Loop Formulas for Description Logic Programs

Description Logic Programs (dl-programs) proposed by Eiter et al. constitute an elegant yet powerful formalism for the integration of answer set programming with description logics, for the Semantic Web. In this paper, we generalize the notions of completion and loop formulas of logic programs to description logic programs and show that the answer sets of a dl-program can be precisely captured by the models of its completion and loop formulas. Furthermore, we propose a new, alternative semantics for dl-programs, called the {\em canonical answer set semantics}, which is defined by the models of completion that satisfy what are called canonical loop formulas. A desirable property of canonical answer sets is that they are free of circular justifications. Some properties of canonical answer sets are also explored.Comment: 29 pages, 1 figures (in pdf), a short version appeared in ICLP'1

Ontologies on the semantic web

As an informational technology, the World Wide Web has enjoyed spectacular success. In just ten years it has transformed the way information is produced, stored, and shared in arenas as diverse as shopping, family photo albums, and high-level academic research. The “Semantic Web” was touted by its developers as equally revolutionary but has not yet achieved anything like the Web’s exponential uptake. This 17 000 word survey article explores why this might be so, from a perspective that bridges both philosophy and IT

Insulin Glargine in the Intensive Care Unit: A Model-Based Clinical Trial Design

Online 4 Oct 2012Introduction: Current succesful AGC (Accurate Glycemic Control) protocols require extra clinical effort and are impractical in less acute wards where patients are still susceptible to stress-induced hyperglycemia. Long-acting insulin Glargine has the potential to be used in a low effort controller. However, potential variability in efficacy and length of action, prevent direct in-hospital use in an AGC framework for less acute wards. Method: Clinically validated virtual trials based on data from stable ICU patients from the SPRINT cohort who would be transferred to such an approach are used to develop a 24-hour AGC protocol robust to different Glargine potencies (1.0x, 1.5x and 2.0x regular insulin) and initial dose sizes (dose = total insulin over prior 12, 18 and 24 hours). Glycemic control in this period is provided only by varying nutritional inputs. Performance is assessed as %BG in the 4.0-8.0mmol/L band and safety by %BG<4.0mmol/L. Results: The final protocol consisted of Glargine bolus size equal to insulin over the previous 18 hours. Compared to SPRINT there was a 6.9% - 9.5% absolute decrease in mild hypoglycemia (%BG<4.0mmol/L) and up to a 6.2% increase in %BG between 4.0 and 8.0mmol/L. When the efficacy is known (1.5x assumed) there were reductions of: 27% BG measurements, 59% insulin boluses, 67% nutrition changes, and 6.3% absolute in mild hypoglycemia. Conclusion: A robust 24-48 clinical trial has been designed to safely investigate the efficacy and kinetics of Glargine as a first step towards developing a Glargine-based protocol for less acute wards. Ensuring robustness to variability in Glargine efficacy significantly affects the performance and safety that can be obtained

Monads and D-instantons

Motivated by twisted N=4 supersymmetric Yang-Mills theory in 4 dimensions, a natural extension of the monad (ADHM) construction relevant to D-instantons is considered. We show that a family of Yang-Mills instantons can be constructed from D-instantons. We discuss some possible roles of reciprocity in D-brane physics. We conjecture the existence of universal instantons together with a generalized Fourier-Nahm transformation as an unifying framework of D-brane physics.Comment: 37 pages, TeX with harvmac.tex and epsf.tex, 3 figure

Quiver Bundles and Wall Crossing for Chains

Holomorphic chains on a Riemann surface arise naturally as fixed points of the natural C*-action on the moduli space of Higgs bundles. In this paper we associate a new quiver bundle to the Hom-complex of two chains, and prove that stability of the chains implies stability of this new quiver bundle. Our approach uses the Hitchin-Kobayashi correspondence for quiver bundles. Moreover, we use our result to give a new proof of a key lemma on chains (due to \'Alvarez-C\'onsul, Garc\'ia-Prada and Schmitt), which has been important in the study of Higgs bundle moduli; this proof relies on stability and thus avoids the direct use of the chain vortex equations

Lanthanoid/Alkali Metal ß-Triketonate Assemblies: A Robust Platform for Efficient NIR Emitters.

