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Universal natural shapes: From unifying shape description to simple methods for shape analysis and boundary value problems

Gielis, J. (author), Caratelli, D. (author), Fougerolle, Y. (author), Ricci, P.E. (author), Tavkelidze, I. (author), Gerats, T. (author)

Gielis curves and surfaces can describe a wide range of natural shapes and they have been used in various studies in biology and physics as descriptive tool. This has stimulated the generalization of widely used computational methods. Here we show that proper normalization of the Levenberg-Marquardt algorithm allows for efficient and robust...

journal article 2012

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NAP1-Assisted Nucleosome Assembly on DNA Measured in Real Time by Single-Molecule Magnetic Tweezers

Vlijm, R. (author), Smitshuijzen, J.S.J. (author), Lusser, A. (author), Dekker, C. (author)

While many proteins are involved in the assembly and (re)positioning of nucleosomes, the dynamics of protein-assisted nucleosome formation are not well understood. We study NAP1 (nucleosome assembly protein 1) assisted nucleosome formation at the single-molecule level using magnetic tweezers. This method allows to apply a well-defined stretching...

journal article 2012

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Accurate Blood Flow Measurements: Are Artificial Tracers Necessary?

Poelma, C. (author), Kloosterman, A. (author), Hierck, B.P. (author), Westerweel, J. (author)

Imaging-based blood flow measurement techniques, such as particle image velocimetry, have become an important tool in cardiovascular research. They provide quantitative information about blood flow, which benefits applications ranging from developmental biology to tumor perfusion studies. Studies using these methods can be classified based on...

journal article 2012

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A mesenchymal stromal cell gene signature for donor age

Alves, H. (author), Van Ginkel, J. (author), Groen, N. (author), Hulsman, N. (author), Mentink, A. (author), Reinders, M.J.T. (author), Van Blitterswijk, C. (author), De Boer, J. (author)

Human aging is associated with loss of function and regenerative capacity. Human bone marrow derived mesenchymal stromal cells (hMSCs) are involved in tissue regeneration, evidenced by their capacity to differentiate into several lineages and therefore are considered the golden standard for cell-based regeneration therapy. Tissue maintenance and...

journal article 2012

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A Synthetic Peptide with the Putative Iron Binding Motif of Amyloid Precursor Protein (APP) Does Not Catalytically Oxidize Iron

Honarmand Ebrahimi, K. (author), Hagedoorn, P.L. (author), Hagen, W.R. (author)

The ?-amyloid precursor protein (APP), which is a key player in Alzheimer's disease, was recently reported to possess an Fe(II) binding site within its E2 domain which exhibits ferroxidase activity [Duce et al. 2010, Cell 142: 857]. The putative ligands of this site were compared to those in the ferroxidase site of ferritin. The activity was...

journal article 2012

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Magnetic Forces and DNA Mechanics in Multiplexed Magnetic Tweezers

De Vlaminck, I. (author), Henighan, T. (author), Van Loenhout, M.T.J. (author), Burnham, D.R. (author), Dekker, C. (author)

Magnetic tweezers (MT) are a powerful tool for the study of DNA-enzyme interactions. Both the magnet-based manipulation and the camera-based detection used in MT are well suited for multiplexed measurements. Here, we systematically address challenges related to scaling of multiplexed magnetic tweezers (MMT) towards high levels of parallelization...

journal article 2012

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Integration of Clinical and Gene Expression Data Has a Synergetic Effect on Predicting Breast Cancer Outcome

Van Vliet, M.H. (author), Horlings, H.M. (author), Van de Vijver, M.J. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

Breast cancer outcome can be predicted using models derived from gene expression data or clinical data. Only a few studies have created a single prediction model using both gene expression and clinical data. These studies often remain inconclusive regarding an obtained improvement in prediction performance. We rigorously compare three different...

journal article 2012

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Understanding Regulation of Metabolism through Feasibility Analysis

