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

The Lyman-limit photon mean free path at the end of late reionization in the Sherwood–Relics simulations

Recent evidence supporting reionization ending at redshift z ≲ 6 includes the rapid redshift evolution of the mean free path, λmfp , for Lyman-limit photons through the intergalactic medium (IGM) at 5 < z < 6. Here, we investigate λmfp predicted by the Sherwood–Relics suite of hybrid radiation hydrodynamical simulations. Simulations with comoving volumes of 40 3 h −3 cMpc 3 (160 3 h −3 cMpc 3 ), calibrated to match the observed Ly α forest transmission with a late end to reionization at z < 6, are consistent with recent λmfp measurements at z < 5 . 9, and are 1 . 2 σ (1 . 8 σ) above the highest redshift λmfp measurement at z = 5 . 93. The majority of the Lyman-limit opacity at the end of reionization is attributable to highly ionized Ly α forest absorbers with neutral hydrogen column densities N HI ≤ 10 16 –10 17 cm −2 . Resolving these systems is critical for capturing the redshift evolution of λmfp during the final stages of reionization. After reionization completes, overdense gas will reduce λmfp by up to 20 per cent around haloes with masses M h ∼ 10 9 –10 11 h −1 M , but during reionization ionized bubbles will instead boost λmfp around haloes by up to an order of magnitude when the IGM is as much as 90 per cent neutral by volume. This effect will play an important role in the visibility of Ly α emitting galaxies at z ≳ 10 discovered with JWST

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

Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation.

Hematopoietic cell transplantation (HCT) uses cytotoxic chemotherapy and/or radiation followed by intravenous infusion of stem cells to cure malignancies, bone marrow failure and inborn errors of immunity, hemoglobin and metabolism. Lung injury is a known complication of the process, due in part to disruption in the pulmonary microenvironment by insults such as infection, alloreactive inflammation and cellular toxicity. How microorganisms, immunity and the respiratory epithelium interact to contribute to lung injury is uncertain, limiting the development of prevention and treatment strategies. Here we used 278 bronchoalveolar lavage (BAL) fluid samples to study the lung microenvironment in 229 pediatric patients who have undergone HCT treated at 32 childrens hospitals between 2014 and 2022. By leveraging paired microbiome and human gene expression data, we identified high-risk BAL compositions associated with in-hospital mortality (P = 0.007). Disadvantageous profiles included bacterial overgrowth with neutrophilic inflammation, microbiome contraction with epithelial fibroproliferation and profound commensal depletion with viral and staphylococcal enrichment, lymphocytic activation and cellular injury, and were replicated in an independent cohort from the Netherlands (P = 0.022). In addition, a broad array of previously occult pathogens was identified, as well as a strong link between antibiotic exposure, commensal bacterial depletion and enrichment of viruses and fungi. Together these lung-immune system-microorganism interactions clarify the important drivers of fatal lung injury in pediatric patients who have undergone HCT. Further investigation is needed to determine how personalized interpretation of heterogeneous pulmonary microenvironments may be used to improve pediatric HCT outcomes