Characterizing & Mitigating Interstellar Scattering in Radio Observations of Pulsars

Pulsars are rapidly rotating neutron stars that emit concentrated beams of radiation from their magnetic poles. Measuring the arrival of these pulses via pulsar timing is a powerful tool in efforts to detect low frequency gravitational waves (GWs). However, the interstellar medium (ISM) presents a significant source of timing uncertainty that must be mitigated to improve the sensitivity of pulsar timing efforts to these GW signals. By examining the effects of pulsar emission interactions with this medium, we can properly correct for the resulting effects in pulsar timing efforts, as well as study the astronomical unit-to-parsec scale structure and behavior of the ISM and characterize this medium across many lines of sight in our Galaxy and localize the regions that dominate these interactions. Emerging data processing techniques that take advantage of the periodic nature of pulsar signals are also now allowing us to probe these features with incredible resolution. This thesis serves to highlight some valuable studies related to understanding the structure and behavior of the ionized ISM via the interstellar scattering of pulsar emission. To examine scattering behavior across many lines of sight, we extract interstellar scintillation parameters for pulsars observed by the North American Nanohertz Observatory for Gravitational Waves (NANOGrav) radio pulsar timing program in the 12.5 year data release. We find good agreement between our scattering delay measurements and electron- density model predictions for most pulsars. For most pulsars for which scattering delays are measurable, we find that time-of-arrival uncertainties for a given epoch are larger than our scattering delay measurements, indicating that variable scattering delays are currently subdominant in our overall noise budget but are important for achieving precisions of tens of nanoseconds or less. Next, we use the Upgraded Giant Metrewave Radio Telescope to measure scin- tillation arc properties in six bright canonical pulsars with simultaneous dual frequency coverage. We perform more robust determinations of arc curvature, scattering delay, and scintillation timescale frequency-dependence, and comparison between arc curvature and pseudo-curvature than allowed by single-frequency-band-per-epoch measurements, which we find to agree with theory and previous literature. We find a strong correlation between arc asymmetry and arc curvature, which we have replicated using simulations, and attribute to a bias in the Hough transform approach to scintillation arc analysis. We then simulate scattering delays from the ISM to examine the effectiveness of three estimators in recovering these delays in pulsar timing data. Two of these estima- tors use the more traditional process of fitting autocorrelation functions (ACFs) to pulsar dynamic spectra to extract scintillation bandwidths, while the third estimator uses the newer technique of cyclic spectroscopy on baseband pulsar data to recover the ISM’s im- pulse response function (IRF). We find that, given sufficient S/N, cyclic spectroscopy is more accurate than both ACF estimators at recovering scattering delays at specific epochs, suggesting that cyclic spectroscopy is a superior method for scattering estimation in high quality data. Finally, we use cyclic spectroscopy to perform high frequency-resolution, frequency dependent analyses of the millisecond pulsar B1937+21. We present among the most robust intra-epoch scattering delay scaling estimations performed at 1.4 GHz, using eight individual measurements across our observing bands, and find our results to agree with those previously quoted in the literature

Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing

Motivation: Transcriptome-based computational drug repurposing has attracted considerable interest by bringing about faster and more cost-effective drug discovery. Nevertheless, key limitations of the current drug connectivity-mapping paradigm have been long overlooked, including the lack of effective means to determine optimal query gene signatures. Results: The novel approach Dr Insight implements a frame-breaking statistical model for the ‘hand-shake’ between disease and drug data. The genome-wide screening of concordantly expressed genes (CEGs) eliminates the need for subjective selection of query signatures, added to eliciting better proxy for potential disease-specific drug targets. Extensive comparisons on simulated and real cancer datasets have validated the superior performance of Dr Insight over several popular drug-repurposing methods to detect known cancer drugs and drug–target interactions. A proof-of-concept trial using the TCGA breast cancer dataset demonstrates the application of Dr Insight for a comprehensive analysis, from redirection of drug therapies, to a systematic construction of disease-specific drug-target networks

Impact of Activity Monitoring on Physical Activity, Sedentary Behavior, and Body Weight during the COVID-19 Pandemic

Decreases in individuals\u27 physical activity and increases in sedentary behavior and bodyweight have been reported during the COVID-19 pandemic. The present study assessed the ability of physical activity monitoring, which may promote physical activity and discourage sedentary behavior, to mitigate these negative outcomes. An evaluation of university samples ( N = 404, 40.5 ± 15.4 years) of self-reported physical activity, sedentary behavior, and bodyweight prior to the closure of campus due to the pandemic in March of 2020 and again at the time of the survey administration (May-June 2020) during pandemic-related restrictions was performed. Participants also reported whether they did ( n = 172) or did not ( n = 232) regularly use physical activity monitoring technology. While physical activity was unchanged during the pandemic ( p ≥ 0.15), participants significantly increased sitting by 67.8 ± 156.6 min/day and gained 0.64 ± 3.5 kg from pre-campus to post-campus closure ( p \u3c 0.001). However, the use of activity monitoring did not moderate these changes. In conclusion, while physical activity was not affected, participants reported significant increases in sedentary behavior and bodyweight during the COVID-19 pandemic. These changes occurred regardless of whether participants regularly used physical activity monitoring or not

