Cyberinfrastructure for Cosmology and Line-of-Sight Projection in Optical Galaxy Clusters.

Upcoming wide-area sky surveys such as the Dark Energy Survey (DES) offer the power to test the source of cosmic acceleration by placing extremely precise constraints on existing cosmological model parameters. These observational surveys will employ multiple tests based on statistical signatures of galaxies and larger-scale structures such as clusters of galaxies. Simulations of large-scale structure provide the means to maximize the power of sky survey tests by characterizing key sources of systematic uncertainties. This dissertation explores two subjects motivated by these facts. First, it explores how grid-aware cyberinfrastructure needs to be utilized in current and upcoming simulation campaigns that support large-area sky surveys. Second, it shows how line-of-sight projection plays into cosmological analysis based on galaxy cluster counts in the same wide-area sky surveys. In the first part, an Apache Airavata-enabled grid-aware application workflow for managing simulations is described. Results pertaining to efficiency in producing N-body simulations are reported. In the second part, bias in cosmological parameter estimates caused by incorrectly assuming a Gaussian (projection-free) mass--observable relation when the true relation is non-Gaussian due to projection is explored. Projection tends to skew the mass--observable relation of galaxy clusters by creating a small fraction of severely blended systems, those for which the measured observable property of a cluster is strongly boosted relative to the value of its primary host halo. A model motivated by optical cluster-finding applied to the Millennium Simulation is introduced for projection and Fisher information matrix parameter bias forecasts are produced for a DES-like sky survey. The model predicts significant biases in the dark energy density and equation of state parameters. The model additional predicts an increase in uncertainties in dark energy parameters to a factor of about two larger than forecast uncertainties. Additionally, new parameters used to characterize the model degrade uncertainties in the dark energy parameters. Motivated by this result, this dissertation also contains preliminary results for a new projection model meant to reduce bias in cluster analysis based on redMaPPer identified clusters for the DES.PHDPhysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/99938/1/bmse_1.pd

Influence of Projection in Cluster Cosmology Studies

Projection tends to skew the mass-observable relation of galaxy clusters by creating a small fraction of severely blended systems, those for which the measured observable property of a cluster is strongly boosted relative to the value of its primary host halo. We examine the bias in cosmological parameter estimates caused by incorrectly assuming a Gaussian (projection-free) mass-observable relation when the true relation is non-Gaussian due to projection. We introduce a mixture model for projection and explore Fisher forecasts for a survey of 5000 sq. deg. to z=1.1 and an equivalent mass threshold of 10^13.7 h^-1 solar masses. Using a blended fraction motivated by optical cluster finding applied to the Millennium Simulation and applying Planck and otherwise weak priors, we find that the biases in Omega_DE and w are significant, being factors of 2.8 and 2.4, respectively, times previous forecast uncertainties. Incorporating eight new degrees of freedom to describe cluster selection with projection increases the forecast uncertainty in Omega_DE and w by similar factors. Knowledge of these additional parameters at the 5% level limits degradation in dark energy constraints to <10% relative to projection-free forecasts. We discuss strategies for using simulations and complementary observations to characterize the fraction of blended clusters and their mass selection properties.Comment: 11 pages, 4 figures to be submitted to phys. rev.

A High Throughput Workflow Environment for Cosmological Simulations

The next generation of wide-area sky surveys offer the power to place extremely precise constraints on cosmological parameters and to test the source of cosmic acceleration. These observational programs will employ multiple techniques based on a variety of statistical signatures of galaxies and large-scale structure. These techniques have sources of systematic error that need to be understood at the percent-level in order to fully leverage the power of next-generation catalogs. Simulations of large-scale structure provide the means to characterize these uncertainties. We are using XSEDE resources to produce multiple synthetic sky surveys of galaxies and large-scale structure in support of science analysis for the Dark Energy Survey. In order to scale up our production to the level of fifty 10^10-particle simulations, we are working to embed production control within the Apache Airavata workflow environment. We explain our methods and report how the workflow has reduced production time by 40% compared to manual management.Comment: 8 pages, 5 figures. V2 corrects an error in figure

