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Search Results: 1 - 10 of 14259 matches for " Evert-Jan Kooi "
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‘Laat uw Naam geheiligd worden’: Een uiting van eerbied aan God
Evert-Jan Vledder
HTS Theological Studies/Teologiese Studies , 2011, DOI: 10.4102/hts.v67i1.839
Abstract: Along with Norman Metzler, I will argue that the first petition of the Lord’s prayer: ‘Hallowed be thy Name’ (Mt 6:9b) is not the first petition in proper sense. It rather can be seen as a ‘parenthetical doxological phrase’ that describes closer the address ‘Our Father in Heaven’ (Mt 6:9b), following examples in both Jewish and Muslim traditions. The question will be raised whether the devotional address to God is not a stronger base for respectful co-existence and dialogue with each other than a rather general moral demand of ‘having respect for each other’? How to cite this article: Vledder, E.-J., 2011, ‘“Laat uw Naam geheiligd worden”: Een uiting van eerbied aan God’, HTS Teologiese Studies/Theological Studies 67(1), Art. #839, 6 pages. DOI: 10.4102/hts.v67i1.839
Clusters of activated microglia in normal-appearing white matter show signs of innate immune activation
Jack van Horssen, Shailender Singh, Susanne van der Pol, Markus Kipp, Jamie L Lim, Laura Peferoen, Wouter Gerritsen, Evert-Jan Kooi, Maarten E Witte, Jeroen J Geurts, Helga E de Vries, Regina Peferoen-Baert, Peter J van den Elsen, Paul van der Valk, Sandra Amor
Journal of Neuroinflammation , 2012, DOI: 10.1186/1742-2094-9-156
Abstract: Here, we document the frequency of preactive lesions and their association with distinct white matter lesions in a cohort of 21 MS patients. Immunohistochemistry was used to gain further insight into the cellular and molecular composition of preactive lesions.Preactive lesions were observed in a majority of MS patients (67%) irrespective of disease duration, gender or subtype of disease. Microglial clusters were predominantly observed in the vicinity of active demyelinating lesions and are not associated with T cell infiltrates, axonal alterations, activated astrocytes or blood–brain barrier disruption. Microglia in preactive lesions consistently express interleukin-10 and TNF-α, but not interleukin-4, whereas matrix metalloproteases-2 and ?9 are virtually absent in microglial nodules. Interestingly, key subunits of the free-radical-generating enzyme NADPH oxidase-2 were abundantly expressed in microglial clusters.The high frequency of preactive lesions suggests that it is unlikely that most of them will progress into full-blown demyelinating lesions. Preactive lesions are not associated with blood–brain barrier disruption, suggesting that an intrinsic trigger of innate immune activation, rather than extrinsic factors crossing a damaged blood–brain barrier, induces the formation of clusters of activated microglia.
Modelling spatial patterns of economic activity in the Netherlands
Jung-Hun Yang,Dick Ettema,Koen Frenken,Frank Van Oort,Evert-Jan Visser
Computer Science , 2012,
Abstract: Understanding how spatial configurations of economic activity emerge is important when formulating spatial planning and economic policy. Not only micro-simulation and agent-based model such as UrbanSim, ILUMAS and SIMFIRMS, but also Simon's model of hierarchical concentration have widely applied, for this purpose. These models, however, have limitations with respect to simulating structural changes in spatial economic systems and the impact of proximity. The present paper proposes a model of firm development that is based on behavioural rules such as growth, closure, spin-off and relocation. An important aspect of the model is that locational preferences of firms are based on agglomeration advantages, accessibility of markets and congestion, allowing for a proper description of concentration and deconcentration tendencies. By comparing the outcomes of the proposed model with real world data, we will calibrate the parameters and assess how well the model predicts existing spatial configurations and decide. The model is implemented as an agent-based simulation model describing firm development in the Netherlands in 21 industrial sectors from 1950 to 2004.
