Moment based estimation of stochastic Kronecker graph parameters

Stochastic Kronecker graphs supply a parsimonious model for large sparse real world graphs. They can specify the distribution of a large random graph using only three or four parameters. Those parameters have however proved difficult to choose in specific applications. This article looks at method of moments estimators that are computationally much simpler than maximum likelihood. The estimators are fast and in our examples, they typically yield Kronecker parameters with expected feature counts closer to a given graph than we get from KronFit. The improvement was especially prominent for the number of triangles in the graph.Comment: 22 pages, 4 figure

Theory, simulation and experimental results of the acoustic detection of magnetization changes in superparamagnetic iron oxide

<p>Abstract</p> <p>Background</p> <p>Magnetic Particle Imaging is a novel method for medical imaging. It can be used to measure the local concentration of a tracer material based on iron oxide nanoparticles. While the resulting images show the distribution of the tracer material in phantoms or anatomic structures of subjects under examination, no information about the tissue is being acquired. To expand Magnetic Particle Imaging into the detection of soft tissue properties, a new method is proposed, which detects acoustic emissions caused by magnetization changes in superparamagnetic iron oxide.</p> <p>Methods</p> <p>Starting from an introduction to the theory of acoustically detected Magnetic Particle Imaging, a comparison to magnetically detected Magnetic Particle Imaging is presented. Furthermore, an experimental setup for the detection of acoustic emissions is described, which consists of the necessary field generating components, i.e. coils and permanent magnets, as well as a calibrated microphone to perform the detection.</p> <p>Results</p> <p>The estimated detection limit of acoustic Magnetic Particle Imaging is comparable to the detection limit of magnetic resonance imaging for iron oxide nanoparticles, whereas both are inferior to the theoretical detection limit for magnetically detected Magnetic Particle Imaging. Sufficient data was acquired to perform a comparison to the simulated data. The experimental results are in agreement with the simulations. The remaining differences can be well explained.</p> <p>Conclusions</p> <p>It was possible to demonstrate the detection of acoustic emissions of magnetic tracer materials in Magnetic Particle Imaging. The processing of acoustic emission in addition to the tracer distribution acquired by magnetic detection might allow for the extraction of mechanical tissue parameters. Such parameters, like for example the velocity of sound and the attenuation caused by the tissue, might also be used to support and improve ultrasound imaging. However, the method can also be used to perform imaging on its own.</p

Ontology-Based Support for Security Requirements Specification Process

The security requirements specification (SRS) is an integral aspect of the development of secured information systems and entails the formal documentation of the security needs of a system in a correct and consistent way. However, in many cases there is lack of sufficiently experienced security experts or security requirements (SR) engineer within an organization, which limits the quality of SR that are specified. This paper presents an approach that leverages ontologies and requirements boilerplates in order to alleviate the effect of lack of highly experienced personnel for SRS. It also offers a credible starting point for the SRS process. A preliminary evaluation of the tool prototype – ReqSec tool - was used to demonstrate the approach and to confirm its usability to support the SRS process. The tool helps to reduce the amount of effort required, stimulate discovery of latent security threats, and enables the specification of good quality SR

Functional characterisation of the mammalian NDR1 and NDR2 protein kinases and their regulation by the mammalian Ste20-like kinase MST3

Protein modification is a common regulatory mechanism in order to transduce a signal from one molecule to another. One of the best-studied protein modifications is phosphorylation. The enzymes that are capable of transferring phosphate groups onto other proteins are called protein kinases. Depending on the acceptor group, kinases can be distinguished into tyrosine, serine/threonine and dual-specificity kinases. This work describes the characterisation of human and mouse NDR1 and NDR2 kinases, members of the AGC group of serine/threonine kinases. The NDR protein kinase family is highly conserved between yeast and human, and several members have been shown to be involved in the regulation of cell morphology and the control of cell cycle progression. For example, the yeast NDR kinases Sid2p (Schizosaccharomyces pombe) and Dbf2p (Saccharomyces cerevisiae) are central components of the septation-initiation network and the mitosis exit network, respectively. The closest yeast relatives Cbk1p and Orb6p, members of the regulation of Ace2p transcription and morphogenesis network and Orb6 signalling pathways, are implicated in the coordination of cell cycle progression and cell morphology. This study, as well as studies using worms and flies, provide evidence that not only NDR is conserved, but also the NDR signalling pathway and regulation. Similar to yeast, NDR kinase activation is regulated by phosphorylation at the activation segment phosphorylation site and the hydrophobic motif phosphorylation site. This phosphorylation is regulated by a conserved signaling module consisting of MOB proteins and a STE20–like kinase. Here we show that the STE20-like kinase MST3 activates NDR by phosphorylation specifically at the hydrophobic motif in vitro and in vivo. Furthermore, MOB1A binding is important for the release of autoinhibition and full kinase activation. The data also indicate that NDR is part of a feedback mechanism, which induces cleavage and nuclear translocation of MST3. The data presented here also show that NDR1 and NDR2 are differentially expressed, but regulated in a similar manner. Mouse Ndr1 mRNA is mainly expressed in spleen, thymus and lung, whereas Ndr2 mRNA is more ubiquitously expressed, with the highest levels in the gastrointestinal tract. Both, NDR1 and NDR2, are activated by S100B protein and okadaic acid stimulated phosphorylation; NDR1 and NDR2 are also indistinguishable in the biochemical assays used: membrane targetting, phosphorylation by MST3, and activation by MOB. Further, this work describes the generation and initial characterisation of a mouse model for NDR1 deficiency. Protein analysis using NDR1 knockout mouse embryonic fibroblasts suggest a compensation of the loss of NDR1 by upregulation of NDR2 expression

Treatment of Patients with the Hypereosinophilic Syndrome with Mepolizumab

BACKGROUND The hypereosinophilic syndrome is a group of diseases characterized by persistent blood eosinophilia, defined as more than 1500 cells per microliter with end-organ involvement and no recognized secondary cause. Although most patients have a response to corticosteroids, side effects are common and can lead to considerable morbidity. METHODS We conducted an international, randomized, double-blind, placebo-controlled trial evaluating the safety and efficacy of an anti–interleukin-5 monoclonal antibody, mepolizumab, in patients with the hypereosinophilic syndrome. Patients were negative for the FIP1L1–PDGFRA fusion gene and required prednisone monotherapy, 20 to 60 mg per day, to maintain a stable clinical status and a blood eosinophil count of less than 1000 per microliter. Patients received either intravenous mepolizumab or placebo while the prednisone dose was tapered. The primary end point was the reduction of the prednisone dose to 10 mg or less per day for 8 or more consecutive weeks. RESULTS The primary end point was reached in 84% of patients in the mepolizumab group, as compared with 43% of patients in the placebo group (hazard ratio, 2.90; 95% confidence interval [CI], 1.59 to 5.26; P CONCLUSIONS Our study shows that treatment with mepolizumab, an agent designed to target eosinophils, can result in corticosteroid-sparing for patients negative for FIP1L1– PDGFRA who have the hypereosinophilic syndrome. (ClinicalTrials.gov number, NCT00086658.