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Hettne, K.M. (author), Kleinjans, J. (author), Stierum, R.H. (author), Boorsma, A. (author), Kors, J.A. (author)This chapter concerns the application of bioinformatics methods to the analysis of toxicogenomics data. The chapter starts with an introduction covering how bioinformatics has been applied in toxicogenomics data analysis, and continues with a description of the foundations of a specific bioinformatics method called text-mining. Next, the...bookPart 2014
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Bosgra, S. (author), van de Steeg, E. (author), Vlaming, M.L. (author), Verhoeckx, K.C. (author), Huisman, M.T. (author), Verwei, M. (author), Wortelboer, H.M. (author)In contrast to primary hepatocytes, estimating carrier-mediated hepatic disposition by using a panel of single transfected cell-lines provides direct information on the contribution of the individual transporters to the net disposition. The most direct way to correct for differences in transporter abundance between cell-lines and tissue is by...article 2014
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Beker van Woudenberg, A. (author), Snel, C. (author), Rijkmans, E. (author), de Groot, D. (author), Bouma, M. (author), Hermsen, S. (author), Piersma, A. (author), Menke, A. (author), Wolterbeek, A. (author)To improve the predictability of the zebrafish embryotoxicity test (ZET) for developmental (neuro)toxicity screening, we used a multiple-endpoints strategy, including morphology, motor activity (MA), histopathology and kinetics. The model compounds used were antiepileptic drugs (AEDs): valproic acid (VPA), carbamazepine (CBZ), ethosuximide (ETH)...article 2014
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Chen, Y. (author), Sun, A. (author), Wang, M. (author), Zhu, Z. (author), Ouwerkerk, P.B.F. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)Glutelins are the most abundant storage proteins in rice grain and can make up to 80 % of total protein content. The promoter region of GluB-1, one of the glutelin genes in rice, has been intensively used as a model to understand regulation of seed-storage protein accumulation. In this study, we describe a zinc finger gene of the Cys3His1 (CCCH...article 2014
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Belzer, C. (author), Gerber, G.K. (author), Roeselers, G. (author), Delaney, M. (author), DuBois, A. (author), Liu, Q. (author), Belavusava, V. (author), Yeliseyev, V. (author), Houseman, A. (author), Onderdonk, A. (author), Cavanaugh, C. (author), Bry, L. (author)Longitudinal studies of the microbiota are important for discovering changes in microbial communities that affect the host. The complexity of these ecosystems requires rigorous integrated experimental and computational methods to identify temporal signatures that promote physiologic or pathophysiologic responses in vivo. Employing a murine model...article 2014
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Mariman, R. (author), Kremer, S.H.A. (author), Koning, F. (author), Nagelkerken, L. (author)Probiotic bacteria express a wide range of molecular structures that bind to receptors on innate immune cells and mediate health-promoting effects in the host. We have recently demonstrated in a colitis model that favourable effects of the probiotic mixture VSL#3 may in part be due to the suppression of intestinal chemokine expression. To obtain...article 2014
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Licht, C.M.M. (author), van Turenhout, L.C. (author), Deijen, J.B. (author), Koppes, L.L.J. (author), van Mechelen, W. (author), Twisk, J.W.R. (author), Drent, M.L. (author)Several studies have demonstrated an association between polymorphisms in the insulin-like growth factor-1 (IGF-1) gene and IGF-1 serum levels. IGF-1 levels have been associated with cognitive functioning in older persons and growth hormone deficient patients. The present study investigates whether IGF-1 polymorphisms, IGF-1 levels, and...article 2014
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Blaauboer, M.E. (author), Emson, C.L. (author), Verschuren, L. (author), van Erk, M. (author), Turner, S.M. (author), Everts, V. (author), Hanemaaijer, R. (author), Stoop, R. (author)Collagen deposition is a key process during idiopathic pulmonary fibrosis; however, little is known about the dynamics of collagen formation during disease development. Tissue samples of early stages of human disease are not readily available and it is difficult to identify changes in collagen content, since standard collagen analyses do not...article 2013
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Martinez, R.C.R. (author), Cardarelli, H.R. (author), Borst, W. (author), Albrecht, S. (author), Schols, H. (author), Gutiérrez, O.P. (author), Maathuis, A.J.H. (author), de Melo Franco, B.D.G. (author), de Martinis, E.C.P. (author), Zoetendal, E.G. (author), Venema, K. (author), Saad, S.M.I. (author), Smidt, H. (author)A validated in vitro model of the large intestine (TIM-2), set up with human or pig faeces, was used to evaluate the impact of potentially probiotic Lactobacillus amylovorus DSM 16698, administered alone (i), in the presence of prebiotic galactooligosaccharides (GOS) (ii), and co-administered with probiotic Bifidobacterium animalis ssp. lactis...article 2013
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Blatchford, P. (author), Ansell, J. (author), de Godoy, M.R.C. (author), Fahey, G. (author), Garcia-Mazcorro, J.F. (author), Gibson, G.R. (author), Goh, Y.J. (author), Hotchkiss, A.T. (author), Hutkins, R. (author), LaCroix, C. (author), Rastall, R.A. (author), Reimer, R.A. (author), Schoterman, M. (author), Van Sinderen, D. (author), Venema, K. (author), Whelan, K. (author)In October 2012, a group of scientists met at the 10th Meeting of the International Scientific Association of Probiotics and Prebiotics (ISAPP) in Cork, Ireland to discuss issues surrounding prebiotics and their development. This article summarises outputs from the meeting. Various prebiotic definitions were discussed and how the concept has...article 2013
