On the Testing of Seismicity Models

Recently a likelihood-based methodology has been developed by the Collaboratory for the Study of Earthquake Predictability (CSEP) with a view to testing and ranking seismicity models. We analyze this approach from the standpoint of possible applications to hazard analysis. We arrive at the conclusion that model testing can be made more efficient by focusing on some integral characteristics of the seismicity distribution. This is achieved either in the likelihood framework but with economical and physically reasonable coarsening of the phase space or by choosing a suitable measure of closeness between empirical and model seismicity rate in this space.Comment: To appear at Acta Geophysic

Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices

Introduction Oligochaetes are recognized as valuable bioindicators of sediment quality in streams and lakes. The development of an oligochaete index based on the identification of specimens using DNA barcodes requires a method for simultaneously preserving the DNA quality and information on the specimen density and oligochaete community composition. Absolute ethanol optimally preserves DNA but fixation of freshwater oligochaetes with this medium can cause disintegration and fragmentation of specimens. Here, we investigated the possibility to preserve oligochaete specimens in low-pH formalin and in neutral buffered formalin for up to four weeks before genetic analyses and tested if the addition of absolute ethanol to formalin-fixed oligochaetes resulted in a loss of specimens and/or species. Methods We performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of a fragment of the cytochrome c oxidase I (COI) gene on tissue fragments preserved in low-pH formalin for up to 3 weeks and in neutral buffered formalin for up to 4 weeks. In addition, we compared the density and taxonomic composition of formalin-fixed oligochaetes of several sieved sediment samples before and after the addition of absolute ethanol. Results The COI fragment of all oligochaete specimens preserved in neutral buffered formalin for up to 28 days was successfully amplified by PCR and obtained sequences were complete and of high quality. The amplification success rate for low-pH formalin fixed specimens declined after 7 days of storage. The addition of absolute ethanol to formalin-fixed oligochaete communities did not alter density or diversity estimates. Discussion Our results indicate that sediment samples can be stored in neutral buffered formalin for up to 4 weeks and the sieved material can then be transferred to absolute ethanol, without affecting DNA quality, density and community composition of oligochaetes. Based on these results, a protocol for preserving freshwater oligochaetes, describing all the steps from collection of sediments to preservation of the biological material in absolute ethanol, is proposed. This method of fixation/preservation is of relevance for establishing DNA barcode reference databases, inventories of genetic diversity and developing genetically based biological indices

The architecture of the simian varicella virus transcriptome

Primary infection with varicella-zoster virus (VZV) causes varicella and the establishment of lifelong latency in sensory ganglion neurons. In one-third of infected individuals VZV reactivates from latency to cause herpes zoster, often complicated by difficult-to-treat chronic pain. Experimental infection of non-human primates with simian varicella virus (SVV) recapitulates most features of human VZV disease, thereby providing the opportunity to study the pathogenesis of varicella and herpes zoster in vivo. However, compared to VZV, the transcriptome and the full coding potential of SVV remains incompletely understood. Here, we performed nanopore direct RNA sequencing to annotate the SVV transcriptome in lytically SVV-infected African green monkey (AGM) and rhesus macaque (RM) kidney epithelial cells. We refined structures of canonical SVV transcripts and uncovered numerous RNA isoforms, splicing events, fusion transcripts and non-coding RNAs, mostly unique to SVV. We verified the expression of canonical and newly identified SVV transcripts in vivo, using lung samples from acutely SVV-infected cynomolgus macaques. Expression of selected transcript isoforms, including those located in the unique left-end of the SVV genome, was confirmed by reverse transcription PCR. Finally, we performed detailed characterization of the SVV homologue of the VZV latency-associated transcript (VLT), located antisense to ORF61. Analogous to VZV VLT, SVV VLT is multiply spliced and numerous isoforms are generated using alternative transcription start sites and extensive splicing. Conversely, low level expression of a single spliced SVV VLT isoform defines in vivo latency. Notably, the genomic location of VLT core exons is highly conserved between SVV and VZV. This work thus highlights the complexity of lytic SVV gene expression and provides new insights into the molecular biology underlying lytic and latent SVV infection. The identification of the SVV VLT homolog further underlines the value of the SVV non-human primate model to develop new strategies for prevention of herpes zoster

Photon-photon correlations and entanglement in doped photonic crystals

We consider a photonic crystal (PC) doped with four-level atoms whose intermediate transition is coupled near-resonantly with a photonic band-gap edge. We show that two photons, each coupled to a different atomic transition in such atoms, can manifest strong phase or amplitude correlations: One photon can induce a large phase shift on the other photon or trigger its absorption and thus operate as an ultrasensitive nonlinear photon-switch. These features allow the creation of entangled two-photon states and have unique advantages over previously considered media: (i) no control lasers are needed; (ii) the system parameters can be chosen to cause full two-photon entanglement via absorption; (iii) a number of PCs can be combined in a network.Comment: Modified, expanded text; added reference

Tunneling times with covariant measurements

We consider the time delay of massive, non-relativistic, one-dimensional particles due to a tunneling potential. In this setting the well-known Hartman effect asserts that often the sub-ensemble of particles going through the tunnel seems to cross the tunnel region instantaneously. An obstacle to the utilization of this effect for getting faster signals is the exponential damping by the tunnel, so there seems to be a trade-off between speedup and intensity. In this paper we prove that this trade-off is never in favor of faster signals: the probability for a signal to reach its destination before some deadline is always reduced by the tunnel, for arbitrary incoming states, arbitrary positive and compactly supported tunnel potentials, and arbitrary detectors. More specifically, we show this for several different ways to define ``the same incoming state'' and ''the same detector'' when comparing the settings with and without tunnel potential. The arrival time measurements are expressed in the time-covariant approach, but we also allow the detection to be a localization measurement at a later time.Comment: 12 pages, 2 figure

