3,969 results on '"Murphy, Michael P."'
Search Results
2. Cultivating Catholic Studies and Charism through Co-Curricular Programs: The Annual John Courtney Murray, S.J., Forum @LUC
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Murphy, Michael P.
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- 2023
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3. Isotopic abundance of carbon in the DLA towards QSO B1331+170
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Milaković, Dinko, Webb, John K., Molaro, Paolo, Lee, Chung-Chi, Jethwa, Prashin, Cupani, Guido, Murphy, Michael T., Welsh, Louise, D'Odorico, Valentina, Cristiani, Stefano, Santos, Ricardo Génova, Martins, Carlos J. A. P., Nunes, Nelson J., Schmidt, Tobias M., Pepe, Francesco A., Osorio, Maria Rosa Zapatero, Alibert, Yann, Hernández, J. I. González, Di Marcantonio, Paolo, Palle, Enric, Santos, Nuno C., and Rebolo, Rafael
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Astrophysics - Astrophysics of Galaxies ,Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
Chemical evolution models predict a gradual build-up of $^{13}$C in the universe, based on empirical nuclear reaction rates and assumptions on the properties of stellar populations. However, old metal-poor stars within the Galaxy contain more $^{13}$C than is predicted, suggesting that further refinements to the models are necessary. Gas at high redshift provides important supplementary information at metallicities $-2\lesssim$ [Fe/H] $\lesssim-1$, for which there are only a few measurements in the Galaxy. We obtained new, high-quality, VLT/ESPRESSO observations of the QSO B1331+170 and used them to measure $^{12}$C/$^{13}$C in the damped Lyman-$\alpha$ system (DLA) at $z_{abs}=1.776$, with [Fe/H]=-1.27. AI-VPFIT, an Artificial Intelligence tool based on genetic algorithms and guided by a spectroscopic information criterion, was used to explore different possible kinematic structures of the carbon gas. Three hundred independent AI-VPFIT models of the absorption system were produced using pre-set $^{12}$C/$^{13}$C values, ranging from 4 to 500. Our results show that $^{12}$C/$^{13}$C$=28.5^{+51.5}_{-10.4}$, suggesting a possibility of $^{13}$C production at low metallicity., Comment: 11 pages, 6 figures. Three appendices. To appear in MNRAS
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- 2024
4. A Security Assessment tool for Quantum Threat Analysis
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Halak, Basel, Csete, Cristian Sebastian, Joyce, Edward, Papaioannou, Jack, Pires, Alexandre, Soma, Jin, Gokkaya, Betul, and Murphy, Michael
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Computer Science - Cryptography and Security ,Computer Science - Computers and Society - Abstract
The rapid advancement of quantum computing poses a significant threat to many current security algorithms used for secure communication, digital authentication, and information encryption. A sufficiently powerful quantum computer could potentially exploit vulnerabilities in these algorithms, rendering data in transit insecure. This threat is expected to materialize within the next 20 years. Immediate transition to quantum-resilient cryptographic schemes is crucial, primarily to mitigate store-now-decrypt-later attacks and to ensure the security of products with decade-long operational lives. This transition requires a systematic approach to identifying and upgrading vulnerable cryptographic implementations. This work developed a quantum assessment tool for organizations, providing tailored recommendations for transitioning their security protocols into a post-quantum world. The work included a systematic evaluation of the proposed solution using qualitative feedback from network administrators and cybersecurity experts. This feedback was used to refine the accuracy and usability of the assessment process. The results demonstrate its effectiveness and usefulness in helping organizations prepare for quantum computing threats. The assessment tool is publicly available at (https://quantum-watch.soton.ac.uk).
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- 2024
5. At least one in a dozen stars exhibits evidence of planetary ingestion
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Liu, Fan, Ting, Yuan-Sen, Yong, David, Bitsch, Bertram, Karakas, Amanda, Murphy, Michael T., Joyce, Meridith, Dotter, Aaron, and Dai, Fei
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Earth and Planetary Astrophysics - Abstract
Stellar chemical compositions can be altered by ingestion of planetary material and/or planet formation which removes refractory material from the proto-stellar disc. These "planet signatures" appear as correlations between elemental abundance differences and the dust condensation temperature. Detecting these planet signatures, however, is challenging due to unknown occurrence rates, small amplitudes, and heterogeneous star samples with large differences in stellar ages, and therefore stars born together (i.e., co-natal) with identical compositions can facilitate such detections. While previous spectroscopic studies were limited to small number of binary stars, the Gaia satellite provides new opportunities for detecting stellar chemical signatures of planets among co-moving pairs of stars confirmed to be co-natal. Here we report high-precision chemical abundances for a homogeneous sample of 91 co-natal pairs of stars with a well-defined selection function and identify at least seven new instances of planetary ingestion, corresponding to an occurrence rate of 8%. An independent Bayesian indicator is deployed, which can effectively disentangle the planet signatures from other factors, such as random abundance variation and atomic diffusion. Our study provides new evidence of planet signatures and facilitates a deeper understanding of the star-planet-chemistry connection by providing new observational constraints on the mechanisms of planet engulfment, formation and evolution., Comment: 29 pages, 11 figures. Author's submitted version before final edits. Published in Nature on March 21, 2024: https://www.nature.com/articles/s41586-024-07091-y
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- 2024
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6. Clinical Validation of Non-invasive Simulation-Based Determination of Vascular Impedance, Wave Intensity, and Hydraulic Work in Patients Undergoing Transcatheter Aortic Valve Replacement
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Brown, Jonathan Y., Fernandez, Gabriela Veiga, De La Torre Hernández, Jose M., Murphy, Michael, Wessler, Benjamin S., and Edelman, Elazer R.
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- 2024
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7. The Role of Dimensions of Social Support in the Relationship Between Stigma and Mental Health: A Moderation Analysis
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Lo Hog Tian, Jason M., Watson, James R., Cioppa, Lynne, Murphy, Michael, Boni, Anthony R., Parsons, Janet A., Maunder, Robert G., and Rourke, Sean B.
