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Background The risk of hemolytic events (HEs) with intravenous immunoglobulin (IVIG) therapy appears to be linked to isoagglutinins (anti-A and anti-B) in the product. Patient risk factors include high IVIG dose, blood group, and underlying inflammatory state. Study design and methods Using published anti-A and anti-B titers for IVIG products and HE rates calculated from HEs spontaneously reported to EudraVigilance, regression models were developed to infer the relationship between HE risk and IVIG isoagglutinin levels for each blood group. Applying estimated model coefficients to isoagglutinin levels associated with an IVIG (Privigen; CSL Behring, King of Prussia, PA), manufactured with and without isoagglutinin reduction steps, predicted HE risk values were generated for each product: 1) without any isoagglutinin reduction, 2) anti-A donor screening, and 3) anti-A/anti-B specific immunoaffinity chromatography (IAC; Ig IsoLo). Results Predicted HE risk was highest for blood group AB, followed by A and B; it was low for O. Projected population shares of HEs by blood group were similar to reported real-world data. Compared with the original process (no isoagglutinin reduction), the model predicts lower hemolytic risk with anti-A donor screening and even lower hemolytic risk with IAC isoagglutinin reduction. Conclusion IAC isoagglutinin reduction is predicted to reduce the HE risk with IVIG substantially. Physicians should be especially vigilant to HE risk in patients with blood group AB and, to a lesser extent, A when using IVIG products with high anti-A titers.

Space Weather (SW) research is a very important topic from the scientific, operational and civic society point of view. Knowledge of interactions in the Sun-Earth system, the physics behind observed SW phenomena, and its direct impact on modern technologies were and will be key areas of interest. The LOFAR for Space Weather (LOFAR4SW) project aim is to prepare a novel tool which can bring new capabilities into this domain. The project is realised in the frame of a Horizon 2020 INFRADEV call. The base for the project is the Low Frequency Array (LOFAR) - the worlds largest low frequency radio telescope, with a dense core near Exloo in The Netherlands and many stations distributed both in the Netherlands and Europe wide with baselines up to 2000 km. The final design of LOFAR4SW will provide a full conceptual and technical description of the LOFAR upgrade, to enable simultaneous operation as a radio telescope for astronomical research as well as an infrastructure working for Space Weather studies. In this work we present the current status of the project, including examples of the capabilities of LOFAR4SW and the project timeline as we plan for the Critical Design Review later in 2021.

Coronal Mass Ejections (CMEs) and their interplanetary counterparts (ICMEs) are key drivers of space weather throughout the heliosphere. Observational studies are used to understand their evolution and for developing existing models and theory in space weather forecasting. Motivated by the future exploration of the solar high-latitudes by Solar Orbiter and complimented by Parker Solar Probe, we aim to contribute to the understanding of high-latitude CMEs as they develop into ICMEs. We examine a high-latitude CME and its subsequent ICME using data from STEREO, Ulysses, and near-Earth spacecraft. We apply a triangulation method to the remote-sensing images from the twin STEREO spacecraft and conduct a multi-spacecraft analysis using the in-situ Ulysses, STEREO, and near-Earth spacecraft data. The Ulysses observations, supported by the other spacecraft, provides a clear picture of the ICME geometry and structure: a shock, followed by a sheath region, and a magnetic flux rope followed by a high-speed stream. This ICME differs from the known ‘over-expanding’ types observed in the high-latitudes by the Ulysses mission, in that it straddles a region between the slow and fast solar winds which in itself drives a shock.

We present a catalogue, IPSCAT, of the results of Interplanetary Scintillation (IPS) analysis applied to observations that are compiled using data from three European radio networks, EISCAT, MERLIN and LOFAR, during the early science phase of the STEREO mission, from 2007 to 2012. These analyses provide a means to study the solar wind and interplanetary transients, which we complement with observations from the Heliospheric Imagers on-board STEREO. Within the IPS data set we identify transient phenomena, specifically Coronal Mass Ejections (CMEs) and Stream Interaction Regions (SIRs), via both visual inspection and an automatic feature-finding algorithm. We study the effectiveness of the automated detection algorithm and find it to be successful at classifying CMEs, whilst the identification of SIRs is less easily established. A discussion of the statistical properties of IPSCAT is presented, together with a comparison between the IPS and HI results. Finally, we present a case study of successive CMEs within the IPSCAT data set, which were also observed by the HIs on both STEREO spacecraft and analysed using the Stereoscopic Self-Similar Expansion (SSSE) method. This work was carried out as part of the EU FP7 HELCATS (Heliospheric Cataloguing, Analysis and Techniques Service) project (http://www.helcats-fp7.eu/).

