The NWRA Classification Infrastructure: Description and Extension to the Discriminant Analysis Flare Forecasting System (DAFFS)

A classification infrastructure built upon Discriminant Analysis has been developed at NorthWest Research Associates for examining the statistical differences between samples of two known populations. Originating to examine the physical differences between flare-quiet and flare-imminent solar active regions, we describe herein some details of the infrastructure including: parametrization of large datasets, schemes for handling "null" and "bad" data in multi-parameter analysis, application of non-parametric multi-dimensional Discriminant Analysis, an extension through Bayes' theorem to probabilistic classification, and methods invoked for evaluating classifier success. The classifier infrastructure is applicable to a wide range of scientific questions in solar physics. We demonstrate its application to the question of distinguishing flare-imminent from flare-quiet solar active regions, updating results from the original publications that were based on different data and much smaller sample sizes. Finally, as a demonstration of "Research to Operations" efforts in the space-weather forecasting context, we present the Discriminant Analysis Flare Forecasting System (DAFFS), a near-real-time operationally-running solar flare forecasting tool that was developed from the research-directed infrastructure.Comment: J. Space Weather Space Climate: Accepted / in press; access supplementary materials through journal; some figures are less than full resolution for arXi

Defect free global minima in Thomson's problem of charges on a sphere

Given $N$ unit points charges on the surface of a unit conducting sphere, what configuration of charges minimizes the Coulombic energy $\sum_{i>j=1}^N 1/r_{ij}$? Due to an exponential rise in good local minima, finding global minima for this problem, or even approaches to do so has proven extremely difficult. For \hbox{$N = 10(h^2+hk+k^2)+ 2$} recent theoretical work based on elasticity theory, and subsequent numerical work has shown, that for $N \sim >500$--1000 adding dislocation defects to a symmetric icosadeltahedral lattice lowers the energy. Here we show that in fact this approach holds for all $N$, and we give a complete or near complete catalogue of defect free global minima.Comment: Revisions in Tables and Reference

Mixing by microorganisms in stratified fluids

We examine the vertical mixing induced by the swimming of microorganisms at low Reynolds and Péclet numbers in a stably stratified ocean, and show that the global contribution of oceanic microswimmers to vertical mixing is negligible. We propose two approaches to estimating the mixing efficiency, η, or the ratio of the rate of potential energy creation to the total rate-of-working on the ocean by microswimmers. The first is based on scaling arguments and estimates η in terms of the ratio between the typical organism size, a, and an intrinsic length scale for the stratified flow, l = (νκ/N2)1/4, where ν is the kinematic viscosity, κ the diffusivity, and N the buoyancy frequency. In particular, for small organisms in the relevant oceanic limit, a/l \u3c\u3c 1, we predict the scaling η ∼ (a/l)3. The second estimate of η is formed by solving the full coupled flow-stratification problem by modeling the swimmer as a regularized force dipole, and computing the efficiency numerically. Our computational results, which are examined for all ratios a/l, validate the scaling arguments in the limit a/l \u3c\u3c 1 and further predict η ≈ 1.2(a/l)3 for vertical swimming and η ≈ 0.15 (a/l)3 for horizontal swimming. These results, relevant for any stratified fluid rich in biological activity, imply that the mixing efficiency of swimming microorganisms in the ocean is at very most 8% and is likely smaller by at least two orders of magnitude

