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2007


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Phenotyping of Chondrocytes In Vivo and In Vitro Using cDNA Array Technology

Zien, A., Gebhard, P., Fundel, K., Aigner, T.

Clinical Orthopaedics and Related Research, 460, pages: 226-233, July 2007 (article)

Abstract
The cDNA array technology is a powerful tool to analyze a high number of genes in parallel. We investigated whether large-scale gene expression analysis allows clustering and identification of cellular phenotypes of chondrocytes in different in vivo and in vitro conditions. In 100% of cases, clustering analysis distinguished between in vivo and in vitro samples, suggesting fundamental differences in chondrocytes in situ and in vitro regardless of the culture conditions or disease status. It also allowed us to differentiate between healthy and osteoarthritic cartilage. The clustering also revealed the relative importance of the investigated culturing conditions (stimulation agent, stimulation time, bead/monolayer). We augmented the cluster analysis with a statistical search for genes showing differential expression. The identified genes provided hints to the molecular basis of the differences between the sample classes. Our approach shows the power of modern bioinformatic algorithms for understanding and class ifying chondrocytic phenotypes in vivo and in vitro. Although it does not generate new experimental data per se, it provides valuable information regarding the biology of chondrocytes and may provide tools for diagnosing and staging the osteoarthritic disease process.

ei

DOI [BibTex]

2007


DOI [BibTex]


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Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

Clark, R., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T., Fu, G., Hinds, D., Chen, H., Frazer, K., Huson, D., Schölkopf, B., Nordborg, M., Rätsch, G., Ecker, J., Weigel, D.

Science, 317(5836):338-342, July 2007 (article)

Abstract
The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and ~4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Graph Laplacians and their Convergence on Random Neighborhood Graphs

Hein, M., Audibert, J., von Luxburg, U.

Journal of Machine Learning Research, 8, pages: 1325-1370, June 2007 (article)

Abstract
Given a sample from a probability measure with support on a submanifold in Euclidean space one can construct a neighborhood graph which can be seen as an approximation of the submanifold. The graph Laplacian of such a graph is used in several machine learning methods like semi-supervised learning, dimensionality reduction and clustering. In this paper we determine the pointwise limit of three different graph Laplacians used in the literature as the sample size increases and the neighborhood size approaches zero. We show that for a uniform measure on the submanifold all graph Laplacians have the same limit up to constants. However in the case of a non-uniform measure on the submanifold only the so called random walk graph Laplacian converges to the weighted Laplace-Beltrami operator.

ei

PDF PDF [BibTex]

PDF PDF [BibTex]


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Dirichlet Process Mixtures of Factor Analysers

Görür, D., Rasmussen, C.

Fifth Workshop on Bayesian Inference in Stochastic Processes (BSP5), June 2007 (talk)

Abstract
Mixture of factor analysers (MFA) is a well-known model that combines the dimensionality reduction technique of Factor Analysis (FA) with mixture modeling. The key issue in MFA is deciding on the latent dimension and the number of mixture components to be used. The Bayesian treatment of MFA has been considered by Beal and Ghahramani (2000) using variational approximation and by Fokoué and Titterington (2003) using birth-and –death Markov chain Monte Carlo (MCMC). Here, we present the nonparametric MFA model utilizing a Dirichlet process (DP) prior on the component parameters (that is, the factor loading matrix and the mean vector of each component) and describe an MCMC scheme for inference. The clustering property of the DP provides automatic selection of the number of mixture components. The latent dimensionality of each component is inferred by automatic relevance determination (ARD). Identifying the action potentials of individual neurons from extracellular recordings, known as spike sorting, is a challenging clustering problem. We apply our model for clustering the waveforms recorded from the cortex of a macaque monkey.

ei

Web [BibTex]

Web [BibTex]


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New BCI approaches: Selective Attention to Auditory and Tactile Stimulus Streams

Hill, N., Raths, C.

Invited talk at the PASCAL Workshop on Methods of Data Analysis in Computational Neuroscience and Brain Computer Interfaces, June 2007 (talk)

Abstract
When considering Brain-Computer Interface (BCI) development for patients in the most severely paralysed states, there is considerable motivation to move away from BCI systems based on either motor cortex activity, or on visual stimuli. Together these account for most of current BCI research. I present the results of our recent exploration of new auditory- and tactile-stimulus-driven BCIs. The talk includes a tutorial on the construction and interpretation of classifiers which extract spatio-temporal features from event-related potential data. The effects and implications of whitening are discussed, and preliminary results on the effectiveness of a low-rank constraint (Tomioka and Aihara 2007) are shown.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Towards Motor Skill Learning in Robotics

Peters, J.

