KIDSpec: An MKID-Based Medium-Resolution, Integral Field Spectrograph

KIDSpec, the Kinetic Inductance Detector Spectrograph, is a concept for a highly sensitive, medium-spectral-resolution optical through near-IR spectrograph. It uses the intrinsic-energy-resolving capability of an array of optical/IR-sensitive MKIDs to distinguish multiple orders from a low-resolution grating. By acting as an ‘order resolver,’ the MKID array replaces the cross-disperser in an echelle spectrograph. This greatly simplifies the optical layout of the spectrograph and enables longer slits than are possible with cross-dispersed instruments (to improve sky subtraction). KIDSpec would have similar capabilities to ESO’s highly successful X-shooter instrument. It would provide an R = 4000–10,000 spectrum covering the optical and near-IR spectral range (0.4–1.5 µm). As well as a ‘long-slit’ mode, the IFU would provide a small ( ∼50 spaxel ) field of view for spatially resolved sources. In addition, the photon-counting operation of MKIDs and their photon-energy-resolving ability enable a read-noise-free spectrum with perfect cosmic ray removal. The spectral resolution would be sufficient to remove the bright night-sky lines without the additional pixel noise, making the instrument more sensitive than an equivalent semiconductor-based instrument. KIDSpec would enhance many existing high-profile science cases, including transient (GRB, SNe, etc.) follow-up, redshift determination of faint objects and transit spectroscopy of exoplanets. In addition, it will enable unique science cases, such as dynamical mass estimates of the compact objects in ultra-compact binaries

Application of the TruCulture® whole blood stimulation system for immune response profiling in cattle

peer-reviewedCapturing the phenotypic variation in immune responses holds enormous promise for the development of targeted treatments for disease as well as tailored vaccination schedules. However, accurate detection of true biological variation can be obscured by the lack of standardised immune assays. The TruCulture® whole blood stimulation system has now been extensively used to detect basal and induced immune responses to a range of pathogen-associated molecular patterns (PAMPs) in human peripheral blood. This study demonstrates the optimisation of this commercially available assay for systemic immune phenotyping in cattle. The early immune response in Holstein-Friesian bull calves (n = 10) was assessed by haematology, flow cytometry and cytokine expression profiling after 24 h ex-vivo PAMP (LPS, poly (I:C) and zymosan) stimulation in TruCulture® tubes. A comparative analysis was also performed with a traditional whole blood stimulation assay and cell viability using both systems was also evaluated. Results: Supernatant collected from TruCulture® tubes showed a significant increase in IL-1β and IL-8 expression compared to null stimulated tubes in response to both LPS and zymosan. In contrast, a detectable immune response was not apparent at the standard concentration of poly (I:C). Conventional whole blood cultures yielded similar response profiles, although the magnitude of the response was higher to both LPS and zymosan, which may be attributed to prokaryotic strain-specificity or batch of the stimulant used. Despite being a closed system, HIF1A expression – used as a measure of hypoxia was not increased, suggesting the TruCulture® assay did not negatively affect cell viability. This represents the first reported use of this novel standardised assay in cattle, and indicates that the concentration of poly (I:C) immunogenic in humans is insufficient to induce cytokine responses in cattle. We conclude that the low blood volume and minimally invasive TruCulture® assay system offers a practical and informative technique to assess basal and induced systemic immune responses in cattle.Teagasc Walsh Fellowship to MO

Design of the VLT-CUBES image slicers: Field re-formatters to provide two spectral resolutions

CUBES is a high efficiency spectrograph designed for a Cassegrain focus of the Very Large Telescope and is expected to be in operation in 2028. It is designed to observe point or compact sources in a spectral range from 300 to 405nm. CUBES will provide two spectral resolving powers: R≥20,000 for high resolution (HR) and R≥5,000 for low resolution (LR). This is achieved by using an image slicer for each resolution mode. The image slicers re-format a rectangular on-sky field of view of either 1.5arcsec by 10arcsec (HR) or 6arcsec by 10arcsec (LR) into six side-by-side slitlets which form the spectrograph slit. The slit dimensions are 0.19mm × 88mm for HR and 0.77mm × 88mm for LR. The on-sky and physical widths of the slicer mirrors are 0.25arcsec/0.5mm (HR) and 1arcsec/2mm (LR). The image slicers reduce the spectrograph entrance slit etendue and hence the size of the spectrograph optics without associated slit losses. Each of the proposed image slicers consists of two arrays of six spherical mirrors (slicer mirror and camera mirror arrays) which provide a straight entrance slit to the spectrograph with almost diffraction-limited optical quality. This paper presents the description of the image slicers at the end of the Phase A conceptual design, including their optical design and expected performance

