An efficient semiparametric maxima estimator of the extremal index

The extremal index $\theta$, a measure of the degree of local dependence in the extremes of a stationary process, plays an important role in extreme value analyses. We estimate $\theta$ semiparametrically, using the relationship between the distribution of block maxima and the marginal distribution of a process to define a semiparametric model. We show that these semiparametric estimators are simpler and substantially more efficient than their parametric counterparts. We seek to improve efficiency further using maxima over sliding blocks. A simulation study shows that the semiparametric estimators are competitive with the leading estimators. An application to sea-surge heights combines inferences about $\theta$ with a standard extreme value analysis of block maxima to estimate marginal quantiles.Comment: 17 pages, 7 figures. Minor edits made to version 1 prior to journal publication. The final publication is available at Springer via http://dx.doi.org/10.1007/s10687-015-0221-

Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma

Abstract: The identification of cancer-promoting genetic alterations is challenging particularly in highly unstable and heterogeneous cancers, such as esophageal adenocarcinoma (EAC). Here we describe a machine learning algorithm to identify cancer genes in individual patients considering all types of damaging alterations simultaneously. Analysing 261 EACs from the OCCAMS Consortium, we discover helper genes that, alongside well-known drivers, promote cancer. We confirm the robustness of our approach in 107 additional EACs. Unlike recurrent alterations of known drivers, these cancer helper genes are rare or patient-specific. However, they converge towards perturbations of well-known cancer processes. Recurrence of the same process perturbations, rather than individual genes, divides EACs into six clusters differing in their molecular and clinical features. Experimentally mimicking the alterations of predicted helper genes in cancer and pre-cancer cells validates their contribution to disease progression, while reverting their alterations reveals EAC acquired dependencies that can be exploited in therapy

An Interconverting Family of Coordination Cages and a meso-Helicate; Effects of Temperature, Concentration, and Solvent on the Product Distribution of a Self-Assembly Process

The self-assembly between a water-soluble bis-bidentate ligand L^18w and Co­(II) salts in water affords three high-spin Co­(II) products: a dinuclear <i>meso</i>-helicate [Co₂(L^18w)₃]­X₄; a tetrahedral cage [Co₄(L^18w)₆]­X₈; and a dodecanuclear truncated-tetrahedral cage [Co₁₂(L^18w)₁₈]­X₂₄ (X = BF₄ or ClO₄). All three products were crystallized under different conditions and structurally characterized. In [Co₂(L^18w)₃]­X₄ all three bridging ligands span a pair of metal ions; in the two larger products, there is a metal ion at each vertex of the Co₄ or Co₁₂ polyhedral cage array with a bridging ligand spanning a pair of metal ions along every edge. All three structural types are known: what is unusual here is the presence of all three from the same reaction. The assemblies <b>Co</b>_<b>2</b>, <b>Co</b>_<b>4</b>, and <b>Co</b>_<b>12</b> are in slow equilibrium (hours/days) in aqueous solution, and this can be conveniently monitored by ¹H NMR spectroscopy because (i) the paramagnetism of Co­(II) disperses the signals over a range of ca. 200 ppm and (ii) the different symmetries of the three species give characteristically different numbers of independent ¹H NMR signals, which makes identification easy. From temperature- and concentration-dependent ¹H NMR studies it is clear that increasing temperature and increasing dilution favors fragmentation to give a larger proportion of the smaller assemblies for entropic reasons. High concentrations and low temperature favor the larger assembly despite the unfavorable entropic and electrostatic factors associated with its formation. We suggest that this arises from the hydrophobic effect: reorganization of several smaller complexes into one larger one results in a smaller proportion of the hydrophobic ligand surface being exposed to water, with a larger proportion of the ligand surface protected in the interior of the assembly. In agreement with this, ¹H NMR spectra in a nonaqueous solvent (MeNO₂) show formation of only [Co₂(L^18w)₃]­X₄ because the driving force for reorganization into larger assemblies is now absent. Thus, we can identify the contributions of temperature, concentration, and solvent on the result of the metal/ligand self-assembly process and have determined the speciation behavior of the <b>Co</b>_<b>2</b>/<b>Co</b>_<b>4</b>/<b>Co</b>_<b>12</b> system in aqueous solution