Scaled-oscillation and regularity

We give sufficient conditions for Sobolev and Lipschitz functions in terms of their lower scaled-oscillation. The sharpness of these conditions is shown by examples. Our examples also show that a Stepanov-type differentiability theorem does not hold under the boundedness assumption of the lower scaled-oscillation.

     

Locally Adaptive Wavelet Empirical Bayes Estimation of a Location Parameter

The traditional empirical Bayes (EB) model is considered with the parameter being a location parameter, in the situation when the Bayes estimator has a finite degree of smoothness and, possibly, jump discontinuities at several points. A nonlinear wavelet EB estimator based on wavelets with bounded supports is constructed, and it is shown that a finite number of jump discontinuities in the Bayes estimator do not affect the rate of convergence of the prior risk of the EB estimator to zero. It is also demonstrated that the estimator adjusts to the degree of smoothness of the Bayes estimator, locally, so that outside the neighborhoods of the points of discontinuities, the posterior risk has a high rate of convergence to zero. Hence, the technique suggested in the paper provides estimators which are significantly superior in several respects to those constructed earlier.     

Atomic layer deposition in nanometer-level replication of cellulosic substances and preparation of photocatalytic TiO2/cellulose composites

TiO2 replicas of filter paper with nanometer-level accuracy were prepared by atomic layer deposition of thin conformal TiO2 coating, followed by a removal of the paper by air-anneal at 450 degrees C. Photocatalytic anatase TiO2/cellulose composites were also made by leaving the paper intact. The TiO2 films were deposited from Ti(OMe)4 and H2O at 150-250 degrees C. The photocatalytic activity of the TiO2/cellulose composite was verified by photocatalytic reduction of Ag(I) from an aqueous solution to Ag nanoparticles on the TiO2 surface. The TiO2/cellulose composites are mechanically more stable than the free-standing TiO2 replicas and are therefore potentially suitable as lightweight, high surface area photocatalysts.     

Toward fully synthetic carbohydrate-based HIV antigen design: on the critical role of bivalency

Synthetic gp120331-335 glycopeptide fragments carrying hybrid and high-mannose type N-linked glycans were evaluated for binding to broadly neutralizing antibody 2G12 using surface plasmon resonance technology. None of the hybrid-type constructs demonstrated binding to 2G12. In the high-mannose series, the "Cys dimer" construct, presenting two undecasaccharide glycans, showed significantly higher binding than the Cys-protected monomer. The binding of the dimeric structure was further investigated in competition with recombinant gp120. The data suggest that gp120 and its designed synthetic epitope construct bind to the same site on 2G12.     

Peptide backbone folding induced by the C(alpha)-tetrasubstituted cyclic alpha-amino acids 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) and 1-aminocyclopentane-1-carboxylic acid (Ac5c). A joint computational and experimental study

The conformational study of a new group of synthetic peptides containing 4-amino-1,2-dithiolane-4-carboxylic acid (Adt), a cysteine-related achiral residue, has been carried out through a joint application of computational and experimental methodologies. Molecular Dynamics simulations clearly suggest the tendency of this molecule to adopt a gamma-turn conformation in vacuum and help in analyzing the complex and crucial conformational behaviour of the dithiolane ring which appears to preferentially adopt a C(S)-like structure. Electronic structure calculations carried out in solution using the Density Functional Theory also indicate the preservation of the gamma-like folding in apolar solvents and the helix-like one in more polar solvents. A comparison with the achiral 1-aminocycloalkane-1-carboxylic acid (Ac5c) has been carried out using the same computational tools. NMR and IR data on dipeptide derivatives containing the Adt or Ac5c residue show that in chloroform solution all the models prefer a gamma-turn structure, centered at the cyclic residue, stabilized by an intramolecular H-bond, whereas in a more polar solvent, i.e. dimethyl sulfoxide, this folding is not maintained. The experimental conformational studies, extended to N-Boc protected tripeptides, clearly indicate the remarkable tendency of both the five-membered C(alpha)-tetrasubstituted cyclic amino acids Adt and Ac5c to induce the gamma-turn structure also in models able to adopt the beta-bend conformation.     