Poly-essential and general Hyperelastic World (brane) models

This article provides a unified treatment of an extensive category of non-linear classical field models whereby the universe is represented (perhaps as a brane in a higher dimensional background) in terms of a structure of a mathematically convenient type describable as hyperelastic, for which a complete set of equations of motion is provided just by the energy-momentum conservation law. Particular cases include those of a perfect fluid in quintessential backgrounds of various kinds, as well as models of the elastic solid kind that has been proposed to account for cosmic acceleration. It is shown how an appropriately generalised Hadamard operator can be used to construct a symplectic structure that controles the evolution of small perturbations, and that provides a characteristic equation governing the propagation of weak discontinuities of diverse (extrinsic and extrinsic) kinds. The special case of a poly-essential model - the k-essential analogue of an ordinary polytropic fluid - is examined and shown to be well behaved (like the fluid) only if the pressure to density ratio $w$ is positive.Comment: 16 pages Latex, Contrib. to 10th Peyresq Pysics Meeting, June 2005: Micro and Macro Structures of Spacetim

Novel Strains of Mice Deficient for the Vesicular Acetylcholine Transporter: Insights on Transcriptional Regulation and Control of Locomotor Behavior

Defining the contribution of acetylcholine to specific behaviors has been challenging, mainly because of the difficulty in generating suitable animal models of cholinergic dysfunction. We have recently shown that, by targeting the vesicular acetylcholine transporter (VAChT) gene, it is possible to generate genetically modified mice with cholinergic deficiency. Here we describe novel VAChT mutant lines. VAChT gene is embedded within the first intron of the choline acetyltransferase (ChAT) gene, which provides a unique arrangement and regulation for these two genes. We generated a VAChT allele that is flanked by loxP sequences and carries the resistance cassette placed in a ChAT intronic region (FloxNeo allele). We show that mice with the FloxNeo allele exhibit differential VAChT expression in distinct neuronal populations. These mice show relatively intact VAChT expression in somatomotor cholinergic neurons, but pronounced decrease in other cholinergic neurons in the brain. VAChT mutant mice present preserved neuromuscular function, but altered brain cholinergic function and are hyperactive. Genetic removal of the resistance cassette rescues VAChT expression and the hyperactivity phenotype. These results suggest that release of ACh in the brain is normally required to “turn down” neuronal circuits controlling locomotion

The United States COVID-19 Forecast Hub dataset

Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages

Effects of Anacetrapib in Patients with Atherosclerotic Vascular Disease

BACKGROUND: Patients with atherosclerotic vascular disease remain at high risk for cardiovascular events despite effective statin-based treatment of low-density lipoprotein (LDL) cholesterol levels. The inhibition of cholesteryl ester transfer protein (CETP) by anacetrapib reduces LDL cholesterol levels and increases high-density lipoprotein (HDL) cholesterol levels. However, trials of other CETP inhibitors have shown neutral or adverse effects on cardiovascular outcomes. METHODS: We conducted a randomized, double-blind, placebo-controlled trial involving 30,449 adults with atherosclerotic vascular disease who were receiving intensive atorvastatin therapy and who had a mean LDL cholesterol level of 61 mg per deciliter (1.58 mmol per liter), a mean non-HDL cholesterol level of 92 mg per deciliter (2.38 mmol per liter), and a mean HDL cholesterol level of 40 mg per deciliter (1.03 mmol per liter). The patients were assigned to receive either 100 mg of anacetrapib once daily (15,225 patients) or matching placebo (15,224 patients). The primary outcome was the first major coronary event, a composite of coronary death, myocardial infarction, or coronary revascularization. RESULTS: During the median follow-up period of 4.1 years, the primary outcome occurred in significantly fewer patients in the anacetrapib group than in the placebo group (1640 of 15,225 patients [10.8%] vs. 1803 of 15,224 patients [11.8%]; rate ratio, 0.91; 95% confidence interval, 0.85 to 0.97; P=0.004). The relative difference in risk was similar across multiple prespecified subgroups. At the trial midpoint, the mean level of HDL cholesterol was higher by 43 mg per deciliter (1.12 mmol per liter) in the anacetrapib group than in the placebo group (a relative difference of 104%), and the mean level of non-HDL cholesterol was lower by 17 mg per deciliter (0.44 mmol per liter), a relative difference of -18%. There were no significant between-group differences in the risk of death, cancer, or other serious adverse events. CONCLUSIONS: Among patients with atherosclerotic vascular disease who were receiving intensive statin therapy, the use of anacetrapib resulted in a lower incidence of major coronary events than the use of placebo. (Funded by Merck and others; Current Controlled Trials number, ISRCTN48678192 ; ClinicalTrials.gov number, NCT01252953 ; and EudraCT number, 2010-023467-18 .)

