Jamming in complex networks with degree correlation

We study the effects of the degree-degree correlations on the pressure congestion J when we apply a dynamical process on scale free complex networks using the gradient network approach. We find that the pressure congestion for disassortative (assortative) networks is lower (bigger) than the one for uncorrelated networks which allow us to affirm that disassortative networks enhance transport through them. This result agree with the fact that many real world transportation networks naturally evolve to this kind of correlation. We explain our results showing that for the disassortative case the clusters in the gradient network turn out to be as much elongated as possible, reducing the pressure congestion J and observing the opposite behavior for the assortative case. Finally we apply our model to real world networks, and the results agree with our theoretical model

Long-term monitoring of the TeV emission from Mrk 421 with the ARGO-YBJ experiment

ARGO-YBJ is an air shower detector array with a fully covered layer of resistive plate chambers. It is operated with a high duty cycle and a large field of view. It continuously monitors the northern sky at energies above 0.3 TeV. In this paper, we report a long-term monitoring of Mrk 421 over the period from 2007 November to 2010 February. This source was observed by the satellite-borne experiments Rossi X-ray Timing Explorer and Swift in the X-ray band. Mrk 421 was especially active in the first half of 2008. Many flares are observed in both X-ray and gamma-ray bands simultaneously. The gamma-ray flux observed by ARGO-YBJ has a clear correlation with the X-ray flux. No lag between the X-ray and gamma-ray photons longer than 1 day is found. The evolution of the spectral energy distribution is investigated by measuring spectral indices at four different flux levels. Hardening of the spectra is observed in both X-ray and gamma-ray bands. The gamma-ray flux increases quadratically with the simultaneously measured X-ray flux. All these observational results strongly favor the synchrotron self-Compton process as the underlying radiative mechanism.Comment: 30 pages, 8 figure

InaudibleKey: Generic Inaudible Acoustic Signal based Key Agreement Protocol for Mobile Devices

Secure Device-to-Device (D2D) communication is becoming increasingly important with the ever-growing number of Internetof-Things (IoT) devices in our daily life. To achieve secure D2D communication, the key agreement between different IoT devices without any prior knowledge is becoming desirable. Although various approaches have been proposed in the literature, they suffer from a number of limitations, such as low key generation rate and short pairing distance. In this paper, we present InaudibleKey, an inaudible acoustic signal based key generation protocol for mobile devices. Based on acoustic channel reciprocity, InaudibleKey exploits the acoustic channel frequency response of two legitimate devices as a common secret to generating keys. InaudibleKey employs several novel technologies to significantly improve its performance. We conduct extensive experiments to evaluate the proposed system in different real environments. Compared to state-of-the-art works, InaudibleKey improves key generation rate by 3-145 times, extends pairing distance by 3.2-44 times, and reduces information reconciliation counts by 2.5 16 times. Security analysis demonstrates that InaudibleKey is resilient to a number of malicious attacks. We also implement InaudibleKey on modern smartphones and resourcelimited IoT devices. Results show that it is energy- efficient and can run on both powerful and resource-limited IoT devices without incurring excessive resource consumption

Measurement of finite-frequency current statistics in a single-electron transistor

Electron transport in nano-scale structures is strongly influenced by the Coulomb interaction which gives rise to correlations in the stream of charges and leaves clear fingerprints in the fluctuations of the electrical current. A complete understanding of the underlying physical processes requires measurements of the electrical fluctuations on all time and frequency scales, but experiments have so far been restricted to fixed frequency ranges as broadband detection of current fluctuations is an inherently difficult experimental procedure. Here we demonstrate that the electrical fluctuations in a single electron transistor (SET) can be accurately measured on all relevant frequencies using a nearby quantum point contact for on-chip real-time detection of the current pulses in the SET. We have directly measured the frequency-dependent current statistics and hereby fully characterized the fundamental tunneling processes in the SET. Our experiment paves the way for future investigations of interaction and coherence induced correlation effects in quantum transport.Comment: 7 pages, 3 figures, published in Nature Communications (open access

Search for Gamma Ray Bursts with the Argo-YBJ Detector in Scaler Mode

We report on the search for Gamma Ray Bursts (GRBs) in the energy range 1-100 GeV in coincidence with the prompt emission detected by satellites using the Astrophysical Radiation with Ground-based Observatory at YangBaJing (ARGO-YBJ) air shower detector. Thanks to its mountain location (Yangbajing, Tibet, P.R. China, 4300 m a.s.l.), active surface (about 6700 m**2 of Resistive Plate Chambers), and large field of view (about 2 sr, limited only by the atmospheric absorption), the ARGO-YBJ air shower detector is particularly suitable for the detection of unpredictable and short duration events such as GRBs. The search is carried out using the "single particle technique", i.e. counting all the particles hitting the detector without measurement of the energy and arrival direction of the primary gamma rays. Between 2004 December 17 and 2009 April 7, 81 GRBs detected by satellites occurred within the field of view of ARGO-YBJ (zenith angle < 45 deg). It was possible to examine 62 of these for >1 GeV counterpart in the ARGO-YBJ data finding no statistically significant emission. With a lack of detected spectra in this energy range fluence upper limits are profitable, especially when the redshift is known and the correction for the extragalactic absorption can be considered. The obtained fluence upper limits reach values as low as 10**{-5} erg cm**{-2} in the 1-100 GeV energy region. Besides this individual search for a higher energy counterpart, a statistical study of the stack of all the GRBs both in time and in phase was made, looking for a common feature in the GRB high energy emission. No significant signal has been detected.Comment: accepted for publication in Ap

