The importance of scale in spatially varying coefficient modeling

While spatially varying coefficient (SVC) models have attracted considerable attention in applied science, they have been criticized as being unstable. The objective of this study is to show that capturing the "spatial scale" of each data relationship is crucially important to make SVC modeling more stable, and in doing so, adds flexibility. Here, the analytical properties of six SVC models are summarized in terms of their characterization of scale. Models are examined through a series of Monte Carlo simulation experiments to assess the extent to which spatial scale influences model stability and the accuracy of their SVC estimates. The following models are studied: (i) geographically weighted regression (GWR) with a fixed distance or (ii) an adaptive distance bandwidth (GWRa), (iii) flexible bandwidth GWR (FB-GWR) with fixed distance or (iv) adaptive distance bandwidths (FB-GWRa), (v) eigenvector spatial filtering (ESF), and (vi) random effects ESF (RE-ESF). Results reveal that the SVC models designed to capture scale dependencies in local relationships (FB-GWR, FB-GWRa and RE-ESF) most accurately estimate the simulated SVCs, where RE-ESF is the most computationally efficient. Conversely GWR and ESF, where SVC estimates are naively assumed to operate at the same spatial scale for each relationship, perform poorly. Results also confirm that the adaptive bandwidth GWR models (GWRa and FB-GWRa) are superior to their fixed bandwidth counterparts (GWR and FB-GWR)

Beyond homozygosity mapping: family-control analysis based on Hamming distance for prioritizing variants in exome sequencing

A major challenge in current exome sequencing in autosomal recessive (AR) families is the lack of an effective method to prioritize single-nucleotide variants (SNVs). AR families are generally too small for linkage analysis, and length of homozygous regions is unreliable for identification of causative variants. Various common filtering steps usually result in a list of candidate variants that cannot be narrowed down further or ranked. To prioritize shortlisted SNVs we consider each homozygous candidate variant together with a set of SNVs flanking it. We compare the resulting array of genotypes between an affected family member and a number of control individuals and argue that, in a family, differences between family member and controls should be larger for a pathogenic variant and SNVs flanking it than for a random variant. We assess differences between arrays in two individuals by the Hamming distance and develop a suitable test statistic, which is expected to be large for a causative variant and flanking SNVs. We prioritize candidate variants based on this statistic and applied our approach to six patients with known pathogenic variants and found these to be in the top 2 to 10 percentiles of ranks

Blocked All-Pairs Shortest Paths Algorithm on Intel Xeon Phi KNL Processor: A Case Study

Manycores are consolidating in HPC community as a way of improving performance while keeping power efficiency. Knights Landing is the recently released second generation of Intel Xeon Phi architecture. While optimizing applications on CPUs, GPUs and first Xeon Phi's has been largely studied in the last years, the new features in Knights Landing processors require the revision of programming and optimization techniques for these devices. In this work, we selected the Floyd-Warshall algorithm as a representative case study of graph and memory-bound applications. Starting from the default serial version, we show how data, thread and compiler level optimizations help the parallel implementation to reach 338 GFLOPS.Comment: Computer Science - CACIC 2017. Springer Communications in Computer and Information Science, vol 79

Oxidation of Nickel in AlCl3-1-Butylpyridinium Chloride at Ambient Temperature

We have studied in detail the electrochemical reaction of nickel in several kinds of molar ratio-controlled molten salts consisting of AlCl(3) and 1-butylpyridinium chloride (BPC) at 40°C. We observed NiCl(2) as an oxidation product from nickel on the surface of the electrode in slightly acidic AlCl(3)/BPC salts with molar ratios of 1.05/1.0 and 1.1/1.0. However, in strongly acidic salt with the ratio of 1.5/1.0, NiCl(2) deposits on the electrode less than when in the above salts, and no NiCl(29) is observed in basic and neutral salts with the ratio of 1.0/1.0 or less AlCl(3) content. This suggests that [NiCl(4)](2−) ions form as the oxidation of nickel in such neutral and basic AlC(3)/BPC (salts)

