Information Extraction in Illicit Domains

Extracting useful entities and attribute values from illicit domains such as human trafficking is a challenging problem with the potential for widespread social impact. Such domains employ atypical language models, have `long tails' and suffer from the problem of concept drift. In this paper, we propose a lightweight, feature-agnostic Information Extraction (IE) paradigm specifically designed for such domains. Our approach uses raw, unlabeled text from an initial corpus, and a few (12-120) seed annotations per domain-specific attribute, to learn robust IE models for unobserved pages and websites. Empirically, we demonstrate that our approach can outperform feature-centric Conditional Random Field baselines by over 18\% F-Measure on five annotated sets of real-world human trafficking datasets in both low-supervision and high-supervision settings. We also show that our approach is demonstrably robust to concept drift, and can be efficiently bootstrapped even in a serial computing environment.Comment: 10 pages, ACM WWW 201

Association of serum-soluble heat shock protein 60 with carotid atherosclerosis: clinical significance determined in a follow-up study

BACKGROUND AND PURPOSE: Previous work has shown that soluble heat shock protein 60 (HSP60; sHSP60), present in circulating blood, is associated with carotid atherosclerosis. In the current evaluation, we tested the hypothesis that sHSP60 levels are associated with the progression of carotid arteriosclerosis, prospectively. METHODS: The association of sHSP60 with early atherogenesis (5-year development and progression of nonstenotic carotid plaques) was investigated as part of the population-based prospective Bruneck Study. The current study focused on the follow-up period between 1995 and 2000 and, thus, included 684 subjects. RESULTS: sHSP60 levels measured in 1995 and 2000 were highly correlated (r=0.40; P<0.001), indicating consistency over a 5-year period. Circulating HSP60 levels were significantly correlated with antilipopolysaccharide and anti-HSP60 antibodies. It was also elevated in subjects with chronic infection (top quintile group of HSP60, among subjects with and without chronic infection: 23.8% versus 17.0%; P=0.003 after adjustment for age and sex). HSP60 levels were significantly associated with early atherogenesis, both in the entire population (multivariate odds ratio, for a comparison between quintile group V versus I+II: 2.0 [1.2 to 3.5] and the subgroup free of atherosclerosis at the 1995 baseline: 3.8 [1.6 to 8.9]). The risk of early atherogenesis was additionally amplified when high-sHSP60 and chronic infection were present together. CONCLUSIONS: Our study provides the first prospective data confirming an association between high levels of sHSP60 and early carotid atherosclerosis. This possibly indicates an involvement of sHSP60 in activating proinflammatory processes associated with early vessel pathology

Spectral Properties of delta-Plutonium: Sensitivity to 5f Occupancy

By combining the local density approximation (LDA) with dynamical mean field theory (DMFT), we report a systematic analysis of the spectral properties of $\delta$-plutonium with varying $5f$ occupancy. The LDA Hamiltonian is extracted from a tight-binding (TB) fit to full-potential linearized augmented plane-wave (FP-LAPW) calculations. The DMFT equations are solved by the exact quantum Monte Carlo (QMC) method and the Hubbard-I approximation. We have shown for the first time the strong sensitivity of the spectral properties to the $5f$ occupancy, which suggests using this occupancy as a fitting parameter in addition to the Hubbard $U$. By comparing with PES data, we conclude that the ``open shell'' $5f^{5}$ configuration gives the best agreement, resolving the controversy over $5f$ ``open shell'' versus ``close shell'' atomic configurations in $\delta$-Pu.Comment: 6 pages, 2 embedded color figures, to appear in Physical Review

Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex

BACKGROUND: Evolutionary analyses of enterohemorrhagic Escherichia coli (EHEC) have identified two distantly related clonal groups: EHEC 1, including serotype O157:H7 and its inferred ancestor O55:H7; and EHEC 2, comprised of several serogroups (O26, O111, O118, etc.). These two clonal groups differ in their virulence and global distribution. Although several fully annotated genomic sequences exist for strains of serotype O157:H7, much less is known about the genomic composition of EHEC 2. In this study, we analyzed a set of 24 clinical EHEC 2 strains representing serotypes O26:H11, O111:H8/H11, O118:H16, O153:H11 and O15:H11 from humans and animals by comparative genomic hybridization (CGH) on an oligoarray based on the O157:H7 Sakai genome. RESULTS: Backbone genes, defined as genes shared by Sakai and K-12, were highly conserved in EHEC 2. The proportion of Sakai phage genes in EHEC 2 was substantially greater than that of Sakai-specific bacterial (non-phage) genes. This proportion was inverted in O55:H7, reiterating that a subset of Sakai bacterial genes is specific to EHEC 1. Split decomposition analysis of gene content revealed that O111:H8 was more genetically uniform and distinct from other EHEC 2 strains, with respect to the Sakai O157:H7 gene distribution. Serotype O26:H11 was the most heterogeneous EHEC 2 subpopulation, comprised of strains with the highest as well as the lowest levels of Sakai gene content conservation. Of the 979 parsimoniously informative genes, 15% were found to be compatible and their distribution in EHEC 2 clustered O111:H8 and O118:H16 strains by serotype. CGH data suggested divergence of the LEE island from the LEE1 to the LEE4 operon, and also between animal and human isolates irrespective of serotype. No correlation was found between gene contents and geographic locations of EHEC 2 strains. CONCLUSION: The gene content variation of phage-related genes in EHEC 2 strains supports the hypothesis that extensive modular shuffling of mobile DNA elements has occurred among EHEC strains. These results suggest that EHEC 2 is a multiform pathogenic clonal complex, characterized by substantial intra-serotype genetic variation. The heterogeneous distribution of mobile elements has impacted the diversification of O26:H11 more than other EHEC 2 serotypes

