"Virus hunting" using radial distance weighted discrimination

Motivated by the challenge of using DNA-seq data to identify viruses in human blood samples, we propose a novel classification algorithm called "Radial Distance Weighted Discrimination" (or Radial DWD). This classifier is designed for binary classification, assuming one class is surrounded by the other class in very diverse radial directions, which is seen to be typical for our virus detection data. This separation of the 2 classes in multiple radial directions naturally motivates the development of Radial DWD. While classical machine learning methods such as the Support Vector Machine and linear Distance Weighted Discrimination can sometimes give reasonable answers for a given data set, their generalizability is severely compromised because of the linear separating boundary. Radial DWD addresses this challenge by using a more appropriate (in this particular case) spherical separating boundary. Simulations show that for appropriate radial contexts, this gives much better generalizability than linear methods, and also much better than conventional kernel based (nonlinear) Support Vector Machines, because the latter methods essentially use much of the information in the data for determining the shape of the separating boundary. The effectiveness of Radial DWD is demonstrated for real virus detection.Comment: Published at http://dx.doi.org/10.1214/15-AOAS869 in the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Playing with the future: social irrealism and the politics of aesthetics

In this paper we wish to explore the political possibilities of video games. Numerous scholars now take seriously the place of popular culture in the remaking of our geographies, but video games still lag behind. For us, this tendency reflects a general response to them as imaginary spaces that are separate from everyday life and 'real' politics. It is this disconnect between abstraction and lived experience that we complicate by defining play as an event of what Brian Massumi calls lived abstraction. We wish to short-circuit the barriers that prevent the aesthetic resonating with the political and argue that through their enactment, video games can animate fantastical futures that require the player to make, and reflect upon, profound ethical decisions that can be antagonistic to prevailing political imaginations. We refer to this as social irrealism to demonstrate that reality can be understood through the impossible and the imagined

Global Hopf bifurcation in the ZIP regulatory system

Regulation of zinc uptake in roots of Arabidopsis thaliana has recently been modeled by a system of ordinary differential equations based on the uptake of zinc, expression of a transporter protein and the interaction between an activator and inhibitor. For certain parameter choices the steady state of this model becomes unstable upon variation in the external zinc concentration. Numerical results show periodic orbits emerging between two critical values of the external zinc concentration. Here we show the existence of a global Hopf bifurcation with a continuous family of stable periodic orbits between two Hopf bifurcation points. The stability of the orbits in a neighborhood of the bifurcation points is analyzed by deriving the normal form, while the stability of the orbits in the global continuation is shown by calculation of the Floquet multipliers. From a biological point of view, stable periodic orbits lead to potentially toxic zinc peaks in plant cells. Buffering is believed to be an efficient way to deal with strong transient variations in zinc supply. We extend the model by a buffer reaction and analyze the stability of the steady state in dependence of the properties of this reaction. We find that a large enough equilibrium constant of the buffering reaction stabilizes the steady state and prevents the development of oscillations. Hence, our results suggest that buffering has a key role in the dynamics of zinc homeostasis in plant cells.Comment: 22 pages, 5 figures, uses svjour3.cl

Cuticular protein with a low complexity sequence becomes cross-linked during insect cuticle sclerotization and is required for the adult molt

Citation: Mun, S., Noh, M. Y., Dittmer, N. T., Muthukrishnan, S., Kramer, K. J., Kanost, M. R., & Arakane, Y. (2015). Cuticular protein with a low complexity sequence becomes cross-linked during insect cuticle sclerotization and is required for the adult molt. Scientific Reports, 5, 11. doi:10.1038/srep10484In the insect cuticle, structural proteins (CPs) and the polysaccharide chitin are the major components. It has been hypothesized that CPs are cross-linked to other CPs and possibly to chitin by quinones or quinone methides produced by the laccase2-mediated oxidation of N-acylcatechols. In this study we investigated functions of TcCP30, the third most abundant CP in protein extracts of elytra (wing covers) from Tribolium castaneum adults. The mature TcCP30 protein has a low complexity and highly polar amino acid sequence. TcCP30 is localized with chitin in horizontal laminae and vertically oriented columnar structures in rigid cuticles, but not in soft and membranous cuticles. Immunoblot analysis revealed that TcCP30 undergoes laccase2-mediated cross-linking during cuticle maturation in vivo, a process confirmed in vitro using recombinant rTcCP30. We identified TcCPR27 and TcCPR18, the two most abundant proteins in the elytra, as putative crosslinking partners of TcCP30. RNAi for the TcCP30 gene had no effect on larval and pupal growth and development. However, during adult eclosion, similar to 70% of the adults were unable to shed their exuvium and died. These results support the hypothesis that TcCP30 plays an integral role as a cross-linked structural protein in the formation of lightweight rigid cuticle of the beetle

Lead-free high-temperature dielectrics with wide operational range

The dielectric, electrical and structural properties of (1-x) (0.94Bi(1/2)Na(1/2)TiO(3)-0.06BaTiO(3))-xK(0.5)Na(0.5)NbO(3) (BNT-BT-xKNN) with x=0.09, 0.12, 0.15, and 0.18 were investigated as potential candidates for high-temperature capacitors with a working temperature far beyond 200 degrees C. Temperature dependent dielectric permittivity (epsilon) showed two local broad maxima that at the optimal composition of KNN (x=0.18) are combined to form a plateau. This then results in a highly temperature-insensitive permittivity up to similar to 300 degrees C at the expense of a small reduction in absolute permittivity values. High-temperature in situ x-ray diffraction study showed pseudocubic symmetry without obvious structural changes, which implies that the dielectric anomalies observed could only be a consequence of a slight change in space group. BNT-BT-0.18KNN showed a permittivity of similar to 2150 at the frequency of 1 kHz at 150 degrees C with a normalized permittivity epsilon/epsilon(150 degrees C) varying no more than +/- 10% from 43 to 319 degrees C. With very good electrical properties persisting up to 300 degrees C, i.e., a resistivity on the order of magnitude of 10(8) Omega m and the RC constant of about 1 s, the examined BNT-BT-xKNN compositions present a good starting point for the development of high-temperature capacitor materials.open343

Constraints on the χ_(c1) versus χ_(c2) polarizations in proton-proton collisions at √s = 8 TeV

The polarizations of promptly produced χ_(c1) and χ_(c2) mesons are studied using data collected by the CMS experiment at the LHC, in proton-proton collisions at √s=8  TeV. The χ_c states are reconstructed via their radiative decays χ_c → J/ψγ, with the photons being measured through conversions to e⁺e⁻, which allows the two states to be well resolved. The polarizations are measured in the helicity frame, through the analysis of the χ_(c2) to χ_(c1) yield ratio as a function of the polar or azimuthal angle of the positive muon emitted in the J/ψ → μ⁺μ⁻ decay, in three bins of J/ψ transverse momentum. While no differences are seen between the two states in terms of azimuthal decay angle distributions, they are observed to have significantly different polar anisotropies. The measurement favors a scenario where at least one of the two states is strongly polarized along the helicity quantization axis, in agreement with nonrelativistic quantum chromodynamics predictions. This is the first measurement of significantly polarized quarkonia produced at high transverse momentum