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- 2024
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8. Fundamental physics with ESPRESSO: a new determination of the D/H ratio towards PKS1937-101
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Guarneri, Francesco, Pasquini, Luca, D'Odorico, Valentina, Cristiani, Stefano, Cupani, Guido, Di Marcantonio, Paolo, Hernández, J. I. González, Martins, C. J. A. P., Mascareño, Alejandro Suárez, Milaković, Dinko, Molaro, Paolo, Murphy, Michael T., Nunes, Nelson J., Palle, Enric, Pepe, Francesco, Rebolo, Rafael, Santos, Nuno C., Santos, Ricardo Génova, Schmidt, Tobias M., Sousa, Sérgio G., Sozzetti, Alessandro, and Trost, Andrea
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
Primordial abundances of light elements are sensitive to the physics of the early Universe and can directly constrain cosmological quantities, such as the baryon-to-photon ratio $\eta_{10}$, the baryon density and the number of neutrino families. Deuterium is especially suited for these studies: its primordial abundance is sensitive and monotonically dependent on $\eta_{10}$, allowing an independent measurement of the cosmic baryon density that can be compared, for instance, against the Planck satellite data. The primordial deuterium abundance can be measured in high $H_I$ column density absorption systems towards distant quasars. We report here a new measurement, based on high-resolution ESPRESSO data, of the primordial $D_I$ abundance of a system at redshift $z \sim 3.572$, towards PKS1937-101. Using only ESPRESSO data, we find a D/H ratio of $2.638\pm0.128 \times 10^{-5}$, while including the available UVES data improves the precision, leading to a ratio of $2.608 \pm 0.102 \times 10^{-5}$. The results of this analysis agree with those of the most precise existing measurements. We find that the relatively low column density of this system ($\log{N_{\rm H_I}/ {\rm cm}^{-2}}\sim18 $) introduces modelling uncertainties, which become the main contributor to the error budget., Comment: Accepted for publication in MNRAS. 16 pages, 10 figures and 6 tables (4 in main text, 2 in Appendix). Full model is available at the end of the manuscript
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- 2024
9. Probing the small scale structure of the Inter-Galactic Medium with ESPRESSO: spectroscopy of the lensed QSO UM673
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Cristiani, Stefano, Cupani, Guido, Trost, Andrea, D'Odorico, Valentina, Guarneri, Francesco, Curto, Gaspare Lo, Meneghetti, Massimo, Di Marcantonio, Paolo, Faria, João P., Hernández, Jonay I. González, Lovis, Christophe, Martins, Carlos J. A. P., Milaković, Dinko, Molaro, Paolo, Murphy, Michael T., Nunes, Nelson J., Pepe, Francesco, Rebolo, Rafael, Santos, Nuno C., Schmidt, Tobias M., Sousa, Sérgio G., Sozzetti, Alessandro, and Osorio, María Rosa Zapatero
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Astrophysics - Cosmology and Nongalactic Astrophysics ,General Relativity and Quantum Cosmology - Abstract
The gravitationally lensed quasar J014516.6-094517 at z=2.719 has been observed with the ESPRESSO instrument at the ESO VLT to obtain high-fidelity spectra of the two images A and B with a resolving power R=70000. At the redshifts under investigation (2.1 < z < 2.7), the Lyman forests along the two sightlines are separated by sub-kiloparsec physical distances and exhibit a strong correlation. We find that the two forests are indistinguishable at the present level of signal-to-noise ratio and do not show any global velocity shift, with the cross-correlation peaking at $\Delta v = 12 \pm 48$ m/s. The distribution of the difference in velocity of individual Lyman-$\alpha$ features is compatible with a null average and a mean absolute deviation of 930 m/s. Significant differences in NHI column density are not detected, putting a limit to the RMS fluctuation in the baryon density on $\leq 1$ proper kpc scales of $\Delta \rho / \rho < 3$%. On the other hand, metal lines show significant differences both in velocity structure and in column density. A toy model shows that the difference in velocity of the metal features between the two sightlines is compatible with the the motions of the baryonic component associated to dark matter halos of typical mass $M\simeq 2\times 10^{10} M_\odot$, also compatible with the observed incidence of the metal systems. The present observations confirm the feasibility of the Sandage test of the cosmic redshift drift with high-fidelity spectroscopy of the Lyman forest of distant, bright quasars, but also provide an element of caution about the intrinsic noise associated to the usage of metal features for the same purpose., Comment: 17 pages, 10 figures, 5 tables, accepted for publication in MNRAS
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- 2024
10. HRMOS White Paper: Science Motivation
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Magrini, Laura, Bensby, Thomas, Brucalassi, Anna, Randich, Sofia, Jeffries, Robin, de Silva, Gayandhi, Skuladottir, Asa, Smiljanic, Rodolfo, Gonzalez, Oscar, Hill, Vanessa, Lagarde, Nadege, Tolstoy, Eline, Arroyo-Polonio, Jose' Maria, Baratella, Martina, Barnes, John R., Battaglia, Giuseppina, Baumgardt, Holger, Bellazzini, Michele, Biazzo, Katia, Bragaglia, Angela, Carter, Bradley, Casali, Giada, Cescutti, Gabriele, Danielski, Camilla, Mena, Elisa Delgado, Drazdauskas, Arnas, Gieles, Mark, Giribaldi, Riano, Hawkins, Keith, Hoeijmakers, H. Jens, Jablonka, Pascale, Kamath, Devika, Louth, Tom, Marino, Anna Fabiola, Martell, Sarah, Merle, Thibault, Montet, Benjamin, Murphy, Michael T., Nisini, Brunella, Nordlander, Thomas, D'Orazi, Valentina, Pino, Lorenzo, Romano, Donatella, Sacco, Germano, Sandford, Nathan R., Sollima, Antonio, Spina, Lorenzo, Tautvaivsiene, Grazina, Ting, Yuan-Sen, Tozzi, Andrea, Van der Swaelmen, Mathieu, Van Eck, Sophie, Watson, Stephen, Worley, C. Clare, and Zocchi, Alice
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Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Solar and Stellar Astrophysics - Abstract
The High-Resolution Multi-Object Spectrograph (HRMOS) is a facility instrument that we plan to propose for the Very Large Telescope (VLT) of the European Southern Observatory (ESO), following the initial presentation at the VLT 2030 workshop held at ESO in June 2019. HRMOS provides a combination of capabilities that are essential to carry out breakthrough science across a broad range of active research areas from stellar astrophysics and exoplanet studies to Galactic and Local Group archaeology. HRMOS fills a gap in capabilities amongst the landscape of future instrumentation planned for the next decade. The key characteristics of HRMOS will be high spectral resolution (R = 60000 - 80000) combined with multi-object (20-100) capabilities and long term stability that will provide excellent radial velocity precision and accuracy (10m/s). Initial designs predict that a SNR~100 will be achievable in about one hour for a star with mag(AB) = 15, while with the same exposure time a SNR~ 30 will be reached for a star with mag(AB) = 17. The combination of high resolution and multiplexing with wavelength coverage extending to relatively blue wavelengths (down to 380\,nm), makes HRMOS a spectrograph that will push the boundaries of our knowledge and that is envisioned as a workhorse instrument in the future. The science cases presented in this White Paper include topics and ideas developed by the Core Science Team with the contributions from the astronomical community, also through the wide participation in the first HRMOS Workshop (https://indico.ict.inaf.it/event/1547/) that took place in Firenze (Italy) in October 2021., Comment: 88 pages, 39 figures. Comments and expressions of interest are welcome by contacting members of the Core Science Team
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- 2023
11. Correlates of Problematic Gambling in Emerging Adult University Students in Ireland
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Murphy, Michael P., Murphy, Raegan, and Roberts, Amanda
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- 2024
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12. A Committee to Manage Innovative Learning Spaces: Balancing Committee Size, Cross-Campus Representation, and Decision-Making Power
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Leger, Andrew B., McRae, Karalyn E., and Murphy, Michael P. A.
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The growth in active learning classrooms represents a major shift in the pedagogy and built environment of higher education. While a robust literature exists to discuss the development, use, and evaluation of these innovative learning spaces, the practical considerations of managing innovative learning spaces has not received the same level of attention. This article describes the management model at Queen's University, outlining key workflow considerations: committee size, cross-campus representation, and decision-making power. The conclusion sets out future research opportunities related to the institutional dynamics of innovative learning space management.
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- 2023
13. Malonate given at reperfusion prevents post-myocardial infarction heart failure by decreasing ischemia/reperfusion injury
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Abe, Jiro, Vujic, Ana, Prag, Hiran A., Murphy, Michael P., and Krieg, Thomas
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- 2024
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14. The experience of teaching in an active learning classroom: a positive/negative perception study
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Murphy, Michael P. A., Phillipson, Andrea, McRae, Karalyn E., and Leger, Andrew B.
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- 2024
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15. Signatures of gas flows-I: Connecting the kinematics of the HI circumgalactic medium to galaxy rotation
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Nateghi, Hasti, Kacprzak, Glenn G., Nielsen, Nikole M., Murphy, Michael T., Churchill, Christopher W., Muzahid, Sowgat, Sameer, and Charlton, Jane C.
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Astrophysics - Astrophysics of Galaxies - Abstract
The CGM hosts many physical processes with different kinematic signatures that affect galaxy evolution. We address the CGM-galaxy kinematic connection by quantifying the fraction of HI that is aligned with galaxy rotation with the equivalent width co-rotation fraction, $f_{\rm EWcorot}$. Using 70 quasar sightlines having HST/COS HI absorption (${12<\log (N(HI)/{\rm cm}^{-2})<20}$) within $5R_{\rm vir}$ of $z<0.6$ galaxies we find that $f_{\rm EWcorot}$ increases with increasing HI column density. $f_{\rm EWcorot}$ is flat at $\sim0.6$ within $R_{\rm vir}$ and decreases beyond $R_{\rm vir}$ to $f_{\rm EWcorot}$$\sim0.35$. $f_{\rm EWcorot}$ also has a flat distribution with azimuthal and inclination angles within $R_{\rm vir}$, but decreases by a factor of two outside of $R_{\rm vir}$ for minor axis gas and by a factor of two for edge-on galaxies. Inside $R_{\rm vir}$, co-rotation dominated HI is located within $\sim 20$ deg of the major and minor axes. We surprisingly find equal amounts of HI absorption consistent with co-rotation along both major and minor axes within $R_{\rm vir}$. However, this co-rotation disappears along the minor axis beyond $R_{\rm vir}$, suggesting that if this gas is from outflows, then it is bound to galaxies. $f_{\rm EWcorot}$ is constant over two decades of halo mass, with no decrease for log(M$_{\rm h}/M_{\odot})>12$ as expected from simulations. Our results suggest that co-rotating gas flows are best found by searching for higher column density gas within $R_{\rm vir}$ and near the major and minor axes., Comment: 22 pages, 11 figures, accepted for publication in MNRAS July 26th 2024
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- 2023
16. Signatures of gas flows-II: Connecting the kinematics of the multiphase circumgalactic medium to galaxy rotation
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Nateghi, Hasti, Kacprzak, Glenn G., Nielsen, Nikole M., Sameer, Murphy, Michael T., Churchill, Christopher W., and Charlton, Jane C.
