Spark: A navigational paradigm for genomic data exploration

Biologists possess the detailed knowledge critical for extracting biological insight from genome-wide data resources, and yet they are increasingly faced with nontrivial computational analysis challenges posed by genome-scale methodologies. To lower this computational barrier, particularly in the early data exploration phases, we have developed an interactive pattern discovery and visualization approach, Spark, designed with epigenomic data in mind. Here we demonstrate Spark's ability to reveal both known and novel epigenetic signatures, including a previously unappreciated binding association between the YY1 transcription factor and the corepressor CTBP2 in human embryonic stem cells

Spin relaxation in (110) and (001) InAs/GaSb superlattices

We report an enhancement of the electron spin relaxation time (T1) in a (110) InAs/GaSb superlattice by more than an order of magnitude (25 times) relative to the corresponding (001) structure. The spin dynamics were measured using polarization sensitive pump probe techniques and a mid-infrared, subpicosecond PPLN OPO. Longer T1 times in (110) superlattices are attributed to the suppression of the native interface asymmetry and bulk inversion asymmetry contributions to the precessional D'yakonov Perel spin relaxation process. Calculations using a nonperturbative 14-band nanostructure model give good agreement with experiment and indicate that possible structural inversion asymmetry contributions to T1 associated with compositional mixing at the superlattice interfaces may limit the observed spin lifetime in (110) superlattices. Our findings have implications for potential spintronics applications using InAs/GaSb heterostructures.Comment: 4 pages, 2 figure

Stripes, Pseudogaps, and Van Hove Nesting in the Three-band tJ Model

Slave boson calculations have been carried out in the three-band tJ model for the high-T_c cuprates, with the inclusion of coupling to oxygen breathing mode phonons. Phonon-induced Van Hove nesting leads to a phase separation between a hole-doped domain and a (magnetic) domain near half filling, with long-range Coulomb forces limiting the separation to a nanoscopic scale. Strong correlation effects pin the Fermi level close to, but not precisely at the Van Hove singularity (VHS), which can enhance the tendency to phase separation. The resulting dispersions have been calculated, both in the uniform phases and in the phase separated regime. In the latter case, distinctly different dispersions are found for large, random domains and for regular (static) striped arrays, and a hypothetical form is presented for dynamic striped arrays. The doping dependence of the latter is found to provide an excellent description of photoemission and thermodynamic experiments on pseudogap formation in underdoped cuprates. In particular, the multiplicity of observed gaps is explained as a combination of flux phase plus charge density wave (CDW) gaps along with a superconducting gap. The largest gap is associated with VHS nesting. The apparent smooth evolution of this gap with doping masks a crossover from CDW-like effects near optimal doping to magnetic effects (flux phase) near half filling. A crossover from large Fermi surface to hole pockets with increased underdoping is found. In the weakly overdoped regime, the CDW undergoes a quantum phase transition ($T_{CDW}\to 0$), which could be obscured by phase separation.Comment: 15 pages, Latex, 18 PS figures Corrects a sign error: major changes, esp. in Sect. 3, Figs 1-4,6 replace