Carbohydrate receptor-mediated gene transfer to human T leukaemic cells

The mucin-type carbohydrate Tn cryptantigen (GalNAcα1-O-Ser/Thr, where GalNAc is N-acetyl-D-galactosamine) is expressed in many carcinomas, in haemopoietic disorders including the Tn syndrome, and on human immunodeficiency virus (HIV) coat glycoproteins, but is not expressed on normal, differentiated cells because of the expression of a Tn-processing galactosyltransferase. Using Jurkat T leukaemic cells which express high levels of Tn antigen due to deficient Tn galactosylation, we have established the Tn antigen-mediated gene transfer and demonstrate the considerable efficiency of this approach. We used poly(L-lysine) conjugates of the monoclonal antibody 1E3 directed against the Tn antigen to deliver the luciferase and β-galactosidase reporter genes to Jurkat cells by receptor-mediated endocytosis. Addition of unconjugated 1E3 reduced transfection efficiency in a concentration-dependent manner and incubation with free GalNAc abolished DNA transfer completely, indicating that gene delivery is indeed mediated by the Tn antigen. Pre-treatment of Jurkat cells with Vibrio cholerae sialidase, which uncovers additional Tn antigens, resulted in an improvement of gene transfection. Both human and chicken adenovirus particles attached to the DNA/polylysine complex strongly augmented transgene expression. When the β-galactosidase (lacZ) gene was delivered to Jurkat cells by Tn-mediated endocytosis, up to 60% of the cells were positive in the cytochemical stain using 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal) as a chromogenic substrate. The efficiency of the transferrin receptor-mediated DNA uptake into Jurkat cells was comparatively low, although these cells were shown to express considerable amounts of transferrin receptor. We show here that a mucin-type carbohydrate antigen mediates highly efficient DNA uptake by endocytosis into Jurkat T cells. This method represents a 50-fold improvement of Jurkat cell transfection efficiency over other physical gene transfer techniques. Specific gene delivery to primary cancer cells exhibiting Tn epitopes may especially be desirable in immunotherapy protocol

The Santa Fe Light Cone Simulation Project: I. Confusion and the WHIM in Upcoming Sunyaev-Zel'dovich Effect Surveys

We present the first results from a new generation of simulated large sky coverage (~100 square degrees) Sunyaev-Zeldovich effect (SZE) cluster surveys using the cosmological adaptive mesh refinement N-body/hydro code Enzo. We have simulated a very large (512^3h^{-3}Mpc^3) volume with unprecedented dynamic range. We have generated simulated light cones to match the resolution and sensitivity of current and future SZE instruments. Unlike many previous studies of this type, our simulation includes unbound gas, where an appreciable fraction of the baryons in the universe reside. We have found that cluster line-of-sight overlap may be a significant issue in upcoming single-dish SZE surveys. Smaller beam surveys (~1 arcmin) have more than one massive cluster within a beam diameter 5-10% of the time, and a larger beam experiment like Planck has multiple clusters per beam 60% of the time. We explore the contribution of unresolved halos and unbound gas to the SZE signature at the maximum decrement. We find that there is a contribution from gas outside clusters of ~16% per object on average for upcoming surveys. This adds both bias and scatter to the deduced value of the integrated SZE, adding difficulty in accurately calibrating a cluster Y-M relationship. Finally, we find that in images where objects with M > 5x10^{13} M_{\odot} have had their SZE signatures removed, roughly a third of the total SZE flux still remains. This gas exists at least partially in the Warm Hot Intergalactic Medium (WHIM), and will possibly be detectable with the upcoming generation of SZE surveys.Comment: 14 pages, 13 figures, version accepted to ApJ. Major revisions mad

Crawling scallop: Friction-based locomotion with one degree of freedom

c We demonstrate that friction-based locomotion with one-degree of freedom is possible. c Locomotion depends on breaking symmetry in both physical properties and kinematics. c This behavior is explained intuitively and through the system's equations of motion. c System locomotion is characterized for a range of physical and kinematic parameters. Fluid-based locomotion at low Reynolds number is subject to the constraints of the scallop theorem, which dictate that body kinematics identical under a time-reversal symmetry (in particular, those with a single degree of freedom) cannot display locomotion on average. The implications of the theorem naturally compel one to ask whether similar symmetry constraints exist for locomotion in different environments. In this work we consider locomotion along a surface where forces are described by isotropic Coulomb friction. To address whether motions with a single degree of freedom can lead to transport, we analyze a model system consisting of two bodies whose separation distance undergoes periodic time variations. The behavior of the two-body system is entirely determined by the kinematic specification of their separation, the friction forces, and the mass of each body. We show that the constraints of the scallop theorem can be escaped in frictional media if two asymmetry conditions are met at the same time: the frictional forces of each body against the surface must be distinct and the time-variation of the body-body separation must vary asymmetrically in time (so quick-slow or slowquick in the extension-contraction phases). Our results are demonstrated numerically and interpreted using asymptotic expansions

