The inactivation of bovine cathepsin B by novel N-chloro-acetyl-dipeptides. Application of the Houghten 'tea bag' methodology to inhibitor synthesis

In this study, a series of N-chloro-acetylated dipeptides were synthesised by the application of Houghten's methodology of multiple analog peptide syntheses. The peptides, all of which contain a C-terminal free acid, were tested as inactivators of bovine cathepsin B, in an attempt at exploiting the known and, amongst the cysteine proteinases, unique carboxy dipeptidyl peptidase activity of the protease. We have succeeded in obtaining a number of effective inactivators, the most potent of which-chloroacetyl-Leu-Leu-OH, inactivates the enzyme with an apparent second-order rate constant of 3.8 x 10(4) M-1 min(-1). In contrast, the esterified analog, chloroacetyl-Leu-Leu-OMe, inactivates the enzyme some three orders of magnitude less efficiently, lending credence to our thesis that a free carboxylic acid moiety is an important determinant for inhibitor effectiveness. This preliminary study has highlighted a number of interesting features about the specificity requirements of the bovine proteinase and we believe that our approach has great potential for the rapid delineation of the subsite specificities of cathepsin B-like proteases from various species. (c) 2005 Elsevier Inc. All rights reserved.

Synthesis, Kinetic Evaluation and Utilization of a Biotinylated Dipeptide Proline Diphenyl Phosphonate for the Disclosure of Dipeptidyl Peptidase IV-like Serine Proteases

In this study, we report on the synthesis, kinetic characterisation, and application of a novel biotinylated and active site-directed inactivator of dipeptidyl peptidase IV (DPP-IV). Thus, the dipeptide-derived proline diphenyl phosphonate NH(2)-Glu(biotinyl-PEG)-Pro(P)(OPh)(2) has been prepared by a combination of classical solution- and solid-phase methodologies and has been shown to be an irreversible inhibitor of porcine DPP-IV, exhibiting an over all second-order rate constant (k(i)/K(i)) for inhibition of 1.57 x 10(3) M(-1) min(-1). This value compares favourably with previously reported rates of inactivation of DPP-IV by dipeptides containing a P(1) proline diphenyl phosphonate grouping [B. Boduszek, J. Oleksyszyn, C.M. Kam, J. Selzler, R.E. Smith, J.C. Powers, Dipeptide phophonates as inhibitors of dipeptidyl peptidase IV, J. Med. Chem. 37 (1994) 3969-3976; B.F. Gilmore, J.F. Lynas, C.J. Scott, C. McGoohan, L. Martin, B. Walker, Dipeptide proline diphenyl phosphonates are potent, irreversible inhibitors of seprase (FAPalpha), Biochem, Biophys. Res. Commun. 346 (2006) 436-446.], thus demonstrating that the incorporation of the side-chain modified (N-biotinyl-3-(2-(2-(3-aminopropyloxy)-ethoxy)-ethoxy)-propyl) glutamic acid residue at the P(2) position is compatible with inhibitor efficacy. The utilisation of this probe for the detection of both purified dipeptidyl peptidase IV and the disclosure of a dipeptidyl peptidase IV-like activity from a clinical isolate of Porphyromonas gingivalis, using established electrophoretic and Western blotting techniques previously developed by our group, is also demonstrated.

Free energy and molecular dynamics calculations for the cubic-tetragonal phase transition in zirconia

The high-temperature cubic-tetragonal phase transition of pure stoichiometric zirconia is studied by molecular dynamics (MD) simulations and within the framework of the Landau theory of phase transformations. The interatomic forces are calculated using an empirical, self-consistent, orthogonal tight-binding model, which includes atomic polarizabilities up to the quadrupolar level. A first set of standard MD calculations shows that, on increasing temperature, one particular vibrational frequency softens. The temperature evolution of the free-energy surfaces around the phase transition is then studied with a second set of calculations. These combine the thermodynamic integration technique with constrained MD simulations. The results seem to support the thesis of a second-order phase transition but with unusual, very anharmonic behavior above the transition temperature.

Total cross sections for transfer ionization in fast ion-helium collisions

The effects of electron correlation and second-order terms on theoretical total cross sections of transfer ionization in collisions of the helium atom with fast H+, He2+ and Li3+ ions are studied and reported. The total cross sections are calculated using highly correlated wavefunctions with expansion of the transition amplitude in the Born series through the second order. The results of these calculations are in sensible agreement with experimental data.

