3,002 results on '"SMITH, DAVID M."'
Search Results
2. The Limp Fatherpizzle
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Klausen, Kristian and Smith, David M.
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- 2023
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3. First joint X-ray solar microflare observations with NuSTAR and Solar Orbiter/STIX
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Bajnoková, Natália, Hannah, Iain G., Cooper, Kristopher, Krucker, Säm, Grefenstette, Brian W., Smith, David M., Jeffrey, Natasha L. S., and Duncan, Jessie
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Astrophysics - Solar and Stellar Astrophysics - Abstract
We present the first joint spectral and imaging analysis of hard X-ray (HXR) emission from 3 microflares observed by the Nuclear Spectroscopic Telescope ARray (NuSTAR) and Solar Orbiter/Spectrometer/Telescope for Imaging X-rays (STIX). We studied 5 joint spectra from GOES A7, B1 and B6 class microflares from active region AR12765 on 2020 June 6 and 7. As these events are very bright for NuSTAR, resulting in extremely low (<1%) livetime, we introduce a pile-up correction method. All five joint spectra were fitted with an isothermal model finding temperatures in the 9-11 MK range. Furthermore, three joint spectra required an additional non-thermal thick-target model finding non-thermal powers of $10^{25}$-$10^{26}$ erg s$^{-1}$. All the fit parameters were within the ranges expected for HXR microflares. The fit results give a relative scaling of STIX and NuSTAR mostly between 6-28% (one outlier at 52%) suggesting each instrument are well calibrated. In addition to spectral analysis, we performed joint HXR imaging of the June 6 and one of the June 7 microflares. In NuSTAR's field of view (FOV), we observed two separate non-thermal sources connected by an elongated thermal source during the June 6 microflares. In STIX's FOV (44 degrees W with respect to NuSTAR), we imaged thermal emission from the hot flare loops which when reprojected to an Earth viewpoint matches the thermal sources seen with NuSTAR and in the hotter EUV channels with the Solar Dynamic Observatory's Atmospheric Imaging Assembly.
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- 2024
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4. Criticality in an imidazolium ionic liquid fully wetting a sapphire support
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Höllring, Kevin, Vučemilović-Alagić, Nataša, Smith, David M., and Smith, Ana-Sunčana
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Condensed Matter - Soft Condensed Matter ,Physics - Computational Physics ,Physics - Data Analysis, Statistics and Probability - Abstract
Hypothesis: Ionic liquids have various applications in catalytic reaction environments. In those systems, their interaction with interfaces is key to their performance as a liquid phase. We hypothesize that the way a monolayer ionic liquid phase interacts with interfaces like a sapphire substrate is significantly dependent on temperature and that critical behavior can be observed in the structural properties of the liquid film. Methods and simulations: We perform molecular dynamics simulations of imidazolium-based ionic liquid monolayers deposited on a sapphire substrate at temperatures from 200K to 400K. We develop computational tools to analyze structural properties of molecular arrangement in the monolayer, the structure of the film and the defects spontaneously forming and healing. Findings: We observe a clear structural phase transition at around 300K from a solid-like to a liquid-like behavior of a film. Below the critical point an alternating crystalline structure of cations and anions with alignment of periodic vectors with the underlying substrate grid is observed, with frozen defects. Above the critical temperature, the pattern becomes isotropic within the contact layer that displays dynamic defects of a characteristic size. Our results highlight the importance of confinement to the phase behavior of the system., Comment: 13 pages, 12 pages pure manuscript, 9 figures, Submitted to JCIS
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- 2024
5. “I Thought I Was Landed!”: The Congested Districts Board and the Women of Western Ireland
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Smith, David M.
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- 2017
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6. Anisotropic molecular diffusion in confinement II: A model for structurally complex particles applied to transport in thin ionic liquid films
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Höllring, Kevin, Baer, Andreas, Vučemilović-Alagić, Nataša, Smith, David M., and Smith, Ana-Sunčana
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Materials Science ,Condensed Matter - Statistical Mechanics ,Physics - Chemical Physics ,Physics - Computational Physics - Abstract
Hypothesis:Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular to interfaces, has been a standing issue and for objects of nanometric size, which structurally fluctuate on a similar time scale as they diffuse, no methodology has been established so far. We hypothesise that the complex, coupled dynamics can be captured and analysed by using a model built on the $2$-dimensional Smoluchowski equation and systematic coarse-graining. Methods and simulations: For large, flexible species, a universal approach is offered that does not make any assumptions about the separation of time scales between translation and other degrees of freedom. The method is validated on Molecular Dynamics simulations of bulk systems of a family of ionic liquids with increasing cation sizes where internal degrees of freedom have little to major effects. Findings: After validation on bulk liquids, where we provide an interpretation of two diffusion constants for each species found experimentally, we clearly demonstrate the anisotropic nature of diffusion coefficients at interfaces. Spatial variations in the diffusivities relate to interface-induced structuring of the ionic liquids. Notably, the length scales in strongly confined ionic liquids vary consistently but differently at the solid-liquid and liquid-vapour interfaces., Comment: 21 pages, 14 figures, 5 tables, pdflatex, submitted to JCIS; This is a follow-up to "Anisotropic molecular diffusion in confinement I: Transport of small particles in potential and density gradients" due to a split of arXiv:archive/2212.09545
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- 2023
7. The “Quality of Life” in Gainesville, Florida: An Application of Territorial Social Indicators
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Dickinson, Joshua C., Gray, Robert J., and Smith, David M.
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- 2013
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8. ProEnd: a comprehensive database for identifying HbYX motif-containing proteins across the tree of life
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Salcedo-Tacuma, David, Howells, Giovanni D., McHose, Coleman, Gutierrez-Diaz, Aimer, Schupp, Jane, and Smith, David M.
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- 2024
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9. An image-based screen for secreted proteins involved in breast cancer G0 cell cycle arrest
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Weston, William A., Holt, Jordan A., Wiecek, Anna J., Pilling, James, Schiavone, Lovisa Holmberg, Smith, David M., Secrier, Maria, and Barr, Alexis R.
