JD
J Dijkstra
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7 records found
1
Journal article
(2018)
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S.N. Best, M. Van der Wegen, J. Dijkstra, P. W.J.M. Willemsen, B. W. Borsje, Dano J.A. Roelvink
This paper aims to fundamentally assess the resilience of salt marsh-mudflat systems under sea level rise. We applied an open-source schematized 2D area model (Delft3D) that couples intertidal flow, wave-action, sediment transport, geomorphological development with a population dynamics approach including temporal and spatial growth of vegetation and bio-accumulation. Wave-action maintains a high sediment concentration on the mudflat while the tidal motion transports the sediments within the vegetated marsh areas during flood. The marsh-mudflat system attained dynamic equilibrium within 120 years. Sediment deposition and bio-accumulation within the marsh make the system initially resilient to sea level rise scenarios. However, after 50–60 years the marsh system starts to drown with vegetated-levees being the last surviving features. Biomass accumulation and sediment supply are critical determinants for the marsh drowning rate and survival. Our model methodology can be applied to assess the resilience of vegetated coast lines and combined engineering solutions for long-term sustainability.
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This paper aims to fundamentally assess the resilience of salt marsh-mudflat systems under sea level rise. We applied an open-source schematized 2D area model (Delft3D) that couples intertidal flow, wave-action, sediment transport, geomorphological development with a population dynamics approach including temporal and spatial growth of vegetation and bio-accumulation. Wave-action maintains a high sediment concentration on the mudflat while the tidal motion transports the sediments within the vegetated marsh areas during flood. The marsh-mudflat system attained dynamic equilibrium within 120 years. Sediment deposition and bio-accumulation within the marsh make the system initially resilient to sea level rise scenarios. However, after 50–60 years the marsh system starts to drown with vegetated-levees being the last surviving features. Biomass accumulation and sediment supply are critical determinants for the marsh drowning rate and survival. Our model methodology can be applied to assess the resilience of vegetated coast lines and combined engineering solutions for long-term sustainability.
An instrumented model pile has been realized to study the displacement pile installation effects in sand in physical model tests. The system includes a model pile, instrumented with axial and horizontal contact stress sensors, and a corresponding calibration apparatus. The development of the instrumented model pile, including numerical analysis of the mechanical response during testing, and an optimization of the instrumentation to minimize thermal effects are described. The performance of this new model pile is demonstrated using calibration measurements and an example application in a physical model test at an elevated stress level in the geotechnical centrifuge.
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An instrumented model pile has been realized to study the displacement pile installation effects in sand in physical model tests. The system includes a model pile, instrumented with axial and horizontal contact stress sensors, and a corresponding calibration apparatus. The development of the instrumented model pile, including numerical analysis of the mechanical response during testing, and an optimization of the instrumentation to minimize thermal effects are described. The performance of this new model pile is demonstrated using calibration measurements and an example application in a physical model test at an elevated stress level in the geotechnical centrifuge.
Journal article
(2018)
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Walid M. Abdelmoula, Nicola Pezzotti, Thomas Hollt, Jouke Dijkstra, Anna Vilanova , Liam A. McDonnell, Boudewijn Lelieveldt
Technological advances in mass spectrometry imaging (MSI) have contributed to growing interest in 3D MSI. However, the large size of 3D MSI data sets has made their efficient analysis and visualization and the identification of informative molecular patterns computationally challenging. Hierarchical stochastic neighbor embedding (HSNE), a nonlinear dimensionality reduction technique that aims at finding hierarchical and multiscale representations of large data sets, is a recent development that enables the analysis of millions of data points, with manageable time and memory complexities. We demonstrate that HSNE can be used to analyze large 3D MSI data sets at full mass spectral and spatial resolution. To benchmark the technique as well as demonstrate its broad applicability, we have analyzed a number of publicly available 3D MSI data sets, recorded from various biological systems and spanning different mass-spectrometry ionization techniques. We demonstrate that HSNE is able to rapidly identify regions of interest within these large high-dimensionality data sets as well as aid the identification of molecular ions that characterize these regions of interest; furthermore, through clearly separating measurement artifacts, the HSNE analysis exhibits a degree of robustness to measurement batch effects, spatially correlated noise, and mass spectral misalignment.
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Technological advances in mass spectrometry imaging (MSI) have contributed to growing interest in 3D MSI. However, the large size of 3D MSI data sets has made their efficient analysis and visualization and the identification of informative molecular patterns computationally challenging. Hierarchical stochastic neighbor embedding (HSNE), a nonlinear dimensionality reduction technique that aims at finding hierarchical and multiscale representations of large data sets, is a recent development that enables the analysis of millions of data points, with manageable time and memory complexities. We demonstrate that HSNE can be used to analyze large 3D MSI data sets at full mass spectral and spatial resolution. To benchmark the technique as well as demonstrate its broad applicability, we have analyzed a number of publicly available 3D MSI data sets, recorded from various biological systems and spanning different mass-spectrometry ionization techniques. We demonstrate that HSNE is able to rapidly identify regions of interest within these large high-dimensionality data sets as well as aid the identification of molecular ions that characterize these regions of interest; furthermore, through clearly separating measurement artifacts, the HSNE analysis exhibits a degree of robustness to measurement batch effects, spatially correlated noise, and mass spectral misalignment.
