On Neutrino Masses and Family Replication

The old issue of why there are more than one family of quarks and leptons is reinvestigated with an eye towards the use of anomaly as a tool for constraining the number of families. It is found that, by assuming the existence of right-handed neutrinos (which would imply that neutrinos will have a mass) and a new chiral SU(2) gauge theory, strong constraints on the number of families can be obtained. In addition, a model, based on that extra SU(2), is constructed where it is natural to have one "very heavy" fourth neutrino and three almost degenerate light neutrinos whose masses are all of the Dirac type.Comment: RevTex, 12 pages with 1 figure, minor changes to the text and added acknowledgment

Neutrino Masses, Mixing and New Physics Effects

We introduce a parametrization of the effects of radiative corrections from new physics on the charged lepton and neutrino mass matrices, studying how several relevant quantities describing the pattern of neutrino masses and mixing are affected by these corrections. We find that the ratio omega = sin theta / tan theta_atm is remarkably stable, even when relatively large corrections are added to the original mass matrices. It is also found that if the lightest neutrino has a mass around 0.3 eV, the pattern of masses and mixings is considerably more stable under perturbations than for a lighter or heavier spectrum. We explore the consequences of perturbations on some flavor relations given in the literature. In addition, for a quasi-degenerate neutrino spectrum it is shown that: (i) starting from a bi-maximal mixing scenario, the corrections to the mass matrices keep tan theta_atm very close to unity while they can lower tan theta_sol to its measured value; (ii) beginning from a scenario with a vanishing Dirac phase, corrections can induce a Dirac phase large enough to yield CP violation observable in neutrino oscillations.Comment: 14 pages, 21 figures. Uses RevTeX4. Added several comments and references. Final version to appear in PR

Thorium speciation in seawater

Author Posting. © The Authors, 2006. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Marine Chemistry 100 (2006): 250-268, doi:10.1016/j.marchem.2005.10.024.Since the 1960’s, thorium isotopes occupy a special place in the oceanographer’s toolbox as tracers for determining rates and mechanisms of oceanic scavenging, particle dynamics, and carbon fluxes. Due to their unique and constant production rates from soluble parent nuclides of uranium and radium, their disequilibrium can be used to calculate rates and time scales of sinking particles. In addition, by ratio-ing particulate 234Th (as well, in principle, other Thnuclides) to carbon (and other elements), and linking this ratio to the parent-daughter disequilibrium in the water column, it is possible to calculate fluxes of carbon and other elements. Most of these applications are possible with little knowledge of the dissolved chemical properties of thorium, other than its oxidation state (IV) and tendency to strongly sorb to surfaces, i.e., its “particle- or surface-activity”. However, the use of any tracer is hindered by a lack of knowledge of its chemical properties. Recent observations in the variability of carbon to 234Th ratios in different particle types, as well as of associations of Th(IV) with various marine organic biomolecules has led to the need for a review of current knowledge and what future endeavors should be taken to understand the marine chemistry of thorium.The writing of this paper was supported, in parts by NSF (OCE-0351559; OCE-0350758, and OCE 0354757)

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Measurements of the qsq dependence of the D0 to K mu nu and D0 to pi mu nu form factors

Using a large sample of D0 to K mu nu and pi mu nu decays collected by the FOCUS photoproduction experiment at Fermilab, we present new measurements of the q^2 dependence for the f+(q^2) form factor. These measured f+(q^2) form factors are fit to common parameterizations such as the pole dominance form and compared to recent unquenched Lattice QCD calculations. We find m_pole = 1.93+-0.05+-0.03 GeV/c^2 for D0 to K mu nu and m_pole = 1.91+0.30-0.15+-0.07 GeV/c^2 for D0 to pi mu nu and f-^{K}(0)/f+^{K}(0) = -1.7+1.5-1.4+-0.3.Comment: 14 pages, 6 figure

Iterative build OMIT maps: Map improvement by iterative model-building and refinement without model bias

A procedure for carrying out iterative model-building, density modification and refinement is presented in which the density in an OMIT region is essentially unbiased by an atomic model. Density from a set of overlapping OMIT regions can be combined to create a composite 'Iterative-Build' OMIT map that is everywhere unbiased by an atomic model but also everywhere benefiting from the model-based information present elsewhere in the unit cell. The procedure may have applications in the validation of specific features in atomic models as well as in overall model validation. The procedure is demonstrated with a molecular replacement structure and with an experimentally-phased structure, and a variation on the method is demonstrated by removing model bias from a structure from the Protein Data Bank

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

Measurement of the azimuthal anisotropy of Y(1S) and Y(2S) mesons in PbPb collisions at √S^{S}NN = 5.02 TeV

The second-order Fourier coefficients (υ$_{2}$) characterizing the azimuthal distributions of Υ(1S) and Υ(2S) mesons produced in PbPb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV are studied. The Υmesons are reconstructed in their dimuon decay channel, as measured by the CMS detector. The collected data set corresponds to an integrated luminosity of 1.7 nb$^{-1}$. The scalar product method is used to extract the υ$_{2}$ coefficients of the azimuthal distributions. Results are reported for the rapidity range |y| < 2.4, in the transverse momentum interval 0 < p$_{T}$ < 50 GeV/c, and in three centrality ranges of 10–30%, 30–50% and 50–90%. In contrast to the J/ψ mesons, the measured υ$_{2}$ values for the Υ mesons are found to be consistent with zero