Chromatin accessibility context identifies regulatory mechanisms for cardiometabolic traits

Cardiovascular diseases (CVD) and associated cardiovascular and metabolic (cardiometabolic) traits pose a significant global health burden. Identifying molecular mechanisms for cardiometabolic traits would improve diagnosis and treatment of disease. Genome-wide association studies (GWAS) have identified thousands of loci associated with cardiometabolic traits. However, the mechanisms of most remain unclear, especially at the large number of noncoding loci. One mechanism of noncoding loci is to regulate gene expression in cell- and context-dependent manners. Regulatory elements can be identified through chromatin accessibility. Therefore, chromatin accessibility in disease-relevant cell types and contexts can be integrated with gene expression and GWAS data to identify regulatory elements that affect gene expression to contribute to cardiometabolic traits. I profiled chromatin accessibility in adipose and liver tissue and in adipocytes exposed to disease-relevant contexts of differentiation, excess free fatty acids, hypoxia, and inflammation. I identified context-dependent regulatory elements that change after exposure to disease-relevant contexts in adipocytes and between sexes in liver tissue. I integrated context-dependent regulatory elements with multiple genomic datasets such as eQTL, Hi-C, and context-dependent gene expression to link elements to candidate genes. Additionally, I integrated context-dependent regulatory elements to GWAS to link elements to traits. Functional testing of candidate regulatory elements identified context- and allele- dependent transcriptional activity. While they require future functional testing, the work in this dissertation identifies hundreds of candidate regulatory mechanisms for noncoding GWAS loci. Furthermore, these chromatin accessibility profiles provide a useful resource for future work on identifying regulatory mechanisms of GWAS loci that may improve diagnosis and treatment of disease.Doctor of Philosoph

Gaps in Protoplanetary Disks as Signatures of Planets: I. Methodology and Validation

We examine the observational consequences of partial gaps being opened by planets in protoplanetary disks. We model the disk using a static alpha-disk model with detailed radiative transfer, parametrizing the shape and size of the partially cleared gaps based on the results of hydrodynamic simulations. Shadowing and illumination by stellar irradiation at the surface of the gap leads to increased contrast as the gap trough is deepened by shadowing and cooling and the far gap wall is puffed up by illumination and heating. In calculating observables, we find that multiple scattering is important and derive an approximation to include these effects. A gap produced by a 200 M_Earth (70 M_Earth) planet at 10 AU can lower/raise the midplane temperature of the disk by up to ~-25/+29% (~-11/+19%) by shadowing in the gap trough and illumination on the far shoulder of the gap. At the distance of Taurus, this gap would be resolvable with ~0.01" angular resolution. The gap contrast is most significant in scattered light and at thermal continuum wavelengths characteristic of the surface temperature, reducing or raising the surface brightness by up to order of magnitude. Since gaps sizes are correlated to planet mass, this is a promising way of finding and determining the masses of planets embedded in protoplanetary disks.Comment: 11 pages, 9 figures. Accepted to Ap

Probing for Exoplanets Hiding in Dusty Debris Disks: Disk Imaging, Characterization, and Exploration with HST/STIS Multi-Roll Coronagraphy

Spatially resolved scattered-light images of circumstellar (CS) debris in exoplanetary systems constrain the physical properties and orbits of the dust particles in these systems. They also inform on co-orbiting (but unseen) planets, systemic architectures, and forces perturbing starlight-scattering CS material. Using HST/STIS optical coronagraphy, we have completed the observational phase of a program to study the spatial distribution of dust in ten CS debris systems, and one "mature" protoplanetrary disk all with HST pedigree, using PSF-subtracted multi-roll coronagraphy. These observations probe stellocentric distances > 5 AU for the nearest stars, and simultaneously resolve disk substructures well beyond, corresponding to the giant planet and Kuiper belt regions in our Solar System. They also disclose diffuse very low-surface brightness dust at larger stellocentric distances. We present new results inclusive of fainter disks such as HD92945 confirming, and better revealing, the existence of a narrow inner debris ring within a larger diffuse dust disk. Other disks with ring-like sub-structures, significant asymmetries and complex morphologies include: HD181327 with a posited spray of ejecta from a recent massive collision in an exo-Kuiper belt; HD61005 suggested interacting with the local ISM; HD15115 & HD32297, discussed also in the context of environmental interactions. These disks, and HD15745, suggest debris system evolution cannot be treated in isolation. For AU Mic's edge-on disk, out-of-plane surface brightness asymmetries at > 5 AU may implicate one or more planetary perturbers. Time resolved images of the MP Mus proto-planetary disk provide spatially resolved temporal variability in the disk illumination. These and other new images from our program enable direct inter-comparison of the architectures of these exoplanetary debris systems in the context of our own Solar System.Comment: 109 pages, 43 figures, accepted for publication in the Astronomical Journa

Sending money home: a mixed-Methods study of remittances by migrant nurses in Ireland

© 2009 Humphries et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

First Resolved Scattered-Light Images of Four Debris Disks in Scorpius-Centaurus with the Gemini Planet Imager

