In vitro processing of herpes simplex virus type 1 DNA replication intermediates by the viral alkaline nuclease, UL12

Herpes simplex virus type 1 (HSV-1) DNA replication intermediates exist in a complex nonlinear structure that does not migrate into a pulsed-field gel. Genetic evidence suggests that the product of the UL12 gene, termed alkaline nuclease, plays a role in processing replication intermediates (R. Martinez, R. T. Sarisky, P. C. Weber, and S. K. Weller, J. Virol. 70:2075-2085, 1996). In this study we have tested the hypothesis that alkaline nuclease acts as a structure-specific resolvase. Cruciform structures generated with oligonucleotides were treated with purified alkaline nuclease; however, instead of being resolved into linear duplexes as would be expected of a resolvase activity, the artificial cruciforms were degraded. DNA replication intermediates were isolated from the well of a pulsed-field gel ("well DNA") and treated with purified HSV-1 alkaline nuclease. Although alkaline nuclease can degrade virion DNA to completion, digestion of well DNA results in a smaller-than-unit-length product that migrates as a heterogeneous smear; this product is resistant to further digestion by alkaline nuclease. The smaller-than-unit-length products are representative of the entire HSV genome, indicating that alkaline nuclease is not inhibited at specific sequences. To further probe the structure of replicating DNA, well DNA was treated with various known nucleases; our results indicate that replicating DNA apparently contains no accessible double-stranded ends but does contain nicks and gaps. Our data suggest that UL12 functions at nicks and gaps in replicating DNA to correctly repair or process the replicating genome into a form suitable for encapsidation.     

A new approach to the design of high-Tc superconductors: Metallised interlayers

We show from muon spin relaxation (SR) studies on mercury HTS superconductors that a 50-fold increase in irreversibility field obtained by partial substitution of Re for Hg is due to metallisation of the Hg/Re layer. Induced superconductivity on this metallic layer doubles the overall superfluid density. This suggests a new approach to the design of high performance HTS materials: metallising one of the non-CuO₂ interlayers and thereby greatly enhancing the superconducting properties.     

Infrastructure Federation Through Virtualized Delegation of Resources and Services

Infrastructure federation is becoming an increasingly important issue for modern Distributed Computing Infrastructures (DCIs): Dynamic elasticity of quasi-static Grid environments, incorporation of special-purpose resources into commoditized Cloud infrastructures, cross-community collaboration for increasingly diverging areas of modern e-Science, and Cloud Bursting pose major challenges on the technical level for many resource and middleware providers. Especially with respect to increasing costs of operating data centers, the intelligent yet automated and secure sharing of resources is a key factor for success. With the D-Grid Scheduler Interoperability (DGSI) project within the German D-Grid Initiative, we provide a strategic technology for the automatically negotiated, SLA-secured, dynamically provisioned federation of resources and services for Grid-and Cloud-type infrastructures. This goal is achieved by complementing current DCI schedulers with the ability to federate infrastructure for the temporary leasing of resources and rechanneling of workloads. In this work, we describe the overall architecture and SLA-secured negotiation protocols within DGSI and depict an advanced mechanism for resource delegation through means of dynamically provisioned, virtualized middleware. Through this methodology, we provide the technological foundation for intelligent capacity planning and workload management in a cross-infrastructure fashion.     

Including R-parity violation in the numerical computation of the spectrum of the minimal supersymmetric standard model: SOFTSUSY3.0

Current publicly available computer programs calculate the spectrum and couplings of the minimal supersymmetric standard model under the assumption of R-parity conservation. Here, we describe an extension to the SOFTSUSY program which includes R-parity violating effects. The user provides a theoretical boundary condition upon the high-scale supersymmetry breaking R-parity violating couplings. Successful radiative electroweak symmetry breaking, electroweak and CKM matrix data are used as weak-scale boundary conditions. The renormalisation group equations are solved numerically between the weak scale and a high energy scale using a nested iterative algorithm. This paper serves as a manual to the R-parity violating mode of the program, detailing the approximations and conventions used.

