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.     

Cos degradation by selected co-utilizing bacteria

Applied Biochemistry and Biotechnology - The results of this study support the hypothesis that several organisms that are capable of utilizing CO are also capable of degrading CO-like compounds,...     

All-trans-1-acyloxy-1,3-pentadiene-5 ols as reactive dienes in new intramolecular diels-alder reactions

The high reactivity of the $\text{all-trans}$-1-acyloxy-1,3-pentadiene-5-ols as dienes in intramolecular Diels-Alder reactions with maleic anhydride and fumaric acid ethylester monochloride is discussed.     

Solvothermal synthesis of new metal organic framework structures in the zinc-terephthalic acid-dimethyl formamide system

Two new metal organic framework (MOF) structures have been obtained from the Zn-terephthalic acid (H₂BDC)-dimethyl formamide (DMF) system and examined by single-crystal X-ray diffraction: Zn(C₈H₄O₄)(C₃H₇NO), 1, monoclinic C2/m, a=11.1369(5), b=14.0217(7), , β=106.316(1)°, , , Z=4, R₁=0.060, wR₂=0.169, S=1.27; Zn(HCO₂)₃(C₂H₈N), 2, trigonal , a=8.1818(1), , , , Z=6, R₁=0.014, wR₂=0.039, S=1.11. Contrary to previously published structures in the same system, the crystals were obtained by solvothermal synthesis at 381 K. Structure 1 consists of 2-D layers stacked in an offset manner to accommodate DMF moieties coordinated to Zn²⁺ within voids in adjacent layers. Structure 2 consists of a 3-D network constructed from Zn²⁺ ions bridged by deprotonated formic acid moieties. Over time, the structure of 1 rearranges to Zn(C₈H₄O₄)(C₃H₇NO)(H₂O) [monoclinic P2₁/n, a=6.6456(2), b=15.2232(5), , β=104.110(2)°, , , Z=4, R₁=0.048, wR₂=0.100, S=1.07], which is identical to the known MOF-2 structure, obtained by crystallization at ambient conditions. The three structures were determined from crystals with similar crystal habits picked from a single solvothermal synthesis batch. The study demonstrates that MOF syntheses can give not only multiple crystal structures under different conditions, but also that numerous different structures, including some that are metastable, can be formed under identical conditions.     

Purification of monoclonal antibodies from cell culture supernatants using a modified zirconia based cation-exchange support

A method suitable for the isolation of monoclonal antibodies (Mabs) is described. The protocol utilizes a zirconia based column modified with ethylenediamine-N,N'-tetra(methylenephosphonic) acid to create a novel cation-exchange chromatographic support. Initial experiments using a linear salt gradient demonstrate the ability of this support to efficiently separate Mab from transferrin and bovine serum albumin in a model matrix. Results of the purification of Mab from an actual cell culture supernatant over a range in protein concentrations are also shown. Analyses by enzyme-linked immunosorbent assay and gel electrophoresis demonstrate that Mabs can be recovered from a cell culture supernatant at high yield (92-98%) and high purity (> 95%) in a single chromatographic step.     

Studies on amino acids and peptides-III. 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane 2,4-disulfide,LR, as a new racemization free coupling reagent in peptide synthesis

The easily accessible 2,4-bis (4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane 2,4-disulfide, $\text{LR}$, has been reacted with salts of N-protected amino acids $\text{1}$ (Z-Gly-OH, Boc-Gly-OH, Boc-S-Ser(Bzl)-OH, Boc-S-Tyr(Bzl)-OH, Z-S-Arg(Z₂)-OH, and Z-S-Pro-OH), at room temperature in CH₂Cl₂ to give the intermediates $\text{2}$, mixed anhydrides. When $\text{2}$ is treated with two moles of a base and one mole of the salt of an amino acid ester $\text{3}$ (TosOH·H-Gly-OBzl, HCl·H-Gly-OBzl, HCl·H-Gly-OEt, and HCl·H-S-Phe-OtBu) at 0°C, the expected peptide $\text{4}$ is isolated in high yields. LR is also found to be a useful reagent in a fragment coupling between Z-Gly-S-Ala-OH and TosOH·H-S-Leu-OBzl). This tripeptide was tested by means of HPLC (deprotection and amino acid analysis according to Izumiya was not necessary), and no epimerization (<0.7 %) was observed.     