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Astrophysics - Astrophysics of Galaxies - Abstract
The multiphase CGM hosts critical processes that affect galaxy evolution such as accretion and outflows. We searched for evidence of these phenomena by using the EW co-rotation fraction ($f_{\rm EWcorot}$) to study the kinematic connection between the multiphase CGM and host galaxy rotation. We examined CGM absorption from HST/COS (including, but not limited to, SiII, CII, SiIII, CIII, and OVI) within $21\leq D\leq~276$ kpc of 27 galaxies. We find the median $f_{\rm EWcorot}$ for all ions is consistent within errors and the $f_{\rm EWcorot}$ increases with increasing N(HI). The $f_{\rm EWcorot}$ of lower ionization gas decreases with increasing $D/R_{\rm vir}$ while OVI and HI are consistent with being flat. The $f_{\rm EWcorot}$ varies minimally as a function of azimuthal angle and is similar for all ions at a fixed azimuthal angle. The larger number of OVI detections enabled us to investigate where the majority of co-rotating gas is found. Highly co-rotating OVI primarily resides along the galaxies' major axis. Looking at the $f_{\rm EWcorot}$ as a function of ionization potential (${d{f_{\rm EWcorot}}}/{d{(eV)}}$), we find a stronger co-rotation signature for lower-ionization gas. There are suggestions of a connection between the CGM metallicity and major axis co-rotation where low-ionization gas with higher $f_{\rm EWcorot}$ exhibits lower metallicity and may trace large-scale filamentary inflows. Higher ionization gas with higher $f_{\rm EWcorot}$ exhibits higher metallicity and may instead trace co-planar recycled gas accretion. Our results stress the importance of comparing absorption originating from a range of ionization phases to differentiate between various gas flow scenarios., Comment: 18 pages, 11 figures, accepted for publication in MNRAS 2024 September 9
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- 2023
17. HIFuzz: Human Interaction Fuzzing for small Unmanned Aerial Vehicles
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Chambers, Theodore, Vierhauser, Michael, Agrawal, Ankit, Murphy, Michael, Brauer, Jason Matthew, Purandare, Salil, Cohen, Myra B., and Cleland-Huang, Jane
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Computer Science - Human-Computer Interaction - Abstract
Small Unmanned Aerial Systems (sUAS) must meet rigorous safety standards when deployed in high-stress emergency response scenarios; however many reported accidents have involved humans in the loop. In this paper, we, therefore, present the HiFuzz testing framework, which uses fuzz testing to identify system vulnerabilities associated with human interactions. HiFuzz includes three distinct levels that progress from a low-cost, limited-fidelity, large-scale, no-hazard environment, using fully simulated Proxy Human Agents, via an intermediate level, where proxy humans are replaced with real humans, to a high-stakes, high-cost, real-world environment. Through applying HiFuzz to an autonomous multi-sUAS system-under-test, we show that each test level serves a unique purpose in revealing vulnerabilities and making the system more robust with respect to human mistakes. While HiFuzz is designed for testing sUAS systems, we further discuss its potential for use in other Cyber-Physical Systems.
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- 2023
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18. C3PO: Towards a complete census of co-moving pairs of stars. I. High precision stellar parameters for 250 stars
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Yong, David, Liu, Fan, Ting, Yuan-Sen, Joyce, Meridith, Bitsch, Bertram, Dai, Fei, Dotter, Aaron, Karakas, Amanda I., and Murphy, Michael T.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Astrophysics of Galaxies - Abstract
We conduct a line-by-line differential analysis of a sample of 125 co-moving pairs of stars (dwarfs and subgiants near solar metallicity). We obtain high precision stellar parameters with average uncertainties in effective temperature, surface gravity and metallicity of 16.5 K, 0.033 dex and 0.014 dex, respectively. We classify the co-moving pairs of stars into two groups, chemically homogeneous (conatal; |Delta[Fe/H]| $\le$ 0.04 dex) and inhomogeneous (non-conatal), and examine the fraction of chemically homogeneous pairs as a function of separation and effective temperature. The four main conclusions from this study are: (1) A spatial separation of \ds = 10$^6$ AU is an approximate boundary between homogeneous and inhomogeneous pairs of stars, and we restrict our conclusions to only consider the 91 pairs with \ds $\le$ 10$^6$ AU; (2) There is no trend between velocity separation and the fraction of chemically homogeneous pairs in the range \dv $\le$ 4 \kms; (3) We confirm that the fraction of chemically inhomogeneous pairs increases with increasing \teff\ and the trend matches a toy model of that expected from planet ingestion; (4) Atomic diffusion is not the main cause of the chemical inhomogeneity. A major outcome from this study is a sample of 56 bright co-moving pairs of stars with chemical abundance differences $\leq$ 0.02 dex (5\%) which is a level of chemical homogeneity comparable to that of the Hyades open cluster. These important objects can be used, in conjunction with star clusters and the \gaia\ ``benchmark'' stars, to calibrate stellar abundances from large-scale spectroscopic surveys., Comment: MNRAS in press (see source file for full versions of long tables)
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- 2023
19. Selenoprotein deficiency disorder predisposes to aortic aneurysm formation.
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Schoenmakers, Erik, Marelli, Federica, Jørgensen, Helle, Visser, W, Moran, Carla, Groeneweg, Stefan, Avalos, Carolina, Jurgens, Sean, Figg, Nichola, Finigan, Alison, Wali, Neha, Agostini, Maura, Wardle-Jones, Hannah, Lyons, Greta, Rusk, Rosemary, Gopalan, Deepa, Twiss, Philip, Visser, Jacob, Goddard, Martin, Nashef, Samer, Heijmen, Robin, Clift, Paul, Sinha, Sanjay, Pirruccello, James, Ellinor, Patrick, Busch-Nentwich, Elisabeth, Ramirez-Solis, Ramiro, Murphy, Michael, Persani, Luca, Bennett, Martin, and Chatterjee, Krishna
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Humans ,Male ,Mice ,Animals ,Zebrafish ,Selenocysteine ,Muscle ,Smooth ,Vascular ,Aortic Aneurysm ,Selenoproteins ,Myocytes ,Smooth Muscle - Abstract
Aortic aneurysms, which may dissect or rupture acutely and be lethal, can be a part of multisystem disorders that have a heritable basis. We report four patients with deficiency of selenocysteine-containing proteins due to selenocysteine Insertion Sequence Binding Protein 2 (SECISBP2) mutations who show early-onset, progressive, aneurysmal dilatation of the ascending aorta due to cystic medial necrosis. Zebrafish and male mice with global or vascular smooth muscle cell (VSMC)-targeted disruption of Secisbp2 respectively show similar aortopathy. Aortas from patients and animal models exhibit raised cellular reactive oxygen species, oxidative DNA damage and VSMC apoptosis. Antioxidant exposure or chelation of iron prevents oxidative damage in patients cells and aortopathy in the zebrafish model. Our observations suggest a key role for oxidative stress and cell death, including via ferroptosis, in mediating aortic degeneration.
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- 2023
20. Potent neutralization of SARS-CoV-2 variants by RBD nanoparticle and prefusion-stabilized spike immunogens
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Miranda, Marcos C., Kepl, Elizabeth, Navarro, Mary Jane, Chen, Chengbo, Johnson, Max, Sprouse, Kaitlin R., Stewart, Cameron, Palser, Anne, Valdez, Adian, Pettie, Deleah, Sydeman, Claire, Ogohara, Cassandra, Kraft, John C., Pham, Minh, Murphy, Michael, Wrenn, Sam, Fiala, Brooke, Ravichandran, Rashmi, Ellis, Daniel, Carter, Lauren, Corti, Davide, Kellam, Paul, Lee, Kelly, Walls, Alexandra C., Veesler, David, and King, Neil P.
