RascalC: A Jackknife Approach to Estimating Single and Multi-Tracer Galaxy Covariance Matrices

To make use of clustering statistics from large cosmological surveys, accurate and precise covariance matrices are needed. We present a new code to estimate large scale galaxy two-point correlation function (2PCF) covariances in arbitrary survey geometries that, due to new sampling techniques, runs $\sim 10^4$ times faster than previous codes, computing finely-binned covariance matrices with negligible noise in less than 100 CPU-hours. As in previous works, non-Gaussianity is approximated via a small rescaling of shot-noise in the theoretical model, calibrated by comparing jackknife survey covariances to an associated jackknife model. The flexible code, RascalC, has been publicly released, and automatically takes care of all necessary pre- and post-processing, requiring only a single input dataset (without a prior 2PCF model). Deviations between large scale model covariances from a mock survey and those from a large suite of mocks are found to be be indistinguishable from noise. In addition, the choice of input mock are shown to be irrelevant for desired noise levels below $\sim 10^5$ mocks. Coupled with its generalization to multi-tracer data-sets, this shows the algorithm to be an excellent tool for analysis, reducing the need for large numbers of mock simulations to be computed.Comment: 29 pages, 8 figures. Accepted by MNRAS. Code is available at http://github.com/oliverphilcox/RascalC with documentation at http://rascalc.readthedocs.io

Probing the Protosolar Disk Using Dust Filtering at Gaps in the Early Solar System

Jupiter and Saturn formed early, before the gas disk dispersed. The presence of gap-opening planets affects the dynamics of the gas and embedded solids and halts the inward drift of grains above a certain size. A drift barrier can explain the absence of calcium aluminium rich inclusions (CAIs) in chondrites originating from parent bodies that accreted in the inner solar system. Employing an interdisciplinary approach, we use a $\mu$-X-Ray-fluorescence scanner to search for large CAIs and a scanning electron microscope to search for small CAIs in the ordinary chondrite NWA 5697. We carry out long-term, two-dimensional simulations including gas, dust, and planets to characterize the transport of grains within the viscous $\alpha$-disk framework exploring the scenarios of a stand-alone Jupiter, Jupiter and Saturn \textit{in situ}, or Jupiter and Saturn in a 3:2 resonance. In each case, we find a critical grain size above which drift is halted as a function of the physical conditions in the disk. From the laboratory search we find four CAIs with a largest size of $\approx$200$\,\mu$m. \Combining models and data, we provide an estimate for the upper limit of the $\alpha$-viscosity and the surface density at the location of Jupiter, using reasonable assumptions about the stellar accretion rate during inward transport of CAIs, and assuming angular momentum transport to happen exclusively through viscous effects. Moreover, we find that the compound gap structure in the presence of Saturn in a 3:2 resonance favors inward transport of grains larger than CAIs currently detected in ordinary chondrites.Comment: 16 pages, 10 figures, updated to match published version in Astrophysical Journa

Planning strategies for inter-fractional robustness in pancreatic patients treated with scanned carbon therapy

Background: Managing inter-fractional anatomy changes is a challenging task in radiotherapy of pancreatic tumors, especially in scanned carbon-ion delivery. This treatment planning study aims to focus on clinically feasible solutions, such as the beam angle selection and margin design to increase the robustness against inter-fractional uncertainties. Methods: This study included 10 patients with weekly 3D-CT imaging and physician-approved Clinical Target Volume (CTV). The study was directed to keep the CTV-coverage using six beam angle configurations in combination with different Internal Target Volume (ITV) concepts. These were: geometric-margin (symmetric 3 and 5 mm margin); range-equivalent margins with an isotropic HU replacement; and to evaluate the need of asymmetric margins the water-equivalent range path (WEPL) was determined per patient from the set of CTs. Plan optimization and forward dose calculation in each week-CT were performed with the research treatment planning system TRiP98 and the plan quality evaluated in terms of CTV coverage (V95CTV) and homogeneity dose (HCTV = D5-D95). Results: The beam geometry had a substantial impact on the target irradiation over the treatment course, with the single posterior or two beams showing the best average coverage of the CTV. The use of geometric margins for the more robust beam geometries showed acceptable results, with a V95CTV of (99.2 ± 1.2)% for the 5 mm-margin. For the non-robust configurations, due to substantial changes in the radiological depth, the use of this margin results in a V95CTV that might be below 80%, only showing improvement when the range changes are included. Conclusions: Selection of adequate beam configurations and treatment margins in ion-beam therapy of pancreatic tumors is of great importance. For a single posterior beam or two beam configurations, application of geometrical margins compensate for dose degradation induced by inter-fractional anatomy changes for the majority of the analyzed treatment fractions

Improving species distribution models for invasive non‐native species with biologically informed pseudo‐absence selection