Studies on organophosphorus compounds: Thiation of 3,1-benzoxathian-4-ones. New routes to 1,2-benzisothiazole-3(2H)-thiones and 3H-1,2-benzodithiol-3-imines

3,1-Benzoxathian-4-ones, 2, when heated with 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane-2, 4-disulfide, 1, or with P₄S₁₀ give one or more of the following products 3,1-benzoxathian-4-thione, 3, 1,3-benzodithian-4-one, 4, 1,3-benzodithian-4-thione, 5, and 3H-1,2-benzodithiole-3-thione, 6. Compounds 2, when heated with primary and secondary amines and with hydrazines, give 2-mercaptobenzamides, 7, and 2-mercaptobenzohydrazides, 8, or their corresponding disulfides, 7' and 8'. 3H-1, 2-Benzodithiol-3-immes, which are in equilibrium with 1,2-benzisothiazole-3(2H)-thiones, (9A ? 9B), are prepared by two new routes (a) by allowing 3 or 5 to react with primary amines or hydrazines, (b) by allowing 7, 8, 7' or 8' to react with 1.     

Biological production of ethanol from coal synthesis gas

The anaerobic bacteriaClostridium ljungdahlii produces ethanol and acetate from CO, CO₂, and H₂ in synthesis gas. Early studies with the bacterium showed that relatively high concentrations of ethanol could be produced by lowering the fermentation pH and eliminating yeast extract from the medium in favor of a defined medium. This article presents the results from a medium development study based on the aerobic bacteriumEscherichia coli. The results of continuous-reactor studies in a continuously stirred tank reactor (CSTR) with and without cell recycle are shown to demonstrate the utility of this improved medium.     

Investigation of tightly coupled porphyrin arrays comprised of identical monomers for multibit information storage

Our prior designs for molecular-based information storage devices have employed multiple redox-active units organized in weakly coupled, covalently linked arrays. To explore a simpler design, we report here the synthesis of porphyrin arrays where porphyrins with identical oxidation potentials are directly linked to one another instead of joined via a molecular linker. Oxidative coupling with AgPF(6) of zinc(II)-5,15-bis(4-tert-butylphenyl)-10-phenylporphyrin, obtained by a rational synthesis, afforded the expected dimer joined by a meso-meso linkage and an unexpected trimer joined by meso-meso linkages. For attachment to an electroactive surface we synthesized a meso-linked porphyrin dimer with a thiol-linker in one of the meso positions. The S-acetyl protecting group was used to avoid handling free thiol groups. Coupling of zinc(II)-5,10,15-tris(3, 5-di-tert-butylphenyl)porphyrin ("upper half") and zinc(II)-5-[4-(S-acetylthio)phenyl]-10,20-bis(3, 5-di-tert-butylphenyl)porphyrin ("lower half") afforded three different meso-linked dimers with the desired dimer as the main product. Electrochemical examination of the meso-linked dimer in solution shows that the first two oxidation potentials of the array differ by approximately 0.15 V and straddle the value exhibited by the monomeric constituents. The third and fourth oxidation potentials of the array are also split although to a lesser extent ( approximately 0.08 V) than the first and second. For the meso-linked trimer, the first three oxidation waves are also split; however, these waves are severely overlapped. The electrochemical behavior of the dimers and trimer is indicative of strong electronic interactions among the porphyrins. The thiol-derivatized meso-linked dimers form self-assembled monolayers (SAMs) on gold via in situ cleavage of the S-acetylthio protecting group. The porphyrin SAM exhibits four well-resolved oxidation waves. Regardless, the meso-meso linkage is relatively unstable upon formation of the pi-cation radical(s). This characteristic indicates that the structural motif is of limited utility for molecular information storage elements.