A Simultaneous Dual-Frequency Scintillation Arc Survey of Six Bright Canonical Pulsars Using the Upgraded Giant Metrewave Radio Telescope

We use the Upgraded Giant Metrewave Radio Telescope to measure scintillation arc properties in six bright canonical pulsars with simultaneous dual frequency coverage. These observations at frequencies from 300 to 750 MHz allowed for detailed analysis of arc evolution across frequency and epoch. We perform more robust determinations of arc curvature, scattering delay, and scintillation timescale frequency-dependence, and comparison between arc curvature and pseudo-curvature than allowed by single-frequency-band-per-epoch measurements, which we find to agree with theory and previous literature. We find a strong correlation between arc asymmetry and arc curvature, which we have replicated using simulations, and attribute to a bias in the Hough transform approach to scintillation arc analysis. Possible evidence for an approximately week long timescale over which a given scattering screen dominates signal propagation was found by tracking visible scintillation arcs in each epoch in PSR J1136+1551. The inclusion of a 155 minute observation allowed us to resolve the scale of scintillation variations on short timescales, which we find to be directly tied to the amount of ISM sampled over the observation. Some of our pulsars showed either consistent or emerging asymmetries in arc curvature, indicating instances of refraction across their lines of sight. Significant features in various pulsars, such as multiple scintillation arcs in PSR J1136+1551 and flat arclets in PSR J1509+5531, that have been found in previous works, were also detected. The multiple band capability of the upgraded GMRT shows excellent promise for future pulsar scintillation work

Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth

One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis, survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 US Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of over 13 000 loci to infer the demographic history of pupfishes in Death Valley. Instead of relicts isolated 2–3 Myr ago throughout repeated flooding of the entire region by inland seas as currently believed, we present evidence for frequent gene flow among Death Valley pupfish species and divergence after the most recent flooding 13 kyr ago. We estimate that Devils Hole was colonized by pupfish between 105 and 830 years ago, followed by genetic assimilation of pelvic fin loss and recent gene flow into neighbouring spring systems. Our results provide a new perspective on an iconic endangered species using the latest population genomic methods and support an emerging consensus that timescales for speciation are overestimated in many groups of rapidly evolving species

Elevated Liver Enzymes and Mortality in Older Individuals: A Prospective Cohort Study

Aim of the study: The aim of the study was to determine the excess risk of all-cause and cardiovascular mortality in older people with elevated liver enzymes [alanine transaminase (ALT) and gamma glutamyltransferase (GGT)]. Methods: We utilized data from a large, prospective, population based study of 2061 people aged 50 to 99 years with linkage to a National Death Registry. Participants were categorized as having elevated liver enzymes using standard thresholds (for males, GGT>51 and ALT>40 IU/L, and GGT>33 and ALT>31 IU/L for females). Adjusted Cox proportional hazards models assessed the association of elevated liver enzymes and mortality with long duration follow-up. Results: Over a median follow-up of 10 years (20,145 person years), 701 people died, including 203 (34%) from cardiovascular disease. Cox regression models adjusted for sex, age, smoking, and alcohol intake indicated that people with elevated liver enzymes had an increased risk of all-cause mortality that was modified by age (test for interaction P=0.01). Age-stratified analyses demonstrated no increased risk at younger ages [age 59 y and below; hazard ratio (HR): 0.46; 95% confidence interval, 0.06-3.49], but increased risk with age; age 60 to 69, HR: 1.05 (0.53-2.07), age 70 to 79 years, HR: 1.54 (0.81 to 2.93), and age 80 years and above, HR: 3.53 (1.55 to 8.04). Similarly, the risk of cardiovascular mortality with elevated liver enzymes was also modified by, and increased with age (test for interaction P=0.02); age 70 to 79, HR: 3.15 (1.37 to 7.23), age 80 years and above, HR: 6.86 (2.44 to 19.30). Conclusions: In community-dwelling elderly persons, an elevation in both ALT and GGT are associated with an excess risk of all-cause and cardiovascular mortality which increases with age

