Taylor’s Modularity Conjecture and Related Problems for Idempotent Varieties

We provide a partial result on Taylor’s modularity conjecture, and several related problems. Namely, we show that the interpretability join of two idempotent varieties that are not congruence modular is not congruence modular either, and we prove an analog for idempotent varieties with a cube term. Also, similar results are proved for linear varieties and the properties of congruence modularity, having a cube term, congruence n-permutability for a fixed n, and satisfying a non-trivial congruence identity.     

Sorption of Sr(II) onto nanocomposites of graphene oxide-polymeric matrix

The simple method for preparation of nanocomposites of graphene oxide or carboxylated graphene oxide on polystyrene matrix and graphene oxide on PA66 matrix were developed and structures of nanocomposites were characterized by X-ray diffraction, infrared spectroscopy, Raman spectroscopy, high-resolution scanning electron microscopy, transmission electron microscopy and scanning transmission electron microscopy. The nanocomposites were investigated for radiostrontium removal from aqueous solutions. The Sr(II) sorption was dependent on pH and ionic strength at pH < 7. The Sr(II) equilibrium data were fitted by Freundlich and Langmuir models. The nanocomposites prepared were evaluated as suitable for the radiostrontium removal from contaminated wastewater.     

Three‐Dimensional Information on the Phase Domain Structure of Thin Films of Polymer Blends Revealed by Secondary Ion Mass Spectrometry

We describe the technique of dynamic secondary ion mass spectrometry developed to determine three‐dimensional phase domain structures of films of polymer blends. The polymers are composed of light elements or are labeled with deuterium or heavy elements. The applicability of this method to various polymer blends forming thin and ultrathin films with flat and undulated air/film interface is discussed.     

On homology modeling of the M2 muscarinic acetylcholine receptor subtype

Twelve homology models of the human M₂ muscarinic receptor using different sets of templates have been designed using the Prime program or the modeller program and compared to crystallographic structure (PDB:3UON). The best models were obtained using single template of the closest published structure, the M₃ muscarinic receptor (PDB:4DAJ). Adding more (structurally distant) templates led to worse models. Data document a key role of the template in homology modeling. The models differ substantially. The quality checks built into the programs do not correlate with the RMSDs to the crystallographic structure and cannot be used to select the best model. Re-docking of the antagonists present in crystallographic structure and relative binding energy estimation by calculating MM/GBSA in Prime and the binding energy function in YASARA suggested it could be possible to evaluate the quality of the orthosteric binding site based on the prediction of relative binding energies. Although estimation of relative binding energies distinguishes between relatively good and bad models it does not indicate the best one. On the other hand, visual inspection of the models for known features and knowledge-based analysis of the intramolecular interactions allows an experimenter to select overall best models manually.     

Thermodynamics of translesion synthesis across a major DNA adduct of antitumor oxaliplatin: differential scanning calorimetric study

Differential scanning calorimetry (DSC) was used to measure the thermodynamic changes associated with translesion synthesis across major lesion induced in DNA by antitumor oxaliplatin [1,2-d(GG) intrastrand cross-link]. Insertion of matched nucleotides dC at the primer terminus (across unique 3'- or 5'-dG in the unplatinated template) and subsequent extensions resulted in an incremental increase in thermodynamic parameters. In contrast, incorporation of dC opposite either platinated dG in the intrastrand cross-link formed in the template strand and subsequent extensions by one nucleotide resulted only in little changes in thermodynamics. A similar thermodynamic delay was observed for a control template primer containing a dG:dT mismatch across 3'- or 5'-dG in the template and subsequent Watson-Crick primer extensions. The thermodynamic scarcity generated by either the lesion or mismatches was not localized but extended to the 5'-downstream sites, which may be connected with the phenomenon termed "short-term memory" of replication errors retained by some DNA polymerases responding to DNA damages or mismatches. Interestingly, formation of the 1,2-d(GG) intrastrand cross-link of oxaliplatin altered the overall DSC profiles of the dG:dT mismatch template/primers only in a very small extent. While addition of matched nucleotide dC across either dG in the template strand was thermodynamically favored over the presence of a mismatched dT (ΔΔG(0)(310) was 7.6 or 6.8 kJ mol(-1), ΔΔH was 14 or 49 kJ mol(-1)), no such thermodynamic advantage was observed with the 1,2-d(GG) intrastrand cross-link of oxaliplatin at these positions (ΔΔG(0)(310) was 2.8 or -0.3 kJ mol(-1), ΔΔH was 4 or 9 kJ mol(-1)). The equilibrium thermodynamic data also provide insight into the processes associated with misincorporation of incorrect nucleotides during replication bypass across major cross-links of antitumor oxaliplatin. On the other hand, besides thermodynamic effects also kinetic factors play an important role in the processing of the cross-links of antitumor platinum drugs. The impact of the two effects in overall processing DNA adducts by a particular DNA polymerase will depend on its nature.     

