Protein Microarray: "Theory" to "Real Practice"

Fueled by ever-growing genomic information and rapid developments of proteomics–the large scale analysis of proteins and mapping its functional role has become one of the most important disciplines for characterizing complex cell function. For building functional linkages between the biomolecules, and for providing insight into the mechanisms of biological processes, last decade witnessed the exploration of combinatorial and chip technology for the detection of bimolecules in a high throughput and spatially addressable fashion. Among the various techniques developed, the protein chip technology has been rapid. Recently we demonstrated a new platform called “Spacially addressable protein array” (SAPA) to profile the ligand receptor interactions. To optimize the platform, the present study investigated various parameters such as the surface chemistry and role of additives for achieving high density and high-throughput detection with minimal nonspecific protein adsorption. In summary the present poster will address some of the critical challenges in protein micro array technology and the process of fine tuning to achieve the optimum system for solving real biological problems.

TU Graz: Course: 707.000 Web Science and Web Technology: Lecture 3: Network Theory and Terminology

In this class, we will discuss network theory fundamentals, including concepts such as diameter, distance, clustering coefficient and others. We will also discuss different types of networks, such as scale-free networks, random networks etc. Readings: Graph structure in the Web, A. Broder and R. Kumar and F. Maghoul and P. Raghavan and S. Rajagopalan and R. Stata and A. Tomkins and J. Wiener Computer Networks 33 309--320 (2000) [Web link, Alternative Link] Optional: The Structure and Function of Complex Networks, M.E.J. Newman, SIAM Review 45 167--256 (2003) [Web link] Original course at: http://kmi.tugraz.at/staff/markus/courses/SS2008/707.000_web-science/

La muerte en la psicoterapia fenomenológico-existencial

El siguiente trabajo pretende, mediante la revisión de diferentes fuentes bibliográficas, mostrar las distintas categorías en las que la muerte se trabaja dentro de la psicoterapia fenomenológico existencial. Es así como se hace un recorrido por los antecedentes filosóficos de este enfoque psicoterapéutico, las diferentes escuelas que dentro de él se desarrollan y sus planteamientos frente a la muerte, las maneras de morir, la muerte y el ciclo vital, y los avances actuales como la Teoría del Manejo del Terror (TMT) . Todos estos elementos se revisan para después ser relacionados y así proponer una serie de acciones prácticas a llevar a cabo dentro del encuentro psicoterapéutico con miras a un trabajo adecuado y productivo con la muerte desde una perspectiva existencial.

Electron localization function at the correlated level

The electron localization function (ELF) has been proven so far a valuable tool to determine the location of electron pairs. Because of that, the ELF has been widely used to understand the nature of the chemical bonding and to discuss the mechanism of chemical reactions. Up to now, most applications of the ELF have been performed with monodeterminantal methods and only few attempts to calculate this function for correlated wave functions have been carried out. Here, a formulation of ELF valid for mono- and multiconfigurational wave functions is given and compared with previous recently reported approaches. The method described does not require the use of the homogeneous electron gas to define the ELF, at variance with the ELF definition given by Becke. The effect of the electron correlation in the ELF, introduced by means of configuration interaction with singles and doubles calculations, is discussed in the light of the results derived from a set of atomic and molecular systems

Fuzzy set Theory and Quantum Chemistry

Es discuteixen breument algunes consideracions sobre l'aplicació de la Teoria dels Conjunts difusos a la Química quàntica. Es demostra aqui que molts conceptes químics associats a la teoria són adequats per ésser connectats amb l'estructura dels Conjunts difusos. També s'explica com algunes descripcions teoriques dels observables quàntics es potencien tractant-les amb les eines associades als esmentats Conjunts difusos. La funció densitat es pren com a exemple de l'ús de distribucions de possibilitat al mateix temps que les distribucions de probabilitat quàntiques

Theory and observations of ice particle evolution in cirrus using Doppler radar: evidence for aggregation

Vertically pointing Doppler radar has been used to study the evolution of ice particles as they sediment through a cirrus cloud. The measured Doppler fall speeds, together with radar-derived estimates for the altitude of cloud top, are used to estimate a characteristic fall time tc for the `average' ice particle. The change in radar reflectivity Z is studied as a function of tc, and is found to increase exponentially with fall time. We use the idea of dynamically scaling particle size distributions to show that this behaviour implies exponential growth of the average particle size, and argue that this exponential growth is a signature of ice crystal aggregation.

