A collateral missing value estimation algorithm for DNA microarrays

Genetic microarray expression data often contains multiple missing values that can significantly affect the performance of statistical and machine learning algorithms. This paper presents an innovative missing value estimation technique, called collateral missing value estimation (CMVE) which has demonstrated superior estimation performance compared with the K-nearest neighbour (KNN) imputation algorithm, the least square impute (LSImpute) and Bayesian principal component analysis (BPCA) techniques. Experimental results confirm that CMVE provides an improvement of 89%, 12% and 10% for the BRCA1, BRCA2 and sporadic ovarian cancer mutations, respectively, compared to the average error rate of KNN, LSImpute and BPCA imputation methods, over a range of randomly selected missing values. The underlying theory behind CMVE also means that it is not restricted to bioinformatics data, but can be successfully applied to any correlated data set

Positronium Decay : Gauge Invariance and Analyticity

The construction of positronium decay amplitudes is handled through the use of dispersion relations. In this way, emphasis is put on basic QED principles: gauge invariance and soft-photon limits (analyticity). A firm grounding is given to the factorization approaches, and some ambiguities in the spin and energy structures of the positronium wavefunction are removed. Non-factorizable amplitudes are naturally introduced. Their dynamics is described, especially regarding the enforcement of gauge invariance and analyticity through delicate interferences. The important question of the completeness of the present theoretical predictions for the decay rates is then addressed. Indeed, some of those non-factorizable contributions are unaccounted for by NRQED analyses. However, it is shown that such new contributions are highly suppressed, being of order alpha^3. Finally, a particular effective form factor formalism is constructed for parapositronium, allowing a thorough analysis of binding energy effects and analyticity implementation.Comment: 34 pages, 13 figure

Tau Polarization in Λb→Xcτνˉ \Lambda_b \to X_c \tau \bar{\nu} and B→XcτνˉB \to X_c \tau \bar{\nu}

We discuss the longitudinal and transverse $\tau$-polarization in inclusive decays of hadrons containing $b$-quarks. The calculation is performed by means of an OPE in HQET. Some mathematical difficulties in calculating transverse polarizations are explained. Numerical results are presented for longitudinal and for transverse polarizations, both in and perpendicular to the decay plane.Comment: LATEX, 20 pages, 5 Postscript figure

Lamin A/C Haploinsufficiency Modulates the Differentiation Potential of Mouse Embryonic Stem Cells

BACKGROUND: Lamins are structural proteins that are the major determinants of nuclear architecture and play important roles in various nuclear functions including gene regulation and cell differentiation. Mutations in the human lamin A gene cause a spectrum of genetic diseases that affect specific tissues. Most available mouse models for laminopathies recapitulate disease symptoms for muscle diseases and progerias. However, loss of human lamin A/C also has highly deleterious effects on fetal development. Hence it is important to understand the impact of lamin A/C expression levels on embryonic differentiation pathways. METHODOLOGY AND PRINCIPAL FINDINGS: We have investigated the differentiation potential of mouse embryonic stem cells containing reduced levels of lamin A/C by detailed lineage analysis of embryoid bodies derived from these cells by culture. We initially carried out a targeted disruption of one allele of the mouse lamin A/C gene (). Undifferentiated wild-type and embryonic stem cells showed similar expression of pluripotency markers and cell cycle profiles. Upon spontaneous differentiation into embryoid bodies, markers for visceral endoderm such as α-fetoprotein were highly upregulated in haploinsufficient cells. However, neuronal markers such as β-III tubulin and nestin were downregulated. Furthermore, we observed a reduction in the commitment of cells into the myogenic lineage, but no discernible effects on cardiac, adipocyte or osteocyte lineages. In the next series of experiments, we derived embryonic stem cell clones expressing lamin A/C short hairpin RNA and examined their differentiation potential. These cells expressed pluripotency markers and, upon differentiation, the expression of lineage-specific markers was altered as observed with embryonic stem cells. CONCLUSIONS: We have observed significant effects on embryonic stem cell differentiation to visceral endoderm, neuronal and myogenic lineages upon depletion of lamin A/C. Hence our results implicate lamin A/C level as an important determinant of lineage-specific differentiation during embryonic development

Z decays into light gluinos: a calculation based on unitarity

The Z boson can decay to a pair of light gluinos through loop-mediated processes. Based on unitarity of the S-matrix, the imaginary part of the decay amplitude is computed in the presence of a light bottom squark. This imaginary part can provide useful information on the full amplitude. Implications are discussed for a recently proposed light gluino and light bottom squark scenario.Comment: 19 pages, LaTeX, 3 figures, submitted to Phys. Rev.