Nikerel, I.E. (author), Berkhout, J. (author), Hu, F. (author), Teusink, B. (author), Reinders, M.J.T. (author), De Ridder, D. (author)

Understanding cellular regulation of metabolism is a major challenge in systems biology. Thus far, the main assumption was that enzyme levels are key regulators in metabolic networks. However, regulation analysis recently showed that metabolism is rarely controlled via enzyme levels only, but through non-obvious combinations of hierarchical ...

journal article 2012

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Exposure Render: An Interactive Photo-Realistic Volume Rendering Framework

Kroes, T. (author), Post, F.H. (author), Botha, C.P. (author)

The field of volume visualization has undergone rapid development during the past years, both due to advances in suitable computing hardware and due to the increasing availability of large volume datasets. Recent work has focused on increasing the visual realism in Direct Volume Rendering (DVR) by integrating a number of visually plausible but...

journal article 2012

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Transcriptional profiling of human familial longevity indicates a role for ASF1A and IL7R

Passtoors, W.M. (author), Boer, J.M. (author), Goeman, J.G. (author), Van den Akker, E.B. (author), Deelen, J. (author), Zwaan, B.J. (author), Scarborough, A. (author), Van der Breggen, R. (author), Vossen, R.H.A.M. (author)

The Leiden Longevity Study consists of families that express extended survival across generations, decreased morbidity in middle-age, and beneficial metabolic profiles. To identify which pathways drive this complex phenotype of familial longevity and healthy aging, we performed a genome-wide gene expression study within this cohort to screen for...

journal article 2012

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Prion uptake in the gut: Identification of the first uptake and replication sites

Kujala, P. (author), Raymond, C.R. (author), Romeijn, M. (author), Godsave, S.F. (author), Van Kasteren, S.I. (author), Wille, H. (author), Prusiner, S.B. (author), Mabbott, N.A. (author), Peters, P.J. (author)

After oral exposure, prions are thought to enter Peyer's patches via M cells and accumulate first upon follicular dendritic cells (FDCs) before spreading to the nervous system. How prions are actually initially acquired from the gut lumen is not known. Using high-resolution immunofluorescence and cryo-immunogold electron microscopy, we report...

journal article 2011

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Time-Resolved Transcriptomics and Bioinformatic Analyses Reveal Intrinsic Stress Responses during Batch Culture of Bacillus subtilis

Blom, E.J. (author), Ridder, A.N.J.A. (author), Lulko, A.T. (author), Roerdink, J.B.T.M. (author), Kuipers, O.P. (author)

We have determined the time-resolved transcriptome of the model gram-positive organism B. subtilis during growth in a batch fermentor on rich medium. DNA microarrays were used to monitor gene transcription using 10-minute intervals at 40 consecutive time points. From the growth curve and analysis of all gene expression levels, we identified 4...

journal article 2011

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Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium

Singer, E. (author), Emerson, D. (author), Webb, E.A. (author), Barco, R.A. (author), Kuenen, J.G. (author), Nelson, W.C. (author), Chan, C.S. (author), Comolli, L.R. (author), Ferriera, S. (author)

Mariprofundus ferrooxydans PV-1 has provided the first genome of the recently discovered Zetaproteobacteria subdivision. Genome analysis reveals a complete TCA cycle, the ability to fix CO2, carbon-storage proteins and a sugar phosphotransferase system (PTS). The latter could facilitate the transport of carbohydrates across the cell membrane and...

journal article 2011

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Facilitating tumor functional assessment by spatially relating 3D tumor histology and in vivo MRI: Image registration approach

Alic, L. (author), Haeck, J.C. (author), Bol, K. (author), Klein, S. (author), Van Tiel, S.T. (author), Wielepolski, P.A. (author), De Jong, M. (author), Niessen, W.J. (author), Bernsen, M. (author), Veenland, J.F. (author)

Background Magnetic resonance imaging (MRI), together with histology, is widely used to diagnose and to monitor treatment in oncology. Spatial correspondence between these modalities provides information about the ability of MRI to characterize cancerous tissue. However, registration is complicated by deformations during pathological processing,...