Interactive Robot Learning - RSS workshop, June 2007 (talk)

ei

Web [BibTex]

Web [BibTex]


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Transductive Support Vector Machines for Structured Variables

Zien, A., Brefeld, U., Scheffer, T.

International Conference on Machine Learning (ICML), June 2007 (talk)

Abstract
We study the problem of learning kernel machines transductively for structured output variables. Transductive learning can be reduced to combinatorial optimization problems over all possible labelings of the unlabeled data. In order to scale transductive learning to structured variables, we transform the corresponding non-convex, combinatorial, constrained optimization problems into continuous, unconstrained optimization problems. The discrete optimization parameters are eliminated and the resulting differentiable problems can be optimized efficiently. We study the effectiveness of the generalized TSVM on multiclass classification and label-sequence learning problems empirically.

ei

PDF PDF Web [BibTex]

PDF PDF Web [BibTex]


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Bayesian Reconstruction of the Density of States

Habeck, M.

Physical Review Letters, 98(20, 200601):1-4, May 2007 (article)

Abstract
A Bayesian framework is developed to reconstruct the density of states from multiple canonical simulations. The framework encompasses the histogram reweighting method of Ferrenberg and Swendsen. The new approach applies to nonparametric as well as parametric models and does not require simulation data to be discretized. It offers a means to assess the precision of the reconstructed density of states and of derived thermodynamic quantities.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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PALMA: mRNA to Genome Alignments using Large Margin Algorithms

Schulze, U., Hepp, B., Ong, C., Rätsch, G.

Bioinformatics, 23(15):1892-1900, May 2007 (article)

Abstract
Motivation: Despite many years of research on how to properly align sequences in the presence of sequencing errors, alternative splicing and micro-exons, the correct alignment of mRNA sequences to genomic DNA is still a challenging task. Results: We present a novel approach based on large margin learning that combines accurate plice site predictions with common sequence alignment techniques. By solving a convex optimization problem, our algorithm – called PALMA – tunes the parameters of the model such that true alignments score higher than other alignments. We study the accuracy of alignments of mRNAs containing artificially generated micro-exons to genomic DNA. In a carefully designed experiment, we show that our algorithm accurately identifies the intron boundaries as well as boundaries of the optimal local alignment. It outperforms all other methods: for 5702 artificially shortened EST sequences from C. elegans and human it correctly identifies the intron boundaries in all except two cases. The best other method is a recently proposed method called exalin which misaligns 37 of the sequences. Our method also demonstrates robustness to mutations, insertions and deletions, retaining accuracy even at high noise levels. Availability: Datasets for training, evaluation and testing, additional results and a stand-alone alignment tool implemented in C++ and python are available at http://www.fml.mpg.de/raetsch/projects/palma.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Impact of target-to-target interval on classification performance in the P300 speller

Martens, S., Hill, J., Farquhar, J., Schölkopf, B.

Scientific Meeting "Applied Neuroscience for Healthy Brain Function", May 2007 (talk)

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Training a Support Vector Machine in the Primal

Chapelle, O.

Neural Computation, 19(5):1155-1178, March 2007 (article)

Abstract
Most literature on Support Vector Machines (SVMs) concentrate on the dual optimization problem. In this paper, we would like to point out that the primal problem can also be solved efficiently, both for linear and non-linear SVMs, and that there is no reason for ignoring this possibilty. On the contrary, from the primal point of view new families of algorithms for large scale SVM training can be investigated.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning

Rätsch, G., Sonnenburg, S., Srinivasan, J., Witte, H., Müller, K., Sommer, R., Schölkopf, B.

PLoS Computational Biology, 3(2, e20):0313-0322, February 2007 (article)

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Statistical Consistency of Kernel Canonical Correlation Analysis

Fukumizu, K., Bach, F., Gretton, A.