Aim: We present a novel strategy for species distribution models (SDMs) aimed at predicting the potential distributions of range‐expanding invasive non‐native species (INNS). The strategy combines two established perspectives on defining the background region for sampling “pseudo‐absences” that have hitherto only been applied separately. These are the accessible area, which accounts for dispersal constraints, and the area outside the environmental range of the species and therefore assumed to be unsuitable for the species. We tested an approach to combine these by fitting SDMs using background samples (pseudo‐absences) from both types of background. Location: Global. Taxon: Invasive non‐native plants: Humulus scandens, Lygodium japonicum, Lespedeza cuneata, Triadica sebifera, Cinnamomum camphora. Methods: Presence‐background (or presence‐only) SDMs were developed for the potential global distributions of five plant species native to Asia, invasive elsewhere and prioritised for risk assessment as emerging INNS in Europe. We compared models where the pseudo‐absences were selected from the accessible background, the unsuitable background (defined using biological knowledge of the species’ key limiting factors) or from both types of background. Results: Combining the unsuitable and accessible backgrounds expanded the range of environments available for model fitting and caused biological knowledge about ecological unsuitability to influence the fitted species‐environment relationships. This improved the realism and accuracy of distribution projections globally and, generally, within the species’ ranges. Main conclusions: Correlative SDMs remain valuable for INNS risk mapping and management, but are often criticised for a lack of biological underpinning. Our approach partly addresses this concern by using prior knowledge of species’ requirements or tolerances to define the unsuitable background for modelling, while also accommodating dispersal constraints through considerations of accessibility. It can be implemented with current SDM software and results in more accurate and realistic distribution projections. As such, wider adoption has potential to improve SDMs that support INNS risk assessment

The Disunity of Consciousness

It is commonplace for both philosophers and cognitive scientists to express their allegiance to the "unity of consciousness". This is the claim that a subject’s phenomenal consciousness, at any one moment in time, is a single thing. This view has had a major influence on computational theories of consciousness. In particular, what we call single-track theories dominate the literature, theories which contend that our conscious experience is the result of a single consciousness-making process or mechanism in the brain. We argue that the orthodox view is quite wrong: phenomenal experience is not a unity, in the sense of being a single thing at each instant. It is a multiplicity, an aggregate of phenomenal elements, each of which is the product of a distinct consciousness-making mechanism in the brain. Consequently, cognitive science is in need of a multi-track theory of consciousness; a computational model that acknowledges both the manifold nature of experience, and its distributed neural basis

Fossilized anuran soft tissues reveal a new taphonomic model for the Eocene Geiseltal Konservat-Lagerstätte, Germany

The Eocene Geiseltal Konservat-Lagerstätte (Germany) is famous for reports of three dimensionally preserved soft tissues with sub-cellular detail. The proposed mode of preservation, direct replication in silica, is not known in other fossils and has not been verified using modern approaches. Here, we investigated the taphonomy of the Geiseltal anurans using diverse microbeam imaging and chemical analytical techniques. Our analyses confirm the preservation of soft tissues in all body regions but fail to yield evidence for silicified soft tissues. Instead, the anuran soft tissues are preserved as two layers that differ in microstructure and composition. Layer 1 comprises sulfur-rich carbonaceous microbodies interpreted as melanosomes. Layer 2 comprises the mid-dermal Eberth-Katschenko layer, preserved in calcium phosphate. In addition, patches of original aragonite crystals define the former position of the endolymphatic sac. The primary modes of soft tissue preservation are therefore sulfurization of melanosomes and phosphatization of more labile soft tissues, i.e., skin. This is consistent with the taphonomy of vertebrates in many other Konservat-Lagerstätten. These findings emphasize an emerging model for pervasive preservation of vertebrate soft tissues via melanosome films, particularly in stagnation-type deposits, with phosphatization of more labile tissues where tissue biochemistry is favorable

A systematic review of management of inadvertent arterial injury during central venous catheterisation

© 2017 Wichtig Publishing. Introduction: Central venous catheterisation (CVC) is a technique commonly used to obtain vascular access and over five million CVCs are inserted annually. This systematic review of CVC-related arterial injury aims to compare outcomes reported with different management strategies. Methods: PRISMA guidelines were followed. A search of Medline, Embase, Central and CINAHL was performed. Results were limited to papers in humans and in English with duplicates removed. Details of cases including site and nature of arterial injury, use of ultrasound, methods for identifying arterial placement, management methods used, and any reported outcomes were collated from all papers. Successful management was defined as control of haemorrhage without evidence of further complications. results: We screened 2187 abstracts and 78 full manuscripts were obtained and reviewed. Twenty-four papers were of relevance and were included in this review. Amongst the papers, 80 cases of arterial injury were reported. Successful treatment by removal and compression, endovascular methods, and open surgical repair were 5.6%, 94.6% and 100%, respectively. Discussion: Removal and compression of the arterial site is a poor management method and is associated with a high rate of complications. Endovascular approaches had a high rate of success with advantages of endovascular techniques including access to arteries which are difficult to expose surgically and avoidance of general anaesthesia. Endovascular repair might be considered depending on site of injury or local expertise though surgical repair reported the best results in this review with no complications seen