The reaction of hydrated lanthanoid chlorides with tribenzoylmethane and an alkali metal hydroxide consistently resulted in the crystallization of neutral tetranuclear assemblies with the general formula [Ln(Ae⋅HOEt)(L)4]2 (Ln=Eu3+, Er3+, Yb3+; Ae=Na+, K+, Rb+). Analysis of the crystal structures of these species revealed a coordination geometry that varied from a slightly distorted square antiprism to a slightly distorted triangular dodecahedron, with the specific geometrical shape being dependent on the degree of lattice solvation and identity of the alkali metal. The near-infrared (NIR)-emitting assemblies of Yb3+ and Er3+ showed remarkably efficient emission, characterized by significantly longer excited-state lifetimes (τobs≈37–47 μs for Yb3+ and τobs≈4–6 μs for Er3+) when compared with the broader family of lanthanoid β-diketonate species, even in the case of perfluorination of the ligands. The Eu3+ assemblies show bright red emission and a luminescence performance (τobs≈0.5 ms, equation image≈35–37 %, ηsens≈68–70 %) more akin to the β-diketonate species. The results highlight that the β-triketonate ligand offers a tunable and facile system for the preparation of efficient NIR emitters without the need for more complicated perfluorination or deuteration synthetic strategies

Molecular determinants for subcellular trafficking of the malarial sheddase PfSUB2.

The malaria merozoite invades erythrocytes in the vertebrate host. Iterative rounds of asexual intraerythrocytic replication result in disease. Proteases play pivotal roles in erythrocyte invasion, but little is understood about their mode of action. The Plasmodium falciparum malaria merozoite surface sheddase, PfSUB2, is one such poorly characterized example. We have examined the molecular determinants that underlie the mechanisms by which PfSUB2 is trafficked initially to invasion-associated apical organelles (micronemes) and then across the surface of the free merozoite. We show that authentic promoter activity is important for correct localization of PfSUB2, likely requiring canonical features within the intergenic region 5' of the pfsub2 locus. We further demonstrate that trafficking of PfSUB2 beyond an early compartment in the secretory pathway requires autocatalytic protease activity. Finally, we show that the PfSUB2 transmembrane domain is required for microneme targeting, while the cytoplasmic domain is essential for surface translocation of the protease to the parasite posterior following discharge from micronemes. The interplay of pre- and post-translational regulatory elements that coordinate subcellular trafficking of PfSUB2 provides the parasite with exquisite control over enzyme-substrate interactions

Imaging Proteins Sensitive to Direct Fusions Using Transient Peptide–Peptide Interactions

Fluorescence microscopy enables specific visualization of proteins in living cells and has played an important role in our understanding of the protein subcellular location and function. Some proteins, however, show altered localization or function when labeled using direct fusions to fluorescent proteins, making themdifficult to study in live cells. Additionally, the resolution of fluorescence microscopy is limited to ∼200 nm, which is 2 orders of magnitude larger than the size of most proteins. To circumvent these challenges, we previously developed LIVE-PAINT, a live-cell superresolution approach that takes advantage of short interacting peptides to transiently bind a fluorescent protein to the protein-ofinterest. Here, we successfully use LIVE-PAINT to image yeastmembrane proteins that do not tolerate the direct fusion of a fluorescent protein by using peptide tags as short as 5-residues. We also demonstrate that it is possible to resolve multiple proteins at the nanoscale concurrently using orthogonal peptide interaction pairs.KEYWORDS: membrane protein, protein−protein interaction, super-resolution microscopy, live-cell imaging, LIVE-PAINT, yeas