Detection efficiency and photometry in supernova surveys - the Stockholm VIMOS Supernova Survey I

The aim of the work presented in this paper is to test and optimise supernova detection methods based on the optimal image subtraction technique. The main focus is on applying the detection methods to wide field supernova imaging surveys and in particular to the Stockholm VIMOS Supernova Survey (SVISS). We have constructed a supernova detection pipeline for imaging surveys. The core of the pipeline is image subtraction using the ISIS 2.2 package. Using real data from the SVISS we simulate supernovae in the images, both inside and outside galaxies. The detection pipeline is then run on the simulated frames and the effects of image quality and subtraction parameters on the detection efficiency and photometric accuracy are studied. The pipeline allows efficient detection of faint supernovae in the deep imaging data. It also allows controlling and correcting for possible systematic effects in the SN detection and photometry. We find such a systematic effect in the form of a small systematic flux offset remaining at the positions of galaxies in the subtracted frames. This offset will not only affect the photometric accuracy of the survey, but also the detection efficiencies. Our study has shown that ISIS 2.2 works well for the SVISS data. We have found that the detection efficiency and photometric accuracy of the survey are affected by the stamp selection for the image subtraction and by host galaxy brightness. With our tools the subtraction results can be further optimised, any systematic effects can be controlled and photometric errors estimated, which is very important for the SVISS, as well as for future SN searches based on large imaging surveys such as Pan-STARRS and LSST.Comment: 17 pages, 10 figure, accepted for publication in A&

Injection-site reactions upon Kineret (anakinra) administration: experiences and explanations

Anakinra (Kineret), a recombinant form of human interleukin-1 (IL-1) receptor antagonist, is approved for the treatment of rheumatoid arthritis (RA) in combination with methotrexate. Kineret is self-administered by daily subcutaneous injections in patients with active RA. The mechanism of action of anakinra is to competitively inhibit the local inflammatory effects of IL-1. Kineret is generally safe and well tolerated and the only major treatment-related side effects that appear are skin reactions at the injection site. Due to the relatively short half-life of anakinra, daily injection of the drug is required. This, in combination with the comparably high rates of injection-site reactions (ISRs) associated with the drug, can become a problem for the patient. The present review summarises published data concerning ISRs associated with Kineret and provides some explanations as to their cause. The objective is also to present some clinical experiences of how the ISRs can be managed

Methods for biogeochemical studies of sea ice: The state of the art, caveats, and recommendations

AbstractOver the past two decades, with recognition that the ocean’s sea-ice cover is neither insensitive to climate change nor a barrier to light and matter, research in sea-ice biogeochemistry has accelerated significantly, bringing together a multi-disciplinary community from a variety of fields. This disciplinary diversity has contributed a wide range of methodological techniques and approaches to sea-ice studies, complicating comparisons of the results and the development of conceptual and numerical models to describe the important biogeochemical processes occurring in sea ice. Almost all chemical elements, compounds, and biogeochemical processes relevant to Earth system science are measured in sea ice, with published methods available for determining biomass, pigments, net community production, primary production, bacterial activity, macronutrients, numerous natural and anthropogenic organic compounds, trace elements, reactive and inert gases, sulfur species, the carbon dioxide system parameters, stable isotopes, and water-ice-atmosphere fluxes of gases, liquids, and solids. For most of these measurements, multiple sampling and processing techniques are available, but to date there has been little intercomparison or intercalibration between methods. In addition, researchers collect different types of ancillary data and document their samples differently, further confounding comparisons between studies. These problems are compounded by the heterogeneity of sea ice, in which even adjacent cores can have dramatically different biogeochemical compositions. We recommend that, in future investigations, researchers design their programs based on nested sampling patterns, collect a core suite of ancillary measurements, and employ a standard approach for sample identification and documentation. In addition, intercalibration exercises are most critically needed for measurements of biomass, primary production, nutrients, dissolved and particulate organic matter (including exopolymers), the CO2 system, air-ice gas fluxes, and aerosol production. We also encourage the development of in situ probes robust enough for long-term deployment in sea ice, particularly for biological parameters, the CO2 system, and other gases.This manuscript is a product of SCOR working group 140 on Biogeochemical Exchange Processes at Sea-Ice Interfaces (BEPSII); we thank BEPSII chairs Jacqueline Stefels and Nadja Steiner and SCOR executive director Ed Urban for their practical and moral support of this endeavour. This manuscript was first conceived at an EU COST Action 735 workshop held in Amsterdam in April 2011; in addition to COST 735, we thank the other participants of the “methods” break-out group at that meeting, namely Gerhard Dieckmann, Christoph Garbe, and Claire Hughes. Our editors, Steve Ackley and Jody Deming, and our reviewers, Mats Granskog and two anonymous reviewers, provided invaluable advice that not only identified and helped fill in some gaps, but also suggested additional ways to make what is by nature a rather dry subject (methods) at least a bit more interesting and accessible. We also thank the librarians at the Institute of Ocean Sciences for their unflagging efforts to track down the more obscure references we required. Finally, and most importantly, we thank everyone who has braved the unknown and made the new measurements that have helped build sea-ice biogeochemistry into the robust and exciting field it has become.This is the final published article, originally published in Elementa: Science of the Anthropocene, 3: 000038, doi: 10.12952/journal.elementa.00003