Journal of Machine Learning Research, 8, pages: 361-383, February 2007 (article)

Abstract
While kernel canonical correlation analysis (CCA) has been applied in many contexts, the convergence of finite sample estimates of the associated functions to their population counterparts has not yet been established. This paper gives a mathematical proof of the statistical convergence of kernel CCA, providing a theoretical justification for the method. The proof uses covariance operators defined on reproducing kernel Hilbert spaces, and analyzes the convergence of their empirical estimates of finite rank to their population counterparts, which can have infinite rank. The result also gives a sufficient condition for convergence on the regularization coefficient involved in kernel CCA: this should decrease as n^{-1/3}, where n is the number of data.

ei

PDF [BibTex]

PDF [BibTex]


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New Margin- and Evidence-Based Approaches for EEG Signal Classification

Hill, N., Farquhar, J.

Invited talk at the FaSor Jahressymposium, February 2007 (talk)

ei

PDF [BibTex]

PDF [BibTex]


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Some observations on the pedestal effect

Henning, G., Wichmann, F.

Journal of Vision, 7(1:3):1-15, January 2007 (article)

Abstract
The pedestal or dipper effect is the large improvement in the detectability of a sinusoidal grating observed when it is added to a masking or pedestal grating of the same spatial frequency, orientation, and phase. We measured the pedestal effect in both broadband and notched noiseVnoise from which a 1.5-octave band centered on the signal frequency had been removed. Although the pedestal effect persists in broadband noise, it almost disappears in the notched noise. Furthermore, the pedestal effect is substantial when either high- or low-pass masking noise is used. We conclude that the pedestal effect in the absence of notched noise results principally from the use of information derived from channels with peak sensitivities at spatial frequencies different from that of the signal and the pedestal. We speculate that the spatial-frequency components of the notched noise above and below the spatial frequency of the signal and the pedestal prevent ‘‘off-frequency looking,’’ that is, prevent the use of information about changes in contrast carried in channels tuned to spatial frequencies that are very much different from that of the signal and the pedestal. Thus, the pedestal or dipper effect measured without notched noise appears not to be a characteristic of individual spatial-frequency-tuned channels.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Cue Combination and the Effect of Horizontal Disparity and Perspective on Stereoacuity

Zalevski, AM., Henning, GB., Hill, NJ.

Spatial Vision, 20(1):107-138, January 2007 (article)

Abstract
Relative depth judgments of vertical lines based on horizontal disparity deteriorate enormously when the lines form part of closed configurations (Westheimer, 1979). In studies showing this effect, perspective was not manipulated and thus produced inconsistency between horizontal disparity and perspective. We show that stereoacuity improves dramatically when perspective and horizontal disparity are made consistent. Observers appear to use unhelpful perspective cues in judging the relative depth of the vertical sides of rectangles in a way not incompatible with a form of cue weighting. However, 95% confidence intervals for the weights derived for cues usually exceed the a-priori [0-1] range.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Frequency-domain displacement sensing with a fiber ring-resonator containing a variable gap

Vollmer, F., Fischer, P.

SENSORS AND ACTUATORS A-PHYSICAL, 134(2):410-413, 2007 (article)

Abstract
Ring-resonators are in general not amenable to strain-free (non-contact) displacement measurements. We show that this limitation may be overcome if the ring-resonator, here a fiber-loop, is designed to contain a gap, such that the light traverses a free-space part between two aligned waveguide ends. Displacements are determined with nanometer sensitivity by measuring the associated changes in the resonance frequencies. Miniaturization should increase the sensitivity of the ring-resonator interferometer. Ring geometries that contain an optical circulator can be used to profile reflective samples. (c) 2006 Elsevier B.V. All rights reserved.

pf

DOI [BibTex]

DOI [BibTex]


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Observation of the Faraday effect via beam deflection in a longitudinal magnetic field

Ghosh, A., Hill, W., Fischer, P.

PHYSICAL REVIEW A, 76(5), 2007 (article)

Abstract
We show that magnetic-field-induced circular differential deflection of light can be observed in reflection or refraction at a single interface. The difference in the reflection or refraction angles between the two circular polarization components is a function of the magnetic-field strength and the Verdet constant, and permits the observation of the Faraday effect not via polarization rotation in transmission, but via changes in the propagation direction. Deflection measurements do not suffer from n-pi ambiguities and are shown to be another means to map magnetic fields with high axial resolution, or to determine the sign and magnitude of magnetic-field pulses in a single measurement.

pf

DOI [BibTex]


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Circular differential double diffraction in chiral media

Ghosh, A., Fazal, F. M., Fischer, P.