Pinned Balseiro-Falicov Model of Tunneling and Photoemission in the Cuprates

The smooth evolution of the tunneling gap of Bi_2Sr_2CaCu_2O_8 with doping from a pseudogap state in the underdoped cuprates to a superconducting state at optimal and overdoping, has been interpreted as evidence that the pseudogap must be due to precursor pairing. We suggest an alternative explanation, that the smoothness reflects a hidden SO(N) symmetry near the (pi,0) points of the Brillouin zone (with N = 3, 4, 5, or 6). Because of this symmetry, the pseudogap could actually be due to any of a number of nesting instabilities, including charge or spin density waves or more exotic phases. We present a detailed analysis of this competition for one particular model: the pinned Balseiro-Falicov model of competing charge density wave and (s-wave) superconductivity. We show that most of the anomalous features of both tunneling and photoemission follow naturally from the model, including the smooth crossover, the general shape of the pseudogap phase diagram, the shrinking Fermi surface of the pseudogap phase, and the asymmetry of the tunneling gap away from optimal doping. Below T_c, the sharp peak at Delta_1 and the dip seen in the tunneling and photoemission near 2Delta_1 cannot be described in detail by this model, but we suggest a simple generalization to account for inhomogeneity, which does provide an adequate description. We show that it should be possible, with a combination of photoemission and tunneling, to demonstrate the extent of pinning of the Fermi level to the Van Hove singularity. A preliminary analysis of the data suggests pinning in the underdoped, but not in the overdoped regime.Comment: 18 pages LaTeX, 26 ps. figure

Collider and Dark Matter Phenomenology of Models with Mirage Unification

We examine supersymmetric models with mixed modulus-anomaly mediated SUSY breaking (MM-AMSB) soft terms which get comparable contributions to SUSY breaking from moduli-mediation and anomaly-mediation. The apparent (mirage) unification of soft SUSY breaking terms at Q=mu_mir not associated with any physical threshold is the hallmark of this scenario. The MM-AMSB structure of soft terms arises in models of string compactification with fluxes, where the addition of an anti-brane leads to an uplifting potential and a de Sitter universe, as first constructed by Kachru {\it et al.}. The phenomenology mainly depends on the relative strength of moduli- and anomaly-mediated SUSY breaking contributions, and on the Higgs and matter field modular weights, which are determined by the location of these fields in the extra dimensions. We delineate the allowed parameter space for a low and high value of tan(beta), for a wide range of modular weight choices. We calculate the neutralino relic density and display the WMAP-allowed regions. We show the reach of the CERN LHC and of the International Linear Collider. We discuss aspects of MM-AMSB models for Tevatron, LHC and ILC searches, muon g-2 and b->s \gamma branching fraction. We also calculate direct and indirect dark matter detection rates, and show that almost all WMAP-allowed models should be accessible to a ton-scale noble gas detector. Finally, we comment on the potential of colliders to measure the mirage unification scale and modular weights in the difficult case where mu_mir>>M_GUT.Comment: 34 pages plus 42 EPS figures; version with high resolution figures is at http://www.hep.fsu.edu/~bae

Pulmonary Delivery of Nanoparticle-Bound Toll-like Receptor 9 Agonist for the Treatment of Metastatic Lung Cancer

CpG oligodeoxynucleotides are potent toll-like receptor (TLR) 9 agonists and have shown promise as anticancer agents in preclinical studies and clinical trials. Binding of CpG to TLR9 initiates a cascade of innate and adaptive immune responses, beginning with activation of dendritic cells and resulting in a range of secondary effects that include the secretion of pro-inflammatory cytokines, activation of natural killer cells, and expansion of T cell populations. Recent literature suggests that local delivery of CpG in tumors results in superior antitumor effects as compared to systemic delivery. In this study, we utilized PRINT (particle replication in nonwetting templates) nanoparticles as a vehicle to deliver CpG into murine lungs through orotracheal instillations. In two murine orthotopic metastasis models of non-small-cell lung cancer-344SQ (lung adenocarcinoma) and KAL-LN2E1 (lung squamous carcinoma), local delivery of PRINT-CpG into the lungs effectively promoted substantial tumor regression and also limited systemic toxicities associated with soluble CpG. Furthermore, cured mice were completely resistant to tumor rechallenge. Additionally, nanodelivery showed extended retention of CpG within the lungs as well as prolonged elevation of antitumor cytokines in the lungs, but no elevated levels of proinflammatory cytokines in the serum. These results demonstrate that PRINT-CpG is a potent nanoplatform for local treatment of lung cancer that has collateral therapeutic effects on systemic disease and an encouraging toxicity profile and may have the potential to treat lung metastasis of other cancer types