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- 2024
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21. Study Protocol: Global Research Initiative on the Neurophysiology of Schizophrenia (GRINS) project
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Wang, Jun, Jiang, Chenguang, Guo, Zhenglin, Chapman, Sinéad, Kozhemiako, Nataliia, Mylonas, Dimitrios, Su, Yi, Zhou, Lin, Shen, Lu, Qin, Shengying, Murphy, Michael, Tan, Shuping, Manoach, Dara S., Stickgold, Robert, Huang, Hailiang, Zhou, Zhenhe, Purcell, Shaun M., Hall, Meihua, Hyman, Steven E., and Pan, Jen Q.
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- 2024
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22. Elevated Na is a dynamic and reversible modulator of mitochondrial metabolism in the heart
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Chung, Yu Jin, Hoare, Zoe, Baark, Friedrich, Yu, Chak Shun, Guo, Jia, Fuller, William, Southworth, Richard, Katschinski, Doerthe M., Murphy, Michael P., Eykyn, Thomas R., and Shattock, Michael J.
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- 2024
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23. “We know what we should be eating, but we don’t always do that.” How and why people eat the way they do: a qualitative study with rural australians
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Van Dyke, Nina, Murphy, Michael, and Drinkwater, Eric J.
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- 2024
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24. Naked mole-rats have distinctive cardiometabolic and genetic adaptations to their underground low-oxygen lifestyles
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Faulkes, Chris G., Eykyn, Thomas R., Miljkovic, Jan Lj., Gilbert, James D., Charles, Rebecca L., Prag, Hiran A., Patel, Nikayla, Hart, Daniel W., Murphy, Michael P., Bennett, Nigel C., and Aksentijevic, Dunja
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- 2024
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25. Nephrectomy for xanthogranulomatous pyelonephritis—a not-so-simple solution
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Kelly, Caroline, Anderson, Steven, Looney, Aisling, Shannon, Naomi, Senaratne, Radha, O’Connor, Eabhann, Breen, Kieran, Lennon, Gerald, McGuire, Barry, Murphy, Michael, Moran, Diarmaid, and Galvin, David
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- 2024
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26. Effect of Force Field Resolution on Membrane Mechanical Response and Mechanoporation Damage under Deformation Simulations
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Vo, Anh T. N., Murphy, Michael A., Phan, Phong K., Prabhu, Raj K., and Stone, Tonya W.
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- 2024
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27. EEG-Meta-Microstates: Towards a More Objective Use of Resting-State EEG Microstate Findings Across Studies
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Koenig, Thomas, Diezig, Sarah, Kalburgi, Sahana Nagabhushan, Antonova, Elena, Artoni, Fiorenzo, Brechet, Lucie, Britz, Juliane, Croce, Pierpaolo, Custo, Anna, Damborská, Alena, Deolindo, Camila, Heinrichs, Markus, Kleinert, Tobias, Liang, Zhen, Murphy, Michael M, Nash, Kyle, Nehaniv, Chrystopher, Schiller, Bastian, Smailovic, Una, Tarailis, Povilas, Tomescu, Miralena, Toplutaş, Eren, Vellante, Federica, Zanesco, Anthony, Zappasodi, Filippo, Zou, Qihong, and Michel, Christoph M
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- 2024
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28. A Potential Source of Bias in Group-Level EEG Microstate Analysis
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Murphy, Michael, Wang, Jun, Jiang, Chenguang, Wang, Lei A., Kozhemiako, Nataliia, Wang, Yining, Pan, Jen Q., and Purcell, Shaun M.
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- 2024
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29. The ESO's Extremely Large Telescope Working Groups
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Padovani, Paolo, Cirasuolo, Michele, van der Burg, Remco, Cantalloube, Faustine, George, Elizabeth, Kasper, Markus, Leschinski, Kieran, Martins, Carlos, Milli, Julien, Möhler, Sabine, Neeser, Mark, Neichel, Benoit, Otarola, Angel, Sánchez-Janssen, Rubén, Serra, Benoit, Smette, Alain, Valenti, Elena, Verinaud, Christophe, Vernet, Joël, Absil, Olivier, Agapito, Guido, Andersen, Morten, Arcidiacono, Carmelo, Arko, Matej, Baudoz, Pierre, Beltramo-Martin, Olivier, Biancalani, Enrico, Bierwirth, Thomas, Burtscher, Leonard, Carlà, Giulia, Castro-Almazán, Julio A., Cheffot, Anne-Laure, Coccato, Lodovico, Correia, Carlos, Fetick, Romain, Fiorentino, Giuliana, Fusco, Thierry, García-Lorenzo, Begoña, Fusillo, Nicola Gentile, Gonzalez, Oscar, Grazian, Andrea, Gullieuszik, Marco, Hainaut, Olivier, Ivanov, Valentin, Kaasinen, Melanie, Kaddad, Darshan, Kamiński, Tomasz, Kausch, Wolfgang, Kerber, Florian, Kimeswenger, Stefan, Kokotanekova, Rosita, Kuznetsov, Arseniy, Lau, Alexis, Louarn, Miska Le, Lemmel, Frédéric, Liske, Jochen, Curto, Gaspare Lo, Lucsanyi, David, Lundin, Lars, Noll, Stefan, Oberti, Sylvain, Osborn, James, Masciadri, Elena, Milaković, Dinko, Murphy, Michael T., Pedichini, Fernando, Santaella, Miguel Pereira, Piazzesi, Roberto, López, Javier Piqueras, Plantet, Cédric, Prod'homme, Thibaut, Przybilla, Norbert, Puech, Mathieu, Reid, Derryck T., Reiners, Ansgar, Rijnenberg, Rutger, Rodrigues, Myriam, Rossi, Fabio, Routledge, Laurence, Smit, Hans, Tecza, Mathias, Thatte, Niranjan, van Boekel, Roy, Verma, Aprajita, and Vigan, Arthur
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Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
Since 2005 ESO has been working with its community and industry to develop an extremely large optical/infrared telescope. ESO's Extremely Large Telescope, or ELT for short, is a revolutionary ground-based telescope that will have a 39-metre main mirror and will be the largest visible and infrared light telescope in the world. To address specific topics that are needed for the science operations and calibrations of the telescope, thirteen specific working groups were created to coordinate the effort between ESO, the instrument consortia, and the wider community. We describe here the goals of these working groups as well as their achievements so far., Comment: 8 pages, 4 figures
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- 2023
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30. Survey for Distant Solar Twins (SDST) -- III. Identification of new solar twin and solar analogue stars
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Lehmann, Christian, Murphy, Michael T., Liu, Fan, Flynn, Chris, Smith, Daniel, and Berke, Daniel A.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Astrophysics of Galaxies - Abstract
The Survey for Distant Solar Twins (SDST) aims to find stars very similar to the Sun at distances 1-4 kpc, several times more distant than any currently known solar twins and analogues. The goal is to identify the best stars with which to test whether the fine-structure constant, alpha, varies with dark matter density in our Galaxy. Here we use EPIC, our line-by-line differential technique, to measure the stellar parameters - effective temperature Teff, surface gravity log g, metallicity [Fe/H] - from moderate resolution (R < 32,000) spectra of 877 solar twin and analogue candidates (547 at 1-4 kpc) observed with the HERMES spectrograph on the Anglo-Australian Telescope. These are consistent with expectations for Teff and log g from photometry, and for [Fe/H] from the Besancon stellar population model. EPIC provides small enough uncertainties (~90 K, 0.08 dex, 0.05 dex, respectively), even at the low signal-to-noise ratios available (S/N >~ 25 per pixel), to identify 299 new solar analogues (> 90% confidence), and 20 solar twins (>50% confidence), 206 and 12 of which are at 1-4 kpc. By extending EPIC to measure line broadening and lithium abundance from HERMES spectra, and with ages derived from isochrone fitting with our stellar parameters, we identify 174 solar analogues at 1-4 kpc which are relatively inactive, slowly rotating, and with no evidence of spectroscopic binarity. These are the preferred targets for follow-up spectroscopy to measure alpha., Comment: 12 pages, 12 figures. Accepted by MNRAS. The full table of stars used in this work can be found at https://doi.org/10.5281/zenodo.7332606
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- 2023
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31. MUSE Analysis of Gas around Galaxies (MAGG) -- V: Linking ionized gas traced by CIV and SiIV absorbers to Ly${\alpha}$ emitting galaxies at $z\approx 3.0-4.5$
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Galbiati, Marta, Fumagalli, Michele, Fossati, Matteo, Lofthouse, Emma K., Dutta, Rajeshwari, Prochaska, J. Xavier, Murphy, Michael T., and Cantalupo, Sebastiano
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Astrophysics - Astrophysics of Galaxies - Abstract
We use 28 quasar fields with high-resolution (HIRES and UVES) spectroscopy from the MUSE Analysis of Gas Around Galaxies survey to study the connection between Ly${\alpha}$ emitters (LAEs) and metal-enriched ionized gas traced by CIV in absorption at redshift $z\approx3-4$. In a sample of 220 CIV absorbers, we identify 143 LAEs connected to CIV gas within a line-of-sight separation ${\rm \pm 500\,km\,s^{-1}}$, equal to a detection rate of $36\pm 5$ per cent once we account for multiple LAEs connected to the same CIV absorber. The luminosity function of LAEs associated with CIV absorbers shows a $\approx 2.4$ higher normalization factor compared to the field. CIV with higher equivalent width and velocity width are associated with brighter LAEs or multiple galaxies, while weaker systems are less often identified near LAEs. The covering fraction in groups is up to $\approx 3$ times larger than for isolated galaxies. Compared to the correlation between optically-thick HI absorbers and LAEs, CIV systems are twice less likely to be found near LAEs especially at lower equivalent width. Similar results are found using SiIV as tracer of ionized gas. We propose three components to model the gas environment of LAEs: i) the circumgalactic medium of galaxies, accounting for the strongest correlations between absorption and emission; ii) overdense gas filaments connecting galaxies, driving the excess of LAEs at a few times the virial radius and the modulation of the luminosity and cross-correlation functions for strong absorbers; iii) an enriched and more diffuse medium, accounting for weaker CIV absorbers farther from galaxies., Comment: 28 pages, 21 figures, 10 tables. Submitted to MNRAS after accounting for reviewer's comments
