An Advanced, Three-Dimensional Plotting Library for Astronomy

We present a new, three-dimensional (3D) plotting library with advanced features, and support for standard and enhanced display devices. The library - S2PLOT - is written in C and can be used by C, C++ and FORTRAN programs on GNU/Linux and Apple/OSX systems. S2PLOT draws objects in a 3D (x,y,z) Cartesian space and the user interactively controls how this space is rendered at run time. With a PGPLOT inspired interface, S2PLOT provides astronomers with elegant techniques for displaying and exploring 3D data sets directly from their program code, and the potential to use stereoscopic and dome display devices. The S2PLOT architecture supports dynamic geometry and can be used to plot time-evolving data sets, such as might be produced by simulation codes. In this paper, we introduce S2PLOT to the astronomical community, describe its potential applications, and present some example uses of the library.Comment: 12 pages, 10 eps figures (higher resolution versions available from http://astronomy.swin.edu.au/s2plot/paperfigures). The S2PLOT library is available for download from http://astronomy.swin.edu.au/s2plo

The Importance Of Multi-Reader Assessment For External Validation Of Prostate Lesion Classification Models Using Quantitative MpMRI

Machine learning for classifying prostate mpMRI lesions may help reduce unnecessary biopsies. However, external validation with multiple scanners and readers is required before the clinical adoption of such models can be considered. Two readers validated a previously published and well-performing logistic regression model on an external cohort. The model performance was not generalisable and offered no advantage to using PSAd cut-offs, and there was marked variation in model score related to contour differences from different readers. This potential variability should be investigated in future models which use quantitative MRI

Spectral Typing of Late Type Stellar Companions to Young Stars from Low Dispersion Near-Infrared Integral Field Unit Data

We used the Project 1640 near-infrared coronagraph and integral field spectrograph to observe 19 young solar type stars. Five of these stars are known binary stars and we detected the late-type secondaries and were able to measure their JH spectra with a resolution of R\sim30. The reduced, extracted, and calibrated spectra were compared to template spectra from the IRTF spectral library. With this comparison we test the accuracy and consistency of spectral type determination with the low-resolution near-infrared spectra from P1640. Additionally, we determine effective temperature and surface gravity of the companions by fitting synthetic spectra calculated with the PHOENIX model atmosphere code. We also present several new epochs of astrometry of each of the systems. Together these data increase our knowledge and understanding of the stellar make up of these systems. In addition to the astronomical results, the analysis presented helps validate the Project 1640 data reduction and spectral extraction processes and the utility of low-resolution, near-infrared spectra for characterizing late-type companions in multiple systems.Comment: Accepted to Astronomical Journal, 25 pages, 8 figure

A new tool for converting food frequency questionnaire data into nutrient and food group values: FETA research methods and availability.

OBJECTIVES: To describe the research methods for the development of a new open source, cross-platform tool which processes data from the European Prospective Investigation into Cancer and Nutrition Norfolk Food Frequency Questionnaire (EPIC-Norfolk FFQ). A further aim was to compare nutrient and food group values derived from the current tool (FETA, FFQ EPIC Tool for Analysis) with the previously validated but less accessible tool, CAFÉ (Compositional Analyses from Frequency Estimates). The effect of text matching on intake data was also investigated. DESIGN: Cross-sectional analysis of a prospective cohort study-EPIC-Norfolk. SETTING: East England population (city of Norwich and its surrounding small towns and rural areas). PARTICIPANTS: Complete FFQ data from 11 250 men and 13 602 women (mean age 59 years; range 40-79 years). OUTCOME MEASURES: Nutrient and food group intakes derived from FETA and CAFÉ analyses of EPIC-Norfolk FFQ data. RESULTS: Nutrient outputs from FETA and CAFÉ were similar; mean (SD) energy intake from FETA was 9222 kJ (2633) in men, 8113 kJ (2296) in women, compared with CAFÉ intakes of 9175 kJ (2630) in men, 8091 kJ (2298) in women. The majority of differences resulted in one or less quintile change (98.7%). Only mean daily fruit and vegetable food group intakes were higher in women than in men (278 vs 212 and 284 vs 255 g, respectively). Quintile changes were evident for all nutrients, with the exception of alcohol, when text matching was not executed; however, only the cereals food group was affected. CONCLUSIONS: FETA produces similar nutrient and food group values to the previously validated CAFÉ but has the advantages of being open source, cross-platform and complete with a data-entry form directly compatible with the software. The tool will facilitate research using the EPIC-Norfolk FFQ, and can be customised for different study populations.This study was supported by programme grants from the MRC Population Health Sciences Research Network (PHSRN), Cancer Research UK(C864/A8257) and the Medical Research Council (G0401527 and G1000143). NGF was supported by the Medical Research Council (MC_UP_A100_1003); APK is funded by a Wellcome Trust Clinical Research Fellowshi

