Review of AdS/CFT Integrability, Chapter III.2: Exact world-sheet S-matrix

We review the derivation of the S-matrix for planar N=4 supersymmetric Yang-Mills theory and type IIB superstring theory on an AdS5xS5 background. After deriving the S-matrix for the su(2) and su(3) sectors at the one-loop level based on coordinate Bethe ansatz, we show how su(2|2) symmetry leads to the exact asymptotic S-matrix up to an overall scalar function. We then briefly review the spectrum of bound states by relating these states to simple poles of the S-matrix. Finally, we review the derivation of the asymptotic Bethe equations, which can be used to determine the asymptotic multiparticle spectrum.Comment: 20 pages, see also overview article arXiv:1012.3982, v2: references to other chapters updated, v3: references added and minor change

New Einstein-Sasaki and Einstein Spaces from Kerr-de Sitter

In this paper, which is an elaboration of our results in hep-th/0504225, we construct new Einstein-Sasaki spaces L^{p,q,r_1,...,r_{n-1}} in all odd dimensions D=2n+1\ge 5. They arise by taking certain BPS limits of the Euclideanised Kerr-de Sitter metrics. This yields local Einstein-Sasaki metrics of cohomogeneity n, with toric U(1)^{n+1} principal orbits, and n real non-trivial parameters. By studying the structure of the degenerate orbits we show that for appropriate choices of the parameters, characterised by the (n+1) coprime integers (p,q,r_1,...,r_{n-1}), the local metrics extend smoothly onto complete and non-singular compact Einstein-Sasaki manifolds L^{p,q,r_1,...,r_{n-1}}. We also construct new complete and non-singular compact Einstein spaces \Lambda^{p,q,r_1,...,r_n} in D=2n+1 that are not Sasakian, by choosing parameters appropriately in the Euclideanised Kerr-de Sitter metrics when no BPS limit is taken.Comment: latex, 26 page

Marginal Deformations of Field Theories with AdS_4 Duals

We generate new AdS_4 solutions of D=11 supergravity starting from AdS_4 x X_7 solutions where X_7 has U(1)^3 isometry. We consider examples where X_7 is weak G_2, Sasaki-Einstein or tri-Sasakian, corresponding to d=3 SCFTs with N=1,2 or 3 supersymmetry, respectively, and where the deformed solutions preserve N=1,2 or 1 supersymmetry, respectively. For the special cases when X_7 is M(3,2), Q(1,1,1) or N(1,1)_I we identify the exactly marginal deformation in the dual field theory. We also show that the volume of supersymmetric 5-cycles of N(1,1)_I agrees with the conformal dimension predicted by the baryons of the dual field theory.Comment: 28 pages, 2 figures; v2. typos correcte

Marginal Deformations with U(1)^3 Global Symmetry

We generate new 11-dimensional supergravity solutions from deformations based on U(1)^3 symmetries. The initial geometries are of the form AdS_4 x Y_7, where Y_7 is a 7-dimensional Sasaki-Einstein space. We consider a general family of cohomogeneity one Sasaki-Einstein spaces, as well as the recently-constructed cohomogeneity three L^{p,q,r,s} spaces. For certain cases, such as when the Sasaki-Einstein space is S^7, Q^{1,1,1} or M^{1,1,1}, the deformed gravity solutions correspond to a marginal deformation of a known dual gauge theory.Comment: 28pp; Refs. added and to appear in JHE

Scattering in Mass-Deformed N>=4 Chern-Simons Models

We investigate the scattering matrix in mass-deformed N>=4 Chern-Simons models including as special cases the BLG and ABJM theories of multiple M2 branes. Curiously the structure of this scattering matrix in three spacetime dimensions is equivalent to (a) the two-dimensional worldsheet matrix found in the context of AdS/CFT integrability and (b) the R-matrix of the one-dimensional Hubbard model. The underlying reason is that all three models are based on an extension of the psu(2|2) superalgebra which constrains the matrix completely. We also compute scattering amplitudes in one-loop field theory and find perfect agreement with scattering unitarity.Comment: 63 pages, v2: minor corrections, v3: minor improvement

Extrinsic CPT Violation in Neutrino Oscillations in Matter

We investigate matter-induced (or extrinsic) CPT violation effects in neutrino oscillations in matter. Especially, we present approximate analytical formulas for the CPT-violating probability differences for three flavor neutrino oscillations in matter with an arbitrary matter density profile. Note that we assume that the CPT invariance theorem holds, which means that the CPT violation effects arise entirely because of the presence of matter. As special cases of matter density profiles, we consider constant and step-function matter density profiles, which are relevant for neutrino oscillation physics in accelerator and reactor long baseline experiments as well as neutrino factories. Finally, the implications of extrinsic CPT violation on neutrino oscillations in matter for several past, present, and future long baseline experiments are estimated.Comment: 47 pages, 7 figures, RevTeX4. Final version to be published in Phys. Rev.

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

Bilarge Neutrino Mixing and \mu - \tau Permutation Symmetry for Two-loop Radiative Mechanism

The presence of approximate electron number conservation and \mu-\tau permutation symmetry of S_2 is shown to naturally provide bilarge neutrino mixing. First, the bimaximal neutrino mixing together with U_{e3}=0 is guaranteed to appear owing to S_2 and, then, the bilarge neutrino mixing together with |U_{e3}|<<1 arises as a result of tiny violation of S_2. The observed mass hierarchy of \Delta m^2_{\odot}<<\Delta m^2_{atm} is subject to another tiny violation of the electron number conservation. This scenario is realized in a specific model based on SU(3)_L x U(1)_N with two-loop radiative mechanism for neutrino masses. The radiative effects from heavy leptons contained in lepton triplets generate the bimaximal structure and those from charged leptons, which break S_2, generate the bilarge structure together with |U_{e3}|<<1. To suppress dangerous flavor-changing neutral current interactions due to Higgs exchanges especially for quarks, this S_2 symmetry is extended to a discrete Z_8 symmetry, which also ensures the absence of one-loop radiative mechanism.Comment: 18 pages, 7 figures, to appear in Phys. Rev.

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