Finding the best visualization of an ontology

An ontology is a classification model for a given domain. In information retrieval, ontologies are used to perform broad searches. An ontology can be visualized as nodes and edges. Each node represents an element and each edge a relation between a parent and a child element. Working with an ontology becomes easier with a visual representation. An idea is to use the expressive power of 3D representation to provide visualization for the user. In this paper, we propose a new method for positioning the elements of the visualized concept lattice in the 3D world based on operations research (OR) methods. One method uses a discrete location model to create an initial solution and we propose heuristic methods to further improve the visual result. We evaluate the visual results according to our success criteria and the feedback from users. Running times of the heuristic indicate that an improved version should be feasible for on-line processing and what-if analysis of ontologies.     

Methane activation on Ni(1 1 1): Effects of poisons and step defects

We have, theoretically and experimentally, investigated the dissociation of methane on the terraces and steps of a Ni(1 1 1) surface. Using Density Functional Theory (DFT) total energy calculations combined with Ultra High Vacuum (UHV) experiments, we find that the steps exhibit a higher activity than the terraces. We have, furthermore, investigated how carbon and sulfur present on the surface will deactivate the steps, leaving only the terraces active. We find the intrinsic sticking probabilities of methane on the steps and terraces at 500 K to be 2.8 × 10⁻⁷ for the steps and 2.1 × 10⁻⁹ for the terraces, in complete agreement with our calculated difference in activation energy of 17 kJ/mol.     

Algorithms for non-linear huber estimation

The Huber criterion for data fitting is a combination of thel ₁ and thel ₂ criteria which is robust in the sense that the influence of wild data points can be reduced. We present a trust region and a Marquardt algorithm for Huber estimation in the case where the functions used in the fit are non-linear. It is demonstrated that the algorithms converge under the usual conditions.     

Photodynamic therapy of human glioma spheroids using 5-aminolevulinic acid

The response of human glioma spheroids to 5-aminolevulinic acid (ALA)-mediated photodynamic therapy (PDT) is investigated. A two-photon fluorescence microscopy technique is used to show that human glioma cells readily convert ALA to protoporphyrin IX throughout the entire spheroid volume. The central finding of this study is that the response of human glioma spheroids to ALA-mediated PDT depends not only on the total fluence, but also on the rate at which the fluence is delivered. At low fluences (< or = 50 J cm-2), lower fluence rates are more effective. At a fluence of 50 J cm-2, near-total spheroid kill is observed at fluence rates of as low as 10 mW cm-2. The fluence rate effect is not as pronounced at higher fluences (> 50 J cm-2), where a favorable response is observed throughout the range of fluence rates investigated. The clinical implications of these findings are discussed.     

Experimental tests of the feasibility of singlet oxygen luminescence monitoring in vivo during photodynamic therapy

Singlet oxygen (1O2) is thought to be the cytotoxic agent in photodynamic therapy (PDT) with current photosensitizers. Direct monitoring of 1O2 concentration in vivo would be a valuable tool in studying biological response. Attempts were made to measure 1O2 IR luminescence during PDT of cell suspensions and two murine tumour models using the photosensitizers Photofrin II and aluminium chlorosulphonated phthalocyanine. Instrumentation was virtually identical to that devised by Parker in the one positive report of in vivo luminescence detection in the literature. Despite the fact that our treatments caused cell killing and tissue necrosis, we were unable to observe 1O2 emission under any conditions. We attribute this negative result to a reduction in 1O2 lifetime in the cellular environment. Quantitative calibration of our system allowed us to estimate that the singlet oxygen lifetime in tissue is less than 0.5 microsecond. Some technical improvements are suggested which would improve detector performance and perhaps make such measurements feasible.     

Acoustic absorption in aqueous potassium phosphate

Measurements of acoustic absorption and velocity as a function of frequency and concentration in KH₂PO₄–K₂HPO₄ buffers at 4°C and pH 5-7 are reported. The dependence of the observed acoustic relaxation parameters on concentration is consistent with that to be expected from perturbation of a monomer-dimer equilibrium with an equilibrium constant [for 2H₂PO ₄ ^– (H₂PO₄)₂ ^2–] of 0.21 M^–1, a bimolecular rate constant of 5×10⁸ M^–1-sec^–1 and a standard volume change of –5 cm³ mole. The equilibrium constant for H₂PO ₄ ^– + HPO₄ ^2–H₃(PO₄)₂ ^3– is estimated to be 0.7 M^–1.     

Thiol- and disulfide-modified oligonucleotide monolayer structures on polycrystalline and single-crystal Au(111) surfaces

We provide a comprehensive study of single- (ss) and double-strand (ds) oligonucleotides with either 25 or 10 bases or base pairs (bp) immobilized on polycrystalline and single-crystal Au(111) surfaces. The study is based on X-ray photoelectron spectroscopy, cyclic and differential pulse voltammetry, interfacial capacitance data, and electrochemical scanning tunnelling microscopy (in situ STM). The sequences used were the 25-bp sequence from the BRCA1 gene (25-mer), while the 10-bp oligonucleotides contained solely linear adenine and thymine sequences. The oligonucleotides were modified by the dimethoxytrityl group (DMT) via a disulfide group [DMT-S-S-ss25-mer and DMT-S-S-ds(AT)₁₀], a pure disulfide group (A₁₀-S-S-T₁₀), or a thiol group [HS-ss25-mer and HS-ds-(AT)₁₀], all via a hexamethylene linker. The overall pattern suggests strategies for controlled adsorption of DNA-based molecules and recognition of complementary strands or other molecules.     

Refinement of borate structures from 11B MAS NMR spectroscopy and density functional theory calculations of 11B electric field gradients

The refinement of borate structures using DFT calculations combined with experimental (11)B quadrupole coupling parameters from solid-state NMR spectroscopy is presented. The (11)B electric field gradient (EFG) tensors, calculated using the WIEN2k software for trigonal and tetrahedral boron sites in a series of model compounds, exhibit a convincing linear correlation with the quadrupole coupling tensor elements, determined from (11)B MAS NMR spectra of the central or satellite transitions. The model compounds include Li(2)B(4)O(7), Mg(2)B(2)O(5), Mg(3)B(2)O(6), NH(4)B(C(6)H(5))(4), and colemanite (CaB(3)O(4)(OH)(3).H(2)O). The (11)B quadrupole moment, Q = 0.0409 +/- 0.0002 barn, derived from the linear correlation, is in excellent agreement with the accepted value for Q((11)B). This demonstrates that DFT (WIEN2k) calculations can provide precise (11)B quadrupole coupling parameters on an absolute scale. On the other hand, DFT calculations based on the reported crystal structures for datolite (CaBSiO(4)(OH)) and danburite (CaB(2)Si(2)O(8)) cannot reproduce the experimental (11)B quadrupole coupling parameters to the same high precision. However, optimization of these structures by minimization of the forces between the atoms (obtained by DFT) results in a significant improvement between the calculated and experimental (11)B quadrupole coupling parameters, which indicates that reliable refinements of the borate structures are obtained by this method. Finally, the DFT calculations also provide important structural information about the sign and orientation of the EFG tensor elements in the crystal frame, a kind of information that cannot be achieved from (11)B NMR experiments on powdered samples.