024
124. Forward modeling fluctuations in the DESI LRGs target sample using image simulations
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Kong, Hui, Ross, Ashley J., Honscheid, Klaus, Lang, Dustin, Porredon, Anna, de Mattia, Arnaud, Rezaie, Mehdi, Zhou, Rongpu, Schlafly, Edward, Moustakas, John, Rosado-Marin, Alberto, Aguilar, Jessica Nicole, Ahlen, Steven, Brooks, David, Chaussidon, Edmond, Claybaugh, Todd, Cole, Shaun, de la Macorra, Axel, Dey, Arjun, Dey, Biprateep, Doel, Peter, Fanning, Kevin, Forero-Romero, Jaime E., Gaztanaga, Enrique, Gontcho, Satya Gontcho A, Gutierrez, Gaston, Howlett, Cullan, Juneau, Stephanie, Kremin, Anthony, Landriau, Martin, Levi, Michael, Manera, Marc, Martini, Paul, Meisner, Aaron, Miquel, Ramon, Mueller, Eva-Maria, Myers, Adam, Newman, Jeffrey A., Nie, Jundan, Niz, Gustavo, Percival, Will, Poppett, Claire, Prada, Francisco, Rossi, Graziano, Sanchez, Eusebio, Schlegel, David, Schubnell, Michael, Seo, Hee-Jong, Sprayberry, David, Tarle, Gregory, Magana, Mariana Vargas, Weaver, Benjamin Alan, and Zou, Hu
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We use the forward modeling pipeline, Obiwan, to study the imaging systematics of the Luminous Red Galaxies (LRGs) targeted by the Dark Energy Spectroscopic Instrument (DESI). We update the Obiwan pipeline, which had previously been developed to simulate the optical images used to target DESI data, to further simulate WISE images in the infrared. This addition makes it possible to simulate the DESI LRGs sample, which utilizes WISE data in the target selection. Deep DESI imaging data combined with a method to account for biases in their shapes is used to define a truth sample of potential LRG targets. We simulate a total of 15 million galaxies to obtain a simulated LRG sample (Obiwan LRGs) that predicts the variations in target density due to imaging properties. We find that the simulations predict the trends with depth observed in the data, including how they depend on the intrinsic brightness of the galaxies. We observe that faint LRGs are the main contributing power of the imaging systematics trend induced by depth. We also find significant trends in the data against Galactic extinction that are not predicted by Obiwan. These trends depend strongly on the particular map of Galactic extinction chosen to test against, implying Large-Scale Structure systematic contamination (e.g. Cosmic-Infrared Background) in the Galactic extinction maps is a likely root cause. We additionally observe that the DESI LRGs sample exhibits a complex dependency on a combination of seeing, depth, and intrinsic galaxy brightness, which is not replicated by Obiwan, suggesting discrepancies between the current simulation settings and the actual observations. The detailed findings we present should be used to guide any observational systematics mitigation treatment for the clustering of the DESI LRG sample., Comment: 46 pages, 26 figures
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- 2024
125. Synthetic high angular momentum spin dynamics in a microwave oscillator
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Roy, Saswata, Senanian, Alen, Wang, Christopher S., Wetherbee, Owen C., Zhang, Luojia, Cole, B., Larson, C. P., Yelton, E., Arora, Kartikeya, McMahon, Peter L., Plourde, B. L. T., Royer, Baptiste, and Fatemi, Valla
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Quantum Physics - Abstract
Spins and oscillators are foundational to much of physics and applied sciences. For quantum information, a spin 1/2 exemplifies the most basic unit, a qubit. High angular momentum spins (HAMSs) and harmonic oscillators provide multi-level manifolds (e.g., qudits) which have the potential for hardware-efficient protected encodings of quantum information and simulation of many-body quantum systems. In this work, we demonstrate a new quantum control protocol that conceptually merges these disparate hardware platforms. Namely, we show how to modify a harmonic oscillator on-demand to implement a continuous range of generators associated to resonant driving of a harmonic qudit, which we can interpret as accomplishing linear and nonlinear control over a harmonic HAMS degree of freedom. The spin-like dynamics are verified by demonstration of linear spin coherent (SU(2)) rotations, nonlinear spin control, and comparison to other manifolds like simply-truncated oscillators. Our scheme allows the first universal control of such a harmonic qudit encoding: we use linear operations to accomplish four logical gates, and further show that nonlinear harmonicity-preserving operations complete the logical gate set. Our results show how motion on a closed Hilbert space can be useful for quantum information processing and opens the door to superconducting circuit simulations of higher angular momentum quantum magnetism., Comment: Additional figures, updated text
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- 2024
126. Dual-comb correlation spectroscopy of thermal light
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Tsao, Eugene J., Lind, Alexander J., Fredrick, Connor, Cole, Ryan K., Chang, Peter, Chang, Kristina F., Lee, Dahyeon, Heyrich, Matthew, Hoghooghi, Nazanin, Quinlan, Franklyn, and Diddams, Scott A.
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Physics - Optics ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
The detection of light of thermal origin is the principal means by which humanity has learned about our world and the cosmos. In optical astronomy, in particular, direct detection of thermal photons and the resolution of their spectra have enabled discoveries of the broadest scope and impact. Such measurements, however, do not capture the phase of the thermal fields--a parameter that has proven crucial to transformative techniques in radio astronomy such as synthetic aperture imaging. Over the last 25 years, tremendous progress has occurred in laser science, notably in the phase-sensitive, broad bandwidth, high resolution, and traceable spectroscopy enabled by the optical frequency comb. In this work, we directly connect the fields of frequency comb laser spectroscopy and passive optical sensing as applied to astronomy, remote sensing, and atmospheric science. We provide fundamental sensitivity analysis of dual-comb correlation spectroscopy (DCCS), whereby broadband thermal light is measured via interferometry with two optical frequency combs. We define and experimentally verify the sensitivity scaling of DCCS at black body temperatures relevant for astrophysical observations. Moreover, we provide comparison with direct detection techniques and more conventional laser heterodyne radiometry. Our work provides the foundation for future exploration of comb-based broadband synthetic aperture hyperspectral imaging across the infrared and optical spectrum., Comment: 54 pages, 7 figures
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- 2024
127. Comparisons of Sequential Experiments for Additively Separable Problems
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Whitmeyer, Mark and Williams, Cole
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Economics - Theoretical Economics - Abstract
For three natural classes of dynamic decision problems; 1. additively separable problems, 2. discounted problems, and 3. discounted problems for a fixed discount factor; we provide necessary and sufficient conditions for one sequential experiment to dominate another in the sense that the dominant experiment is preferred to the other for any decision problem in the specified class. We use these results to study the timing of information arrival in additively separable problems.
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- 2024
128. Euclid. I. Overview of the Euclid mission