Current and Nascent SETI Instruments

Here we describe our ongoing efforts to develop high-performance and sensitive instrumentation for use in the search for extra-terrestrial intelligence (SETI). These efforts include our recently deployed Search for Extraterrestrial Emissions from Nearby Developed Intelligent Populations Spectrometer (SERENDIP V.v) and two instruments currently under development; the Heterogeneous Radio SETI Spectrometer (HRSS) for SETI observations in the radio spectrum and the Optical SETI Fast Photometer (OSFP) for SETI observations in the optical band. We will discuss the basic SERENDIP V.v instrument design and initial analysis methodology, along with instrument architectures and observation strategies for OSFP and HRSS. In addition, we will demonstrate how these instruments may be built using low-cost, modular components and programmed and operated by students using common languages, e.g. ANSI C.Comment: 12 pages, 5 figures, Original version appears as Chapter 2 in "The Proceedings of SETI Sessions at the 2010 Astrobiology Science Conference: Communication with Extraterrestrial Intelligence (CETI)," Douglas A. Vakoch, Edito

Massive stars at low metallicity: Evolution and surface abundances of O dwarfs in the SMC

We study the evolution, rotation, and surface abundances of O-type dwarfs in the Small Magellanic Cloud. We analyzed the UV and optical spectra of twenty-three objects and derived photospheric and wind properties. The observed binary fraction of the sample is ~ 26%, which is compatible with more systematic studies, if one considers that the actual binary fraction is potentially larger owing to low-luminosity companions and that the sample excluded obvious spectroscopic binaries. The location of the fastest rotators in the H-R diagram indicates that these could be several Myr old. The offset in the position of these fast rotators compared with the other stars confirms the predictions of evolutionary models that fast-rotating stars tend to evolve more vertically in the H-R diagram. Only one star of luminosity-class Vz, expected to best characterize extreme youth, is located on the ZAMS, the other two stars are more evolved. The distribution of nitrogen abundance of O and B stars suggests that the mechanisms responsible for the chemical enrichment of slowly rotating massive stars depends only weakly on the star's mass. We confirm that the group of slowly rotating N-rich stars is not reproduced by the evolutionary tracks. Our results call for stronger mixing in the models to explain the range of observed N abundances. All stars have an N/C ratio as a function of stellar luminosity that matches the predictions of the stellar evolution models well. More massive stars have a higher N/C ratio than the less massive stars. Faster rotators show on average a higher N/C ratio than slower rotators. The N/O versus N/C ratios agree qualitatively well with those of stellar evolution models. The only discrepant behavior is observed for the youngest two stars of the sample, which both show very strong signs of mixing, which is unexpected for their evolutionary status.Comment: Accepted for publication in A&A (43 pages, 60 figures

Carbohydrate receptor-mediated gene transfer to human T leukaemic cells

The mucin-type carbohydrate Tn cryptantigen (GalNAcα1-O-Ser/Thr, where GalNAc is N-acetyl-D-galactosamine) is expressed in many carcinomas, in haemopoietic disorders including the Tn syndrome, and on human immunodeficiency virus (HIV) coat glycoproteins, but is not expressed on normal, differentiated cells because of the expression of a Tn-processing galactosyltransferase. Using Jurkat T leukaemic cells which express high levels of Tn antigen due to deficient Tn galactosylation, we have established the Tn antigen-mediated gene transfer and demonstrate the considerable efficiency of this approach. We used poly(L-lysine) conjugates of the monoclonal antibody 1E3 directed against the Tn antigen to deliver the luciferase and β-galactosidase reporter genes to Jurkat cells by receptor-mediated endocytosis. Addition of unconjugated 1E3 reduced transfection efficiency in a concentration-dependent manner and incubation with free GalNAc abolished DNA transfer completely, indicating that gene delivery is indeed mediated by the Tn antigen. Pre-treatment of Jurkat cells with Vibrio cholerae sialidase, which uncovers additional Tn antigens, resulted in an improvement of gene transfection. Both human and chicken adenovirus particles attached to the DNA/polylysine complex strongly augmented transgene expression. When the β-galactosidase (lacZ) gene was delivered to Jurkat cells by Tn-mediated endocytosis, up to 60% of the cells were positive in the cytochemical stain using 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal) as a chromogenic substrate. The efficiency of the transferrin receptor-mediated DNA uptake into Jurkat cells was comparatively low, although these cells were shown to express considerable amounts of transferrin receptor. We show here that a mucin-type carbohydrate antigen mediates highly efficient DNA uptake by endocytosis into Jurkat T cells. This method represents a 50-fold improvement of Jurkat cell transfection efficiency over other physical gene transfer techniques. Specific gene delivery to primary cancer cells exhibiting Tn epitopes may especially be desirable in immunotherapy protocol