CUBES: application of image slicers to reformat the field for two spectral resolving powers

The Cassegrain U-Band Efficient Spectrograph (CUBES) is a high-efficiency spectrograph designed for observations from 305 to 400nm. It will be integrated at a Cassegrain focus of the Very Large Telescope (VLT). The image slicer technology is applied to reformat the field of view reducing the spectrograph entrance slit etendue and minimising the spectrograph volume and weight without slit losses. Two image slicers will provide CUBES with two spectral resolving powers: R≥20,000 for high resolution (HR) and R≥5,000 for low resolution (LR). Both image slicers are composed of two arrays of six spherical mirrors. For the HR mode, a rectangular field of view of 1.5arcsec by 10arcsec is reorganised into a slit of 0.19mm × 88mm; for the LR mode, a field of view of 6arcsec by 10arcsec is reformatted into a slit of 0.77mm × 88mm, with slicer mirrors of width 0.5mm and 2mm, respectively. CUBES is currently in the Preliminary Design Phase (Phase B). This communication presents the Conceptual (Phase A) design and the main performance for the HR and LR image slicers addressing the following technological challenges: compact layout with the minimum number of optical components to optimise throughput, near diffraction limited optical quality, telecentric design with overlapped exit pupils for all slices of the field of view, distribution of the slicer mirrors to reduce shadows and selection of the best substrate for the very short wavelengths at which CUBES will operate

A jet model for the fast IR variability of the black hole X-ray binary GX 339-4

Using the simultaneous Infra-Red (IR) and X-ray light curves obtained by Kalamkar et al., we perform a Fourier analysis of the IR/X-ray timing correlations of the black hole X-ray binary (BHB) GX 339-4. The resulting IR vs X-ray Fourier coherence and lag spectra are similar to those obtained in previous studies of GX 339-4 using optical light curves. In particular, above 1 Hz, the lag spectrum features an approximately constant IR lag of about 100 ms. We model simultaneously the radio to IR Spectral Energy Distribution (SED), the IR Power Spectral Density (PSD), and the coherence and lag spectra using the jet internal shock model ISHEM assuming that the fluctuations of the jet Lorentz factor are driven by the accretion flow. It turns out that most of the spectral and timing features, including the 100-ms lag, are remarkably well-reproduced by this model. The 100-ms time-scale is then associated with the travel time from the accretion flow to the IR emitting zone. Our exploration of the parameter space favours a jet which is at most mildly relativistic (¯ < 3), and a linear and positive relation between the jet Lorentz factor and X-ray light curve i.e. (t) − 1∝LX(t). The presence of a strong Low-Frequency Quasi-Periodic Oscillation (LFQPO) in the IR light curve could be caused by jet precession driven by Lense–Thirring precession of the jet-emitting accretion flow. Our simulations confirm that this mechanism can produce an IR LFQPO similar to that observed in GX 339-4

Silver(I)-Catalyzed Synthesis of Cuneanes from Cubanes and their Investigation as Isosteres

Bridged or caged polycyclic hydrocarbons have rigid structures that project substituents into precise regions of 3D space, making them attractive as linking groups in materials science and as building blocks for medicinal chemistry. The efficient synthesis of new or underexplored classes of such compounds is, therefore, an important objective. Herein, we describe the silver(I)-catalyzed rearrangement of 1,4-disubstituted cubanes to cuneanes, which are strained hydrocarbons that have not received much attention since they were first described in 1970. The synthesis of 2,6-disubstituted or 1,3-disubstituted cuneanes can be achieved with high regioselectivities, with the regioselectivity being dependent on the electronic character of the cubane substituents. A preliminary assessment of cuneanes as scaffolds for medicinal chemistry suggests cuneanes could serve as isosteric replacements of trans-1,4-disubstituted cyclohexanes and 1,3-disubstituted benzenes. An analogue of the anticancer drug sonidegib was synthesized, in which the 1,2,3-trisubstituted benzene was replaced with a 1,3-disubstituted cuneane