Emission lines of Na-like ions in spectra obtained with the Solar EUV Research Telescope and Spectrograph (SERTS)

Theoretical emission-line ratios involving transitions in the 236-412 Angstrom wavelength range are presented for the Na-like ions Ar viii, Cr xiv, Mn xv, Fe xvi, Co xvii, Ni xviii and Zn xx. A comparison of these with an extensive data set of the solar active region, quiet-Sun, subflare and off-limb observations, obtained during rocket flights by the Solar EUV Research Telescope and Spectrograph (SERTS), reveals generally very good agreement between theory and experiment. This indicates that most of the Na-like ion lines are reliably detected in the SERTS observations, and hence may be employed with confidence in solar spectral analyses. However, the features in the SERTS spectra at 236.34 and 300.25 Angstrom, originally identified as the Ni xviii 3p (2) P-3/2 -3d (2) D- 3/2 and Cr xiv 3p (2) P-3/2 -3d (2) D-5/2 transitions, respectively, are found to be due to emission lines of Ar xiii (236.34 Angstrom) and possibly S v or Ni vi (300.25 Angstrom). The Co xvii 3s (2) S-3p (2) P-3/2 line at 312.55 Angstrom is always badly blended with an Fe xv feature at the same wavelength, but Mn xv 3s (2) S-3p (2) P-1/2 at 384.75 Angstrom may not always be as affected by second-order emission from Fe xii 192.37 Angstrom as previously thought. On the other hand, we find that the Zn xx 3s (2) S-3p (2) P-3/2 transition can sometimes make a significant contribution to the Zn xx/Fe xiii 256.43- Angstrom blend, and hence care must be taken when using this feature as an Fe xiii electron density diagnostic. A line in the SERTS-89 active region spectrum at 265.00 Angstrom has been re-assessed, and we confirm its identification as the Fe xvi 3p (2) P-3/2 -3d (2) D-3/2 transition.

Thickness-induced stabilization of ferroelectricity in SrRuO3/Ba0.5Sr0.5TiO3/Au thin film capacitors

Pulsed-laser deposition has been used to fabricate Au/Ba0.5Sr0.5TiO3/SrRuO3/MgO thin film capacitor structures. Crystallographic and microstructural investigations indicated that the Ba0.5Sr0.5TiO3 (BST) had grown epitaxially onto the SrRuO3 lower electrode, inducing in-plane compressive and out- of-plane tensile strain in the BST. The magnitude of strain developed increased systematically as film thickness decreased. At room temperature this composition of BST is paraelectric in bulk. However, polarization measurements suggested that strain had stabilized the ferroelectric state, and that the decrease in film thickness caused an increase in remanent polarization. An increase in the paraelectric-ferroelectric transition temperature upon a decrease in thickness was confirmed by dielectric measurements. Polarization loops were fitted to Landau-Ginzburg-Devonshire (LGD) polynomial expansion, from which a second order paraelectric-ferroelectric transition in the films was suggested at a thickness of similar to500 nm. Further, the LGD analysis showed that the observed changes in room temperature polarization were entirely consistent with strain coupling in the system. (C) 2002 American Institute of Physics.

Intrinsic dielectric response in ferroelectric nano-capacitors

Measurements on 'free-standing' single-crystal barium titanate capacitors with thickness down to 75 nm show a dielectric response typical of large single crystals, rather than conventional thin films. There is a notable absence of any broadening or temperature shift of the dielectric peak or loss tangent. Peak dielectric constants of similar to25 000 are observed, and Curie-Weiss analysis demonstrates first order transformation behaviour. This is in dramatic contrast to results on conventionally deposited thin film capacitor heterostructures, which show large dielectric peak broadening and temperature shifts (e.g. Parker et al 2002 Appl. Phys. Lett. 81 340), as well as an apparent change in the nature-of the paraelectric-ferroelectric transition from first to second order. Our data are compatible with a recent model by Bratkovsky and Levanyuk (2004 Preprint cond-mat/0402100), which attributes dielectric peak broadening to gradient terms that will exist in any thin film capacitor heterostructure. The observed recovery of first order transformation behaviour is consistent with the absence of significant substrate clamping in our experiment, as modelled by Pertsev et al (1998,Phys. Rev. Lett. 80 1988), and illustrates that the second order behaviour seen in conventionally deposited thin films cannot be attributed to the effects of reduced dimensionality in the system, nor to the influence of an intrinsic universal interfacial capacitance associated with the electrode- ferroelectric interface.