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- 2024
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10. The Stokes-Einstein-Sutherland equation at the nanoscale revisited
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Baer, Andreas, Wawra, Simon E., Bielmeier, Kristina, Uttinger, Maximilian J., Smith, David M., Peukert, Wolfgang, Walter, Johannes, and Smith, Ana-Sunčana
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Condensed Matter - Mesoscale and Nanoscale Physics - Abstract
The Stokes-Einstein-Sutherland (SES) equation is at the foundation of statistical physics, relating a particle's diffusion coefficient and size with the fluid viscosity, temperature and the boundary condition for the particle-solvent interface. It is assumed that it relies on the separation of scales between the particle and the solvent, hence it is expected to break down for diffusive transport on the molecular scale. This assumption is however challenged by a number of experimental studies showing a remarkably small, if any, violation, while simulations systematically report the opposite. To understand these discrepancies, analytical ultracentrifugation experiments are combined with molecular simulations, both performed at unprecedented accuracies, to study the transport of buckminsterfullerene C60 in toluene at infinite dilution. This system is demonstrated to clearly violate the conditions of slow momentum relaxation. Yet, through a linear response to a constant force, the SES equation can be recovered in the long time limit with no more than 4% uncertainty both in experiments and in simulations. This nonetheless requires partial slip on the particle interface, extracted consistently from all the data. These results, thus, resolve a long-standing discussion on the validity and limits of the SES equation at the molecular scale., Comment: The data that support the findings of this study are openly available in Zenodo at http://doi.org/10.5281/zenodo.8281244, reference number 8281244
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- 2023
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11. The Geographical Basis of American Life: Space and Society in the Development of the United States
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Smith, David M., primary
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- 2024
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12. Anisotropic molecular diffusion in confinement I: Transport of small particles in potential and density gradients
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Höllring, Kevin, Baer, Andreas, Vučemilović-Alagić, Nataša, Smith, David M., and Smith, Ana-Sunčana
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Materials Science ,Condensed Matter - Statistical Mechanics ,Physics - Chemical Physics ,Physics - Computational Physics - Abstract
Hypothesis: Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular to interfaces, has been a standing issue. In the vicinity of interfaces, density fluctuations as a consequence of layering locally impose statistical drift, which impedes the analysis of spatially dependent diffusion coefficients even further. We hypothesise, that we can derive a model to spatially resolve interface-perpendicular diffusion coefficients based on local lifetime statistics with an extension to explicitly account for the effect of local drift using the Smoluchowski equation, that allows us to resolve anisotropic and spatially dependent diffusivity landscapes at interfaces. Methods and simulations: An analytic relation between local crossing times in system slices and diffusivity as well as an explicit term for calculating drift-induced systematic errors is presented. The method is validated on Molecular Dynamics simulations of bulk water and applied to simulations of water in slit pores. Findings: After validation on bulk liquids, we clearly demonstrate the anisotropic nature of diffusion coefficients at interfaces. Significant spatial variations in the diffusivities correlate with interface-induced structuring but cannot be solely attributed to the drift induced by local density fluctuations., Comment: 13 pages, 6 figures, submitted to JCIS, PDFLaTex; updated for submission to new Journal and split in two due to length; second accompanying publication: "Anisotropic molecular diffusion in confinement II: A model for structurally complex particles applied to transport in thin ionic liquid films" (both due to a split of arXiv:archive/2212.09545 )
- Published
- 2022
13. The First Survey of Quiet Sun Features Observed in Hard X-Rays with NuSTAR
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Paterson, Sarah, Hannah, Iain G, Grefenstette, Brian W, Hudson, Hugh S, Krucker, Säm, Glesener, Lindsay, White, Stephen M, and Smith, David M
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Astronomical Sciences ,Physical Sciences ,Corona ,quiet ,Heating ,coronal ,Jets ,Spectrum ,X-ray ,X-ray bursts ,hard ,Astronomical and Space Sciences ,Astronomy & Astrophysics ,Astronomical sciences ,Space sciences - Abstract
Abstract: We present the first survey of quiet Sun features observed in hard X-rays (HXRs), using the Nuclear Spectroscopic Telescope ARray (NuSTAR), a HXR focusing optics telescope. The recent solar minimum, combined with NuSTAR’s high sensitivity, has presented a unique opportunity to perform the first HXR imaging spectroscopy on a range of features in the quiet Sun. By studying the HXR emission of these features, we can detect or constrain the presence of high temperature (> 5 MK) or non-thermal sources, to help understand how they relate to larger, more energetic solar phenomena, and determine their contribution to heating the solar atmosphere. We report on several features observed in the 28 September 2018 NuSTAR full-disk quiet Sun mosaics, the first of the NuSTAR quiet Sun observing campaigns, which mostly include steady features of X-ray bright points and an emerging flux region, which later evolved into an active region, as well as a short-lived jet. We find that the features’ HXR spectra are well fitted with isothermal models with temperatures ranging between 2.0 – 3.2 MK. Combining the NuSTAR data with softer X-ray emission from Hinode/XRT and EUV from SDO/AIA, we recover the differential emission measures, confirming little significant emission above 4 MK. The NuSTAR HXR spectra allow us to constrain the possible non-thermal emission that would still be consistent with a null HXR detection. We found that for only one of the features (the jet) was there a potential non-thermal upper limit capable of powering the heating observed. However, even here, the non-thermal electron distribution had to be very steep (effectively mono-energetic) with a low energy cut-off between 3 – 4 keV.
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- 2023
14. Geant4 Modeling of a Cerium Bromide Scintillator Detector for the IMPRESS CubeSat Mission
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Setterberg, William, Glesener, Lindsay, Egziabher, Demoz Gebre, Sample, John G., Smith, David M., Caspi, Amir, Faulkner, Allan, Clemmer, Lestat, Hildebrandt, Kate, Skinner, Evan, Greathouse, Annsley, Kozic, Ty, Wieber, Meredith, Savadogo, Mansour, Nightingale, Mel, and Knuth, Trevor
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - High Energy Astrophysical Phenomena ,Astrophysics - Instrumentation and Methods for Astrophysics ,Physics - Space Physics - Abstract
Solar flares are some of the most energetic events in the solar system and can be studied to investigate the physics of plasmas and stellar processes. One interesting aspect of solar flares is the presence of accelerated (nonthermal) particles, whose signatures appear in solar flare hard X-ray emissions. Debate has been ongoing since the early days of the space age as to how these particles are accelerated, and one way to probe relevant acceleration mechanisms is by investigating short-timescale (tens of milliseconds) variations in solar flare hard X-ray flux. The Impulsive Phase Rapid Energetic Solar Spectrometer (IMPRESS) CubeSat mission aims to measure these fast hard X-ray variations. In order to produce the best possible science data from this mission, we characterize the IMPRESS scintillator detectors using Geant4 Monte Carlo models. We show that the Geant4 Monte Carlo detector model is consistent with an analytical model. We find that Geant4 simulations of X-ray and optical interactions explain observed features in experimental data, but do not completely account for our measured energy resolution. We further show that nonuniform light collection leads to double-peak behavior at the 662 keV $^{137}$Cs photopeak and can be corrected in Geant4 models and likely in the lab., Comment: 12 pages, 9 figures. SPIE 2022 Astronomical Telescopes and Instrumentation proceedings paper
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- 2022
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15. The First Survey of Quiet Sun Features Observed in Hard X-Rays With NuSTAR
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Paterson, Sarah, Hannah, Iain G., Grefenstette, Brian W., Hudson, Hugh, Krucker, Säm, Glesener, Lindsay, White, Stephen M., and Smith, David M.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
We present the first survey of quiet Sun features observed in hard X-rays (HXRs), using the the Nuclear Spectroscopic Telescope ARray (NuSTAR), a HXR focusing optics telescope. The recent solar minimum combined with NuSTAR's high sensitivity has presented a unique opportunity to perform the first HXR imaging spectroscopy on a range of features in the quiet Sun. By studying the HXR emission of these features we can detect or constrain the presence of high temperature (>5 MK) or non-thermal sources, to help understand how they relate to larger more energetic solar phenomena, and determine their contribution to heating the solar atmosphere. We report on several features observed in the 28 September 2018 NuSTAR full-disk quiet Sun mosaics, the first of the NuSTAR quiet Sun observing campaigns, which mostly include steady features of X-ray bright points and an emerging flux region which later evolved into an active region, as well as a short-lived jet. We find that the features' HXR spectra are well fitted with isothermal models with temperatures ranging between 2.0-3.2 MK. Combining the NuSTAR data with softer X-ray emission from Hinode/XRT and EUV from SDO/AIA we recover the differential emission measures, confirming little significant emission above 4 MK. The NuSTAR HXR spectra allow us to constrain the possible non-thermal emission that would still be consistent with a null HXR detection. We found that for only one of the features (the jet) was there a potential non-thermal upper limit capable of powering the heating observed. However, even here the non-thermal electron distribution had to be very steep (effectively mono-energetic) with a low energy cut-off between 3-4 keV. The higher temperature or non-thermal sources in the typical quiet Sun features found in this September 2018 data are therefore found to be very weak, if present at all., Comment: Accepted for publication in Solar Physics
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- 2022
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16. Austerity, Health and Public Safety in Low-Income Neighborhoods: Grassroots Responses to the Decline of Local Services in Southeast England
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Smith, David M.
