Peak alignment of urine NMR spectra using fuzzy warping

Proton nuclear magnetic resonance (1H NMR) spectroscopic analysis of mixtures has been used extensively for a variety of applications ranging from the analysis of plant extracts, wine, and food to the evaluation of toxicity in animals. For example, NMR analysis of urine samples has been used extensively for biomarker discovery and, more simply, for the construction of classification models of toxicity, disease, and biochemical phenotype. However, NMR spectra of complex mixtures typically show unwanted local peak shifts caused by matrix and instrument variability, which must be compensated for prior to statistical analysis and interpretation of the data. One approach is to align the spectral peaks across the data set. An efficient and fast warping algorithm is required as the signals typically contain ca. 32,000-64,000 data points and there can be several thousand spectra in a data set. As demonstrated in our study, the iterative fuzzy warping algorithm fulfills these requirements and can be used on-line for an alignment of the NMR spectra. Correlation coefficients between the aligned and target spectra are used as the evaluation function for the algorithm, and its performance is compared with those of other published warping methods.     

Parallel analysis of v-Src mutant protein function using reverse transfection cell arrays

The conversion of the genomic information produced by the recent sequencing projects into a comprehensive understanding of the human proteome has yet to occur. A new technology that represents a potential bridge between genomics and proteomics is reverse transfection. Reverse transfection cell microarrays are produced by overlaying cDNA arrays with mammalian cells, generating localized clusters of transfected cells with each cluster overexpressing a unique protein. This miniaturized cell-based microarray format affords parallel functional analysis of thousands of cDNA constructs in a high throughput format. In this report we document the development of a co-transfection methodology for reverse transfection applications. The demonstrated high co-transfection efficiency with a "marker" plasmid encoding for GFP enables the identification of transfected cells and eliminates the need for epitope-tagged constructs in cell-based high throughput screening applications using reverse transfection. This co-transfection method was used to study in parallel the structure/function of multiple versions of the v-Src protein using automated fluorescence microscopy. The wild-type v-Src protein and four mutants having insertions or deletions in the SH2 or SH3 domains displayed high levels of tyrosine kinase activity in HEK293T cells. Three other mutated v-Src proteins, including a kinase-dead version, were shown to be defective for tyrosine kinase activity. This reverse co-transfection approach is applicable for high throughput screening of both cDNA libraries and positional scanning recombinant protein libraries.     

Near Infrared Studies of Polymer Blends

Abstract

The dependence of absorption in the near-infrared region of cellulose acetate-polyaniline/camphorsulfonic acid blends on their conductivity and homogeneity has been studied. Thin films (10 to 100 μm) of the blends containing various amounts of protonated polyaniline show very high absorption in the NIR region. The absorption increases with increasing of conductivity and homogeneity of the sample.     

Electronically tunable surface-coil-type resonator for L-band EPR spectroscopy

The automatic frequency control (AFC) circuit in conventional electron paramagnetic resonance (EPR) spectrometers automatically tunes the microwave source to the resonance frequency of the resonator. The circuit works satisfactorily for samples stable enough that the geometric relations in the resonance structure do not change in a significant way. When EPR signals are measured during in vivo experiments with small rodents, however, the distance between the signal source and the surface-coil detector can change rapidly. When a conventional AFC circuit keeps the oscillator tuned to the resonator under those conditions, the resultant frequency change may exceed +/-5 MHz and markedly shift the position of the EPR signal. Such a shift results in unacceptable effects on the spectra, especially when the experimenter is dealing with narrow EPR lines. The animal movement also causes a mismatching of the resonator and the 50-ohm transmission line. Direct results of this mismatching are increased noise; shifts in the position of the baseline; and a high probability of overdriving the signal preamplifier with consequent loss of the EPR signal. We therefore designed, built, and tested a new surface-coil resonator using varactor diodes for tuning the resonance frequency to the fixed frequency oscillator and for capacitive matching of the resonator to the 50-ohm transmission line. The performance of the automatic matching system was tested in vivo by measuring EPR spectra of lithium phthalocyanine implanted in rats. Stability and sensitivity of the spectrometer were evaluated by measuring EPR spectra with and without the use of the automatic matching system. The overall experimental performance of the spectrometer was found to significantly improve during in vivo experiments using the automatic matching system. Excellent matching between the 50-ohm transmission line and the resonator was maintained under all experimental circumstances that were tested. This should allow us now to carry out experiments that previously were not possible.     

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.     

Development of Zinc‐Specific iCEST MRI as an Imaging Biomarker for Prostate Cancer

The healthy prostate contains the highest concentration of mobile zinc in the body. As this level decreases dramatically during the initial development of prostate cancer, in vivo detection of prostate zinc content may be applied for diagnosis of prostate cancer. Using ¹⁹F ion chemical exchange saturation transfer magnetic resonance imaging (iCEST MRI) and TF‐BAPTA as a fluorinated Zn‐binding probe with micromolar sensitivity, we show that iCEST MRI is able to differentiate between normal and malignant prostate cells with a 10‐fold difference in contrast following glucose‐stimulated zinc secretion in vitro. The iCEST signal decreased in normal prostate cells upon downregulation of the ZIP1 zinc transporter. In vivo, using an orthotopic prostate cancer mouse model and a transgenic adenocarcinoma of the mouse prostate (TRAMP) model, a gradual decrease of >300 % in iCEST contrast following the transition of normal prostate epithelial cells to cancer cells was detected.     