SHARQnet – Sophisticated harmonic artifact reduction in quantitative susceptibility mapping using a deep convolutional neural network

Quantitative susceptibility mapping (QSM) reveals pathological changes in widespread diseases such as Parkinson's disease, Multiple Sclerosis, or hepatic iron overload. QSM requires multiple processing steps after the acquisition of magnetic resonance imaging (MRI) phase measurements such as unwrapping, background field removal and the solution of an ill-posed field-to-source-inversion. Current techniques utilize iterative optimization procedures to solve the inversion and background field correction, which are computationally expensive and lead to suboptimal or over-regularized solutions requiring a careful choice of parameters that make a clinical application of QSM challenging. We have previously demonstrated that a deep convolutional neural network can invert the magnetic dipole kernel with a very efficient feed forward multiplication not requiring iterative optimization or the choice of regularization parameters. In this work, we extended this approach to remove background fields in QSM. The prototype method, called SHARQnet, was trained on simulated background fields and tested on 3T and 7T brain datasets. We show that SHARQnet outperforms current background field removal procedures and generalizes to a wide range of input data without requiring any parameter adjustments. In summary, we demonstrate that the solution of ill-posed problems in QSM can be achieved by learning the underlying physics causing the artifacts and removing them in an efficient and reliable manner and thereby will help to bring QSM towards clinical applications

Assessing the assessments: Evidencing and benchmarking student learning outcomes in chemistry

Background Higher Education in Australia is in a phase of rapid change due to a number of regulatory changes. Over the past five years the Australian Chemistry community has agreed on a list of Chemistry Threshold Learning Outcomes (CTLOs) that every student graduating from an Australian University will have attained. In addition, the Royal Australian Chemical Institute (RACI) has changed its accreditation process for Chemistry degrees and now uses these CTLOs as the basis for accreditation. Therefore, it is now paramount to ensure that our assessment items allow students to demonstrate attainment of the CTLOs during a degree (Elmgren, Ho, Åkesson, Schmid & Towns 2015). The “Assessing the Assessments” project, funded by the Australian Government’s Office for Learning and Teaching (OLT ID14-3562) is developing a framework designed to help academics at tertiary institutions to determine the alignment of their assessment items with the CTLOs. The project is also collating a database of exemplary standards-based assessment items. Outcomes The project team has developed an online pro-forma, allowing self-assessment and submission of assessment items. Through workshops, colleagues are guided through a deeper evaluation of assessment items to determine how they meet or fall short of attainment of specific CTLOs. These workshops are designed to support evaluation of assessment items to ensure that they are CTLO compliant, using a tool developed over the course of the project. Results of evaluations conducted using this tool provide information regarding which portions of each CTLO students engage with through the task’s design, the level of scope and complexity at which they are engaged and the extent to which the attainment of each CTLO is assessed. Results also reveal which features of the CTLOs may need to be assessed more explicitly or rigorously in order to confirm student attainment or otherwise. References Elmgren, M., Ho, F., Åkesson, E., Schmid S. & Towns, M. J. Chem. Educ. 92, 427- 432 (2015). Comparison and evaluation of learning outcomes from an international perspective: Development of a best-practice process. Proceedings of the Australian Conference on Science and Mathematics Education, The University of Queensland, Sept 28th to 30th, 2016, page X, ISBN Number 978-0-9871834-4-6

Assessment of learning outcomes workshop: How do you know that your assessment tasks are effective?

