Neural networks for model-free and scale-free automated planning

Knowledge and Information Systems - Automated planning for problems without an explicit model is an elusive research challenge. However, if tackled, it could provide a general approach to problems...     

Search for speaker identity in historical oral archives

We present our ongoing research focused on speaker recognition in historical oral archives. This research is part of our long-term effort aimed at enabling versatile access to the archive of the Czech Radio (CRo). Based on a manually annotated partition of the archive, we compiled a database covering a time span of more than 30 years to carry out our experimental study. Hence we were able to investigate the impact of various aspects that make it challenging to process historical data. We show the shift of scores for target (genuine) speaker trials introduced by the aging effect, the value of the signal-to-noise ratio or by the variable amount of the enrollment and test data. Scores for speaker detection trials were assessed by a system based on the i-vector paradigm and probabilistic linear discriminative analysis. We also assessed the performance of this system using an evaluation database containing contemporary recordings collected over a time span of approximately 4 years. Although using state-of-the-art techniques, capable of dealing with nuisance inter-session variability, we demonstrate remarkable degradation in the performance of the system in the evaluation containing historical data compared to the one containing contemporary data only. Specifically, the Equal Error Rate (EER) of the system rose to 8.27 % from 1.93 %. The revealed difference thus exemplifies that compensation techniques need to be employed to cope with additional variability introduced in the historical data by various sources.     

The Anticancer Drug Ellipticine Activated with Cytochrome P450 Mediates DNA Damage Determining Its Pharmacological Efficiencies: Studies with Rats,Hepatic Cytochrome P450 Reductase Null (HRN?) Mice and Pure Enzymes

Ellipticine is a DNA-damaging agent acting as a prodrug whose pharmacological efficiencies and genotoxic side effects are dictated by activation with cytochrome P450 (CYP). Over the last decade we have gained extensive experience in using pure enzymes and various animal models that helped to identify CYPs metabolizing ellipticine. In this review we focus on comparison between the in vitro and in vivo studies and show a necessity of both approaches to obtain valid information on CYP enzymes contributing to ellipticine metabolism. Discrepancies were found between the CYP enzymes activating ellipticine to 13-hydroxy- and 12-hydroxyellipticine generating covalent DNA adducts and those detoxifying this drug to 9-hydroxy- and 7-hydroellipticine in vitro and in vivo. In vivo, formation of ellipticine-DNA adducts is dependent not only on expression levels of CYP3A, catalyzing ellipticine activation in vitro, but also on those of CYP1A that oxidize ellipticine in vitro mainly to the detoxification products. The finding showing that cytochrome b₅ alters the ratio of ellipticine metabolites generated by CYP1A1/2 and 3A4 explained this paradox. Whereas the detoxification of ellipticine by CYP1A and 3A is either decreased or not changed by cytochrome b₅, activation leading to ellipticine-DNA adducts increased considerably. We show that (I) the pharmacological effects of ellipticine mediated by covalent ellipticine-derived DNA adducts are dictated by expression levels of CYP1A, 3A and cytochrome b₅, and its own potency to induce these enzymes in tumor tissues, (II) animal models, where levels of CYPs are either knocked out or induced are appropriate to identify CYPs metabolizing ellipticine in vivo, and (III) extrapolation from in vitro data to the situation in vivo is not always possible, confirming the need for these animal models.     

Polymerase Synthesis and Restriction Enzyme Cleavage of DNA Containing 7‐Substituted 7‐Deazaguanine Nucleobases

Previous studies of polymerase synthesis of base‐modified DNAs and their cleavage by restriction enzymes have mostly related only to 5‐substituted pyrimidine and 7‐substituted 7‐deazaadenine nucleotides. Here we report the synthesis of a series of 7‐substituted 7‐deazaguanine 2′‐deoxyribonucleoside 5′‐O‐triphosphates (dG^RTPs), their use as substrates for polymerase synthesis of modified DNA and the influence of the modification on their cleavage by type II restriction endonucleases (REs). The dG^RTPs were generally good substrates for polymerases but the PCR products could not be visualised on agarose gels by intercalator staining, due to fluorescence quenching. The presence of 7‐substituted 7‐deazaguanine residues in recognition sequences of REs in most cases completely blocked the cleavage.     