We show in situ observations of ICMEs during the first year of Solar Orbiter observations based on magnetic field data from the MAG instrument in conjunction with in situ and imaging observations from the Heliospheric System Observatory. The in situ magnetic field data from four other currently active spacecraft - Parker Solar Probe, BepiColombo, STEREO-Ahead and Wind - are also searched for ICME signatures, and all clear ICME events that could be identified by classic signatures such as elevated and rotating magnetic fields of sufficiently long durations are included in a living online catalog. Furthermore, we provide a visualization of the in situ magnetic field data alongside spacecraft positions and propagating CME fronts, which are based on modeling of STEREO-A heliospheric imager data. This allows us to identify ICME events that could be unambiguously followed from their inception on the Sun to their impact at the aforementioned spacecraft, and highlights sought-after lineup events, in which the same ICME is observed at multiple points in space, such as the well-studied 2020 April 15-20 ICME. We discuss the ICME rate observed so far, and provide an outlook on the expected ICME rate in solar cycle 25 based on different forecasts for the cycle amplitude (see Möstl et al. 2020, https://doi.org/10.3847/1538-4357/abb9a1).

The Low Frequency Array (LOFAR) is an advanced phased-array radio-telescope system based across Europe. It is capable of observing over a wide radio bandwidth of ~10-250 MHz at both high spatial and temporal resolutions. LOFAR has capabilities that enable studies of many aspects of what we class as space weather (from the Sun to the Earth and afar) to be progressed beyond today’s state-of-the-art. However, with the present setup and organisation behind the operations of the telescope, it can only be used for space-weather campaign studies with limited triggering availability. This severely limits our ability to effectively use LOFAR to contribute to space-weather monitoring/forecast beyond its core strength of enabling world-leading scientific research. LOFAR itself is made up of a dense core of 24 stations near Exloo in The Netherlands with an additional 14 stations spread across the northeast Netherlands. In addition to those, there are a further 13 stations based internationally across Europe. These international stations are, currently, six in Germany, three in northern Poland, and one each in France, Ireland, Latvia, Sweden, and the UK. Further sites are under preparations (for example, in Italy). We are undertaking a Horizon 2020 (H2020) INFRADEV design study to undertake investigations into upgrading LOFAR to allow for regular space-weather science/monitoring observations in parallel with normal radio-astronomy/scientific operations. This project is called the LOFAR For Space Weather (LOFAR4SW) project (see: http://lofar4sw.eu/). Our work involves all aspects of scientific and engineering work along with end-user and political engagements with various stakeholders. This is with the full recognition that space weather is a worldwide threat with varying local, regional, continent-wide impacts, and also global impacts – and hence is a global concern. Here, we summarise the most-recent key aspects of the LOFAR4SW progress including outputs/progress following the Detailed Design Review (DDR) that took place at ASTRON, The Netherlands, in March 2020, as well as the implementation of recommendations from the earlier Preliminary Design Review (PDR) with an outlook to the LOFAR4SW User Workshop the week following EGU 2020. We also aim to briefly summarise a key set of the longer-term goals envisaged for LOFAR to become one of Europe’s most-comprehensive space-weather observing systems capable of shedding new light on several aspects of the space-weather system, from the Sun to the solar wind to Jupiter and Earth’s ionosphere.

Public transport is designed to move people efficiently and affordably around their communities. Millions of people internationally with disabilities rely on public transport every day to connect them to services, work, educational and social events. Many of these people attempt to board public transport using a powered mobility aid (such as an electric wheelchair, mobility scooter, or gopher) and this number is expected to rise as the population ages. Evidence suggests that many people have difficulty getting their powered mobility aids on and off public transport vehicles, and consumers, vendors and the health care-professionals involved in recommending mobility aids have no way of knowing which powered mobility aids are compatible with existing public transport configurations. The purpose of this paper is to demonstrate how existing 3D technologies and software can be applied to solve this real world problem using the example of buses. This proof-of-principle paper describes the process of scanning buses and powered mobility aids in 3D, together with descriptions of the prototype software to undertake the computerised process, to determine the compatibility of powered mobility aids for access on buses. Feasibility is then demonstrated using an example of one bus and one powered mobility aid. This paper is of interest to researchers wishing to examine the application of 3D technologies, health care providers and consumers who select powered mobility aids, as well as transport policy makers and conveyance commissioners who can access 3D data to optimise transport network accessibility for all community members.

