Optical and ultraviolet spectroscopic analysis of SN 2011fe at late times

We present optical spectra of the nearby Type Ia supernova SN 2011fe at 100, 205, 311, 349, and 578 days post-maximum light, as well as an ultraviolet spectrum obtained with Hubble Space Telescope at 360 days post-maximum light. We compare these observations with synthetic spectra produced with the radiative transfer code PHOENIX. The day +100 spectrum can be well fit with models which neglect collisional and radiative data for forbidden lines. Curiously, including this data and recomputing the fit yields a quite similar spectrum, but with different combinations of lines forming some of the stronger features. At day +205 and later epochs, forbidden lines dominate much of the optical spectrum formation; however, our results indicate that recombination, not collisional excitation, is the most influential physical process driving spectrum formation at these late times. Consequently, our synthetic optical and UV spectra at all epochs presented here are formed almost exclusively through recombination-driven fluorescence. Furthermore, our models suggest that the ultraviolet spectrum even as late as day +360 is optically thick and consists of permitted lines from several iron-peak species. These results indicate that the transition to the "nebular" phase in Type Ia supernovae is complex and highly wavelength-dependent.Comment: 22 pages, 21 figuress, 1 table, submitted to MNRA

Developing a Machine Learning-Based Clinical Decision Support Tool for Uterine Tumor Imaging

Uterine leiomyosarcoma (LMS) is a rare but aggressive malignancy. On imaging, it is difficult to differentiate LMS from, for example, degenerated leiomyoma (LM), a prevalent but benign condition. We curated a data set of 115 axial T2-weighted MRI images from 110 patients (mean [range] age=45 [17-81] years) with UTs that included five different tumor types. These data were randomly split stratifying on tumor volume into training (n=85) and test sets (n=30). An independent second reader (reader 2) provided manual segmentations for all test set images. To automate segmentation, we applied nnU-Net and explored the effect of training set size on performance by randomly generating subsets with 25, 45, 65 and 85 training set images. We evaluated the ability of radiomic features to distinguish between types of UT individually and when combined through feature selection and machine learning. Using the entire training set the mean [95% CI] fibroid DSC was measured as 0.87 [0.59-1.00] and the agreement between the two readers was 0.89 [0.77-1.0] on the test set. When classifying degenerated LM from LMS we achieve a test set F1-score of 0.80. Classifying UTs based on radiomic features we identify classifiers achieving F1-scores of 0.53 [0.45, 0.61] and 0.80 [0.80, 0.80] on the test set for the benign versus malignant, and degenerated LM versus LMS tasks. We show that it is possible to develop an automated method for 3D segmentation of the uterus and UT that is close to human-level performance with fewer than 150 annotated images. For distinguishing UT types, while we train models that merit further investigation with additional data, reliable automatic differentiation of UTs remains a challenge

Age-related human small intestine methylation: evidence for stem cell niches

BACKGROUND: The small intestine is constructed of many crypts and villi, and mouse studies suggest that each crypt contains multiple stem cells. Very little is known about human small intestines because mouse fate mapping strategies are impractical in humans. However, it is theoretically possible that stem cell histories are inherently written within their genomes. Genomes appear to record histories (as exemplified by use of molecular clocks), and therefore it may be possible to reconstruct somatic cell dynamics from somatic cell errors. Recent human colon studies suggest that random somatic epigenetic errors record stem cell histories (ancestry and total numbers of divisions). Potentially age-related methylation also occurs in human small intestines, which would allow characterization of their stem cells and comparisons with the colon. METHODS: Methylation patterns in individual crypts from 13 small intestines (17 to 78 years old) were measured by bisulfite sequencing. The methylation patterns were analyzed by a quantitative model to distinguish between immortal or niche stem cell lineages. RESULTS: Age-related methylation was observed in the human small intestines. Crypt methylation patterns were more consistent with stem cell niches than immortal stem cell lineages. Human large and small intestine crypt niches appeared to have similar stem cell dynamics, but relatively less methylation accumulated with age in the small intestines. There were no apparent stem cell differences between the duodenum and ileum, and stem cell survival did not appear to decline with aging. CONCLUSION: Crypt niches containing multiple stem cells appear to maintain human small intestines. Crypt niches appear similar in the colon and small intestine, and the small intestinal stem cell mitotic rate is the same as or perhaps slower than that of the colon. Although further studies are needed, age-related methylation appears to record somatic cell histories, and a somatic epigenetic molecular clock strategy may potentially be applied to other human tissues to reconstruct otherwise occult stem cell histories

A transient search using combined human and machine classifications

Large modern surveys require efficient review of data in order to find transient sources such as supernovae, and to distinguish such sources from artefacts and noise. Much effort has been put into the development of automatic algorithms, but surveys still rely on human review of targets. This paper presents an integrated system for the identification of supernovae in data from Pan-STARRS1, combining classifications from volunteers participating in a citizen science project with those from a convolutional neural network. The unique aspect of this work is the deployment, in combination, of both human and machine classifications for near real-time discovery in an astronomical project. We show that the combination of the two methods outperforms either one used individually. This result has important implications for the future development of transient searches, especially in the era of Large Synoptic Survey Telescope and other large-throughput surveys

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The estimated number of potential PrEP users among gay-identifying men who have sex with men in Australia

We estimated the size of the population of gay-identified men who have sex with men (gay men) eligible for PrEP in Australia under the current national PrEP guidelines. Using input indicators from the Australian Bureau of Statistics, the national representative survey Second Australian Study of Health and Relationships, and national HIV- behavioural surveillance, we calculated the size of the population of sexually active gay men and estimated a range for the number eligible for PrEP using different scenarios based on the guidelines. In 2015, an estimated 108,850 sexually-active 16-69-year-old gay men were classified as at risk of acquiring HIV in Australia. Of these men, 10,558 to 30,913 (9.7%-28.4%) were classified as being at high risk and therefore eligible for PrEP, most commonly due to recent receptive condomless intercourse with casual partners (6.1% to 15.5%), STI infections (5.4% to 10.6%) or the use of crystal methamphetamine (1.4% to 9.4%). The higher estimates included men who may have been at HIV risk for shorter time periods or with fewer partners. Australian PrEP guidelines recommend targeting PrEP to people at high HIV risk. Our estimation of potential PrEP users informed PrEP implementation in Australia. The choice of PrEP eligibility criteria, and interpretation of the guidelines, strongly affects the population estimates. In the future, higher numbers of gay men may become eligible for PrEP, because the estimates are largely defined by and follow trends in condomless anal intercourse. Our estimation methods can be adapted to other settings