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- 2023
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17. Compromised chronic efficacy of a glucokinase activator AZD1656 in mouse models for common human GCKR variants
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Ford, Brian E., Chachra, Shruti S., Alshawi, Ahmed, Oakley, Fiona, Fairclough, Rebecca J., Smith, David M., Tiniakos, Dina, and Agius, Loranne
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- 2024
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18. The glucose transporter 2 regulates CD8+ T cell function via environment sensing
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Fu, Hongmei, Vuononvirta, Juho, Fanti, Silvia, Bonacina, Fabrizia, D’Amati, Antonio, Wang, Guosu, Poobalasingam, Thanushiyan, Fankhaenel, Maria, Lucchesi, Davide, Coleby, Rachel, Tarussio, David, Thorens, Bernard, Hearnden, Robert J., Longhi, M. Paula, Grevitt, Paul, Sheikh, Madeeha H., Solito, Egle, Godinho, Susana A., Bombardieri, Michele, Smith, David M., Cooper, Dianne, Iqbal, Asif J., Rathmell, Jeffrey C., Schaefer, Samuel, Morales, Valle, Bianchi, Katiuscia, Norata, Giuseppe Danilo, and Marelli-Berg, Federica M.
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- 2023
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19. NuSTAR observations of a repeatedly microflaring active region
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Cooper, Kristopher, Hannah, Iain G., Grefenstette, Brian W., Glesener, Lindsay, Krucker, Säm, Hudson, Hugh S., White, Stephen M., Smith, David M., and Duncan, Jessie
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
We investigate the spatial, temporal, and spectral properties of 10 microflares from AR12721 on 2018 September 9 and 10 observed in X-rays using the Nuclear Spectroscopic Telescope ARray (NuSTAR) and the Solar Dynamic Observatory's Atmospheric Imaging Assembly and Helioseismic and Magnetic Imager (SDO/AIA and HMI). We find GOES sub-A class equivalent microflare energies of 10$^{26}$-10$^{28}$ erg reaching temperatures up to 10 MK with consistent quiescent or hot active region core plasma temperatures of 3-4 MK. One microflare (SOL2018-09-09T10:33), with an equivalent GOES class of A0.1, has non-thermal HXR emission during its impulsive phase (of non-thermal power $\sim$7$\times$10$^{24}$ erg s$^{-1}$) making it one of the faintest X-ray microflares to have direct evidence for accelerated electrons. In 4 of the 10 microflares, we find that the X-ray time profile matches fainter and more transient sources in the EUV, highlighting the need for observations sensitive to only the hottest material that reaches temperatures higher than those of the active region core ($>$5 MK). Evidence for corresponding photospheric magnetic flux cancellation/emergence present at the footpoints of 8 microflares is also observed., Comment: Accepted for published in MNRAS
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- 2021
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20. High resolution structures define divergent and convergent mechanisms of archaeal proteasome activation
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Chuah, Janelle J. Y., Rexroad, Matthew S., and Smith, David M.
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- 2023
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21. Minimal mechanistic component of HbYX-dependent proteasome activation that reverses impairment by neurodegenerative-associated oligomers
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Chuah, Janelle J. Y., Thibaudeau, Tiffany A., and Smith, David M.
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- 2023
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22. A small-molecule PI3Kα activator for cardioprotection and neuroregeneration
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Gong, Grace Q., Bilanges, Benoit, Allsop, Ben, Masson, Glenn R., Roberton, Victoria, Askwith, Trevor, Oxenford, Sally, Madsen, Ralitsa R., Conduit, Sarah E., Bellini, Dom, Fitzek, Martina, Collier, Matt, Najam, Osman, He, Zhenhe, Wahab, Ben, McLaughlin, Stephen H., Chan, A. W. Edith, Feierberg, Isabella, Madin, Andrew, Morelli, Daniele, Bhamra, Amandeep, Vinciauskaite, Vanesa, Anderson, Karen E., Surinova, Silvia, Pinotsis, Nikos, Lopez-Guadamillas, Elena, Wilcox, Matthew, Hooper, Alice, Patel, Chandni, Whitehead, Maria A., Bunney, Tom D., Stephens, Len R., Hawkins, Phillip T., Katan, Matilda, Yellon, Derek M., Davidson, Sean M., Smith, David M., Phillips, James B., Angell, Richard, Williams, Roger L., and Vanhaesebroeck, Bart
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- 2023
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23. Anisotropic molecular diffusion in confinement II: A model for structurally complex particles applied to transport in thin ionic liquid films
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Höllring, Kevin, Baer, Andreas, Vučemilović-Alagić, Nataša, Smith, David M., and Smith, Ana-Sunčana
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- 2024
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24. Measuring structural parameters of crosslinked and entangled semiflexible polymer networks with single-filament tracing
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Händler, Tina, Tutmarc, Cary, Glaser, Martin, Freitag, Jessica S., Smith, David M., and Schnauß, Jörg
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Condensed Matter - Soft Condensed Matter - Abstract
Single-filament tracing has been a valuable tool to directly determine geometrical and mechanical properties of entangled polymer networks. However, systematically verifying how the stiffness of the tracer filament or its molecular interactions with the surrounding network impacts the measurement of these parameters has not been possible with the established experimental systems. Here, we use mechanically programmable DNA nanotubes embedded in crosslinked and entangled F-actin networks, as well as in synthetic DNA networks, in order to measure fundamental, structural network properties like tube width and mesh size with respect to the stiffness of the tracers. While we confirm some predictions derived from models based purely on steric interactions, our results indicate that these models should be expanded to account for additional inter-filament interactions, thus describing the behavior of real polymer networks., Comment: 6 pages, 4 figures, supplemental information
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- 2020
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25. NuSTAR Observation of Energy Release in Eleven Solar Microflares
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Duncan, Jessie, Glesener, Lindsay, Grefenstette, Brian W., Vievering, Juliana, Hannah, Iain G., Smith, David M., Krucker, Säm, White, Stephen M., and Hudson, Hugh
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Astrophysics - Solar and Stellar Astrophysics - Abstract
