X-ray enabled MOCASSIN: a 3D code for photoionized media

We present a new version of the fully 3D photoionization and dust radiative transfer code, MOCASSIN, that uses a Monte Carlo approach for the transfer of radiation. The X-ray enabled MOCASSIN allows a fully geometry independent description of low-density gaseous environments strongly photoionized by a radiation field extending from radio to gamma rays. The code has been thoroughly benchmarked against other established codes routinely used in the literature, using simple plane parallel models designed to test performance under standard conditions. We show the results of our benchmarking exercise and discuss applicability and limitations of the new code, which should be of guidance for future astrophysical studies with MOCASSIN.Comment: Accepted for publication in ApJS 9 pages, 5 figure

The lipid droplet protein DHRS3 is a regulator of melanoma cell state

Lipid droplets are fat storage organelles composed of a protein envelope and lipid rich core. Regulation of this protein envelope underlies differential lipid droplet formation and function. In melanoma, lipid droplet formation has been linked to tumor progression and metastasis, but it is unknown whether lipid droplet proteins play a role. To address this, we performed proteomic analysis of the lipid droplet envelope in melanoma. We found that lipid droplet proteins were differentially enriched in distinct melanoma states; from melanocytic to undifferentiated. DHRS3, which converts all-trans-retinal to all-trans-retinol, is upregulated in the MITFLO/undifferentiated/neural crest-like melanoma cell state and reduced in the MITFHI/melanocytic state. Increased DHRS3 expression is sufficient to drive MITFHI/melanocytic cells to a more undifferentiated/invasive state. These changes are due to retinoic acid mediated regulation of melanocytic genes. Our data demonstrate that melanoma cell state can be regulated by expression of lipid droplet proteins which affect downstream retinoid signaling

Natural language processing to automatically extract the presence and severity of esophagitis in notes of patients undergoing radiotherapy

Radiotherapy (RT) toxicities can impair survival and quality-of-life, yet remain under-studied. Real-world evidence holds potential to improve our understanding of toxicities, but toxicity information is often only in clinical notes. We developed natural language processing (NLP) models to identify the presence and severity of esophagitis from notes of patients treated with thoracic RT. We fine-tuned statistical and pre-trained BERT-based models for three esophagitis classification tasks: Task 1) presence of esophagitis, Task 2) severe esophagitis or not, and Task 3) no esophagitis vs. grade 1 vs. grade 2-3. Transferability was tested on 345 notes from patients with esophageal cancer undergoing RT. Fine-tuning PubmedBERT yielded the best performance. The best macro-F1 was 0.92, 0.82, and 0.74 for Task 1, 2, and 3, respectively. Selecting the most informative note sections during fine-tuning improved macro-F1 by over 2% for all tasks. Silver-labeled data improved the macro-F1 by over 3% across all tasks. For the esophageal cancer notes, the best macro-F1 was 0.73, 0.74, and 0.65 for Task 1, 2, and 3, respectively, without additional fine-tuning. To our knowledge, this is the first effort to automatically extract esophagitis toxicity severity according to CTCAE guidelines from clinic notes. The promising performance provides proof-of-concept for NLP-based automated detailed toxicity monitoring in expanded domains.Comment: 17 pages, 6 tables, 1figure, submiting to JCO-CCI for revie

The Coronae of AR Lac

We observed the coronally active eclipsing binary, AR Lac, with the High Energy Transmission Grating on Chandra for a total of 97 ks, spaced over five orbits, at quadratures and conjunctions. Contemporaneous and simultaneous EUV spectra and photometry were also obtained with the Extreme Ultraviolet Explorer. Significant variability in both X-ray and EUV fluxes were observed, dominated by at least one X-ray flare and one EUV flare. We saw no evidence of primary or secondary eclipses. X-ray flux modulation was largest at high temperature, indicative of flare heating of coronal plasma. Line widths interpreted in terms of Doppler broadening suggest that both binary stellar components are active. From line fluxes obtained from total integrated spectra, we have modeled the emission measure and abundance distributions. A strong maximum was found in the differential emission measure, characterized by peaks at log T = 6.9 and 7.4, together with a weak but significant cooler maximum near log T=6.2, and a moderately strong hot tail from log T= 7.6-8.2. Coronal abundances have a broad distribution and show no simple correlation with first ionization potential. While the resulting model spectrum generally agrees very well with the observed spectrum, there are some significant discrepancies, especially among the many Fe L-lines. Both the emission measure and abundance distributions are qualitatively similar to prior determinations from other X-ray and ultraviolet spectra, indicating some long-term stability in the overall coronal structure.Comment: 31 pages, 8 figures, 3 tables; Accepted for publication in the Astrophysical Journal (tentatively October 1, 2003

Unrelated Helpers in a Primitively Eusocial Wasp: Is Helping Tailored Towards Direct Fitness?

