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Search Results: 1 - 10 of 183149 matches for " Frank de Vos "
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The Oldest Gibbon Fossil (Hylobatidae) from Insular Southeast Asia: Evidence from Trinil, (East Java, Indonesia), Lower/Middle Pleistocene
Thomas Ingicco, John de Vos, O. Frank Huffman
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0099531
Abstract: A fossil femur excavated by Eugène Dubois between 1891–1900 in the Lower/Middle Pleistocene bonebed of the Trinil site (Java, Indonesia) was recognised by us as that of a Hylobatidae. The specimen, Trinil 5703 of the Dubois Collection (Leiden, The Netherlands), has the same distinctive form of fossilization that is seen in many of the bonebed fossils from Trinil in the collection. Anatomical comparison of Trinil 5703 to a sample of carnivore and primate femora, supported by morphometric analyses, lead to the attribution of the fossil to gibbon. Trinil 5703 therefore provides the oldest insular record of this clade, one of the oldest known Hylobatidae fossils from Southeast Asia. Because living Hylobatidae only inhabit evergreen rain forests, the paleoenvironment within the river drainage in the greater Trinil area evidently included forests of this kind during the Lower/Middle Pleistocene as revealed here.
How Molecular Competition Influences Fluxes in Gene Expression Networks
Dirk De Vos, Frank J. Bruggeman, Hans V. Westerhoff, Barbara M. Bakker
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028494
Abstract: Often, in living cells different molecular species compete for binding to the same molecular target. Typical examples are the competition of genes for the transcription machinery or the competition of mRNAs for the translation machinery. Here we show that such systems have specific regulatory features and how they can be analysed. We derive a theory for molecular competition in parallel reaction networks. Analytical expressions for the response of network fluxes to changes in the total competitor and common target pools indicate the precise conditions for ultrasensitivity and intuitive rules for competitor strength. The calculations are based on measurable concentrations of the competitor-target complexes. We show that kinetic parameters, which are usually tedious to determine, are not required in the calculations. Given their simplicity, the obtained equations are easily applied to networks of any dimension. The new theory is illustrated for competing sigma factors in bacterial transcription and for a genome-wide network of yeast mRNAs competing for ribosomes. We conclude that molecular competition can drastically influence the network fluxes and lead to negative response coefficients and ultrasensitivity. Competitors that bind a large fraction of the target, like bacterial σ70, tend to influence competing pathways strongly. The less a competitor is saturated by the target, the more sensitive it is to changes in the concentration of the target, as well as to other competitors. As a consequence, most of the mRNAs in yeast turn out to respond ultrasensitively to changes in ribosome concentration. Finally, applying the theory to a genome-wide dataset we observe that high and low response mRNAs exhibit distinct Gene Ontology profiles.
Optimality and evolution of transcriptionally regulated gene expression
Frank J Poelwijk, Philip D Heyning, Marjon GJ de Vos, Daniel J Kiviet, Sander J Tans
BMC Systems Biology , 2011, DOI: 10.1186/1752-0509-5-128
Abstract: We addressed this problem by decoupling the regulatory and metabolic function of the Escherichia coli lac system, using an inducer that cannot be metabolized and a carbon source that does not induce. Growth rate measurements directly identified the induced expression level that maximizes the metabolism benefits minus the protein production costs, without relying on models. Using these results, we established a controlled mismatch between sensing and metabolism, resulting in sub-optimal transcriptional regulation with the potential to improve by evolution. Next, we tested the evolutionary response by serial transfer. Constant environments showed cells evolving to the predicted expression optimum. Phenotypes with decreased expression emerged several hundred generations later than phenotypes with increased expression, indicating a higher genetic accessibility of the latter. Environments alternating between low and high expression demands resulted in overall rather than differential changes in expression, which is explained by the concave shape