Solar flares are explosive releases of magnetic energy. Hard X-ray (HXR) flare emission originates from both hot (millions of Kelvin) plasma and nonthermal accelerated particles, giving insight into flare energy release. The Nuclear Spectroscopic Telescope ARray (NuSTAR) utilizes direct focusing optics to attain much higher sensitivity in the HXR range than that of previous indirect imagers. This paper presents eleven NuSTAR microflares from two active regions (AR 12671 on 2017 August 21, and AR 12712 on 2018 May 29). The temporal, spatial, and energetic properties of each are discussed in context with previously published HXR brightenings. They are seen to display several 'large-flare' properties, such as impulsive time profiles and earlier peaktimes in higher energy HXRs. For two events where active region background could be removed, microflare emission did not display spatial complexity: differing NuSTAR energy ranges had equivalent emission centroids. Finally, spectral fitting showed a high energy excess over a single thermal model in all events. This excess was consistent with additional higher-temperature plasma volumes in 10/11 microflares, and consistent only with an accelerated particle distribution in the last. Previous NuSTAR studies focused on one or a few microflares at a time, making this the first to collectively examine a sizable number of events. Additionally, this paper introduces an observed variation in the NuSTAR gain unique to the extremely low-livetime (<1%) regime, and establishes a correction method to be used in future NuSTAR solar spectral analysis., Comment: Accepted for publication in ApJ
- Published
- 2020
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26. NuSTAR Observation of a Minuscule Microflare in a Solar Active Region
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Cooper, Kristopher, Hannah, Iain G., Grefenstette, Brian W., Glesener, Lindsay, Krucker, Säm, Hudson, Hugh S., White, Stephen M., and Smith, David M.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
We present X-ray imaging spectroscopy of one of the weakest active region (AR) microflares ever studied. The microflare occurred at $\sim$11:04 UT on 2018 September 9 and we studied it using the Nuclear Spectroscopic Telescope ARray (NuSTAR) and the Solar Dynamic Observatory's Atmospheric Imaging Assembly (SDO/AIA). The microflare is observed clearly in 2.5-7 keV with NuSTAR and in Fe XVIII emission derived from the hotter component of the 94 $\unicode{x212B}$ SDO/AIA channel. We estimate the event to be three orders of magnitude lower than a GOES A class microflare with an energy of 1.1$\times$10$^{26}$ erg. It reaches temperatures of 6.7 MK with an emission measure of 8.0$\times$10$^{43}$ cm$^{-3}$. Non-thermal emission is not detected but we instead determine upper limits to such emission. We present the lowest thermal energy estimate for an AR microflare in literature, which is at the lower limits of what is still considered an X-ray microflare., Comment: Accepted for publication in ApJL
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- 2020
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27. Accelerated electrons observed down to <7 keV in a NuSTAR solar microflare
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Glesener, Lindsay, Krucker, S"am, Duncan, Jessie, Hannah, Iain G., Grefenstette, Brian W., Chen, Bin, Smith, David M., White, Stephen M., and Hudson, Hugh
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
We report the detection of emission from a non-thermal electron distribution in a small solar microflare (GOES class A5.7) observed by the Nuclear Spectroscopic Telescope Array (NuSTAR), with supporting observation by the Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI). The flaring plasma is well accounted for by a thick-target model of accelerated electrons collisionally thermalizing within the loop, akin to the "coronal thick target" behavior occasionally observed in larger flares. This is the first positive detection of non-thermal hard X-rays from the Sun using a direct imager (as opposed to indirectly imaging instruments). The accelerated electron distribution has a spectral index of 6.3 +/- 0.7, extends down to at least 6.5 keV, and deposits energy at a rate of ~2x1027 erg/s, heating the flare loop to at least 10 MK. The existence of dominant non-thermal emission in X-rays down to <5 keV means that RHESSI emission is almost entirely non-thermal, contrary to what is usually assumed in RHESSI spectroscopy. The ratio of non-thermal to thermal energies is similar to that of large flares, in contrast to what has been found in previous studies of small RHESSI flares. We suggest that a coronal thick target may be a common property of many small microflares based on the average electron energy and collisional mean free path. Future observations of this kind will enable understanding of how flare particle acceleration changes across energy scales, and will aid the push toward the observational regime of nanoflares, which are a possible source of significant coronal heating.
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- 2020
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28. X-ray spectral and flux variability of the microquasar GRS 1758-258 on timescales from weeks to years
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Hirsch, Maria, Pottschmidt, Katja, Smith, David M., Bodaghee, Arash, Bel, Marion Cadolle, Grinberg, Victoria, Hell, Natalie, Krauss, Felicia, Kreykenbohm, Ingo, Lohfink, Anne, Nowak, Michael A., Rodrigues, Barbara H., Soria, Roberto, Tomsick, John A., and Wilms, Joern
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Astrophysics - High Energy Astrophysical Phenomena - Abstract
We present the spectral and timing evolution of the persistent black hole X-ray binary GRS 1758-258 based on almost 12 years of observations using the Rossi X-ray Timing Explorer Proportional Counter Array. While the source was predominantly found in the hard state during this time, it entered the thermally dominated soft state seven times. In the soft state GRS 1758-258 shows a strong decline in flux above 3 keV rather than the pivoting flux around 10 keV more commonly shown by black hole transients. In its 3-20 keV hardness intensity diagram, GRS 1758-258 shows a hysteresis of hard and soft state fluxes typical for transient sources in outburst. The RXTE-PCA and RXTE-ASM long-term light curves do not show any orbital modulations in the range of 2 to 30 d. However, in the dynamic power spectra significant peaks drift between 18.47d and 18.04d for the PCA data, while less significant signatures between 19d and 20d are seen for the ASM data as well as for the Swift/BAT data. We discuss different models for the hysteresis behavior during state transitions as well as possibilities for the origin of the long term variation in the context of a warped accretion disk., Comment: 12 pages, 13 figures, accepted by Astronomy & Astrophysics
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- 2019
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29. The Art of Designing DNA Nanostructures with CAD Software.
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Glaser, Martin, Deb, Sourav, Seier, Florian, Agrawal, Amay, Liedl, Tim, Douglas, Shawn, Gupta, Manish K, and Smith, David M
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DNA ,Nucleic Acid Conformation ,Nanotechnology ,Nanostructures ,Software ,CAD software ,DNA bricks ,DNA nanotechnology ,DNA origami ,DNA tiles ,nanofabrication ,self-assembly ,simulation ,Organic Chemistry ,Medicinal and Biomolecular Chemistry ,Theoretical and Computational Chemistry - Abstract
Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.
