Multiple Gaps in the Disk of the Class I Protostar GY 91

We present the highest spatial resolution ALMA observations to date of the Class I protostar GY 91 in the $\rho$ Ophiuchus L1688 molecular cloud complex. Our 870 $\mu$m and 3 mm dust continuum maps show that the GY 91 disk has a radius of $\sim$80 AU, and an inclination of $\sim$40$^{\circ}$, but most interestingly that the disk has three dark lanes located at 10 AU, 40 AU, and 70 AU. We model these features assuming they are gaps in the disk surface density profile and find that their widths are 7 AU, 30 AU, and 10 AU. These gaps bear a striking resemblance to the gaps seen in the HL Tau disk, suggesting that there may be Saturn-mass planets hiding in the disk. To constrain the relative ages of GY 91 and HL Tau, we also model the disk and envelope of HL Tau and find that they are of similar ages, although GY 91 may be younger. Although snow lines and magnetic dead zones can also produce dark lanes, if planets are indeed carving these gaps then Saturn-mass planets must form within the first $\sim$0.5 Myr of the lifetime of protoplanetary disks.Comment: 9 pages, 6 figures, 2 tables. Accepted for publication in Ap

WL 17: A Young Embedded Transition Disk

We present the highest spatial resolution ALMA observations to date of the Class I protostar WL 17 in the $\rho$ Ophiuchus L1688 molecular cloud complex, which show that it has a 12 AU hole in the center of its disk. We consider whether WL 17 is actually a Class II disk being extincted by foreground material, but find that such models do not provide a good fit to the broadband SED and also require such high extinction that it would presumably arise from dense material close to the source such as a remnant envelope. Self-consistent models of a disk embedded in a rotating collapsing envelope can nicely reproduce both the ALMA 3 mm observations and the broadband SED of WL 17. This suggests that WL 17 is a disk in the early stages of its formation, and yet even at this young age the inner disk has been depleted. Although there are multiple pathways for such a hole to be created in a disk, if this hole were produced by the formation of planets it could place constraints on the timescale for the growth of planetesimals in protoplanetary disks.Comment: 7 pages, 3 figures, 2 tables, accepted for publication in ApJ

Benefits of the Snakemake Workflow Management Software in Comparison to Traditional Programming (Paper)

Tools surrounding bioinformatics have increased data acquisition and accuracy significantly, especially with near-real time results using nanopore DNA sequencing. With large amounts of data, reproducibility is of high importance, and long workflows can become convoluted. Snakemake, built on the Common Workflow Language and Python, aims to alleviate this with readable formatting, reproducibility, and portability for any machine. Using 97 fastq files, the usability of these three traits were compared between a Bash and Snakemake workflow using a range of one to twelve threads. In every test, Snakemake was faster than Bash. At its fastest, Snakemake was 27% faster than Bash. Reproducibility of both workflows was verified using an MD5 hash of results. The hashes differed between the workflows; this may be a result of executing the workflows in two different terminal environments. Despite this, it is a valid method of validating reproducibility between tests within individual workflows. Outside speed tests, Snakemake offers quality of life features that allow it to pull ahead from Bash. Containerization of workflows using Conda is one example of this. The ability to require specific versions of software within a workflow boosts reproducibility. Additionally, portability is increased because the container can be deployed almost anywhere, and the required software can be downloaded on an as-needed basis. With readability comes maintainability. Snakemake will almost always pull ahead of Bash in this regard with its simple input, output, and shell fields. The field of Bioinformatics is moving very quickly, and it can be difficult for traditional Bash scripts to keep up in certain aspects. While Bash is paramount in the execution of some software, more powerful tools like Snakemake are required to handle the execution of an entire, complex workflow.https://openprairie.sdstate.edu/honors_isp/1007/thumbnail.jp

A VLA Survey For Faint Compact Radio Sources in the Orion Nebula Cluster

We present Karl G. Janksy Very Large Array (VLA) 1.3 cm, 3.6 cm, and 6 cm continuum maps of compact radio sources in the Orion Nebular Cluster. We mosaicked 34 square arcminutes at 1.3 cm, 70 square arcminutes at 3.6 cm and 109 square arcminutes at 6 cm, containing 778 near-infrared detected YSOs and 190 HST-identified proplyds (with significant overlap between those characterizations). We detected radio emission from 175 compact radio sources in the ONC, including 26 sources that were detected for the first time at these wavelengths. For each detected source we fit a simple free-free and dust emission model to characterize the radio emission. We extrapolate the free-free emission spectrum model for each source to ALMA bands to illustrate how these measurements could be used to correctly measure protoplanetary disk dust masses from sub-millimeter flux measurements. Finally, we compare the fluxes measured in this survey with previously measured fluxes for our targets, as well as four separate epochs of 1.3 cm data, to search for and quantify variability of our sources.Comment: 13 pages, 6 figures, 4 tables, ApJ, in pres

Is incident rheumatoid arthritis interstitial lung disease associated with methotrexate treatment? Results from a multivariate analysis in the ERAS and ERAN inception cohorts

© Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.Objectives To assess predictive factors for rheumatoid arthritis interstitial lung disease (RA-ILD) in two early RA inception cohorts with a focus on methotrexate (MTX) exposure. Design Multicenter prospective early RA inception cohort studies; the early RA study (ERAS) and the early RA network (ERAN) Setting Secondary care, ERAS 9 centers, ERAN 23 centers in England, Wales and the Republic of Ireland Participants Patients with new diagnosis of RA, n=2701.Standardised data including demographics, drug therapies and clinical outcomes including the presence of RA-ILD were collected at baseline, within 3- 6 months, at 12 months and annually thereafter. Primary and secondary outcome measures Primary outcome was the association of MTX exposure on RA-ILD diagnosis. Secondary outcomes were the association of demographic, comorbid and RA specific factors on RA-ILD diagnosis and the association of MTX exposure on time to RA-ILD diagnosis. Results Of 92 eligible ILD cases, 39 occurred in 1578 (2.5%) MTX exposed and 53 in 1114 (4.8%) non-MTX exposed cases. The primary analysis of RA-ILD cases only developing after any csDMARD treatment (n=67) showed MTX exposure not to be associated with incident RA-ILD (O.R. 0.85 CI 0.49, 1.49 p=0.578) and a non-significant trend for delayed ILD diagnosis (O.R. 0.54 CI 0.28, 1.06 p=0.072). In an extended analysis including RA-ILD cases present at RA diagnosis (n=92), MTX exposure was associated with a significantly reduced risk of incident RA-ILD (O.R. 0.48, CI 0.3, 0.79 p=0.004) and longer time to ILD diagnosis (O.R. 0.41, CI 0.23, 0.75 p=0.004). Other independent baseline associations with incident RA-ILD were higher age of RA onset, ever smoking, male gender, rheumatoid nodules and longer time from first RA symptom to first out-patient visit. Conclusions MTX treatment was not associated with an increased risk of RA-ILD diagnosis. On the contrary evidence suggested that MTX may delay the onset of ILD.Peer reviewe