Impurity Effects on Quantum Depinning of Commensurate Charge Density Waves

We investigate quantum depinning of the one-dimensional (1D) commensurate charge-density wave (CDW) in the presence of one impurity theoretically. Quantum tunneling rate below but close to the threshold field is calculated at absolute zero temperature by use of the phase Hamiltonian within the WKB approximation. We show that the impurity can induce localized fluctuation and enhance the quantum depinning. The electric field dependence of the tunneling rate in the presence of the impurity is different from that in its absence.Comment: 14 pages with 13 figures. Submitted to J. Phys. Soc. Jp

Untangling CP Violation and the Mass Hierarchy in Long Baseline Experiments

In the overlap region, for the normal and inverted hierarchies, of the neutrino-antineutrino bi-probability space for $\nu_\mu \to \nu_e$ appearance, we derive a simple identity between the solutions in the ($\sin^2 2\theta_{13}$, $\sin \delta$) plane for the different hierarchies. The parameter $\sin^2 2\theta_{13}$ sets the scale of the $\nu_\mu \to \nu_e$ appearance probabilities at the atmospheric $\delta m^2_{atm} \approx 2.4 \times 10^{-3}$ eV$^2$ whereas $\sin \delta$ controls the amount of CP violation in the lepton sector. The identity between the solutions is that the difference in the values of $\sin \delta$ for the two hierarchies equals twice the value of $\sqrt{\sin^2 2\theta_{13}}$ divided by the {\it critical} value of $\sqrt{\sin^2 2\theta_{13}}$. We apply this identity to the two proposed long baseline experiments, T2K and NO$\nu$A, and we show how it can be used to provide a simple understanding of when and why fake solutions are excluded when two or more experiments are combined. The identity demonstrates the true complimentarity of T2K and NO$\nu$A.Comment: 15 pages, Latex, 4 postscript figures. Submitted to New Journal of Physics, ``Focus on Neutrino Physics'' issu

Application of Hamamatsu MPPC to T2K Neutrino Detectors

A special type of Hamamatsu MPPC, with a sensitive area of 1.3x1.3mm^2 containing 667 pixels with 50x50um^2 each, has been developed for the near neutrino detector in the T2K long baseline neutrino experiment. About 60 000 MPPCs will be used in total to read out the plastic scintillator detectors with wavelength shifting fibers. We report on the basic performance of MPPCs produced for T2K.Comment: Contribution to the proceedings of NDIP 2008, Aix-les-Bains, France, June 15-20, 200

Numerical computations of facetted pattern formation in snow crystal growth

Facetted growth of snow crystals leads to a rich diversity of forms, and exhibits a remarkable sixfold symmetry. Snow crystal structures result from diffusion limited crystal growth in the presence of anisotropic surface energy and anisotropic attachment kinetics. It is by now well understood that the morphological stability of ice crystals strongly depends on supersaturation, crystal size and temperature. Until very recently it was very difficult to perform numerical simulations of this highly anisotropic crystal growth. In particular, obtaining facet growth in combination with dendritic branching is a challenging task. We present numerical simulations of snow crystal growth in two and three space dimensions using a new computational method recently introduced by the authors. We present both qualitative and quantitative computations. In particular, a linear relationship between tip velocity and supersaturation is observed. The computations also suggest that surface energy effects, although small, have a larger effect on crystal growth than previously expected. We compute solid plates, solid prisms, hollow columns, needles, dendrites, capped columns and scrolls on plates. Although all these forms appear in nature, most of these forms are computed here for the first time in numerical simulations for a continuum model.Comment: 12 pages, 28 figure

Global analysis of neutrino masses, mixings and phases: entering the era of leptonic CP violation searches

We perform a global analysis of neutrino oscillation data, including high-precision measurements of the neutrino mixing angle theta_13 at reactor experiments, which have confirmed previous indications in favor of theta_13>0. Recent data presented at the Neutrino 2012 Conference are also included. We focus on the correlations between theta_13 and the mixing angle theta_23, as well as between theta_13 and the neutrino CP-violation phase delta. We find interesting indications for theta_23< pi/4 and possible hints for delta ~ pi, with no significant difference between normal and inverted mass hierarchy.Comment: Updated version, including recent data released at the Neutrino 2012 Conference. Some references adde