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Euclid Collaboration, Mellier, Y., Abdurro'uf, Barroso, J. A. Acevedo, Achúcarro, A., Adamek, J., Adam, R., Addison, G. E., Aghanim, N., Aguena, M., Ajani, V., Akrami, Y., Al-Bahlawan, A., Alavi, A., Albuquerque, I. S., Alestas, G., Alguero, G., Allaoui, A., Allen, S. W., Allevato, V., Alonso-Tetilla, A. V., Altieri, B., Alvarez-Candal, A., Alvi, S., Amara, A., Amendola, L., Amiaux, J., Andika, I. T., Andreon, S., Andrews, A., Angora, G., Angulo, R. E., Annibali, F., Anselmi, A., Anselmi, S., Arcari, S., Archidiacono, M., Aricò, G., Arnaud, M., Arnouts, S., Asgari, M., Asorey, J., Atayde, L., Atek, H., Atrio-Barandela, F., Aubert, M., Aubourg, E., Auphan, T., Auricchio, N., Aussel, B., Aussel, H., Avelino, P. P., Avgoustidis, A., Avila, S., Awan, S., Azzollini, R., Baccigalupi, C., Bachelet, E., Bacon, D., Baes, M., Bagley, M. B., Bahr-Kalus, B., Balaguera-Antolinez, A., Balbinot, E., Balcells, M., Baldi, M., Baldry, I., Balestra, A., Ballardini, M., Ballester, O., Balogh, M., Bañados, E., Barbier, R., Bardelli, S., Baron, M., Barreiro, T., Barrena, R., Barriere, J. -C., Barros, B. J., Barthelemy, A., Bartolo, N., Basset, A., Battaglia, P., Battisti, A. J., Baugh, C. M., Baumont, L., Bazzanini, L., Beaulieu, J. -P., Beckmann, V., Belikov, A. N., Bel, J., Bellagamba, F., Bella, M., Bellini, E., Benabed, K., Bender, R., Benevento, G., Bennett, C. L., Benson, K., Bergamini, P., Bermejo-Climent, J. R., Bernardeau, F., Bertacca, D., Berthe, M., Berthier, J., Bethermin, M., Beutler, F., Bevillon, C., Bhargava, S., Bhatawdekar, R., Bianchi, D., Bisigello, L., Biviano, A., Blake, R. P., Blanchard, A., Blazek, J., Blot, L., Bosco, A., Bodendorf, C., Boenke, T., Böhringer, H., Boldrini, P., Bolzonella, M., Bonchi, A., Bonici, M., Bonino, D., Bonino, L., Bonvin, C., Bon, W., Booth, J. T., Borgani, S., Borlaff, A. S., Borsato, E., Bose, B., Botticella, M. T., Boucaud, A., Bouche, F., Boucher, J. S., Boutigny, D., Bouvard, T., Bouwens, R., Bouy, H., Bowler, R. A. A., Bozza, V., Bozzo, E., Branchini, E., Brando, G., Brau-Nogue, S., Brekke, P., Bremer, M. N., Brescia, M., Breton, M. -A., Brinchmann, J., Brinckmann, T., Brockley-Blatt, C., Brodwin, M., Brouard, L., Brown, M. L., Bruton, S., Bucko, J., Buddelmeijer, H., Buenadicha, G., Buitrago, F., Burger, P., Burigana, C., Busillo, V., Busonero, D., Cabanac, R., Cabayol-Garcia, L., Cagliari, M. S., Caillat, A., Caillat, L., Calabrese, M., Calabro, A., Calderone, G., Calura, F., Quevedo, B. Camacho, Camera, S., Campos, L., Canas-Herrera, G., Candini, G. P., Cantiello, M., Capobianco, V., Cappellaro, E., Cappelluti, N., Cappi, A., Caputi, K. I., Cara, C., Carbone, C., Cardone, V. F., Carella, E., Carlberg, R. G., Carle, M., Carminati, L., Caro, F., Carrasco, J. M., Carretero, J., Carrilho, P., Duque, J. Carron, Carry, B., Carvalho, A., Carvalho, C. S., Casas, R., Casas, S., Casenove, P., Casey, C. M., Cassata, P., Castander, F. J., Castelao, D., Castellano, M., Castiblanco, L., Castignani, G., Castro, T., Cavet, C., Cavuoti, S., Chabaud, P. -Y., Chambers, K. C., Charles, Y., Charlot, S., Chartab, N., Chary, R., Chaumeil, F., Cho, H., Chon, G., Ciancetta, E., Ciliegi, P., Cimatti, A., Cimino, M., Cioni, M. -R. L., Claydon, R., Cleland, C., Clément, B., Clements, D. L., Clerc, N., Clesse, S., Codis, S., Cogato, F., Colbert, J., Cole, R. E., Coles, P., Collett, T. E., Collins, R. S., Colodro-Conde, C., Colombo, C., Combes, F., Conforti, V., Congedo, G., Conseil, S., Conselice, C. J., Contarini, S., Contini, T., Conversi, L., Cooray, A. R., Copin, Y., Corasaniti, P. -S., Corcho-Caballero, P., Corcione, L., Cordes, O., Corpace, O., Correnti, M., Costanzi, M., Costille, A., Courbin, F., Mifsud, L. Courcoult, Courtois, H. M., Cousinou, M. -C., Covone, G., Cowell, T., Cragg, C., Cresci, G., Cristiani, S., Crocce, M., Cropper, M., Crouzet, P. E, Csizi, B., Cuby, J. -G., Cucchetti, E., Cucciati, O., Cuillandre, J. -C., Cunha, P. A. C., Cuozzo, V., Daddi, E., D'Addona, M., Dafonte, C., Dagoneau, N., Dalessandro, E., Dalton, G. B., D'Amico, G., Dannerbauer, H., Danto, P., Das, I., Da Silva, A., da Silva, R., Doumerg, W. d'Assignies, Daste, G., Davies, J. E., Davini, S., Dayal, P., de Boer, T., Decarli, R., De Caro, B., Degaudenzi, H., Degni, G., de Jong, J. T. A., de la Bella, L. F., de la Torre, S., Delhaise, F., Delley, D., Delucchi, G., De Lucia, G., Denniston, J., De Paolis, F., De Petris, M., Derosa, A., Desai, S., Desjacques, V., Despali, G., Desprez, G., De Vicente-Albendea, J., Deville, Y., Dias, J. D. F., Díaz-Sánchez, A., Diaz, J. J., Di Domizio, S., Diego, J. M., Di Ferdinando, D., Di Giorgio, A. M., Dimauro, P., Dinis, J., Dolag, K., Dolding, C., Dole, H., Sánchez, H. Domínguez, Doré, O., Dournac, F., Douspis, M., Dreihahn, H., Droge, B., Dryer, B., Dubath, F., Duc, P. -A., Ducret, F., Duffy, C., Dufresne, F., Duncan, C. A. J., Dupac, X., Duret, V., Durrer, R., Durret, F., Dusini, S., Ealet, A., Eggemeier, A., Eisenhardt, P. R. M., Elbaz, D., Elkhashab, M. Y., Ellien, A., Endicott, J., Enia, A., Erben, T., Vigo, J. A. Escartin, Escoffier, S., Sanz, I. Escudero, Essert, J., Ettori, S., Ezziati, M., Fabbian, G., Fabricius, M., Fang, Y., Farina, A., Farina, M., Farinelli, R., Farrens, S., Faustini, F., Feltre, A., Ferguson, A. M. N., Ferrando, P., Ferrari, A. G., Ferré-Mateu, A., Ferreira, P. G., Ferreras, I., Ferrero, I., Ferriol, S., Ferruit, P., Filleul, D., Finelli, F., Finkelstein, S. L., Finoguenov, A., Fiorini, B., Flentge, F., Focardi, P., Fonseca, J., Fontana, A., Fontanot, F., Fornari, F., Fosalba, P., Fossati, M., Fotopoulou, S., Fouchez, D., Fourmanoit, N., Frailis, M., Fraix-Burnet, D., Franceschi, E., Franco, A., Franzetti, P., Freihoefer, J., Frenk, C. . S., Frittoli, G., Frugier, P. -A., Frusciante, N., Fumagalli, A., Fumagalli, M., Fumana, M., Fu, Y., Gabarra, L., Galeotta, S., Galluccio, L., Ganga, K., Gao, H., García-Bellido, J., Garcia, K., Gardner, J. P., Garilli, B., Gaspar-Venancio, L. -M., Gasparetto, T., Gautard, V., Gavazzi, R., Gaztanaga, E., Genolet, L., Santos, R. Genova, Gentile, F., George, K., Gerbino, M., Ghaffari, Z., Giacomini, F., Gianotti, F., Gibb, G. P. S., Gillard, W., Gillis, B., Ginolfi, M., Giocoli, C., Girardi, M., Giri, S. K., Goh, L. W. K., Gómez-Alvarez, P., Gonzalez-Perez, V., Gonzalez, A. H., Gonzalez, E. J., Gonzalez, J. C., Beauchamps, S. Gouyou, Gozaliasl, G., Gracia-Carpio, J., Grandis, S., Granett, B. R., Granvik, M., Grazian, A., Gregorio, A., Grenet, C., Grillo, C., Grupp, F., Gruppioni, C., Gruppuso, A., Guerbuez, C., Guerrini, S., Guidi, M., Guillard, P., Gutierrez, C. M., Guttridge, P., Guzzo, L., Gwyn, S., Haapala, J., Haase, J., Haddow, C. R., Hailey, M., Hall, A., Hall, D., Hamaus, N., Haridasu, B. S., Harnois-Déraps, J., Harper, C., Hartley, W. G., Hasinger, G., Hassani, F., Hatch, N. A., Haugan, S. V. H., Häußler, B., Heavens, A., Heisenberg, L., Helmi, A., Helou, G., Hemmati, S., Henares, K., Herent, O., Hernández-Monteagudo, C., Heuberger, T., Hewett, P. C., Heydenreich, S., Hildebrandt, H., Hirschmann, M., Hjorth, J., Hoar, J., Hoekstra, H., Holland, A. D., Holliman, M. S., Holmes, W., Hook, I., Horeau, B., Hormuth, F., Hornstrup, A., Hosseini, S., Hu, D., Hudelot, P., Hudson, M. J., Huertas-Company, M., Huff, E. M., Hughes, A. C. N., Humphrey, A., Hunt, L. K., Huynh, D. D., Ibata, R., Ichikawa, K., Iglesias-Groth, S., Ilbert, O., Ilić, S., Ingoglia, L., Iodice, E., Israel, H., Israelsson, U. E., Izzo, L., Jablonka, P., Jackson, N., Jacobson, J., Jafariyazani, M., Jahnke, K., Jain, B., Jansen, H., Jarvis, M. J., Jasche, J., Jauzac, M., Jeffrey, N., Jhabvala, M., Jimenez-Teja, Y., Muñoz, A. Jimenez, Joachimi, B., Johansson, P. H., Joudaki, S., Jullo, E., Kajava, J. J. E., Kang, Y., Kannawadi, A., Kansal, V., Karagiannis, D., Kärcher, M., Kashlinsky, A., Kazandjian, M. V., Keck, F., Keihänen, E., Kerins, E., Kermiche, S., Khalil, A., Kiessling, A., Kiiveri, K., Kilbinger, M., Kim, J., King, R., Kirkpatrick, C. C., Kitching, T., Kluge, M., Knabenhans, M., Knapen, J. H., Knebe, A., Kneib, J. -P., Kohley, R., Koopmans, L. V. E., Koskinen, H., Koulouridis, E., Kou, R., Kovács, A., Kovačić, I., Kowalczyk, A., Koyama, K., Kraljic, K., Krause, O., Kruk, S., Kubik, B., Kuchner, U., Kuijken, K., Kümmel, M., Kunz, M., Kurki-Suonio, H., Lacasa, F., Lacey, C. G., La