Beurling zeta functions, generalised primes, and fractal membranes

We study generalised prime systems P (1 < p(1) <= p(2) <= ..., with p(j) is an element of R tending to infinity) and the associated Beurling zeta function zeta p(s) = Pi(infinity)(j=1)(1 - p(j)(-s))(-1). Under appropriate assumptions, we establish various analytic properties of zeta p(s), including its analytic continuation, and we characterise the existence of a suitable generalised functional equation. In particular, we examine the relationship between a counterpart of the Prime Number Theorem (with error term) and the properties of the analytic continuation of zeta p(s). Further we study 'well-behaved' g-prime systems, namely, systems for which both the prime and integer counting function are asymptotically well-behaved. Finally, we show that there exists a natural correspondence between generalised prime systems and suitable orders on N-2. Some of the above results are relevant to the second author's theory of 'fractal membranes', whose spectral partition functions are given by Beurling-type zeta functions, as well as to joint work of that author and R. Nest on zeta functions attached to quasicrystals.

Radar scattering by aggregate snowflakes

The radar scattering properties of realistic aggregate snowflakes have been calculated using the Rayleigh-Gans theory. We find that the effect of the snowflake geometry on the scattering may be described in terms of a single universal function, which depends only on the overall shape of the aggregate and not the geometry or size of the pristine ice crystals which compose the flake. This function is well approximated by a simple analytic expression at small sizes; for larger snowflakes we fit a curve to Our numerical data. We then demonstrate how this allows a characteristic snowflake radius to be derived from dual wavelength radar measurements without knowledge of the pristine crystal size or habit, while at the same time showing that this detail is crucial to using such data to estimate ice water content. We also show that the 'effective radius'. characterizing the ratio of particle volume to projected area, cannot be inferred from dual wavelength radar data for aggregates. Finally, we consider the errors involved in approximating snowflakes by 'air-ice spheres', and show that for small enough aggregates the predicted dual wavelength ratio typically agrees to within a few percent, provided some care is taken in choosing the radius of the sphere and the dielectric constant of the air-ice mixture; at larger sizes the radar becomes more sensitive to particle shape, and the errors associated with the sphere model are found to increase accordingly.

Turbulent flow at 190 m height above London during 2006-2008: A climatology and the applicability of similarity theory

Flow and turbulence above urban terrain is more complex than above rural terrain, due to the different momentum and heat transfer characteristics that are affected by the presence of buildings (e.g. pressure variations around buildings). The applicability of similarity theory (as developed over rural terrain) is tested using observations of flow from a sonic anemometer located at 190.3 m height in London, U.K. using about 6500 h of data. Turbulence statistics—dimensionless wind speed and temperature, standard deviations and correlation coefficients for momentum and heat transfer—were analysed in three ways. First, turbulence statistics were plotted as a function only of a local stability parameter z/Λ (where Λ is the local Obukhov length and z is the height above ground); the σ_i/u_* values (i = u, v, w) for neutral conditions are 2.3, 1.85 and 1.35 respectively, similar to canonical values. Second, analysis of urban mixed-layer formulations during daytime convective conditions over London was undertaken, showing that atmospheric turbulence at high altitude over large cities might not behave dissimilarly from that over rural terrain. Third, correlation coefficients for heat and momentum were analyzed with respect to local stability. The results give confidence in using the framework of local similarity for turbulence measured over London, and perhaps other cities. However, the following caveats for our data are worth noting: (i) the terrain is reasonably flat, (ii) building heights vary little over a large area, and (iii) the sensor height is above the mean roughness sublayer depth.

The calculation of accurate normal coordinates I: general theory, and application to methane

The calculation of accurate and reliable vibrational potential functions and normal co-ordinates is discussed, for such simple polyatomic molecules as it may be possible. Such calculations should be corrected for the effects of anharmonicity and of resonance interactions between the vibrational states, and should be fitted to all the available information on all isotopic species: particularly the vibrational frequencies, Coriolis zeta constants and centrifugal distortion constants. The difficulties of making these corrections, and of making use of the observed data are reviewed. A programme for the Ferranti Mercury Computer is described by means of which harmonic vibration frequencies and normal co-ordinate vectors, zeta factors and centrifugal distortion constants can be calculated, from a given force field and from given G-matrix elements, etc. The programme has been used on up to 5 × 5 secular equations for which a single calculation and output of results takes approximately l min; it can readily be extended to larger determinants. The best methods of using such a programme and the possibility of reversing the direction of calculation are discussed. The methods are applied to calculating the best possible vibrational potential function for the methane molecule, making use of all the observed data.