OPTICS LETTERS, 32(13):1836-1838, 2007 (article)

Abstract
In an optically active liquid the diffraction angle depends on the circular polarization state of the incident light beam. We report the observation of circular differential diffraction in an isotropic chiral medium, and we demonstrate that double diffraction is an alternate means to determine the handedness (enantiomeric excess) of a solution. (c) 2007 Optical Society of America.

pf

DOI [BibTex]

DOI [BibTex]


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Bacterial flagella-based propulsion and on/off motion control of microscale objects

Behkam, B., Sitti, M.

Applied Physics Letters, 90(2):023902, AIP, 2007 (article)

pi

[BibTex]

[BibTex]


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Friction of partially embedded vertically aligned carbon nanofibers inside elastomers

Aksak, B., Sitti, M., Cassell, A., Li, J., Meyyappan, M., Callen, P.

Applied Physics Letters, 91(6):061906, AIP, 2007 (article)

pi

[BibTex]

[BibTex]


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Enhanced friction of elastomer microfiber adhesives with spatulate tips

Kim, S., Aksak, B., Sitti, M.

Applied Physics Letters, 91(22):221913, AIP, 2007 (article)

pi

Project Page [BibTex]

Project Page [BibTex]


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The new robotics - towards human-centered machines

Schaal, S.

HFSP Journal Frontiers of Interdisciplinary Research in the Life Sciences, 1(2):115-126, 2007, clmc (article)

Abstract
Research in robotics has moved away from its primary focus on industrial applications. The New Robotics is a vision that has been developed in past years by our own university and many other national and international research instiutions and addresses how increasingly more human-like robots can live among us and take over tasks where our current society has shortcomings. Elder care, physical therapy, child education, search and rescue, and general assistance in daily life situations are some of the examples that will benefit from the New Robotics in the near future. With these goals in mind, research for the New Robotics has to embrace a broad interdisciplinary approach, ranging from traditional mathematical issues of robotics to novel issues in psychology, neuroscience, and ethics. This paper outlines some of the important research problems that will need to be resolved to make the New Robotics a reality.

am

link (url) [BibTex]

link (url) [BibTex]


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Hydrogen storage in metal-organic frameworks

Hirscher, M., Panella, B.

{Scripta Materialia}, 56, pages: 809-812, 2007 (article)

mms

[BibTex]

[BibTex]


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Substrate-induced current anisotropy in YBa2Cu3O7-δthin films

Djupmyr, M., Albrecht, J.

{Physica C}, 460-462, pages: 1190-1191, 2007 (article)

mms

DOI [BibTex]

DOI [BibTex]


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A micellar approach to magnetic ultrahigh-density data-storage media: extending the limits of current colloidal methods

Ethirajan, A., Wiedwald, U., Boyen, H.-G., Kern, B., Han, L., Klimmer, A., Weigl, F., Kästle, G., Ziemann, P., Fauth, K., Cai, J., Behm, J., Romanyuk, A., Oelhafen, P., Walther, P., Biskupek, J., Kaiser, U.

{Advanced Materials}, 19, pages: 406-410, 2007 (article)

mms

[BibTex]

[BibTex]


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Size dependence in the magnetization reversal of Fe/Gd multilayers on self-assembled arrays of nanospheres

Amaladass, E., Ludescher, B., Schütz, G., Tyliszczak, T., Eimüller, T.

{Applied Physics Letters}, 91, 2007 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Ma\ssgeschneiderte Wasserstoffspeicher

Hirscher, M., Panella, B.

{Nachrichten aus der Gdch-Energieinitiative}, (Sonderheft April 2007):12-13, 2007 (article)

mms

[BibTex]

[BibTex]


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Reconstruction of historical alloys for pipe organs brings true Baroque music back to life.

Baretzky, B., Friesel, M., Straumal, B.

{MRS Bulletin}, 32, pages: 249-255, 2007 (article)

mms

[BibTex]

[BibTex]


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Analysis of results from X-ray magnetic reflectometry for magnetic multilayer systems

Fähnle, M., Steiauf, D., Martosiswoyo, L., Goering, E., Brück, S., Schütz, G.

{Physical Review B}, 75, 2007 (article)

mms

[BibTex]

[BibTex]


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Dramatic role of critical current anisotropy on flux avalanches in MgB2 films

Albrecht, J., Matveev, A. T., Strempfer, J., Habermeier, H.-U., Shantsev, D. V., Galperin, Y. M., Johansen, T. H.