Franca, F., Lagarde, N., Lahav, O., Laigle, C., La Marca, A., La Marle, O., Lamine, B., Lam, M. C., Lançon, A., Landt, H., Langer, M., Lapi, A., Larcheveque, C., Larsen, S. S., Lattanzi, M., Laudisio, F., Laugier, D., Laureijs, R., Laurent, V., Lavaux, G., Lawrenson, A., Lazanu, A., Lazeyras, T., Boulc'h, Q. Le, Brun, A. M. C. Le, Brun, V. Le, Leclercq, F., Lee, S., Graet, J. Le, Legrand, L., Leirvik, K. N., Jeune, M. Le, Lembo, M., Mignant, D. Le, Lepinzan, M. D., Lepori, F., Reun, A. Le, Leroy, G., Lesci, G. F., Lesgourgues, J., Leuzzi, L., Levi, M. E., Liaudat, T. I., Libet, G., Liebing, P., Ligori, S., Lilje, P. B., Lin, C. -C., Linde, D., Linder, E., Lindholm, V., Linke, L., Li, S. -S., Liu, S. J., Lloro, I., Lobo, F. S. N., Lodieu, N., Lombardi, M., Lombriser, L., Lonare, P., Longo, G., López-Caniego, M., Lopez, X. Lopez, Alvarez, J. Lorenzo, Loureiro, A., Loveday, J., Lusso, E., Macias-Perez, J., Maciaszek, T., Maggio, G., Magliocchetti, M., Magnard, F., Magnier, E. A., Magro, A., Mahler, G., Mainetti, G., Maino, D., Maiorano, E., Malavasi, N., Mamon, G. A., Mancini, C., Mandelbaum, R., Manera, M., Manjón-García, A., Mannucci, F., Mansutti, O., Outeiro, M. Manteiga, Maoli, R., Maraston, C., Marcin, S., Marcos-Arenal, P., Margalef-Bentabol, B., Marggraf, O., Marinucci, D., Marinucci, M., Markovic, K., Marleau, F. R., Marpaud, J., Martignac, J., Martín-Fleitas, J., Martin-Moruno, P., Martin, E. L., Martinelli, M., Martinet, N., Martin, H., Martins, C. J. A. P., Marulli, F., Massari, D., Massey, R., Masters, D. C., Matarrese, S., Matsuoka, Y., Matthew, S., Maughan, B. J., Mauri, N., Maurin, L., Maurogordato, S., McCarthy, K., McConnachie, A. W., McCracken, H. J., McDonald, I., McEwen, J. D., McPartland, C. J. R., Medinaceli, E., Mehta, V., Mei, S., Melchior, M., Melin, J. -B., Ménard, B., Mendes, J., Mendez-Abreu, J., Meneghetti, M., Mercurio, A., Merlin, E., Metcalf, R. B., Meylan, G., Migliaccio, M., Mignoli, M., Miller, L., Miluzio, M., Milvang-Jensen, B., Mimoso, J. P., Miquel, R., Miyatake, H., Mobasher, B., Mohr, J. J., Monaco, P., Monguió, M., Montoro, A., Mora, A., Dizgah, A. Moradinezhad, Moresco, M., Moretti, C., Morgante, G., Morisset, N., Moriya, T. J., Morris, P. W., Mortlock, D. J., Moscardini, L., Mota, D. F., Mottet, S., Moustakas, L. A., Moutard, T., Müller, T., Munari, E., Murphree, G., Murray, C., Murray, N., Musi, P., Nadathur, S., Nagam, B. C., Nagao, T., Naidoo, K., Nakajima, R., Nally, C., Natoli, P., Navarro-Alsina, A., Girones, D. Navarro, Neissner, C., Nersesian, A., Nesseris, S., Nguyen-Kim, H. N., Nicastro, L., Nichol, R. C., Nielbock, M., Niemi, S. -M., Nieto, S., Nilsson, K., Noller, J., Norberg, P., Nouri-Zonoz, A., Ntelis, P., Nucita, A. A., Nugent, P., Nunes, N. J., Nutma, T., Ocampo, I., Odier, J., Oesch, P. A., Oguri, M., Oliveira, D. Magalhaes, Onoue, M., Oosterbroek, T., Oppizzi, F., Ordenovic, C., Osato, K., Pacaud, F., Pace, F., Padilla, C., Paech, K., Pagano, L., Page, M. J., Palazzi, E., Paltani, S., Pamuk, S., Pandolfi, S., Paoletti, D., Paolillo, M., Papaderos, P., Pardede, K., Parimbelli, G., Parmar, A., Partmann, C., Pasian, F., Passalacqua, F., Paterson, K., Patrizii, L., Pattison, C., Paulino-Afonso, A., Paviot, R., Peacock, J. A., Pearce, F. R., Pedersen, K., Peel, A., Peletier, R. F., Ibanez, M. Pellejero, Pello, R., Penny, M. T., Percival, W. J., Perez-Garrido, A., Perotto, L., Pettorino, V., Pezzotta, A., Pezzuto, S., Philippon, A., Pierre, M., Piersanti, O., Pietroni, M., Piga, L., Pilo, L., Pires, S., Pisani, A., Pizzella, A., Pizzuti, L., Plana, C., Polenta, G., Pollack, J. E., Poncet, M., Pöntinen, M., Pool, P., Popa, L. A., Popa, V., Popp, J., Porciani, C., Porth, L., Potter, D., Poulain, M., Pourtsidou, A., Pozzetti, L., Prandoni, I., Pratt, G. W., Prezelus, S., Prieto, E., Pugno, A., Quai, S., Quilley, L., Racca, G. D., Raccanelli, A., Rácz, G., Radinović, S., Radovich, M., Ragagnin, A., Ragnit, U., Raison, F., Ramos-Chernenko, N., Ranc, C., Rasera, Y., Raylet, N., Rebolo, R., Refregier, A., Reimberg, P., Reiprich, T. H., Renk, F., Renzi, A., Retre, J., Revaz, Y., Reylé, C., Reynolds, L., Rhodes, J., Ricci, F., Ricci, M., Riccio, G., Ricken, S. O., Rissanen, S., Risso, I., Rix, H. -W., Robin, A. C., Rocca-Volmerange, B., Rocci, P. -F., Rodenhuis, M., Rodighiero, G., Monroy, M. Rodriguez, Rollins, R. P., Romanello, M., Roman, J., Romelli, E., Romero-Gomez, M., Roncarelli, M., Rosati, P., Rosset, C., Rossetti, E., Roster, W., Rottgering, H. J. A., Rozas-Fernández, A., Ruane, K., Rubino-Martin, J. A., Rudolph, A., Ruppin, F., Rusholme, B., Sacquegna, S., Sáez-Casares, I., Saga, S., Saglia, R., Sahlén, M., Saifollahi, T., Sakr, Z., Salvalaggio, J., Salvaterra, R., Salvati, L., Salvato, M., Salvignol, J. -C., Sánchez, A. G., Sanchez, E., Sanders, D. B., Sapone, D., Saponara, M., Sarpa, E., Sarron, F., Sartori, S., Sartoris, B., Sassolas, B., Sauniere, L., Sauvage, M., Sawicki, M., Scaramella, R., Scarlata, C., Scharré, L., Schaye, J., Schewtschenko, J. A., Schindler, J. -T., Schinnerer, E., Schirmer, M., Schmidt, F., Schmidt, M., Schneider, A., Schneider, M., Schneider, P., Schöneberg, N., Schrabback, T., Schultheis, M., Schulz, S., Schuster, N., Schwartz, J., Sciotti, D., Scodeggio, M., Scognamiglio, D., Scott, D., Scottez, V., Secroun, A., Sefusatti, E., Seidel, G., Seiffert, M., Sellentin, E., Selwood, M., Semboloni, E., Sereno, M., Serjeant, S., Serrano, S., Setnikar, G., Shankar, F., Sharples, R. M., Short, A., Shulevski, A., Shuntov, M., Sias, M., Sikkema, G., Silvestri, A., Simon, P., Sirignano, C., Sirri, G., Skottfelt, J., Slezak, E., Sluse, D., Smith, G. P., Smith, L. C., Smith, R. E., Smit, S. J. A., Soldano, F., Solheim, B. G. B., Sorce, J. G., Sorrenti, F., Soubrie, E., Spinoglio, L., Mancini, A. Spurio, Stadel, J., Stagnaro, L., Stanco, L., Stanford, S. A., Starck, J. -L., Stassi, P., Steinwagner, J., Stern, D., Stone, C., Strada, P., Strafella, F., Stramaccioni, D., Surace, C., Sureau, F., Suyu, S. H., Swindells, I., Szafraniec, M., Szapudi, I., Taamoli, S., Talia, M., Tallada-Crespí, P., Tanidis, K., Tao, C., Tarrío, P., Tavagnacco, D., Taylor, A. N., Taylor, J. E., Taylor, P. L., Teixeira, E. M., Tenti, M., Idiago, P. Teodoro, Teplitz, H. I., Tereno, I., Tessore, N., Testa, V., Testera, G., Tewes, M., Teyssier, R., Theret, N., Thizy, C., Thomas, P. D., Toba, Y., Toft, S., Toledo-Moreo, R., Tolstoy, E., Tommasi, E., Torbaniuk, O., Torradeflot, F., Tortora, C., Tosi, S., Tosti, S., Trifoglio, M., Troja, A., Trombetti, T., Tronconi, A., Tsedrik, M., Tsyganov, A., Tucci, M., Tutusaus, I., Uhlemann, C., Ulivi, L., Urbano, M., Vacher, L., Vaillon, L., Valageas, P., Valdes, I., Valentijn, E. A., Valenziano, L., Valieri, C., Valiviita, J., Broeck, M. Van den, Vassallo, T., Vavrek, R., Vega-Ferrero, J., Venemans, B., Venhola, A., Ventura, S., Kleijn, G. Verdoes, Vergani, D., Verma, A., Vernizzi, F., Veropalumbo, A., Verza, G., Vescovi, C., Vibert, D., Viel, M., Vielzeuf, P., Viglione, C., Viitanen, A., Villaescusa-Navarro, F., Vinciguerra, S., Visticot, F., Voggel, K., von Wietersheim-Kramsta, M., Vriend, W. J., Wachter, S., Walmsley, M., Walth, G., Walton, D. M., Walton, N. A., Wander, M., Wang, L., Wang, Y., Weaver, J. R., Weller, J., Wetzstein, M., Whalen, D. J., Whittam, I. H., Widmer, A., Wiesmann, M., Wilde, J., Williams, O. R., Winther, H. -A., Wittje, A., Wong, J. H. W., Wright, A. H., Yankelevich, V., Yeung, H. W., Yoon, M., Youles, S., Yung, L. Y. A., Zacchei, A., Zalesky, L., Zamorani, G., Vitorelli, A. Zamorano, Marc, M. Zanoni, Zennaro, M., Zerbi, F. M., Zinchenko, I. A., Zoubian, J., Zucca, E., and Zumalacarregui, M.
