Prolog/Rex-a way to extend Prolog for better knowledgerepresentation

Prolog/Rex represents a powerful amalgamation of the latest techniques for knowledge representation and processing, rich in semantic features that ease the difficult task of encoding heterogeneous knowledge of real-world applications. The Prolog/Rex concept mechanism lets a user represent domain entities in terms of their structural and behavioral properties, including multiple inheritance, arbitrary user-defined relations among entities, annotated values (demons), incomplete knowledge, etc. A flexible rule language helps the knowledge engineer capture human expertise and provide flexible control of the reasoning process. Additional Prolog/Rex strength that cannot be found in any other hybrid language made on top of Prolog is language level support for keeping many potentially contradictory solutions to a problem, allowing possible solutions and their implications to be automatically generated and completely explored before they are committed. The same mechanism is used to model time-states, which are useful in planning and scheduling applications of Prolog/Rex     

Morphometric and some immunohistochemical characteristics of human choroids plexus stroma and psammoma bodies

Psammoma bodies (PBs) are one of many choroids plexus aging changes. The aim of our research was to perform the quantification of PBs' presence in human choroids plexus stroma, as well as to evaluate the characteristics of choroids plexus stroma in cases in which PBs were present. Afterwards, the observations of the histochemical analysis would be confirmed by immunohistochemical analysis. Choroid plexuses of 30 cadavers were used for the histochemical and, choroids plexuses of 15 cadavers in which PBs' presence was confirmed during the histochemical analysis, were used as material for the immunohistochemical analysis. Light microscopy, histochemical, immunohistochemical, and morphometric method were applied during the study. Classification of the cases was performed by cluster analysis. We observed increase of choroids plexus PBs' presence during the aging process. But this increase is not linear. Their presence is the largest in the second cluster that is younger than the third and older than the first. Nuclear morphometric parameters of the stroma in these cases showed that the cellular composition in this cluster is different than in other two and, that contain larger number of lymphoid cells. Immunohistochemical analysis showed PBs' positive reaction on vimentin, CD45R0, and LCA markers, while in their vicinity, as well as inside them, numerous T-cells were observed. So, the presence of CD45R0 and LCA-positive T cells, PBs' positive reaction on the same markers, indirectly connect these cells with PBs' formation process.     

Prolog/Rex inference engine

Abstract: Prolog/Rex supports the construction of knowledge-based systems, allowing frames (Prolog/Rex concepts) and rules to be combined, and providing language level support for hypothetical reasoning and assumption-based truth maintenance (Prolog/Rex viewpoint mechanism). To increase run-time performance during rule execution, Prolog/Rex provides two complementary rule compilation techniques: the simple indexing scheme and the heavily modified Rete expansion method. To improve the efficiency of the inference engine, we built an agenda-based rule manager that uses priority mechanism and/or heuristics embedded in meta-rules to control the rule firing order. Forward- and backward-chaining can be combined within the same program.     

A Comprehensive Study of the Interaction between Peptidoglycan Fragments and the Extracellular Domain of Mycobacterium tuberculosis Ser/Thr Kinase PknB

The Mycobacterium tuberculosis Ser/Thr kinase PknB is implicated in the regulation of bacterial cell growth and cell division. The intracellular kinase function of PknB is thought to be triggered by peptidoglycan (PGN) fragments that are recognized by the extracytoplasmic domain of PknB. The PGN in the cell wall of M. tuberculosis has several unusual modifications, including the presence of N-glycolyl groups (in addition to N-acetyl groups) in the muramic acid residues and amidation of d -Glu in the peptide chains. Using synthetic PGN fragments incorporating these diverse PGN structures, we analyzed their binding characters through biolayer interferometry (BLI), NMR spectroscopy, and native mass spectrometry (nMS) techniques. The results of BLI showed that muropeptides containing 1,6-anhydro-MurNAc and longer glycan chains exhibited higher binding potency and that the fourth amino acid of the peptide stem, d -Ala, was crucial for protein recognition. Saturation transfer difference (STD) NMR spectroscopy indicated the major involvement of the stem peptide region in the PASTA-PGN fragment binding. nMS suggested that the binding stoichiometry was 1:1. The data provide the first molecular basis for the specific interaction of PGN with PknB and firmly establish PGNs as the effective ligands of PknB.     

Arylpiperazine dopamineric ligands protect neuroblastoma cells from nitric oxide (NO)-induced mitochondrial damage and apoptosis

The protective ability of novel arylpiperazine-based dopaminergic ligands against nitric oxide (NO)-mediated neurotoxicity is investigated. The most potent neuroprotective arylpiperazine identified during the study was N-{4-[2-(4-phenyl-piperazin-1-yl)ethyl]-phenyl}picolinamide, which protected SH-SY5Y human neuron-like cells from the proapoptotic effect of NO donor sodium nitroprusside (SNP) by decreasing oxidative stress, mitochondrial membrane depolarization, caspase activation and subsequent phosphatydilserine externalization/DNA fragmentation. The protective effect was associated with the inhibition of proapoptotic (JNK, ERK, AMPK) and activation of antiapoptotic (Akt) signaling pathways, in the absence of interference with intracellular NO accumulation. The neuroprotective action of arylpiperazines was shown to be independent of dopamine receptor binding, as it was not affected by the high-affinity D?/D? receptor blocker butaclamol. These results reported support the further study of arylpiperazines as potential neuroprotective agents.     

Deconstruction of GCN4/GCRE into a monomeric peptide-DNA complex

Here we describe a system that enables short peptides to bind DNA sequence-specifically. Linking the peptide covalently to DNA through a disulphide bond eliminates the unfavourable energetic cost of diffusion and thus potentiates the peptide-DNA interaction. By this approach we have deconstructed the GCN4/DNA complex into its elemental DNA recognition units. We find that the GCN4 basic region contacts the two half-sites with very different affinities and propose that this thermodynamic asymmetry plays a role in differential regulation of gene expression. Specific binding of the peptide to DNA stabilizes the disulphide bond toward reduction suggesting a novel approach to the discovery of new DNA-binding specificities.     

Application of the electrochemical quartz crystal microbalance technique to copper sonoelectrochemistry: Part 1. Sulfate-based electrolytes

The applicability of the electrochemical quartz crystal microbalance technique in an ultrasonic field created by an ultrasound probe is demonstrated for the electrodeposition of copper. Cyclic voltammetry and potentiostatic depositions in acidic sulfate-based copper electrolytes were performed at different ultrasonic intensities. The electrochemical quartz crystal microbalance was operated in ultrasonic fields with intensities up to 30 W cm⁻². For cyclic voltammetry, potential resolved and averaged (apparent) current efficiencies were calculated from mass and charge data in function of the amplitude of the ultrasonic horn. Ultrasound slightly affected the current efficiencies during copper deposition in cyclic voltammetry, but did not change the efficiencies during dissolution. During potentiostatic depositions the current efficiency increased from 84% to almost 100% upon application of ultrasound. Morphology of deposits prepared by potentiostatic depositions was analyzed by scanning electron microscopy, and found to be different at high ultrasonic intensities.     

Exploring the interatomic forces between tip and single molecules during STM manipulation

The interaction between a single molecule and the STM tip during intramolecular manipulation is investigated in detail. We show that the conformational change of complex organic molecules can be induced reversibly and very reliably by using exclusively attractive forces. By studying the dependence of this process on the bias voltage and the tip position, the driving forces are characterized. Different regimes of tip-molecule interactions are observed as a function of the distance.