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de Boer, P. (author), Bronkhof, J. (author), Duki, K. (author), Kerkman, R. (author), Touw, H. (author), van den Berg, M. (author), Offringa, R. (author)The industrial production of β-lactam antibiotics by Penicillium chrysogenum has increased tremendously over the last decades, however, further optimization via classical strain and process improvement has reached its limits. The availability of the genome sequence provides new opportunities for directed strain improvement, but this requires the...article 2013
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Bastiaansen-Jenniskens, Y.M. (author), Siawash, M. (author), van de Lest, C.H.A. (author), Verhaar, J.A.N. (author), Kloppenburg, M. (author), Zuurmond, A.M. (author), Stojanovic-Susulic, V. (author), van Osch, G.J.V.M. (author), Clockaerts, S. (author)Purpose: Osteoarthritis (OA) is associated with obesity in which altered fatty acid levels have been observed. We investigated whether the most common fatty acids in synovial fluid influence cartilage deterioration in OA. Design: Cartilage was obtained from OA patients undergoing total knee arthroplasty. Chondrocytes or cartilage explants were...article 2013
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Zeegers, M.P. (author), Nekeman, D. (author), Khan, H.S. (author), van Dijk, B.A.C. (author), Goldbohm, R.A. (author), Schalken, J. (author), Shajahan, S. (author), Pearlman, A. (author), Oddoux, C. (author), van den Brandt, P.A. (author), Schouten, L.J. (author), Ostrer, H. (author), TNO Preventie en Gezondheid (author)Background:Prostate cancer is the most commonly diagnosed cancer in men in Europe and the United States. Numerous studies have indicated genetics to have a major role in the aetiology of this disease; as much as 42% of the risk may be explained by heritable factors. Genome-wide association studies have detected an association between prostate...article 2013
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Hettne, K.M. (author), Boorsma, A. (author), van Dartel, D.A.M. (author), Goeman, J.J. (author), de Jong, E. (author), Piersma, A.H. (author), Stierum, R.H. (author), Kleinjans, J.C. (author), Kors, J.A. (author)Background: Availability of chemical response-specific lists of genes (gene sets) for pharmacological and/or toxic effect prediction for compounds is limited. We hypothesize that more gene sets can be created by next-generation text mining (next-gen TM), and that these can be used with gene set analysis (GSA) methods for chemical treatment...article 2013
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TNO Voeding (author), Fleuren, W.W.M. (author), Toonen, E.J.M. (author), Verhoeven, S. (author), Frijters, R. (author), Hulsen, T. (author), Rullmann, T. (author), van Schaik, R. (author), de Vlieg, J. (author), Alkema, W. (author)Background: Glucocorticoids are potent anti-inflammatory agents used for the treatment of diseases such as rheumatoid arthritis, asthma, inflammatory bowel disease and psoriasis. Unfortunately, usage is limited because of metabolic side-effects, e.g. insulin resistance, glucose intolerance and diabetes. To gain more insight into the mechanisms...article 2013
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Wopereis, S. (author), Radonjic, M. (author), Rubingh, C. (author), van Erk, M. (author), Smilde, A. (author), van Duyvenvoorde, W. (author), Cnubben, N. (author), Kooistra, T. (author), van Ommen, B. (author), Kleemann, R. (author)The prevalence of diabetes mellitus Type 2 could be significantly reduced by early identification of subjects at risk, allowing for better prevention and earlier treatment. Glucose intolerance (GI) is a hallmark of the prediabetic stage. This study aims at identifying 1) prognostic biomarkers predicting the risk of developing GI later in life...article 2012
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Mariman, R. (author), Kremer, S.H.A. (author), van Erk, M. (author), Lagerweij, T. (author), Koning, F. (author), Nagelkerken, L. (author)Background: Host-microbiota interactions in the intestinal mucosa play a major role in intestinal immune homeostasis and control the threshold of local inflammation. The aim of this study was to evaluate the efficacy of probiotics in the recurrent trinitrobenzene sulfonic acid (TNBS)-induced colitis model and gain more insight into protective...article 2012
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Terhal, P.A. (author), van Dommelen, P. (author), Le Merrer, M. (author), Zankl, A. (author), Simon, M.E. (author), Smithson, S.F. (author), Marcelis, C. (author), Kerr, B. (author), Kinning, E. (author), Mansour, S. (author), Hennekam, R.C. (author), van der Hout, A.H. (author), Cormier-Daire, V. (author), Lund, A.M. (author), Goodwin, L. (author), Mégarbané, A. (author), Lees, M. (author), Betz, R.C. (author), Tobias, E.S. (author), Coucke, P. (author), Mortier, G.R. (author)From data collected via a large international collaborative study, we have constructed a growth chart for patients with molecularly confirmed congenital spondylo-epiphyseal dysplasia (SEDC) and other COL2A1 related dysplasias. The growth chart is based on longitudinal height measurements of 79 patients with glycine substitutions in the triple...article 2012
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- Venema, K. (author) article 2012
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van Eunen, K. (author), Rossell, S. (author), Bouwman, J. (author), Westerhoff, H.V. (author), Bakker, B.M. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)Regulation analysis is a methodology that quantifies to what extent a change in the flux through a metabolic pathway is regulated by either gene expression or metabolism. Two extensions to regulation analysis were developed over the past years: (i) the regulation of Vmax can be dissected into the various levels of the gene-expression cascade,...conference paper 2011