Mapping and controlling molecular processes: The application of control theory and system identification algorithms to ASOPS and other fast pulse spectroscopies

Asynchronous Optical Sampling (ASOPS) [1,2] and frequency comb spectrometry [3] based on dual Ti:saphire resonators operated in a master/slave mode have the potential to improve signal to noise ratio in THz transient and IR sperctrometry. The multimode Brownian oscillator time-domain response function described by state-space models is a mathematically robust framework that can be used to describe the dispersive phenomena governed by Lorentzian, Debye and Drude responses. In addition, the optical properties of an arbitrary medium can be expressed as a linear combination of simple multimode Brownian oscillator functions. The suitability of a range of signal processing schemes adopted from the Systems Identification and Control Theory community for further processing the recorded THz transients in the time or frequency domain will be outlined [4,5]. Since a femtosecond duration pulse is capable of persistent excitation of the medium within which it propagates, such approach is perfectly justifiable. Several de-noising routines based on system identification will be shown. Furthermore, specifically developed apodization structures will be discussed. These are necessary because due to dispersion issues, the time-domain background and sample interferograms are non-symmetrical [6-8]. These procedures can lead to a more precise estimation of the complex insertion loss function. The algorithms are applicable to femtosecond spectroscopies across the EM spectrum. Finally, a methodology for femtosecond pulse shaping using genetic algorithms aiming to map and control molecular relaxation processes will be mentioned.

Modelling risk perception and trust in food safety information within the theory of planned behaviour

This study suggests a statistical strategy for explaining how food purchasing intentions are influenced by different levels of risk perception and trust in food safety information. The modelling process is based on Ajzen's Theory of Planned Behaviour and includes trust and risk perception as additional explanatory factors. Interaction and endogeneity across these determinants is explored through a system of simultaneous equations, while the SPARTA equation is estimated through an ordered probit model. Furthermore, parameters are allowed to vary as a function of socio-demographic variables. The application explores chicken purchasing intentions both in a standard situation and conditional to an hypothetical salmonella scare. Data were collected through a nationally representative UK wide survey of 533 UK respondents in face-to-face, in-home interviews. Empirical findings show that interactions exist among the determinants of planned behaviour and socio-demographic variables improve the model's performance. Attitudes emerge as the key determinant of intention to purchase chicken, while trust in food safety information provided by media reduces the likelihood to purchase. (C) 2006 Elsevier Ltd. All rights reserved.

Sparse multioutput radial basis function network construction using combined locally regularised orthogonal least square and D-optimality experimental design

A construction algorithm for multioutput radial basis function (RBF) network modelling is introduced by combining a locally regularised orthogonal least squares (LROLS) model selection with a D-optimality experimental design. The proposed algorithm aims to achieve maximised model robustness and sparsity via two effective and complementary approaches. The LROLS method alone is capable of producing a very parsimonious RBF network model with excellent generalisation performance. The D-optimality design criterion enhances the model efficiency and robustness. A further advantage of the combined approach is that the user only needs to specify a weighting for the D-optimality cost in the combined RBF model selecting criterion and the entire model construction procedure becomes automatic. The value of this weighting does not influence the model selection procedure critically and it can be chosen with ease from a wide range of values.

Modified radial basis function neural network using output transformation

A modified radial basis function (RBF) neural network and its identification algorithm based on observational data with heterogeneous noise are introduced. The transformed system output of Box-Cox is represented by the RBF neural network. To identify the model from observational data, the singular value decomposition of the full regression matrix consisting of basis functions formed by system input data is initially carried out and a new fast identification method is then developed using Gauss-Newton algorithm to derive the required Box-Cox transformation, based on a maximum likelihood estimator (MLE) for a model base spanned by the largest eigenvectors. Finally, the Box-Cox transformation-based RBF neural network, with good generalisation and sparsity, is identified based on the derived optimal Box-Cox transformation and an orthogonal forward regression algorithm using a pseudo-PRESS statistic to select a sparse RBF model with good generalisation. The proposed algorithm and its efficacy are demonstrated with numerical examples.