Complexity, Development, and Evolution in Morphogenetic Collective Systems

Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief overview of our recent effort that investigated various aspects of such morphogenetic collective systems. We first propose a theoretical classification scheme that distinguishes four complexity levels of morphogenetic collective systems based on the nature of their components and interactions. We conducted a series of computational experiments using a self-propelled particle swarm model to investigate the effects of (1) heterogeneity of components, (2) differentiation/re-differentiation of components, and (3) local information sharing among components, on the self-organization of a collective system. Results showed that (a) heterogeneity of components had a strong impact on the system's structure and behavior, (b) dynamic differentiation/re-differentiation of components and local information sharing helped the system maintain spatially adjacent, coherent organization, (c) dynamic differentiation/re-differentiation contributed to the development of more diverse structures and behaviors, and (d) stochastic re-differentiation of components naturally realized a self-repair capability of self-organizing morphologies. We also explored evolutionary methods to design novel self-organizing patterns, using interactive evolutionary computation and spontaneous evolution within an artificial ecosystem. These self-organizing patterns were found to be remarkably robust against dimensional changes from 2D to 3D, although evolution worked efficiently only in 2D settings.Comment: 13 pages, 8 figures, 1 table; submitted to "Evolution, Development, and Complexity: Multiscale Models in Complex Adaptive Systems" (Springer Proceedings in Complexity Series

Inconsistency of ammonium–sulfate aerosol ratios with thermodynamic models in the eastern US: a possible role of organic aerosol

Thermodynamic models predict that sulfate aerosol (S(VI)  ≡  H2SO4(aq) + HSO4−+ SO42−) should take up available ammonia (NH3) quantitatively as ammonium (NH4+) until the ammonium sulfate stoichiometry (NH4)2SO4 is close to being reached. This uptake of ammonia has important implications for aerosol mass, hygroscopicity, and acidity. When ammonia is in excess, the ammonium–sulfate aerosol ratio R =  [NH4+] ∕ [S(VI)] should approach 2, with excess ammonia remaining in the gas phase. When ammonia is in deficit, it should be fully taken up by the aerosol as ammonium and no significant ammonia should remain in the gas phase. Here we report that sulfate aerosol in the eastern US in summer has a low ammonium–sulfate ratio despite excess ammonia, and we show that this is at odds with thermodynamic models. The ammonium–sulfate ratio averages only 1.04 ± 0.21 mol mol−1 in the Southeast, even though ammonia is in large excess, as shown by the ammonium–sulfate ratio in wet deposition and by the presence of gas-phase ammonia. It further appears that the ammonium–sulfate aerosol ratio is insensitive to the supply of ammonia, remaining low even as the wet deposition ratio exceeds 6 mol mol−1. While the ammonium–sulfate ratio in wet deposition has increased by 5.8 % yr−1 from 2003 to 2013 in the Southeast, consistent with SO2 emission controls, the ammonium–sulfate aerosol ratio decreased by 1.4–3.0 % yr−1. Thus, the aerosol is becoming more acidic even as SO2 emissions decrease and ammonia emissions stay constant; this is incompatible with simple sulfate–ammonium thermodynamics. A tentative explanation is that sulfate particles are increasingly coated by organic material, retarding the uptake of ammonia. Indeed, the ratio of organic aerosol (OA) to sulfate in the Southeast increased from 1.1 to 2.4 g g−1 over the 2003–2013 period as sulfate decreased. We implement a simple kinetic mass transfer limitation for ammonia uptake to sulfate aerosols in the GEOS-Chem chemical transport model and find that we can reproduce both the observed ammonium–sulfate aerosol ratios and the concurrent presence of gas-phase ammonia. If sulfate aerosol becomes more acidic as OA ∕ sulfate ratios increase, then controlling SO2 emissions to decrease sulfate aerosol will not have the co-benefit of suppressing acid-catalyzed secondary organic aerosol (SOA) formation

Interferometric Constraints on Gravity Darkening with Application to the Modeling of Spica A & B

In 2005 we obtained very precise interferometric measurements of the pole-on rapid rotator Vega (A0 V) with the longest baselines of the Center for High Angular Angular Resolution (CHARA) Array and the Fiber Linked Unit for Optical Recombination (FLUOR). For the analysis of these data, we developed a code for mapping sophisticated PHOENIX model atmospheres on to the surface of rotationally distorted stars described by a Roche-von Zeipel formalism. Given a set of input parameters for a star or binary pair, this code predicts the interferometric visibility, spectral energy distribution and high-resolution line spectrum expected for the system. For the gravity-darkened Vega, our model provides a very good match to the K-band interferometric data, a good match to the spectral energy distribution - except below 160 nm - and a rather poor match to weak lines in the high dispersion spectrum where the model appears overly gravity darkened. In 2006, we used the CHARA Array and FLUOR to obtain high precision measurements of the massive, non-eclipsing, double-line spectroscopic binary Spica, a 4-day period system where both components are gravity darkened rapid rotators. These data supplement recent data obtained with the Sydney University Stellar Interferometer (SUSI). Our study follows the classic 1971 study by Herbison-Evans et al. who resolved Spica as a binary with the Narrabri Stellar Intensity Interferometer (NSII). We will report on our progress modeling the new interferometric and archival spectroscopic data, with the goal towards better constraining the apsidal constan