Charge Transfer in c-Si(n)/TiO(ALD) at the Amorphous/Anatase Transition: A Transient Surface Photovoltage Spectroscopy Study.

Electronic properties and charge transfer processes were studied in an n-Si(n)/TiO(ALD) system at an amorphous TiO/anatase transition by transient surface photovoltage spectroscopy at constant photon flux. The TiO layers were deposited by atomic layer deposition (ALD) onto highly doped silicon (c-Si(n)), and the phase composition of the TiO layers changed with increasing thickness from amorphous to the anatase polymorph as anatase crystallites started to grow at the surface. Depending on phase composition, the band gap of TiO correlated with the characteristic energy of exponential tails.

Semantic localization-driven partial image retrieval in CT series.

Background: Picture archiving and communication systems (PACS) contain very large amounts of computed tomography (CT) data. When querying a PACS for a particular series, the user is often not interested in the complete series but in a certain region of interest (ROI), described e.g.

2D image registration in CT images using radial image descriptors.

Registering CT scans in a body atlas is an important technique for aligning and comparing different CT scans. It is also required for navigating automatically to certain regions of a scan or if sub volumes should be identified automatically. Common solutions to this problem employ landmark detectors and interpolation techniques.

Supervised ensembles of prediction methods for subcellular localization.

In the past decade, many automated prediction methods for the subcellular localization of proteins have been proposed, utilizing a wide range of principles and learning approaches. Based on an experimental evaluation of different methods and their theoretical properties, we propose to combine a well-balanced set of existing approaches to new, ensemble-based prediction methods. The experimental evaluation shows that our ensembles improve substantially over the underlying base methods.

Extraction of semantic biomedical relations from text using conditional random fields.

Background: The increasing amount of published literature in biomedicine represents an immense source of knowledge, which can only efficiently be accessed by a new generation of automated information extraction tools. Named entity recognition of well-defined objects, such as genes or proteins, has achieved a sufficient level of maturity such that it can form the basis for the next step: the extraction of relations that exist between the recognized entities. Whereas most early work focused on the mere detection of relations, the classification of the type of relation is also of great importance and this is the focus of this work.

Graph kernels for disease outcome prediction from protein-protein interaction networks.

It is widely believed that comparing discrepancies in the protein-protein interaction (PPI) networks of individuals will become an important tool in understanding and preventing diseases. Currently PPI networks for individuals are not available, but gene expression data is becoming easier to obtain and allows us to represent individuals by a co-integrated gene expression/protein interaction network. Two major problems hamper the application of graph kernels - state-of-the-art methods for whole-graph comparison - to compare PPI networks.

Class prediction from time series gene expression profiles using dynamical systems kernels.

We present a kernel-based approach to the classification of time series of gene expression profiles. Our method takes into account the dynamic evolution over time as well as the temporal characteristics of the data. More specifically, we model the evolution of the gene expression profiles as a Linear Time Invariant (LTI) dynamical system and estimate its model parameters.

Integrating structured biological data by Kernel Maximum Mean Discrepancy.

Motivation: Many problems in data integration in bioinformatics can be posed as one common question: Are two sets of observations generated by the same distribution? We propose a kernel-based statistical test for this problem, based on the fact that two distributions are different if and only if there exists at least one function having different expectation on the two distributions. Consequently we use the maximum discrepancy between function means as the basis of a test statistic. The Maximum Mean Discrepancy (MMD) can take advantage of the kernel trick, which allows us to apply it not only to vectors, but strings, sequences, graphs, and other common structured data types arising in molecular biology.

Protein function prediction via graph kernels.

Motivation: Computational approaches to protein function prediction infer protein function by finding proteins with similar sequence, structure, surface clefts, chemical properties, amino acid motifs, interaction partners or phylogenetic profiles. We present a new approach that combines sequential, structural and chemical information into one graph model of proteins. We predict functional class membership of enzymes and non-enzymes using graph kernels and support vector machine classification on these protein graphs.

Nearest neighbor classification in 3D protein databases.

In molecular databases, structural classification is a basic task that can be successfully approached by nearest neighbor methods. The underlying similarity models consider spatial properties such as shape and extension as well as thematic attributes. We introduce 3D shape histograms as an intuitive and powerful approach to model similarity for solid objects such as molecules.

Solvent accessible surface representation in a database system for protein docking.