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Astrophysics - Cosmology and Nongalactic Astrophysics ,Astrophysics - Astrophysics of Galaxies ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
The current standard model of cosmology successfully describes a variety of measurements, but the nature of its main ingredients, dark matter and dark energy, remains unknown. Euclid is a medium-class mission in the Cosmic Vision 2015-2025 programme of the European Space Agency (ESA) that will provide high-resolution optical imaging, as well as near-infrared imaging and spectroscopy, over about 14,000 deg^2 of extragalactic sky. In addition to accurate weak lensing and clustering measurements that probe structure formation over half of the age of the Universe, its primary probes for cosmology, these exquisite data will enable a wide range of science. This paper provides a high-level overview of the mission, summarising the survey characteristics, the various data-processing steps, and data products. We also highlight the main science objectives and expected performance., Comment: Accepted for publication in the A&A special issue`Euclid on Sky'
- Published
- 2024
129. Euclid. II. The VIS Instrument
- Author
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Euclid Collaboration, Cropper, M., Al-Bahlawan, A., Amiaux, J., Awan, S., Azzollini, R., Benson, K., Berthe, M., Boucher, J., Bozzo, E., Brockley-Blatt, C., Candini, G. P., Cara, C., Chaudery, R. A., Cole, R. E., Danto, P., Denniston, J., Di Giorgio, A. M., Dryer, B., Endicott, J., Dubois, J. -P., Farina, M., Galli, E., Genolet, L., Gow, J. P. D., Guttridge, P., Hailey, M., Hall, D., Harper, C., Holland, A. D., Horeau, B., Hu, D., King, R., James, R. E., Larcheveque, C., Khalil, A., Lawrenson, A., Liebing, P., Martignac, J., McCracken, H. J., Murray, N., Nakajima, R., Niemi, S. -M., Pendem, A., Paltani, S., Philippon, A., Pool, P., Plana, C., Pottinger, S., Racca, G. D., Rousseau, A., Ruane, K., Salatti, M., Salvignol, J. -C., Sciortino, A., Short, Alexander, Liu, S. J., Skottfelt, J., Swindells, I., Smit, S. J. A., Szafraniec, M., Thomas, P. D., Thomas, W., Tommasi, E., Winter, B., Tosti, S., Visticot, F., Walton, D. M., Willis, G., Mora, A., Kohley, R., Massey, R., Nightingale, J. W., Kitching, T., Hoekstra, H., Aghanim, N., Altieri, B., Amara, A., Andreon, S., Auricchio, N., Aussel, H., Baldi, M., Balestra, A., Bardelli, S., Basset, A., Bender, R., Bodendorf, C., Boenke, T., Bonino, D., Branchini, E., Brescia, M., Brinchmann, J., Camera, S., Capobianco, V., Carbone, C., Cardone, V. F., Carretero, J., Casas, R., Casas, S., Castander, F. J., Castellano, M., Cavuoti, S., Cimatti, A., Congedo, G., Conselice, C. J., Conversi, L., Copin, Y., Courbin, F., Courtois, H. M., Cuby, J. -G., Cuillandre, J. -C., Da Silva, A., Degaudenzi, H., Dinis, J., Dolding, C., Douspis, M., Duncan, C. A. J., Dupac, X., Dusini, S., Ealet, A., Fabricius, M., Farrens, S., Ferriol, S., Fosalba, P., Fotopoulou, S., Frailis, M., Franceschi, E., Franzetti, P., Frugier, P. -A., Fumana, M., Galeotta, S., Garilli, B., Gillard, W., Gillis, B., Giocoli, C., Gómez-Alvarez, P., Granett, B. R., Grazian, A., Grupp, F., Guzzo, L., Haugan, S. V. H., Herent, O., Hoar, J., Holliman, M. S., Hook, I., Hormuth, F., Hornstrup, A., Hudelot, P., Jahnke, K., Jhabvala, M., Joachimi, B., Keihänen, E., Kermiche, S., Kilbinger, M., Kubik, B., Kuijken, K., Kümmel, M., Kunz, M., Kurki-Suonio, H., Lahav, O., Laureijs, R., Ligori, S., Lilje, P. B., Lindholm, V., Lloro, I., Alvarez, J. Lorenzo, Maino, D., Maiorano, E., Mansutti, O., Marggraf, O., Martinet, N., Marulli, F., Masters, D. C., Maurogordato, S., Medinaceli, E., Mei, S., Melchior, M., Mellier, Y., Meneghetti, M., Merlin, E., Meylan, G., Miller, L., Mohr, J. J., Moresco, M., Moscardini, L., Nichol, R. C., Nutma, T., Padilla, C., Paech, K., Pasian, F., Peacock, J. A., Pedersen, K., Percival, W. J., Pettorino, V., Pires, S., Polenta, G., Poncet, M., Popa, L. A., Pozzetti, L., Raison, F., Rebolo, R., Refregier, A., Renzi, A., Riccio, G., Rix, Hans-Walter, Romelli, E., Roncarelli, M., Rosset, C., Rossetti, E., Rottgering, H. J. A., Saglia, R., Sapone, D., Sauvage, M., Scaramella, R., Schirmer, M., Schneider, P., Schrabback, T., Secroun, A., Seidel, G., Serrano, S., Sirignano, C., Sirri, G., Stanco, L., Starck, J. -L., Tallada-Crespí, P., Tavagnacco, D., Taylor, A. N., Teplitz, H. I., Tereno, I., Toledo-Moreo, R., Torradeflot, F., Tutusaus, I., Valentijn, E. A., Valenziano, L., Vassallo, T., Kleijn, G. Verdoes, Veropalumbo, A., Wachter, S., Wang, Y., Weller, J., Zamorani, G., Zoubian, J., Zucca, E., Baccigalupi, C., Bernardeau, F., Biviano, A., Bolzonella, M., Boucaud, A., Burigana, C., Calabrese, M., Casenove, P., Colodro-Conde, C., Crocce, M., De Lucia, G., Di Ferdinando, D., Vigo, J. A. Escartin, Fabbian, G., Farinelli, R., Finelli, F., George, K., Gracia-Carpio, J., Ilić, S., Israel, H., Mainetti, G., Marcin, S., Martinelli, M., Mauri, N., Neissner, C., Nguyen-Kim, H. N., Pezzotta, A., Pöntinen, M., Porciani, C., Sakr, Z., Scottez, V., Sefusatti, E., Tenti, M., Viel, M., Wiesmann, M., Akrami, Y., Allevato, V., Anselmi, S., Aubourg, E., Ballardini, M., Bertacca, D., Bethermin, M., Blanchard, A., Blot, L., Borgani, S., Borlaff, A. S., Bruton, S., Cabanac, R., Calabro, A., Calderone, G., Canas-Herrera, G., Cappi, A., Carvalho, C. S., Castignani, G., Castro, T., Chambers, K. C., Chary, R., Contarini, S., Cooray, A. R., Cordes, O., Costanzi, M., Cucciati, O., Davini, S., De Caro, B., Desprez, G., Díaz-Sánchez, A., Di Domizio, S., Dole, H., Escoffier, S., Ferrari, A. G., Ferreira, P. G., Ferrero, I., Finoguenov, A., Fontana, A., Fornari, F., Gabarra, L., Ganga, K., García-Bellido, J., Gautard, V., Gaztanaga, E., Giacomini, F., Gianotti, F., Gozaliasl, G., Gregorio, A., Hall, A., Hartley, W. G., Hildebrandt, H., Hjorth, J., Huertas-Company, M., Ilbert, O., Joudaki, S., Kajava, J. J. E., Kansal, V., Karagiannis, D., Kirkpatrick, C. C., Lacasa, F., Graet, J. Le, Legrand, L., Libet, G., Loureiro, A., Macias-Perez, J., Magliocchetti, M., Mancini, C., Mannucci, F., Maoli, R., Martins, C. J. A. P., Matthew, S., Maurin, L., McPartland, C. J. R., Metcalf, R. B., Migliaccio, M., Miluzio, M., Monaco, P., Moretti, C., Morgante, G., Nadathur, S., Walton, Nicholas A., Odier, J., Oguri, M., Patrizii, L., Popa, V., Potter, D., Pourtsidou, A., Reimberg, P., Risso, I., Rocci, P. -F., Rollins, R. P., Rusholme, B., Sahlén, M., Sánchez, A. G., Scarlata, C., Schaye, J., Schewtschenko, J. A., Schneider, A., Schultheis, M., Sereno, M., Shankar, F., Sikkema, G., Silvestri, A., Simon, P., Mancini, A. Spurio, Stadel, J., Stanford, S. A., Steinwagner, J., Tanidis, K., Tao, C., Tessore, N., Testera, G., Tewes, M., Teyssier, R., Toft, S., Tosi, S., Troja, A., Tucci, M., Valieri, C., Valiviita, J., Vergani, D., Vernizzi, F., Verza, G., Vielzeuf, P., Weaver, J. R., Zalesky, L., Zinchenko, I. A., Archidiacono, M., Atrio-Barandela, F., Bouvard, T., Caro, F., Dimauro, P., Duc, P. -A., Fang, Y., Ferguson, A. M. N., Gasparetto, T., Gutierrez, C. M., Kova{č}ić, I., Kruk, S., Brun, A. M. C. Le, Liaudat, T. I., Montoro, A., Murray, C., Pagano, L., Paoletti, D., Sarpa, E., Viitanen, A., Lesgourgues, J., and Martín-Fleitas, J.
