Second Nature: Hamilton College and the Natural Environment

The following histories explore the boundaries between the human and natural environment on Hamilton College’s campus. They were written for the Environmental Studies course “Interpreting the American Environment” and incorporated site visits and consultations of the historical record in order to better understand familiar places on Hamilton’s campus. Through this research, the contributors identified the human imprint on natural places and located nature in the built environment.https://digitalcommons.hamilton.edu/books/1012/thumbnail.jp

New quasar proximity zone size measurements at z∼6z\sim 6 using the enlarged XQR-30 sample

Proximity zones of high-redshift quasars are unique probes of their central supermassive black holes as well as the intergalactic medium in the last stages of reionization. We present 22 new measurements of proximity zones of quasars with redshifts between 5.8 and 6.6, using the enlarged XQR-30 sample of high-resolution, high-SNR quasar spectra. The quasars in our sample have UV magnitudes of $M_{1450}\sim -27$ and black hole masses of $10^9$\unicode{x2013}$10^{10}$ M$_\odot$. Our inferred proximity zone sizes are 2\unicode{x2013}7 physical Mpc, with a typical uncertainty of less than 0.5 physical Mpc, which, for the first time, also includes uncertainty in the quasar continuum. We find that the correlation between proximity zone sizes and the quasar redshift, luminosity, or black hole mass, indicates a large diversity of quasar lifetimes. Two of our proximity zone sizes are exceptionally small. The spectrum of one of these quasars, with $z=6.02$, displays, unusually for this redshift, damping wing absorption without any detectable metal lines, which could potentially originate from the IGM. The other quasar has a high-ionization absorber $\sim$0.5 pMpc from the edge of the proximity zone. This work increases the number of proximity zone measurements available in the last stages of cosmic reionization to 87. This data will lead to better constraints on quasar lifetimes and obscuration fractions at high redshift, which in turn will help probe the seed mass and formation redshift of supermassive black holes.Comment: 16 pages, 9 figures, Accepted in MNRA

BioModels—15 years of sharing computational models in life science

Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform allows submission of models encoded in diverse modelling formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication. The curation also involves encoding models in standard formats and annotation with controlled vocabularies following MIRIAM (minimal information required in the annotation of biochemical models) guidelines. BioModels now accepts large-scale submission of auto-generated computational models. With gradual growth in content over 15 years, BioModels currently hosts about 2000 models from the published literature. With about 800 curated models, BioModels has become the world’s largest repository of curated models and emerged as the third most used data resource after PubMed and Google Scholar among the scientists who use modelling in their research. Thus, BioModels benefits modellers by providing access to reliable and semantically enriched curated models in standard formats that are easy to share, reproduce and reuse

Evidence of patchy hydrogen reionization from an extreme Lyα trough below redshift six

We report the discovery of an extremely long (∼110 Mpc/h) and dark (τeff≳7) Lyα trough extending down to z≃5.5 towards the zem≃6.0 quasar ULAS J0148+0600. We use these new data in combination with Lyα forest measurements from 42 quasars at 4.5≤zem≤6.4 to conduct an updated analysis of the line-of-sight variance in the intergalactic Lyα opacity over 4≤z≤6. We find that the scatter in transmission among lines of sight near z∼6 significantly exceeds theoretical expectations for either a uniform ultraviolet background (UVB) or simple fluctuating UVB models in which the mean free path to ionizing photons is spatially invariant. The data, particularly near z≃5.6-5.8, instead require fluctuations in the volume-weighted hydrogen neutral fraction that are a factor of 3 or more beyond those expected from density variations alone. We argue that these fluctuations are most likely driven by large-scale variations in the mean free path, consistent with expectations for the final stages of inhomogeneous hydrogen reionization. Even by z≃5.6, however, a large fraction of the data are consistent with a uniform UVB, and by z∼5 the data are fully consistent with opacity fluctuations arising solely from the density field. This suggests that while reionization may be ongoing at z∼6, it has fully completed by z∼5

Genome-Wide Association Study of Coronary Heart Disease and Its Risk Factors in 8,090 African Americans: The NHLBI CARe Project

Coronary heart disease (CHD) is the leading cause of mortality in African Americans. To identify common genetic polymorphisms associated with CHD and its risk factors (LDL- and HDL-cholesterol (LDL-C and HDL-C), hypertension, smoking, and type-2 diabetes) in individuals of African ancestry, we performed a genome-wide association study (GWAS) in 8,090 African Americans from five population-based cohorts. We replicated 17 loci previously associated with CHD or its risk factors in Caucasians. For five of these regions (CHD: CDKN2A/CDKN2B; HDL-C: FADS1-3, PLTP, LPL, and ABCA1), we could leverage the distinct linkage disequilibrium (LD) patterns in African Americans to identify DNA polymorphisms more strongly associated with the phenotypes than the previously reported index SNPs found in Caucasian populations. We also developed a new approach for association testing in admixed populations that uses allelic and local ancestry variation. Using this method, we discovered several loci that would have been missed using the basic allelic and global ancestry information only. Our conclusions suggest that no major loci uniquely explain the high prevalence of CHD in African Americans. Our project has developed resources and methods that address both admixture- and SNP-association to maximize power for genetic discovery in even larger African-American consortia

The Role of Galaxies and AGN in Reionising the IGM - I: Keck Spectroscopy of 5 < z < 7 Galaxies in the QSO Field J1148+5251

We introduce a new method for determining the influence of galaxies and active galactic nuclei (AGN) on the physical state of the intergalactic medium (IGM) at high redshift and illustrate its potential via a first application to the field of the $z=6.42$ QSO J1148+5251. By correlating the spatial positions of spectroscopically-confirmed Lyman break galaxies (LBGs) with fluctuations in the Lyman alpha forest seen in the high signal-to-noise spectrum of a background QSO, we provide a statistical measure of the typical escape fraction of Lyman continuum photons close to the end of cosmic reionisation. Here we use Keck DEIMOS spectroscopy to locate 7 colour-selected LBGs in the redshift range $5.3\lesssim z\lesssim 6.4$ and confirm a faint $z=5.701$ AGN. We then examine the spatial correlation between this sample and Ly$\alpha$/Ly$\beta$ transmission fluctuations in a Keck ESI spectrum of the QSO. Interpreting the statistical HI proximity effect as arising from faint galaxies clustered around the detected LBGs, we translate the observed mean Ly$\alpha$ transmitted flux around an average detected LBG into a constraint on the mean escape fraction $\langle f_{\rm esc}\rangle\geq0.08$ at $z\simeq6$. We also report evidence of the individual transverse HI proximity effect of a $z=6.177$ luminous LBG via a Ly$\beta$ transmission spike and two broad Ly$\alpha$ transmission spikes around the $z=5.701$ AGN. We discuss the possible origin of such associations which suggest that while faint galaxies are primarily driving reionisation, luminous galaxies and AGN may provide important contributions to the UV background or thermal fluctuations of the IGM at $z\simeq6$. Although a limited sample, our results demonstrate the potential of making progress using this method in resolving one of the most challenging aspects of the contribution of galaxies and AGN to cosmic reionisation.Comment: 21 pages, 16 figures, the version accepted in MNRA