Serum testing of genetically modified soybeans with special emphasis on potential allergenicity of the heterologous protein CP4 EPSPS

Roundup Ready soy contains the CP4-enolpyruvylshikimate-3-phosphate synthase (CP4 EPSPS) protein. Serum IgE from two distinct populations of soy-allergic patients were recruited to determine their IgE-binding specificity. One population consisted of 10 adult patients from Europe, whose primary diagnosis was soy food allergy with some also having mite allergy. In addition, 6 primarily mite-allergic, 6 food-allergic (celery, carrot, milk, shrimp, walnut, and apple), and 5 non-allergic patients were tested. Another population consisted of 13 children from Korea, whose primary diagnosis was atopic dermatitis and secondarily soy and egg sensitization. In addition, 11 non-allergic patients were tested. Each patient population was extensively characterized with respect to clinical symptoms, specific IgE (CAP) scores, and total IgE. Immunoblots and ELISA assays were developed using serum IgE from these patients and soy extracts, CP4 EPSPS, rice extract, ovalbumin, rubisco, purified major peanut allergen Ara h 2, the putative soy allergen Gly m Bd 30k and mite allergen Der f 2 proteins as the intended targets. Immunoblot results indicated that soy-allergic patients bound soy extracts but did not specifically bind rubisco or CP4 EPSPS. ELISA results were in general agreement with the immunoblot results except that rubisco bound significant quantities of serum IgE from some patients. These results indicate that the CP4 EPSPS protein does not bind significant quantities of IgE from two geographically distinct sensitive populations and there is no evidence for an increased allergenic potential of this biotech protein.     

Boysenberry and blackcurrant drinks increased the plasma antioxidant capacity in an elderly population but had little effect on other markers of oxidative stress

BACKGROUND: The consumption of fruit and vegetables promotes good health by protecting against various degenerative diseases. Even though the constituents responsible are not known, some evidence indicates that the antioxidant properties of fruit and vegetable phytochemicals are responsible. Previous studies have shown that blackcurrant and Boysenberry reduce oxidative stress using in vitro cell systems. The aim of this study was to determine if blackcurrant or Boysenberry drinks could improve measures of oxidative stress and inflammation in an elderly population with below‐average memory abilities. The intervention parallel study was fully blinded with a placebo control. RESULTS: Of the six measures of oxidative stress assessed, only plasma antioxidant capacity significantly increased for both the Boysenberry and blackcurrant treatments compared with the placebo. Plasma malondialdehyde decreased in both the Boysenberry and blackcurrant treatments although the decrease was not statistically significant. Measures of oxidative stress for protein oxidation and lipid peroxidation improved for the berryfruit treatments during the study but were not statistically different from the placebo. CONCLUSION: Long‐term consumption of both the Boysenberry and blackcurrant drinks raised the plasma total antioxidant capacity of the study participants suggesting that Boysenberry and blackcurrant may help protect against oxidative stress‐related health conditions. Copyright © 2007 Society of Chemical Industry     

Hydrolyzed fumonisins HFB1 and HFB2 are acylated in vitro and in vivo by ceramide synthase to form cytotoxic N-acyl-metabolites

