High Precision Galaxy Cluster Mass Estimation: Building a Model for Stacked Caustics in Simulations and its Application to Galaxy Cluster Survey Data

Honors (Bachelor's)Astronomy and AstrophysicsUniversity of Michiganhttp://deepblue.lib.umich.edu/bitstream/2027.42/112141/1/nkern.pd

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction.

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2-3 × 10-4 (ΔE/E). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (ΔE/E = 3 × 10-3) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction

Emulating Simulations of Cosmic Dawn for 21cm Power Spectrum Constraints on Cosmology, Reionization, and X-ray Heating

Current and upcoming radio interferometric experiments are aiming to make a statistical characterization of the high-redshift 21cm fluctuation signal spanning the hydrogen reionization and X-ray heating epochs of the universe. However, connecting 21cm statistics to underlying physical parameters is complicated by the theoretical challenge of modeling the relevant physics at computational speeds quick enough to enable exploration of the high dimensional and weakly constrained parameter space. In this work, we use machine learning algorithms to build a fast emulator that mimics expensive simulations of the 21cm signal across a wide parameter space to high precision. We embed our emulator within a Markov-Chain Monte Carlo framework, enabling it to explore the posterior distribution over a large number of model parameters, including those that govern the Epoch of Reionization, the Epoch of X-ray Heating, and cosmology. As a worked example, we use our emulator to present an updated parameter constraint forecast for the Hydrogen Epoch of Reionization Array experiment, showing that its characterization of a fiducial 21cm power spectrum will considerably narrow the allowed parameter space of reionization and heating parameters, and could help strengthen Planck's constraints on $\sigma_8$. We provide both our generalized emulator code and its implementation specifically for 21cm parameter constraints as publicly available software.Comment: 22 pages, 9 figures; accepted to Ap

Results from EDGES High-Band: II. Constraints on Parameters of Early Galaxies

We use the sky-average spectrum measured by EDGES High-Band ($90-190$ MHz) to constrain parameters of early galaxies independent of the absorption feature at $78$~MHz reported by Bowman et al. (2018). These parameters represent traditional models of cosmic dawn and the epoch of reionization produced with the 21cmFAST simulation code (Mesinger & Furlanetto 2007, Mesinger et al. 2011). The parameters considered are: (1) the UV ionizing efficiency ($\zeta$), (2) minimum halo virial temperature hosting efficient star-forming galaxies ($T^{\rm min}_{\rm vir}$), (3) integrated soft-band X-ray luminosity ($L_{\rm X\,<\,2\,keV}/{\rm SFR}$), and (4) minimum X-ray energy escaping the first galaxies ($E_{0}$), corresponding to a typical H${\rm \scriptstyle I}$ column density for attenuation through the interstellar medium. The High-Band spectrum disfavors high values of $T^{\rm min}_{\rm vir}$ and $\zeta$, which correspond to signals with late absorption troughs and sharp reionization transitions. It also disfavors intermediate values of $L_{\rm X\,<\,2\,keV}/{\rm SFR}$, which produce relatively deep and narrow troughs within the band. Specifically, we rule out $39.4<\log_{10}\left(L_{\rm X\,<\,2\,keV}/{\rm SFR}\right)<39.8$ ($95\%$ C.L.). We then combine the EDGES High-Band data with constraints on the electron scattering optical depth from Planck and the hydrogen neutral fraction from high-$z$ quasars. This produces a lower degeneracy between $\zeta$ and $T^{\rm min}_{\rm vir}$ than that reported in Greig & Mesinger (2017a) using the Planck and quasar constraints alone. Our main result in this combined analysis is the estimate $4.5$~$\leq \log_{10}\left(T^{\rm min}_{\rm vir}/\rm K\right)\leq$~$5.7$ ($95\%$ C.L.). We leave for future work the evaluation of $21$~cm models using simultaneously data from EDGES Low- and High-Band.Comment: Accepted in Ap