of the cross-environmental tradeoff curve that limits the selective advantage of altering the regulatory response.This work indicates that the decoupling of regulatory and metabolic functions allows one to directly measure the costs and benefits that underlie the natural selection of gene regulation. Regulated gene expression is shown to evolve within several hundreds of generations to optima that are predicted by these costs and benefits. The results provide a step towards a quantitative understanding of the adaptive origins of regulatory systems.Evolution is often viewed as an optimization process, in which selection drives the fixation of fitness-increasing mutations until the optimal phenotype that maximizes fitness is reached [1-5]. It is routinely observed that organisms, when challenged with novel environments, can adapt and increase fitness by genetic changes [6-8]. However, adaptation alone does not necessarily imply opt
arf3DS4: An Integrated Framework for Localization and Connectivity Analysis of fMRI Data
Wouter D. Weeda,Frank de Vos,Lourens J. Waldorp,Raoul Grasman
Journal of Statistical Software , 2011,
Abstract: In standard fMRI analysis all voxels are tested in a massive univariate approach, that is, each voxel is tested independently. This requires stringent corrections for multiple comparisons to control the number of false positive tests (i.e., marking voxels as active while they are actually not). As a result, fMRI analyses may suffer from low power to detect activation, especially in studies with high levels of noise in the data, for example developmental or single-subject studies. Activated region fitting (ARF) yields a solution by modeling fMRI data by multiple Gaussian shaped regions. ARF only requires a small number of parameters and therefore has increased power to detect activation. If required, the estimated regions can be directly used as regions of interest in a functional connectivity analysis. ARF is implemented in the R package arf3DS4. In this paper ARF and its implementation are described and illustrated with an example.
Overlay of conventional angiographic and en-face OCT images enhances their interpretation
Mirjam EJ van Velthoven, Koos de Vos, Frank D Verbraak, Chris W Pool, Marc D de Smet
BMC Ophthalmology , 2005, DOI: 10.1186/1471-2415-5-12
Abstract: In various patients, en-face OCT C-scans (made with a prototype OCT-Ophthalmoscope (OTI, Canada) in use at the Department of Ophthalmology (Academic Medical Centre, Amsterdam, The Netherlands)) and conventional fluorescein angiography (FA) were performed. ImagePro, with a custom made plug-in, was used to make an overlay-image. The confocal part of the OCT C-scan was used to spatially transform the FA image onto the OCT C-scan, using the vascular arcades as a reference. To facilitate visualization the transformed angiographic image and the OCT C-scan were combined in an RGB image.The confocal part of the OCT C-scan could easily be fused with angiographic images. Overlay showed a direct correspondence between retinal thickening and FA leakage in Birdshot retinochoroiditis, localized the subretinal neovascular membrane and correlated anatomic and vascular leakage features in myopia, and showed the extent of retinal and pigment epithelial detachment in retinal angiomatous proliferation as FA leakage was subject to blocked fluorescence. The overlay mode provided additional insight not readily available in either mode alone.Combining conventional angiographic images and en-face OCT C-scans assists in the interpretation of both imaging modalities. By combining the physiopathological information in the angiograms with the structural information in the OCT scan, zones of leakage can be correlated to structural changes in the retina or pigment epithelium. This strategy could be used in the evaluation and monitoring of patients with complex central macular pathology.The combined use of morphological and functional information has been shown to improve diagnostic accuracy in many clinical disciplines [1-3]. In the management of patients with malignancies, coronary heart disease and diseases of the brain, fusion of different image modalities, such as CT, MRI, PET and various other nuclear diagnostic tests, is widely used [3-7]. Retinal diseases are also very complex, and often m
Environmental Dependence of Genetic Constraint
Marjon G. J. de Vos,Frank J. Poelwijk,Nico Battich,Joseph D. T. Ndika,Sander J. Tans
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003580
Abstract: The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data.