Mechanisms of fibrinogen adsorption at solid substrates

Adsorption of fibrinogen, modeled as a linear chain of touching beads of various sizes, was theoretically studied using the random sequential adsorption (RSA) model. The adsorption process was assumed to consist of two steps: (i) formation of an irreversibly bound fibrinogen monolayer under the side-on orientation, which is independent of the bulk protein concentration and (ii) formation of the reversibly bound, end-on monolayer, whose coverage was dependent on the bulk concentration. Calculation based on the RSA model showed that the maximum surface concentration of the end-on (reversible) monolayer equals N(⊥∞) = 6.13 × 10(3) μm(-2) which is much larger than the previously found value for the side-on (irreversible) monolayer, equal to N(∞) = 2.27 × 10(3) μm(-2). Hence, the maximum surface concentration of fibrinogen in both orientations is determined to be 8.40 × 10(3) μm(-2) corresponding to the protein coverage of 5.70 mg m(-2) assuming 20% hydration. Additionally, the surface blocking function (ASF) was determined for the end-on fibrinogen adsorption, approximated for the entire range of coverage by the interpolating polynomial. For the coverage approaching the jamming limit, the surface blocking function (ASF) was shown to vanish proportionally to (θ(⊥∞) - θ(⊥))(2). These calculation allowed one to theoretically predict adsorption isotherms for the end-on regime of fibrinogen and adsorption kinetics under various transport conditions (diffusion and convection). Using these theoretical results, a quantitative interpretation of experimental data obtained by TIRF and ellipsometry was successfully performed. The equilibrium adsorption constant for the end-on adsorption regime was found to be 8.04 × 10(-3) m. On the basis of this value, the depth of the adsorption energy minimum, equal to -17.4 kT, was predicted, which corresponds to ΔG = -41.8 kJ mol(-1). This is in accordance with adsorption energy derived as the sum of the van der Waals and electrostatic interactions. Besides having significance for predicting fibrinogen adsorption, theoretical results derived in this work also have implications for basic science providing information on mechanisms of anisotropic protein molecule adsorption on heterogeneous surfaces.     

Evaluation of comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry for the diagnosis of inherited metabolic disorders using an automated data processing strategy

Organic acidurias are a large group of inherited metabolic disorders (IMDs), commonly diagnosed by GC-MS analysis of organic acids in urine after acidic extraction and trimethylsilylation. In this study, a GC×GC-ToF-MS method has been optimized for the analysis of pathological metabolites in urine. An automated data processing strategy based on the use of mass spectra and GC retention times for the target search and quantification of pathological metabolites has been developed. Using this procedure, each unknown sample is automatically examined for the presence of markers of several diseases at the same time. The method has been applied for the analysis of 6 challenging proficiency testing samples from patients with IMDs (thymidine phosphorylase deficiency, mevalonic aciduria, hawkinsinuria, aromatic l-amino acid decarboxylase deficiency, propionic acidemia and medium-chain acyl-CoA dehydrogenase deficiency). Using the GC×GC-ToF-MS method, we were able to determine complete sets of markers for all the IMDs. The quality of the mass spectral matches for the pathological markers was higher than 800 (out of 1000).     

Generalized Specker lattice-ordered groups and two types of distributivity

Let A be a lattice-ordered group, B a generalized Boolean algebra. The Boolean extension A _B of A has been investigated in the literature; we will refer to A _B as a generalized Specker lattice-ordered group (namely, if A is the linearly ordered group of all integers, then A _B is a Specker lattice-ordered group). The paper establishes that some distributivity laws extend from A _B to both A and B, and (under certain circumstances) also conversely.     

Triangle-Free Geometric Intersection Graphs with Large Chromatic Number

Several classical constructions illustrate the fact that the chromatic number of a graph may be arbitrarily large compared to its clique number. However, until very recently no such construction was known for intersection graphs of geometric objects in the plane. We provide a general construction that for any arc-connected compact set $X$ X in $\mathbb{R }^2$ R 2 that is not an axis-aligned rectangle and for any positive integer $k$ k produces a family $\mathcal{F }$ F of sets, each obtained by an independent horizontal and vertical scaling and translation of $X$ X , such that no three sets in $\mathcal{F }$ F pairwise intersect and $\chi (\mathcal{F })>k$ χ ( F ) > k . This provides a negative answer to a question of Gyárfás and Lehel for L-shapes. With extra conditions we also show how to construct a triangle-free family of homothetic (uniformly scaled) copies of a set with arbitrarily large chromatic number. This applies to many common shapes, like circles, square boundaries or equilateral L-shapes. Additionally, we reveal a surprising connection between coloring geometric objects in the plane and on-line coloring of intervals on the line.