Regulation of Lipoprotein Lipase by Protein Kinase Cα in 3T3-F442A Adipocytes

Lipoprotein lipase (LPL) is an important enzyme in adipocyte and lipid metabolism with complex cellular regulation. Previous studies demonstrated an inhibition of LPL activity and synthesis following depletion of protein kinase C (PKC) isoforms with long term treatment of 3T3-F442A adipocytes with 12-O-tetradecanoylphorbol-13-acetate. To identify the specific PKC isoforms involved, we treated cells with antisense oligonucleotides that block expression of specific PKC isoforms. An antisense oligonucleotide to PKCα inhibited LPL activity by 78 ± 8%, whereas antisense oligonucleotides directed against PKCδ or PKCε had no effect on LPL activity. The change in LPL activity was maximal at 72 h and was accompanied by a decrease in LPL protein and LPL synthetic rate but no change in LPL mRNA, suggesting regulation at the level of translation. However, PKC depletion resulted in no change in the polysome profile, indicating that translation initiation was not affected. However, the addition of cytoplasmic extracts from adipocytes treated with 12-O-tetradecanoylphorbol-13-acetate or PKCα antisense oligomers inhibited LPL translation in vitro. This inhibition of LPL translation in vitro was lost when the LPL mRNA transcript did not contain nucleotides 1599-3200, thus implicating the 3′-untranslated region of LPL in the regulation of translation by PKC depletion. Both LPL activity and Raf1 activity were decreased in parallel following depletion of either total PKC or specific inhibition of PKCα. An antisense oligonucleotide to RAF1, which inhibited RAF1 activity, also inhibited LPL activity by 48 ± 10%, and this decrease in LPL activity was not accompanied by a change in LPL mRNA. Cells were treated with U0126, a specific inhibitor of the ERK-activating kinases MEK1 and MEK2. Although U0126 inhibited ERK1 and ERK2 phosphorylation, U0126 had no effect on LPL activity, indicating that MEK/ERK pathways were not involved in this mechanism of LPL regulation. Together, these data indicate that PKCα and RAF1 are important in the translational regulation of LPL in adipocytes and that the mechanism of regulation is probably through an ERK-independent pathway

Polarized Redundant-Baseline Calibration for 21 cm Cosmology Without Adding Spectral Structure

21 cm cosmology is a promising new probe of the evolution of visible matter in our universe, especially during the poorly-constrained Cosmic Dawn and Epoch of Reionization. However, in order to separate the 21 cm signal from bright astrophysical foregrounds, we need an exquisite understanding of our telescopes so as to avoid adding spectral structure to spectrally-smooth foregrounds. One powerful calibration method relies on repeated simultaneous measurements of the same interferometric baseline to solve for the sky signal and for instrumental parameters simultaneously. However, certain degrees of freedom are not constrained by asserting internal consistency between redundant measurements. In this paper, we review the origin of these "degeneracies" of redundant-baseline calibration and demonstrate how they can source unwanted spectral structure in our measurement and show how to eliminate that additional, artificial structure. We also generalize redundant calibration to dual-polarization instruments, derive the degeneracy structure, and explore the unique challenges to calibration and preserving spectral smoothness presented by a polarized measurement.Comment: 12 pages, 3 figures, updated to match the published MNRAS versio

On the use of temporal filtering for mitigating galactic synchrotron calibration bias in 21 cm reionization observations

Precision antenna calibration is required for mitigating the impact of foreground contamination in 21 cm cosmological radio surveys. One widely studied source of error is the effect of missing point sources in the calibration sky model; however, poorly understood diffuse galactic emission also creates a calibration bias that can complicate the clean separation of foregrounds from the 21 cm signal. In this work, we present a technique for suppressing this bias with temporal filtering of radio interferometric visibilities observed in a drift-scan mode. We demonstrate this technique on mock simulations of the Hydrogen Epoch of Reionization Array (HERA) experiment. Inspecting the recovered calibration solutions, we find that our technique reduces spurious errors by over an order of magnitude. This improved accuracy approaches the required accuracy needed to make a fiducial detection of the 21 cm signal with HERA, but is dependent on a number of external factors that we discuss. We also explore different types of temporal filtering techniques and discuss their relative performance and tradeoffs

Smart Alarms: Multivariate Medical Alarm Integration for Post CABG Surgery Patients

In order to monitor patients in the Intensive Care Unit, healthcare practitioners set threshold alarms on each of many individual vital sign monitors. The current alarm algorithms elicit numerous false positive alarms producing an inefficient healthcare system, where nurses habitually ignore low level alarms due to their overabundance. In this paper, we describe an algorithm that considers multiple vital signs when monitoring a post coronary artery bypass graft (post-CABG) surgery patient. The algorithm employs a Fuzzy Expert System to mimic the decision processes of nurses. In addition, it includes a Clinical Decision Support tool that uses Bayesian theory to display the possible CABG-related complications the patient might be undergoing at any point in time, as well as the most relevant risk factors. As a result, this multivariate approach decreases clinical alarms by an average of 59% with a standard deviation of 17% (Sample of 32 patients, 1,451 hours of vital sign data). Interviews comparing our proposed system with the approach currently used in hospitals have also confirmed the potential efficiency gains from this approach