SMT-Solvers in Action: Encoding and Solving Selected Problems in NP and EXPTIME

We compare the efficiency of seven modern SMT-solvers for several decision and combinatorial problems: the bounded Post correspondence problem (BPCP), the extended string correction problem (ESCP), and the Towers of Hanoi (ToH) of exponential solutions. For this purpose, we define new original reductions to SMT for all the above problems, and show their complexity. Our extensive experimental results allow for drawing quite interesting conclusions on efficiency and applicability of SMT-solvers depending on the theory used in the encoding

FÖRSTER TRANSFER CALCULATIONS BASED ON CRYSTAL STRUCTURE DATA FROM Agmenellum quadruplicatum C-PHYCOCYANIN

Excitation energy transfer in C-phycocyanin is modeled using the Forster inductive resonance mechanism. Detailed calculations are carried out using coordinates and orientations of the chromophores derived from X-ray crystallographic studies of C-phycocyanin from two different species (Schirmer et al, J. Mol. Biol. 184, 257–277 (1985) and ibid., 188, 651-677 (1986)). Spectral overlap integrals are estimated from absorption and fluorescence spectra of C-phycocyanin of Mastigocladus laminosus and its separated subunits. Calculations are carried out for the β-subunit, αβ-monomer, (αβ)3-trimer and (αβ)0-hexamer species with the following chromophore assignments: β155 = 's’(sensitizer), β84 =‘f (fluorescer) and α84 =‘m’(intermediate):]:. The calculations show that excitation transfer relaxation occurs to 3=98% within 200 ps in nearly every case; however, the rates increase as much as 10-fold for the higher aggregates. Comparison with experimental data on fluorescence decay and depolarization kinetics from the literature shows qualitative agreement with these calculations. We conclude that Forster transfer is sufficient to account for all of the observed fluorescence properties of C-phycocyanin in aggregation states up to the hexamer and in the absence of linker polypeptides

Learning valued relations from data

Driven by a large number of potential applications in areas like bioinformatics, information retrieval and social network analysis, the problem setting of inferring relations between pairs of data objects has recently been investigated quite intensively in the machine learning community. To this end, current approaches typically consider datasets containing crisp relations, so that standard classification methods can be adopted. However, relations between objects like similarities and preferences are in many real-world applications often expressed in a graded manner. A general kernel-based framework for learning relations from data is introduced here. It extends existing approaches because both crisp and valued relations are considered, and it unifies existing approaches because different types of valued relations can be modeled, including symmetric and reciprocal relations. This framework establishes in this way important links between recent developments in fuzzy set theory and machine learning. Its usefulness is demonstrated on a case study in document retrieval

Genotypic and phenotypic variation among Staphylococcus saprophyticus from human and animal isolates

<p>Abstract</p> <p>Background</p> <p>The main aim of this study was to examine the genotypic and phenotypic diversity of <it>Staphylococcus saprophyticus </it>isolates from human and animal origin.</p> <p>Findings</p> <p>In total, 236 clinical isolates and 15 animal isolates of <it>S. saprophyticus </it>were characterized in respect of the occurrence of 9 potential virulence genes and four surface properties. All strains were PCR positive for the regulatory genes <it>agr</it>, <it>sar</it>>it>A and <it>rot </it>as well as for the surface proteins UafA and Aas. Nearly 90% of the clinical isolates were found to possess the gene for the surface-associated lipase Ssp and 10% for the collagen binding MSCRAMM SdrI. All animal isolates were negative for<it>sdrI</it>. Lipolytic activity could be detected in 66% of the clinical and 46% of the animal isolates. Adherence to collagen type I was shown of 20% of the clinical strains and 6% of the strains of animal origin. Most <it>S. saprophyticus </it>strains showed hydrophobic properties and only few could agglutinate sheep erythrocytes.</p> <p>Conclusions</p> <p>We described a broad analysis of animal and human <it>S. saprophyticus </it>isolates regarding virulence genes and phenotypic properties such as lipase activity, hydrophobicity, and adherence. While <it>S. saprophyticus </it>strains from animal sources have prerequisites for colonization of the urinary tract like the D-serine-deaminase, out findings suggested that they need to acquire new genes e.g. MSCRAMMS for adherence like sdrI and to modulate their existing properties e.g. increasing the lipase activity or reducing hydrophobicity. These apparently important new genes or properties for virulence have to be further analyzed.</p

Could Direct Killing by Larger Dingoes Have Caused the Extinction of the Thylacine from Mainland Australia?

