Structural analysis of prion proteins by means of drift cell and traveling wave ion mobility mass spectrometry

The prion protein (PrP) is implicitly involved in the pathogenesis of transmissible spongiform encephalopathies (TSEs). The conversion of normal cellular PrP (PrP^C), a protein that is predominantly α-helical, to a β-sheet-rich isoform (PrP^Sc), which has a propensity to aggregate, is the key molecular event in prion diseases. During its short life span, PrP can experience two different pH environments; a mildly acidic environment, whilst cycling within the cell, and a neutral pH when it is glycosyl phosphatidylinositol (GPI)-anchored to the cell membrane. Ion mobility (IM) combined with mass spectrometry has been employed to differentiate between two conformational isoforms of recombinant Syrian hamster prion protein (SHaPrP). The recombinant proteins studied were α-helical SHaPrP(90-231) and β-sheet-rich SHaPrP(90-231) at pH 5.5 and pH 7.0. The recombinant proteins have the same nominal mass-to-charge ratio (m/z) but differ in their secondary and tertiary structures. A comparison of traveling-wave (T-Wave) ion mobility and drift cell ion mobility (DCIM) mass spectrometry estimated and absolute cross-sections showed an excellent agreement between the two techniques. The use of T-Wave ion mobility as a shape-selective separation technique enabled differentiation between the estimated cross-sections and arrival time distributions (ATDs) of α-helical SHaPrP(90-231) and β-sheet-rich SHaPrP(90-231) at pH 5.5. No differences in cross-section or ATD profiles were observed between the protein isoforms at pH 7.0. The findings have potential implications for a new ante-mortem screening assay, in bodily fluids, for prion misfolding diseases such as TSEs.     

On the representability of totally unimodular matrices on bidirected graphs

We present a polynomial time algorithm to construct a bidirected graph for any totally unimodular matrix B by finding node-edge incidence matrices Q and S such that QB=S. Seymour’s famous decomposition theorem for regular matroids states that any totally unimodular (TU) matrix can be constructed through a series of composition operations called k-sums starting from network matrices and their transposes and two compact representation matrices B₁,B₂ of a certain ten element matroid. Given that B₁,B₂ are binet matrices we examine the k-sums of network and binet matrices. It is shown that thek-sum of a network and a binet matrix is a binet matrix, but binet matrices are not closed under this operation for k=2,3. A new class of matrices is introduced, the so-called tour matrices, which generalise network, binet and totally unimodular matrices. For any such matrix there exists a bidirected graph such that the columns represent a collection of closed tours in the graph. It is shown that tour matrices are closed under k-sums, as well as under pivoting and other elementary operations on their rows and columns. Given the constructive proofs of the above results regarding the k-sum operation and existing recognition algorithms for network and binet matrices, an algorithm is presented which constructs a bidirected graph for any TU matrix.     

Safe density ratio modeling

An important problem in logistic regression modeling is the existence of the maximum likelihood estimators. In particular, when the sample size is small, the maximum likelihood estimator of the regression parameters does not exist if the data are completely, or quasicompletely separated. Recognizing that this phenomenon has a serious impact on the fitting of the density ratio model–which is a semiparametric model whose profile empirical log-likelihood has the logistic form because of the equivalence between prospective and retrospective sampling–we suggest a linear programming methodology for examining whether the maximum likelihood estimators of the finite dimensional parameter vector of the model exist. It is shown that the methodology can be effectively utilized in the analysis of case–control gene expression data by identifying cases where the density ratio model cannot be applied. It is demonstrated that naive application of the density ratio model yields erroneous conclusions.     

Multifunctional lanthanum tetraphosphonates: flexible, ultramicroporous and proton-conducting hybrid frameworks

A new flexible ultramicroporous solid, La(H(5)DTMP)·7H(2)O (1), has been crystallized at room temperature using the tetraphosphonic acid H(8)DTMP, hexamethylenediamine-N,N,N',N'-tetrakis(methylenephosphonic acid). Its crystal structure, solved by synchrotron powder X-ray diffraction, is characterised by a 3D pillared open-framework containing 1D channels filled with water. Upon dehydration, a new related crystalline phase, La(H(5)DTMP) (2) is formed. Partial rehydration of 2 led to La(H(5)DTMP)·2H(2)O (3). These new phases contain highly corrugated layers showing different degrees of conformational flexibility of the long organic chain. The combination of the structural study and the gas adsorption characterization (N(2) and CO(2)) suggests an ultramicroporous flexible framework. NO isotherms are indicative of a strong irreversible adsorption of NO within the pores. Impedance data indicates that 1 is a proton-conductor with a conductivity of 8 × 10(-3) S cm(-1) at 297 K and 98% of relative humidity, and an activation energy of 0.25 eV.     