Cardiac MRI: Standardized Right and Left Ventricular Quantification by Briefly Coaching Inexperienced Personnel
Niek H. Prakken, Birgitta K. Velthuis, Evert-Jan J. Vonken, Willem P. Mali and Maarten-Jan J. Cramer
The Open Magnetic Resonance Journal , 2008, DOI: 10.2174/1874769800801010104]
Abstract: MRI quantification of the cardiac ventricles is time-consuming, especially for the right ventricle due to its complex geometry. Using a short axis MRI protocol, we tested if briefly coaching persons inexperienced in cardiac MRI provides reliable right and left ventricular quantification. 22 healthy subjects (mean age 26 ± 4.2 years) underwent short-axis breath-hold SSFP sequence cardiac MRI. Two persons inexperienced in cardiac MRI independently traced endocardial and epicardial contours of both ventricles with a predefined contour tracing protocol. Measurements were repeated after visual correction of each two most basal slices of the endocardial contours and epicardial contours in the learning curve. Five random short-axis cines were retraced for intraobserver variability. Measurements were performed blinded within 4 months. Agreement was assessed with the Bland- Altman method. No systematic bias was observed and measurements were within acceptable limits of agreement after brief coaching. Repeat measurements following visual correction significantly improved inter-observer differences, especially for mass calculations. Maximum interobserver and intraobserver disagreement of the final protocol were respectively ≥ 8% and ≥ 5%. Brief coaching of persons inexperienced in cardiac MRI, using the short axis MRI protocol, provides reliable volume, function and mass quantification of both ventricles.
Time-Resolved Transcriptomics and Bioinformatic Analyses Reveal Intrinsic Stress Responses during Batch Culture of Bacillus subtilis
Evert-Jan Blom, Anja N. J. A. Ridder, Andrzej T. Lulko, Jos B. T. M. Roerdink, Oscar P. Kuipers
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0027160
Abstract: 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 distinct growth phases and one clear transition point: a lag phase, an exponential growth phase, the transition point and the very clearly separated early and late stationary growth phases. The gene expression profiles suggest the occurrence of stress responses at specific times although no external stresses were applied. The first one is a small induction of the SigB regulon that occurs at the transition point. Remarkably, a very strong response is observed for the SigW regulon, which is highly upregulated at the onset of the late stationary phase. Bioinformatic analyses that were performed on our data set suggest several novel putative motifs for regulator binding. In addition, the expression profiles of several genes appeared to correlate with the oxygen concentration. This data set of the expression profiles of all B. subtilis genes during the entire growth curve on rich medium constitutes a rich repository that can be further mined by the scientific community.
DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites
Evert-Jan Blom, Sacha AFT van Hijum, Klaas J Hofstede, Remko Silvis, Jos BTM Roerdink, Oscar P Kuipers
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-535
Abstract: We developed an exploratory application that benchmarks the results of clustering methods using functional annotations. In addition, a de novo DNA motif discovery algorithm is integrated in our program which identifies overrepresented DNA binding sites in the upstream DNA sequences of genes from the clusters that are indicative of sites of transcriptional control. The performance of our program was evaluated by comparing the original results of a time course experiment with the findings of our application.DISCLOSE assists researchers in the prokaryotic research community in systematically evaluating results of the application of a range of clustering algorithms to transcriptome data. Different performance measures allow to quickly and comprehensively determine the best suited clustering approach for a given dataset.DNA microarray technology is commonly used to study mRNA expression levels of genes under different experimental conditions. Clustering approaches are widely used in the analysis of gene expression data. The ability to identify groups of genes exhibiting similar expression patterns by clustering allows for detailed biological insights into global regulation of gene expression and cellular processes. Clustering methodology is considered a potent means to infer putative gene function [1,2].In the process of the analysis of transcriptome data, researchers are often faced with the choice between a wide variety of clustering methods and associated parameters. The results of the application of different clustering algorithms to the same dataset will place genes in different clusters and therefore result in different biological interpretations of the same dataset. Moreover, selecting the most appropriate clustering method and parameters heavily depends on the experience of the researcher and on the nature of the dataset analyzed.Several studies have shown the relevance of applying external measures (i.e., using prior biological knowledge) to more objectively eva
