DanNet: the challenge of compiling a wordnet for Danish by reusing a monolingual dictionary

This paper is a contribution to the discussion on compiling computational lexical resources from conventional dictionaries. It describes the theoretical as well as practical problems that are encountered when reusing a conventional dictionary for compiling a lexical-semantic resource in terms of a wordnet. More specifically, it describes the methodological issues of compiling a wordnet for Danish, DanNet, from a monolingual basis, and not—as is often seen—by applying the translational expansion method with Princeton WordNet as the English source. Thus, we apply as our basis a large, corpus-based printed dictionary of modern Danish. Using this approach, we discuss the issues of readjusting inconsistent and/or underspecified hyponymy hierarchies taken from the conventional dictionary, sense distinctions as opposed to the synonym sets of wordnets, generating semantic wordnet relations on the basis of sense definitions, and finally, supplementing missing or implicit information.     

Detection of phosphorylated peptides in proteomic analyses using microfluidic compact disk technology

A compact disk (CD)-based microfluidic method for selective detection of phosphopeptides by mass spectrometry is described. It combines immobilized metal affinity chromatography (IMAC) and enzymatic dephosphorylation. Phosphoproteins are digested with trypsin and processed on the CD using nanoliter scale IMAC with and without subsequent in situ alkaline phosphatase treatment. This is followed by on-CD matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Dephosphorylation of the IMAC-enriched peptides allows selective phosphopeptide detection based on the differential mass maps generated (mass shifts of 80 Da or multiples of 80 Da). The CD contains 96 microstructures, each with a 16 nL IMAC microfluidic column. Movement of liquid is controlled by differential spinning of the disk. Up to 48 samples are distributed onto the CD in two equal sets. One set is for phosphopeptide enrichment only, the other for identical phosphopeptide enrichment but combined with in situ dephosphorylation. Peptides are eluted from the columns directly into MALDI target areas, still on the CD, using a solvent containing the MALDI matrix. After crystallization, the CD is inserted into a MALDI mass spectrometer for analysis down to the femtomole level. The average success rate in phosphopeptide detection is over 90%. Applied to noncharacterized samples, the method identified two novel phosphorylation sites, Thr 735 and Ser 737, in the ligand-binding domain of the human mineralocorticoid receptor.     

Peptide/β-Peptoid Hybrids with Activity against Vancomycin-Resistant Enterococci: Influence of Hydrophobicity and Structural Features on Antibacterial and Hemolytic Properties

Infections with enterococci are challenging to treat due to intrinsic resistance to several antibiotics. Especially vancomycin-resistant Enterococcus faecium and Enterococcus faecalis are of considerable concern with a limited number of efficacious therapeutics available. From an initial screening of 20 peptidomimetics, 11 stable peptide/β-peptoid hybrids were found to have antibacterial activity against eight E. faecium and E. faecalis isolates. Microbiological characterization comprised determination of minimal inhibitory concentrations (MICs), probing of synergy with antibiotics in a checkerboard assay, time–kill studies, as well as assessment of membrane integrity. E. faecium isolates proved more susceptible than E. faecalis isolates, and no differences in susceptibility between the vancomycin-resistant (VRE) and -susceptible E. faecium isolates were observed. A test of three peptidomimetics (Ac-[hArg-βNsce]₆-NH₂, Ac-[hArg-βNsce-Lys-βNspe]₃-NH₂ and Oct-[Lys-βNspe]₆-NH₂) in combination with conventional antibiotics (vancomycin, gentamicin, ciprofloxacin, linezolid, rifampicin or azithromycin) revealed no synergy. The same three potent analogues were found to have a bactericidal effect with a membrane-disruptive mode of action. Peptidomimetics Ac-[hArg-βNsce-Lys-βNspe]₃-NH₂ and Oct-[Lys-βNspe]₆-NH₂ with low MIC values (in the ranges 2–8 µg/mL and 4–16 µg/mL against E. faecium and E. faecalis, respectively) and displaying weak cytotoxic properties (i.e., <10% hemolysis at a ~100-fold higher concentration than their MICs; IC₅₀ values of 73 and 41 µg/mL, respectively, against HepG2 cells) were identified as promising starting points for further optimization studies.     

Systematic Verb Polysemy in MT: A Study of Danish Motion Verbs with Comparisons with Spanish

In this paper we propose a semantic apparatus based on Frame Semanticswhich enables us to treat the systematic polysemy of Danish motionverbs in a satisfactory way in relation to Machine Translation (MT).Abandoning the strategy applied in more traditional MT systems whererelated and unrelated meanings are in essence treated alike, i.e. asunrelated, we suggest an approach where relatedness in meaning isexpressed via frame element assignments and where systematicallyderived senses can thus be generated on the basis of prototypicalsenses. By contrasting Danish data with Spanish, we demonstrate thatthe identified meaning variations in Danish motion verbs are crucialnot only for analysis but also in the transfer phase where deviationsin evoked frame elements prove to trigger translations which differfrom the prototypical translations of the relevant verbs.     

Sphaerechinorhynchus ophiograndis n. sp. (Acanthocephala:Plagiorhynchidae:Sphaerechinorhynchinae), described from the intestine of a king cobra, Ophiophagus hannah

BACKGROUND/AIMS: The mechanism of action of recombinant interferon-alpha (rIFN alpha) treatment in chronic hepatitis C is not fully understood, and may include modulation of the immune system as well as a direct antiviral effect. We have therefore evaluated the plasma concentrations of pro- and anti-inflammatory cytokines in patients with chronic hepatitis C before and during treatment with rIFN alpha. METHODS: Twenty-three patients were studied. Plasma concentrations of IL-1 beta, IL-6, TNF, IL-1 receptor antagonist (IL-1RA) and soluble TNF receptors (sTNFRs) type I and type II were determined twice before rIFN alpha treatment (on day -11 and day 1), and on days 11, 32 and 120 of treatment. RESULTS: IL-1 beta, IL-6 and TNF plasma concentrations were rarely increased before treatment (in one, six and seven patients, respectively), and usually declined during treatment. sTNFRs I and II plasma concentrations were not increased either before or during treatment. This was not the case for IL-1RA. In untreated patients, the plasma concentration of IL-1RA was higher than normal in 16 out of 23 patients. When rIFN alpha treatment was initiated, there was a constant and dramatic increase in IL-1RA levels, which reached 8 times the upper limit of the normal range (p < 0.001 as compared to pretreatment values). This increase was sustained up to day 120. CONCLUSIONS: These results indicate that induction of an anti-inflammatory status through modulation of the IL-1/IL-1RA balance may be a key mechanism of action of rIFN alpha treatment in chronic hepatitis C.     

An algorithm for Exact Satisfiability analysed with the number of clauses as parameter

We give an algorithm for Exact Satisfiability with polynomial space usage and a time bound of poly(L)⋅m!, where m is the number of clauses and L is the length of the formula. Skjernaa has given an algorithm for Exact Satisfiability with time bound poly(L)⋅m² but using exponential space. We leave the following problem open: Is there an algorithm for Exact Satisfiability using only polynomial space with a time bound of cm, where c is a constant and m is the number of clauses?