Identification of gene expression levels in primary melanoma associated with clinically meaningful characteristics

Factors influencing melanoma survival include sex, age, clinical stage, lymph node involvement, as well as Breslow thickness, presence of tumor-infiltrating lymphocytes based on histological analysis of primary melanoma, mitotic rate, and ulceration. Identification of genes whose expression in primary tumors is associated with these key tumor/patient characteristics can shed light on molecular mechanisms of melanoma survival. Here, we show results from a gene expression analysis of formalin-fixed paraffin-embedded primary melanomas with extensive clinical annotation. The Cancer Genome Atlas data on primary melanomas were used for validation of nominally significant associations. We identified five genes that were significantly associated with the presence of tumor-infiltrating lymphocytes in the joint analysis after adjustment for multiple testing: IL1R2, PPL, PLA2G3, RASAL1, and SGK2. We also identified two genes significantly associated with melanoma metastasis to the regional lymph nodes (PIK3CG and IL2RA), and two genes significantly associated with sex (KDM5C and KDM6A). We found that LEF1 was significantly associated with Breslow thickness and CCNA2 and UBE2T with mitosis. RAD50 was the gene most significantly associated with survival, with a higher level of expression associated with worse survival

Timed patterns: TCOZ to timed automata

Abstract. The integrated logic-based modeling language, Timed Communicating Object Z (TCOZ), is well suited for presenting complete and coherent requirement models for complex real-time systems. However, the challenge is how to verify the TCOZ models with tool support, especially for analyzing timing properties. Specialized graph-based modeling technique, Timed Automata (TA), has powerful mechanisms for designing real-time models using multiple clocks and has well developed automatic tool support. One weakness of TA is the lack of high level composable graphical patterns to support systematic designs for complex systems. The investigation of possible links between TCOZ and TA may benefit both techniques. For TCOZ, TA’s tool support can be reused to check timing properties. For TA, a set of composable graphical patterns can be defined based on the semantics of the TCOZ constructs, so that those patterns can be re-used in a generic way. This paper firstly defines the composable TA graphical patterns, and then presents sound transformation rules and a tool for projecting TCOZ specifications into TA. A case study of a railroad crossing system is demonstrated

K\"{a}hler-Einstein metrics on strictly pseudoconvex domains

The metrics of S. Y. Cheng and S.-T. Yau are considered on a strictly pseudoconvex domains in a complex manifold. Such a manifold carries a complete K\"{a}hler-Einstein metric if and only if its canonical bundle is positive. We consider the restricted case in which the CR structure on $\partial M$ is normal. In this case M must be a domain in a resolution of the Sasaki cone over $\partial M$. We give a condition on a normal CR manifold which it cannot satisfy if it is a CR infinity of a K\"{a}hler-Einstein manifold. We are able to mostly determine those normal CR 3-manifolds which can be CR infinities. Many examples are given of K\"{a}hler-Einstein strictly pseudoconvex manifolds on bundles and resolutions.Comment: 30 pages, 1 figure, couple corrections, improved a couple example

The fermion dynamical symmetry model for the even--even and even--odd nuclei in the Xe--Ba region

The even--even and even--odd nuclei $^{126}$Xe-$^{132}$Xe and $^{131}$Ba-$^{137}$Ba are shown to have a well-realized $SO_8 \supset SO_6 \supset SO_3$ fermion dynamical symmetry. Their low-lying energy levels can be described by a unified analytical expression with two (three) adjustable parameters for even--odd (even--even) nuclei that is derived from the fermion dynamical symmetry model. Analytical expressions are given for wavefunctions and for $E2$ transition rates that agree well with data. The distinction between the FDSM and IBM $SO_6$ limits is discussed. The experimentally observed suppression of the the energy levels with increasing $SO_5$ quantum number $\tau$ can be explained as a perturbation of the pairing interaction on the $SO_6$ symmetry, which leads to an $SO_5$ Pairing effect for $SO_6$ nuclei.Comment: submitted to Phys. Rev. C, LaTeX, 31 pages, 8 figures with postscript files available on request at [email protected]

Charming penguin contributions to charmless B decays into two pseudoscalar mesons

We present estimates of the charming penguin contribution to B => K pi, pi pi,K eta, K eta' decays due to intermediate charmed meson states. We find that this contribution is indeed significant for B => K pi decays, and its inclusion, together with the tree and penguin terms, produces large branching ratios in agreement with data, though the analysis is affected by large theoretical uncertainties. On the other hand, for B => pi pi, K eta, K eta' decays, the effect of the charming penguin contribution is more modest. We also compute CP asymmetries for B => K pi, pi pi decays and we obtain rather large results.Comment: 12 pages, 4 figures, LaTeX2e with epsfig. Minor changes in the text, this version will appear in Phys. Rev.

