A “Density-Based” Algorithm for Cluster Analysis Using Species Sampling Gaussian Mixture Models

We propose a new model for cluster analysis in a Bayesian nonparametric framework. Our model combines two ingredients, species sampling mixture models of Gaussian distributions on one hand, and a deterministic clustering procedure (DBSCAN) on the other. Here, two observations from the underlying species sampling mixture model share the same cluster if the distance between the densities corresponding to their latent parameters is smaller than a threshold; this yields a random partition which is coarser than the one induced by the species sampling mixture. Since this procedure depends on the value of the threshold, we suggest a strategy to fix it. In addition, we discuss implementation and applications of the model; comparison with more standard clustering algorithms will be given as well. Supplementary materials for the article are available online.     

Molecular insights into azumamide e histone deacetylases inhibitory activity

Azumamide E, a cyclotetrapeptide isolated from the sponge Mycale izuensis, is the most powerful carboxylic acid containing natural histone deacetylase (HDAC) inhibitor known to date. In this paper, we describe design and synthesis of two stereochemical variants of the natural product. These compounds have allowed us to clarify the influence of side chain topology on the HDAC-inhibitory activity. The present contribution also reveals the identity of the recognition pattern between azumamides and the histone deacetylase-like protein (HDLP) model receptor and reports the azumamide E unprecedented isoform selectivity on histone deacetylases class subtypes. From the present studies, a plausible model for the interaction of azumamides with the receptor binding pocket is derived, providing a framework for the rational design of new cyclotetrapeptide-based HDAC inhibitors as antitumor agents.     

Nitrogen oxide interaction with copper complexes formed by small peptides belonging to the prion protein octa-repeat region

The interaction between NO and copper(II) complexes formed by peptides coming from the N-terminal prion protein octa-repeat region was studied. Aqueous solutions of the Cu-Ac-HGGG-NH(2) and the Cu-Ac-PHGGGWGQ-NH(2) systems around pH 7.5 were tested after the addition of NONOates as a source of NO. UV-Vis, room temperature and frozen solution EPR spectra showed the occurrence of copper(ii) reduction in all these complexes. The reduction of these complexes is probably mediated by the formation of a labile NO adduct, which, after re-oxidation, leads to a relatively stable NO(2)(-) adduct through the apical coordination along the void site of their square pyramidal structure. In fact, the most significant shifts in EPR magnetic parameters (g(||) and A(||) or g(iso) and A(iso)) as well as in the optical parameters (lambda(max) and epsilon(max)) gave a reason for geometrical changes of the copper coordination polyhedron from a distorted square pyramid to a pseudo-octahedron. The presence of oxygen in the aqueous solution hindered the reduction ability of NO towards copper, but it made it easier to return to the original species. In order to elucidate the possible mechanism of this interaction, the reduction of copper complexed by these ligands was followed by means of zinc powder addition. The further addition of nitrite to the solution containing reduced copper led to the conclusion that nitrite could easily form an adduct, which after re-oxidation presented the same spectral features of the species obtained when the NO interaction was followed. The complexity of this interaction could involve both an inner or an outer-sphere electron transfer mechanism.     

Influence of Excitation Wavelength (UV or Visible Light) on the Photocatalytic Activity of Titania Containing Gold Nanoparticles for the Generation of Hydrogen or Oxygen from Water

Gold nanoparticles supported on P25 titania (Au/TiO(2)) exhibit photocatalytic activity for UV and visible light (532 nm laser or polychromatic light λ > 400 nm) water splitting. The efficiency and operating mechanism are different depending on whether excitation occurs on the titania semiconductor (gold acting as electron buffer and site for gas generation) or on the surface plasmon band of gold (photoinjection of electrons from gold onto the titania conduction band and less oxidizing electron hole potential of about -1.14 V). For the novel visible light photoactivity of Au/TiO(2), it has been determined that gold loading, particle size and calcination temperature play a role in the photocatalytic activity, the most active material (Φ(H2) = 7.5% and Φ(O2) = 5.0% at 560 nm) being the catalyst containing 0.2 wt % gold with 1.87 nm average particle size and calcined at 200 °C.     

Low temperature kinetics, crossed beam dynamics and theoretical studies of the reaction S((1)D) + CH4 and low temperature kinetics of S((1)D) + C2H2

The reaction between sulfur atoms in the first electronically excited state, S((1)D), and methane (CH(4)), has been investigated in a complementary fashion in (a) crossed-beam dynamics experiments with mass spectrometric detection and time-of-flight (TOF) analysis at two collision energies (30.4 and 33.6 kJ mol(-1)), (b) low temperature kinetics experiments ranging from 298 K down to 23 K, and (c) electronic structure calculations of stationary points and product energetics on the CH(4)S singlet potential energy surface. The rate coefficients for total loss of S((1)D) are found to be very large (ca. 2 × 10(-10) cm(3) molec(-1) s(-1)) down to very low temperatures indicating that the overall reaction is barrier-less. Similar measurements are also performed for S((1)D) + C(2)H(2), and also for this system the rate coefficients are found to be very large (ca. 3 × 10(-10) cm(3) molec(-1) s(-1)) down to very low temperatures. From laboratory angular and TOF distributions at different product masses for the reaction S((1)D) + CH(4), it is found that the only open reaction channel at the investigated collision energies is that leading to SH + CH(3). The product angular, T(θ), and translational energy, P(E'(T)), distributions in the center-of-mass frame are derived. The reaction dynamics are discussed in terms of two different micromechanisms: a dominant long-lived complex mechanism at small and intermediate impact parameters with a strongly polarized T(θ), and a direct pickup-type (stripping) mechanism occurring at large impact parameters with a strongly forward peaked T(θ). Interpretation of the experimental results on the S((1)D) + CH(4) reaction kinetics and dynamics is assisted by high-level theoretical calculations on the CH(4)S singlet potential energy surface. The dynamics of the SH + CH(3) forming channel are compared with those of the corresponding channel (leading to OH + CH(3)) in the related O((1)D) + CH(4) reaction, previously investigated in crossed-beams in other laboratories at comparable collision energies. The possible astrophysical relevance of S((1)D) reactions with hydrocarbons, especially in the chemistry of cometary comae, is discussed.     