Comparison of mass spectrometric methods for studying thermally labile compounds: Rifapentine

Results of 16 different mass spectrometric ionization and sample-introduction methods are compared for the case of a thermally very labile antibiotic, rifapentine. These suggest that extensive thermal decomposition occurs during evaporation when the sample can come into contact with hot metal parts, usually the source housing. The intensity of the molecular ion and the extent of fragmentation depend on various parameters, such as the ionization process, positive or negative-ion detection and the type of sample introduction. The most informative methods for rifapentine seem to be ‘in-beam’ electron impact, negative ionization with particle beam and direct liquid introduction interfaces and positive- and negative-ion fast atom bombardment.     

Synthesis and stereochemical studies of 6-substituted 1H,3H,6H,7aH-3,3-dimethylimidazo-[1,5-c]thiazol-5-one-7-thiones

The reaction of (4S)-5,5-dimethyl-4-thiazolidine-carboxylic acid 1 with alkyl and aryl isothiocyanates 2 gave bicyclic thiohydantoins 3 . The (2R,4S)- and (2S,4S)-mixtures of 2-substituted 5,5-dimethyl-4-thiazolidine-carboxylic acids 4 and 8 containing two centers of chirality in the analogous reaction afforded thiohydantoins 7 and 10 , respectively, with (1R)-configuration. In some cases we managed to isolate the thioureido acid intermediates 6 and 9 or their triethylamine salts which afforded the corresponding bicycles 7 and 10 under thermal cyclization or acidification. The stereochemistry has been elucidated by high resolution ram studies, optical rotation measurements and X-ray crystallography.     

Determination of the enantiomeric composition of guest molecules by chemometric analysis of the UV-visible spectra of cyclodextrin guest-host complexes

Multivariate statistical techniques were applied to the UV spectra of a series of solutions at pH 12 containing a fixed concentration (30 mM) of beta-cyclodextrin (beta-CD) and a fixed concentration (15 mM) of 2-phenylglycine (phi-Gly) with various known enantiomeric compositions. Multivariate correlation of the spectral data for the solutions containing the phi-Gly/beta-CD guest-host complexes with the known enantiomeric composition of the phi-Gly samples was accomplished by partial-least-squares regression. When the multivariate model was used to predict the enantiomeric purity of a test set of samples over the mol fraction range of 0.5-0.9 R-phi-Gly, the average magnitude of the relative errors in the mol fraction determination of enantiomeric composition was 3%. A plot of the enantiomeric composition predicted by the model versus the known enantiomeric composition of the calibration set gave a straight line with a correlation coefficient of 0.955, a slope of 1.05, and an offset of 5.61 x 10-4.     

An Extensive Assessment of Network Embedding in PPI Network Alignment

Network alignment is a fundamental task in network analysis. In the biological field, where the protein–protein interaction (PPI) is represented as a graph, network alignment allowed the discovery of underlying biological knowledge such as conserved evolutionary pathways and functionally conserved proteins throughout different species. A recent trend in network science concerns network embedding, i.e., the modelling of nodes in a network as a low-dimensional feature vector. In this survey, we present an overview of current PPI network embedding alignment methods, a comparison among them, and a comparison to classical PPI network alignment algorithms. The results of this comparison highlight that: (i) only five network embeddings for network alignment algorithms have been applied in the biological context, whereas the literature presents several classical network alignment algorithms; (ii) there is a need for developing an evaluation framework that may enable a unified comparison between different algorithms; (iii) the majority of the proposed algorithms perform network embedding through matrix factorization-based techniques; (iv) three out of five algorithms leverage external biological resources, while the remaining two are designed for domain agnostic network alignment and tested on PPI networks; (v) two algorithms out of three are stated to perform multi-network alignment, while the remaining perform pairwise network alignment.