Spin-Charge Separation in the t−Jt-J Model: Magnetic and Transport Anomalies

A real spin-charge separation scheme is found based on a saddle-point state of the $t-J$ model. In the one-dimensional (1D) case, such a saddle-point reproduces the correct asymptotic correlations at the strong-coupling fixed-point of the model. In the two-dimensional (2D) case, the transverse gauge field confining spinon and holon is shown to be gapped at {\em finite doping} so that a spin-charge deconfinement is obtained for its first time in 2D. The gap in the gauge fluctuation disappears at half-filling limit, where a long-range antiferromagnetic order is recovered at zero temperature and spinons become confined. The most interesting features of spin dynamics and transport are exhibited at finite doping where exotic {\em residual} couplings between spin and charge degrees of freedom lead to systematic anomalies with regard to a Fermi-liquid system. In spin dynamics, a commensurate antiferromagnetic fluctuation with a small, doping-dependent energy scale is found, which is characterized in momentum space by a Gaussian peak at ($\pi/a$, $\pi/a$) with a doping-dependent width ($\propto \sqrt{\delta}$, $\delta$ is the doping concentration). This commensurate magnetic fluctuation contributes a non-Korringa behavior for the NMR spin-lattice relaxation rate. There also exits a characteristic temperature scale below which a pseudogap behavior appears in the spin dynamics. Furthermore, an incommensurate magnetic fluctuation is also obtained at a {\em finite} energy regime. In transport, a strong short-range phase interference leads to an effective holon Lagrangian which can give rise to a series of interesting phenomena including linear-$T$ resistivity and $T^2$ Hall-angle. We discuss the striking similarities of these theoretical features with those found in the high-$T_c$ cuprates and give aComment: 70 pages, RevTex, hard copies of 7 figures available upon request; minor revisions in the text and references have been made; To be published in July 1 issue of Phys. Rev. B52, (1995

Measurement of Mass and Width of the W Boson at LEP

We report on measurements of the mass and total decay width of the W boson with the L3 detector at LEP. W-pair events produced in $\mathrm{e^+e^-}$ interactions between 161 GeV and 183 GeV centre-of-mass energy are selected in a data sample corresponding to a total luminosity of 76.7 pb$^{-1}$. Combining all final states in W-pair production, the mass and total decay width of the W boson are determined to be $\mathrm{M_W}=80.61\pm0.15$ GeV and $\Gamma_{\mathrm{W}}=1.97\pm0.38$ GeV, respectively

Measurement of W Polarisation at LEP

The three different helicity states of W bosons produced in the reaction e+ e- -> W+ W- -> l nu q q~ at LEP are studied using leptonic and hadronic W decays. Data at centre-of-mass energies \sqrt s = 183-209 GeV are used to measure the polarisation of W bosons, and its dependence on the W boson production angle. The fraction of longitudinally polarised W bosons is measured to be 0.218 \pm 0.027 \pm 0.016 where the first uncertainty is statistical and the second systematic, in agreement with the Standard Model expectation

Search for Heavy Neutral and Charged Leptons in e+^+e−^- Annihilation at s\sqrt{s} = 183 and 189 GeV

A search for unstable neutral and charged heavy leptons as well as for stable charged heavy leptons is performed at center-of-mass energies $\sqrt{s}$ = 183 and 189 GeV with the L3 detector at LEP. No evidence for their existence is found. We exclude neutral heavy leptons which couple to the electron, muon or tau family, of the Dirac type for masses below 92.4, 93.3 and 83.3 GeV, and of the Majorana type for masses below 81.8, 84.1 and 73.5 GeV, respectively. We exclude unstable charged heavy leptons for masses below 93.9 GeV for a wide range of the associated neutral heavy lepton mass. If the unstable charged heavy lepton decays to a light neutrino, we exclude masses below 92.4 GeV. The production of stable charged heavy leptons with mass less than 93.5 GeV is also excluded