Synthesising Strategy Improvement and Recursive Algorithms for Solving 2.5 Player Parity Games

2.5 player parity games combine the challenges posed by 2.5 player reachability games and the qualitative analysis of parity games. These two types of problems are best approached with different types of algorithms: strategy improvement algorithms for 2.5 player reachability games and recursive algorithms for the qualitative analysis of parity games. We present a method that - in contrast to existing techniques - tackles both aspects with the best suited approach and works exclusively on the 2.5 player game itself. The resulting technique is powerful enough to handle games with several million states

Lazy Probabilistic Model Checking without Determinisation

The bottleneck in the quantitative analysis of Markov chains and Markov decision processes against specifications given in LTL or as some form of nondeterministic B\"uchi automata is the inclusion of a determinisation step of the automaton under consideration. In this paper, we show that full determinisation can be avoided: subset and breakpoint constructions suffice. We have implemented our approach---both explicit and symbolic versions---in a prototype tool. Our experiments show that our prototype can compete with mature tools like PRISM.Comment: 38 pages. Updated version for introducing the following changes: - general improvement on paper presentation; - extension of the approach to avoid full determinisation; - added proofs for such an extension; - added case studies; - updated old case studies to reflect the added extensio

Cell-Specific Aptamers as Emerging Therapeutics

Aptamers are short nucleic acids that bind to defined targets with high affinity and specificity. The first aptamers have been selected about two decades ago by an in vitro process named SELEX (systematic evolution of ligands by exponential enrichment). Since then, numerous aptamers with specificities for a variety of targets from small molecules to proteins or even whole cells have been selected. Their applications range from biosensing and diagnostics to therapy and target-oriented drug delivery. More recently, selections using complex targets such as live cells have become feasible. This paper summarizes progress in cell-SELEX techniques and highlights recent developments, particularly in the field of medically relevant aptamers with a focus on therapeutic and drug-delivery applications

Regional and temporal parasite loads in bumble bees associated with cranberry landscapes

Abstract. There are concerns that the fitness of bumble bees that provide pollination services to cranberry could suffer within intensively managed agricultural lands. In the cranberry region of Massachusetts, the crop occurs within urbanized coastal and sand plains that generally lack floral resources. Additional stressors that compromise the health of bumble bee colonies could be the reduction of habitat and infections by parasites. In contrast to the lack of floral resources in the region, the mass bloom of managed cranberry provides abundant floral resources around July. We examined the prevalence and intensity of pathogen infection in bumble bees collected across areas of varying cranberry bloom. To determine how the amount of cranberry acreage affects the prevalence of these parasites, bumble bee queens and workers of multiple Bombus spp. were assessed for parasite presence and load. The amount of cranberry bog within 2 km of each collected bee was calculated and included in a model testing its effect on parasite prevalence and intensity. Initial investigations appeared to show higher prevalence and intensity of the trypanosome Crithidia bombi in areas with little to no acreage of cranberry bog in comparison to areas with higher acreage of cranberry. This did not hold true for Nosema bombi, Apicystis bombi, and parasitism by conopid flies. We speculate on the reasons behind our findings, including the potential effects of fungicide use and phytochemicals on the health of bumble bees

FT-ICR-massenspektrometrische Untersuchungen zur Fragmentierung isomerer Oligosaccharide