Fumonisins B1 and B2 (FB1 and FB2) are the most abundant members of the fumonisins--mycotoxins that are produced by Fusarium verticillioides and are natural inhibitors of ceramide synthase. Their hydrolyzed forms, HFB1 and HFB2 (also called AP1 and AP2) are found in some foods, and they are not only inhibitors of ceramide synthase but also undergo acylation by this enzyme. This study characterized the conversion of HFB1 and HFB2 by ceramide synthase to their respective N-acylated metabolites using rat liver microsomes and palmitoyl-CoA or nervonoyl-CoA as cosubstrates, and examined animals that had been dosed with hydrolyzed fumonisins to ascertain if acylation occurs in vivo. Using an HPLC-MS/MS method that allowed the sensitive and selective detection of the acylation products, both HFB1 and HFB2 were found to be metabolized in vitro to nervonoyl- or palmitoyl-HFB1 and -HFB2 (i.e. C24:1-HFB1/2 and C16-HFB1/2, respectively). The apparent vmax was considerably higher for formation of C24:1HFB1 (157 pmol/min/mg protein) than for formation of C16HFB1 (8.7 pmol/min/mg protein). The acylation products also inhibited ceramide synthase and significantly reduced the number of viable cells in an in vitro [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)] assay using a human colonic cell line (HT29). Furthermore, HPLC-MS/MS analysis of tissues from rats given intraperitoneal doses of HFB1 confirmed that formation of N-acyl-HFB1 occurs in vivo to produce metabolites with fatty acids of various chain lengths. The contribution of acylated HFB1 and HFB2 metabolites to fumonisin toxicity in vivo warrants further investigation.     

Assessment of green cleaning effectiveness on polychrome surfaces by MALDI‐TOF mass spectrometry and microscopic imaging

This article proposes an innovative methodology which employs nondestructive techniques to assess the effectiveness of new formulations based on ionic liquids, as alternative solvents for enzymes (proteases), for the removal of proteinaceous materials from painted surfaces during restoration treatments. Ionic liquids (ILs), also known as “designer” solvents, because of their peculiar properties which can be adjusted by selecting different cation‐anion combinations, are potentially green solvents due totheir low vapour pressure. In this study, two ionic liquids were selected: IL1 (1‐butyl‐3‐methylimidazolium tetrafluoroborate ([BMIM][BF₄])) and IL2 (1‐ethyl‐3‐methylimidazolium ethylsulphate ([EMIM][EtSO₄])). New formulations were prepared with these ILs and two different proteases (E): one acid (E1—pepsin) and one alkaline (E2—obtained from Aspergillus sojae). These formulations were tested on tempera and oil mock‐up samples, prepared in accordance with historically documented recipes, and covered with two different types of protein‐based varnishes (egg white and isinglass—fish glue). A noninvasive multiscale imaging methodology was applied before and after the treatment to evaluate the cleaning's effectiveness. Different microscopic techniques—optical microscopy (OM) with visible and fluorescent light, scanning electron microscopy (SEM) and atomic force microscopy (AFM)—together with Matrix‐Assisted Laser Desorption/Ionization—Time of Flight Mass Spectrometry (MALDI‐TOF MS) were applied on areas cleaned with the new formulations (IL + E) and reference areas cleaned only with the commercial enzyme formulations (gels). MALDI‐TOF proved particularly very useful for comparing the diversity and abundance of peptides released by using different enzymatic systems. Microsc. Res. Tech. 77:574–585, 2014. © 2014 Wiley Periodicals, Inc.     

Chemical,technological, and nutritional characteristics of two lines of “farro” (Triticum turgidum ssp. dicoccum)

In recent years, the renewed interest for foods with a natural image has increased the demand for dry pasta produced from “hulled” wheat such as the Triticum turgidum ssp. dicoccum, also known as “farro”. In order to contribute to the general knowledge, two lines of farro were considered in this study. To have a comparison, an old cultivar of Triticum turgidum ssp. durum (Senatore Cappelli) in addition to a commercial semolina were also examined. All semolina samples were used to produce pasta samples. Results showed some differences among pasta samples that seem to be due not to the presence of specific protein subunits but especially to the quantitative ratio between the different subunits. Results also reconfirmed the role played by the drying technology that is able to affect the sensory characteristics of pasta products.