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Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
This paper presents the specification, design, and development of the Visible Camera (VIS) on the ESA Euclid mission. VIS is a large optical-band imager with a field of view of 0.54 deg^2 sampled at 0.1" with an array of 609 Megapixels and spatial resolution of 0.18". It will be used to survey approximately 14,000 deg^2 of extragalactic sky to measure the distortion of galaxies in the redshift range z=0.1-1.5 resulting from weak gravitational lensing, one of the two principal cosmology probes of Euclid. With photometric redshifts, the distribution of dark matter can be mapped in three dimensions, and, from how this has changed with look-back time, the nature of dark energy and theories of gravity can be constrained. The entire VIS focal plane will be transmitted to provide the largest images of the Universe from space to date, reaching m_AB>24.5 with S/N >10 in a single broad I_E~(r+i+z) band over a six year survey. The particularly challenging aspects of the instrument are the control and calibration of observational biases, which lead to stringent performance requirements and calibration regimes. With its combination of spatial resolution, calibration knowledge, depth, and area covering most of the extra-Galactic sky, VIS will also provide a legacy data set for many other fields. This paper discusses the rationale behind the VIS concept and describes the instrument design and development before reporting the pre-launch performance derived from ground calibrations and brief results from the in-orbit commissioning. VIS should reach fainter than m_AB=25 with S/N>10 for galaxies of full-width half-maximum of 0.3" in a 1.3" diameter aperture over the Wide Survey, and m_AB>26.4 for a Deep Survey that will cover more than 50 deg^2. The paper also describes how VIS works with the other Euclid components of survey, telescope, and science data processing to extract the cosmological information., Comment: Paper submitted as part of the A&A special issue `Euclid on Sky', which contains Euclid key reference papers and first results from the Euclid Early Release Observations
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- 2024
130. Extreme Flaring of Starlink Satellites
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Mallama, Anthony and Cole, Richard E.
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Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
Starlink satellites can become extremely bright when sunlight reflects specularly to an observer on the ground. The observed brightness of such flares is consistent with a bidirectional reflectance function of the Starlink satellite chassis. These findings are applied to the case of an extreme flare that was reported as an Unidentified Aerial Phenomena by the pilots of two commercial aircraft.
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- 2024
131. The Brightness of Starlink Mini Satellites During Orbit-Raising
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Mallama, Anthony, Cole, Richard E., Respler, Jay, Harrington, Scott, Lee, Ron, and Worley, Aaron
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Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
Observations of Starlink V2 Mini satellites during orbit-raising suggest that SpaceX applies brightness mitigation when they reach a height of 357 km. The mean apparent magnitudes for objects below that height threshold is 2.68 while the mean for those above is 6.46. When magnitudes are adjusted to a uniform distance of 1000 km the means are 4.58 and 7.52, respectively. The difference of 2.94 between distance-adjusted magnitudes above and below threshold implies that mitigation is 93% effective in reducing the brightness of orbit-raising spacecraft. Orbit-raising Mini spacecraft have a smaller impact on astronomical observations than higher altitude on-station spacecraft because they are relatively few in number. They also spend less time traversing the sky and spend longer in the Earth's shadow. These low-altitude objects will be more out-of-focus in large telescopes such as the LSST which reduces their impact, too. However, they attract considerable public attention and airline pilots have reported them as Unidentified Aerial Phenomena.
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- 2024
132. Beyond Calibration: Assessing the Probabilistic Fit of Neural Regressors via Conditional Congruence
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Young, Spencer, Edgren, Cole, Sinema, Riley, Hall, Andrew, Dong, Nathan, and Jenkins, Porter
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
While significant progress has been made in specifying neural networks capable of representing uncertainty, deep networks still often suffer from overconfidence and misaligned predictive distributions. Existing approaches for addressing this misalignment are primarily developed under the framework of calibration, with common metrics such as Expected Calibration Error (ECE). However, calibration can only provide a strictly marginal assessment of probabilistic alignment. Consequently, calibration metrics such as ECE are distribution-wise measures and cannot diagnose the point-wise reliability of individual inputs, which is important for real-world decision-making. We propose a stronger condition, which we term conditional congruence, for assessing probabilistic fit. We also introduce a metric, Conditional Congruence Error (CCE), that uses conditional kernel mean embeddings to estimate the distance, at any point, between the learned predictive distribution and the empirical, conditional distribution in a dataset. We show that using CCE to measure congruence 1) accurately quantifies misalignment between distributions when the data generating process is known, 2) effectively scales to real-world, high dimensional image regression tasks, and 3) can be used to gauge model reliability on unseen instances.
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- 2024
133. A Test of the Thermodynamics of Evolution
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Sadasivan, Daniel, Cantu, Cole, Marsh, Cecilia, and Graham, Andrew
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Quantitative Biology - Populations and Evolution - Abstract
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine learning, and thermodynamics. We present simulations of biological evolution used to test this framework. The test simulates organisms whose behavior is determined by specific parameters that play the role of genes. These genes are passed on to new simulated organisms with the capacity to mutate, allowing adaption of the organisms to the environment. With this simulation, we are able to test the the framework in question. The results of our simulation are consistent with the work being tested, providing evidence for it., Comment: 10 pages, 3 figures
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- 2024
134. Edwards-Wilkinson fluctuations in subcritical 2D stochastic heat equations
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Dunlap, Alexander and Graham, Cole
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Mathematics - Probability ,60F05 (Primary), 60H15, 35R60, 82B44 (Secondary) - Abstract
We study 2D nonlinear stochastic heat equations under a logarithmically attenuated white-noise limit with subcritical coupling. We show that solutions asymptotically exhibit Edwards-Wilkinson fluctuations. This extends work of Ran Tao, which required a stricter condition on the coupling. Part of the limiting fluctuation is measurable with respect to the original noise and the remainder is independent., Comment: 11 pages
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- 2024
135. Coherent $\pi^0\eta d$ photoproduction at forward deuteron angles measured at BGOOD
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Figueiredo, A. J. Clara, Jude, T. C., Alef, S., Cole, P. L., Di Salvo, R., Elsner, D., Fantini, A., Freyermuth, O., Frommberger, F., Ghio, F., Groß, J., Kohl, K., Sandri, P. Levi, Mandaglio, G., Pedroni, P., Reitz, B. -E., Romaniuk, M., Scheluchin, G., Schmieden, H., Sonnenschein, A., and Tillmanns, C.
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Nuclear Experiment - Abstract
The coherent reaction, $\gamma d \rightarrow \pi^0\eta d$ was studied with the BGOOD experiment at ELSA from threshold to a centre-of-mass energy of 3200\,MeV. A full kinematic reconstruction was made, with final state deuterons identified in the forward spectrometer and $\pi^0$ and $\eta$ decays in the central BGO Rugby Ball. The strength of the differential cross section exceeds what can be described by models of coherent photoproduction at forward angles by orders of magnitude. The distribution of the differential cross section has an excellent agreement with a model including quasi-free $\Delta \pi$ photoproduction, pion re-scattering and $N(1535)$ formation and subsequent nucleon coalescence to the deuteron. This also gives a reasonable description of the two-body invariant mass distributions and naturally explains the similar magnitudes of this channel and $\pi^0\pi^0 d$ coherent photoproduction., Comment: 7 pages, 5 figures
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- 2024
136. A practical guide to light-sheet microscopy for nanoscale imaging: Looking beyond the cell
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Kramer, Stephanie N., Antarasen, Jeanpun, Reinholt, Cole R., and Kisley, Lydia
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Physics - Optics ,Physics - Instrumentation and Detectors - Abstract
We present a comprehensive guide to light-sheet microscopy (LSM) to assist scientists in navigating the practical implementation of this microscopy technique. Emphasizing the applicability of LSM to image both static microscale and nanoscale features, as well as diffusion dynamics, we present the fundamental concepts of microscopy, progressing through beam profile considerations, to image reconstruction. We outline key practical decisions in constructing a home-built system and provide insight into the alignment and calibration processes. We briefly discuss the conditions necessary for constructing a continuous 3D image and introduce our home-built code for data analysis. By providing this guide, we aim to alleviate the challenges associated with designing and constructing LSM systems and offer scientists new to LSM a valuable resource in navigating this complex field., Comment: 65 pages, 16 figures, submitted to Journal of Applied Physics
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- 2024
137. Artificial intelligence for abnormality detection in high volume neuroimaging: a systematic review and meta-analysis
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Agarwal, Siddharth, Wood, David A., Grzeda, Mariusz, Suresh, Chandhini, Din, Munaib, Cole, James, Modat, Marc, and Booth, Thomas C
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Purpose: Most studies evaluating artificial intelligence (AI) models that detect abnormalities in neuroimaging are either tested on unrepresentative patient cohorts or are insufficiently well-validated, leading to poor generalisability to real-world tasks. The aim was to determine the diagnostic test accuracy and summarise the evidence supporting the use of AI models performing first-line, high-volume neuroimaging tasks. Methods: Medline, Embase, Cochrane library and Web of Science were searched until September 2021 for studies that temporally or externally validated AI capable of detecting abnormalities in first-line CT or MR neuroimaging. A bivariate random-effects model was used for meta-analysis where appropriate. PROSPERO: CRD42021269563. Results: Only 16 studies were eligible for inclusion. Included studies were not compromised by unrepresentative datasets or inadequate validation methodology. Direct comparison with radiologists was available in 4/16 studies. 15/16 had a high risk of bias. Meta-analysis was only suitable for intracranial haemorrhage detection in CT imaging (10/16 studies), where AI systems had a pooled sensitivity and specificity 0.90 (95% CI 0.85 - 0.94) and 0.90 (95% CI 0.83 - 0.95) respectively. Other AI studies using CT and MRI detected target conditions other than haemorrhage (2/16), or multiple target conditions (4/16). Only 3/16 studies implemented AI in clinical pathways, either for pre-read triage or as post-read discrepancy identifiers. Conclusion: The paucity of eligible studies reflects that most abnormality detection AI studies were not adequately validated in representative clinical cohorts. The few studies describing how abnormality detection AI could impact patients and clinicians did not explore the full ramifications of clinical implementation.