A Weighted Estimate for the Square Function on the Unit Ball in \C^n

We show that the Lusin area integral or the square function on the unit ball of \C^n, regarded as an operator in weighted space $L^2(w)$ has a linear bound in terms of the invariant $A_2$ characteristic of the weight. We show a dimension-free estimate for the ``area-integral'' associated to the weighted $L^2(w)$ norm of the square function. We prove the equivalence of the classical and the invariant $A_2$ classes.Comment: 11 pages, to appear in Arkiv for Matemati

Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium

<p>Abstract</p> <p>Background:</p> <p>Global patterns of gene expression of <it>Escherichia coli </it>K-12 during growth transitions have been deeply investigated, however, comparable studies of <it>E. coli </it>O157:H7 have not been explored, particularly with respect to factors regulating virulence genes and genomic islands specific to this pathogen. To examine the impact of growth phase on the dynamics of the transcriptome, O157:H7 Sakai strain was cultured in MOPS minimal media (0.1% glucose), RNA harvested at 10 time points from early exponential to full stationary phase, and relative gene expression was measured by co-hybridization on high-density DNA microarrays. Expression levels of 14 genes, including those encoding Shiga toxins and other virulence factors associated with the locus of enterocyte effacement (LEE), were confirmed by Q-PCR.</p> <p>Results:</p> <p>Analysis of variance (R/MAANOVA, Fs test) identified 442 (36%) of 1239 O157-specific ORFs and 2110 (59%) of 3647 backbone ORFs that changed in expression significantly over time. QT cluster analysis placed 2468 of the 2552 significant ORFs into 12 groups; each group representing a distinct expression pattern. ORFs from the largest cluster (<it>n </it>= 1078) decreased in expression from late exponential to early stationary phase: most of these ORFs are involved in functions associated with steady state growth. Also represented in this cluster are ORFs of the TAI island, encoding tellurite resistance and urease activity, which decreased ~4-fold. Most ORFs of the LEE pathogenicity island also decreased ~2-fold by early stationary phase. The ORFs encoding proteins secreted via the LEE encoded type III secretion system, such as <it>tccP </it>and <it>espJ</it>, also decreased in expression from exponential to stationary phase. Three of the clusters (<it>n </it>= 154) comprised genes that are transiently upregulated at the transition into stationary phase and included genes involved in nutrient scavenging. Upregulated genes with an increase in mRNA levels from late exponential to early stationary phase belonged to one cluster (<it>n </it>= 923) which includes genes involved in stress responses (e.g. <it>gadAB</it>, <it>osmBC</it>, and <it>dps</it>). These transcript levels remained relatively high for > 3 h in stationary phase. The Shiga toxin genes (<it>stx</it>1AB and <it>stx</it>2B) were significantly induced after transition into stationary phase.</p> <p>Conclusion:</p> <p>Expression of more than 300 O157-specific ORFs, many implicated in virulence of the O157 pathogen, was modulated in a growth dependent manner. These results provide a baseline transcriptional profile that can be compared to patterns of gene expression of this important foodborne pathogen under adverse environmental conditions.</p

The Rotation Average in Lightcone Time-Ordered Perturbation Theory

We present a rotation average of the two-body scattering amplitude in the lightcone time($\tau$)-ordered perturbation theory. Using a rotation average procedure, we show that the contribution of individual time-ordered diagram can be quantified in a Lorentz invariant way. The number of time-ordered diagrams can also be reduced by half if the masses of two bodies are same. In the numerical example of $\phi^{3}$ theory, we find that the higher Fock-state contribution is quite small in the lightcone quantization.Comment: 25 pages, REVTeX, epsf.sty, 69 eps file

Solving the inhomogeneous Bethe-Salpeter equation

We develop an advanced method of solving homogeneous and inhomogeneous Bethe-Salpeter equations by using the expansion over the complete set of 4-dimensional spherical harmonics. We solve Bethe-Salpeter equations for bound and scattering states of scalar and spinor particles for the case of one meson exchange kernels. Phase shifts calculated for the scalar model are in agreement with the previously published results. We discuss possible manifestations of separability for one meson exchange interaction kernels.Comment: 9 pages, 11 eps-figures. Talk presented by S. S. Semikh at XVII International Baldin Seminar on High Energy Physics Problems "Relativistic Nuclear Physics and Quantum Chromodynamics", September 27 - October 2, 2004, Dubna, Russia; to appear in the proceedings of this conferenc