Causal hierarchy within the thalamo-cortical network in spike and wave discharges

Background: Generalised spike wave (GSW) discharges are the electroencephalographic (EEG) hallmark of absence seizures, clinically characterised by a transitory interruption of ongoing activities and impaired consciousness, occurring during states of reduced awareness. Several theories have been proposed to explain the pathophysiology of GSW discharges and the role of thalamus and cortex as generators. In this work we extend the existing theories by hypothesizing a role for the precuneus, a brain region neglected in previous works on GSW generation but already known to be linked to consciousness and awareness. We analysed fMRI data using dynamic causal modelling (DCM) to investigate the effective connectivity between precuneus, thalamus and prefrontal cortex in patients with GSW discharges. Methodology and Principal Findings: We analysed fMRI data from seven patients affected by Idiopathic Generalized Epilepsy (IGE) with frequent GSW discharges and significant GSW-correlated haemodynamic signal changes in the thalamus, the prefrontal cortex and the precuneus. Using DCM we assessed their effective connectivity, i.e. which region drives another region. Three dynamic causal models were constructed: GSW was modelled as autonomous input to the thalamus (model A), ventromedial prefrontal cortex (model B), and precuneus (model C). Bayesian model comparison revealed Model C (GSW as autonomous input to precuneus), to be the best in 5 patients while model A prevailed in two cases. At the group level model C dominated and at the population-level the p value of model C was ∼1. Conclusion: Our results provide strong evidence that activity in the precuneus gates GSW discharges in the thalamo-(fronto) cortical network. This study is the first demonstration of a causal link between haemodynamic changes in the precuneus - an index of awareness - and the occurrence of pathological discharges in epilepsy. © 2009 Vaudano et al

Periodate-treated, non-anticoagulant heparin-carrying polystyrene (NAC-HCPS) affects angiogenesis and inhibits subcutaneous induced tumour growth and metastasis to the lung

