Jenny Wagner

Inductively coupled, polymer coated surface acoustic wave sensor for organic vapors

Abstract We introduce a new device architecture for polymer coated surface acoustic wave (SAW) sensors for the detection of organic vapors. This new design differs from conventional devices because the sensor is inductively coupled to the rf circuitry so that no bonding wires and sockets are necessary. Two designs of SAW sensors operating in different modes were investigated: a one port device for measurements with a network analyzer or a vector voltmeter and a two port device for oscillator applications.

Nuclear Position and Shape Deformation of Chromosome 8 Territories in Pancreatic Ductal Adenocarcinoma

Cell type specific radial positioning of chromosome territories (CTs) and their sub-domains in the interphase seem to have functional relevance in non-neoplastic human nuclei, while much less is known about nuclear architecture in carcinoma cells and its development during tumor progression. We analyzed the 3D-architecture of the chromosome 8 territory (CT8) in carcinoma and corresponding non-neoplastic ductal pancreatic epithelium. Fluorescence-in-situ-hybridization (FISH) with whole chromosome painting (WCP) probes on sections from formalin-fixed, paraffin wax-embedded tissues from six patients with ductal adenocarcinoma of the pancreas was used. Radial positions and shape parameters of CT8 were analyzed by 3D-microscopy. None of the parameters showed significant inter-individual changes. CT8 was localized in the nuclear periphery in carcinoma cells and normal ductal epithelial cells. Normalized volume and surface of CT8 did not differ significantly. In contrast, the normalized roundness was significantly lower in carcinoma cells, implying an elongation of neoplastic cell nuclei. Unexpectedly, radial positioning of CT8, a dominant parameter of nuclear architecture, did not change significantly when comparing neoplastic with non-neoplastic cells. A significant deformation of CT8, however, accompanies nuclear atypia of carcinoma cells. This decreased roundness of CTs may reflect the genomic and transcriptional alterations in carcinoma.

High-Precision Combinatorial Deposition of Micro Particle Patterns on a Microelectronic Chip

The behavior of charged bio polymer micro particles when deposited onto a CMOS chip can be analytically modeled in form of the incompressible Navier-Stokes equation and the electrostatic Poisson equation, as we describe in this article. Based on these models, numerical simulations of depositions can be implemented in COMSOL that lead to improvements in the experimental setup, optimizing the size and charge distribution of the micro particles. Adapting the experiments according to the simulation results, we will show the powerful gain in deposition precision, which is essential for a contamination-free deposition and hence high quality combinatorial deposition.

Model-independent characterisation of strong gravitational lenses

We develop a new approach to extracting model-independent information from observations of strong gravitational lenses. The approach is based on the generic properties of images near the fold and cusp catastrophes in caustics and critical curves. Observables used are the relative image positions, the magnification ratios and ellipticities of extended images, and time delays between images with temporally varying intensity. We show how these observables constrain derivatives and ratios of derivatives of the lensing potential near a critical curve. Based on these measured properties of the lensing potential, classes of parametric lens models can then easily be restricted to such parameter values compatible with the measurements, thus allowing fast scans of large varieties of models. Applying our approach to a representative galaxy (JVAS B1422+231) and a galaxy-cluster lens (MACS J1149.5+2223), we show which model-independent information can be extracted in those cases and demonstrate that the parameters obtained by our approach for known parametric lens models agree well with those found by detailed model fitting.

Combinatorial selection of short triplex forming oligonucleotides for fluorescence in situ hybridisation COMBO-FISH

Abstract For the selection of short triplex forming oligonucleotides for COMBO-FISH hybridisations used in research and medicine for 3D-structure investigations of the nucleus, the human genome has to be scanned for polypurine or poly-pyrimidine sequences which colocalise at the desired genomic region. Further binding sites of the selected oligonucleotides are required not to cluster anywhere else. We present an implementation of algorithms which design such oligonucleotide sets and exemplify the existence of COMBO-FISH probe sets by designing labelling sets for 29 genes and subsets thereof. The algorithms can be trivially parallelised and run on clusters, grids, and clouds.

Generalised model-independent characterisation of strong gravitational lenses - I. Theoretical foundations

We extend the model-independent approach to characterise strong gravitational lenses of \cite{bib:Wagner} to its most general form to leading order by using the orientation angles of a set of multiple images with respect to their connection line(s) in addition to the relative distances between the images, their ellipticities and time-delays. For two symmetric images that straddle the critical curve, the orientation angle additionally allows to determine the slope of the critical curve and a second (reduced) flexion coefficient at the critical point on the connection line between the images. It also allows to drop the symmetry assumption that the axis of largest image extension is orthogonal to the critical curve. For three images almost forming a giant arc, the degree of assumed image symmetry is also reduced to the most general case, allowing to describe image configurations for which the source need not be placed on the symmetry axis of the two folds that unite at the cusp. For a given set of multiple images, we set limits on the applicability of our approach, show which information can be obtained in cases of merging images, and analyse the accuracy achievable due to the Taylor expansion of the lensing potential for the fold case on a galaxy cluster scale NFW-profile. The position of the critical curve deviates from its true position up to 7\% of the relative distance between the images and the ratio of potential derivatives is retrieved within an accuracy of 22\% of the true value for images as far away from the critical curve as 40\% of the Einstein radius.

