Propositional Dynamic Logic for Message-Passing Systems

We examine a bidirectional propositional dynamic logic (PDL) for finite and infinite message sequence charts (MSCs) extending LTL and TLC-. By this kind of multi-modal logic we can express properties both in the entire future and in the past of an event. Path expressions strengthen the classical until operator of temporal logic. For every formula defining an MSC language, we construct a communicating finite-state machine (CFM) accepting the same language. The CFM obtained has size exponential in the size of the formula. This synthesis problem is solved in full generality, i.e., also for MSCs with unbounded channels. The model checking problem for CFMs and HMSCs turns out to be in PSPACE for existentially bounded MSCs. Finally, we show that, for PDL with intersection, the semantics of a formula cannot be captured by a CFM anymore

Characterizing mixed mode oscillations shaped by noise and bifurcation structure

Many neuronal systems and models display a certain class of mixed mode oscillations (MMOs) consisting of periods of small amplitude oscillations interspersed with spikes. Various models with different underlying mechanisms have been proposed to generate this type of behavior. Stochastic versions of these models can produce similarly looking time series, often with noise-driven mechanisms different from those of the deterministic models. We present a suite of measures which, when applied to the time series, serves to distinguish models and classify routes to producing MMOs, such as noise-induced oscillations or delay bifurcation. By focusing on the subthreshold oscillations, we analyze the interspike interval density, trends in the amplitude and a coherence measure. We develop these measures on a biophysical model for stellate cells and a phenomenological FitzHugh-Nagumo-type model and apply them on related models. The analysis highlights the influence of model parameters and reset and return mechanisms in the context of a novel approach using noise level to distinguish model types and MMO mechanisms. Ultimately, we indicate how the suite of measures can be applied to experimental time series to reveal the underlying dynamical structure, while exploiting either the intrinsic noise of the system or tunable extrinsic noise.Comment: 22 page

Field evaluation of entomopathogenic nematodes against orchard pests

Survival of pest in micro-plot trials (container studies) or field plot trials was monitored after exposure to commercially used EPN strains. Experimental plots were artificially infested with pest larvae that naturally burrowed into the soil for diapause. Either larval mortality or adult emergence, was assessed to estimate the control effect of the EPN treatment. Here we present preliminary results from three ongoing projects

The Injector Layout of BERLinPro

BERLinPro is an Energy Recovery Linac Project running since 2011 at the HZB in Berlin. A conceptual design report has been published in 2012 [1]. One of the key components of the project is the 100 mA superconducting RF photocathode gun under development at the HZB since 2010. Starting in 2016 the injector will go into operation, providing 6.6 MeV electrons with an emittance well below 1mm mrad and bunches shorter than 5 ps. In 2017 the 50 MeV linac will be set up and full recirculation is planned for 2018. The injector design has been finalized and is described in detail in this paper. Emphasis is further laid on beam dynamics aspects and performance simulations of two different gun cavitie

BIOCHEMICAL AND FUNCTIONAL CHARACTERIZATION OF A POTENTIAL 2’, 3’-CYCLIC-NUCLEOTIDE 3’-PHOSPHODIESTERASE (CNPASE) FOUND IN TUMORIGENIC FISH RETROVIRUSES

Tumorigenic retroviruses cause seasonal cancer in fish. Many of these retroviruses contain an interesting unknown gene of cellular origin. Computational programs predict that this gene encodes a CNPase (2’,3’-Cyclic-nucleotide 3’-phosphodiesterase). In mammals, the natural function of CNPase is unknown. The purpose of the experiment is to isolate and characterize the potential viral CNPase. Utilizing a vector from zebrafish endogenous retrovirus (ZFERV), the potential CNPase genetic sequence will be isolated and analyzed. Thereafter, the potential CNPase protein will be expressed and purified, and characterization will include enzymatic activity assays, inhibition activity studies, and NMR studies. Future studies involve functional characterization of the potential CNPase, including binding and transformation studies. Potential CNPase is predicted to function as an oncogene that promotes tumorigenesis in fish. Exploring this potential CNPase may aide in the treatment of affected fish as well as provide insight into the function of this enzyme in humans

The Isomorphism Relation Between Tree-Automatic Structures

An $\omega$-tree-automatic structure is a relational structure whose domain and relations are accepted by Muller or Rabin tree automata. We investigate in this paper the isomorphism problem for $\omega$-tree-automatic structures. We prove first that the isomorphism relation for $\omega$-tree-automatic boolean algebras (respectively, partial orders, rings, commutative rings, non commutative rings, non commutative groups, nilpotent groups of class n >1) is not determined by the axiomatic system ZFC. Then we prove that the isomorphism problem for $\omega$-tree-automatic boolean algebras (respectively, partial orders, rings, commutative rings, non commutative rings, non commutative groups, nilpotent groups of class n >1) is neither a $\Sigma_2^1$-set nor a $\Pi_2^1$-set

Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076

Members of the bacterial phylum Acidobacteria are widespread in soils and sediments worldwide, and are abundant in many soils. Acidobacteria are challenging to culture in vitro, and many basic features of their biology and functional roles in the soil have not been determined. Candidatus Solibacter usitatus strain Ellin6076 has a 9.9 Mb genome that is approximately 2–5 times as large as the other sequenced Acidobacteria genomes. Bacterial genome sizes typically range from 0.5 to 10 Mb and are influenced by gene duplication, horizontal gene transfer, gene loss and other evolutionary processes. Our comparative genome analyses indicate that the Ellin6076 large genome has arisen by horizontal gene transfer via ancient bacteriophage and/or plasmid-mediated transduction, and widespread small-scale gene duplications, resulting in an increased number of paralogs. Low amino acid sequence identities among functional group members, and lack of conserved gene order and orientation in regions containing similar groups of paralogs, suggest that most of the paralogs are not the result of recent duplication events. The genome sizes of additional cultured Acidobacteria strains were estimated using pulsed-field gel electrophoresis to determine the prevalence of the large genome trait within the phylum. Members of subdivision 3 had larger genomes than those of subdivision 1, but none were as large as the Ellin6076 genome. The large genome of Ellin6076 may not be typical of the phylum, and encodes traits that could provide a selective metabolic, defensive and regulatory advantage in the soil environment

Machine Protection Considerations for BERLinPro

The Berlin energy recovery linac project BERLinPro at the HZB is a 50 MeV ERL test facility, which addresses physical and technological questions for future superconducting rf based high brightness, high current electron beam sources. The combination of a 100 mA cw beam, electron bunches with normalized emittances lower than 1 mm mrad and the magnet optics of BERLinPro leads to power densities capable to harm the accelerator components within microseconds if total beam loss occurs. Furthermore, continuous beam loss on the level of 10 5 has to be controlled to avoid activation and to protect the SRF, beam diagnostics and other infrastructure components. In this paper, we present the evaluation of the required key parameters of the BERLinPro machine protection system and present its first conceptual desig