- Published
- 2021
30. AI-guided discovery of the invariant host response to viral pandemics
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Sahoo, Debashis, Katkar, Gajanan D, Khandelwal, Soni, Behroozikhah, Claire, Amanraj, Castillo, Vanessa, Tindle, Courtney, Fuller, MacKenzie, Taheri, Sahar, Rogers, Thomas F, Beutler, Nathan, Ramirez, Sydney I, Rawlings, Stephen A, Pretorius, Victor, Smith, David M, Burton, Dennis R, Alexander, Laura E Crotty, Duran, Jason, Crotty, Shane, Dan, Jennifer M, Das, Soumita, and Ghosh, Pradipta
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Biomedical and Clinical Sciences ,Immunology ,Lung ,Coronaviruses ,Biodefense ,Coronaviruses Therapeutics and Interventions ,Infectious Diseases ,Genetics ,Emerging Infectious Diseases ,2.1 Biological and endogenous factors ,Infection ,Good Health and Well Being - Abstract
UNLABELLED: We sought to define the host immune response, a.k.a, the "cytokine storm" that has been implicated in fatal COVID-19 using an AI-based approach. Over 45,000 transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a 'seed' gene; ACE2 was rationalized because it encodes the receptor that facilitates the entry of SARS-CoV-2 (the virus that causes COVID-19) into host cells. Surprisingly, this 166-gene signature was conserved in all vi ral p andemics, including COVID-19, and a subset of 20-genes classified disease severity, inspiring the nomenclatures ViP and severe-ViP signatures, respectively. The ViP signatures pinpointed a paradoxical phenomenon wherein lung epithelial and myeloid cells mount an IL15 cytokine storm, and epithelial and NK cell senescence and apoptosis determines severity/fatality. Precise therapeutic goals were formulated and subsequently validated in high-dose SARS-CoV-2-challenged hamsters using neutralizing antibodies that abrogate SARS-CoV-2•ACE2 engagement or a directly acting antiviral agent, EIDD-2801. IL15/IL15RA were elevated in the lungs of patients with fatal disease, and plasma levels of the cytokine tracked with disease severity. Thus, the ViP signatures provide a quantitative and qualitative framework for titrating the immune response in viral pandemics and may serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs. ONE SENTENCE SUMMARY: The host immune response in COVID-19. PANEL RESEARCH IN CONTEXT: Evidence before this study: The SARS-CoV-2 pandemic has inspired many groups to find innovative methodologies that can help us understand the host immune response to the virus; unchecked proportions of such immune response have been implicated in fatality. We searched GEO and ArrayExpress that provided many publicly available gene expression data that objectively measure the host immune response in diverse conditions. However, challenges remain in identifying a set of host response events that are common to every condition. There are no studies that provide a reproducible assessment of prognosticators of disease severity, the host response, and therapeutic goals. Consequently, therapeutic trials for COVID-19 have seen many more 'misses' than 'hits'. This work used multiple (> 45,000) gene expression datasets from GEO and ArrayExpress and analyzed them using an unbiased computational approach that relies upon fundamentals of gene expression patterns and mathematical precision when assessing them.Added value of this study: This work identifies a signature that is surprisingly conserved in all viral pandemics, including Covid-19, inspiring the nomenclature ViP-signature. A subset of 20-genes classified disease severity in respiratory pandemics. The ViP signatures pinpointed the nature and source of the 'cytokine storm' mounted by the host. They also helped formulate precise therapeutic goals and rationalized the repurposing of FDA-approved drugs.Implications of all the available evidence: The ViP signatures provide a quantitative and qualitative framework for assessing the immune response in viral pandemics when creating pre-clinical models; they serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs.
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- 2021
31. Anisotropic molecular diffusion in confinement I: Transport of small particles in potential and density gradients
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Höllring, Kevin, Baer, Andreas, Vučemilović-Alagić, Nataša, Smith, David M., and Smith, Ana-Sunčana
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- 2023
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32. NuSTAR Observation of Energy Release in 11 Solar Microflares
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Duncan, Jessie, Glesener, Lindsay, Grefenstette, Brian W, Vievering, Juliana, Hannah, Iain G, Smith, David M, Krucker, Säm, White, Stephen M, and Hudson, Hugh
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Astronomical Sciences ,Physical Sciences ,Affordable and Clean Energy ,The Sun ,Solar flare spectra ,Solar x-ray flares ,Non-thermal radiation sources ,Solar flares ,Solar physics ,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
Solar flares are explosive releases of magnetic energy. Hard X-ray (HXR) flare emission originates from both hot (millions of Kelvin) plasma and nonthermal accelerated particles, giving insight into flare energy release. The Nuclear Spectroscopic Telescope ARray (NuSTAR) utilizes direct-focusing optics to attain much higher sensitivity in the HXR range than that of previous indirect imagers. This paper presents 11 NuSTAR microflares from two active regions (AR 12671 on 2017 August 21 and AR 12712 on 2018 May 29). The temporal, spatial, and energetic properties of each are discussed in context with previously published HXR brightenings. They are seen to display several "large flare" properties, such as impulsive time profiles and earlier peak times in higher-energy HXRs. For two events where the active region background could be removed, microflare emission did not display spatial complexity; differing NuSTAR energy ranges had equivalent emission centroids. Finally, spectral fitting showed a high-energy excess over a single thermal model in all events. This excess was consistent with additional higher-temperature plasma volumes in 10/11 microflares and only with an accelerated particle distribution in the last. Previous NuSTAR studies focused on one or a few microflares at a time, making this the first to collectively examine a sizable number of events. Additionally, this paper introduces an observed variation in the NuSTAR gain unique to the extremely low livetime (
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- 2021
33. A Space-based All-sky MeV gamma-ray Survey with the Electron Tracking Compton Camera
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Hamaguchi, Kenji, Tanimori, Toru, Takada, Atsushi, Beacom, John F., Gunji, Shuichi, Mori, Masaki, Nakamori, Takeshi, Shrader, Chris R., Smith, David M., Tamagawa, Toru, and Tsurutani, Bruce T.
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Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
A sensitive survey of the MeV gamma-ray sky is needed to understand important astrophysical problems such as gamma-ray bursts in the early universe, progenitors of Type Ia supernovae, and the nature of dark matter. However, the study has not progressed remarkably since the limited survey by COMPTEL onboard CGRO in the 1990s. Tanimori et al. have developed a Compton camera that tracks the trajectory of each recoil electron in addition to the information obtained by the conventional Compton cameras, leading to superior imaging. This Electron Tracking Compton Camera (ETCC) facilitates accurate reconstruction of the incoming direction of each MeV photon from a wide sky at ~degree angular resolution and with minimized particle background using trajectory information. The latest ETCC model, SMILE-2+, made successful astronomical observations during a day balloon flight in 2018 April and detected diffuse continuum and 511 keV annihilation line emission from the Galactic Center region at a high significance in ~2.5 hours. We believe that MeV observations from space with upgraded ETCCs will dramatically improve our knowledge of the MeV universe. We advocate for a space-based all-sky survey mission with multiple ETCCs onboard and detail its expected benefits., Comment: 14 pages, 5 figures, 1 table, Astro 2020 APC white paper
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- 2019
34. Structural Characterization of an Ionic Liquid in bulk and in nano-confined environment from MD simulations
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Vucemilovic-Alagic, Natasa, Banhatti, Radha D., Stepic, Robert, Wick, Christian R., Berger, Daniel, Gaimann, Mario, Bear, Andreas, Harting, Jens, Smith, David M., and Smith, Ana-Suncana
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Physics - Chemical Physics ,Condensed Matter - Mesoscale and Nanoscale Physics ,Physics - Computational Physics - Abstract
This article contains data on structural characterization of the [C2Mim][NTf2] in bulk and in nano-confined environment obtained using MD simulations. These data supplement those presented in the paper Insights from Molecular Dynamics Simulations on Structural Organization and Diffusive Dynamics of an Ionic Liquid at Solid and Vacuum Interfaces, where force fields with three different charge methods and three charge scaling factors were used for the analysis of the IL in the bulk, at the interface with the vacuum and the IL film in the contact with a hydroxylated alumina surface. Here, we present details on the construction of the model systems in an extended detailed methods section. Furthermore, for best parametrization, structural and dynamic properties of IL in different environment are studied with certain features presented herein., Comment: 13 pages, 12 figures. arXiv admin note: substantial text overlap with arXiv:1903.09450
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- 2019
35. Insights from Molecular Dynamics Simulations on Structural Organization and Diffusive Dynamics of an Ionic Liquid at Solid and Vacuum Interfaces
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Vucemilovic-Alagic, Natasa, Banhatti, Radha D., Stepic, Robert, Wick, Christian R., Berger, Daniel, Gaimann, Mario U., Baer, Andreas, Harting, Jens, Smith, David M., and Smith, Ana-Suncana
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Condensed Matter - Materials Science ,Condensed Matter - Mesoscale and Nanoscale Physics - Abstract
Hypothesis A prototypical modelling approach is required for a full characterisation of the static and equilibrium dynamical properties of confined ionic liquids (ILs), in order to gain predictive power of properties that are difficult to extract from experiments. Such a protocol needs to be constructed by benchmarking molecular dynamics simulations against available experiments. Simulations We perform an in-depth study of [C2Mim][NTf2] in bulk, at the vacuum and at hydroxylated alumina surface. Using the charge methods CHelpG, RESP-HF and RESP-B3LYP with charge scaling factors 1.0, 0.9 and 0.85, we search for an optimum non-polarizable force field by benchmarking against self-diffusion coefficients, surface tension, X-ray reflectivity data, and structural data. Findings Benchmarking, which relies on establishing the significance of an appropriate size of the model systems and the length of the simulations, yields RESP-HF/0.9 as the best suited force field for this IL overall. A complete and accurate characterisation of the spatially-dependent internal configurational space and orientation of IL molecules relative to the solid and vacuum interfaces is obtained. Furthermore, the density and mobility of IL ions in the plane parallel and normal to the interfaces is evaluated and the correlation between the stratification and dynamics in the interfacial layers is detectable deep into the films., Comment: 14 pages, 9 figures in main text and 14 figures in Supporting Information
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- 2019
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36. The Role of Stickiness in the Rheology of Semiflexible Polymers
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Golde, Tom, Glaser, Martin, Tutmarc, Cary, Elbalasy, Iman, Huster, Constantin, Busteros, Gaizka, Smith, David M., Herrmann, Harald, Käs, Josef A., and Schnauß, Jörg
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Condensed Matter - Soft Condensed Matter - Abstract
Semiflexible polymers form central structures in biological material. Modeling approaches usually neglect influences of polymer-specific molecular features aiming to describe semiflexible polymers universally. Here, we investigate the influence of molecular details on networks assembled from filamentous actin, intermediate filaments, and synthetic DNA nanotubes. In contrast to prevalent theoretical assumptions, we find that bulk properties are affected by various inter-filament interactions. We present evidence that these interactions can be merged into a single parameter in the frame of the glassy wormlike chain model. The interpretation of this parameter as a polymer specific stickiness is consistent with observations from macro-rheological measurements and reptation behavior. Our findings demonstrate that stickiness should generally not be ignored in semiflexible polymer models.