We analyse in this work the propagation and geoeffectiveness of four successive coronal mass ejections (CMEs) that erupted from the Sun during 21--23 May 2013 and that were detected in interplanetary space by the Wind and/or STEREO-A spacecraft. All these CMEs featured critical aspects for understanding so-called "problem space weather storms" at Earth. In the first three events a limb CMEs resulted in moderately geoeffective in-situ structures at their target location in terms of the disturbance storm time (Dst) index (either measured or estimated). The fourth CME, which also caused a moderate geomagnetic response, erupted from close to the disc centre as seen from Earth, but it was not visible in coronagraph images from the spacecraft along the Sun--Earth line and appeared narrow and faint from off-angle viewpoints. Making the correct connection between CMEs at the Sun and their in-situ counterparts is often difficult for problem storms. We investigate these four CMEs using multiwavelength and multipoint remote-sensing observations (extreme ultraviolet, white light, and radio), aided by 3D heliospheric modelling, in order to follow their propagation in the corona and in interplanetary space and to assess their impact at 1 AU. Finally, we emphasise the difficulties in forecasting moderate space weather effects provoked by problematic and ambiguous events and the importance of multispacecraft data for observing and modelling problem storms., 20 pages, 10 figures, 3 tables, accepted for publication in The Astrophysical Journal

Background Whole-genome sequencing (WGS) is a powerful method for revealing the diversity and complexity of the somatic mutation burden of tumours. Here, we investigated the utility of tumour and matched germline WGS for understanding aetiology and treatment opportunities for high-risk individuals with familial breast cancer. Patients and methods We carried out WGS on 78 paired germline and tumour DNA samples from individuals carrying pathogenic variants in BRCA1 (n = 26) or BRCA2 (n = 22) or from non-carriers (non-BRCA1/2; n = 30). Results Matched germline/tumour WGS and somatic mutational signature analysis revealed patients with unreported, dual pathogenic germline variants in cancer risk genes (BRCA1/BRCA2; BRCA1/MUTYH). The strategy identified that 100% of tumours from BRCA1 carriers and 91% of tumours from BRCA2 carriers exhibited biallelic inactivation of the respective gene, together with somatic mutational signatures suggestive of a functional deficiency in homologous recombination. A set of non-BRCA1/2 tumours also had somatic signatures indicative of BRCA-deficiency, including tumours with BRCA1 promoter methylation, and tumours from carriers of a PALB2 pathogenic germline variant and a BRCA2 variant of uncertain significance. A subset of 13 non-BRCA1/2 tumours from early onset cases were BRCA-proficient, yet displayed complex clustered structural rearrangements associated with the amplification of oncogenes and pathogenic germline variants in TP53, ATM and CHEK2. Conclusions Our study highlights the role that WGS of matched germline/tumour DNA and the somatic mutational signatures can play in the discovery of pathogenic germline variants and for providing supporting evidence for variant pathogenicity. WGS-derived signatures were more robust than germline status and other genomic predictors of homologous recombination deficiency, thus impacting the selection of platinum-based or PARP inhibitor therapy. In this first examination of non-BRCA1/2 tumours by WGS, we illustrate the considerable heterogeneity of these tumour genomes and highlight that complex genomic rearrangements may drive tumourigenesis in a subset of cases.

Although large-scale stereoscopic 3D environments like CAVEs are a favorable location for group presentations, the perspective projection and stereoscopic optimization usually follows a navigator-centric approach. Therefore, these presentations are usually accompanied by strong side-effects, such as motion sickness which is often caused by a disturbed stereoscopic vision. The reason is that the stereoscopic visualization is usually optimized for the only head-tracked person in the CAVE – the navigator – ignoring the needs of the real target group – the audience. To overcome this misconception, this work proposes an alternative to the head tracking-based stereoscopic effect optimization. By using an interactive virtual overview map in 3D, the pre-tour and on-tour configuration of the stereoscopic effect is provided, partly utilizing our previously published interactive projection plane approach. This Stereoscopic Space Map is visualized by the zSpace 200®, whereas the virtual world is shown on a panoramic 330° CAVE2TM. A pilot expert study with eight participants was conducted using pre-configured tours through 3D models. The comparison of the manual and automatic stereoscopic adjustment showed that the proposed approach is an appropriate alternative to the nowadays commonly used head tracking-based stereoscopic adjustment.