Multi-zone TAP-reactors theory and application - IV. Ideal and non-ideal boundary conditions

We study the influence of non-ideal boundary and initial conditions (BIC) of a temporal analysis of products (TAP) reactor model on the data (observed exit flux) analysis. The general theory of multi-response state-defining experiments for a multi-zone TAP reactor is extended and applied to model several alternative boundary and initial conditions proposed in the literature. The method used is based on the Laplace transform and the transfer matrix formalism for multi-response experiments. Two non-idealities are studied: (1) the inlet pulse not being narrow enough (gas pulse not entering the reactor in Dirac delta function shape) and (2) the outlet non-ideality due to imperfect vacuum. The effect of these non-idealities is analyzed to the first and second order of approximation. The corresponding corrections were obtained and discussed in detail. It was found that they are negligible. Therefore, the model with ideal boundary conditions is proven to be completely adequate to the description and interpretation of transport-reaction data obtained with TAP-2 reactors.

Synthesis of Peptidyl Ene Diones: Selective Inactivators of the Cysteine Proteinases

A series of synthetic peptides in which the C-terminal carboxyl grouping (-CO2H) of each has been chemically converted into a variety of ene dione derivatives (-CO-CH CH-CO-X; X -H, -Me, -OBut, - OEt, -OMe, -CO-OMe), have been prepared and tested as inactivators against typical members of the serine and cysteine protease families. For example, the sequences Cbz-Pro-Phe-CH CH-CO-OEt (I) which fulfils the known primary and secondary specificity requirements of the serine protease chymotrypsin, and Cbz-Phe-Ala-CH CH-CO-OEt (II) which represents a general recognition sequence for cysteine proteases such as cathepsins B, L and S, have been tested as putative irreversible inactivators of their respective target proteases. It was found that, whereas II, for example, functioned as a time-dependent, irreversible inactivator of each of the cysteine proteases, I behaved only as a modest competitive reversible inhibitor of chymotrypsin. Within the simple ester sequences Cbz- Phe-Ala-CH CH-CO-R, the rank order of inhibitor effectiveness decreases in the order R -OMe > - OEt >> -OBut. It was also found that the presence of both an unsaturated double bond and an ester (or a-keto ester) moiety were indispensable for obtaining irreversible inactivators. Of the irreversible inactivators synthesized, Cbz-Phe-Ala-CH CHCO- CO-OEt (which contains a highly electrophilic a-keto ester grouping) was found to be the most effective exhibiting, for example, second-order rate constants of approximately 1.7 106/M/min and approximately 4.9 104/M/min against recombinant human cathepsin S and human spleenic cathepsin B, respectively. This initial study thus holds out the promise that this class of inactivator may well be specific for the cysteine protease subclass.

An FPGA Based Coprocessor for GLCM and Haralick Texture Features and Their Application in Prostate Cancer Classification

Grey Level Co-occurrence Matrix (GLCM), one of the best known tool for texture analysis, estimates image properties related to second-order statistics. These image properties commonly known as Haralick texture features can be used for image classification, image segmentation, and remote sensing applications. However, their computations are highly intensive especially for very large images such as medical ones. Therefore, methods to accelerate their computations are highly desired. This paper proposes the use of programmable hardware to accelerate the calculation of GLCM and Haralick texture features. Further, as an example of the speedup offered by programmable logic, a multispectral computer vision system for automatic diagnosis of prostatic cancer has been implemented. The performance is then compared against a microprocessor based solution.

Magnetic tight binding and the iron-chromium enthalpy anomaly

We describe a self-consistent magnetic tight-binding theory based in an expansion of the Hohenberg-Kohn density functional to second order, about a non-spin-polarized reference density. We show how a first order expansion about a density having a trial input magnetic moment leads to a fixed moment model. We employ a simple set of tight-binding parameters that accurately describes electronic structure and energetics, and show these to be transferable between first row transition metals and their alloys. We make a number of calculations of the electronic structure of dilute Cr impurities in Fe, which we compare with results using the local spin density approximation. The fixed moment model provides a powerful means for interpreting complex magnetic configurations in alloys; using this approach, we are able to advance a simple and readily understood explanation for the observed anomaly in the enthalpy of mixing.

