Hypersparse Neural Network Analysis of Large-Scale Internet Traffic

The Internet is transforming our society, necessitating a quantitative understanding of Internet traffic. Our team collects and curates the largest publicly available Internet traffic data containing 50 billion packets. Utilizing a novel hypersparse neural network analysis of "video" streams of this traffic using 10,000 processors in the MIT SuperCloud reveals a new phenomena: the importance of otherwise unseen leaf nodes and isolated links in Internet traffic. Our neural network approach further shows that a two-parameter modified Zipf-Mandelbrot distribution accurately describes a wide variety of source/destination statistics on moving sample windows ranging from 100,000 to 100,000,000 packets over collections that span years and continents. The inferred model parameters distinguish different network streams and the model leaf parameter strongly correlates with the fraction of the traffic in different underlying network topologies. The hypersparse neural network pipeline is highly adaptable and different network statistics and training models can be incorporated with simple changes to the image filter functions.Comment: 11 pages, 10 figures, 3 tables, 60 citations; to appear in IEEE High Performance Extreme Computing (HPEC) 201

Two-dimensional mapping of triaxial strain fields in a multiferroic BiFeO3 thin film using scanning x-ray microdiffraction

The dramatically enhanced polarizations and saturation magnetizations observed in the epitaxially constrained BiFeO3 (BFO) thin films with their pronounced grain-orientation dependence have attracted much attention and are attributed largely to the constrained in-plane strain. Thus, it is highly desirable to directly obtain information on the two-dimensional (2D) distribution of the in-plane strain and its correlation with the grain orientation of each corresponding microregion. Here the authors report a 2D quantitative mapping of the grain orientation and the local triaxial strain field in a 250 nm thick multiferroic BFO film using a synchrotron x-ray microdiffraction technique. This direct scanning measurement demonstrates that the deviatoric component of the in-plane strain tensor is between 5x10(-3) and 6x10(-3) and that the local triaxial strain is fairly well correlated with the grain orientation in that particular region. (c) 2007 American Institute of Physics.X1145Nsciescopu

Plasmonic colloidal nanoparticles with open eccentric cavities via acid-induced chemical transformation

Surface-enhanced Raman spectroscopy (SERS) has been considered a promising technique for the detection of trace molecules in biomedicine and environmental monitoring. The ideal metal nanoparticles for SERS must not only fulfill important requirements such as high near-field enhancement and a tunable far-field response but also overcome the diffusion limitation at extremely lower concentrations of a target material. Here, we introduce a novel method to produce gold nanoparticles with open eccentric cavities by selectively adapting the structure of non-plasmonic nanoparticles via acid-mediated surface replacement. Copper oxide nanoparticles with open eccentric cavities are first prepared using a microwave-irradiation-assisted surfactant-free hydrothermal reaction and are then transformed into gold nanoparticles by an acidic gold precursor while maintaining their original structure. Because of the strong near-field enhancement occurring at the mouth of the open cavities and the very rough surfaces resulting from the uniformly covered hyperbranched sharp multi-tips and the free access of SERS molecules inside of the nanoparticles without diffusion limitation, adenine, one of the four bases in DNA, in an extremely diluted aqueous solution (1.0 pM) was successfully detected with excellent reproducibility upon laser excitation with a 785-nm wavelength. The gold nanoparticles with open eccentric cavities provide a powerful platform for the detection of ultra-trace analytes in an aqueous solution within near-infrared wavelengths, which is essential for highly sensitive, reliable and direct in vivo analysis.None1132sciescopu

A study on the effect of COX-2 inhibitors on gastric mucosal prostaglandin synthesis

published_or_final_versio

High prevalence of mixed infections by Helicobacter pylori in Hong Kong: Metronidazole sensitivity and overall genotype

Background: Diversity in metronidazole susceptibility and genotypes of Helicobacter pylori have been reported with varying results in different areas. Aims: To investigate the prevalence of multiple strain infection in a symptomatic Chinese population and to determine the metronidazole susceptibility pattern and genotypic characteristics of these infecting strains. Methods: Gastric biopsies from antrum, body and cardia were taken during upper endoscopy in symptomatic patients referred to our department. Pooled cultures and single colony isolates were obtained and tested for metronidazole susceptibility and random amplified polymorphic DNA (RAPD) fingerprint patterns. Results: A total of 461 isolates were successfully cultured from 46 patients. Fifty-seven per cent of subjects had metronidazole-resistant strains. Among them, 77% carried a mixture of sensitive and resistant strains, non-uniformly distributed in the gastric mucosa. Mixed genotypes were found by RAPD typing in 24% of subjects. These did not correlate with the metronidazole susceptibility/resistance pattern. Conclusion: H. pylori infections with mixed metronidazole sensitive/resistant strains and mixed genotypes are common in Hong Kong. This makes it prudent to use bacterial strains from several biopsy sites when testing for traits such as drug resistance or virulence in relation to disease.postprin

Molecular lens applied to benzene and carbon disulfide molecular beams

A molecular lens of the nonresonant dipole force formed by focusing a nanosecond IR laser pulse has been applied to benzene and CS2 molecular beams. Using the velocity map imaging technique for molecular ray tracing, characteristic molecular lens parameters including the focal length (f ), minimum beam width (W), and distance to the minimum beam width position (D) were determined. The laser intensity dependence of the observed lens parameters was in good agreement with theoretical predictions. W was independent of the laser peak intensity (I-0), whereas f and D varied linearly with 1/I-0. The differences in lens parameters between the molecular species were well correlated with the polarizability per mass values of the molecules. A high chromatographic resolution of Rs = 0.84 was achieved between the images of benzene molecular beams undeflected and deflected by the lens. The possibilities for a new type of chromatography are discussed.open293