Assessment of the effects of wastewater treatment plant effluents on receiving streams using oligochaete communities of the porous matrix

Human activities can disturb the natural dynamics of exchanges between surface water and groundwater in rivers. Such exchanges contribute to the self-purification of the environment and an excess of infiltration can lead to contamination of groundwater. In addition, the porous matrix (coarse surface sediments and hyporheic zone), through which water exchanges occur, is a sink for pollutants. For environmental monitoring programs, it is therefore essential to take into account both the dynamics of vertical hydrological exchanges and the biological quality of this matrix. The functional trait (FTR) method, which is based on the study of oligochaete communities in coarse surface sediments and the hyporheic zone, was proposed as a tool to simultaneously assess the dynamics of vertical hydrological exchanges and the effects of pollutants present in the porous matrix. Here, we applied this method during two different periods (in March and September 2016), upstream and downstream of locations affected by discharges from wastewater treatment plants (WWTP) located in Switzerland. The biological quality of surface sediments and the hyporheic zone was shown to be better upstream of the WWTP in both campaigns. In addition, results suggested that the capacity for self-purification was lower downstream of the WWTP, and that groundwater at these locations was vulnerable to pollution by surface water. The FTR method proved valuable as a field method for detecting the effects of point source contamination on receiving streams. In the near future, this community-based approach will benefit from advances in the use of DNA barcodes for oligochaete species identification

Homogeneous nucleation of quark-gluon plasma, finite size effects and long-lived metastable objects

The general formalism of homogeneous nucleation theory is applied to study the hadronization pattern of the ultra-relativistic quark-gluon plasma (QGP) undergoing a first order phase transition. A coalescence model is proposed to describe the evolution dynamics of hadronic clusters produced in the nucleation process. The size distribution of the nucleated clusters is important for the description of the plasma conversion. The model is most sensitive to the initial conditions of the QGP thermalization, time evolution of the energy density, and the interfacial energy of the plasma-hadronic matter interface. The rapidly expanding QGP is first supercooled by about $\Delta T = T - T_c = 4-6$. Then it reheats again up to the critical temperature T_c. Finally it breaks up into hadronic clusters and small droplets of plasma. This fast dynamics occurs within the first $5-10 fm/c$. The finite size effects and fluctuations near the critical temperature are studied. It is shown that a drop of longitudinally expanding QGP of the transverse radius below 4.5 fm can display a long-lived metastability. However, both in the rapid and in the delayed hadronization scenario, the bulk pion yield is emitted by sources as large as 3-4.5 fm. This may be detected experimentally both by a HBT interferometry signal and by the analysis of the rapidity distributions of particles in narrow p_T-intervals at small p_T on an event-by-event basis.Comment: 29 pages, incl. 12 figures and 1 table; to be published in Phys. Rev.

Aging without disorder on long time scales

We study the Metropolis dynamics of a simple spin system without disorder, which exhibits glassy dynamics at low temperatures. We use an implementation of the algorithm of Bortz, Kalos and Lebowitz \cite{bortz}. This method turns out to be very efficient for the study of glassy systems, which get trapped in local minima on many different time scales. We find strong evidence of aging effects at low temperatures. We relate these effects to the distribution function of the trapping times of single configurations.Comment: 8 pages Revtex, 7 figures uuencoded (Revised version: the figures are now present

Light-Front Quantisation as an Initial-Boundary Value Problem

In the light front quantisation scheme initial conditions are usually provided on a single lightlike hyperplane. This, however, is insufficient to yield a unique solution of the field equations. We investigate under which additional conditions the problem of solving the field equations becomes well posed. The consequences for quantisation are studied within a Hamiltonian formulation by using the method of Faddeev and Jackiw for dealing with first-order Lagrangians. For the prototype field theory of massive scalar fields in 1+1 dimensions, we find that initial conditions for fixed light cone time {\sl and} boundary conditions in the spatial variable are sufficient to yield a consistent commutator algebra. Data on a second lightlike hyperplane are not necessary. Hamiltonian and Euler-Lagrange equations of motion become equivalent; the description of the dynamics remains canonical and simple. In this way we justify the approach of discretised light cone quantisation.Comment: 26 pages (including figure), tex, figure in latex, TPR 93-

On the nature of cosmic rays above the Greisen--Zatsepin--Kuz'min cut off

A re-examination of the atmospheric cascade profile of the highest energy cosmic ray is presented. The study includes air-shower simulations considering different cross sections, particle multiplicity and variation of the hadronic-event-generator to model interactions above 200 GeV. The analysis provides evidence that a medium mass nucleus primary reproduces the shower profile quite well. This result does not support the idea, increasingly popular at present, that the highest energy particles are protons, derived from the decay of supermassive relic particles. On the other hand, we show that debris of relativistic super-heavy nuclei, which can survive a 100 Mpc journey through the primeval radiation are likely to generate such a kind of cascade.Comment: Revised version, improvements per referee's suggestions. To be published in Phys. Lett.