{Physical Review Letters}, 98, 2007 (article)

mms

[BibTex]

[BibTex]


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Transport properties of LCMO/YBCO hybrid structures

Soltan, S., Albrecht, J., Habermeier, H.-U.

{Materials Science and Engineering B}, 144, pages: 15-18, 2007 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Microscale and nanoscale robotics systems [grand challenges of robotics]

Sitti, M.

IEEE Robotics \& Automation Magazine, 14(1):53-60, IEEE, 2007 (article)

pi

[BibTex]

[BibTex]


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A new biomimetic adhesive for therapeutic capsule endoscope applications in the gastrointestinal tract

Glass, P., Sitti, M., Appasamy, R.

Gastrointestinal Endoscopy, 65(5):AB91, Mosby, 2007 (article)

pi

[BibTex]

[BibTex]


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Visual servoing-based autonomous 2-D manipulation of microparticles using a nanoprobe

Onal, C. D., Sitti, M.

IEEE Transactions on control systems technology, 15(5):842-852, IEEE, 2007 (article)

pi

[BibTex]

[BibTex]


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Cluster expansions in multicomponent systems: precise expansions from noisy databases

Diaz-Ortiz, A., Dosch, H., Drautz, R.

{Journal of Physics: Condensed Matter}, 19, 2007 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Unusual propagation of magnetic avalanches in gold covered MgB2

Albrecht, J., Matveev, A. T., Habermeier, H.-U.

{Physica C}, 460-462, pages: 1245-1246, 2007 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Lowering of the L10 ordering temperature of FePt nanoparticles by He+ ion irradiation

Wiedwald, U., Klimmer, A., Kern, B., Han, L., Boyen, H.-G., Ziemann, P., Fauth, K.

{Applied Physics Letters}, 90, 2007 (article)

mms

[BibTex]

[BibTex]


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Magnetic core shell nanoparticles characterized by X-ray absorption and magnetic circular dichroism

Fauth, K.

{Modern Physics Letters B}, 21(18):1179-1187, 2007 (article)

mms

[BibTex]

[BibTex]


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Magnetic moment of Fe in oxide-free FePt nanoparticles

Dmitrieva, O., Spasova, M., Antoniak, C., Acet, M., Dumpich, G., Kästner, J., Farle, M., Fauth, K., Wiedwald, U., Boyen, H.-G., Ziemann, P.

{Physical Review B}, 76, 2007 (article)

mms

[BibTex]

[BibTex]


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The effect of bismuth segregation on the faceting of \Sigma3 and \Sigma9 coincidence boundaries in copper bicrystals

Straumal, B. B., Polyakov, S. A., Chang, L.-S., Mittemeijer, E. J.

{International Journal of Materials Research}, 98, pages: 451-456, 2007 (article)

mms

[BibTex]

[BibTex]


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Hot isostatic pressing of Cu-Bi polycrystals with liquid-like grain boundary layers

Chang, L.-S., Straumal, B., Rabkin, E., Lojkowski, W., Gust, W.

{Acta Materialia}, 55, pages: 335-343, 2007 (article)

mms

[BibTex]

[BibTex]


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Spatially resolved magnetic response in core shell nanoparticles

Fauth, K., Goering, E., Theil Kuhn, L.

{Modern Physics Letters B}, 21(18):1197-1200, 2007 (article)

mms

[BibTex]

[BibTex]


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Interfaces in semiconductor/metal radial superlattices

Deneke, C., Sigle, W., Eigenthaler, U., van Aken, P. A., Schütz, G., Schmidt, O. G.

{Applied Physics Letters}, 90, 2007 (article)

mms

[BibTex]

[BibTex]


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Live cell adhesion assay with attenuated total reflection infrared spectroscopy

Schmidt, M., Wolfram, T., Rumpler, M., Tripp, C. P., Grunze, M.

{Biointerphases}, 2(1):1-5, 2007 (article)

mms

[BibTex]

[BibTex]


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Unusual Co moment reduction in the NiCoO/Co exchange bias system

Brück, S., Goering, E., Tang, Y. J., Schütz, G., Berkowitz, A. E.

{Journal of Magnetism and Magnetic Materials}, 310, pages: 2316-2318, 2007 (article)

mms

[BibTex]

[BibTex]