Liberalizing trade in environmental goods and services

We examine the effects of trade liberalization in environmental goods in a model with one domestic downstream polluting firm and two upstream firms (one domestic, one foreign). The upstream firms offer their technologies to the downstream firm at a flat fee. The domestic government sets the emission tax rate after the outcome of R&D is known. The effect of liberalization on the domestic upstream firm's R&D incentive is ambiguous. Liberalization usually results in cleaner production, which allows the country to reach higher welfare. However this increase in welfare is typically achieved at the expense of the environment (a backfire effect)

Aperture Mask Interferometry with an Integral Field Spectrograph

A non-redundant pupil mask placed in front of a low-resolution integral field spectrograph (IFS) adds a spectral dimension to high angular resolution imaging behind adaptive optics systems. We demonstrate the first application of this technique, using the spectroscopic binary star system β CrB as our target. The mask and IFS combination enabled us to measure the first low-resolution spectrum of the F3-F5 dwarf secondary component of β CrB, at an angular separation 141 mas from its A5-A7Vp primary star. To record multi-wavelength closure phases, we collected interferograms simultaneously in 23 spectral channels spanning the J and H bands (1.1 μm-1.8 μm), using the Project 1640 IFS behind the 249-channel PalAO adaptive optics system on the Hale telescope at Palomar Observatory. In addition to providing physical information about the source, spectrally resolved mask fringes have the potential to enhance detection limits over single filter observations. While the overall dynamic range of our observation suffers from large systematic calibration errors, the information gleaned from the full channel range improves the dynamic range by a factor of 3 to 4 over the best single channel

Loss of Integrin-linked kinase sensitizes breast cancer to SRC inhibitors

SRC is a nonreceptor tyrosine kinase with key roles in breast cancer development and progression. Despite this, SRC tyrosine kinase inhibitors have so far failed to live up to their promise in clinical trials, with poor overall response rates. We aimed to identify possible synergistic gene–drug interactions to discover new rational combination therapies for SRC inhibitors. An unbiased genome-wide CRISPR-Cas9 knockout screen in a model of triple-negative breast cancer revealed that loss of integrin-linked kinase (ILK) and its binding partners α-Parvin and PINCH-1 sensitizes cells to bosutinib, a clinically approved SRC/ABL kinase inhibitor. Sensitivity to bosutinib did not correlate with ABL dependency; instead, bosutinib likely induces these effects by acting as a SRC tyrosine kinase inhibitor. Furthermore, in vitro and in vivo models showed that loss of ILK enhanced sensitivity to eCF506, a novel and highly selective inhibitor of SRC with a unique mode of action. Whole-genome RNA sequencing following bosutinib treatment in ILK knockout cells identified broad changes in the expression of genes regulating cell adhesion and cell–extracellular matrix. Increased sensitivity to SRC inhibition in ILK knockout cells was associated with defective adhesion, resulting in reduced cell number as well as increased G(1) arrest and apoptosis. These findings support the potential of ILK loss as an exploitable therapeutic vulnerability in breast cancer, enhancing the effectiveness of clinical SRC inhibitors. SIGNIFICANCE: A CRISPR-Cas9 screen reveals that loss of integrin-linked kinase synergizes with SRC inhibition, providing a new opportunity for enhancing the clinical effectiveness of SRC inhibitors in breast cancer