Periodate-treated, non-anticoagulant heparin-carrying polystyrene consists of about ten periodate-oxidized, alkaline-degraded low molecular weight-heparin chains linked to a polystyrene core and has a markedly lower anti-coagulant activity than heparin. In this study, we evaluated the effect of non-anticoagulant heparin-carrying polystyrene on tumour growth and metastasis. Non-anticoagulant heparin-carrying polystyrene has a higher activity to inhibit vascular endothelial growth factor-165-, fibroblast growth factor-2- or hepatocyte growth factor-induced human microvascular endothelial cell growth than heparin, ten periodate-oxidized-heparin and ten periodate-oxidized-low molecular weight-heparin, which is probably due to the heparin-clustering effect of non-anticoagulant heparin-carrying polystyrene. Non-anticoagulant heparin-carrying polystyrene inhibited human microvascular endothelial cell, B16 melanoma and Lewis lung cancer cell adhesion to Matrigel-coated plates. Non-anticoagulant heparin-carrying polystyrene also showed strong inhibitory activities in the tubular formation of endothelial cells on Matrigel and B16-melanoma and Lewis lung cancer cell invasion in a Matrigel-coated chamber assay. In vivo studies showed that growth of subcutaneous induced tumours and lung metastasis of B16-melanoma and Lewis lung cancer cells were more effectively inhibited by non-anticoagulant heparin-carrying polystyrene than ten periodate-oxidized-heparin and ten periodate-oxidized-low molecular weight-heparin. Furthermore, non-anticoagulant heparin-carrying polystyrene markedly reduced the number of CD34-positive vessels in subcutaneous Lewis lung cancer tumours, indicating a strong inhibition of angiogenesis. These results suggest that non-anticoagulant heparin-carrying polystyrene has an inhibitory activity on angiogenesis and tumour invasion and may be very useful in cancer therapy

Spectroscopy of the Type Ia supernova 2011fe past 1000d

In this Letter we present an optical spectrum of SN 2011fe taken 1034 d after the explosion, several hundred days later than any other spectrum of a Type Ia supernova (disregarding light-echo spectra and Local Group remnants). The spectrum is still dominated by broad emission features, with no trace of a light echo or interaction of the supernova ejecta with surrounding interstellar material. Comparing this extremely late spectrum to an earlier one taken 331 d after the explosion, we find that the most prominent feature at 331 d - [Fe III] emission around 4700 Å - has entirely faded away, suggesting a significant change in the ionization state. Instead, [Fe II] lines are probably responsible for most of the emission at 1034 d. An emission feature at 6300-6400 Å has newly developed at 1034 d, which we tentatively identify with Fe I λ6359, [Fe I] λλ6231, 6394 or [O I] λλ6300, 6364. Interestingly, the features in the 1034 d spectrum seem to be collectively redshifted, a phenomenon that we currently have no convincing explanation for. We discuss the implications of our findings for explosion models, but conclude that sophisticated spectral modelling is required for any firm statement

Dominant Mutations in GRHL3 Cause Van der Woude Syndrome and Disrupt Oral Periderm Development

Peer reviewe

The discovery and classification of 16 supernovae at high redshifts in ELAIS-S1 - the Stockholm VIMOS Supernova Survey II

Supernova surveys can be used to study a variety of subjects such as: (i) cosmology through type Ia supernovae (SNe), (ii) star-formation rates through core-collapse SNe, and (iii) supernova properties and their connection to host galaxy characteristics. The Stockholm VIMOS Supernova Survey (SVISS) is a multi-band imaging survey aiming to detect supernovae at redshift ~0.5 and derive thermonuclear and core-collapse supernova rates at high redshift. In this paper we present the supernovae discovered in the survey along with light curves and a photometric classification into thermonuclear and core-collapse types. To detect the supernovae in the VLT/VIMOS multi-epoch images, we used difference imaging and a combination of automatic and manual source detection to minimise the number of spurious detections. Photometry for the found variable sources was obtained and careful simulations were made to estimate correct errors. The light curves were typed using a Bayesian probability method and Monte Carlo simulations were used to study misclassification. We detected 16 supernovae, nine of which had a core-collapse origin and seven had a thermonuclear origin. The estimated misclassification errors are quite small, in the order of 5%, but vary with both redshift and type. The mean redshift of the supernovae is 0.58. Additionally, we found a variable source with a very extended light curve that could possibly be a pair instability supernova.Comment: 30 pages, 15 figures, Accepted for publication in A&A. Version with high resolution images available at: http://www.astro.su.se/~jens/sviss_sne.pd