Fitting the Gamma-Ray Spectrum from Dark Matter with DMFIT: GLAST and the Galactic Center Region

We study the potential of GLAST to unveil particle dark matter properties with gamma-ray observations of the Galactic center region. We present full GLAST simulations including all gamma-ray sources known to date in a region of 4 degrees around the Galactic center, in addition to the diffuse gamma-ray background and to the dark matter signal. We introduce DMFIT, a tool that allows one to fit gamma-ray emission from pair-annihilation of generic particle dark matter models and to extract information on the mass, normalization and annihilation branching ratios into Standard Model final states. We assess the impact and systematic effects of background modeling and theoretical priors on the reconstruction of dark matter particle properties. Our detailed simulations demonstrate that for some well motivated supersymmetric dark matter setups with one year of GLAST data it will be possible not only to significantly detect a dark matter signal over background, but also to estimate the dark matter mass and its dominant pair-annihilation mode.Comment: 37 pages, 16 figures, submitted to JCA

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles

<p>Abstract</p> <p>Background</p> <p>Post-translational modifications have a substantial influence on the structure and functions of protein. Post-translational phosphorylation is one of the most common modification that occur in intracellular proteins. Accurate prediction of protein phosphorylation sites is of great importance for the understanding of diverse cellular signalling processes in both the human body and in animals. In this study, we propose a new machine learning based protein phosphorylation site predictor, SiteSeek. SiteSeek is trained using a novel compact evolutionary and hydrophobicity profile to detect possible protein phosphorylation sites for a target sequence. The newly proposed method proves to be more accurate and exhibits a much stable predictive performance than currently existing phosphorylation site predictors.</p> <p>Results</p> <p>The performance of the proposed model was compared to nine existing different machine learning models and four widely known phosphorylation site predictors with the newly proposed PS-Benchmark_1 dataset to contrast their accuracy, sensitivity, specificity and correlation coefficient. SiteSeek showed better predictive performance with 86.6% accuracy, 83.8% sensitivity, 92.5% specificity and 0.77 correlation-coefficient on the four main kinase families (CDK, CK2, PKA, and PKC).</p> <p>Conclusion</p> <p>Our newly proposed methods used in SiteSeek were shown to be useful for the identification of protein phosphorylation sites as it performed much better than widely known predictors on the newly built PS-Benchmark_1 dataset.</p

Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data

Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein∶protein interactions might yield useful insights into the cellular responses. The large-scale protein interaction data sets are, however, unable to capture the changes in the profile of protein∶protein interactions. In order to understand how these interactions change dynamically, we have constructed conditional protein linkages for Escherichia coli by integrating functional linkages and gene expression information. As a case study, we have chosen to analyze UV exposure in wild-type and SOS deficient E. coli at 20 minutes post irradiation. The conditional networks exhibit similar topological properties. Although the global topological properties of the networks are similar, many subtle local changes are observed, which are suggestive of the cellular response to the perturbations. Some such changes correspond to differences in the path lengths among the nodes of carbohydrate metabolism correlating with its loss in efficiency in the UV treated cells. Similarly, expression of hubs under unique conditions reflects the importance of these genes. Various centrality measures applied to the networks indicate increased importance for replication, repair, and other stress proteins for the cells under UV treatment, as anticipated. We thus propose a novel approach for studying an organism at the systems level by integrating genome-wide functional linkages and the gene expression data

An EMT-Driven Alternative Splicing Program Occurs in Human Breast Cancer and Modulates Cellular Phenotype

Epithelial-mesenchymal transition (EMT), a mechanism important for embryonic development, plays a critical role during malignant transformation. While much is known about transcriptional regulation of EMT, alternative splicing of several genes has also been correlated with EMT progression, but the extent of splicing changes and their contributions to the morphological conversion accompanying EMT have not been investigated comprehensively. Using an established cell culture model and RNA–Seq analyses, we determined an alternative splicing signature for EMT. Genes encoding key drivers of EMT–dependent changes in cell phenotype, such as actin cytoskeleton remodeling, regulation of cell–cell junction formation, and regulation of cell migration, were enriched among EMT–associated alternatively splicing events. Our analysis suggested that most EMT–associated alternative splicing events are regulated by one or more members of the RBFOX, MBNL, CELF, hnRNP, or ESRP classes of splicing factors. The EMT alternative splicing signature was confirmed in human breast cancer cell lines, which could be classified into basal and luminal subtypes based exclusively on their EMT–associated splicing pattern. Expression of EMT–associated alternative mRNA transcripts was also observed in primary breast cancer samples, indicating that EMT–dependent splicing changes occur commonly in human tumors. The functional significance of EMT–associated alternative splicing was tested by expression of the epithelial-specific splicing factor ESRP1 or by depletion of RBFOX2 in mesenchymal cells, both of which elicited significant changes in cell morphology and motility towards an epithelial phenotype, suggesting that splicing regulation alone can drive critical aspects of EMT–associated phenotypic changes. The molecular description obtained here may aid in the development of new diagnostic and prognostic markers for analysis of breast cancer progression.National Institutes of Health (U.S.) (R01-HG002439)National Science Foundation (U.S.) (equipment grant)National Institutes of Health (U.S.) (Integrative Cancer Biology Program Grant U54-CA112967)David H. Koch Institute for Integrative Cancer Research at MIT (Ludwig Center for Metastasis Research)David H. Koch Institute for Integrative Cancer Research at MITMassachusetts Institute of Technology (Croucher Scholarship)Massachusetts Institute of Technology (Ludwig Fund postdoctoral fellowship)National Institutes of Health (U.S.) (NIH CA100324)National Institutes of Health (U.S.) (AECC9526-5267