Identifying the source of the material within coronal mass ejections (CMEs) and understanding CME onset mechanisms are fundamental issues in solar and space physics. Parameters relating to plasma composition, such as charge states and He abundance (\ahe), may be different for plasmas originating from differing processes or regions on the Sun. Thus, it is crucial to examine the relationship between in-situ measurements of CME composition and activity on the Sun. We study the CME that erupted on 2014 September 10, in association with an X1.6 flare, by analyzing AIA imaging and IRIS spectroscopic observations and its in-situ signatures detected by Wind and ACE. We find that during the slow expansion and intensity increase of the sigmoid, plasma temperatures of 9 MK, and higher, first appear at the footpoints of the sigmoid, associated with chromospheric brightening. Then the high-temperature region extends along the sigmoid. IRIS observations confirm that this extension is caused by transportation of hot plasma upflow. Our results show that chromospheric material can be heated to 9 MK, and above, by chromospheric evaporation at the sigmoid footpoints before flare onset. The heated chromospheric material can transport into the sigmoidal structure and supply mass to the CME. The aforementioned CME mass supply scenario provides a reasonable explanation for the detection of high charge states and elevated \ahe\ in the associated ICME. The observations also demonstrate that the quasi-steady evolution in the precursor phase is dominated by magnetic reconnection between the rising flux rope and the overlying magnetic field structure., 10 pages, 5 figures, accepted for publication in ApJL

We present a statistical analysis of coronal mass ejections (CMEs) imaged by the Heliospheric Imager (HI) instruments aboard NASAs twin-spacecraft STEREO mission between April 2007 and August 2017 for STEREO-A and between April 2007 and September 2014 for STEREO-B. The analysis exploits a catalogue that was generated within the FP7 HELCATS project. Here, we focus on the observational characteristics of CMEs imaged in the heliosphere by the inner (HI-1) cameras. More specifically, in this paper we present distributions of the basic observational parameters - namely occurrence frequency, central position angle (PA) and PA span - derived from nearly 2000 detections of CMEs in the heliosphere by HI-1 on STEREO-A or STEREO-B from the minimum between Solar Cycles 23 and 24 to the maximum of Cycle 24; STEREO-A analysis includes a further 158 CME detections from the descending phase of Cycle 24, by which time communication with STEREO-B had been lost. We compare heliospheric CME characteristics with properties of CMEs observed at coronal altitudes, and with sunspot number. As expected, heliospheric CME rates correlate with sunspot number, and are not inconsistent with coronal rates once instrumental factors/differences in cataloguing philosophy are considered. As well as being more abundant, heliospheric CMEs, like their coronal counterparts, tend to be wider during solar maximum. Our results confirm previous coronagraph analyses suggesting that CME launch sites don't simply migrate to higher latitudes with increasing solar activity. At solar minimum, CMEs tend to be launched from equatorial latitudes while, at maximum, CMEs appear to be launched over a much wider latitude range; this has implications for understanding the CME/solar source association. Our analysis provides some supporting evidence for the systematic dragging of CMEs to lower latitude as they propagate outwards., 26 pages, 8 figures, in press at Solar Physics. The abstract has been shortened to comply with the allowed length at arxiv.org

Facing the rapidly shrinking trend of in-store shopping, this study aims at developing an interactive environmental prototype that provides the in-store customer with a more intuitive and enjoyable experience. Based on an intensive market research and evaluation process, we suggest that it is necessary to establish a new type of connection among customers, products, and retailers. Therefore, it is vital to provide stores with a better solution which could integrate an advanced product displaying method with object tracking and recognition and user behaviour interaction approaches. The designed solution proposes an interactive show-window, which emphasizes customized product visualization and direct interactivity to reinforce the connection, during physical shopping, between goods and consumers. We explore the possible feedback when people interact with the interactive show-window using a qualitative study, which has also been facilitated through an interactive show-window installation. The results demonstrated a meaningful outcome for this designed solution.