Quality analysis of selective microparticle deposition on electrically programmable surfaces

Image processing and pattern analysis can evaluate the deposition quality of triboelectrically charged microparticles on charged surfaces. The image processing method presented in this paper aims at controlling the quality of peptide arrays generated by particle based solid phase Merrifield combinatorial peptide synthesis. Incorrectly deposited particles are detected before the amino acids therein are coupled to the growing peptide. The calibration of the image acquisition is performed in a supervised training step in which all parameters of the quality analyzing algorithm are learnt given one representative image. Then, the correct deposition pattern is determined by a linear support vector machine. Knowing the pattern, contaminated areas can be detected by comparing the pattern with the actual deposition. Taking into account the resolution of the image acquisition system and its magnification factor, the number and size of contaminating particles can be calculated out of the number of connected foreground pixels.

Generalised model-independent characterisation of strong gravitational lenses. II. Transformation matrix between multiple images

(shortened) We determine the transformation matrix T that maps multiple images with resolved features onto one another and that is based on a Taylor-expanded lensing potential close to a point on the critical curve within our model-independent lens characterisation approach. From T, the same information about the critical curve at fold and cusp points is derived as determined by the quadrupole moment of the individual images as observables. In addition, we read off the relative parities between the images, so that the parity of all images is determined, when one is known. We compare all retrievable ratios of potential derivatives to the actual ones and to those obtained by using the quadrupole moment as observable for two and three image configurations generated by a galaxy-cluster scale singular isothermal ellipse. We conclude that using the quadrupole moments as observables, the properties of the critical curve at the cusp points are retrieved to higher accuracy, at the fold points to lower accuracy, and the ratios of second order potential derivatives to comparable accuracy. We show that the approach using ratios of convergences and reduced shear is equivalent to ours close to the critical curve but yields more accurate results and is more robust because it does not require a special coordinate system like the approach using potential derivatives. T is determined by mapping manually assigned reference points in the images onto each other. If the assignment of reference points is subject to measurement uncertainties under noise, we find that the confidence intervals of the lens parameters can be as large as the values, when the uncertainties are larger than one pixel. Observed multiple images with resolved features are more extended than unresolved ones, so that higher order moments should be taken into account to improve the reconstruction.

Efficient clustering earth mover's distance

The two-class clustering problem is formulated as an integer convex optimisation problem which determines the maximum of the Earth Movers Distance (EMD) between two classes, constructing a bipartite graph with minimum flow and maximum inter-class EMD between two sets. Subsequently including the nearest neighbours of the start point in feature space and calculating the EMD for this labellings quickly converges to a robust optimum. A histogram of grey values with the number of bins b as the only parameter is used as feature, which makes run time complexity independent of the number of pixels. After convergence in O(b) steps, spatial correlations can be taken into account by total variational smoothing. Testing the algorithm on real world images from commonly used databases reveals that it is competitive to state-of-theart methods, while it deterministically yields hard assignments without requiring any a priori knowledge of the input data or similarity matrices to be calculated.

Generalised model-independent characterisation of strong gravitational lenses: III. Perturbed axisymmetric lenses

In galaxy-galaxy strong gravitational lensing, Einstein rings are generated when the lensing galaxy has an axisymmetric lensing potential and the source galaxy is aligned with its symmetry centre along the line of sight. Using a Taylor expansion around the Einstein radius and eliminating the unknown source, I derive a set of analytic equations that determine differences of the deflection angle of the perturber weighted by the convergence of the axisymmetric lens and ratios of the convergences at the positions of the arcs from the measurable thickness of the arcs. In the same manner, asymmetries in the brightness distributions along an arc determine differences in the deflection angle of the perturber if the source has a symmetric brightness profile and is oriented parallel to or orthogonal to the caustic. These equations are the only model-independent information retrievable from observations to leading order in the Taylor expansion. General constraints on the derivatives of the perturbing lens are derived such that the perturbation does not change the number of critical curves. To infer physical properties such as the mass of the perturber or its position, models need to be inserted. The same conclusions about the scale of detectable masses and model-dependent degeneracies as in other approaches are then found and supported by analysing B1938 as an example. Yet, the model-independent equations show that there is a fundamental degeneracy between the main lens and the perturber that can only be broken if their relative position is known. This explains the degeneracies between lens models already found in simulations from a more general viewpoint. Depending on the properties of the pertuber, this degeneracy can be broken by characterising the surrounding of the lens or by measuring the time delay between quasar images embedded in the perturbed Einstein ring of the host galaxy.