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- 2024
138. Exploring a Cognitive Architecture for Learning Arithmetic Equations
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Gawin, Cole
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Quantitative Biology - Neurons and Cognition ,Computer Science - Artificial Intelligence - Abstract
The acquisition and performance of arithmetic skills and basic operations such as addition, subtraction, multiplication, and division are essential for daily functioning, and reflect complex cognitive processes. This paper explores the cognitive mechanisms powering arithmetic learning, presenting a neurobiologically plausible cognitive architecture that simulates the acquisition of these skills. I implement a number vectorization embedding network and an associative memory model to investigate how an intelligent system can learn and recall arithmetic equations in a manner analogous to the human brain. I perform experiments that provide insights into the generalization capabilities of connectionist models, neurological causes of dyscalculia, and the influence of network architecture on cognitive performance. Through this interdisciplinary investigation, I aim to contribute to ongoing research into the neural correlates of mathematical cognition in intelligent systems., Comment: 16 pages, 6 figures, 2 tables
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- 2024
139. A self-supervised text-vision framework for automated brain abnormality detection
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Wood, David A., Guilhem, Emily, Kafiabadi, Sina, Busaidi, Ayisha Al, Dissanayake, Kishan, Hammam, Ahmed, Mansoor, Nina, Townend, Matthew, Agarwal, Siddharth, Wei, Yiran, Mazumder, Asif, Barker, Gareth J., Sasieni, Peter, Ourselin, Sebastien, Cole, James H., and Booth, Thomas C.
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Artificial neural networks trained on large, expert-labelled datasets are considered state-of-the-art for a range of medical image recognition tasks. However, categorically labelled datasets are time-consuming to generate and constrain classification to a pre-defined, fixed set of classes. For neuroradiological applications in particular, this represents a barrier to clinical adoption. To address these challenges, we present a self-supervised text-vision framework that learns to detect clinically relevant abnormalities in brain MRI scans by directly leveraging the rich information contained in accompanying free-text neuroradiology reports. Our training approach consisted of two-steps. First, a dedicated neuroradiological language model - NeuroBERT - was trained to generate fixed-dimensional vector representations of neuroradiology reports (N = 50,523) via domain-specific self-supervised learning tasks. Next, convolutional neural networks (one per MRI sequence) learnt to map individual brain scans to their corresponding text vector representations by optimising a mean square error loss. Once trained, our text-vision framework can be used to detect abnormalities in unreported brain MRI examinations by scoring scans against suitable query sentences (e.g., 'there is an acute stroke', 'there is hydrocephalus' etc.), enabling a range of classification-based applications including automated triage. Potentially, our framework could also serve as a clinical decision support tool, not only by suggesting findings to radiologists and detecting errors in provisional reports, but also by retrieving and displaying examples of pathologies from historical examinations that could be relevant to the current case based on textual descriptors., Comment: Under Review
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- 2024
140. A Classification-Based Adaptive Segmentation Pipeline: Feasibility Study Using Polycystic Liver Disease and Metastases from Colorectal Cancer CT Images
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Wang, Peilong, Kline, Timothy L., Missert, Andy D., Cook, Cole J., Callstrom, Matthew R., Chan, Alex, Hartman, Robert P., Kelm, Zachary S., and Korfiatis, Panagiotis
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Physics - Medical Physics - Abstract
Automated segmentation tools often encounter accuracy and adaptability issues when applied to images of different pathology. The purpose of this study is to explore the feasibility of building a workflow to efficiently route images to specifically trained segmentation models. By implementing a deep learning classifier to automatically classify the images and route them to appropriate segmentation models, we hope that our workflow can segment the images with different pathology accurately. The data we used in this study are 350 CT images from patients affected by polycystic liver disease and 350 CT images from patients presenting with liver metastases from colorectal cancer. All images had the liver manually segmented by trained imaging analysts. Our proposed adaptive segmentation workflow achieved a statistically significant improvement for the task of total liver segmentation compared to the generic single segmentation model (non-parametric Wilcoxon signed rank test, n=100, p-value << 0.001). This approach is applicable in a wide range of scenarios and should prove useful in clinical implementations of segmentation pipelines., Comment: J Digit Imaging. Inform. med. (2024)
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- 2024
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141. Planet Hunters TESS V: a planetary system around a binary star, including a mini-Neptune in the habitable zone
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Eisner, Nora L., Grunblatt, Samuel K., Barragán, Oscar, Faridani, Thea H., Lintott, Chris, Aigrain, Suzanne, Johnston, Cole, Mason, Ian R., Stassun, Keivan G., Bedell, Megan, Boyle, Andrew W., Ciardi, David R., Clark, Catherine A., Hebrard, Guillaume, Hogg, David W., Howell, Steve B., Klein, Baptiste, Llama, Joe, Winn, Joshua N., Zhao, Lily L., Murphy, Joseph M. Akana, Beard, Corey, Brinkman, Casey L., Chontos, Ashley, Cortes-Zuleta, Pia, Delfosse, Xavier, Giacalone, Steven, Gilbert, Emily A., Heidari, Neda, Holcomb, Rae, Jenkins, Jon M., Kiefer, Flavien, Lubin, Jack, Martioli, Eder, Polanski, Alex S., Saunders, Nicholas, Seager, Sara, Shporer, Avi, Tyler, Dakotah, Van Zandt, Judah, Alhassan, Safaa, Amratlal, Daval J., Antonel, Lais I., Bentzen, Simon L. S., Bosch, Milton K. D., Bundy, David, Chitsiga, Itayi, Delaunay, Jérôme F., Doisy, Xavier, Ferstenou, Richard, Fynø, Mark, Geary, James M., Haynaly, Gerry, Hermes, Pete, Huten, Marc, Lee, Sam, Metcalfe, Paul, Pennell, Garry J., Puszkarska, Joanna, Schäfer, Thomas, Stiller, Lisa, Tanner, Christopher, Tarr, Allan, and Wilkinson, Andrew
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Astrophysics - Earth and Planetary Astrophysics - Abstract
We report on the discovery and validation of a transiting long-period mini-Neptune orbiting a bright (V = 9.0 mag) G dwarf (TOI 4633; R = 1.05 RSun, M = 1.10 MSun). The planet was identified in data from the Transiting Exoplanet Survey Satellite by citizen scientists taking part in the Planet Hunters TESS project. Modeling of the transit events yields an orbital period of 271.9445 +/- 0.0040 days and radius of 3.2 +/- 0.20 REarth. The Earth-like orbital period and an incident flux of 1.56 +/- 0.2 places it in the optimistic habitable zone around the star. Doppler spectroscopy of the system allowed us to place an upper mass limit on the transiting planet and revealed a non-transiting planet candidate in the system with a period of 34.15 +/- 0.15 days. Furthermore, the combination of archival data dating back to 1905 with new high angular resolution imaging revealed a stellar companion orbiting the primary star with an orbital period of around 230 years and an eccentricity of about 0.9. The long period of the transiting planet, combined with the high eccentricity and close approach of the companion star makes this a valuable system for testing the formation and stability of planets in binary systems., Comment: 24 pages, 16 figures, 4 tables
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- 2024
- Full Text
- View/download PDF
142. Double Robust Variance Estimation with Parametric Working Models
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Shook-Sa, Bonnie E., Zivich, Paul N., Lee, Chanhwa, Xue, Keyi, Ross, Rachael K., Edwards, Jessie K., Stringer, Jeffrey S. A., and Cole, Stephen R.
