Synthesis and Anticancer Evaluation of New Indole-Based Tyrphostin Derivatives and Their (p-Cymene)dichloridoruthenium(II) Complexes

New N-alkylindole-substituted 2-(pyrid-3-yl)-acrylonitriles with putative kinase inhibitory activity and their (p-cymene)Ru(II) piano-stool complexes were prepared and tested for their antiproliferative efficacy in various cancer models. Some of the indole-based derivatives inhibited tumor cell proliferation at (sub-)micromolar concentrations with IC₅₀ values below those of the clinically relevant multikinase inhibitors gefitinib and sorafenib, which served as positive controls. A focus was set on the investigation of drug mechanisms in HCT-116 p53-knockout colon cancer cells in order to evaluate the dependence of the test compounds on p53. Colony formation assays as well as experiments with tumor spheroids confirmed the excellent antineoplastic efficacy of the new derivatives. Their mode of action included an induction of apoptotic caspase-3/7 activity and ROS formation, as well as anti-angiogenic properties. Docking calculations with EGFR and VEGFR-2 identified the two 3-aryl-2-(pyrid-3-yl)acrylonitrile derivatives 2a and 2b as potential kinase inhibitors with a preferential activity against the VEGFR-2 tyrosine kinase. Forthcoming studies will further unveil the underlying mode of action of the promising new derivatives as well as their suitability as an urgently needed novel approach in cancer treatment.     

Active learning for extended finite state machines

We present a black-box active learning algorithm for inferring extended finite state machines (EFSM)s by dynamic black-box analysis. EFSMs can be used to model both data flow and control behavior of software and hardware components. Different dialects of EFSMs are widely used in tools for model-based software development, verification, and testing. Our algorithm infers a class of EFSMs called register automata. Register automata have a finite control structure, extended with variables (registers), assignments, and guards. Our algorithm is parameterized on a particular theory, i.e., a set of operations and tests on the data domain that can be used in guards.Key to our learning technique is a novel learning model based on so-called tree queries. The learning algorithm uses tree queries to infer symbolic data constraints on parameters, e.g., sequence numbers, time stamps, identifiers, or even simple arithmetic. We describe sufficient conditions for the properties that the symbolic constraints provided by a tree query in general must have to be usable in our learning model. We also show that, under these conditions, our framework induces a generalization of the classical Nerode equivalence and canonical automata construction to the symbolic setting. We have evaluated our algorithm in a black-box scenario, where tree queries are realized through (black-box) testing. Our case studies include connection establishment in TCP and a priority queue from the Java Class Library.     

Salmonella contamination in pigs at slaughter and on the farm: a field study using an antibody ELISA test and a PCR technique

An antibody ELISA test and a PCR method for identifying the risk of Salmonella contamination were compared in a field study on the same lots of animals in a slaughterhouse. The results were compared to investigations carried out on two farms with different prevalences of Salmonella antibody-positive animals. Salmonella antibody ELISA testing was carried out on all 383 meat juice samples derived from the diaphragm pillar muscle of each pig. Salmonella DNA analysis was performed by PCR technique on small intestine samples with lymph nodes from all 383 pigs, and on tonsils from the last 129 pigs. The 383 animals tested came from 32 different pig farms. Furthermore, the herd antibody blood serum status against Salmonella spp. of weaners was determined on two selected pig fattening farms, one with low and one with high seroprevalence in meat juice. A total of 7.0% (ELISA cut-off OD% > or =40) of the slaughtered pigs from 6 of 32 fattening farms were seropositive. Salmonella DNA was found in 16.4% of the jejunum/lymph nodes (383 animals) and in 15.5% of the tonsils (129 animals). Salmonella DNA was found in the jejunum/lymph nodes of 41% of the seropositive pigs. However, serotitres were also positive in only 17.5% of all pigs positive in the jejunum DNA test. Two farms were selected for further investigation: farm 13 (F13), with a high prevalence of seropositive pigs, 29.0%, Category II; and F11, with 9.4%, Category I. However, categorization according to the blood serum tests of the fattening pigs after on-farm testing was very different: F13 had 5% positive animals (Category I); and F11, 23.3% (Category II). The study led to the following results and recommendations: First, ELISA tests are useful for the detection of farms that are regularly contaminated with Salmonella, but such tests cannot give information on the infectious status of a single animal (or a group) at the point of slaughter. Second, it is crucial that management measures are taken to prevent the spread of infections by trade and transport: piglets should be supplied exclusively by a single, well-known producer, and finishers should be tested serologically on farm before going to slaughter. Third, ELISA tests and the PCR method are suitable for the detection of Salmonella and are recommended as analytical tools for all pork quality control programmes. Fourth, animals from suspicious farms should always be slaughtered at the end of the slaughter day, followed by thorough cleaning and disinfection.     