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- 2023
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32. Efficiently predicting high resolution mass spectra with graph neural networks
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Murphy, Michael, Jegelka, Stefanie, Fraenkel, Ernest, Kind, Tobias, Healey, David, and Butler, Thomas
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Computer Science - Machine Learning ,Quantitative Biology - Quantitative Methods - Abstract
Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over molecular formulas. We discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and orders-of-magnitude faster runtime than state-of-the-art methods.
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- 2023
33. From prosumer to flexumer: Case study on the value of flexibility in decarbonizing the multi-energy system of a manufacturing company
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Fleschutz, Markus, Bohlayer, Markus, Braun, Marco, and Murphy, Michael D.
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Electrical Engineering and Systems Science - Systems and Control ,Economics - Econometrics ,Statistics - Applications - Abstract
Digitalization and sector coupling enable companies to turn into flexumers. By using the flexibility of their multi-energy system (MES), they reduce costs and carbon emissions while stabilizing the electricity system. However, to identify the necessary investments in energy conversion and storage technologies to leverage demand response (DR) potentials, companies need to assess the value of flexibility. Therefore, this study quantifies the flexibility value of a production company's MES by optimizing the synthesis, design, and operation of a decarbonizing MES considering self-consumption optimization, peak shaving, and integrated DR based on hourly prices and carbon emission factors (CEFs). The detailed case study of a beverage company in northern Germany considers vehicle-to-X of powered industrial trucks, power-to-heat on multiple temperatures, wind turbines, photovoltaic systems, and energy storage systems (thermal energy, electricity, and hydrogen). We propose and apply novel data-driven metrics to evaluate the intensity of price-based and CEF-based DR. The results reveal that flexibility usage reduces decarbonization costs (by 19-80% depending on electricity and carbon removal prices), total annual costs, operating carbon emissions, energy-weighted average prices and CEFs, and fossil energy dependency. The results also suggest that a net-zero operational carbon emission MES requires flexibility, which, in an economic case, is provided by a combination of different flexible technologies and storage systems that complement each other. While the value of flexibility depends on various market and consumer-specific factors such as electricity or carbon removal prices, this study highlights the importance of demand flexibility for the decarbonization of MESs., Comment: 23 pages, 28 figures, research paper
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- 2023
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34. Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains
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Wang, Jing Yang, Khmelinskaia, Alena, Sheffler, William, Miranda, Marcos C, Antanasijevic, Aleksandar, Borst, Andrew J, Torres, Susana V, Shu, Chelsea, Hsia, Yang, Nattermann, Una, Ellis, Daniel, Walkey, Carl, Ahlrichs, Maggie, Chan, Sidney, Kang, Alex, Nguyen, Hannah, Sydeman, Claire, Sankaran, Banumathi, Wu, Mengyu, Bera, Asim K, Carter, Lauren, Fiala, Brooke, Murphy, Michael, Baker, David, Ward, Andrew B, and King, Neil P
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Medical Biotechnology ,Biological Sciences ,Biomedical and Clinical Sciences ,Bioengineering ,Vaccine Related ,Biotechnology ,Nanotechnology ,Generic health relevance ,Proteins ,Nanoparticles ,Vaccines ,biochemistry ,protein design ,nanoparticles - Abstract
Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.
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- 2023
35. A limit on variations in the fine-structure constant from spectra of nearby Sun-like stars
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Murphy, Michael T., Berke, Daniel A., Liu, Fan, Flynn, Chris, Lehmann, Christian, Dzuba, Vladimir A., and Flambaum, Victor V.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Astrophysics of Galaxies ,Astrophysics - High Energy Astrophysical Phenomena ,Physics - Atomic Physics - Abstract
The fine structure constant, $\alpha$, sets the strength of the electromagnetic force. The Standard Model of particle physics provides no explanation for its value, which could potentially vary. The wavelengths of stellar absorption lines depend on $\alpha$, but are subject to systematic effects owing to astrophysical processes in stellar atmospheres. We measured precise line wavelengths using 17 stars, selected to have almost identical atmospheric properties to those of the Sun (solar twins), which reduces those systematic effects. We found that $\alpha$ varies by $\lesssim$50 parts-per-billion (ppb) within 50 parsecs from Earth. Combining the results from all 17 stars provides an empirical, local reference for stellar measurements of $\alpha$ with an ensemble precision of 12 ppb., Comment: 33 pages, 6 figures. Published in Science (11 November 2022). This is the accepted version which includes 20 pages of Supplementary Materials
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- 2022
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36. Survey for Distant Solar Twins (SDST) -- II. Design, observations and data
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Liu, Fan, Murphy, Michael T., Lehmann, Christian, Flynn, Chris, Smith, Daniel, Kos, Janez, Berke, Daniel A., and Martell, Sarah L.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Astrophysics of Galaxies - Abstract
Studies of solar twins have key impacts on the astronomical community, but only $\sim$100--200 nearby solar twins ($<$ 1 kpc) have been reliably identified over the last few decades. The aim of our survey (SDST) is to identify $\sim$150--200 distant solar twins and analogues (up to $\lesssim$ 4 kpc) closer to the Galactic Centre. We took advantage of the precise Gaia and Skymapper surveys to select Sun-like candidates in a 2-degree field, which were observed with the HERMES spectrograph on the Anglo-Australian Telescope. We successfully built up the required signal-to-noise ratio (25-per-pixel in the HERMES red band) for most targets as faint as Gaia G of 17.4 mag. The stellar photometric/astrometric parameters (e.g., \teff, \logg, mass) of our candidates are derived in this paper, while the spectroscopic parameters will be presented in the third paper in this SDST series. The selection success rate - the fraction of targets which belong to solar twins or analogues - was estimated from simulated survey data and the Besan\c{c}on stellar population model, and compared with the actual success rate of the survey. We find that expected and actual success rates agree well, indicating that the numbers of solar twins and analogues we discover in SDST are consistent with expectations, affirming the survey approach. These distant solar analogues are prime targets for testing for any variation in the strength of electromagnetism in regions of higher dark matter density, and can make additional contributions to our understanding of, e.g., Galactic chemical evolution in the inner Milky Way., Comment: 15 pages, 13 figures. Accepted by MNRAS
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- 2022
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37. Probing Galactic variations in the fine-structure constant using solar twin stars: methodology and results
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Berke, Daniel A., Murphy, Michael T., Flynn, Chris, and Liu, Fan
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Astrophysics of Galaxies ,Physics - Atomic Physics - Abstract
The rich absorption spectra of Sun-like stars are enticing probes for variations in the fine-structure constant, $\alpha$, which gauges the strength of electromagnetism. While individual line wavelengths are sensitive to $\alpha$, they are also sensitive to physical processes in the stellar atmospheres, which has precluded their use so far. Here we demonstrate a new, differential approach using solar twins: velocity separations between close pairs of transitions are compared across stars with very similar physical properties, strongly suppressing astrophysical and instrumental systematic errors. We utilise 423 archival exposures of 18 solar twins from the High-Accuracy Radial velocity Planetary Searcher (HARPS), in which calibration errors can be reduced to $\lesssim$3 m/s. For stars with $\approx$10 high signal-to-noise ratio spectra ($\ge$200 per pixel), velocity separations between pairs are measured with $\approx$10 m/s statistical precision. A companion paper assesses a range of systematic error sources using 130 stars, with a greater range of stellar parameters, providing accurate corrections for astrophysical effects and a residual, intrinsic star-to-star scatter of 0-13 m/s. Within these uncertainties, we find no evidence for velocity separation differences in 17 transition pairs between solar twins. In a second companion paper, this is found to limit local ($\lesssim$50 pc) variations in $\alpha$ to $\approx$50 parts per billion, $\sim$2 orders of magnitude less than other Galactic constraints., Comment: 15 pages, 5 figures. Accepted by MNRAS. The VarConLib (Varying Constants Library) software used in this work is available at https://github.com/DBerke/varconlib. The measurements and results in this work are available at https://github.com/DBerke/Berke_et_alia_2022_supplemental_data