The paper wasp Polistes dominulus is unique among the social insects in that nearly one-third of co-foundresses are completely unrelated to the dominant individual whose offspring they help to rear and yet reproductive skew is high. These unrelated subordinates stand to gain direct fitness through nest inheritance, raising the question of whether their behaviour is adaptively tailored towards maximizing inheritance prospects. Unusually, in this species, a wealth of theory and empirical data allows us to predict how unrelated subordinates should behave. Based on these predictions, here we compare helping in subordinates that are unrelated or related to the dominant wasp across an extensive range of field-based behavioural contexts. We find no differences in foraging effort, defense behaviour, aggression or inheritance rank between unrelated helpers and their related counterparts. Our study provides no evidence, across a number of behavioural scenarios, that the behaviour of unrelated subordinates is adaptively modified to promote direct fitness interests

Models and Studies of Aging: Executive Summary of a Report from the U13 Conference Series

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148241/1/jgs15788.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148241/2/jgs15780-sup-0001-supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148241/3/jgs15788_am.pd

The past and future roles of competition and habitat in the range-wide occupancy dynamics of Northern Spotted Owls

Slow ecological processes challenge conservation. Short-term variability can obscure the importance of slower processes that may ultimately determine the state of a system. Furthermore, management actions with slow responses can be hard to justify. One response to slow processes is to explicitly concentrate analysis on state dynamics. Here, we focus on identifying drivers of Northern Spotted Owl (Strix occidentalis caurina) territorial occupancy dynamics across 11 study areas spanning their geographic range and forecasting response to potential management actions. Competition with Barred Owls (Strix varia) has increased Spotted Owl territory extinction probabilities across all study areas and driven recent declines in Spotted Owl populations. Without management intervention, the Northern Spotted Owl subspecies will be extirpated from parts of its current range within decades. In the short term, Barred Owl removal can be effective. Over longer time spans, however, maintaining or improving habitat conditions can help promote the persistence of northern spotted owl populations. In most study areas, habitat effects on expected Northern Spotted Owl territorial occupancy are actually greater than the effects of competition from Barred Owls. This study suggests how intensive management actions (removal of a competitor) with rapid results can complement a slower management action (i.e., promoting forest succession)

Description and Demonstration of the Coupled Community Earth System Model v2-Community Ice Sheet Model v2 (CESM2-CISM2)

Earth system/ice-sheet coupling is an area of recent, major Earth System Model (ESM) development. This work occurs at the intersection of glaciology and climate science and is motivated by a need for robust projections of sea-level rise. The Community Ice Sheet Model version 2 (CISM2) is the newest component model of the Community Earth System Model version 2 (CESM2). This study describes the coupling and novel capabilities of the model, including: (1) an advanced energy-balance-based surface mass balance calculation in the land component with downscaling via elevation classes; (2) a closed freshwater budget from ice sheet to the ocean from surface runoff, basal melting, and ice discharge; (3) dynamic land surface types; and (4) dynamic atmospheric topography. The Earth system/ice-sheet coupling is demonstrated in a simulation with an evolving Greenland Ice Sheet (GrIS) under an idealized high CO2 scenario. The model simulates a large expansion of ablation areas (where surface ablation exceeds snow accumulation) and a large increase in surface runoff. This results in an elevated freshwater flux to the ocean, as well as thinning of the ice sheet and area retreat. These GrIS changes result in reduced Greenland surface albedo, changes in the sign and magnitude of sensible and latent heat fluxes, and modified surface roughness and overall ice sheet topography. Representation of these couplings between climate and ice sheets is key for the simulation of ice and climate interactions. </div