A characterization of the circle group via uniqueness of roots

It was shown in Bíró et al. (2001) [7] that every cyclic subgroup C of the circle group T admits a characterizing sequence (un) of integers in the sense that unx→0 for some x∈T iff x∈C. More generally, for a subgroup H of a topological (abelian) group G one can define:

(a)

g(H) to be the set of all elements x of G such that unx→0 in G for all sequences (un) of integers such that unh→0 in G for all h∈H;

(b)

H to be g-closed if H=g(H).

We show then that an infinite compact abelian group G has all its cyclic subgroups g-closed iff G≅T.     

Tuning in-meso-crystallized lysozyme polymorphism by lyotropic liquid crystal symmetry

Lipid-based lyotropic liquid crystals (LLCs) show great potential for applications in fields as diverse as food technology, cosmetics, pharmaceutics, or structural biology. Recently, these systems have provided a viable alternative to the difficult process of membrane protein crystallization, owing to their similarities with cell membranes. Nonetheless, the process of in-meso crystallization of proteins still remains poorly understood. In this study, we demonstrate that in-meso crystal morphologies of lysozyme (LSZ), a model hydrophilic protein, can be controlled by both the composition and symmetry of the mesophase, inferring a possible general influence of the LLC space group on the protein crystal polymorphism. Lysozyme was crystallized in-meso from three common LLC phases (lamellar, inverse hexagonal, and inverse bicontinuous cubic) composed of monolinolein and water. Different mixing ratios of mesophase to crystallization buffer were used in order to tune crystallization both in the bulk mesophase and in excess water conditions. Two distinct mechanisms of crystallization were shown to take place depending on available water in the mesophases. In the bulk mesophases, protein nuclei form and grow within structural defects of the mesophase and partially dehydrate the system inducing order-to-order transitions of the liquid crystalline phase toward stable symmetries in conditions of lower hydration. The formed protein crystals eventually macrophase separate from the mesophase allowing the system to reach its final symmetry. On the other hand, when excess water is available, protein molecules diffuse from the water channels into the excess water, where the crystallization process can take place freely, and with little to no effect on the structure and symmetry of the lyotropic liquid crystals.     

Ionic strength effects on the critical micellar concentration of ionic and nonionic surfactants: the binding model

We have recently investigated the aggregation behavior of zwitterionic n-dodecyl phosphocholine in the presence of high salt. As double logarithmic Corrin-Harkins plots of the critical micellar concentration versus the salt concentration were not linear, here we re-examine those data in the context of the binding model of surfactant aggregation, as previously developed by us for ionic surfactants. We have also re-examined plenty of data available in the literature on the salt-dependent aggregation of neutral surfactants. The use of double-logarithmic plots allowed us to show that the binding model is of general applicability. Indeed, it permits unified treatment of ionic and uncharged aggregation without requiring the introduction of linear terms in the salt concentration, as needed in the empirical Corrin-Harkins treatment of nonionic surfactants. The use of this model could be of help in a broad range of surfactant-based applications in the presence of high salt.     

Improved postharvest quality in patagonian squash (Cucurbita moschata) coated with radiation depolymerized chitosan

Different molecular weight chitosans were evaluated on the decay of coated Anquito squashes (Cucurbita moschata) as well as the maintenance of the fruit quality along five storage months. The original chitosan (Mw=391 kDa, 83% DD), was depolymerized by gamma radiation. Apart from chain scission, other chemical changes were not detected by FTIR or UV–vis analyses. The molecular weight characterization of chitosans was done by size exclusion chromatography with dual light scattering and concentration detection (SEC-MALLS-RI). The coating effectiveness was evaluated on the following parameters: fungal decay incidence, weight loss, firmness, total reducing sugar, soluble solid, flesh color, carotene content, pH and titratable acidity. No sign of fungal decay was observed in squashes coated with 122 and 56 kDa chitosans, which were also the most effective treatments in reducing the weight loss. The chitosan with Mw=122 kDa was also the best treatment considering firmness, internal aspect, sugar and carotene content. Then, radiation degraded chitosan was better in C. moschata preservation than the original chitosan.     

New Developments and Results for Mathematical Models in Environment Evaluations

A new mathematical model capable to provide a detailed evaluation of the ecological state of an environmental system is here presented. The mathematical model consists in a set of ordinary differential equations. The state variable of the system is the so-called Biological Territorial Capacity. The analysis is performed at the scale of each biotope that is the patch of land cover with homogeneous vegetation. Since the model consists in a very large number of ODE, in order to implement numerical computations with a fast algorithm, an approximated solution procedure is proposed. Finally a study case with comparisons between different designs and plans of the territory under investigation is performed.