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- 2022
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38. Probing Galactic variations in the fine-structure constant using solar twin stars: systematic errors
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Berke, Daniel A., Murphy, Michael T., Flynn, Chris, and Liu, Fan
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Astrophysics of Galaxies ,Physics - Atomic Physics - Abstract
Sun-like stars are a new probe of variations in the fine-structure constant, $\alpha$, via the solar twins approach: velocity separations of close pairs of absorption lines are compared between stars with very similar stellar parameters, i.e. effective temperature, metallicity and surface gravity within 100K, 0.1 dex and 0.2 dex of the Sun's values. Here we assess possible systematic errors in this approach by analysing $\gtrsim$10,000 archival exposures from the High-Accuracy Radial velocity Planetary Searcher (HARPS) of 130 stars covering a much broader range of stellar parameters. We find that each transition pair's separation shows broad, low-order variations with stellar parameters which can be accurately modelled, leaving only a small residual, intrinsic star-to-star scatter of 0-33 m/s (average $\approx$7 m/s, $\approx$10$^{-4}$\r{A} at 5000\r{A}). This limits the precision available from a single pair in one star. We consider potential systematic errors from a range of instrumental and astrophysical sources (e.g. wavelength calibration, charge transfer inefficiency, stellar magnetic activity, line blending) and conclude that variations in elemental abundances, isotope ratios and stellar rotational velocities may explain this star-to-star scatter. Finally, we find that the solar twins approach can be extended to solar analogues - within 300K, 0.3 dex and 0.4 dex of the Sun's parameters - without significant additional systematic errors, allowing a much larger number of stars to be used as probes of variation in $\alpha$, including at much larger distances., Comment: 18 pages, 12 figures. Accepted by MNRAS. The VarConLib (Varying Constants Library) software used in this work is available at https://github.com/DBerke/varconlib. The measurements and results in this work are available at https://github.com/DBerke/Berke_et_alia_2022_supplemental_data
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- 2022
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39. MUSE Analysis of Gas around Galaxies (MAGG) -- IV: The gaseous environment of $z\sim$ 3-4 Lyman-alpha emitting galaxies
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Lofthouse, Emma K., Fumagalli, Michele, Fossati, Matteo, Dutta, Rajeshwari, Galbiati, Marta, Battaia, Fabrizio Arrigoni, Cantalupo, Sebastiano, Christensen, Lise, Cooke, Ryan J., Longobardi, Alessia, Murphy, Michael T., and Prochaska, J. Xavier.
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Astrophysics - Astrophysics of Galaxies - Abstract
We study the link between galaxies and HI-selected absorption systems at z~3-4 in the MUSE Analysis of Gas around Galaxies (MAGG) survey, an ESO large programme consisting of integral field pectroscopic observations of 28 quasar fields hosting 61 strong absorbers with $\rm N_{\rm HI}\gtrsim 10^{16.5}~\rm cm^{-2}$. We identify 127 Ly$\alpha$ emitting galaxies (LAEs) around the absorbers, corresponding to a detection rate of 82$\pm$16 per cent. The luminosity function of these LAEs is approximately 5 times higher in normalization than the field population and we detect a significant clustering of galaxies with respect to the gas, confirming that high column density absorbers and LAEs trace each other. Between 30 and 40 per cent of the absorbers are associated with multiple LAEs, which lie preferentially along filaments. Galaxies in groups also exhibit a three times higher covering factor of optically-thick gas compared to isolated systems. No significant correlations are identified between the emission properties of LAEs and the absorption properties of optically-thick gas clouds, except for a weak preference of brighter and multiple galaxies to reside near broad absorbers. Based on the measured impact parameters and the covering factor, we conclude that the near totality of optically-thick gas in the Universe can be found in the outer circumgalactic medium (CGM) of LAEs or in the intergalactic medium (IGM) in proximity to these galaxies. Thus, LAEs act as tracers of larger scale structures within which both galaxies and optically-thick clouds are embedded. The patchy and inhomogeneous nature of the CGM and IGM explains the lack of correlations between absorption and emission properties. This implies that very large samples are needed to unveil the trends that encode the properties of the baryon cycle., Comment: 30 pages, 19 figures, submitted to MNRAS
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- 2022
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40. PSFs of coadded images
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Mandelbaum, Rachel, Jarvis, Mike, Lupton, Robert H., Bosch, James, Kannawadi, Arun, Murphy, Michael D., Zhang, Tianqing, and Collaboration, the LSST Dark Energy Science
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Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
We provide a detailed exploration of the connection between choice of coaddition schemes and the point-spread function (PSF) of the resulting coadded images. In particular, we investigate what properties of the coaddition algorithm lead to the final coadded image having a well-defined PSF. The key elements of this discussion are as follows: 1. We provide an illustration of how linear coaddition schemes can produce a coadd that lacks a well-defined PSF even for relatively simple scenarios and choices of weight functions. 2. We provide a more formal demonstration of the fact that a linear coadd only has a well-defined PSF in the case that either (a) each input image has the same PSF or (b) the coadd is produced with weights that are independent of the signal. 3. We discuss some reasons that two plausible nonlinear coaddition algorithms (median and clipped-mean) fail to produce a consistent PSF profile for stars. 4. We demonstrate that all nonlinear coaddition procedures fail to produce a well-defined PSF for extended objects. In the end, we conclude that, for any purpose where a well-defined PSF is desired, one should use a linear coaddition scheme with weights that do not correlate with the signal and are approximately uniform across typical objects of interest., Comment: 13 pages, 4 figures; pedagogical article; v2 accepted for publication in the Open Journal of Astrophysics
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- 2022
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41. The probabilistic random forest applied to the QUBRICS survey: improving the selection of high-redshift quasars with synthetic data
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Guarneri, Francesco, Calderone, Giorgio, Cristiani, Stefano, Porru, Matteo, Fontanot, Fabio, Boutsia, Konstantina, Cupani, Guido, Grazian, Andrea, D'Odorico, Valentina, Murphy, Michael T., Bongiorno, Angela, Saccheo, Ivano, and Nicastro, Luciano
- Subjects
Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Astrophysics of Galaxies - Abstract
Several recent works have focused on the search for bright, high-z quasars (QSOs) in the South. Among them, the QUasars as BRIght beacons for Cosmology in the Southern hemisphere (QUBRICS) survey has now delivered hundreds of new spectroscopically confirmed QSOs selected by means of machine learning algorithms. Building upon the results obtained by introducing the probabilistic random forest (PRF) for the QUBRICS selection, we explore in this work the feasibility of training the algorithm on synthetic data to improve the completeness in the higher redshift bins. We also compare the performances of the algorithm if colours are used as primary features instead of magnitudes. We generate synthetic data based on a composite QSO spectral energy distribution. We first train the PRF to identify QSOs among stars and galaxies, then separate high-z quasar from low-z contaminants. We apply the algorithm on an updated dataset, based on SkyMapper DR3, combined with Gaia eDR3, 2MASS and WISE magnitudes. We find that employing colours as features slightly improves the results with respect to the algorithm trained on magnitude data. Adding synthetic data to the training set provides significantly better results with respect to the PRF trained only on spectroscopically confirmed QSOs. We estimate, on a testing dataset, a completeness of ~86% and a contamination of ~36%. Finally, 207 PRF-selected candidates were observed: 149/207 turned out to be genuine QSOs with z > 2.5, 41 with z < 2.5, 3 galaxies and 14 stars. The result confirms the ability of the PRF to select high-z quasars in large datasets., Comment: 18 pages, 15 figures. Accepted for publication (MNRAS). Removed a source from the catalogue due to uncertain classification (a star, QID = 1016233)
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- 2022
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42. Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8+ T cells in persons with previous COVID-19
- Author
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Ford, Emily S., Mayer-Blackwell, Koshlan, Jing, Lichen, Laing, Kerry J., Sholukh, Anton M., St. Germain, Russell, Bossard, Emily L., Xie, Hong, Pulliam, Thomas H., Jani, Saumya, Selke, Stacy, Burrow, Carlissa J., McClurkan, Christopher L., Wald, Anna, Greninger, Alexander L., Holbrook, Michael R., Eaton, Brett, Eudy, Elizabeth, Murphy, Michael, Postnikova, Elena, Robins, Harlan S., Elyanow, Rebecca, Gittelman, Rachel M., Ecsedi, Matyas, Wilcox, Elise, Chapuis, Aude G., Fiore-Gartland, Andrew, and Koelle, David M.