Porphyromonas Gingivalis and E-coli Induce Different Cytokine Production Patterns in Pregnant Women
Marijke M. Faas, Alina Kunnen, Daphne C. Dekker, Hermie J. M. Harmsen, Jan G. Aarnoudse, Frank Abbas, Paul De Vos, Maria G. Van Pampus
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0086355
Abstract: Objective Pregnant individuals of many species, including humans, are more sensitive to various bacteria or their products as compared with non-pregnant individuals. Pregnant individuals also respond differently to different bacteria or their products. Therefore, in the present study, we evaluated whether the increased sensitivity of pregnant women to bacterial products and their heterogeneous response to different bacteria was associated with differences in whole blood cytokine production upon stimulation with bacteria or their products. Methods Blood samples were taken from healthy pregnant and age-matched non-pregnant women and ex vivo stimulated with bacteria or LPS from Porphyromonas Gingivalis (Pg) or E-coli for 24 hrs. TNFα, IL-1?, IL-6, IL-12 and IL-10 were measured using a multiplex Luminex system. Results We observed a generally lower cytokine production after stimulation with Pg bacteria or it’s LPS as compared with E-coli bacteria. However, there was also an effect of pregnancy upon cytokine production: in pregnant women the production of IL-6 upon Pg stimulation was decreased as compared with non-pregnant women. After stimulation with E-coli, the production of IL-12 and TNFα was decreased in pregnant women as compared with non-pregnant women. Conclusion Our results showed that cytokine production upon bacterial stimulation of whole blood differed between pregnant and non-pregnant women, showing that the increased sensitivity of pregnant women may be due to differences in cytokine production. Moreover, pregnancy also affected whole blood cytokine production upon Pg or E-coli stimulation differently. Thus, the different responses of pregnant women to different bacteria or their products may result from variations in cytokine production.
Echo state networks as an alternative to traditional artificial neural networks in rainfall–runoff modelling
N. J. de Vos
Hydrology and Earth System Sciences (HESS) & Discussions (HESSD) , 2013,
Abstract: Despite theoretical benefits of recurrent artificial neural networks over their feedforward counterparts, it is still unclear whether the former offer practical advantages as rainfall–runoff models. The main drawback of recurrent networks is the increased complexity of the training procedure due to their architecture. This work uses the recently introduced and conceptually simple echo state networks for streamflow forecasts on twelve river basins in the Eastern United States, and compares them to a variety of traditional feedforward and recurrent approaches. Two modifications on the echo state network models are made that increase the hydrologically relevant information content of their internal state. The results show that the echo state networks outperform feedforward networks and are competitive with state-of-the-art recurrent networks, across a range of performance measures. This, along with their simplicity and ease of training, suggests that they can be considered promising alternatives to traditional artificial neural networks in rainfall–runoff modelling.
A new locality for the sand tampan ornithodoros savignyi (audouin) in Southern Africa
V. de Vos
Koedoe : African Protected Area Conservation and Science , 1977, DOI: 10.4102/koedoe.v20i1.944
Abstract: A new locality for the sand tampan (Omithodoros savignyi) in southern Africa is described. Sand tampans were found in the Nwambiya sandveld (22degrees31'S., 31 degrees 20'E.) in the northern sector of the Kruger National Park. Environmental conditions for the area is described. The possibility of an earlier linkage of the Nwambiya area with the arid western regions of southern Africa is raised in an attempt to explain this seemingly anomalous locality record.
A new potent analgesic for chemical immobilization of gemsbok oryx gazella gazella
V. de Vos
Koedoe : African Protected Area Conservation and Science , 1978, DOI: 10.4102/koedoe.v21i1.971
Abstract: The successful chemical immobilization of gemsbok Oryx gazella gazella with a new potent analgesic, R33799 (Janssen Pharmaceutica), and the major sedative xylazine hydro-chloride (Rompun; Bayer) is described. Evidence, which is presented, show that the R33799 - xylazine mixture is an improvement over previously used drug mixtures for the immobilization of gemsbok. The following optimal dosage rates and application are recommended: 10-20 ug R33 799 per kg + 100 ug xylazine per kg deep intra-muscularly. It is concluded that with the use of the above-mentioned drug mixtures and deposition site, almost predictable short induction periods of about 5 minutes or less can be achieved. High dosage levels of xylazine was found to produce a delayed or persistent somnolent state which has the disadvantage of a long and hazardous recovery phase, especially in predator prone surroundings. Results show that the action of R33799 could be effectively reversed with the usual morphine antagonists. Propionylpromazine (Combelen; Bayer) was found to be a useful post-capture tranquilizer.
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