Nicotine-activated descending facilitation on spinal NMDA-dependent reflex potentiation from pontine tegmentum in rats

This study was conducted to investigate the possible neurotransmitter that activates the descending pathways coming from the dorsolateral pontine tegmentum (DPT) to modulate spinal pelvic-urethra reflex potentiation. External urethra sphincter electromyogram (EUSE) activity in response to test stimulation (TS, 1/30 Hz) and repetitive stimulation (RS, 1 Hz) on the pelvic afferent nerve of 63 anesthetized rats were recorded with or without microinjection of nicotinic cholinergic receptor (nAChR) agonists, ACh and nicotine, to the DPT. TS evoked a baseline reflex activity with a single action potential (1.00 +/- 0.00 spikes/stimulation, n = 40), whereas RS produced a long-lasting reflex potentiation (16.14 +/- 0.96 spikes/stimulation, n = 40) that was abolished by D-2-amino-5-phosphonovaleric acid (1.60 +/- 0.89 spikes/stimulation, n = 40) and was attenuated by 2,3-dihydroxy-6-nitro-7sulfamoyl-benzo (F) quinoxaline (7.10 +/- 0.84 spikes/stimulation, n = 40). ACh and nicotine microinjections to DPT both produced facilitation on the RS-induced reflex potentiation (23.57 +/- 2.23 and 28.29 +/- 2.36 spikes/stimulation, P = 0.01, n = 10 and 20, respectively). Pretreatment of selective nicotinic receptor antagonist, chlorisondamine, reversed the facilitation on RS-induced reflex potentiation caused by nicotine (19.41 +/- 1.21 spikes/stimulation, P = 0.01, n = 10) Intrathecal WAY-100635 and spinal transection at the T(1) level both abolished the facilitation on reflex potentiation resulting from the DPT nicotine injection (12.86 +/- 3.13 and 15.57 +/- 1.72 spikes/stimulation, P < 0.01, n = 10 each). Our findings suggest that activation of nAChR at DPT may modulate N-methyl-D-aspartic acid-dependent reflex potentiation via descending serotonergic neurotransmission. This descending modulation may have physiological/pathological relevance in the neural controls of urethral closure

Green functions for generalized point interactions in 1D: A scattering approach

Recently, general point interactions in one dimension has been used to model a large number of different phenomena in quantum mechanics. Such potentials, however, requires some sort of regularization to lead to meaningful results. The usual ways to do so rely on technicalities which may hide important physical aspects of the problem. In this work we present a new method to calculate the exact Green functions for general point interactions in 1D. Our approach differs from previous ones because it is based only on physical quantities, namely, the scattering coefficients, $R$ and $T$, to construct $G$. Renormalization or particular mathematical prescriptions are not invoked. The simple formulation of the method makes it easy to extend to more general contexts, such as for lattices of $N$ general point interactions; on a line; on a half-line; under periodic boundary conditions; and confined in a box.Comment: Revtex, 9 pages, 3 EPS figures. To be published in PR

Fabrication of Nickel Nanostructure Arrays Via a Modified Nanosphere Lithography

In this paper, we present a modified nanosphere lithographic scheme that is based on the self-assembly and electroforming techniques. The scheme was demonstrated to fabricate a nickel template of ordered nanobowl arrays together with a nickel nanostructure array-patterned glass substrate. The hemispherical nanobowls exhibit uniform sizes and smooth interior surfaces, and the shallow nanobowls with a flat bottom on the glass substrate are interconnected as a net structure with uniform thickness. A multiphysics model based on the level set method (LSM) was built up to understand this fabricating process by tracking the interface between the growing nickel and the electrolyte. The fabricated nickel nanobowl template can be used as a mold of long lifetime in soft lithography due to the high strength of nickel. The nanostructure–patterned glass substrate can be used in optical and magnetic devices due to their shape effects. This fabrication scheme can also be extended to a wide range of metals and alloys

CDMS, Supersymmetry and Extra Dimensions

The CDMS experiment aims to directly detect massive, cold dark matter particles originating from the Milky Way halo. Charge and lattice excitations are detected after a particle scatters in a Ge or Si crystal kept at ~30 mK, allowing to separate nuclear recoils from the dominating electromagnetic background. The operation of 12 detectors in the Soudan mine for 75 live days in 2004 delivered no evidence for a signal, yielding stringent limits on dark matter candidates from supersymmetry and universal extra dimensions. Thirty Ge and Si detectors are presently installed in the Soudan cryostat, and operating at base temperature. The run scheduled to start in 2006 is expected to yield a one order of magnitude increase in dark matter sensitivity.Comment: To be published in the proceedings of the 7th UCLA symposium on sources and detection of dark matter and dark energy in the universe, Marina del Rey, Feb 22-24, 200

A High Statistics Search for Ultra-High Energy Gamma-Ray Emission from Cygnus X-3 and Hercules X-1

We have carried out a high statistics (2 Billion events) search for ultra-high energy gamma-ray emission from the X-ray binary sources Cygnus X-3 and Hercules X-1. Using data taken with the CASA-MIA detector over a five year period (1990-1995), we find no evidence for steady emission from either source at energies above 115 TeV. The derived upper limits on such emission are more than two orders of magnitude lower than earlier claimed detections. We also find no evidence for neutral particle or gamma-ray emission from either source on time scales of one day and 0.5 hr. For Cygnus X-3, there is no evidence for emission correlated with the 4.8 hr X-ray periodicity or with the occurrence of large radio flares. Unless one postulates that these sources were very active earlier and are now dormant, the limits presented here put into question the earlier results, and highlight the difficulties that possible future experiments will have in detecting gamma-ray signals at ultra-high energies.Comment: 26 LaTeX pages, 16 PostScript figures, uses psfig.sty to be published in Physical Review