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- 2024
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43. A Complex Multiphase DLA Associated with a Compact Group at z=2.431 Traces Accretion, Outflows, and Tidal Streams
- Author
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Nielsen, Nikole M., Kacprzak, Glenn G., Sameer, Murphy, Michael T., Nateghi, Hasti, Charlton, Jane C., and Churchill, Christopher W.
- Subjects
Astrophysics - Astrophysics of Galaxies - Abstract
As part of our program to identify host galaxies of known z=2-3 MgII absorbers with the Keck Cosmic Web Imager (KCWI), we discovered a compact group giving rise to a z=2.431 DLA with ultra-strong MgII absorption in quasar field J234628+124859. The group consists of four star-forming galaxies within 8-28 kpc and $v\sim40-340$ km s$^{-1}$ of each other, where tidal streams are weakly visible in deep HST imaging. The group geometric centre is D=25 kpc from the quasar (D=20-40 kpc for each galaxy). Galaxy G1 dominates the group ($1.66L_{\ast}$, ${\rm SFR}_{\rm FUV}=11.6$ M$_{\odot}$ yr$^{-1}$) while G2, G3, and G4 are less massive ($0.1-0.3L_{\ast}$, ${\rm SFR}_{\rm FUV}=1.4-2.0$ M$_{\odot}$ yr$^{-1}$). Using a VLT/UVES quasar spectrum covering the HI Lyman series and metal lines such as MgII, SiIII, and CIV, we characterised the kinematic structure and physical conditions along the line-of-sight with cloud-by-cloud multiphase Bayesian modelling. The absorption system has a total $\log(N(HI)/{\rm cm}^{-2})=20.53$ and an $N(HI)$-weighted mean metallicity of $\log(Z/Z_{\odot})=-0.68$, with a very large MgII linewidth of $\Delta v\sim700$ km s$^{-1}$. The highly kinematically complex profile is well-modelled with 30 clouds across low and intermediate ionisation phases with values ${13\lesssim\log(N(HI)/{\rm cm}^{-2})\lesssim20}$ and $-3\lesssim\log(Z/Z_{\odot})\lesssim1$. Comparing these properties to the galaxy properties, we infer a wide range of gaseous environments, including metal-rich outflows, metal-poor IGM accretion, and tidal streams from galaxy--galaxy interactions. This diversity of structures forms the intragroup medium around a complex compact group environment at the epoch of peak star formation activity. Surveys of low redshift compact groups would benefit from obtaining a more complete census of this medium for characterising evolutionary pathways., Comment: 29 pages, 10 figures. Accepted for publication in MNRAS 28 June 2022
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- 2022
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44. Discovery of three new near-pristine absorption clouds at $z=2.6$-4.4
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Robert, P. Frédéric, Murphy, Michael T., O'Meara, John M., Crighton, Neil H. M., and Fumagalli, Michele
- Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics ,Astrophysics - Astrophysics of Galaxies - Abstract
We report the discovery of three new "near-pristine" Lyman Limit Systems (LLSs), with metallicities ~1/1000 solar, at redshifts 2.6, 3.8 and 4.0, with a targeted survey at the Keck Observatory. High resolution echelle spectra of eight candidates yielded precise column densities of hydrogen and weak, but clearly detected, metal lines in seven LLSs; we previously reported the one remaining, apparently metal-free LLS, to have metallicity <1/10000 solar. Robust photoionisation modelling provides metallicities [Si/H] = -3.05 to -2.94, with 0.26 dex uncertainties (95% confidence) for three LLSs, and [Si/H] >~ -2.5 for the remaining four. Previous simulations suggest that near-pristine LLSs could be the remnants of PopIII supernovae, so comparing their detailed metal abundances with nucleosynthetic yields from supernovae models is an important goal. Unfortunately, at most two different metals were detected in each new system, despite their neutral hydrogen column densities (10^{19.2-19.4} cm^{-2}) being two orders of magnitude larger than the two previous, serendipitously discovered near-pristine LLSs. Nevertheless, the success of this first targeted survey for near-pristine systems demonstrates the prospect that a much larger, future survey could identify clear observational signatures of PopIII stars. With a well-understood selection function, such a survey would also yield the number density of near-pristine absorbers which, via comparison to future simulations, could reveal the origin(s) of these rare systems., Comment: Accepted by MNRAS. 21 pages, 27 figures
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- 2022
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45. Prolonged Length of Stay after Elective Carotid Revascularization
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Aridi, Hanaa, Murphy, Michael P, Malas, Mahmoud, Schermerhorn, Marc L, Kashyap, Vikram S, Wang, Grace J, Eldrup-jorgensen, Jens, and Motaganahalli, Raghunandan L
- Subjects
Clinical Sciences ,Surgery ,Clinical sciences - Published
- 2023
46. Late Silurian to earliest Devonian vertebrate biostratigraphy of the Birch Creek II section, Roberts Mountains, Nevada, U.S.A.
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Burrow, Carole Jan, Murphy, Michael, and Turner, Susan
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paleobiogeography ,‘Acanthodii’ ,Funicristata ,Thelodonti ,Heterostraci ,Chondrichthyes ,stem Osteichthyes - Abstract
Intensive sampling of uppermost Silurian to lowermost Devonian levels of the marine sequence of the Roberts Mountains Formation exposed in the Birch Creek II section, Nevada has yielded assemblages of vertebrate microremains dominated by acanthodian scales. Taxonomic assessment of the vertebrates represented shows a suite and succession of taxa most similar to those recorded from contemporary circum-Arctic assemblages, with scales of the poracanthodid acanthodians Poracanthodes punctatus, P. canadensis, Radioporacanthodes porosus and ischnacanthid Gomphonchus sandelensis most abundant below the Silurian–Devonian (S–D) boundary (as previously determined by conodont and graptolite occurrences), and stem chondrichthyan ‘acanthodians’ Nostovicina laticristata and other Nostovicina spp. (order, family indet.) the most abundant above the boundary. Just one endemic acanthodian taxon, Funicristata nevadaensis nov. gen. nov. sp., was found, in the uppermost Silurian. Agnathan vertebrate remains are rare relative to acanthodian scales, with dermal fragments of heterostracans at fewer than 10 levels and scales of thelodonts from 12 levels scattered throughout the whole section. Thelodonts Apalolepis, Barlowodus spp., ?Boreania, Gonioporus alatus, Lanarkia, Loganellia, Nikolivia, Talivalia, Thelodus, ?Turinia sp. and Trimerolepis spp. are found below the purported S–D boundary. Rare thelodont scales including Boreania sp. cf. minima, N. gutta and a single scale of ?Amaltheolepis sp. are found above the S–D boundary level. The only identifiable gnathostome remains of groups other than acanthodians are from the putative osteichthyan Lophosteus sp. and chondrichthyans Ellesmereia schultzei and Polymerolepis sp., in the uppermost Silurian levels.