High prevalence of Helicobacter pylori infection with dual resistance to metronidazole and clarithromycin in Hong Kong

Background: Metronidazole resistance is a common problem in most Asian countries, and clarithromycin has been widely used in Hong Kong. Aim: To determine the prevalence of Helicobacter pylori strains resistant to metronidazole and clarithromycin in Hong Kong and to assess the effect on eradication rates. Also to determine the genetic mutation in relation to phenotypic divergence in clarithromycin-resistant strains. Methods: H. pylori were cultured from gastric biopsies obtained from 87 patients during upper endoscopy. Minimal inhibitory concentrations of metronidazole and clarithromycin were determined by Etest and agar dilution methods. Mutations in clarithromycin-resistant strains were identified by polymerase chain reaction and restriction analysis. Random amplified polymorphic DNA fingerprinting was performed on clarithromycin-resistant and susceptible isolates. Results: The prevalences of H. pylori strains resistant to metronidazole and clarithromycin were 49.4% and 10.8%, respectively, in Hong Kong. Dual resistance to metronidazole and clarithromycin were found in 7.2% of patients. The agreement between E-test and agar dilution methods was determined by error-rate bound analysis as 95.4% for metronidazole and 100% for clarithromycin. Dual resistant strains reduced the eradication rate to 66.7%. Among clarithromycin-resistant strains tested, all were due to A2144G point mutation in 23S rRNA gene. Random amplified polymorphic DNA fingerprinting suggested various phenotypically mixed populations. Conclusions: The prevalence of metronidazole-resistant H. pylori strains remained static whilst the prevalence of clarithromycin-resistant strains was not rare in Hong Kong. An alarming 7.2% of patients were resistant to both the antimicrobials, which had a definite impact on treatment success. All cases of resistance to clarithromycin were due to A2144G mutation in 23S rRNA of H. pylori.postprin

The effect of umbilical cord blood derived mesenchymal stem cells in monocrotaline-induced pulmonary artery hypertension rats

Pulmonary arterial hypertension (PAH) causes right ventricular failure due to a gradual increase in pulmonary vascular resistance. The purposes of this study were to confirm the engraftment of human umbilical cord blood-mesenchymal stem cells (hUCB-MSCs) placed in the correct place in the lung and research on changes of hemodynamics, pulmonary pathology, immunomodulation and several gene expressions in monocrotaline (MCT)induced PAH rat models after hUCB-MSCs transfusion. The rats were grouped as follows: the control (C) group; the M group (MCT 60 mg/kg); the U group (hUCB-MSCs transfusion). They received transfusions via the external jugular vein a week after MCT injection. The mean right ventricular pressure (RVP) was significantly reduced in the U group after the 2 week. The indicators of RV hypertrophy were significantly reduced in the U group at week 4. Reduced medial wall thickness in the pulmonary arteriole was noted in the U group at week 4. Reduced number of intra-acinar muscular pulmonary arteries was observed in the U group after 2 week. Protein expressions such as endothelin (ET)-1, endothelin receptor A (ERA), endothelial nitric oxide synthase (eNOS) and matrix metalloproteinase (MMP)-2 significantly decreased at week 4. The decreased levels of ERA, eNOS and MMP-2 immunoreactivity were noted by immnohistochemical staining. After hUCB-MSCs were administered, there were the improvement of RVH and mean RVP. Reductions in several protein expressions and immunomodulation were also detected. It is suggested that hUCB-MSCs may be a promising therapeutic option for PAH.1174Ysciescopu

Up-regulation of adipogenin, an adipocyte plasma transmembrane protein, during adipogenesis

The original publication is available at www.springerlink.com.ArticleMOLECULAR AND CELLULAR BIOCHEMISTRY. 276(1-2): 133-141 (2005)journal articl

UNCLES: Method for the identification of genes differentially consistently co-expressed in a specific subset of datasets

Background: Collective analysis of the increasingly emerging gene expression datasets are required. The recently proposed binarisation of consensus partition matrices (Bi-CoPaM) method can combine clustering results from multiple datasets to identify the subsets of genes which are consistently co-expressed in all of the provided datasets in a tuneable manner. However, results validation and parameter setting are issues that complicate the design of such methods. Moreover, although it is a common practice to test methods by application to synthetic datasets, the mathematical models used to synthesise such datasets are usually based on approximations which may not always be sufficiently representative of real datasets. Results: Here, we propose an unsupervised method for the unification of clustering results from multiple datasets using external specifications (UNCLES). This method has the ability to identify the subsets of genes consistently co-expressed in a subset of datasets while being poorly co-expressed in another subset of datasets, and to identify the subsets of genes consistently co-expressed in all given datasets. We also propose the M-N scatter plots validation technique and adopt it to set the parameters of UNCLES, such as the number of clusters, automatically. Additionally, we propose an approach for the synthesis of gene expression datasets using real data profiles in a way which combines the ground-truth-knowledge of synthetic data and the realistic expression values of real data, and therefore overcomes the problem of faithfulness of synthetic expression data modelling. By application to those datasets, we validate UNCLES while comparing it with other conventional clustering methods, and of particular relevance, biclustering methods. We further validate UNCLES by application to a set of 14 real genome-wide yeast datasets as it produces focused clusters that conform well to known biological facts. Furthermore, in-silico-based hypotheses regarding the function of a few previously unknown genes in those focused clusters are drawn. Conclusions: The UNCLES method, the M-N scatter plots technique, and the expression data synthesis approach will have wide application for the comprehensive analysis of genomic and other sources of multiple complex biological datasets. Moreover, the derived in-silico-based biological hypotheses represent subjects for future functional studies.The National Institute for Health Research (NIHR) under its Programme Grants for Applied Research Programme (Grant Reference Number RP-PG-0310-1004)