Spherical coordinate systems, which are ubiquitous in astronomy, cannot be shown without distortion on flat, two-dimensional surfaces. This poses challenges for the two complementary phases of visual exploration -- making discoveries in data by looking for relationships, patterns or anomalies -- and publication -- where the results of an exploration are made available for scientific scrutiny or communication. This is a long-standing problem, and many practical solutions have been developed. Our allskyVR approach provides a workflow for experimentation with commodity virtual reality head-mounted displays. Using the free, open source S2PLOT programming library, and the A-Frame WebVR browser-based framework, we provide a straightforward way to visualise all-sky catalogues on a user-centred, virtual celestial sphere. The allskyVR distribution contains both a quickstart option, complete with a gaze-based menu system, and a fully customisable mode for those who need more control of the immersive experience. The software is available for download from: https://github.com/cfluke/allskyVR, 11 pages, 3 figures, accepted for publication in Publications of the Astronomical Society of Australia

An FPGA-based digital-receiver has been developed for a low-frequency imaging radio interferometer, the Murchison Widefield Array (MWA). The MWA, located at the Murchison Radio-astronomy Observatory (MRO) in Western Australia, consists of 128 dual-polarized aperture-array elements (tiles) operating between 80 and 300\,MHz, with a total processed bandwidth of 30.72 MHz for each polarization. Radio-frequency signals from the tiles are amplified and band limited using analog signal conditioning units; sampled and channelized by digital-receivers. The signals from eight tiles are processed by a single digital-receiver, thus requiring 16 digital-receivers for the MWA. The main function of the digital-receivers is to digitize the broad-band signals from each tile, channelize them to form the sky-band, and transport it through optical fibers to a centrally located correlator for further processing. The digital-receiver firmware also implements functions to measure the signal power, perform power equalization across the band, detect interference-like events, and invoke diagnostic modes. The digital-receiver is controlled by high-level programs running on a single-board-computer. This paper presents the digital-receiver design, implementation, current status, and plans for future enhancements., Comment: 14 pages, 7 figures

A gunfight between police and a gang of men led by the self-styled "Captain Moonlite", a.k.a. George Scott, occurred on 16th November 1879 at a farmhouse near Wantabadgery Station in the colony of New South Wales. The skirmish resulted in the deaths of two bushrangers and one police officer. As a result, Captain Moonlite and Thomas Rogan were hung in Sydney's Darlinghurst Gaol on 20 January 1880 for the murder of Constable Edward Webb-Bowen. Culpability for firing the fatal shot, however, has remained a source of controversy. Information obtained from an analysis of historical records was used to guide an archeological excavation at the scene of the shooting in which Terrestrial Laser Scanning (TLS) technology was employed to produce a digital (3D) terrain model of the siege location. Utilizing the terrain model, the relative positions of Moonlite, Webb-Bowen, and the other gang members were established with possible projectile trajectories plotted. This, in combination with inquest evidence from a gun maker and the medical practitioner who examined Constable Webb-Bowen's wound, indicates that the most likely shooter was Gus Warnicke, aged 15 years, the youngest member of the gang, who was also killed in the exchange of fire.

PurposeTo improve the accuracy of automated vein segmentation by combining susceptibility-weighted images (SWI), quantitative susceptibility maps (QSM), and a vein atlas to produce a resultant image called a composite vein image (CV image).MethodAn atlas was constructed in common space from 1072 manually traced 2D-slices. The composite vein image was derived for each subject as a weighted sum of three inputs; a SWI image, a QSM image and the vein atlas. The weights for each input and each anatomical location, called template priors, were derived by assessing the accuracy of each input over an independent data set. The accuracy of venograms derived automatically from each of the CV image, SWI, and QSM image sets was assessed by comparison with manual tracings. Three different automated vein segmentation techniques were used, and ten performance metrics evaluated.ResultsVein segmentations using the CV image were comprehensively better than those derived from SWI or QSM images (mean Cohen’s d = 1.1). Sixty permutations of performance metric and automated segmentation technique were evaluated. Vein identification improvements that were both large and significant (Cohen’s d>0.80, pConclusionThe accuracy of automated venograms derived from the composite vein image was overwhelmingly superior to venograms derived from SWI or QSM alone.

The magnetic susceptibility of haemoglobin is modulated by oxygen saturation, providing a mechanism to non-invasively measure oxygen extraction fraction. When combined with perfusion techniques, quantitative susceptibility mapping facilitates regional measurement of cerebral metabolic rate of oxygen consumption. However, accurate measurement requires a complete vein map to measure anatomical variance in the metabolic demands of tissue. In this work we present a novel shape-based Markov Random Field technique to segmentation the cerebral veins that provides accurate and complete vein maps. The shape-based graph underpinning the model controls the spatial relationships between voxels and enforces cylindrical geometry, allowing increased sensitivity with accurate vein boundaries.