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- 2023
47. A multi-omics longitudinal aging dataset in primary human fibroblasts with mitochondrial perturbations.
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Sturm, Gabriel, Monzel, Anna, Karan, Kalpita, Michelson, Jeremy, Ware, Sarah, Cardenas, Andres, Lin, Jue, Bris, Céline, Santhanam, Balaji, Murphy, Michael, Levine, Morgan, Horvath, Steve, Belsky, Daniel, Wang, Shuang, Procaccio, Vincent, Kaufman, Brett, Hirano, Michio, and Picard, Martin
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Humans ,Aging ,Fibroblasts ,Longevity ,Cellular Senescence ,Glycolysis - Abstract
Aging is a process of progressive change. To develop biological models of aging, longitudinal datasets with high temporal resolution are needed. Here we report a multi-omics longitudinal dataset for cultured primary human fibroblasts measured across their replicative lifespans. Fibroblasts were sourced from both healthy donors (n = 6) and individuals with lifespan-shortening mitochondrial disease (n = 3). The dataset includes cytological, bioenergetic, DNA methylation, gene expression, secreted proteins, mitochondrial DNA copy number and mutations, cell-free DNA, telomere length, and whole-genome sequencing data. This dataset enables the bridging of mechanistic processes of aging as outlined by the hallmarks of aging, with the descriptive characterization of aging such as epigenetic age clocks. Here we focus on bridging the gap for the hallmark mitochondrial metabolism. Our dataset includes measurement of healthy cells, and cells subjected to over a dozen experimental manipulations targeting oxidative phosphorylation (OxPhos), glycolysis, and glucocorticoid signaling, among others. These experiments provide opportunities to test how cellular energetics affect the biology of cellular aging. All data are publicly available at our webtool: https://columbia-picard.shinyapps.io/shinyapp-Lifespan_Study/.
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- 2022
48. Fundamental physics with ESPRESSO: Constraints on Bekenstein and dark energy models from astrophysical and local probes
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Martins, C. J. A. P., Cristiani, S., Cupani, G., D'Odorico, V., Santos, R. Génova, Leite, A. C. O., Marques, C. M. J., Milaković, D., Molaro, P., Murphy, Michael T., Nunes, N. J., Schmidt, Tobias M., Adibekyan, V., Alibert, Y., Di Marcantonio, Paolo, Hernández, J. I. González, Mégevand, D., Palle, E., Pepe, F. A., Santos, N. C., Sousa, S. G., Sozzetti, A., Mascareño, A. Suárez, and Osorio, M. R. Zapatero
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Astrophysics - Cosmology and Nongalactic Astrophysics ,General Relativity and Quantum Cosmology ,High Energy Physics - Phenomenology - Abstract
Dynamical scalar fields in an effective four-dimensional field theory are naturally expected to couple to the rest of the theory's degrees of freedom, unless some new symmetry is postulated to suppress these couplings. In particular, a coupling to the electromagnetic sector will lead to spacetime variations of the fine-structure constant, $\alpha$. Astrophysical tests of the space-time stability of $\alpha$ are therefore a powerful probe of new physics. Here we use ESPRESSO and other contemporary measurements of $\alpha$, together with background cosmology data, local laboratory atomic clock and Weak Equivalence Principle measurements, to place stringent constraints on the simplest examples of the two broad classes of varying $\alpha$ models: Bekenstein models and quintessence-type dark energy models, both of which are parametric extensions of the canonical $\Lambda$CDM model. In both cases, previously reported constraints are improved by more than a factor of ten. This improvement is largely due to the very strong local constraints, but astrophysical measurements can help to break degeneracies between cosmology and fundamental physics parameters., Comment: 8 pages, 2 figures, 2 tables; in press at Phys. Rev. D
- Published
- 2022
- Full Text
- View/download PDF
49. Fundamental Physics with ESPRESSO, Constraining a simple parametrisation for varying $\alpha$
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da Fonseca, Vitor, Barreiro, Tiago, Nunes, Nelson J., Cristiani, Stefano, Cupani, Guido, D'Odorico, Valentina, Santos, Ricardo Génova, Leite, Ana C. O., Marques, Catarina M. J., Martins, Carlos J. A. P., Milaković, Dinko, Molaro, Paolo, Murphy, Michael T., Schmidt, Tobias M., Abreu, Manuel, Adibekyan, Vardan, Cabral, Alexandre, Di Marcantonio, Paolo, Hernández, Jonay I. González, Palle, Enric, Pepe, Francesco A., Rebolo, Rafael, Santos, Nuno C., Sousa, Sérgio G., Sozzetti, Alessandro, Mascareño, Alejandro Suárez, and Osorio, Maria-Rosa Zapatero
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
The spectrograph ESPRESSO recently obtained a limit on the variation of the fine-structure constant, $\alpha$, through measurements along the line of sight of a bright quasar with a precision of $1.36$ ppm at $1\sigma$ level. This imposes new constraints on cosmological models with a varying $\alpha$. We assume such a model where the electromagnetic sector is coupled to a scalar field dark energy responsible for the current acceleration of the Universe. We parametrise the variation of $\alpha$ with two extra parameters, one defining the cosmological evolution of the quintessence component and the other fixing the coupling with the electromagnetic field. The objective of this work is to constrain these parameters with both astrophysical and local probes. We also carried out a comparative analysis of how each data probe may constrain our parametrisation. We performed a Bayesian analysis by comparing the predictions of the model with observations. The astrophysical datasets are composed of quasar spectra measurements, including the latest ESPRESSO data point, as well as Planck observations of the cosmic microwave background. We combined these with local results from atomic clocks and the MICROSCOPE experiment. The constraints placed on the quintessence parameter are consistent with a null variation of the field, and are therefore compatible with a $\Lambda$CDM cosmology. The constraints on the coupling to the electromagnetic sector are dominated by the E\"otv\"os parameter local bound. More precise measurements with ESPRESSO will be extremely important to study the cosmological evolution of $\alpha$ as it probes an interval of redshift not accessible to other types of observations. However, for this particular model, current available data favour a null variation of $\alpha$ resulting mostly from the strong MICROSCOPE limits., Comment: 9 pages, 7 figures, as published in A&A
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- 2022
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50. Extending MAPE-K to support Human-Machine Teaming
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Cleland-Huang, Jane, Agrawal, Ankit, Vierhauser, Michael, Murphy, Michael, and Prieto, Mike
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Computer Science - Robotics ,Computer Science - Software Engineering - Abstract
The MAPE-K feedback loop has been established as the primary reference model for self-adaptive and autonomous systems in domains such as autonomous driving, robotics, and Cyber-Physical Systems. At the same time, the Human Machine Teaming (HMT) paradigm is designed to promote partnerships between humans and autonomous machines. It goes far beyond the degree of collaboration expected in human-on-the-loop and human-in-the-loop systems and emphasizes interactions, partnership, and teamwork between humans and machines. However, while MAPE-K enables fully autonomous behavior, it does not explicitly address the interactions between humans and machines as intended by HMT. In this paper, we present the MAPE-K-HMT framework which augments the traditional MAPE-K loop with support for HMT. We identify critical human-machine teaming factors and describe the infrastructure needed across the various phases of the MAPE-K loop in order to effectively support HMT. This includes runtime models that are constructed and populated dynamically across monitoring, analysis, planning, and execution phases to support human-machine partnerships. We illustrate MAPE-K-HMT using examples from an autonomous multi-UAV emergency response system, and present guidelines for integrating HMT into MAPE-K., Comment: Final published version appearing in 17th Symposium on Software Engineering for Adaptive and Self-Managing Systems (SEAMS 2022)
- Published
- 2022
- Full Text
- View/download PDF
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