Food Allergens: Is There a Correlation between Stability to Digestion and Allergenicity?

Food allergy is a major health problem in the Western countries, affecting 3–8% of the population. It has not yet been established what makes a dietary protein a food allergen. Several characteristics have been proposed to be shared by food allergens. One of these is resistance to digestion. This paper reviews data from digestibility studies on purified food allergens and evaluates the predictive value of digestibility tests on the allergenic potential. We point out that food allergens do not necessarily resist digestion. We discuss how the choice of in vitro digestibility assay condition and the method used for detection of residual intact protein as well as fragments hereof may greatly influence the outcome as well as the interpretation of results. The finding that digests from food allergens may retain allergenicity, stresses the importance of using immunological assays for evaluating the allergenic potential of food allergen digestion products. Studies assessing the allergenicity of digestion products, by either IgE-binding, elicitation or sensitizing capacity, shows that digestion may abolish, decrease, have no effect, or even increase the allergenicity of food allergens. Therefore, the predictive value of the pepsin resistance test for assessing the allergenic potential of novel proteins can be questioned.     

Purification and characterisation of relevant natural and recombinant apple allergens

Apple (Malus domestica) is the most widely cultivated fruit crop in Europe and frequently causes allergic reactions with a variable degree of severity. So far, four apple allergens Mal d 1, Mal d 2, Mal d 3 and Mal d 4 have been identified. Mal d 1, a Bet v 1 related allergen, and Mal d 4, apple profilin, are sensitive to proteolytic degradation, whereas Mal d 2, a thaumatin-like protein and Mal d 3, a nonspecific lipid transfer protein, are rather stable to proteolytic processes. Mal d 1 and Mal d 4 were purified after expression in Escherichia coli expression system, while Mal d 2 and Mal d 3 were purified from apple fruit tissue. All purified proteins were subjected to detailed physicochemical characterisation to confirm their structural integrity and maintained IgE binding capacity. Detailed investigations of carbohydrate moieties of Mal d 2 demonstrated their involvement in the overall IgE binding capacity of this allergen. It was concluded that the folded structure and IgE binding capacity of all four allergens were preserved during purification.     

Including R-parity violation in the numerical computation of the spectrum of the minimal supersymmetric standard model: SOFTSUSY3.0

Current publicly available computer programs calculate the spectrum and couplings of the minimal supersymmetric standard model under the assumption of R-parity conservation. Here, we describe an extension to the SOFTSUSY program which includes R-parity violating effects. The user provides a theoretical boundary condition upon the high-scale supersymmetry breaking R-parity violating couplings. Successful radiative electroweak symmetry breaking, electroweak and CKM matrix data are used as weak-scale boundary conditions. The renormalisation group equations are solved numerically between the weak scale and a high energy scale using a nested iterative algorithm. This paper serves as a manual to the R-parity violating mode of the program, detailing the approximations and conventions used.