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- 2019
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37. The GCKR-P446L gene variant predisposes to raised blood cholesterol and lower blood glucose in the P446L mouse-a model for GCKR rs1260326
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Ford, Brian E., Chachra, Shruti S., Rodgers, Katrina, Moonira, Tabassum, Al-Oanzi, Ziad H., Anstee, Quentin M., Reeves, Helen L., Schattenberg, Jörn M., Fairclough, Rebecca J., Smith, David M., Tiniakos, Dina, and Agius, Loranne
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- 2023
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38. Joint X-ray, EUV and UV Observations of a Small Microflare
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Hannah, Iain G., Kleint, Lucia, Krucker, Säm, Grefenstette, Brian W., Glesener, Lindsay, Hudson, Hugh S., White, Stephen M., and Smith, David M.
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Astrophysics - Solar and Stellar Astrophysics - Abstract
We present the first joint observation of a small microflare in X-rays with the Nuclear Spectroscopic Telescope ARray (NuSTAR), UV with the Interface Region Imaging Spectrograph (IRIS) and EUV with the Solar Dynamics Observatory/Atmospheric Imaging Assembly (SDO/AIA). These combined observations allows us to study the microflare's hot coronal and cooler chromospheric/transition region emission. This small microflare peaks from SOL2016-07-26T23:35 to 23:36UT, in both NuSTAR, SDO/AIA and IRIS. Spatially this corresponds to a small loop visible in the SDO/AIA Fe XVIII emission, which matches a similar structure lower in the solar atmosphere seen by IRIS in SJI1330{\AA} and 1400\AA. The NuSTAR emission in both 2.5-4 keV and 4-6 keV, is located in a small source at this loop location. The IRIS slit was over the microflaring loop, and fits show little change in Mg II but do show intensity increases, slight width enhancements and redshifts in Si IV andO IV, indicating that this microflare had most significance in and above the upper chromosphere. The NuSTAR microflare spectrum is well fitted by a thermal component of 5.8MK and $2.3\times10^{44}$ cm$^{-3}$, which corresponds to a thermal energy of $10^{26}$ erg, making it considerably smaller than previously studied X-ray microflares. No non-thermal emission was detected but this could be due to the limited effective exposure time of the observation. This observation shows that even ordinary features seen in UV and EUV, can remarkably have a higher energy component that is clear in X-rays., Comment: Accepted for publication in ApJ
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- 2018
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39. ProEnd: A Comprehensive Database for Identifying HbYX Motif-Containing Proteins Across the Tree of Life
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Salcedo-Tacuma, David M, primary, Howells, Giovanni, additional, McHose, Coleman, additional, Gutierrez-Diaz, Aimer, additional, and Smith, David M, additional
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- 2024
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40. Opposing effects on regulated insulin secretion of acute vs chronic stimulation of AMP-activated protein kinase
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Nguyen-Tu, Marie-Sophie, Harris, Joseph, Martinez-Sanchez, Aida, Chabosseau, Pauline, Hu, Ming, Georgiadou, Eleni, Pollard, Alice, Otero, Pablo, Lopez-Noriega, Livia, Leclerc, Isabelle, Sakamoto, Kei, Schmoll, Dieter, Smith, David M., Carling, David, and Rutter, Guy A.
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- 2022
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41. Water in an electric field does not dance alone: The relation between equilibrium structure, time dependent viscosity and molecular motions
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Baer, Andreas, Miličević, Zoran, Smith, David M., and Smith, Ana-Sunčana
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Condensed Matter - Soft Condensed Matter - Abstract
Dynamic structuring of water is a key player in a large class of processes underlying biochemical and technological developments today, the latter often involving electric fields. However, the anisotropic coupling between the water structure and the field has not been understood on a molecular level so far. Here we perform extensive molecular dynamics simulations to explore the influence of an externally imposed electric field on liquid water under ambient conditions. Using self-developed analysis tools and rigorous statistical analysis, we unambiguously show that water hydration shells break into subcompartments, which were hitherto not observed due to radial averaging. The shape of subcompartments is sensitive to the field magnitude, and affects excitations of the hydrogen bond network including the femtosecond stretching and the sub-picosecond restructuring of hydrogen bonds. Furthermore, by analysing the reorientational dynamics of water molecules, we ascertain the existence of cooperative excitations of small water clusters. Enabled by the interplay between hydrogen bonding, and the coupling of water dipoles to the field, these coordinated motions, occurring on the picosecond time scale, are associated with fluctuations between torque-free states of water dipoles. We show that unlike the coupling between translation and reorientation of water molecules, which takes place on even longer time scales, these coordinated motions are the key for understanding the emergent anisotropy of diffusion and viscosity of water. Particular effort is invested to provide an analysis that allows for future experimental validation.
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- 2018
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42. Towards Cytoskeleton Computers. A proposal
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Adamatzky, Andrew, Tuszynski, Jack, Pieper, Joerg, Nicolau, Dan V., Rinalndi, Rossalia, Sirakoulis, Georgios, Erokhin, Victor, Schnauss, Joerg, and Smith, David M.