Program summary

Program title:SOFTSUSY v3.0Catalogue identifier: ADPM_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADPM_v2_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 75 927No. of bytes in distributed program, including test data, etc.: 570 916Distribution format: tar.gzProgramming language: C++, FortranComputer: Personal computerOperating system: Tested on Linux 4.xWord size: 32 bitsClassification: 11.6Catalogue identifier of previous version: ADPM_v1_0Journal reference of previous version: Comput. Phys. Comm. 143 (2002) 305Does the new version supersede the previous version?: YesNature of problem: Calculating supersymmetric particle spectrum and mixing parameters in the R-parity violating minimal supersymmetric standard model. The solution to the renormalisation group equations must be consistent with a high-scale boundary condition on supersymmetry breaking parameters and Rp parameters, as well as a weak-scale boundary condition on gauge couplings, Yukawa couplings and the Higgs potential parameters.Solution method: Nested iterative algorithmReasons for new version: This is an extension to the SOFTSUSY program which includes R-parity violating effects. The user provides a theoretical boundary condition upon the high-scale supersymmetry breaking R-parity violating couplings. Successful radiative electroweak symmetry breaking, electroweak and CKM matrix data are used as weak-scale boundary conditions. The renormalisation group equations are solved numerically between the weak scale and a high energy scale using a nested iterative algorithm. The paper serves as a manual to the R-parity violating mode of the program, detailing the approximations and conventions used.Restrictions:SOFTSUSY3.0 will provide a solution only in the perturbative regime and it assumes that all couplings of the MSSM are real (i.e. CP-conserving). The iterative SOFTSUSY algorithm will not converge if parameters are too close to a boundary of successful electroweak symmetry breaking, but a warning flag will alert the user to this fact.Running time: A few seconds per parameter point.     

Smooth velocity approximation for constrained systems in real-time simulation

The rapidly increasing complexity of multi-body system models in applications like vehicle dynamics, robotics and bio-mechanics requires qualitative new solution methods to slash computing times for the dynamical simulation.     

Online segmentation of time series based on polynomial least-squares approximations

The paper presents SwiftSeg, a novel technique for online time series segmentation and piecewise polynomial representation. The segmentation approach is based on a least-squares approximation of time series in sliding and/or growing time windows utilizing a basis of orthogonal polynomials. This allows the definition of fast update steps for the approximating polynomial, where the computational effort depends only on the degree of the approximating polynomial and not on the length of the time window. The coefficients of the orthogonal expansion of the approximating polynomial-obtained by means of the update steps-can be interpreted as optimal (in the least-squares sense) estimators for average, slope, curvature, change of curvature, etc., of the signal in the time window considered. These coefficients, as well as the approximation error, may be used in a very intuitive way to define segmentation criteria. The properties of SwiftSeg are evaluated by means of some artificial and real benchmark time series. It is compared to three different offline and online techniques to assess its accuracy and runtime. It is shown that SwiftSeg-which is suitable for many data streaming applications-offers high accuracy at very low computational costs.     

Tests and Proofs

This special issue collects current advances in the ongoing attempt to obtain synergies from the combination of Tests and Proofs.     

The physiological mirror—a system for unconscious control of a virtual environment through physiological activity

This paper introduces a system for real-time physiological measurement, analysis, and metaphorical visualization within a virtual environment (VE). Our goal is to develop a method that allows humans to unconsciously relate to parts of an environment more strongly than to others, purely induced by their own physiological responses to the virtual reality (VR) displays. In particular, we exploit heart rate, respiration, and galvanic skin response in order to control the behavior of virtual characters in the VE. Such unconscious processes may become a useful tool for storytelling or assist guiding participants through a sequence of tasks in order to make the application more interesting, e.g., in rehabilitation. We claim that anchoring of subjective bodily states to a virtual reality (VR) can enhance a person’s sense of realism of the VR and ultimately create a stronger relationship between humans and the VR.