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Statistics - Methodology ,Statistics - Applications - Abstract
Doubly robust estimators have gained popularity in the field of causal inference due to their ability to provide consistent point estimates when either an outcome or exposure model is correctly specified. However, for nonrandomized exposures the influence function based variance estimator frequently used with doubly robust estimators of the average causal effect is only consistent when both working models (i.e., outcome and exposure models) are correctly specified. Here, the empirical sandwich variance estimator and the nonparametric bootstrap are demonstrated to be doubly robust variance estimators. That is, they are expected to provide valid estimates of the variance leading to nominal confidence interval coverage when only one working model is correctly specified. Simulation studies illustrate the properties of the influence function based, empirical sandwich, and nonparametric bootstrap variance estimators in the setting where parametric working models are assumed. Estimators are applied to data from the Improving Pregnancy Outcomes with Progesterone (IPOP) study to estimate the effect of maternal anemia on birth weight among women with HIV., Comment: 32 pages, 14 figures, 13 tables
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- 2024
143. Why not a thin plate spline for spatial models? A comparative study using Bayesian inference
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Cavieres, Joaquin, Moraga, Paula, and Monnahan, Cole C.
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Statistics - Methodology ,Statistics - Computation - Abstract
Spatial modelling often uses Gaussian random fields to capture the stochastic nature of studied phenomena. However, this approach incurs significant computational burdens (O(n3)), primarily due to covariance matrix computations. In this study, we propose to use a low-rank approximation of a thin plate spline as a spatial random effect in Bayesian spatial models. We compare its statistical performance and computational efficiency with the approximated Gaussian random field (by the SPDE method). In this case, the dense matrix of the thin plate spline is approximated using a truncated spectral decomposition, resulting in computational complexity of O(kn2) operations, where k is the number of knots. Bayesian inference is conducted via the Hamiltonian Monte Carlo algorithm of the probabilistic software Stan, which allows us to evaluate performance and diagnostics for the proposed models. A simulation study reveals that both models accurately recover the parameters used to simulate data. However, models using a thin plate spline demonstrate superior execution time to achieve the convergence of chains compared to the models utilizing an approximated Gaussian random field. Furthermore, thin plate spline models exhibited better computational efficiency for simulated data coming from different spatial locations. In a real application, models using a thin plate spline as spatial random effect produced similar results in estimating a relative index of abundance for a benthic marine species when compared to models incorporating an approximated Gaussian random field. Although they were not the more computational efficient models, their simplicity in parametrization, execution time and predictive performance make them a valid alternative for spatial modelling under Bayesian inference., Comment: Preliminary results of this analysis were presented in CMStatistics, 2023 (Berlin)
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- 2024
144. An analysis of parameter compression and full-modeling techniques with Velocileptors for DESI 2024 and beyond
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Maus, M., Chen, S., White, M., Aguilar, J., Ahlen, S., Aviles, A., Brieden, S., Brooks, D., Claybaugh, T., Cole, S., de la Macorra, A., Dey, Arjun, Doel, P., Ferraro, S., Findlay, N., Forero-Romero, J. E., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Hahn, C., Honscheid, K., Howlett, C., Ishak, M., Juneau, S., Kremin, A., Lai, Y., Landriau, M., Levi, M. E., Manera, M., Miquel, R., Mueller, E., Myers, A. D., Nadathur, S., Nie, J., Noriega, H. E., Palanque-Delabrouille, N., Percival, W. J., Poppett, C., Ramirez-Solano, S., Rezaie, M., Rocher, A., Rossi, G., Sanchez, E., Schlegel, D., Schubnell, M., Seo, H., Sprayberry, D., Tarlé, G., Vargas-Magaña, M., Weaver, B. A., Yuan, S., Zarrouk, P., Zhang, H., Zhou, R., and Zou, H.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
In anticipation of forthcoming data releases of current and future spectroscopic surveys, we present the validation tests and analysis of systematic effects within \texttt{velocileptors} modeling pipeline when fitting mock data from the \texttt{AbacusSummit} N-body simulations. We compare the constraints obtained from parameter compression methods to the direct fitting (Full-Modeling) approaches of modeling the galaxy power spectra, and show that the ShapeFit extension to the traditional template method is consistent with the Full-Modeling method within the standard $\Lambda$CDM parameter space. We show the dependence on scale cuts when fitting the different redshift bins using the ShapeFit and Full-Modeling methods. We test the ability to jointly fit data from multiple redshift bins as well as joint analysis of the pre-reconstruction power spectrum with the post-reconstruction BAO correlation function signal. We further demonstrate the behavior of the model when opening up the parameter space beyond $\Lambda$CDM and also when combining likelihoods with external datasets, namely the Planck CMB priors. Finally, we describe different parametrization options for the galaxy bias, counterterm, and stochastic parameters, and employ the halo model in order to physically motivate suitable priors that are necessary to ensure the stability of the perturbation theory., Comment: 56 pages, 23 figures. Supporting publication of DESI 2024 V: Analysis of the full shape of two-point clustering statistics from galaxies and quasars
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- 2024
145. Validating the Galaxy and Quasar Catalog-Level Blinding Scheme for the DESI 2024 analysis
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Andrade, U., Mena-Fernández, J., Awan, H., Ross, A. J., Brieden, S., Pan, J., de Mattia, A., Aguilar, J., Ahlen, S., Alves, O., Brooks, D., Buckley-Geer, E., Chaussidon, E., Claybaugh, T., Cole, S., de la Macorra, A., Dey, Arjun, Doel, P., Fanning, K., Forero-Romero, J. E., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Guy, J., Hahn, C., Hanif, M. M. S, Honscheid, K., Howlett, C., Huterer, D., Juneau, S., Kremin, A., Landriau, M., Guillou, L. Le, Levi, M. E., Manera, M., Martini, P., Meisner, A., Miquel, R., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Newman, J. A., Nie, J., Niz, G., Palanque-Delabrouille, N., Percival, W. J., Pinon, M., Poppett, C., Prada, F., Rashkovetskyi, M., Rezaie, M., Rossi, G., Sanchez, E., Schlegel, D., Schubnell, M., Seo, H., Sprayberry, D., Tarlé, G., Vargas-Magaña, M., Verde, L., and Weaver, B. A.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
In the era of precision cosmology, ensuring the integrity of data analysis through blinding techniques is paramount -- a challenge particularly relevant for the Dark Energy Spectroscopic Instrument (DESI). DESI represents a monumental effort to map the cosmic web, with the goal to measure the redshifts of tens of millions of galaxies and quasars. Given the data volume and the impact of the findings, the potential for confirmation bias poses a significant challenge. To address this, we implement and validate a comprehensive blind analysis strategy for DESI Data Release 1 (DR1), tailored to the specific observables DESI is most sensitive to: Baryonic Acoustic Oscillations (BAO), Redshift-Space Distortion (RSD) and primordial non-Gaussianities (PNG). We carry out the blinding at the catalog level, implementing shifts in the redshifts of the observed galaxies to blind for BAO and RSD signals and weights to blind for PNG through a scale-dependent bias. We validate the blinding technique on mocks, as well as on data by applying a second blinding layer to perform a battery of sanity checks. We find that the blinding strategy alters the data vector in a controlled way such that the BAO and RSD analysis choices do not need any modification before and after unblinding. The successful validation of the blinding strategy paves the way for the unblinded DESI DR1 analysis, alongside future blind analyses with DESI and other surveys., Comment: Supporting publication of "DESI 2024 II: Sample definitions, characteristics, and two-point clustering statistics", "DESI 2024 III: Baryon Acoustic Oscillations from Galaxies and Quasars", and "DESI 2024 V: Analysis of the full shape of two-point clustering statistics from galaxies and quasars". (v2 - update DESI references)
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- 2024
146. A comparison of effective field theory models of redshift space galaxy power spectra for DESI 2024 and future surveys
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Maus, M., Lai, Y., Noriega, H. E., Ramirez-Solano, S., Aviles, A., Chen, S., Fromenteau, S., Gil-Marín, H., Howlett, C., Vargas-Magaña, M., White, M., Zarrouk, P., Aguilar, J., Ahlen, S., Alves, O., Brieden, S., Brooks, D., Burtin, E., Claybaugh, T., Cole, S., Dawson, K., Icaza-Lizaola, M., de la Macorra, A., de Mattia, A., Doel, P., Ferraro, S., Findlay, N., Forero-Romero, J. E., Gaztañaga, E., Gontcho, S. Gontcho A, Hahn, C., Honscheid, K., Ishak, M., Kremin, A., Landriau, M., Guillou, L. Le, Manera, M., Miquel, R., Mueller, E., Nadathur, S., Niz, G., Palanque-Delabrouille, N., Percival, W. J., Poppett, C., Prada, F., Rezaie, M., Rocher, A., Rossi, G., Sanchez, E., Schlegel, D., Schubnell, M., Sprayberry, D., Tarlé, G., Yuan, S., Zhao, R., Zhou, R., and Zou, H.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
In preparation for the next generation of galaxy redshift surveys, and in particular the year-one data release from the Dark Energy Spectroscopic Instrument (DESI), we investigate the consistency of a variety of effective field theory models that describe the galaxy-galaxy power spectra in redshift space into the quasi-linear regime using 1-loop perturbation theory. These models are employed in the pipelines \texttt{velocileptors}, \texttt{PyBird}, and \texttt{Folps$\nu$}. While these models have been validated independently, a detailed comparison with consistent choices has not been attempted. After briefly discussing the theoretical differences between the models we describe how to provide a more apples-to-apples comparison between them. We present the results of fitting mock spectra from the \texttt{AbacusSummit} suite of N-body simulations provided in three redshift bins to mimic the types of dark time tracers targeted by the DESI survey. We show that the theories behave similarly and give consistent constraints in both the forward-modeling and ShapeFit compressed fitting approaches. We additionally generate (noiseless) synthetic data from each pipeline to be fit by the others, varying the scale cuts in order to show that the models agree within the range of scales for which we expect 1-loop perturbation theory to be applicable. This work lays the foundation of Full-Shape analysis with DESI Y1 galaxy samples where in the tests we performed, we found no systematic error associated with the modeling of the galaxy redshift space power spectrum for this volume., Comment: 33 pages, 12 figures. Supporting publication of DESI 2024 V: Analysis of the full shape of two-point clustering statistics from galaxies and quasars
