Playing with parameters: structural parameterization in graphs

When considering a graph problem from a parameterized point of view, the parameter chosen is often the size of an optimal solution of this problem (the "standard" parameter). A natural subject for investigation is what happens when we parameterize such a problem by various other parameters, some of which may be the values of optimal solutions to different problems. Such research is known as parameterized ecology. In this paper, we investigate seven natural vertex problems, along with their respective parameters: the size of a maximum independent set, the size of a minimum vertex cover, the size of a maximum clique, the chromatic number, the size of a minimum dominating set, the size of a minimum independent dominating set and the size of a minimum feedback vertex set. We study the parameterized complexity of each of these problems with respect to the standard parameter of the others.Comment: 17 page

Requirement for PRC1 subunit BMI1 in host gene activation by Epstein-Barr virus potein EBNA3C

Epstein–Barr virus proteins EBNA3A, EBNA3B and EBNA3C control hundreds of host genes after infection. Changes in epigenetic marks around EBNA3-regulated genes suggest that they exert transcriptional control in collaboration with epigenetic factors. The roles of polycomb repressive complex (PRC)2 subunit SUZ12 and of PRC1 subunit BMI1 were assessed for their importance in EBNA3-mediated repression and activation. ChIP-seq experiments for SUZ12 and BMI1 were performed to determine their global localization on chromatin and analysis offered further insight into polycomb protein distribution in differentiated cells. Their localization was compared to that of each EBNA3 to resolve longstanding questions about the EBNA3–polycomb relationship. SUZ12 did not co-localize with any EBNA3, whereas EBNA3C co-localized significantly and co-immunoprecipitated with BMI1. In cells expressing a conditional EBNA3C, BMI1 was sequestered to EBNA3C-binding sites after EBNA3C activation. When SUZ12 or BMI1 was knocked down in the same cells, SUZ12 did not contribute to EBNA3C-mediated regulation. Surprisingly, after BMI1 knockdown, EBNA3C repressed equally efficiently but host gene activation by EBNA3C was impaired. This overturns previous assumptions about BMI1/PRC1 functions during EBNA3C-mediated regulation, for the first time identifies directly a host factor involved in EBNA3-mediated activation and provides a new insight into how PRC1 can be involved in gene activation

Tau Polarization in Tau-Neutrino Nucleon Scattering

We investigate the spin polarization of \tau^{\pm} leptons produced in \nu_{\tau} and \bar{\nu}_{\tau} nucleon scattering via charged currents. Quasi-elastic scattering, \Delta resonance production and deep inelastic scattering processes are studied. The polarization information is essential for measuring the \tau^{\pm} appearance rate in long baseline neutrino oscillation experiments, because the decay particle distributions depend crucially on the \tau^{\pm} spin. In this article, we calculate the spin density matrix of each process and estimate the spin polarization vector in medium and high neutrino energy interactions. We find that the produced \tau^{\pm}'s have high degree of polarization, and their spin direction depends non-trivially on the energy and the scattering angle of \tau^{\pm} in the laboratory frame.Comment: 23 pages, 35 figures; compile errors corrected; notation errors in Eq.(30) and (31) corrected, typo error in Eq.(40) corrected, references and comments in footnote adde

Resonance production by neutrinos: I. J=3/2 Resonances

The article contains general formulas for the production of J=3/2 resonances by neutrinos and antineutrinos. It specializes to the P_{33}(1232) resonance whose form factors are determined by theory and experiment and then are compared with experimental results at low and high energies. It is shown that the minimum in the low Q^2 region is a consequence of a combined effect from the vanishing of the vector form factors, the muon mass and Pauli blocking. Several improvements for the future investigations are suggested.Comment: 10 pages, LaTeX, misprints corrected, 1 reference adde

Core binding factor (CBF) is required for Epstein-Barr virus EBNA3 proteins to regulate target gene expression

ChIP-seq performed on lymphoblastoid cell lines (LCLs), expressing epitope-tagged EBNA3A, EBNA3B or EBNA3C from EBV-recombinants, revealed important principles of EBNA3 binding to chromatin. When combined with global chromatin looping data, EBNA3-bound loci were found to have a singular character, each directly associating with either EBNA3-repressed or EBNA3-activated genes, but not with both. EBNA3A and EBNA3C showed significant association with repressed and activated genes. Significant direct association for EBNA3B loci could only be shown with EBNA3B-repressed genes. A comparison of EBNA3 binding sites with known transcription factor binding sites in LCL GM12878 revealed substantial co-localization of EBNA3s with RUNX3-a protein induced by EBV during B cell transformation. The beta-subunit of core binding factor (CBFβ), that heterodimerizes with RUNX3, could co-immunoprecipitate robustly EBNA3B and EBNA3C, but only weakly EBNA3A. Depletion of either RUNX3 or CBFβ with lentivirus-delivered shRNA impaired epitope-tagged EBNA3B and EBNA3C binding at multiple regulated gene loci, indicating a requirement for CBF heterodimers in EBNA3 recruitment during target-gene regulation. ShRNA-mediated depletion of CBFβ in an EBNA3C-conditional LCL confirmed the role of CBF in the regulation of EBNA3C-induced and -repressed genes. These results reveal an important role for RUNX3/CBF during B cell transformation and EBV latency that was hitherto unexplored