Program summary

Program title:SOFTSUSY v3.0Catalogue identifier: ADPM_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADPM_v2_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 75 927No. of bytes in distributed program, including test data, etc.: 570 916Distribution format: tar.gzProgramming language: C++, FortranComputer: Personal computerOperating system: Tested on Linux 4.xWord size: 32 bitsClassification: 11.6Catalogue identifier of previous version: ADPM_v1_0Journal reference of previous version: Comput. Phys. Comm. 143 (2002) 305Does the new version supersede the previous version?: YesNature of problem: Calculating supersymmetric particle spectrum and mixing parameters in the R-parity violating minimal supersymmetric standard model. The solution to the renormalisation group equations must be consistent with a high-scale boundary condition on supersymmetry breaking parameters and Rp parameters, as well as a weak-scale boundary condition on gauge couplings, Yukawa couplings and the Higgs potential parameters.Solution method: Nested iterative algorithmReasons for new version: This is an extension to the SOFTSUSY program which includes R-parity violating effects. The user provides a theoretical boundary condition upon the high-scale supersymmetry breaking R-parity violating couplings. Successful radiative electroweak symmetry breaking, electroweak and CKM matrix data are used as weak-scale boundary conditions. The renormalisation group equations are solved numerically between the weak scale and a high energy scale using a nested iterative algorithm. The paper serves as a manual to the R-parity violating mode of the program, detailing the approximations and conventions used.Restrictions:SOFTSUSY3.0 will provide a solution only in the perturbative regime and it assumes that all couplings of the MSSM are real (i.e. CP-conserving). The iterative SOFTSUSY algorithm will not converge if parameters are too close to a boundary of successful electroweak symmetry breaking, but a warning flag will alert the user to this fact.Running time: A few seconds per parameter point.     

Iron-mediated oxidation of antimony(III) by oxygen and hydrogen peroxide compared to arsenic(III) oxidation

Antimony is used in large quantities in a variety of products, though it has been declared as a pollutant of priority interest by the Environmental Protection Agency of the United States (USEPA). Oxidation processes critically affect the mobility of antimony in the environment since Sb(V) has a greater solubility than Sb(lll). In this study, the cooxidation reactions of Sb(lIl) with Fe(ll) and both O2 and H2O2 were investigated and compared to those of As(III). With increasing pH, the oxidation rate coefficients of Sb(lll) in the presence of Fe(ll) and O2 increased and followed a similar pH trend as the Fe(ll) oxidation by O2. Half-lives of Sb(lll) were 35 and 1.4 h at pH 5.0 and pH 6.2, respectively. The co-oxidation with Fe(ll) and H2O2 is about 7000 and 20 times faster than with Fe(ll) and O2 at pH 3 and pH 7, respectively. For both systems, *OH radicals appear to be the predominant oxidant below approximately pH 4, while at more neutral pH values, other unknown intermediates become important. The oxidation of As(lll) follows a similar pH trend as the Sb(lll) oxidation; however, As(lll) oxidation was roughly 10 times slower and only partly oxidized in most of the experiments. This study shows that the Fe(ll)-mediated oxidation of Sb(Ill) can be an important oxidation pathway at neutral pH values.     

How platinum oxide affects the degradation analysis of PEM fuel cell cathodes

In this work, proton exchange membrane fuel cell cathodes are degraded with accelerated-stress-tests.These PtCo containing cathodes are analyzed at begin-of-life and end-of-test with a dedicated diagnostic procedure. For every individual load point, the oxygen transport resistance and voltage losses due to the formation of platinum oxides were obtained in addition to commonly measured electrochemical surface area, high frequency resistance, as well as cathode ionomer resistance. These data were used to break down the voltage losses into six different contributors. With this break down, performance gains and performance losses were determined at end-of-test. At low current densities, it was found that voltage losses due to degradation are dominated by the loss of specific activity and catalyst surface area - in line with the state-of-the-art knowledge. But by quantifying the losses from platinum oxide formation explicitly, we show that end-of-test an unassigned voltage loss is not only present at highest current densities, but already at low current density. More precisely, the unassigned voltage loss shows a linear increase with decreasing half cell voltage and is independent from the chosen accelerated stress test. As this unassigned loss depends on half cell voltage, it might arise from ionomer adsorption.