Interpretation of UV Absorption Lines in SN1006

We present a theoretical interpretation of the broad silicon and iron UV absorption features observed with the Hubble Space Telescope in the spectrum of the Schweizer-Middleditch star behind the remnant of Supernova 1006. These features are caused by supernova ejecta in SN1006. We propose that the redshifted SiII2 1260 A feature consists of both unshocked and shocked SiII. The sharp red edge of the line at 7070 km/s indicates the position of the reverse shock, while its Gaussian blue edge reveals shocked Si with a mean velocity of 5050 km/s and a dispersion of 1240 km/s, implying a reverse shock velocity of 2860 km/s. The measured velocities satisfy the energy jump condition for a strong shock, provided that all the shock energy goes into ions, with little or no collisionless heating of electrons. The line profiles of the SiIII and SiIV absorption features indicate that they arise mostly from shocked Si. The total mass of shocked and unshocked Si inferred from the SiII, SiIII and SiIV profiles is M_Si = 0.25 \pm 0.01 Msun on the assumption of spherical symmetry. Unshocked Si extends upwards from 5600 km/s. Although there appears to be some Fe mixed with the Si at lower velocities < 7070 km/s, the absence of FeII absorption with the same profile as the shocked SiII suggests little Fe mixed with Si at higher (before being shocked) velocities. The column density of shocked SiII is close to that expected for SiII undergoing steady state collisional ionization behind the reverse shock, provided that the electron to SiII ratio is low, from which we infer that most of the shocked Si is likely to be of a fairly high degree of purity, unmixed with other elements. We propose that the ambient interstellar density on the far side of SN1006 is anomalously low compared to the density around the rest of the remnant. ThisComment: 24 pages, with 8 figures included. Accepted for publication in the Astrophysical Journa

Comparison of reproducibility, accuracy, sensitivity, and specificity of miRNA quantification platforms

Given the increasing interest in their use as disease biomarkers, the establishment of reproducible, accurate, sensitive, and specific platforms for microRNA (miRNA) quantification in biofluids is of high priority. We compare four platforms for these characteristics: small RNA sequencing (RNA-seq), FirePlex, EdgeSeq, and nCounter. For a pool of synthetic miRNAs, coefficients of variation for technical replicates are lower for EdgeSeq (6.9%) and RNA-seq (8.2%) than for FirePlex (22.4%); nCounter replicates are not performed. Receiver operating characteristic analysis for distinguishing present versus absent miRNAs shows small RNA-seq (area under curve 0.99) is superior to EdgeSeq (0.97), nCounter (0.94), and FirePlex (0.81). Expected differences in expression of placenta-associated miRNAs in plasma from pregnant and non-pregnant women are observed with RNA-seq and EdgeSeq, but not FirePlex or nCounter. These results indicate that differences in performance among miRNA profiling platforms impact ability to detect biological differences among samples and thus their relative utility for research and clinical use

TRANSMIT: Training Research and Applications Network to Support the Mitigation of Ionospheric Threats