In dieser Arbeit werden zwei neue Ansätze zur Fragmentierung und Unterscheidung von isomeren Oligosacchariden beschrieben. Zum einen wurde die Photodissoziation von Oligosacchariden mit sichtbarem Licht (VisPD) durchgeführt. Als Analysator wurde dabei ein Fouriertransformations-Ionenzyklotronresonanz-Massenspektrometer (FT-ICR-MS) verwendet. Maltopentaose (MP), Lacto-N-fucopentaose I (LNFP I) und Lacto-N-fucopentaose II (LNFP II) wurden zur Verbesserung der Absorption mit verschiedenen Chromophoren derivatisiert. Je nach verwendeter Ionenspezies des Derivats werden unterschiedliche Fragmentierungsmuster beobachtet. Die Ionen fragmentieren überwiegend durch glycosidische Bindungsbrüche. Intensive Ringbrüche finden nur bei der deprotonierten Spezies [MP - H]- statt. Bei allen protonierten Spezies [M+H]+ werden überwiegend Y-Typ-Ionen gebildet. In den Spektren der Spezies [M+Na]+, [M+K]+ und [M+2Na]2+ dominieren B- und Y-Typ-Ionen, aber auch C-Typ-Ionen und ein intensiver 0,1A-Bindungsbruch am reduzierenden Ende wird beobachtet. Bei der VisPD der Spezies [M+H+Li]2+, [M+H+Na]2+ und [M+H+K]2+ werden B- und Y-, aber auch Z- und C-Typ-Ionen gebildet. Eine massenspektrometrische Unterscheidung der Isomere LNFPI und LNFPII ist anhand dieser Fragmentspektren und der Fragmentspektren der deprotonierten Derivate [M - H]- möglich. Bei der VisPD entstehen eine größere Anzahl von Fragmenten als bei der Collision Induced Dissoziation (CID). Zum anderen wurden dimere und trimere Cluster von LNFPI und LNFPII massenspektrometrisch untersucht. Die dimeren Cluster [2M+H+A]2+ bzw. [2M+B]2+ bilden sich bei Additiv-Ionenradien zwischen 113pm und 164 pm. Als Additive wurden dabei (A) Li+, Na+, K+, Rb+, Cs+ und NH4+ oder (B) Sr2+ und Ba2+ verwendet. Bei Ionenradien zwischen 132pm und 152pm besitzen die Cluster zusätzlich ein auffälliges Fragmentierungsverhalten. In den CID-Spektren dieser Cluster ([2M+H+K]2+, [2M+Sr]2+ und [2M+Ba]2+) können dimere Clusterfragment und auch isomerenspezifische Signale identifiziert werden

Opening a next-generation black box: Ecological trends for hundreds of species-like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit

Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. The faster evolving protein-encoding gene priB was used to reveal ecological patterns hidden within a single operational taxonomic unit (OTU) defined by >99% 16S rRNA sequence similarity. The studied subcluster PnecC of the genus Polynucleobacter represents a ubiquitous group of abundant freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3,400 km (42 degrees N to 71 degrees N) and a pH gradient of 4.2 to 8.6. In addition to the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. An unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca2+-rich and Ca2+-poor habitats. This compositional pattern strongly resembled the vicariance of plant species on silicate and limestone soils. The new cultivation-independent approach presented opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria

Scenario Approach for Parametric Markov Models

In this paper, we propose an approximating framework for analyzing parametric Markov models. Instead of computing complex rational functions encoding the reachability probability and the reward values of the parametric model, we exploit the scenario approach to synthesize a relatively simple polynomial approximation. The approximation is probably approximately correct (PAC), meaning that with high confidence, the approximating function is close to the actual function with an allowable error. With the PAC approximations, one can check properties of the parametric Markov models. We show that the scenario approach can also be used to check PRCTL properties directly, without synthesizing the polynomial at first hand. We have implemented our algorithm in a prototype tool and conducted thorough experiments. The experimental results demonstrate that our tool is able to compute polynomials for more benchmarks than state of the art tools such as PRISM and Storm, confirming the efficacy of our PAC-based synthesis.Comment: 24 pages, 8 figure

ISCASMC: A Web-Based Probabilistic Model Checker

We introduce the web-based model checker iscasMc for probabilistic systems (see http://iscasmc.ios.ac.cn/IscasMC). This Java application offers an easy-to-use web interface for the evaluation of Markov chains and decision processes against PCTL and PCTL specifications. Compared to PRISM or MRMC, iscasMc is particularly efficient in evaluating the probabilities of LTL properties. © 2014 Springer International Publishing Switzerland.We introduce the web-based model checker iscasMc for probabilistic systems (see http://iscasmc.ios.ac.cn/IscasMC). This Java application offers an easy-to-use web interface for the evaluation of Markov chains and decision processes against PCTL and PCTL specifications. Compared to PRISM or MRMC, iscasMc is particularly efficient in evaluating the probabilities of LTL properties. © 2014 Springer International Publishing Switzerland