The Long Wavelength Array Software Library

The Long Wavelength Array Software Library (LSL) is a Python module that provides a collection of utilities to analyze and export data collected at the first station of the Long Wavelength Array, LWA1. Due to the nature of the data format and large-N ($\gtrsim$100 inputs) challenges faced by the LWA, currently available software packages are not suited to process the data. Using tools provided by LSL, observers can read in the raw LWA1 data, synthesize a filter bank, and apply incoherent de-dispersion to the data. The extensible nature of LSL also makes it an ideal tool for building data analysis pipelines and applying the methods to other low frequency arrays.Comment: accepted to the Journal of Astronomical Instrumentation; 24 pages, 4 figure

THE BEAMING STRUCTURES OF JUPITER’S DECAMETRIC COMMON S-BURSTS OBSERVED FROM THE LWA1, NDA, AND URAN2 RADIO TELESCOPES

On 2015 February 21, simultaneous observations of Jupiter's decametric radio emission between 10 and 33 MHz were carried out using three powerful low-frequency radio telescopes: the Long Wavelength Array Station One in the USA, the Nançay Decameter Array in France, and the URAN2 telescope in Ukraine. We measured the lag times of short-bursts (S-bursts) for 105 minutes of data over effective baselines of up to 8460 km by using cross-correlation analysis of the spectrograms from each instrument. Of particular interest is the measurement of the beaming thickness of S-bursts, testing if either flashlight- or beacon-like beaming is emanating from Jupiter. We find that the lag times for all pairs drift slightly as time elapses, in agreement with expectations from the flashlight-like beaming model. This leads to a new constraint of the minimum beaming thickness of 2farcs66. Also, we find that most of the analyzed data abound with S-bursts, whose occurrence probability peaks at 17–18 MHz

PAM50 Breast Cancer Subtyping by RT-qPCR and Concordance with Standard Clinical Molecular Markers

Abstract Background Many methodologies have been used in research to identify the “intrinsic” subtypes of breast cancer commonly known as Luminal A, Luminal B, HER2-Enriched (HER2-E) and Basal-like. The PAM50 gene set is often used for gene expression-based subtyping; however, surrogate subtyping using panels of immunohistochemical (IHC) markers are still widely used clinically. Discrepancies between these methods may lead to different treatment decisions. Methods We used the PAM50 RT-qPCR assay to expression profile 814 tumors from the GEICAM/9906 phase III clinical trial that enrolled women with locally advanced primary invasive breast cancer. All samples were scored at a single site by IHC for estrogen receptor (ER), progesterone receptor (PR), and Her2/neu (HER2) protein expression. Equivocal HER2 cases were confirmed by chromogenic in situ hybridization (CISH). Single gene scores by IHC/CISH were compared with RT-qPCR continuous gene expression values and “intrinsic” subtype assignment by the PAM50. High, medium, and low expression for ESR1, PGR, ERBB2, and proliferation were selected using quartile cut-points from the continuous RT-qPCR data across the PAM50 subtype assignments. Results ESR1, PGR, and ERBB2 gene expression had high agreement with established binary IHC cut-points (area under the curve (AUC) ≥ 0.9). Estrogen receptor positivity by IHC was strongly associated with Luminal (A and B) subtypes (92%), but only 75% of ER negative tumors were classified into the HER2-E and Basal-like subtypes. Luminal A tumors more frequently expressed PR than Luminal B (94% vs 74%) and Luminal A tumors were less likely to have high proliferation (11% vs 77%). Seventy-seven percent (30/39) of ER-/HER2+ tumors by IHC were classified as the HER2-E subtype. Triple negative tumors were mainly comprised of Basal-like (57%) and HER2-E (30%) subtypes. Single gene scoring for ESR1, PGR, and ERBB2 was more prognostic than the corresponding IHC markers as shown in a multivariate analysis. Conclusions The standard immunohistochemical panel for breast cancer (ER, PR, and HER2) does not adequately identify the PAM50 gene expression subtypes. Although there is high agreement between biomarker scoring by protein immunohistochemistry and gene expression, the gene expression determinations for ESR1 and ERBB2 status was more prognostic

Erratum: “The Beaming Structures of Jupiter's Decametric Common S-bursts Observed from the LWA1, NDA, and URAN2 Radio Telescopes” (<A href="http://iopscience.iop.org/article/10.3847/0004-637X/826/2/176">2016, ApJ, 826, 176</A>)

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Assessing Treatment Integrity in Alcohol Behavioral Couple Therapy

OBJECTIVES: Alcohol Behavioral Couple Therapy (ABCT) is an efficacious treatment for alcohol use disorders. Coding treatment integrity can shed light on the active ingredients of ABCT, but there are no published studies of treatment integrity instruments for ABCT. The present study describes the development and initial reliability of the Treatment Integrity Rating System – Couples Version (C-TIRS) for ABCT. METHODS: The C-TIRS was used to rate 284 first- and mid-treatment ABCT sessions of 188 couples in four randomized clinical trials. RESULTS: Average inter-rater reliability for distinguishing ratings between C-TIRS items was fair-to-good for quantity items (intraclass correlation [ICC] = 0.64) and poor-to-fair for quality items (ICC = 0.41). Five C-TIRS subscales were defined a priori to measure treatment components involving cognitive-behavioral therapy, spouse involvement, couple therapy, common therapeutic factors, and overall adherence to the treatment protocol and had adequate internal reliability (α = 0.74–0.89). Inter-rater reliability was fair to good on seven of ten scales but poor on three scales (ICC range = 0.17–0.72). CONCLUSIONS: The C-TIRS was designed to provide information about quantity and quality of the delivery of ABCT components; however, further refinement of the C-TIRS is warranted before it should be used in frontline practice. Clinical implications and recommendations for future research are discussed