PACE: Pattern Accurate Computationally Efficient Bootstrapping for Timely Discovery of Cyber-Security Concepts

Public disclosure of important security information, such as knowledge of vulnerabilities or exploits, often occurs in blogs, tweets, mailing lists, and other online sources months before proper classification into structured databases. In order to facilitate timely discovery of such knowledge, we propose a novel semi-supervised learning algorithm, PACE, for identifying and classifying relevant entities in text sources. The main contribution of this paper is an enhancement of the traditional bootstrapping method for entity extraction by employing a time-memory trade-off that simultaneously circumvents a costly corpus search while strengthening pattern nomination, which should increase accuracy. An implementation in the cyber-security domain is discussed as well as challenges to Natural Language Processing imposed by the security domain.Comment: 6 pages, 3 figures, ieeeTran conference. International Conference on Machine Learning and Applications 201

Unravelling the Dodecahedral Spaces

The hyperbolic dodecahedral space of Weber and Seifert has a natural non-positively curved cubulation obtained by subdividing the dodecahedron into cubes. We show that the hyperbolic dodecahedral space has a 6-sheeted irregular cover with the property that the canonical hypersurfaces made up of the mid-cubes give a very short hierarchy. Moreover, we describe a 60-sheeted cover in which the associated cubulation is special. We also describe the natural cubulation and covers of the spherical dodecahedral space (aka Poincar\'e homology sphere).Comment: 15 pages + 6 pages appendix, 7 figures, 4 table

The HD5980 multiple system: Masses and evolutionary status

New spectroscopic observations of the LBV/WR multiple system HD5980 in the Small Magellanic Cloud are used to address the question of the masses and evolutionary status of the two very luminous stars in the 19.3d eclipsing binary system. Two distinct components of the N V 4944 A line are detected in emission and their radial velocity variations are used to derive masses of 61 and 66 Mo, under the assumption that binary interaction effects on this atomic transition are negligible. We propose that this binary system is the product of quasi-chemically homogeneous evolution with little or no mass transfer. Thus, both of these binary stars may be candidates for gamma-ray burst progenitors or even pair instability supernovae. Analysis of the photospheric absorption lines belonging to the third-light object in the system confirm that it consists of an O-type star in a 96.56d eccentric orbit (e=0.82) around an unseen companion. The 5:1 period ratio and high eccentricities of the two binaries suggest that they may constitute a hierarchical quadruple system.Comment: 27 pages, 8 tables, 15 figures; accepted A

The role of cell cycle–regulated expression in the localization of spatial landmark proteins in yeast

In Saccharomyces cerevisiae, Bud8p and Bud9p are homologous plasma membrane glycoproteins that appear to mark the distal and proximal cell poles, respectively, as potential sites for budding in the bipolar pattern. Here we provide evidence that Bud8p is delivered to the presumptive bud site (and thence to the distal pole of the bud) just before bud emergence, and that Bud9p is delivered to the bud side of the mother-bud neck (and thence to the proximal pole of the daughter cell) after activation of the mitotic exit network, just before cytokinesis. Like the delivery of Bud8p, that of Bud9p is actin dependent; unlike the delivery of Bud8p, that of Bud9p is also septin dependent. Interestingly, although the transcription of BUD8 and BUD9 appears to be cell cycle regulated, the abundance of BUD8 mRNA peaks in G2/M and that of BUD9 mRNA peaks in late G1, suggesting that the translation and/or delivery to the cell surface of each protein is delayed and presumably also cell cycle regulated. The importance of time of transcription in localization is supported by promoter-swap experiments: expression of Bud8p from the BUD9 promoter leads to its localization predominantly to the sites typical for Bud9p, and vice versa. Moreover, expression of Bud8p from the BUD9 promoter fails to rescue the budding-pattern defect of a bud8 mutant but fully rescues that of a bud9 mutant. However, although expression of Bud9p from the BUD8 promoter fails to rescue a bud9 mutant, it also rescues only partially the budding-pattern defect of a bud8 mutant, suggesting that some feature(s) of the Bud8p protein is also important for Bud8p function. Experiments with chimeric proteins suggest that the critical element(s) is somewhere in the extracytoplasmic domain of Bud8p

Thermal denaturation of fluctuating finite DNA chains: the role of bending rigidity in bubble nucleation

Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of broken bonds, or bubble, compared to the double stranded state, the inclusion of the molecular conformational degrees of freedom in a more general mesoscopic model is needed. In this paper we do so by presenting a 1D Ising model, which describes the internal base pair states, coupled to a discrete worm like chain model describing the chain configurations [J. Palmeri, M. Manghi, and N. Destainville, Phys. Rev. Lett. 99, 088103 (2007)]. This coupled model is exactly solved using a transfer matrix technique that presents an analogy with the path integral treatment of a quantum two-state diatomic molecule. When the chain fluctuations are integrated out, the denaturation transition temperature and width emerge naturally as an explicit function of the model parameters of a well defined Hamiltonian, revealing that the transition is driven by the difference in bending (entropy dominated) free energy between bubble and double-stranded segments. The calculated melting curve (fraction of open base pairs) is in good agreement with the experimental melting profile of polydA-polydT. The predicted variation of the mean-square-radius as a function of temperature leads to a coherent novel explanation for the experimentally observed thermal viscosity transition. Finally, the influence of the DNA strand length is studied in detail, underlining the importance of finite size effects, even for DNA made of several thousand base pairs.Comment: Latex, 28 pages pdf, 9 figure

Perspectives on Gamma-Ray Burst Physics and Cosmology with Next Generation Facilities

High-redshift Gamma-Ray Bursts (GRBs) beyond redshift $\sim6$ are potentially powerful tools to probe the distant early Universe. Their detections in large numbers and at truly high redshifts call for the next generation of high-energy wide-field instruments with unprecedented sensitivity at least one order of magnitude higher than the ones currently in orbit. On the other hand, follow-up observations of the afterglows of high-redshift GRBs and identification of their host galaxies, which would be difficult for the currently operating telescopes, require new, extremely large facilities of at multi-wavelengths. This chapter describes future experiments that are expected to advance this exciting field, both being currently built and being proposed. The legacy of Swift will be continued by SVOM, which is equipped with a set of space-based multi-wavelength instruments as well as and a ground segment including a wide angle camera and two follow-up telescopes. The established Lobster-eye X-ray focusing optics provides a promising technology for the detection of faint GRBs at very large distances, based on which the {THESEUS}, {Einstein Probe} and other mission concepts have been proposed. Follow-up observations and exploration of the reionization era will be enabled by large facilities such as {SKA} in the radio, the 30m class telescopes in the optical/near-IR, and the space-borne {WFIRST} and {JWST} in the optical/near-IR/mid-IR. In addition, the X-ray and $\gamma$-ray polarization experiment POLAR is also introduced.Comment: accepted for publication in Space Science Review; reprinted as a chapter in a book of the Space Sciences Series of ISSI for the proceedings of the ISSI-Beijing workshop " Gamma-Ray Bursts: a Tool to Explore the Young Universe

Allele-Specific Copy Number Profiling by Next-Generation DNA Sequencing

The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. We describe a new method, Falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normals. Falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, Falcon more effectively pools evidence from sites with low coverage. A modified Bayesian information criterion is used to guide model selection for determining the number of copy number events. Falcon is evaluated on in silico spike-in data and applied to the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by Falcon allows us to draw detailed conclusions regarding the clonal history of the individual\u27s colon cancer