Purpose: Quantitative susceptibility mapping (QSM) enables cerebral venous characterization and physiological measurements, such as oxygen extraction fraction (OEF). The exquisite sensitivity of QSM to deoxygenated blood makes it possible to image small veins; however partial volume effects must be addressed for accurate quantification. We present a new method, Iterative Cylindrical Fitting (ICF), to estimate voxel-based partial volume effects for susceptibility maps and use it to improve OEF quantification of small veins with diameters between 1.5 and 4 voxels. Materials and Methods: Simulated QSM maps were generated to assess the performance of the ICF method over a range of vein geometries with varying echo times and noise levels. The ICF method was also applied to in vivo human brain data to assess the feasibility and behavior of OEF measurements compared to the maximum intensity voxel (MIV) method. Results: Improved quantification of OEF measurements was achieved for vessels with contrast to noise greater than 3.0 and vein radii greater than 0.75 voxels. The ICF method produced improved quantitative accuracy of OEF measurement compared to the MIV approach (mean OEF error 7.7 vs. 12.4%). The ICF method provided estimates of vein radius (mean error

Using the final 128 antenna locations of the Murchison Widefield Array (MWA), we calculate its sensitivity to the epoch of reionization (EoR) power spectrum of redshifted 21 cm emission for a fiducial model and provide the tools to calculate the sensitivity for any model. Our calculation takes into account synthesis rotation, chromatic and asymmetrical baseline effects, and excludes modes that will be contaminated by foreground subtraction. For the fiducial model, the MWA will be capable of a 14σ detection of the EoR signal with one full season of observation on two fields (900 and 700 h)., National Science Foundation (U.S.) (Grant AST CAREER-0847753), National Science Foundation (U.S.) (Grant AST-0457585), National Science Foundation (U.S.) (Grant AST-0908884), National Science Foundation (U.S.) (Grant PHY-0835713), United States. Air Force Office of Scientific Research (Grant FA9550-0510247), Smithsonian Astrophysical Observatory, MIT School of Science

Radio survey datasets comprise an increasing number of individual observations stored as sets of multidimensional data. In large survey projects, astronomers commonly face limitations regarding: 1) interactive visual analytics of sufficiently large subsets of data; 2) synchronous and asynchronous collaboration; and 3) documentation of the discovery workflow. To support collaborative data inquiry, we present encube, a large-scale comparative visual analytics framework. Encube can utilise advanced visualization environments such as the CAVE2 (a hybrid 2D and 3D virtual reality environment powered with a 100 Tflop/s GPU-based supercomputer and 84 million pixels) for collaborative analysis of large subsets of data from radio surveys. It can also run on standard desktops, providing a capable visual analytics experience across the display ecology. Encube is composed of four primary units enabling compute-intensive processing, advanced visualisation, dynamic interaction, parallel data query, along with data management. Its modularity will make it simple to incorporate astronomical analysis packages and Virtual Observatory capabilities developed within our community. We discuss how encube builds a bridge between high-end display systems (such as CAVE2) and the classical desktop, preserving all traces of the work completed on either platform -- allowing the research process to continue wherever you are., Comment: Accepted for Proceedings of IAU Symposium 325

Antenna layout is an important design consideration for radio interferometers because it determines the quality of the snapshot point spread function (PSF, or array beam). This is particularly true for experiments targeting the 21 cm Epoch of Reionization signal as the quality of the foreground subtraction depends directly on the spatial dynamic range and thus the smoothness of the baseline distribution. Nearly all sites have constraints on where antennas can be placed---even at the remote Australian location of the MWA (Murchison Widefield Array) there are rock outcrops, flood zones, heritages areas, emergency runways and trees. These exclusion areas can introduce spatial structure into the baseline distribution that enhance the PSF sidelobes and reduce the angular dynamic range. In this paper we present a new method of constrained antenna placement that reduces the spatial structure in the baseline distribution. This method not only outperforms random placement algorithms that avoid exclusion zones, but surprisingly outperforms random placement algorithms without constraints to provide what we believe are the smoothest constrained baseline distributions developed to date. We use our new algorithm to determine antenna placements for the originally planned MWA, and present the antenna locations, baseline distribution, and snapshot PSF for this array choice.