Force Sensing in Surgical Sutures
Tim Horeman, Evert-jan Meijer, Joris J. Harlaar, Johan F. Lange, John J. van den Dobbelsteen, Jenny Dankelman
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0084466
Abstract: The tension in a suture is an important factor in the process of wound healing. If there is too much tension in the suture, the blood flow is restricted and necrosis can occur. If the tension is too low, the incision opens up and cannot heal properly. The purpose of this paper is to describe the design and evaluation of the Stitch Force (SF) sensor and the Hook-In Force (HIF) sensor. These sensors were developed to measure the force on a tensioned suture inside a closed incision and to measure the pulling force used to close the incision. The accuracy of both sensors is high enough to determine the relation between the force in the thread of a stitch and the pulling force applied on the suture by the physician. In a pilot study, a continuous suture of 7 stitches was applied on the fascia of the abdominal wall of multiple pigs to study this relationship. The results show that the max force in the thread of the second stitch drops from 3 (SD 1.2) to 1 (SD 0.3) newton after the 4th stitch was placed. During placement of the 5th, 6th and 7th stitch, the force in the 2nd stitch was not influenced anymore. This study indicates that in a continuous suture the force in the thread remains constant up to more than 3 stiches away from the pulled loose end of the suture. When a force feedback tool is developed specially for suturing in surgery on patients, the proposed sensors can be used to determine safety threshold for different types of tissue and sutures.
Dimerization of Peptides by Calcium Ions: Investigation of a Calcium-Binding Motif
Azadeh Jamalian,Evert-Jan Sneekes,Lennard J. M. Dekker,Mario Ursem,Theo M. Luider,Peter C. Burgers
International Journal of Proteomics , 2014, DOI: 10.1155/2014/153712
Abstract: We investigated calcium-binding motifs of peptides and their recognition of active functionalities for coordination. This investigation generates the fundamentals to design carrier material for calcium-bound peptide-peptide interactions. Interactions of different peptides with active calcium domains were investigated. Evaluation of selectivity was performed by electrospray ionization mass spectrometry by infusing solutions containing two different peptides (P1 and P2) in the presence of calcium ions. In addition to signals for monomer species, intense dimer signals are observed for the heterodimer ions ( represents the noncovalent binding of calcium with the peptide) in the positive ion mode and for ions in the negative ion mode. Monitoring of the dissociation from these mass selected dimer ions via the kinetic method provides information on the calcium affinity order of different peptide sequences. The authors fondly remember the late Mario Ursem as a passionate person and friend interested in research and in the researchers themselves. In particular, the exploration and discovery of new chromatography materials was one of his great achievements 1. Introduction Calcium is one of the most abundant cations in living organisms [1, 2]. As an intracellular signaling ion, Ca2+ plays crucial roles in an array of cellular functions from fertilization, muscle contraction, and cell differentiation/proliferation to apoptosis and, in the case of dysregulation, cancer and neural diseases [3–6]. The impact of monitoring calcium in proteins can be extremely high. For example, mutations in calcium ion transport proteins can disrupt channel functions and have been associated with various diseases, like Alzheimer’s disease [6]. However, Ca2+ does not act alone. Many cells contain a variety of cytosolic calcium-binding proteins (CaBPs) which either modulate or mediate the actions of this ion [7–9]. Depending on the role and cellular locations of the CaBPs, their affinities may vary by as much as 106-fold [10]. These proteins may be found just in specific cell types or are distributed in variety of cells and tissues. For instance, Table 1 summarizes major calcium-binding proteins present in the nervous system [7]. Table 1: Major calcium-binding proteins in the nervous system. Three major classes of Ca2+-sensing structural modules have been identified as EF-hands [11], C2 domains, and annexin folds [12]. The EF-hand domain is one of the common known motifs to bind calcium to proteins [13, 14]. Falke et al. [15] and Linse and Forsén [16] have shown the finely tuned