On CP Asymmetries in Two-, Three- and Four-Body D Decays

Indirect and direct CP violations have been established in K_L and B_d decays. They have been found in two-body decay channels -- with the exception of K_L to pi^+ pi^- e^+ e^- transitions. Evidence for direct CP asymmetry has just appeared in LHCb data on A_{CP}(D^0 to K^+ K^-) - A_{CP}(D^0 to pi^+ pi^-) with 3.5 sigma significance. Manifestations of New Dynamics (ND) can appear in CP asymmetries just below experimental bounds. We discuss D^{\pm}_{(s)}, D^0/\bar D^0 and D_L/D_S transitions to 2-, 3- and 4-body final states with a comment on predictions for inclusive vs. exclusive CP asymmetries. In particular we discuss T asymmetries in D to h_1 h_2 l^+ l^- in analogy with K_L to pi^+ pi^- e^+ e^- transitions due to interference between M1, internal bremsstrahlung and possible E1 amplitudes. Such an effect depends on the strength of CP violation originating from the ND -- as discussed here for Little Higgs Models with T parity and non-minimal Higgs sectors -- but also in the interferences between these amplitudes even in the Standard Model (SM). More general lessons can be learnt for T asymmetries in non-leptonic D decays like D to h_1h_2 h_3 h_4. Such manifestations of ND can be tested at LHCb and other Super-Flavour Factories like the projects at KEK near Tokyo and at Tor Vergata/Frascati near Rome.Comment: 27 pages, 6 figures. Revised with current results from LHCb and HFAG and further interpretation

Shock Breakout in Core-Collapse Supernovae and its Neutrino Signature

(Abridged) We present results from dynamical models of core-collapse supernovae in one spatial dimension, employing a newly-developed Boltzmann neutrino radiation transport algorithm, coupled to Lagrangean hydrodynamics and a consistent high-density nuclear equation of state. We focus on shock breakout and its neutrino signature and follow the dynamical evolution of the cores of 11 M_sun, 15 M_sun, and 20 M_sun progenitors through collapse and the first 250 milliseconds after bounce. We examine the effects on the emergent neutrino spectra, light curves, and mix of species of artificial opacity changes, the number of energy groups, the weak magnetism/recoil corrections, nucleon-nucleon bremsstrahlung, neutrino-electron scattering, and the compressibility of nuclear matter. Furthermore, we present the first high-resolution look at the angular distribution of the neutrino radiation field both in the semi-transparent regime and at large radii and explore the accuracy with which our tangent-ray method tracks the free propagation of a pulse of radiation in a near vacuum. Finally, we fold the emergent neutrino spectra with the efficiencies and detection processes for a selection of modern underground neutrino observatories and argue that the prompt electron-neutrino breakout burst from the next galactic supernova is in principle observable and usefully diagnostic of fundamental collapse/supernova behavior. Though we are not in this study focusing on the supernova mechanism per se, our simulations support the theoretical conclusion (already reached by others) that spherical (1D) supernovae do not explode when good physics and transport methods are employed.Comment: 16 emulateapj pages, plus 24 postscript figures, accepted to The Astrophysical Journal; text revised; neutrino oscillation section expanded; Fig. 22 correcte

Dynamical and thermal descriptions in parton distribution functions

We suggest a duality between the standard (dynamical) and statistical distributions of partons in the nucleons. The temperature parameter entering into the statistical form for the quark distributions is estimated. It is found that this effective temperature is practically the same for the dependence on longitudinal and transverse momenta and, in turn, it is close to the freeze-out temperature in high energy heavy-ion collisions.Comment: 8 pages, 1 figure. Talk given at the 6th International Workshop on Critical Point and Onset of Deconfinement (CPOD), JINR, Dubna, 23-29 August 201

New Fermions at e+^+e−^- Colliders: I. Production and Decay

We analyze the production in $e^+e^-$ collisions of new heavy fermions stemming from extensions of the Standard Model. We write down the most general expression for the production of two heavy fermions and their subsequent decays, allowing for the polarization of the e$^+$e$^-$ initial state and taking into account the final polarization of the fermions. We then discuss the various decay modes including cascade and three body decays, and the production mechanisms, both pair production and single production in association with ordinary fermions.Comment: 21 pages (no figures), Preprint UdeM-LPN-TH-93-15

The Roles of Individual Mammalian Argonautes in RNA Interference In Vivo

Argonaute 2 (Ago2) is the only mammalian Ago protein capable of mRNA cleavage. It has been reported that the activity of the short interfering RNA targeting coding sequence (CDS), but not 3′ untranslated region (3′UTR) of an mRNA, is solely dependent on Ago2 in vitro. These studies utilized extremely high doses of siRNAs and overexpressed Ago proteins, as well as were directed at various highly expressed reporter transgenes. Here we report the effect of Ago2 in vivo on targeted knockdown of several endogenous genes by siRNAs, targeting both CDS and 3′UTR. We show that siRNAs targeting CDS lose their activity in the absence of Ago2, whereas both Ago1 and Ago3 proteins contribute to residual 3′UTR-targeted siRNA-mediated knockdown observed in the absence of Ago2 in mouse liver. Our results provide mechanistic insight into two components mediating RNAi under physiological conditions: mRNA cleavage dependent and independent. In addition our results contribute a novel consideration for designing most efficacious siRNA molecules with the preference given to 3′UTR targeting as to harness the activity of several Ago proteins.Alnylam Pharmaceuticals (Firm