We present the first spatially resolved scattered-light images of four debris disks around members of the Scorpius-Centaurus (Sco-Cen) OB association with high-contrast imaging and polarimetry using the Gemini Planet Imager (GPI). All four disks are resolved for the first time in polarized light, and one disk is also detected in total intensity. The three disks imaged around HD 111161, HD 143675, and HD 145560 are symmetric in both morphology and brightness distribution. The three systems span a range of inclinations and radial extents. The disk imaged around HD 98363 shows indications of asymmetries in morphology and brightness distribution, with some structural similarities to the HD 106906 planet-disk system. Uniquely, HD 98363 has a wide comoving stellar companion, Wray 15-788, with a recently resolved disk with very different morphological properties. HD 98363 A/B is the first binary debris disk system with two spatially resolved disks. All four targets have been observed with ALMA, and their continuum fluxes range from one nondetection to one of the brightest disks in the region. With the new results, a total of 15 A/F stars in Sco-Cen have resolved scattered-light debris disks, and approximately half of these systems exhibit some form of asymmetry. Combining the GPI disk structure results with information from the literature on millimeter fluxes and imaged planets reveals a diversity of disk properties in this young population. Overall, the four newly resolved disks contribute to the census of disk structures measured around A/F stars at this important stage in the development of planetary systems

JWST-TST DREAMS: Quartz Clouds in the Atmosphere of WASP-17b

Clouds are prevalent in many of the exoplanet atmospheres that have been observed to date. For transiting exoplanets, we know if clouds are present because they mute spectral features and cause wavelength-dependent scattering. While the exact composition of these clouds is largely unknown, this information is vital to understanding the chemistry and energy budget of planetary atmospheres. In this work, we observe one transit of the hot Jupiter WASP-17b with JWST's MIRI LRS and generate a transmission spectrum from 5-12 $\rm{\mu}$m. These wavelengths allow us to probe absorption due to the vibrational modes of various predicted cloud species. Our transmission spectrum shows additional opacity centered at 8.6 $\rm{\mu}$m, and detailed atmospheric modeling and retrievals identify this feature as SiO$_2$(s) (quartz) clouds. The SiO$_2$(s) clouds model is preferred at 3.5-4.2$\sigma$ versus a cloud-free model and at 2.6$\sigma$ versus a generic aerosol prescription. We find the SiO$_2$(s) clouds are comprised of small ${\sim}0.01$ $\rm{\mu}$m particles, which extend to high altitudes in the atmosphere. The atmosphere also shows a depletion of H$_2$O, a finding consistent with the formation of high-temperature aerosols from oxygen-rich species. This work is part of a series of studies by our JWST Telescope Scientist Team (JWST-TST), in which we will use Guaranteed Time Observations to perform Deep Reconnaissance of Exoplanet Atmospheres through Multi-instrument Spectroscopy (DREAMS).Comment: 19 pages, 7 figures, accepted for publication in ApJ

First Resolved Scattered-light Images of Four Debris Disks in Scorpius-Centaurus with the Gemini Planet Imager

We present the first spatially resolved scattered-light images of four debris disks around members of the Scorpius-Centaurus (Sco-Cen) OB association with high-contrast imaging and polarimetry using the Gemini Planet Imager (GPI). All four disks are resolved for the first time in polarized light, and one disk is also detected in total intensity. The three disks imaged around HD 111161, HD 143675, and HD 145560 are symmetric in both morphology and brightness distribution. The three systems span a range of inclinations and radial extents. The disk imaged around HD 98363 shows indications of asymmetries in morphology and brightness distribution, with some structural similarities to the HD 106906 planet–disk system. Uniquely, HD 98363 has a wide comoving stellar companion, Wray 15-788, with a recently resolved disk with very different morphological properties. HD 98363 A/B is the first binary debris disk system with two spatially resolved disks. All four targets have been observed with ALMA, and their continuum fluxes range from one nondetection to one of the brightest disks in the region. With the new results, a total of 15 A/F stars in Sco-Cen have resolved scattered-light debris disks, and approximately half of these systems exhibit some form of asymmetry. Combining the GPI disk structure results with information from the literature on millimeter fluxes and imaged planets reveals a diversity of disk properties in this young population. Overall, the four newly resolved disks contribute to the census of disk structures measured around A/F stars at this important stage in the development of planetary systems

Twenty-three unsolved problems in hydrology (UPH) – a community perspective

This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through on-line media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focussed on process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come

The Science Performance of JWST as Characterized in Commissioning

This paper characterizes the actual science performance of the James Webb Space Telescope (JWST), as determined from the six month commissioning period. We summarize the performance of the spacecraft, telescope, science instruments, and ground system, with an emphasis on differences from pre-launch expectations. Commissioning has made clear that JWST is fully capable of achieving the discoveries for which it was built. Moreover, almost across the board, the science performance of JWST is better than expected; in most cases, JWST will go deeper faster than expected. The telescope and instrument suite have demonstrated the sensitivity, stability, image quality, and spectral range that are necessary to transform our understanding of the cosmos through observations spanning from near-earth asteroids to the most distant galaxies.Comment: 5th version as accepted to PASP; 31 pages, 18 figures; https://iopscience.iop.org/article/10.1088/1538-3873/acb29