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Computer Science - Emerging Technologies - Abstract
We propose a road-map to experimental implementation of cytoskeleton-based computing devices. An overall concept is described in the following. Collision-based cytoskeleton computers implement logical gates via interactions between travelling localisation (voltage solitons on AF/MT chains and AF/MT polymerisation wave fronts). Cytoskeleton networks are grown via programmable polymerisation. Data are fed into the AF/MT computing networks via electrical and optical means. Data signals are travelling localisations (solitons, conformational defects) at the network terminals. The computation is implemented via collisions between the localisations at structural gates (branching sites) of the AF/MT network. The results of the computation are recorded electrically and/or optically at the output terminals of the protein networks. As additional options, optical I/O elements are envisaged via direct excitation of the protein network and by coupling to fluorescent molecules., Comment: To be published as a chapter in the book Adamatzky A., Akl S., Sirakoulis G., Editors. From Parallel to Emergent Computing, CRC Press/Taylor & Francis, 2019
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- 2018
43. Hard X-Ray Constraints on Small-Scale Coronal Heating Events
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Marsh, Andrew J., Smith, David M., Glesener, Lindsay, Klimchuk, James A., Bradshaw, Stephen J., Vievering, Juliana, Hannah, Iain G., Christe, Steven, Ishikawa, Shin-nosuke, and Krucker, Sam
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Astrophysics - Solar and Stellar Astrophysics - Abstract
Much evidence suggests that the solar corona is heated impulsively, meaning that nanoflares may be ubiquitous in quiet and active regions (ARs). Hard X-ray (HXR) observations with unprecedented sensitivity $>$3~keV are now enabled by focusing instruments. We analyzed data from the \textit{Focusing Optics X-ray Solar Imager (FOXSI)} rocket and the \textit{Nuclear Spectroscopic Telescope Array (NuSTAR)} spacecraft to constrain properties of AR nanoflares simulated by the EBTEL field-line-averaged hydrodynamics code. We generated model X-ray spectra by computing differential emission measures for homogeneous nanoflare sequences with heating amplitudes $H_0$, durations $\tau$, delay times between events $t_N$, and filling factors $f$. The single quiescent AR observed by \textit{FOXSI-2} on 2014 December 11 is well fit by nanoflare sequences with heating amplitudes 0.02 erg cm$^{-3}$ s$^{-1}$ $<$ $H_0$ $<$ 13 erg cm$^{-3}$ s$^{-1}$ and a wide range of delay times and durations. We exclude delays between events shorter than $\sim$900 s at the 90\% confidence level for this region. Three of five regions observed by {\nustar} on 2014 November 1 are well fit by homogeneous nanoflare models, while two regions with higher fluxes are not. Generally, the {\nustar} count spectra are well fit by nanoflare sequences with smaller heating amplitudes, shorter delays, and shorter durations than the allowed \textit{FOXSI-2} models. These apparent discrepancies are likely due to differences in spectral coverage between the two instruments and intrinsic differences among the regions. Steady heating ($t_N$ = $\tau$) was ruled out with $>$99\% confidence for all regions observed by either instrument., Comment: 17 pages, 21 figures. Accepted for publication in The Astrophysical Journal
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- 2018
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44. Termination of Electron Acceleration in Thundercloud by Intra/Inter-cloud Discharge
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Wada, Yuuki, Bowers, Gregory S., Enoto, Teruaki, Kamogawa, Masashi, Nakamura, Yoshitaka, Morimoto, Takeshi, Smith, David M., Furuta, Yoshihiro, Nakazawa, Kazuhiro, Yuasa, Takayuki, Matsuki, Atsushi, Kubo, Mamoru, Tamagawa, Toru, Makishima, Kazuo, and Tsuchiya, Harufumi
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Physics - Atmospheric and Oceanic Physics ,High Energy Physics - Experiment - Abstract
An on-ground observation program for high energy atmospheric phenomena in winter thunderstorms along Japan Sea has been performed via measurements of gamma-ray radiation, atmospheric electric field and low-frequency radio band. On February 11, 2017, the radiation detectors recorded gamma-ray emission lasting for 75 sec. The gamma-ray spectrum extended up to 20 MeV and was reproduced by a cutoff power-law model with a photon index of $1.36^{+0.03}_{-0.04}$, being consistent with a Bremsstrahlung radiation from a thundercloud (as known as a gamma-ray glow and a thunderstorm ground enhancement). Then the gamma-ray glow was abruptly terminated with a nearby lightning discharge. The low-frequency radio monitors, installed $\sim$50 km away from the gamma-ray observation site recorded leader development of an intra/inter-cloud discharge spreading over $\sim$60 km area with a $\sim$300 ms duration. The timing of the gamma-ray termination coincided with the moment when the leader development of the intra/inter-cloud discharge passed 0.7 km horizontally away from the radiation monitors. The intra/inter-cloud discharge started $\sim$15 km away from the gamma-ray observation site. Therefore, the glow was terminated by the leader development, while it did not trigger the lightning discharge in the present case., Comment: 12 pages, 4 figures, accepted for publication in Geophysical Research Letters
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- 2018
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45. NuSTAR Detection of X-Ray Heating Events in the Quiet Sun
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Kuhar, Matej, Krucker, Säm, Glesener, Lindsay, Hannah, Iain G., Grefenstette, Brian W., Smith, David M., Hudson, Hugh S., and White, Stephen M.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
The explanation of the coronal heating problem potentially lies in the existence of nanoflares, numerous small-scale heating events occuring across the whole solar disk. In this paper, we present the first imaging spectroscopy X-ray observations of three quiet Sun flares during the NuSTAR solar campaigns on 2016 July 26 and 2017 March 21, concurrent with SDO/AIA observations. Two of the three events showed time lags of a few minutes between peak X-ray and extreme ultraviolet (EUV) emissions. Isothermal fits with rather low temperatures in the range $3.2-4.1$ MK and emission measures of $(0.6-15)\times10^{44} \textrm{ cm}^{-3}$ describe their spectra well, resulting in thermal energies in the range $(2-6)\times10^{26}\textrm{ ergs}$. NuSTAR spectra did not show any signs of a nonthermal or higher temperature component. However, since the estimated upper limits of (hidden) nonthermal energy are comparable to the thermal energy estimates, the lack of a nonthermal component in the observed spectra is not a constraining result. The estimated GOES classes from the fitted values of temperature and emission measure fall between $1/1000 \textrm{ and } 1/100$ A class level, making them 8 orders of magnitude fainter in soft X-ray flux than the largest solar flares., Comment: Accepted for publication in ApJL
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- 2018
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46. Evaluating the predictive character of the method of constrained geometries simulate external force with density functional theory
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Wick, Christian R., Topraksal, Ece, Smith, David M., and Smith, Ana-Sunčana
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- 2022
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47. Direct observation and rational design of nucleation behavior in addressable self-assembly
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Sajfutdinow, Martin, Jacobs, William M., Reinhardt, Aleks, Schneider, Christoph, and Smith, David M.
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Condensed Matter - Soft Condensed Matter - Abstract
In order to optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model system for addressable, multicomponent self-assembly based on a prototypical 'DNA-brick' structure. By combining temperature-dependent dynamic light scattering and atomic force microscopy with coarse-grained simulations, we show how subtle changes in the nucleation pathway profoundly affect the yield of the correctly formed structures. In particular, we can increase the range of conditions over which self-assembly occurs by utilizing stable multi-subunit clusters that lower the nucleation barrier for assembling subunits in the interior of the structure. Consequently, modifying only a small portion of a structure is sufficient to optimize its assembly. Due to the generality of our coarse-grained model and the excellent agreement that we find with our experimental results, the design principles reported here are likely to apply generically to addressable, multicomponent self-assembly.