Background Higher Education in Australia is in a phase of rapid change due to regulatory changes (TEQSA) and a shift towards a standards based framework. Over the past five years, the Chemistry community in Australia has developed the Chemistry Threshold Learning Outcomes (CTLOs) which articulate the outcomes that every student graduating from an Australian university with a major in Chemistry will have attained. In keeping with this development, the Royal Australian Chemical Institute (RACI) now bases its accreditation for Chemistry degrees on the CTLOs. Therefore, it is now vital to the Chemistry community to ensure that the assessment items we use allow students to demonstrate attainment of all CTLOs during their chemistry degree. Our OLT funded project (Assessing the assessments: Evidencing and benchmarking student learning outcomes in Chemistry (OLT ID14-3562)) has developed a diagnostic framework that will help you to determine whether your assessment items actually deliver reliable measures of student performance and provide evidence of achievement of the CTLOs. An additional outcome of the project will be a database of standards-based assessment items to be shared with the Chemistry community. Workshop Format We invite you to attend this half-day workshop where project team members will guide you through evaluating your assessment items for their ‘fitness for purpose’ in providing evidence of achievement of the CTLOs. Ideally you will bring along one of your 2nd or 3rd year Chemistry assessment items (in electronic format) so that the workshop team can guide you through an online submission and evaluation to determine: 1. Which CTLOs are explicitly demonstrated by students through successful completion of the item? 2. Is your task suited to a developing or graduate level understanding? 3. To what extent can your task be said to help confirm student attainment of the CTLOs? A critical aspect of this process is consideration of marking schemes and student work for the assessment items. We strongly encourage you to bring one or two pieces of marked pass level student work (de-identified) that can be used to evidence successful attainment of a particular CTLO. A central part of the workshop will be a ‘calibration’ exercise, which allows developing a mutual understanding of what constitutes demonstrating attainment of a particular CTLO. While the content of this workshop is Chemistry specific, the process is not. Therefore we are confident that all ACSME attendees will find this to be a valuable experience. All are invited. Attendance is free, however, registration is required for catering purposes. Proceedings of the Australian Conference on Science and Mathematics Education, The University of Queensland, Sept 28th to 30th, 2016, page X, ISBN Number 978-0-9871834-4-6

The MANGO study: a prospective investigation of oxygen enhanced and blood-oxygen level dependent MRI as imaging biomarkers of hypoxia in glioblastoma

BackgroundGlioblastoma (GBM) is the most aggressive type of brain cancer, with a 5-year survival rate of ~5% and most tumours recurring locally within months of first-line treatment. Hypoxia is associated with worse clinical outcomes in GBM, as it leads to localized resistance to radiotherapy and subsequent tumour recurrence. Current standard of care treatment does not account for tumour hypoxia, due to the challenges of mapping tumour hypoxia in routine clinical practice. In this clinical study, we aim to investigate the role of oxygen enhanced (OE) and blood-oxygen level dependent (BOLD) MRI as non-invasive imaging biomarkers of hypoxia in GBM, and to evaluate their potential role in dose-painting radiotherapy planning and treatment response assessment.MethodsThe primary endpoint is to evaluate the quantitative and spatial correlation between OE and BOLD MRI measurements and [18F]MISO values of uptake in the tumour. The secondary endpoints are to evaluate the repeatability of MRI biomarkers of hypoxia in a test-retest study, to estimate the potential clinical benefits of using MRI biomarkers of hypoxia to guide dose-painting radiotherapy, and to evaluate the ability of MRI biomarkers of hypoxia to assess treatment response. Twenty newly diagnosed GBM patients will be enrolled in this study. Patients will undergo standard of care treatment while receiving additional OE/BOLD MRI and [18F]MISO PET scans at several timepoints during treatment. The ability of OE/BOLD MRI to map hypoxic tumour regions will be evaluated by assessing spatial and quantitative correlations with areas of hypoxic tumour identified via [18F]MISO PET imaging.DiscussionMANGO (Magnetic resonance imaging of hypoxia for radiation treatment guidance in glioblastoma multiforme) is a diagnostic/prognostic study investigating the role of imaging biomarkers of hypoxia in GBM management. The study will generate a large amount of longitudinal multimodal MRI and PET imaging data that could be used to unveil dynamic changes in tumour physiology that currently limit treatment efficacy, thereby providing a means to develop more effective and personalised treatments