Genome sequence of enterovirus D68 from St. Louis, Missouri, USA, 2016

Enterovirus D68 (EV-D68) was rarely observed prior to a widespread outbreak in 2014. We observed its reemergence in St. Louis in 2016 and sequenced the EV-D68 genomes from two patient samples. The 2016 viruses in St. Louis differed from those we had sequenced from the 2014 outbreak but were similar to other viruses circulating nationally in 2016

The Seiberg-Witten prepotential and the Euler class of the reduced moduli space of instantons

The n-instanton contribution to the Seiberg-Witten prepotential of N=2 supersymmetric d=4 Yang Mills theory is represented as the integral of the exponential of an equivariantly exact form. Integrating out an overall scale and a U(1) angle the integral is rewritten as (4n-3) fold product of a closed two form. This two form is, formally, a representative of the Euler class of the Instanton moduli space viewed as a principal U(1) bundle, because its pullback under bundel projection is the exterior derivative of an angular one-form.Comment: LaTex, 15 page

Enhanced virome sequencing using targeted sequence capture

Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications

Application of the direct Liapunov method to the problem of symmetric stability in the atmosphere

The problem of symmetric stability is examined within the context of the direct Liapunov method. The sufficient conditions for stability derived by Fjørtoft are shown to imply finite-amplitude, normed stability. This finite-amplitude stability theorem is then used to obtain rigorous upper bounds on the saturation amplitude of disturbances to symmetrically unstable flows.By employing a virial functional, the necessary conditions for instability implied by the stability theorem are shown to be in fact sufficient for instability. The results of Ooyama are improved upon insofar as a tight two-sided (upper and lower) estimate is obtained of the growth rate of (modal or nonmodal) symmetric instabilities.The case of moist adiabatic systems is also considered

The backbone of the climate network

We propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system, relying on the nonlinear mutual information of time series analysis and betweenness centrality of complex network theory. We show, that this approach reveals a rich internal structure in complex climate networks constructed from reanalysis and model surface air temperature data. Our novel method uncovers peculiar wave-like structures of high energy flow, that we relate to global surface ocean currents. This points to a major role of the oceanic surface circulation in coupling and stabilizing the global temperature field in the long term mean (140 years for the model run and 60 years for reanalysis data). We find that these results cannot be obtained using classical linear methods of multivariate data analysis, and have ensured their robustness by intensive significance testing.Comment: 6 pages, 5 figure

Renormalization group theory for finite-size scaling in extreme statistics

We present a renormalization group (RG) approach to explain universal features of extreme statistics, applied here to independent, identically distributed variables. The outlines of the theory have been described in a previous Letter, the main result being that finite-size shape corrections to the limit distribution can be obtained from a linearization of the RG transformation near a fixed point, leading to the computation of stable perturbations as eigenfunctions. Here we show details of the RG theory which exhibit remarkable similarities to the RG known in statistical physics. Besides the fixed points explaining universality, and the least stable eigendirections accounting for convergence rates and shape corrections, the similarities include marginally stable perturbations which turn out to be generic for the Fisher-Tippett-Gumbel class. Distribution functions containing unstable perturbations are also considered. We find that, after a transitory divergence, they return to the universal fixed line at the same or at a different point depending on the type of perturbation.Comment: 15 pages, 8 figures, to appear in Phys. Rev.

Loss of CLN7 results in depletion of soluble lysosomal proteins and impaired mTOR reactivation

Defects in the MFSD8 gene encoding the lysosomal membrane protein CLN7 lead to CLN7 disease, a neurodegenerative lysosomal storage disorder belonging to the group of neuronal ceroid lipofuscinoses (NCLs). Here we have performed a SILAC-based quantitative analysis of the lysosomal proteome using Cln7-deficient mouse embryonic fibroblasts (MEFs) from a Cln7 knockout (ko) mouse model. From 3335 different proteins identified, we detected 56 soluble lysosomal proteins and 29 highly abundant lysosomal membrane proteins. Quantification revealed that the amounts of 12 different soluble lysosomal proteins were significantly reduced in Cln7 ko MEFs compared with wild type controls. One of the most significantly depleted lysosomal proteins was Cln5 protein that underlies another distinct NCL disorder. Expression analyses showed that the mRNA expression, biosynthesis, intracellular sorting and proteolytic processing of Cln5 were not affected, whereas the depletion of mature Cln5 protein was due to increased proteolytic degradation by cysteine proteases in Cln7 ko lysosomes. Considering the similar phenotypes of CLN5 and CLN7 patients, our data suggest that depletion of CLN5 may play an important part in the pathogenesis of CLN7 disease. In addition, we found a defect in the ability of Cln7 ko MEFs to adapt to starvation conditions as shown by impaired mammalian target of rapamycin complex 1 reactivation, reduced autolysosome tubulation and increased perinuclear accumulation of autolysosomes compared to controls. In summary, depletion of multiple soluble lysosomal proteins suggest a critical role of CLN7 for lysosomal function, which may contribute to the pathogenesis and progression of CLN7 disease

The social construct of climate and climate change

Different time scales of climate change and their differential perception in society are discussed. A historical examination of natural climate changes during the past millennium suggests that short-term changes, especially crucial changes, trigger a significant response in and by society. Short-term changes correspond to the "time horizon of everyday life", that is, to a time scale from days and weeks to a few years. The anticipated anthropogenic climate changes, however, are expected to occur on a longer time scale. They require a response by society not on the basis of primary experience but on the basis of scientifically constructed scenarios and ways in which such information is represented in the modern media for example. Socio—economic impact research relies on concepts that are based on the premise of perfectly informed actors for the development of optimal adaptation strategies. In contrast to such a conception, we develop the concept of a "social construct of climate" as decisive for the public perception of scientific knowledge about climate and for public policy on climate change. The concept is illustrated using a number of examples