DFT study of Co-C bond cleavage in the neutral and one-electron-reduced alkyl-cobalt(III) phthalocyanines

Density functional theory (DFT) has been applied to the analysis of the structural and electronic properties of the alkyl-cobalt(III) phthalocyanine complexes, [CoIIIPc]-R (Pc = phthalocyanine, R = Me or Et), and their pyridine adducts. The BP86/6-31G(d) level of theory shows good reliability for the optimized axial bond lengths and bond dissociation energies (BDEs). The mechanism of the reductive cleavage was probed for the [CoIIIPc]-Me complex which is known as a highly effective methyl group donor. In the present analysis, which follows a recent study on the reductive Co-C bond cleavage in methylcobalamin (J. Phys. Chem. B 2007, 111, 7638-7645), it is demonstrated that addition of an electron and formation of the pi-anion radical [CoIII(Pc*)]-Me- significantly lowers the energetic barrier required for homolytic Co-C bond dissociation. Such BDE lowering in [CoIII(Pc*)]-Me- arises from the involvement of two electronic states: upon electron addition, a quasi-degenerate pi*Pc state is initially formed, but when the cobalt-carbon bond is stretched, the unpaired electron moves to a sigma*Co-C state and the final cleavage involves the three-electron (sigma)2(sigma*)1 bond. As in corrin complexes, the pi*Pc-sigma*Co-C states crossing does not take place at the equilibrium geometry of [CoIII(Pc*)]-Me- but only when the Co-C bond is stretched to approximately 2.3 A. The DFT computed Co-C BDE of 23.3 kcal/mol in the one-electron-reduced phthalocyanine species, [CoIII(Pc*)]-Me-, is lowered by approximately 37% compared to the neutral Py-[CoIIIPc]-Me complex where BDE = 36.8 kcal/mol. A similar comparison for the corrin-containing complexes shows that a DFT computed BDE of 20.4 kcal/mol for [CoIII(corrin*)]-Me leads to approximately 45% bond strength reduction, in comparison to 37.0 kcal/mol for Im-[CoIII(corrin)]-Me+. These results suggest some preference by the alkylcorrinoids for the reductive cleavage mechanism.     

Classification of genomic data: some aspects of feature selection

Feature selection, while working with genomic data sets, is of particular interest, not only for classification (diagnostics) improvement, but also for the data interpretability. Application of the multivariate feature selection approaches allows an efficient reduction of data dimensionality, but as demonstrated in our study, sets of the selected variables depend on the objective function of the classifier. It is possible to select different subset of genes for classification due to the correlation of genes but their interpretation ought to be cautiously made.     

Thermal properties of the gel made by low molecular weight gelator 1,2-O-(1-ethylpropylidene)-alpha-D-glucofuranose with toluene and molecular dynamics of solvent

The studies of the gel-to-sol phase transition by the Raman, FT-IR, and 1H NMR methods of the gel made by low molecular weight organogelator 1,2-O-(1-ethylpropylidene)-alpha-D-glucofuranose with toluene as the solvent are reported. The FT-IR spectra revealed the existence of a hydrogen bond network formed by gelator molecules in the crystalline and gel phase. In both phases, the network formation is dominated by the gelator self-interaction. Upon gelation, only one stretching band of infrared absorption modes nualpha, assigned to the O(6)H hydroxyl protons of gelator, is shifted by Deltaupsilonalpha = 25 cm-1, which indicates the involvement of this proton in the interaction with the solvent molecules. The phase transition measurements performed as a function of gelator concentration allowed the calculation of the energy correlated with the transition from gel to solution phase. The obtained value of 72 kJ/mol is the largest one reported up until now for monosaccharide-based gels. The analysis of the temperature measurements of the toluene 1H NMR spectra provides evidence for a different chemical environment of toluene molecules in the gel. The toluene spin-lattice relaxation in bulk and gel indicate that the viscosity is most likely the main factor that influences the dynamics of toluene.     

Exchange narrowing of the J band of molecular dye aggregates

The exchange narrowing of the J band of certain dye monomers upon aggregation in solution has been known since the 1930s. Here, we analyze the theoretical explanations put forward to account for these narrow absorption bands. Although the theories range from models of identical monomers interacting with vibrations to the opposite of rigid monomers with statistically distributed electronic site energies, all approaches exhibit exchange narrowing. However, we show that the origins of the narrowing are different. A unified theory incorporating the two approaches is presented in which features of both narrowing mechanisms are evident.