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- 2017
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48. New Star Observations with NuSTAR: Flares from Young Stellar Objects in the ρ Ophiuchi Cloud Complex in Hard X-Rays
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Vievering, Juliana T, Glesener, Lindsay, Grefenstette, Brian W, and Smith, David M
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Pre-main sequence stars ,Star forming regions ,Stellar activity ,Stellar flares ,Stellar x-ray flares ,Young stellar objects ,Astronomical and Space Sciences ,Atomic ,Molecular ,Nuclear ,Particle and Plasma Physics ,Physical Chemistry (incl. Structural) ,Astronomy & Astrophysics - Abstract
We study the structure and dynamics of extreme flaring events on young stellar objects (YSOs) observed in hard X-rays by the Nuclear Spectroscopic Telescope Array (NuSTAR). During 2015 and 2016, NuSTAR made three observations of the star-forming region ρ Ophiuchi, each with an exposure ~50 ks. NuSTAR offers unprecedented sensitivity above ~7 keV, making this data set the first of its kind. Through improved coverage of hard X-rays, it is finally possible to directly measure the high-energy thermal continuum for hot plasmas and to sensitively search for evidence of nonthermal emission from YSO flares. During these observations, multiple flares were observed, and spectral and timing analyses were performed on three of the brightest flares. By fitting an optically thin thermal plasma model to each of these events, we found flare plasma heated to high temperatures (~40-80 MK) and determined that these events are ~1000 times brighter than the brightest flares observed on the Sun. Two of the studied flares showed excess emission at 6.4 keV, and this excess may be attributable to iron fluorescence in the circumstellar disk. No clear evidence for a nonthermal component was observed, but upper limits on nonthermal emission allow for enough nonthermal energy to account for the estimated thermal energy in the flare on protostar IRS 43, which is consistent with the standard model for solar and stellar flares.
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- 2019
49. HIV-1 drug resistance before initiation or re-initiation of first-line ART in eight regions of Mexico: a sub-nationally representative survey
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Ávila-Ríos, Santiago, García-Morales, Claudia, Valenzuela-Lara, Marisol, Chaillon, Antoine, Tapia-Trejo, Daniela, Pérez-García, Marissa, López-Sánchez, Dulce M, Maza-Sánchez, Liliana, del Arenal-Sánchez, Silvia J, Paz-Juárez, Héctor E, Quiroz-Morales, Verónica S, Mehta, Sanjay R, Smith, David M, León-Juárez, Eddie A, Magis-Rodríguez, Carlos, Reyes-Terán, Gustavo, Gamboa-Marroquín, Jorge A, Espinoza-Fernández, Alan F, Lam-Enríquez, Mario, Castillo-Soria, Oscar A, Navarro-Álvarez, Samuel, Varela-Lara, Noemí, Ortiz-Batanero, Rogelio, Flores-Gómez, Andrés, Velasco-Robledo, Luis, Alatorre-Manjarrez, Arturo, Gutiérrez-Zúñiga, Rita E, Peña-Gutiérrez, Jesús, Rivera-Marroquín, Alejandro, Robles, Berenice, Gálvez-Martínez, Maribel, Hernández-Gutiérrez, Raúl, Solís-Grajales, David, Mora-Castellanos, María G, Vidal-López, Manuel, González-Pacheco, Maribel A, Salazar-Pérez, Carmen, Padilla-Acosta, Juan CA, González-Rodríguez, Andrea, Badial-Hernández, Florentino, Tecalero-Hernández, José C, García-Martínez, Patricia G, Cendejas-Hernández, Arturo, Mosqueda-Gómez, Juan L, Benítez-Carrasco, José M, Bello, José L Sánchez, Fierro-Teliz, Benjamín, Arellano-Torreblanca, Jazmín, Manríquez-Gómez, Ramiro, Zaragoza-Zapata, Elizabeth, Ruiz-Torrez, Saúl O, González-Hernández, Luz A, Soria-Rodríguez, Raúl, Quintero-Pérez, Nora P, Amaya-Tapia, Gerardo, Arredondo-Fuentes, Juana, Santiesteban-Garay, Javier, Mendoza-García, María S, Durán-Arias, Gustavo, Rosas-Dossetti, Margarita M, Chacón-Sánchez, Juana C, Uribe-Iturbide, Angélica, Castro-Melchor, Pedro, Castillo-Reyna, Luis G, Rivera-Abarca, Lesvia M, de la Cruz-Castillo, Jorge E, Papaqui-Limón, Elizabeth, Velázquez-Esqueda, María P, Domínguez-Sánchez, Alexandra S, Magdaleno-Sandoval, Zoila, Silva-Herrera, Jorge, Esparza-Pérez, Mario A, Muñoz-Doana, Alejandro, Aldapa, Gabriela, Arrollo-Romero, Fernando, Salazar-Arriola, Sergio A, Vásquez-Bañuelos, Elva C, Hernández-Morales, Mario J, Prado-Rosas, Daniel, Santos-Villegas, Mercedes, Sánchez-Hernández, Esteban, Jiménez-Jiménez, Adonay, Cárdenas-Anzures, Alejandro, Ortiz-Brisuela, Juan F, Díaz-García, Juana, Carrillo-Garza, Carlos A, Beltrán-Saldaña, Juan, Sánchez-Rivas, Santos, Domínguez-Ramírez, Lizbeth, de la Roca-Chiapas, Jorge M, Basilio-Badillo, Hilda, Torruco-García, Uri, Pérez-Alonso, Juan A, Arias-Tlacuilo, Luis E, and Palacios-Lara, Omar
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Medical Microbiology ,Biomedical and Clinical Sciences ,Antimicrobial Resistance ,Infectious Diseases ,HIV/AIDS ,Infection ,Good Health and Well Being ,Adult ,Anti-HIV Agents ,Antiretroviral Therapy ,Highly Active ,Drug Resistance ,Viral ,Female ,Gene Frequency ,Genotype ,HIV Infections ,HIV-1 ,Humans ,Male ,Mexico ,Mutation ,Prevalence ,Sequence Analysis ,DNA ,Socioeconomic Factors ,Viral Load ,Young Adult ,HIVDR MexNet Group ,Microbiology ,Pharmacology and Pharmaceutical Sciences ,Clinical sciences ,Pharmacology and pharmaceutical sciences - Abstract
BackgroundHIV pretreatment drug resistance (PDR) to NNRTIs in persons initiating ART is increasing in Mexico.ObjectivesTo compare HIV PDR in eight sub-regions of Mexico.Patients and methodsA large PDR survey was implemented in Mexico (September 2017-March 2018) across eight sub-regions. All larger clinics (which provide ART to 90% of all initiators) were included, allocating sample size using the probability-proportional-to-size method. Both antiretroviral-naive and prior antiretroviral-exposed persons were included. HIV PDR levels were estimated from pol Sanger sequences obtained at a WHO-designated laboratory.ResultsA total of 2006 participants were enrolled from 74 clinics. PDR to NNRTIs was higher than to other drug classes (P
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- 2019
50. Proteasome activator 28γ (PA28γ) allosterically activates trypsin-like proteolysis by binding to the α-ring of the 20S proteasome
- Author
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Thomas, Taylor A. and Smith, David M.
- Published
- 2022
- Full Text
- View/download PDF
Catalog
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