The most frequently encountered patients with primary immunodeficiency disease (PID) are those with antibody deficiencies. These patients require life-long immunoglobulin (IgG) replacement therapy to prevent severe and reoccurring infections. IgG is traditionally administered intravenously (IVIG) on an outpatient basis, although in some Scandinavian countries subcutaneous administration of IgG (SCIG) as home self-infusion has become the predominant mode of delivery. Compared with IVIG, SCIG therapy leads to a more physiologic IgG profile since the large variations between peak and trough levels of serum IgG are blunted by slow absorption and maintenance of closer equilibrium between intra- and extravascular compartments. SCIG therapy has been shown to be as effective as IVIG in preventing infections and has a better safety profile, with fewer systemic side effects. While local tissue reactions are common with SCIG, they are usually mild, tend to improve over time and typically do not interfere with therapy. Switching to SCIG therapy from IVIG can lead to significant improvements in health-related quality of life, appears to be more convenient for the patient, and can make it easier for the patient to travel. In those patients with difficult vascular access and intolerable side-effects with IVIG therapy, SCIG therapy may be the only treatment option. Selected patients can be expected to benefit greatly from SCIG therapy, although implementation of a successful home-treatment program requires proper education, training, and supportive care.

Incoherent dedispersion is a computationally intensive problem that appears frequently in pulsar and transient astronomy. For current and future transient pipelines, dedispersion can dominate the total execution time, meaning its computational speed acts as a constraint on the quality and quantity of science results. It is thus critical that the algorithm be able to take advantage of trends in commodity computing hardware. With this goal in mind, we present analysis of the 'direct', 'tree' and 'sub-band' dedispersion algorithms with respect to their potential for efficient execution on modern graphics processing units (GPUs). We find all three to be excellent candidates, and proceed to describe implementations in C for CUDA using insight gained from the analysis. Using recent CPU and GPU hardware, the transition to the GPU provides a speed-up of 9x for the direct algorithm when compared to an optimised quad-core CPU code. For realistic recent survey parameters, these speeds are high enough that further optimisation is unnecessary to achieve real-time processing. Where further speed-ups are desirable, we find that the tree and sub-band algorithms are able to provide 3-7x better performance at the cost of certain smearing, memory consumption and development time trade-offs. We finish with a discussion of the implications of these results for future transient surveys. Our GPU dedispersion code is publicly available as a C library at: this http URL

Background Melanotic neuroectodermal tumor of infancy (MNTI) is exceptionally rare and occurs predominantly in the head and neck (92.8 % cases). The patient reported here is only the eighth case of MNTI presenting in an extremity, and the first reported in the fibula. Case presentation A 2-month-old female presented with a mass arising in the fibula. Exhaustive genomic, transcriptomic, epigenetic and pathological characterization was performed on the excised primary tumor and a derived cell line. Whole-exome analysis of genomic DNA from both the tumor and blood indicated no somatic, non-synonymous coding mutations within the tumor, but a heterozygous, unique germline, loss of function mutation in CDKN2A (p16INK4A, D74A). SNP-array CGH on DNA samples revealed the tumor to be euploid, with no detectable gene copy number variants. Multiple chromosomal translocations were identified by RNA-Seq, and fusion genes included RPLP1-C19MC, potentially deregulating the C19MC cluster, an imprinted locus containing microRNA genes reactivated by gene fusion in embryonal tumors with multilayered rosettes. Since the presumed cell of origin of MNTI is from the neural crest, we also compared gene expression with a dataset from human neural crest cells and identified 185 genes with significantly different expression. Consistent with the melanotic phenotype of the tumor, elevated expression of tyrosinase was observed. Other highly expressed genes encoded muscle proteins and modulators of the extracellular matrix. A derived MNTI cell line was sensitive to inhibitors of lysine demethylase, but not to compounds targeting other epigenetic regulators. Conclusions In the absence of somatic copy number variations or mutations, the fully transformed phenotype of the MNTI may have arisen in infancy because of the combined effects of a germline CDKN2A mutation, tumor promoting somatic fusion genes and epigenetic deregulation. Very little is known about the etiology of MNTI and this report advances knowledge of these rare tumors by providing the first comprehensive genomic, transcriptomic and epigenetic characterization of a case. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2669-3) contains supplementary material, which is available to authorized users.