Microneedle-mediated intradermal delivery of 5-aminolevulinic acid: potential for enhanced topical photodynamic therapy

Photodynamic therapy of deep or nodular skin tumours is currently limited by the poor tissue penetration of the porphyrin precursor 5-aminolevulinic acid (ALA). In this study, silicon microneedle arrays were used, for the first time, to enhance skin penetration of ALA in vitro and in vivo. Puncturing excised murine skin with 6x7 arrays of microneedles 270 mum in height, with a diameter of 240 mum at the base and an interspacing of 750 mum led to a significant increase in transdermal delivery of ALA released from a bioadhesive patch containing 19 mg ALA cm(-2). Microneedle puncture enhanced ALA delivery to the upper regions of excised porcine skin but, at mean depths of 1.875 mm, ALA concentrations were similar to control values, possibly reflecting binding of ALA by tissue components. However, and importantly, in vivo experiments using nude mice showed that microneedle puncture could reduce application time and ALA dose required to induce high levels of the photosensitiser protoporphyrin IX in skin. This clearly has implications for clinical practice, as shorter application times would mean improved patient and clinician convenience and also that more patients could be treated in the same session. As ALA is expensive and degrades rapidly via a second order reaction, reducing the required dose is also a notable advantage.

A new Jacobian matrix for optimal learning of single-layer neural networks

This paper investigates the learning of a wide class of single-hidden-layer feedforward neural networks (SLFNs) with two sets of adjustable parameters, i.e., the nonlinear parameters in the hidden nodes and the linear output weights. The main objective is to both speed up the convergence of second-order learning algorithms such as Levenberg-Marquardt (LM), as well as to improve the network performance. This is achieved here by reducing the dimension of the solution space and by introducing a new Jacobian matrix. Unlike conventional supervised learning methods which optimize these two sets of parameters simultaneously, the linear output weights are first converted into dependent parameters, thereby removing the need for their explicit computation. Consequently, the neural network (NN) learning is performed over a solution space of reduced dimension. A new Jacobian matrix is then proposed for use with the popular second-order learning methods in order to achieve a more accurate approximation of the cost function. The efficacy of the proposed method is shown through an analysis of the computational complexity and by presenting simulation results from four different examples.

Kinetic analysis of the reaction between electrogenerated superoxide and carbon dioxide in the room temperature ionic liquids 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide and hexyltriethylammonium bis(trifluoromethylsulfonyl)imide

The reduction of oxygen in the presence of carbon dioxide has been investigated by cyclic voltammetry at a gold microdisk electrode in the two room-temperature ionic liquids 1-ethyl-3-methylimidazolium bis-(trifluoromethylsulfonyl)imide ([EMIM][N(Tf)(2)]) and hexyltriethylammonium bis(trifluoromethylsulfonyl)imide ([N-6222] [N(Tf)(2)]). With increasing levels of CO2, cyclic voltammetry shows an increase in the reductive wave and diminishing of the oxidative wave, indicating that the generated superoxide readily reacts with carbon dioxide. The kinetics of this reaction are investigated in both ionic liquids. The reaction was found to proceed via a DISP1 type mechanism in [EMIM][N(Tf)(2)] with an overall second-order rate constant of 1.4 +/- 0.4 x 10(3) M-1 s(-1). An ECE or DISP1 mechanism was determined to be the most likely pathway for the reaction in [N-6222][N(Tf)(2)], with an overall second-order rate constant of 1.72 +/- 0.45 x 10(3) m(-1) s(-1).

Kinetics of the oxidation of methyl tert-butyl ether (MTBE) by potassium permanganate

The occurrence of the fuel oxygenate methyl tert-butyl ether (MTBE) in the environment has received considerable scientific attention. The pollutant is frequently found in the groundwater due to leaking of underground storage tanks or pipelines. Concentrations of more than several mg/L MTBE were detected in groundwater at several places in the US and Germany in the last few years. In situ chemical oxidation is a promising treatment method for MTBE-contaminated plumes. This research investigated the reaction kinetics for the oxidation of MTBE by permanganate. Batch tests demonstrated that the oxidation of MTBE by permanganate is second order overall and first order individually with respect to permanganate and MTBE. The second-order rate constant was 1.426 x 10(-6) L/mg/h. The influence of pH on the reaction rate was demonstrated to have no significant effect. However, the rate of MTBE oxidation by potassium permanganate is 2-3 orders of magnitude lower than of other advanced oxidation processes. The slower rates of MTBE oxidation by permanganate limit the applicability of this process for rapid MTBE cleanup strategies. However, permanganate oxidation of MTBE has potential for passive oxidation risk management strategies. (C) 2002 Elsevier Science Ltd. All rights reserved.