A Set of Nonparametric Tests for Experiments with Lattice-Ordered Means: Theory, Programs, and Applications

In many factorial experiments where the factors have levels that are ordinal or quantitative, a researcher may predict that the mean response in certain treatments will be higher or lower than those in other treatments. One type of order that may be anticipated is called lattice order, where average response tends to increase (or decrease) as the levels of any one of the factors is increased, holding the others fixed. A Kendall-type statistic, which measures the degree of lattice order in the data, can also be used to carry out a test involving lattice-ordered means. In this article, tests for individual factors are developed to complement the overall test of lattice order, and the methods are then applied to relevant and current data. Programs in R and FORTRAN are included to carry out the tests.

Representability of the local motivic Brouwer degree

We study which quadratic forms are representable as the local degree of a map f:An→An with an isolated zero at 0 , following the work of Kass and Wickelgren who established the connection to the quadratic form of Eisenbud, Khimshiashvili, and Levine. Our main observation is that over some base fields k , not all quadratic forms are representable as a local degree. Empirically the local degree of a map f:An→An has many hyperbolic summands, and we prove that in fact this is the case for local degrees of low rank. We establish a complete classification of the quadratic forms of rank at most 7 that are representable as the local degree of a map over all base fields of characteristic different from 2 . The number of hyperbolic summands was also studied by Eisenbud and Levine, where they establish general bounds on the number of hyperbolic forms that must appear in a quadratic form that is representable as a local degree. Our proof method is elementary and constructive in the case of rank 5 local degrees, while the work of Eisenbud and Levine is more general. We provide further families of examples that verify that the bounds of Eisenbud and Levine are tight in several cases

Identifying Structural Variation in Haploid Microbial Genomes from Short-Read Resequencing Data Using Breseq

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for similar to 25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.U.S. National Institutes of Health R00-GM087550U.S. National Science Foundation (NSF) DEB-0515729NSF BEACON Center for the Study of Evolution in Action DBI-0939454Cancer Prevention & Research Institute of Texas (CPRIT) RP130124University of Texas at Austin startup fundsUniversity of Texas at AustinCPRIT Cancer Research TraineeshipMolecular Bioscience

Community Seismic Network

The article describes the design of the Community Seismic Network, which is a dense open seismic network based on low cost sensors. The inputs are from sensors hosted by volunteers from the community by direct connection to their personal computers, or through sensors built into mobile devices. The server is cloud-based for robustness and to dynamically handle the load of impulsive earthquake events. The main product of the network is a map of peak acceleration, delivered within seconds of the ground shaking. The lateral variations in the level of shaking will be valuable to first responders, and the waveform information from a dense network will allow detailed mapping of the rupture process. Sensors in buildings may be useful for monitoring the state-of-health of the structure after major shaking

LASAGNA PLOTS: A SAUCY ALTERNATIVE TO SPAGHETTI PLOTS

Longitudinal repeated measures data has often been visualized with spaghetti plots for continuous out- comes. For large datasets, this often leads to over-plotting and consequential obscuring of trends in the data. This is primarily due to overlapping of trajectories. Here, we suggest a framework called lasagna plot ting that constrains the subject-specific trajectories to prevent overlapping and utilizes gradients of color to depict the outcome. Dynamic sorting and visualization is demonstrated as an exploratory data analysis tool. Supplemental material in the form of sample R code additional illustrated examples are available online

First principles calculations of optical properties for oxygen vacancies in binary metal oxides

Using an advanced computational methodology implemented in CP2K, a non-local PBE0-TC-LRC density functional and the recently implemented linear response formulation of the Time-dependent Density Functional Theory equations, we test the interpretation of the optical absorption and photoluminescence signatures attributed by previous experimental and theoretical studies to O-vacancies in two widely used oxides—cubic MgO and monoclinic (m)-HfO2. The results obtained in large periodic cells including up to 1000 atoms emphasize the importance of accurate predictions of defect-induced lattice distortions. They confirm that optical transitions of O-vacancies in 0, +1, and +2 charge states in MgO all have energies close to 5 eV. We test the models of photoluminescence of O-vacancies proposed in the literature. The photoluminescence of V+2O centers in m-HfO2 is predicted to peak at 3.7 eV and originate from radiative tunneling transition between a V+1O center and a self-trapped hole created by the 5.2 eV excitation