Single pixel feeds on large aperture radio telescopes have the ability to detect weak (∼10 mJy) impulsive bursts of radio emission and sub-mJy radio pulsars. Unfortunately, in large-scale blind surveys, radio frequency interference (RFI) mimics both radio bursts and radio pulsars, greatly reducing the sensitivity to new discoveries as real signals of astronomical origin get lost among the millions of false candidates. In this paper a technique that takes advantage of multipixel feeds to use eigenvector decomposition of common signals is used to greatly facilitate radio burst and pulsar discovery. Since the majority of RFI occurs with zero dispersion, the method was tested on the total power present in the 13 beams of the Parkes multibeam receiver using data from archival intermediate-latitude surveys. The implementation of this method greatly reduced the number of false candidates and led to the discovery of one new rotating radio transient or RRAT, six new pulsars and five new pulses that shared the swept-frequency characteristics similar in nature to the `Lorimer burst'. These five new signals occurred within minutes of 11 previous detections of a similar type. When viewed together, they display temporal characteristics related to integer seconds, with non-random distributions and characteristic ‘gaps’ between them, suggesting they are not from a naturally occurring source. Despite the success in removing RFI, false candidates present in the data that are only visible after integrating in time or at non-zero dispersion remained. It is demonstrated that with some computational penalty, the method can be applied iteratively at all trial dispersions and time resolutions to remove the vast majority of spurious candidates.

Astronomy depends on ever increasing computing power. Processor clock-rates have plateaued, and increased performance is now appearing in the form of additional processor cores on a single chip. This poses significant challenges to the astronomy software community. Graphics Processing Units (GPUs), now capable of general-purpose computation, exemplify both the difficult learning-curve and the significant speedups exhibited by massively-parallel hardware architectures. We present a generalised approach to tackling this paradigm shift, based on the analysis of algorithms. We describe a small collection of foundation algorithms relevant to astronomy and explain how they may be used to ease the transition to massively-parallel computing architectures. We demonstrate the effectiveness of our approach by applying it to four well-known astronomy problems: Hogbom CLEAN, inverse ray-shooting for gravitational lensing, pulsar dedispersion and volume rendering. Algorithms with well-defined memory access patterns and high arithmetic intensity stand to receive the greatest performance boost from massively-parallel architectures, while those that involve a significant amount of decision-making may struggle to take advantage of the available processing power.

We investigate the neutral hydrogen (HI) content of sixteen groups for which we have multi-wavelength data including X-ray observations. Wide-field imaging of the groups was obtained with the 20-cm multibeam system on the 64-m Parkes telescope. We have detected ten previously uncatalogued HI sources, one of which has no visible optical counterpart. We examine the HI properties of the groups, compared to their X-ray characteristics, finding that those groups with a higher X-ray temperature and luminosity contain less HI per galaxy. The HI content of a group depends on its morphological make-up, with those groups dominated by early-type galaxies containing the least total HI. We determined the expected HI for the spiral galaxies in the groups, and found that a number of the galaxies were HI deficient. The HI deficient spirals were found both in groups with and without a hot intra-group medium. The HI deficient galaxies were not necessarily found at the centre of the groups, however, we did find that two thirds of HI deficient galaxies were found within about 1 Mpc from the group centre, indicating that the group environment is affecting the gas-loss from these galaxies. We determined the HI mass function for a composite sample of 15 groups, and found that it is significantly flatter than the field HI mass function. We also find a lack of high HI-mass galaxies in groups. One possible cause of this effect is the tidal stripping of HI gas from spiral galaxies as they are pre-processed in groups.

Two human pathogenic bacteria, Staphylococcus aureus CIP 68.5 and Pseudomonas aeruginosa ATCC 9025, were adsorbed onto surfaces containing Ti thin films of varying thickness to determine the extent to which nanoscale surface roughness influences the extent of bacterial attachment. A magnetron sputter thin film system was used to deposit titanium films with thicknesses of 3, 12, and 150 nm on glass substrata with corresponding surface roughness parameters of R(q) 1.6, 1.2, and 0.7 nm (on a 4 microm x 4 microm scanning area). The chemical composition, wettability, and surface architecture of titanium thin films were characterized using X-ray photoelectron spectroscopy, contact angle measurements, atomic force microscopy, three-dimensional interactive visualization, and statistical approximation of the topographic profiles. Investigation of the dynamic evolution of the Ti thin film topographic parameters indicated that three commonly used parameters, R(a), R(q), and R(max), were insufficient to effectively characterize the nanoscale rough/smooth surfaces. Two additional parameters, R(skw) and R(kur), which describe the statistical distributions of roughness character, were found to be useful for evaluating the surface architecture. Analysis of bacterial retention profiles indicated that bacteria responded differently to the surfaces on a scale of less than 1 nm change in the R(a) and R(q) Ti thin film surface roughness parameters by (i) an increased number of retained cells by a factor of 2-3, and (ii) an elevated level of secretion of extracellular polymeric substances.