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- 2024
147. Comparing Compressed and Full-modeling Analyses with FOLPS: Implications for DESI 2024 and beyond
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Noriega, H. E., Aviles, A., Gil-Marín, H., Ramirez-Solano, S., Fromenteau, S., Vargas-Magaña, M., Aguilar, J., Ahlen, S., Alves, O., Brieden, S., Brooks, D., Cervantes-Cota, J. L., Chen, S., Claybaugh, T., Cole, S., Dawson, K., de la Macorra, A., de Mattia, A., Doel, P., Findlay, N., Forero-Romero, J. E., Gaztañaga, E., Gontcho, S. Gontcho A, Honscheid, K., Hou, J., Howlett, C., Ishak, M., Juneau, S., Lai, Y., Landriau, M., Manera, M., Maus, M., Miquel, R., Morales-Navarrete, G., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Niz, G., Palanque-Delabrouille, N., Percival, W. J., Poppett, C., Rezaie, M., Rocher, A., Rossi, G., Sanchez, E., Schlegel, D., Schubnell, M., Sprayberry, D., Tarlé, G., Verde, L., Yuan, S., Zarrouk, P., and Zou, H.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
The Dark Energy Spectroscopic Instrument (DESI) will provide unprecedented information about the large-scale structure of our Universe. In this work, we study the robustness of the theoretical modelling of the power spectrum of FOLPS, a novel effective field theory-based package for evaluating the redshift space power spectrum in the presence of massive neutrinos. We perform this validation by fitting the AbacusSummit high-accuracy $N$-body simulations for Luminous Red Galaxies, Emission Line Galaxies and Quasar tracers, calibrated to describe DESI observations. We quantify the potential systematic error budget of FOLPS, finding that the modelling errors are fully sub-dominant for the DESI statistical precision within the studied range of scales. Additionally, we study two complementary approaches to fit and analyse the power spectrum data, one based on direct Full-Modelling fits and the other on the ShapeFit compression variables, both resulting in very good agreement in precision and accuracy. In each of these approaches, we study a set of potential systematic errors induced by several assumptions, such as the choice of template cosmology, the effect of prior choice in the nuisance parameters of the model, or the range of scales used in the analysis. Furthermore, we show how opening up the parameter space beyond the vanilla $\Lambda$CDM model affects the DESI observables. These studies include the addition of massive neutrinos, spatial curvature, and dark energy equation of state. We also examine how relaxing the usual Cosmic Microwave Background and Big Bang Nucleosynthesis priors on the primordial spectral index and the baryonic matter abundance, respectively, impacts the inference on the rest of the parameters of interest. This paper pathways towards performing a robust and reliable analysis of the shape of the power spectrum of DESI galaxy and quasar clustering using FOLPS., Comment: Supporting publication of DESI 2024 VII: Cosmological constraints from full-shape analyses of the two-point clustering statistics measurements, in preparation (2024)
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- 2024
148. Full Modeling and Parameter Compression Methods in configuration space for DESI 2024 and beyond
- Author
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Ramirez-Solano, S., Icaza-Lizaola, M., Noriega, H. E., Vargas-Magaña, M., Fromenteau, S., Aviles, A., Rodriguez-Martinez, F., Aguilar, J., Ahlen, S., Alves, O., Brieden, S., Brooks, D., Claybaugh, T., Cole, S., de la Macorra, A., Dey, Arjun, Dey, B., Doel, P., Fanning, K., Forero-Romero, J. E., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Honscheid, K., Howlett, C., Juneau, S., Lai, Y., Landriau, M., Manera, M., Maus, M., Miquel, R., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Nie, J., Percival, W. J., Poppett, C., Rezaie, M., Rossi, G., Sanchez, E., Schlegel, D., Schubnell, M., Seo, H., Sprayberry, D., Tarlé, G., Verde, L., Weaver, B. A., Wechsler, R. H., Yuan, S., Zarrouk, P., and Zou, H.
- Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
In the contemporary era of high-precision spectroscopic surveys, led by projects like DESI, there is an increasing demand for optimizing the extraction of cosmological information from clustering data. This work conducts a thorough comparison of various methodologies for modeling the full shape of the two-point statistics in configuration space. We investigate the performance of both direct fits (Full-Modeling) and the parameter compression approaches (ShapeFit and Standard). We utilize the ABACUS-SUMMIT simulations, tailored to exceed DESI's precision requirements. Particularly, we fit the two-point statistics of three distinct tracers (LRG, ELG, and QSO), by employing a Gaussian Streaming Model in tandem with Convolution Lagrangian Perturbation Theory and Effective Field Theory. We explore methodological setup variations, including the range of scales, the set of galaxy bias parameters, the inclusion of the hexadecapole, as well as model extensions encompassing varying $n_s$ and allowing for $w_0w_a$CDM dark energy model. Throughout these varied explorations, while precision levels fluctuate and certain configurations exhibit tighter parameter constraints, our pipeline consistently recovers the parameter values of the mocks within $1\sigma$ in all cases for a 1-year DESI volume. Additionally, we compare the performance of configuration space analysis with its Fourier space counterpart using three models: PyBird, FOLPS and velocileptors, presented in companion papers. We find good agreement with the results from all these models., Comment: Supporting publication of DESI 2024 KP5
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- 2024
149. KATch: A Fast Symbolic Verifier for NetKAT
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Moeller, Mark, Jacobs, Jules, Belanger, Olivier Savary, Darais, David, Schlesinger, Cole, Smolka, Steffen, Foster, Nate, and Silva, Alexandra
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Computer Science - Programming Languages - Abstract
We develop new data structures and algorithms for checking verification queries in NetKAT, a domain-specific language for specifying the behavior of network data planes. Our results extend the techniques obtained in prior work on symbolic automata and provide a framework for building efficient and scalable verification tools. We present KATch, an implementation of these ideas in Scala, featuring an extended set of NetKAT operators that are useful for expressing network-wide specifications, and a verification engine that constructs a bisimulation or generates a counter-example showing that none exists. We evaluate the performance of our implementation on real-world and synthetic benchmarks, verifying properties such as reachability and slice isolation, typically returning a result in well under a second, which is orders of magnitude faster than previous approaches. Our advancements underscore NetKAT's potential as a practical, declarative language for network specification and verification.
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- 2024
- Full Text
- View/download PDF
150. Identifying Quasars from the DESI Bright Galaxy Survey
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Juneau, S., Canning, R., Alexander, D. M., Pucha, R., Fawcett, V. A., Myers, A. D., Moustakas, J., Ruiz-Macias, O., Cole, S., Pan, Z., Aguilar, J., Ahlen, S., Alam, S., Bailey, S., Brooks, D., Chaussidon, E., Circosta, C., Claybaugh, T., Dawson, K., de la Macorra, A., Dey, Arjun, Doel, P., Fanning, K., Forero-Romero, J. E., Gaztañaga, E., Gontcho, S. Gontcho A, Gutierrez, G., Hahn, C., Honscheid, K., Kehoe, R., Kisner, T., Kremin, A., Lambert, A., Landriau, M., Guillou, L. Le, Manera, M., Martini, P., Meisner, A., Miquel, R., Muñoz-Gutiérrez, A., Nie, J., Palanque-Delabrouille, N., Percival, W. J., Poppett, C., Prada, F., Ravoux, C., Rezaie, M., Rossi, G., Sanchez, E., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Silber, J., Siudek, M., Sprayberry, D., Tarlé, G., Zhou, Z., and Zou, H.
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Astrophysics - Astrophysics of Galaxies ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
The Dark Energy Spectroscopic Instrument (DESI) cosmology survey includes a Bright Galaxy Survey (BGS) which will yield spectra for over ten million bright galaxies (r<20.2 AB mag). The resulting sample will be valuable for both cosmological and astrophysical studies. However, the star/galaxy separation criterion implemented in the nominal BGS target selection algorithm excludes quasar host galaxies in addition to bona fide stars. While this excluded population is comparatively rare (~3-4 per square degrees), it may hold interesting clues regarding galaxy and quasar physics. Therefore, we present a target selection strategy that was implemented to recover these missing active galactic nuclei (AGN) from the BGS sample. The design of the selection criteria was both motivated and confirmed using spectroscopy. The resulting BGS-AGN sample is uniformly distributed over the entire DESI footprint. According to DESI survey validation data, the sample comprises 93% quasi-stellar objects (QSOs), 3% narrow-line AGN or blazars with a galaxy contamination rate of 2% and a stellar contamination rate of 2%. Peaking around redshift z=0.5, the BGS-AGN sample is intermediary between quasars from the rest of the BGS and those from the DESI QSO sample in terms of redshifts and AGN luminosities. The stacked spectrum is nearly identical to that of the DESI QSO targets, confirming that the sample is dominated by quasars. We highlight interesting small populations reaching z>2 which are either faint quasars with nearby projected companions or very bright quasars with strong absorption features including the Lyman-apha forest, metal absorbers and/or broad absorption lines., Comment: 41 pages, 31 figures, submitted to the AAS journals. Comments are welcome
- Published
- 2024
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