Probing Supersymmetry With Third-Generation Cascade Decays

The chiral structure of supersymmetric particle couplings involving third generation Standard Model fermions depends on left-right squark and slepton mixings as well as gaugino-higgsino mixings. The shapes and intercorrelations of invariant mass distributions of a first or second generation lepton with bottoms and taus arising from adjacent branches of SUSY cascade decays are shown to be a sensitive probe of this chiral structure. All possible cascade decays that can give rise to such correlations within the MSSM are considered. For bottom-lepton correlations the distinctive structure of the invariant mass distributions distinguishes between decays originating from stop or sbottom squarks through either an intermediate chargino or neutralino. For decay through a chargino the spins of the stop and chargino are established by the form of the distribution. When the bottom charge is signed through soft muon tagging, the structure of the same-sign and opposite-sign invariant mass distributions depends on a set function of left-right and gaugino-higgsino mixings, as well as establishes the spins of all the superpartners in the sequential two-body cascade decay. Tau-lepton and tau-tau invariant mass distributions arising from MSSM cascade decays are likewise systematically considered with particular attention to their dependence on tau polarization. All possible tau-lepton and tau-tau distributions are plotted using a semi-analytic model for hadronic one-prong taus. Algorithms for fitting tau-tau and tau-lepton distributions to data are suggested.Comment: 35 pages, 17 .eps figure

Dimerization and Incommensurate Spiral Spin Correlations in the Zigzag Spin Chain: Analogies to the Kondo Lattice

Using the density matrix renormalization group and a bosonization approach, we study a spin-1/2 antiferromagnetic Heisenberg chain with near-neighbor coupling $J_1$ and frustrating second-neighbor coupling $J_2$, particularly in the limit $J_2 >> J_1$. This system exhibits both dimerization and incommensurate spiral spin correlations. We argue that this system is closely related to a doped, spin-gapped phase of the one-dimensional Kondo lattice.Comment: 18 pages, with 13 embedded encapsulated Postscript figures, uses epsf.sty. Corrects a misstatement about the pitch angle, and contains additional reference

On the 3-particle scattering continuum in quasi one dimensional integer spin Heisenberg magnets

We analyse the three-particle scattering continuum in quasi one dimensional integer spin Heisenberg antiferromagnets within a low-energy effective field theory framework. We exactly determine the zero temperature dynamical structure factor in the O(3) nonlinear sigma model and in Tsvelik's Majorana fermion theory. We study the effects of interchain coupling in a Random Phase Approximation. We discuss the application of our results to recent neutron-scattering experiments on the Haldane-gap material ${\rm CsNiCl_3}$.Comment: 8 pages of revtex, 5 figures, small changes, to appear in PR

Haldane-Gapped Spin Chains as Luttinger Liquids: Correlation Functions at Finite Field

We study the behavior of Heisenberg, antiferromagnetic, integer-spin chains in the presence of a magnetic field exceeding the attendant spin gap. For temperatures much smaller than the gap, the spin chains exhibit Luttinger liquid behavior. We compute exactly both the corresponding Luttinger parameter and the Fermi velocity as a function of magnetic field. This enables the computation of a number of correlators from which we derive the spin conductance, the expected form of the dynamic structure factor relevant to inelastic neutron scattering experiments, and NMR relaxation rates. We also comment upon the robustness of the magnetically induced gapless phase both to finite temperature and finite couplings between neighbouring chains.Comment: 32 pages, 8 figures; published version includes additions discussing the robustness of the magnetically induced gapless phase to ordering between chains as well as the relationship between the spin-1 chains and spin-1/2 ladders in the presence of a magnetic fiel

Phase diagrams of spin ladders with ferromagnetic legs

The low-temperature properties of the spin S=1/2 ladder with anisotropic ferromagnetic legs are studied using the continuum limit bosonization approach. The weak-coupling ground state phase diagram of the model is obtained for a wide range of coupling constants and several unconventional gapless ''spin-liquid'' phases are shown to exist for ferromagnetic coupling. The behavior of the ladder system in the vicinity of the ferromagnetic instability point is discussed in detail.Comment: 11 pages, 4 figure

Competing Orders in Coupled Luttinger Liquids

We consider the problem of two coupled Luttinger liquids both at half filling and at low doping levels, to investigate the problem of competing orders in quasi-one-dimensional strongly correlated systems. We use bosonization and renormalization group equations to investigate the phase diagrams, to determine the allowed phases and to establish approximate boundaries among them. Because of the chiral translation and reflection symmetry in the charge mode away from half filling, orders of charge density wave (CDW) and spin-Peierls (SP) diagonal current (DC) and $d$-density wave (DDW) form two doublets and thus can be at most quasi-long range ordered. At half-filling, umklapp terms break this symmetry down to a discrete group and thus Ising-type ordered phases appear as a result of spontaneous breaking of the residual symmetries. Quantum disordered Haldane phases are also found, with finite amplitudes of pairing orders and triplet counterparts of CDW, SP, DC and DDW. Relations with recent numerical results and implications to similar problems in two dimensions are discussed.Comment: 16 pages, 5 figures, 4 tables. Revised manuscript; a misprint in Eq. B3 has been corrected. The paper is already in print in PR

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

Enhanced genome assembly and a new official gene set for Tribolium castaneum

Background. The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality. Results. Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI. Conclusions. The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis