"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

Feasible alternatives to green growth

Climate change and increasing income inequality have emerged as twin threats to contemporary standards of living, peace and democracy. These two problems are usually tackled separately in the policy agenda. A new breed of radical proposals have been advanced to manage a fair low-carbon transition. In this spirit, we develop a dynamic macrosimulation model to investigate the long-term effects of three scenarios: green growth, policies for social equity, and degrowth. The green growth scenario, based on technological progress and environmental policies, achieves a significant reduction in greenhouse gas emissions at the cost of increasing income inequality and unemployment. The policies for social equity scenario adds direct labour market interventions that result in an environmental performance similar to green growth while improving social conditions at the cost of increasing public deficit. The degrowth scenario further adds a reduction in consumption and exports, and achieves a greater reduction in emissions and inequality with higher public deficit, despite the introduction of a wealth tax. We argue that new radical social policies can combine social prosperity and low-carbon emissions and are economically and politically feasible

Stac Proteins Suppress Ca2+-Dependent Inactivation of Neuronal L-type Ca2+ Channels

Stac protein (named for its SH3-and cysteine-rich domains) was first identified in brain 20 years ago and is currently known to have three isoforms. Stac2, Stac1, and Stac3 transcripts are found at high, modest, and very low levels, respectively, in the cerebellum and forebrain, but their neuronal functions have been little investigated. Here, we tested the effects of Stac proteins on neuronal, high-voltage-activated Ca2+ channels. Overexpression of the three Stac isoforms eliminated Ca2+-dependent inactivation (CDI) ofL-type current in rat neonatal hippocampal neurons (sex unknown), but not CDI of non-L-type current. Using heterologous expression in tsA201 cells (together with β and α2-δ1 auxiliary subunits), we found that CDI for CaV1.2 and CaV1.3 (the predominant, neuronalL-type Ca2+ channels) was suppressed by all three Stac isoforms, whereas CDI for the P/Q channel, CaV2.1, was not. For CaV1.2, the inhibition of CDI by the Stac proteins appeared to involve their direct interaction with the channel’s C terminus. Within the Stac proteins, a weakly conserved segment containing ~100 residues and linking the structurally conserved PKC C1 and SH3_1 domains was sufficient to fully suppress CDI. The presence of CDI forL-type current in control neonatal neurons raised the possibility that endogenous Stac levels are low in these neurons and Western blotting indicated that the expression of Stac2 was substantially increased in adult forebrain and cerebellum compared with neonate. Together, our results indicate that one likely function of neuronal Stac proteins is to tune Ca2+ entry via neuronal L-type channels. © 2018 the authors

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

Local heating method for growth of aligned carbon nanotubes at low ambient temperature

We use a highly localised resistive heating technique to grow vertically aligned multiwalled nanotube films and aligned single-walled nanotubes on substrates with an average temperature of less than 100°C. The temperature at the catalyst can easily be as high as 1000 °C but an extremely high temperature gradient ensures that the surrounding chip is held at much lower temperatures, even as close as 1μm away from the local heater. We demonstrate the influence of temperature on the height of multi-walled nanotube films, illustrate the feasibility of sequential growth of single-walled nanotubes by switching between local heaters and also show that nanotubes can be grown over temperature sensitive materials such as resist polymer

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