Invasive predators can impose strong selection pressure on species that evolved in their absence and drive species to extinction. Interactions between coexisting predators may be particularly strong, as larger predators frequently kill smaller predators and suppress their abundances. Until 3500 years ago the marsupial thylacine was Australia's largest predator. It became extinct from the mainland soon after the arrival of a morphologically convergent placental predator, the dingo, but persisted in the absence of dingoes on the island of Tasmania until the 20th century. As Tasmanian thylacines were larger than dingoes, it has been argued that dingoes were unlikely to have caused the extinction of mainland thylacines because larger predators are rarely killed by smaller predators. By comparing Holocene specimens from the same regions of mainland Australia, we show that dingoes were similarly sized to male thylacines but considerably larger than female thylacines. Female thylacines would have been vulnerable to killing by dingoes. Such killing could have depressed the reproductive output of thylacine populations. Our results support the hypothesis that direct killing by larger dingoes drove thylacines to extinction on mainland Australia. However, attributing the extinction of the thylacine to just one cause is problematic because the arrival of dingoes coincided with another the potential extinction driver, the intensification of the human economy

Micromechanical Properties of Injection-Molded Starch–Wood Particle Composites

The micromechanical properties of injection molded starch–wood particle composites were investigated as a function of particle content and humidity conditions. The composite materials were characterized by scanning electron microscopy and X-ray diffraction methods. The microhardness of the composites was shown to increase notably with the concentration of the wood particles. In addition,creep behavior under the indenter and temperature dependence were evaluated in terms of the independent contribution of the starch matrix and the wood microparticles to the hardness value. The influence of drying time on the density and weight uptake of the injection-molded composites was highlighted. The results revealed the role of the mechanism of water evaporation, showing that the dependence of water uptake and temperature was greater for the starch–wood composites than for the pure starch sample. Experiments performed during the drying process at 70°C indicated that the wood in the starch composites did not prevent water loss from the samples.Peer reviewe

Isolation and characterization of a putative collagen receptor from Staphylococcus aureus strain Cowan 1

In a previous study we demonstrated that cells of Staphylococcus aureus strain Cowan bind 125I-collagen in a receptor-ligand type of interaction (Speziale, P., Raucci, G., Visai, L., Switalski, L.M., Timpl, R., and Höök, M. (1986) J. Bacteriol. 167, 77-81). In the present communication we report on the isolation and preliminary characterization of a putative collagen receptor from a lysate of S. aureus strain Cowan. Antibodies raised against a collagen receptor positive strain inhibit the binding of 125I-collagen to bacterial cells, whereas antibodies raised against a collagen receptor negative strain were without effect. Solubilized cell surface components did not exhibit any measurable affinity for collagen-Sepharose. However, the inhibitory effect of the antibodies against bacterial cells was neutralized by the lysate from a receptor-positive but not receptor-negative strain. A collagen receptor assay was designed based on this observation and used to develop a receptor purification protocol involving anion exchange chromatography, ammonium sulfate precipitation, and gel chromatography. Using this procedure a protein with an apparent Mr of 135,000 was purified. This protein which was present on a collagen receptor-positive strain but not on a receptor-negative strain could completely neutralize the inhibitory activity of the antibodies raised against S. aureus strain Cowan. Furthermore, antibodies raised against the 135-kDa protein inhibited the binding of collagen to bacteria, and this protein is tentatively identified as a collagen receptor