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

Magnetic and axial vector form factors as probes of orbital angular momentum in the proton

We have recently examined the static properties of the baryon octet (magnetic moments and axial vector coupling constants) in a generalized quark model in which the angular momentum of a polarized nucleon is partly spin $\langle S_z \rangle$ and partly orbital $\langle L_z \rangle$. The orbital momentum was represented by the rotation of a flux-tube connecting the three constituent quarks. The best fit is obtained with $\langle S_z \rangle = 0.08\pm 0.15$, $\langle L_z \rangle = 0.42\pm 0.14$. We now consider the consequences of this idea for the $q^2$-dependence of the magnetic and axial vector form factors. It is found that the isovector magnetic form factor $G_M^{\mathrm{isovec}}(q^2)$ differs in shape from the axial form factor $F_A(q^2)$ by an amount that depends on the spatial distribution of orbital angular momentum. The model of a rigidly rotating flux-tube leads to a relation between the magnetic, axial vector and matter radii, $\langle r^2 \rangle_{\mathrm{mag}} = f_{\mathrm{spin}} \langle r^2 \rangle_{\mathrm{axial}} + \frac{5}{2} f_{\mathrm{orb}} \langle r^2 \rangle_{\mathrm{matt}}$, where $f_{\mathrm{orb}}/ f_{\mathrm{spin}} = \frac{1}{3}\langle L_z \rangle / G_A$, $f_{\mathrm{spin}} + f_{\mathrm{orb}} = 1$. The shape of $F_A(q^2)$ is found to be close to a dipole with $M_A = 0.92\pm 0.06$ GeV.Comment: 18 pages, 5 ps-figures, uses RevTe

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

How to Improve Postgenomic Knowledge Discovery Using Imputation

While microarrays make it feasible to rapidly investigate many complex biological problems, their multistep fabrication has the proclivity for error at every stage. The standard tactic has been to either ignore or regard erroneous gene readings as missing values, though this assumption can exert a major influence upon postgenomic knowledge discovery methods like gene selection and gene regulatory network (GRN) reconstruction. This has been the catalyst for a raft of new flexible imputation algorithms including local least square impute and the recent heuristic collateral missing value imputation, which exploit the biological transactional behaviour of functionally correlated genes to afford accurate missing value estimation. This paper examines the influence of missing value imputation techniques upon postgenomic knowledge inference methods with results for various algorithms consistently corroborating that instead of ignoring missing values, recycling microarray data by flexible and robust imputation can provide substantial performance benefits for subsequent downstream procedures

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

Alien chromosome segment from Aegilops speltoides and Dasypyrum villosum increases drought tolerance in wheat via profuse and deep root system

BackgroundRecurrent drought associated with climate change is a major constraint to wheat (Triticum aestivum L.) productivity. This study aimed to (i) quantify the effects of addition/substitution/translocation of chromosome segments from wild relatives of wheat on the root, physiological and yield traits of hexaploid wheat under drought, and (ii) understand the mechanism(s) associated with drought tolerance or susceptibility in wheat-alien chromosome lines.MethodsA set of 48 wheat-alien chromosome lines (addition/substitution/translocation lines) with Chinese Spring background were used. Seedling root traits were studied on solid agar medium. To understand the influence of drought on the root system of adult plants, these 48 lines were grown in 150-cm columns for 65 d under full irrigation or withholding water for 58 d. To quantify the effect of drought on physiological and yield traits, the 48 lines were grown in pots under full irrigation until anthesis; after that, half of the plants were drought stressed by withholding water for 16 d before recording physiological and yield-associated traits.ResultsThe alien chromosome lines exhibited altered root architecture and decreased photochemical efficiency and seed yield and its components under drought. The wheat-alien chromosome lines T5DS5S#3L (TA5088) with a chromosome segment from Aegilops speltoides (5S) and T5DL(.)5V#3S (TA5638) with a chromosome segment from Dasypyrum villosum (5V) were identified as drought tolerant, and the drought tolerance mechanism was associated with a deep, thin and profuse root system.ConclusionsThe two germplasm lines (TA5088 and TA5638) could be used in wheat breeding programs to improve drought tolerance in wheat and understand the underlying molecular genetic mechanisms of root architecture and drought tolerance

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

Survey strategy optimization for the Atacama Cosmology Telescope

In recent years there have been significant improvements in the sensitivity and the angular resolution of the instruments dedicated to the observation of the Cosmic Microwave Background (CMB). ACTPol is the first polarization receiver for the Atacama Cosmology Telescope (ACT) and is observing the CMB sky with arcmin resolution over about 2000 sq. deg. Its upgrade, Advanced ACTPol (AdvACT), will observe the CMB in five frequency bands and over a larger area of the sky. We describe the optimization and implementation of the ACTPol and AdvACT surveys. The selection of the observed fields is driven mainly by the science goals, that is, small angular scale CMB measurements, B-mode measurements and cross-correlation studies. For the ACTPol survey we have observed patches of the southern galactic sky with low galactic foreground emissions which were also chosen to maximize the overlap with several galaxy surveys to allow unique cross-correlation studies. A wider field in the northern galactic cap ensured significant additional overlap with the BOSS spectroscopic survey. The exact shapes and footprints of the fields were optimized to achieve uniform coverage and to obtain cross-linked maps by observing the fields with different scan directions. We have maximized the efficiency of the survey by implementing a close to 24 hour observing strategy, switching between daytime and nighttime observing plans and minimizing the telescope idle time. We describe the challenges represented by the survey optimization for the significantly wider area observed by AdvACT, which will observe roughly half of the low-foreground sky. The survey strategies described here may prove useful for planning future ground-based CMB surveys, such as the Simons Observatory and CMB Stage IV surveys.Comment: 14 Pages, 9 Figures, 4 Table

Impact of Systematic Errors in Sunyaev-Zel'dovich Surveys of Galaxy Clusters

Future high-resolution microwave background measurements hold the promise of detecting galaxy clusters throughout our Hubble volume through their Sunyaev-Zel'dovich (SZ) signature, down to a given limiting flux. The number density of galaxy clusters is highly sensitive to cluster mass through fluctuations in the matter power spectrum, as well as redshift through the comoving volume and the growth factor. This sensitivity in principle allows tight constraints on such quantities as the equation of state of dark energy and the neutrino mass. We evaluate the ability of future cluster surveys to measure these quantities simultaneously when combined with PLANCK-like CMB data. Using a simple effective model for uncertainties in the cluster mass-SZ flux relation, we evaluate systematic shifts in cosmological constraints from cluster SZ surveys. We find that a systematic bias of 10% in cluster mass measurements can give rise to shifts in cosmological parameter estimates at levels larger than the $1\sigma$ statistical errors. Systematic errors are unlikely to be detected from the mass and redshift dependence of cluster number counts alone; increasing survey size has only a marginal effect. Implications for upcoming experiments are discussed.Comment: 12 pages, 6 figures; accepted to JCAP; revised to match submitted versio

Orbital Angular Momentum Parton Distributions in Light-Front Dynamics

We study the quark angular momentum distribution in the nucleon within a light-front covariant quark model. Special emphasis is put into the orbital angular momentum: a quantity which is very sensitive to the relativistic treatment of the spin in a light-front dynamical approach. Discrepancies with the predictions of the low-energy traditional quark models where relativistic spin effects are neglected, are visible also after perturbative evolution to higher momentum scales. Orbital angular momentum distributions and their contribution to the spin sum rule are calculated for different phenomenological mass operators and compared with the results of the MIT bag model.Comment: 14 pages; latex; 3 ps figure