Lake Superior Manoomin cultural and ecosystem characterization study

Manoomin, wild rice, is integral to the culture, livelihood, and identity of the Anishinaabeg, the indigenous peoples of Canada and the United States that include the Odawa, Ojibwe, Potawatomi, and Algonquin peoples. In addition to the vital role Manoomin has in the lives of the Anishinaabeg, Manoomin is recognized as being ecologically important, feeding migrating and resident wildlife species, providing a nursery for fish and nesting and breeding habitats for many waterfowl and muskrat, and stabilizing shorelines. This study was initiated by a team of Lake Superior basin Anishinaabe communities and federal and state agencies to document and characterize (1) the importance of Manoomin habitat to Anishinaabe cultural perspectives and identity, community connections, spiritual practices, food sovereignty, and food security; and (2) the ecological importance of Manoomin habitat as an indicator of a high-quality, high-functioning, and biodiverse ecosystem. The team applied a set of cultural and ecological metrics to characterize seven case study sites around Lake Superior and used a habitat equivalency analysis to determine the amount of restoration needed to counterbalance the lost Manoomin habitat functionality. Results from this study highlight the difficulty in restoring the cultural and ecological functionality of degraded Manoomin habitat and the importance of preserving and protecting existing Manoomin habitat

Paradoxical Association Between Relative Cerebral Blood Volume Dynamics Following Chemoradiation and Increased Progression-Free Survival in Newly Diagnosed IDH Wild-Type MGMT Promoter Methylated Glioblastoma With Measurable Disease.

Background and purposeWhile relative cerebral blood volume (rCBV) may be diagnostic and prognostic for survival in glioblastoma (GBM), changes in rCBV during chemoradiation in the subset of newly diagnosed GBM with subtotal resection and the impact of MGMT promoter methylation status on survival have not been explored. This study aimed to investigate the association between rCBV response, MGMT methylation status, and progression-free (PFS) and overall survival (OS) in newly diagnosed GBM with measurable enhancing lesions.Methods1,153 newly diagnosed IDH wild-type GBM patients were screened and 53 patients (4.6%) had measurable post-surgical tumor (&gt;1mL). rCBV was measured before and after patients underwent chemoradiation. Patients with a decrease in rCBV &gt;10% were considered rCBV Responders, while patients with an increase or a decrease in rCBV &lt;10% were considered rCBV Non-Responders. The association between change in enhancing tumor volume, change in rCBV, MGMT promotor methylation status, and PFS or OS were explored.ResultsA decrease in tumor volume following chemoradiation trended towards longer OS (p=0.12; median OS=26.8 vs. 16.3 months). Paradoxically, rCBV Non-Responders had a significantly improved PFS compared to Responders (p=0.047; median PFS=9.6 vs. 7.2 months). MGMT methylated rCBV Non-Responders exhibited a significantly longer PFS compared to MGMT unmethylated rCBV Non-Responders (p&lt;0.001; median PFS=0.5 vs. 7.1 months), and MGMT methylated rCBV Non-Responders trended towards longer PFS compared to methylated rCBV Responders (p=0.089; median PFS=20.5 vs. 13.8 months).ConclusionsThis preliminary report demonstrates that in newly diagnosed IDH wild-type GBM with measurable enhancing disease after surgery (5% of patients), an enigmatic non-response in rCBV was associated with longer PFS, particularly in MGMT methylated patients