Effect of Aqueous Ozone on the NF-κB System

Ozone has been proposed as an alternative oral antiseptic in dentistry, due to its antimicrobial power reported for gaseous and aqueous forms, the latter showing a high biocompatibility with mammalian cells. New therapeutic strategies for the treatment of periodontal disease and apical periodontitis should consider not only antibacterial effects, but also their influence on the host immune response. Therefore, our aim was to investigate the effect of aqueous ozone on the NF-κB system, a paradigm for inflammationassociated signaling/transcription. We showed that NF-κB activity in oral cells stimulated with TNF, and in periodontal ligament tissue from root surfaces of periodontally damaged teeth, was inhibited following incubation with ozonized medium. Under this treatment, IκBalpah proteolysis, cytokine expression, and κB-dependent transcription were prevented. Specific ozonized amino acids were shown to represent major inhibitory components of ozonized medium. In summary, our study establishes a condition under which aqueous ozone exerts inhibitory effects on the NF-κB system, suggesting that it has an antiinflammatory capacity

On the Complexity of Local Search for Weighted Standard Set Problems

In this paper, we study the complexity of computing locally optimal solutions for weighted versions of standard set problems such as SetCover, SetPacking, and many more. For our investigation, we use the framework of PLS, as defined in Johnson et al., [JPY88]. We show that for most of these problems, computing a locally optimal solution is already PLS-complete for a simple neighborhood of size one. For the local search versions of weighted SetPacking and SetCover, we derive tight bounds for a simple neighborhood of size two. To the best of our knowledge, these are one of the very few PLS results about local search for weighted standard set problems

The cooperative functions of the EBNA3 Proteins are central to EBV persistence and latency

The Epstein–Barr nuclear antigen 3 (EBNA3) family of proteins, comprising EBNA3A, EBNA3B, and EBNA3C, play pivotal roles in the asymptomatic persistence and life-long latency of Epstein–Barr virus (EBV) in the worldwide human population. EBNA3-mediated transcriptional reprogramming of numerous host cell genes promotes in vitro B cell transformation and EBV persistence in vivo. Despite structural and sequence similarities, and evidence of substantial cooperative activity between the EBNA3 proteins, they perform quite different, often opposing functions. Both EBNA3A and EBNA3C are involved in the repression of important tumour suppressive pathways and are considered oncogenic. In contrast, EBNA3B exhibits tumour suppressive functions. This review focuses on how the EBNA3 proteins achieve the delicate balance required to support EBV persistence and latency, with emphasis on the contribution of the Allday laboratory to the field of EBNA3 biology

Polarization effects in tau production by neutrino

We studied polarization effects in tau production by neutrino-nucleon scattering. Quasi-elastic scattering, $Delta$ resonance production and deep inelastic scattering processes are taken into account for the CERN-to-Gran Sasso projects. We show that the tau produced by neutrino has high degree of polarization, and its spin direction depends non-trivially on the energy and the scattering angle of tau in the laboratory frame.Comment: 6 pages, 5 eps figures, espcrc2.sty; Proceedings of the 3rd International Workshop on Neutrino-Nucleus Interactions in the Few GeV Region (NuInt04), March 17-21, 2004, Gran Sasso, Italy; minor changes, typos in Eq. (6) correcte

Search for energetic cosmic axions utilizing terrestrial/celestial magnetic fields

Orbiting $\gamma$-detectors combined with the magnetic field of the Earth or the Sun can work parasitically as cosmic axion telescopes. The relatively short field lengths allow the axion-to-photon conversion to be coherent for $m_{axion} \sim 10^{-4}$ eV, if the axion kinetic energy is above $\sim 500$ keV (Earth's field), or, $\sim 50$ MeV (Sun's field), allowing thus to search for axions from $e^+e^-$ annihilations, from supernova explosions, etc. With a detector angular resolution of $\sim 1^o$, a more efficient sky survey for energetic cosmic axions passing {\it through the Sun} can be performed. Axions or other axion-like particles might be created by the interaction of the cosmic radiation with the Sun, similarly to the axion searches in accelerator beam dump experiments; the enormous cosmic energy combined with the built-in coherent Primakoff effect might provide a sensitive detection scheme, being out of reach with accelerators. The axion signal will be an excess in $\gamma$-rays coming either from a specific celestial place behind the Sun, e.g. the Galactic Center, or, from any other direction in the sky being associated with a violent astrophysical event, e.g. a supernova. Earth bound detectors are also of potential interest. The axion scenario also applies to other stars or binary systems in the Universe, in particular to those with superstrong magnetic fields.Comment: 9 pages, LaTeX, small changes in text and bibliograph