journal article 2011

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An evaluation protocol for subtype-specific breast cancer event prediction

Sontrop, H.M.J. (author), Verhaegh, W.F.J. (author), Reinders, M.J.T. (author), Moerland, P.D. (author)

In recent years increasing evidence appeared that breast cancer may not constitute a single disease at the molecular level, but comprises a heterogeneous set of subtypes. This suggests that instead of building a single monolithic predictor, better predictors might be constructed that solely target samples of a designated subtype, which are...

journal article 2011

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GATA3 Expression Is Decreased in Psoriasis and during Epidermal Regeneration: Induction by Narrow-Band UVB and IL-4

Rácz, E. (author), Kurek, D. (author), Kant, M. (author), Baerveldt, E.M. (author), Florencia, E. (author), Mourits, S. (author), De Ridder, D. (author), Laman, J.D. (author), Van der Fits, L. (author), Prens, E.P. (author)

Psoriasis is characterized by hyperproliferation of keratinocytes and by infiltration of activated Th1 and Th17 cells in the (epi)dermis. By expression microarray, we previously found the GATA3 transcription factor significantly downregulated in lesional psoriatic skin. Since GATA3 serves as a key switch in both epidermal and T helper cell...

journal article 2011

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Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features

Saulnier, D.M. (author), santos, F. (author), Roos, S. (author), Mistretta, T.A. (author), Spinler, J.K. (author), Molenaar, D. (author), Teusink, B. (author), Versalovic, J. (author)

The genomes of four Lactobacillus reuteri strains isolated from human breast milk and the gastrointestinal tract have been recently sequenced as part of the Human Microbiome Project. Preliminary genome comparisons suggested that these strains belong to two different clades, previously shown to differ with respect to antimicrobial production,...

journal article 2011

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Comparison of Two Methods for In Vivo Estimation of the Glenohumeral Joint Rotation Center (GH-JRC) of the Patients with Shoulder Hemiarthroplasty

Asadi Nikooyan, A. (author), Van der Helm, F.C.T. (author), Westerhoff, P. (author), Graichen, F. (author), Bergmann, G. (author), Veeger, H.E.J. (author)

Determination of an accurate glenohumeral-joint rotation center (GH-JRC) from marker data is essential for kinematic and dynamic analysis of shoulder motions. Previous studies have focused on the evaluation of the different functional methods for the estimation of the GH-JRC for healthy subjects. The goal of this paper is to compare two widely...

journal article 2011

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Clinically Translatable Cell Tracking and Quantification by MRI in Cartilage Repair Using Superparamagnetic Iron Oxides

Van Buul, G. (author), Kotek, G. (author), Wielopolski, P.A. (author), Farrell, E. (author), Bos, P.K. (author), Weinans, H. (author), Grohnert, A.U. (author), Jahr, H. (author), Verhaar, J.A.N. (author), Krestin, G.P. (author), Van Osch, G.J.V.M. (author), Bernsen, M.R. (author)

Background: Articular cartilage has very limited intrinsic regenerative capacity, making cell-based therapy a tempting approach for cartilage repair. Cell tracking can be a major step towards unraveling and improving the repair process of these therapies. We studied superparamagnetic iron oxides (SPIO) for labeling human bone marrow-derived...

journal article 2011

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Genome-Wide Analysis of PDZ Domain Binding Reveals Inherent Functional Overlap within the PDZ Interaction Network

Te Veldhuis, A.J.W. (author), Sakalis, P.A. (author), Fowler, D.A. (author), Bagowski, C.P. (author)

Binding selectivity and cross-reactivity within one of the largest and most abundant interaction domain families, the PDZ family, has long been enigmatic. The complete human PDZ domain complement (the PDZome) consists of 267 domains and we applied here a Bayesian selectivity model to predict hundreds of human PDZ domain interactions, using...

journal article 2011