TRANSMIT is an initiative funded by the European Commission through a Marie Curie Initial Training Network (ITN). Main aim of such networks is to improve the career perspectives of researchers who are in the first five years of their research career in both public and private sectors. In particular TRANSMIT will provide a coordinated program of academic and industrial training, focused on atmospheric phenomena that can significantly impair a wide range of systems and applications that are at the core of several activities embedded in our daily life. TRANSMIT deals with the harmful effects of the ionosphere on these systems, which will become increasingly significant as we approach the next solar maximum, predicted for 2013. Main aim of the project is to develop real time integrated state of the art tools to mitigate ionospheric threats to Global Navigation Satellite Systems (GNSS) and several related applications, such as civil aviation, marine navigation and land transportation. The project will provide Europe with the next generation of researchers in this field, equipping them with skills developed through a comprehensive and coordinated training program. Theirs research projects will develop real time integrated state of the art tools to mitigate these ionospheric threats to GNSS and several applications that rely on these systems. The main threat to the reliable and safe operation of GNSS is the variable propagation conditions encountered by GNSS signals as they pass through the ionosphere. At a COST 296 MIERS (Mitigation of Ionospheric Effects on Radio Systems) workshop held at the University of Nottingham in 2008, the establishment of a sophisticated Ionospheric Perturbation Detection and Monitoring (IPDM) network (http://ipdm.nottingham.ac.uk/) was proposed by European experts and supported by the European Space Agency (ESA) as the way forward to deliver the state of the art to protect the range of essential systems vulnerable to these ionospheric threats. Through a set of carefully designed research work packages TRANSMIT will be the enabler of the IPDM network. The goal of TRANSMIT is therefore to provide a concerted training programme including taught courses, research training projects, secondments at the leading European institutions, and a set of network wide events, with summer schools, workshops and a conference, which will arm the researchers of tomorrow with the necessary skills and knowledge to set up and run the proposed service. TRANSMIT will count on an exceptional set of partners, encompassing both academia and end users, including the aerospace and satellite communications sectors, as well as GNSS system designers and service providers, major user operators and receiver manufacturers. TRANSMIT's objectives are: A. Develop new techniques to detect and monitor ionospheric threats, with the introduction of new prediction and forecasting models, mitigation tools and improved system design; B. Advance the physical modeling of the underlying processes associated with the ionospheric plasma environment and the knowledge of its influences on human activity; C. Establish a prototype of a real time system to monitor the ionosphere, capable of providing useful assistance to users, which exploits all available resources and adds value for European services and products; D. Incorporate solutions to this system that respond to all end user needs and that are applicable in all geographical regions of European interest (polar, high and mid-latitudes, equatorial region). TRANSMIT will pave the way to establish in Europe a system capable of mitigating ionospheric threats on GNSS signals in real tim

Bubbles and denaturation in DNA

The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without the unwinding of the DNA double helix. Although these biological processes are driven by proteins, there might well be a relation between these biological openings and the spontaneous bubble formation due to thermal fluctuations. Mesoscopic models, like the Peyrard-Bishop-Dauxois model, have fairly accurately reproduced some experimental denaturation curves and the sharp phase transition in the thermodynamic limit. It is, hence, tempting to see whether these models could be used to predict the biological activity of DNA. In a previous study, we introduced a method that allows to obtain very accurate results on this subject, which showed that some previous claims in this direction, based on molecular dynamics studies, were premature. This could either imply that the present PBD should be improved or that biological activity can only be predicted in a more complex frame work that involves interactions with proteins and super helical stresses. In this article, we give detailed description of the statistical method introduced before. Moreover, for several DNA sequences, we give a thorough analysis of the bubble-statistics as function of position and bubble size and the so-called $l$-denaturation curves that can be measured experimentally. These show that some important experimental observations are missing in the present model. We discuss how the present model could be improved.Comment: 15 pages, 5 figures, published as Eur. Phys. J. E 20 : 421-434 AUG 200

Urinary MicroRNA Profiling in the Nephropathy of Type 1 Diabetes

Background: Patients with Type 1 Diabetes (T1D) are particularly vulnerable to development of Diabetic nephropathy (DN) leading to End Stage Renal Disease. Hence a better understanding of the factors affecting kidney disease progression in T1D is urgently needed. In recent years microRNAs have emerged as important post-transcriptional regulators of gene expression in many different health conditions. We hypothesized that urinary microRNA profile of patients will differ in the different stages of diabetic renal disease. Methods and Findings: We studied urine microRNA profiles with qPCR in 40 T1D with >20 year follow up 10 who never developed renal disease (N) matched against 10 patients who went on to develop overt nephropathy (DN), 10 patients with intermittent microalbuminuria (IMA) matched against 10 patients with persistent (PMA) microalbuminuria. A Bayesian procedure was used to normalize and convert raw signals to expression ratios. We applied formal statistical techniques to translate fold changes to profiles of microRNA targets which were then used to make inferences about biological pathways in the Gene Ontology and REACTOME structured vocabularies. A total of 27 microRNAs were found to be present at significantly different levels in different stages of untreated nephropathy. These microRNAs mapped to overlapping pathways pertaining to growth factor signaling and renal fibrosis known to be targeted in diabetic kidney disease. Conclusions: Urinary microRNA profiles differ across the different stages of diabetic nephropathy. Previous work using experimental, clinical chemistry or biopsy samples has demonstrated differential expression of many of these microRNAs in a variety of chronic renal conditions and diabetes. Combining expression ratios of microRNAs with formal inferences about their predicted mRNA targets and associated biological pathways may yield useful markers for early diagnosis and risk stratification of DN in T1D by inferring the alteration of renal molecular processes. © 2013 Argyropoulos et al