Endovascular Treatment of Internal Iliac Artery Stenosis in Patients with Buttock Claudication
Jip F. Prince, Maarten L. J. Smits, Joost A. van Herwaarden, Mark J. Arntz, Evert-Jan P. A. Vonken, Maurice A. A. J. van den Bosch, Gert Jan de Borst
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0073331
Abstract: Aim To assess the technical feasibility and clinical outcome of percutaneous transluminal angioplasty (PTA) with and without stent placement for treatment of buttock claudication caused by internal iliac artery (IIA) stenosis. Methods Between September 2001 and July 2011, thirty-four patients with buttock claudication underwent endovascular treatment. After angiographic lesion evaluation PTA with or without stent placement was performed. Technical success was recorded. Clinical outcome post-treatment was assessed at three months post-intervention and was classified as: 1) complete relief of symptoms, 2) partial relief, or 3) no relief of symptoms. Complications during follow-up were recorded. Results Forty-four lesions in 34 symptomatic patients were treated with PTA. Eight lesions were treated with additional stent placement. Technical success was achieved in 40/44 lesions (91%). Three procedure-related minor complications occurred, i.e. asymptomatic conservatively treated intimal dissections. After a median of 2.9 months, patients experienced no relief of symptoms in 7/34 cases (21%), partial relief in 14/34 cases (41%), and complete relief in 13/34 cases (38%). Six patients required a reintervention during follow-up. Conclusion Endovascular treatment of IIA stenosis has a high technical success rate and a low complication rate. Complete or partial relief of symptoms is achieved in the majority (79%) of patients.
Assessment of distribution and evolution of Mechanical dyssynchrony in a porcine model of myocardial infarction by cardiovascular magnetic resonance
Khaled Z Abd-Elmoniem, Miguel Tomas, Tetsuo Sasano, Sahar Soleimanifard, Evert-Jan P Vonken, Amr Youssef, Harsh Agarwal, Veronica L Dimaano, Hugh Calkins, Matthias Stuber, Jerry L Prince, Theodore P Abraham, M Abraham
Journal of Cardiovascular Magnetic Resonance , 2012, DOI: 10.1186/1532-429x-14-1
Abstract: Cine, gadolinium-contrast, and tagged cardiovascular magnetic resonance (CMR) were performed pre-MI, 9 ± 2 days (early post-MI), and 33 ± 10 days (late post-MI) post-MI in 6 pigs to characterize cardiac morphology, location and extent of MI, and regional mechanics. LV mechanics were assessed by circumferential strain (eC). Electro-anatomic mapping (EAM) was performed within 24 hrs of CMR and prior to sacrifice.Mean infarct size was 21 ± 4% of LV volume with evidence of post-MI remodeling. Global eC significantly decreased post MI (-27 ± 1.6% vs. -18 ± 2.5% (early) and -17 ± 2.7% (late), p < 0.0001) with no significant change in peri-MI and MI segments between early and late time-points. Time to peak strain (TTP) was significantly longer in MI, compared to normal and peri-MI segments, both early (440 ± 40 ms vs. 329 ± 40 ms and 332 ± 36 ms, respectively; p = 0.0002) and late post-MI (442 ± 63 ms vs. 321 ± 40 ms and 355 ± 61 ms, respectively; p = 0.012). The standard deviation of TTP in 16 segments (SD16) significantly increased post-MI: 28 ± 7 ms to 50 ± 10 ms (early, p = 0.012) to 54 ± 19 ms (late, p = 0.004), with no change between early and late post-MI time-points (p = 0.56). TTP was not related to reduction of segmental contractility. EAM revealed late electrical activation and greatly diminished conduction velocity in the infarct (5.7 ± 2.4 cm/s), when compared to peri-infarct (18.7 ± 10.3 cm/s) and remote myocardium (39 ± 20.5 cm/s).Mechanical dyssynchrony occurs early after MI and is the result of delayed electrical and mechanical activation in the infarct.Cardiac resynchronization therapy (CRT) relieves symptoms, induces reverse remodeling, reduces heart failure hospitalizations, and improves survival in symptomatic heart failure patients with left ventricular systolic dysfunction and conduction abnormality [1-4]. However, CRT is plagued by a high non-responder rate of ~30% [5]. Differences between ischemic and non-ischemic cardiomyopathy (CM) have generally
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