Protein docking is a new and challenging application for query processing in database systems. Our architecture for an efficient support of docking queries is based on the multistep query processing paradigm, a technique well-known from spatial database system. Along with physicochemical parameters, the geometry of the molecules plays a fundamental role for docking retrieval.

Autoradiography of lymph nodes with 99mTc-dextran in rabbits.

99mTc-dextran (D) was further evaluated in the present study as a lymphoscintigraphic agent compared to radiocolloids. It was injected intra-dermally into the web space between the second and third toes in both hind feet of two rabbits. 99mTc-nanocolloid (NC) was injected subcutaneously in both hind feet of two other rabbits.

Curative radioimmunotherapy of human mammary carcinoma xenografts with iodine-131-labeled monoclonal antibodies.

The radioiodinated monoclonal antibody BW 495/36 showed an exceptionally high uptake and long residence time in human ductal mammary carcinoma xenografts in nude mice. There was a mean tumor uptake of 82%/g 24 hr p.i.

Improved radioimmunoscintigraphy of human mammary carcinoma xenografts after injection of an anti-antibody.

The low tumor-to-background ratio obtained after administration of radiolabeled whole monoclonal antibodies (MAbs) is one of the major problems in immunoscintigraphy and -therapy. To reduce the blood pool label caused by the circulation of radiolabeled MAb we have investigated the advantage of injecting an anti-antibody after administration of a tumor-specific MAb in nude mice bearing human mammary carcinoma xenografts. The MAb MA 10-11 of rat origin, used in these studies, had shown a high affinity to human mammary carcinoma tissue on frozen sections and low cross-reactivity with various normal human tissues.

Measurement of myocardial fatty acid metabolism: kinetics of iodine-123 heptadecanoic acid in normal dog hearts.

To define the potential of iodine-123 heptadecanoic acid (IHA) for the noninvasive assessment of myocardial fatty acid metabolism with gamma camera imaging, the influence of myocardial oxygen consumption (MVO2) and blood flow (MBF) on extraction and half-times of IHA were investigated in dogs. Following IHA injection into the left circumflex coronary artery, extraction fraction and half-times were derived from the peak and slope of the IHA time activity curve, which consisted of a vascular, early, and late phase. Single-pass extraction fraction of IHA averaged 0.

Comparative distribution on niobium-95 in maternal and fetal rats and rabbits.

Pregnant rats and rabbits were injected with Nb95 towards the end of gestation. In rats, all maternal tissues showed higher concentrations compared to the fetal organs; the highest ratio was 0.6 in bone.

The ingrowth quota of autologous spongiosa from different points of removal--experimental study in sheep. A preliminary report.

The importance of the point of removal for the ingrowth quota of autologous spongiosa was examined in seven sheep. In six sheep spongiosa was taken from five different regions (proximal radius, olecranon, pelvic crest, trochanter major, and proximal tibia) and was transplanted autologously. Defined corticalis defects of the tibia were the chosen sites for the heterotopic implantations.

Performance of two new solid-phase ligand assays for TSH using monoclonal antibodies.

Three ligand assays for TSH using monoclonal antibodies, an IRMA, an ELISA and a DELFIA were compared with a standard DAB RIA technique. The IRMA proved to be superior in respect to sensitivity, precision, reproducibility and practicality. The highest sensitivity yet, was achieved by DELFIA.

Uptake mechanism of interstitially injected 99mTc-labeled antimony trisulphide colloid in the popliteal lymph node of rabbits.

The right popliteal lymph node was studied in rabbits by well counting, histoautoradiography and electron microscopy, after interstitial injection of 99mTc-labeled antimony trisulphide (Sb2S3) colloid into the right hind pad. The highest radioactivity concentration (96.8%/g) was measured 6 hr following injection.

Transfer and distribution of niobium-95 in adult, fetal, and newborn rats after injection during pregnancy.

Following i.v. injection of Nb-95 into pregnant rats, fetuses and newborns were dissected and measured for radioactivity after several time intervals.

Correlations between the degree and type of forebrain malformations and the simultaneous neuro-oncogenic properties of ethylnitrosourea after diaplacental exposure in rats, alone and in combination with X-irradiation.

Single and combined treatments were performed in rats on day 13 of gestation with either ENU or ENU subsequent to various X-irradiation doses between 0.5 and 1.5 Gy.