Towards Understanding Reasoning Complexity in Practice

Although the computational complexity of the logic underlying the standard OWL 2 for the Web Ontology Language (OWL) appears discouraging for real applications, several contributions have shown that reasoning with OWL ontologies is feasible in practice. It turns out that reasoning in practice is often far less complex than is suggested by the established theoretical complexity bound, which reflects the worstcase scenario. State-of-the reasoners like FACT++, HERMIT, PELLET and RACER have demonstrated that, even with fairly expressive fragments of OWL 2, acceptable performances can be achieved. However, it is still not well understood why reasoning is feasible in practice and it is rather unclear how to study this problem. In this paper, we suggest first steps that in our opinion could lead to a better understanding of practical complexity. We also provide and discuss some initial empirical results with HERMIT on prominent ontologie

Task-set switching with natural scenes: Measuring the cost of deploying top-down attention

In many everyday situations, we bias our perception from the top down, based on a task or an agenda. Frequently, this entails shifting attention to a specific attribute of a particular object or scene. To explore the cost of shifting top-down attention to a different stimulus attribute, we adopt the task-set switching paradigm, in which switch trials are contrasted with repeat trials in mixed-task blocks and with single-task blocks. Using two tasks that relate to the content of a natural scene in a gray-level photograph and two tasks that relate to the color of the frame around the image, we were able to distinguish switch costs with and without shifts of attention. We found a significant cost in reaction time of 23–31 ms for switches that require shifting attention to other stimulus attributes, but no significant switch cost for switching the task set within an attribute. We conclude that deploying top-down attention to a different attribute incurs a significant cost in reaction time, but that biasing to a different feature value within the same stimulus attribute is effortless

ChlamyCyc - a comprehensive database and web-portal centered on _Chlamydomonas reinhardtii_

*Background* - The unicellular green alga _Chlamydomonas reinhardtii_ is an important eukaryotic model organism for the study of photosynthesis and growth, as well as flagella development and other cellular processes. In the era of high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the whole cellular system of a single organism.
*Results* - In the framework of the German Systems Biology initiative GoFORSYS a pathway/genome database and web-portal for _Chlamydomonas reinhardtii_ (ChlamyCyc) was established, which currently features about 270 metabolic pathways with related genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification.
*Conclusion* - Chlamycyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in _Chlamydomonas reinhardtii_. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de

PDL with Negation of Atomic Programs

Propositional dynamic logic (PDL) is one of the most succesful variants of modal logic. To make it even more useful for applications, many extensions of PDL have been considered in the literature. A very natural and useful such extension is with negation of programs. Unfortunately, it is long-known that reasoning with the resulting logic is undecidable. In this paper, we consider the extension of PDL with negation of atomic programs, only. We argue that this logic is still useful, e.g. in the context of description logics, and prove that satisfiability is decidable and EXPTIME-complete using an approach based on Büchi tree automata

Quantitative temporal logics over the reals: PSpace and below

AbstractIn many cases, the addition of metric operators to qualitative temporal logics (TLs) increases the complexity of satisfiability by at least one exponential: while common qualitative TLs are complete for NP or PSpace, their metric extensions are often ExpSpace-complete or even undecidable. In this paper, we exhibit several metric extensions of qualitative TLs of the real line that are at most PSpace-complete, and analyze the transition from NP to PSpace for such logics. Our first result is that the logic obtained by extending since-until logic of the real line with the operators ‘sometime within n time units in the past/future’ is still PSpace-complete. In contrast to existing results, we also capture the case where n is coded in binary and the finite variability assumption is not made. To establish containment in PSpace, we use a novel reduction technique that can also be used to prove tight upper complexity bounds for many other metric TLs in which the numerical parameters to metric operators are coded in binary. We then consider metric TLs of the reals that do not offer any qualitative temporal operators. In such languages, the complexity turns out to depend on whether binary or unary coding of parameters is assumed: satisfiability is still PSpace-complete under binary coding, but only NP-complete under unary coding

Quantitative Temporal Logics: PSpace and below

Often the addition of metric operators to qualitative temporal logics leads to an increase of the complexity of satisfiability by at least one exponential. In this paper, we exhibit a number of metric extensions of qualitative temporal logics of the real line that do not lead to an increase in computational complexity. The main result states that the language obtained by extending since/until logic of the real line with the operators 'sometime within n time units', n coded in binary, is PSpace-complete even without the finite variability assumption. Without qualitative temporal operators the complexity of this language turns out to depend on whether binary or unary coding of parameters is assumed: it is still PSpace-hard under binary coding but in NP under unary coding

Biogenesis of β-barrel membrane proteins in bacteria and eukaryotes: evolutionary conservation and divergence

Membrane-embedded β-barrel proteins span the membrane via multiple amphipathic β-strands arranged in a cylindrical shape. These proteins are found in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. This situation is thought to reflect the evolutionary origin of mitochondria and chloroplasts from Gram-negative bacterial endosymbionts. β-barrel proteins fulfil a variety of functions; among them are pore-forming proteins that allow the flux of metabolites across the membrane by passive diffusion, active transporters of siderophores, enzymes, structural proteins, and proteins that mediate protein translocation across or insertion into membranes. The biogenesis process of these proteins combines evolutionary conservation of the central elements with some noticeable differences in signals and machineries. This review summarizes our current knowledge of the functions and biogenesis of this special family of proteins