Investigation of viscosity and crystallization in supercooled-liquid region of Zr-based glassy alloys

Using viscosity measurement method and in-situ heating synchrotron radiation, the viscosity of the (Zr_0.55Al_0.1Ni_0.05Cu_0.3)_100 ? xY_x (x = 0, 0.5, 1, 2) bulk metallic glasses (BMGs) in their supercooled liquid regions (SLRs) and the in-situ heating nucleation were investigated, respectively. In the SLR, the (Zr_0.55Al_0.1Ni_0.05Cu_0.3)₉₉Y₁ metallic glass which shows distinct plastic strain in compression exhibits higher viscosity than the other three BMGs, however their Poisson's ratios are almost the same. The synchrotron diffraction results show that crystallization happened in the SLR of the (Zr_0.55Al_0.1Ni_0.05Cu_0.3)₉₉Y₁ glassy alloy, which could be the reason for the higher viscosity and larger plastic strain in compression compared to the other three alloys. The fracture surfaces of the glassy alloys were observed and analyzed.     

Dual-cardiac marker capillary waveguide fluoroimmunosensor based on tyramide signal amplification

The early diagnosis of acute myocardial infarction requires the determination of several markers in serum shortly after its incidence. The markers most widely employed are the isoenzyme MB of creatine kinase (CK-MB) and the cardiac troponin I (cTnI). In the present work, a capillary waveguide fluoroimmunosensor for fast and highly sensitive simultaneous determination of these markers in serum samples is demonstrated. The dual-analyte immunosensor was realized using glass capillaries internally modified with an ultrathin poly(dimethylsiloxane) film by creating discrete bands of analyte-specific antibodies. The capillary was then filled with a mixture of sample and biotinylated detection antibodies followed by reaction with streptavidin–horseradish peroxidase and incubation with a fluorescently labeled tyramide derivative to accumulate fluorescent labels onto immunoreaction bands. Upon scanning the capillary with a laser beam, part of the emitted fluorescence is trapped and waveguided through the capillary wall to a photomultiplier placed on one of its ends. The employment of tyramide signal amplification provided detection limits of 0.2 and 0.5 ng/mL for cTnI and CK-MB, respectively, in a total assay time of 30 min compared to 0.8 and 0.6 ng/mL obtained for the corresponding assays when the conventional fluorescent label R-phycoerythrin was used in a 65-min assay. In addition, the proposed immunosensor provided accurate and repeatable measurements (intra-assay and interassay coefficients of variation lower than 10%), and the values determined in serum samples were in good agreement with those obtained with commercially available enzyme immunoassays. Thus, the proposed capillary waveguide fluoroimmunosensor has all the required characteristics for fast and reliable diagnosis of acute myocardial infarction.      

Photoacoustic imaging in attenuating acoustic media based on strongly causal models

In this paper, we derive time reversal imaging functionals for two strongly causal acoustic attenuation models, which have been proposed recently. The time reversal techniques are based on recently proposed ideas of Ammari et al. for the thermo‐viscous wave equation. Here and there, an asymptotic analysis provides reconstruction functionals from first order corrections for the attenuating effect. In addition, we present a novel approach for higher order corrections. Copyright © 2013 John Wiley & Sons, Ltd.     

Dielectric‐loaded plasmonic waveguide components: Going practical

Surface plasmon propagating modes supported by metal/dielectric interfaces in various configurations can be used for radiation guiding similarly to conventional dielectric waveguides. Plasmonic waveguides offer two attractive features: subdiffraction mode confinement and the presence of conducting elements at the mode‐field maximum. The first feature can be exploited to realize ultrahigh density of nanophotonics components, whereas the second feature enables the development of dynamic components controlling the plasmon propagation with ultralow signals, minimizing heat dissipation in switching elements. While the first feature is yet to be brought close to the domain of practical applications because of high propagation losses, the second one is already being investigated for bringing down power requirements in optical communication systems. In this review, the latest application‐oriented research on radiation modulation and routing using thermo‐optic dielectric‐loaded plasmonic waveguide components integrated with silicon‐based photonic waveguides is overviewed. Their employment under conditions of real telecommunications is addressed, highlighting challenges and perspectives.     

Ab initio calculations of the O1s XPS spectra of ZnO and Zn oxo compounds

O1s core level binding energies of oxygen atoms in bulk ZnO, at different ZnO surfaces, and in some Zn oxo compounds were calculated by means of wave function based quantum chemical ab initio methods. Initial and final state effects were obtained by Koopmans' theorem and at the DeltaSCF level, respectively. After correction for scalar relativistic effects and electron correlation, the calculated XPS peak positions are in excellent agreement with the available experimental data for all systems included in the present study. The O1s core level shifts between an isolated H2O molecule and the Zn oxo compounds or ZnO, as well as between oxygen atoms in bulk ZnO and at various ZnO surfaces, can be understood by means of Madelung potentials and electronic relaxation or screening. XPS spectra were calculated for various cluster models which are designed to describe different possibilities of stabilizing the polar O-terminated ZnO(0001) surface by the adsorption of H atoms. The experimental spectra are only compatible with the theoretical results for the fully hydroxylated H-ZnO(0001) surface exhibiting a (1x1) surface structure.