A cost effective method to measure pore water pressures in mixed granular media is described using 40 miniature MEMS pore pressure transducers. High accuracy in a single point is exchanged for lower accuracy full field measurements adjacent to the strongbox wall. The system is easily de-aired and calibrated due to the fact that the transducers are installed inside the strongbox wall. Additionally, the proof of concept test shows that the transducers are sufficiently accurate for problems with large pressure difference such as consolidation of clay while being subjected to elevated stress levels in the geotechnical centrifuge.
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A cost effective method to measure pore water pressures in mixed granular media is described using 40 miniature MEMS pore pressure transducers. High accuracy in a single point is exchanged for lower accuracy full field measurements adjacent to the strongbox wall. The system is easily de-aired and calibrated due to the fact that the transducers are installed inside the strongbox wall. Additionally, the proof of concept test shows that the transducers are sufficiently accurate for problems with large pressure difference such as consolidation of clay while being subjected to elevated stress levels in the geotechnical centrifuge.
Journal article
(2016)
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Harald Homulle, F Powolny, E Dubikovskaya, Edoardo Charbon, C Bruschini, PL Stegehuis, J Dijkstra, DU Li, K Homicsko, D. Rimoldi, K. Muehlethaler, JO Prior, R Sinisi
In near infrared fluorescence-guided surgical oncology, it is challenging to distinguish healthy from cancerous tissue. One promising research avenue consists in the analysis of the exogenous fluorophores’ lifetime, which are however in the (sub-)nanosecond range. We have integrated a single-photon pixel array, based on standard CMOS SPADs (single-photon avalanche diodes), in a compact, time-gated measurement system, named FluoCam. In vivo measurements were carried out with indocyanine green (ICG)-modified derivatives targeting the αvβ3 integrin, initially on a genetically engineered mouse model of melanoma injected with ICG conjugated with tetrameric cyclic pentapeptide (ICG−E[c(RGD f K)4]), then on mice carrying tumour xenografts of U87-MG (a human primary glioblastoma cell line) injected with monomeric ICG−c(RGD f K). Measurements on tumor, muscle and tail locations allowed us to demonstrate the feasibility of in vivo lifetime measurements with the FluoCam, to determine the characteristic lifetimes (around 500 ps) and subtle lifetime differences between bound and unbound ICG-modified fluorophores (10% level), as well as to estimate the available photon fluxes under realistic conditions
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In near infrared fluorescence-guided surgical oncology, it is challenging to distinguish healthy from cancerous tissue. One promising research avenue consists in the analysis of the exogenous fluorophores’ lifetime, which are however in the (sub-)nanosecond range. We have integrated a single-photon pixel array, based on standard CMOS SPADs (single-photon avalanche diodes), in a compact, time-gated measurement system, named FluoCam. In vivo measurements were carried out with indocyanine green (ICG)-modified derivatives targeting the αvβ3 integrin, initially on a genetically engineered mouse model of melanoma injected with ICG conjugated with tetrameric cyclic pentapeptide (ICG−E[c(RGD f K)4]), then on mice carrying tumour xenografts of U87-MG (a human primary glioblastoma cell line) injected with monomeric ICG−c(RGD f K). Measurements on tumor, muscle and tail locations allowed us to demonstrate the feasibility of in vivo lifetime measurements with the FluoCam, to determine the characteristic lifetimes (around 500 ps) and subtle lifetime differences between bound and unbound ICG-modified fluorophores (10% level), as well as to estimate the available photon fluxes under realistic conditions
Conference paper
(2016)
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Shengnan Liu, Jeroen Eggermont, Shimpei Nakatani, Boudewijn Lelieveldt, J Dijkstra
Currently two commercial intravascular optical coherence tomography (IVOCT) systems are available: Illumien Optis from St. Jude Medical (SJM) and Lunawave from Terumo. Both systems store the light intensity data in a raw vendor specic polar format. However, whereas SJM uses 16-bits per pixel Terumo uses 8-bits meaning the intensity values are in dierent ranges. This complicates quantitative light intensity based analysis when comparing results based on data from both systems. Therefore, this work aims to find an intensity transformation function from Terumo's 8-bit OFDI data to SJM's 16-bit range. The data consists of 8 pullbacks, 4 acquired with each system in the same arteries of 2 dierent patents pre- and post-stenting implantation. A total of 133 matching sections without stent struts from the two sets of pullbacks were identied based on landmarks such as side-branches and calcied regions. Since the main region of interest in the image is the tissue region only the pixels within 2mm behind the lumen border are used. In order to match the SJM data range, the Terumo data
was rescaled and cumulative distribution functions (CDF) were calculated based on the histogram distributions. Comparing these CDFs, the transformation function can be determined. Application of this transformation function not only improves the visual similarity of matching slices it can also be used for further quantitative analysis.
...
Currently two commercial intravascular optical coherence tomography (IVOCT) systems are available: Illumien Optis from St. Jude Medical (SJM) and Lunawave from Terumo. Both systems store the light intensity data in a raw vendor specic polar format. However, whereas SJM uses 16-bits per pixel Terumo uses 8-bits meaning the intensity values are in dierent ranges. This complicates quantitative light intensity based analysis when comparing results based on data from both systems. Therefore, this work aims to find an intensity transformation function from Terumo's 8-bit OFDI data to SJM's 16-bit range. The data consists of 8 pullbacks, 4 acquired with each system in the same arteries of 2 dierent patents pre- and post-stenting implantation. A total of 133 matching sections without stent struts from the two sets of pullbacks were identied based on landmarks such as side-branches and calcied regions. Since the main region of interest in the image is the tissue region only the pixels within 2mm behind the lumen border are used. In order to match the SJM data range, the Terumo data
was rescaled and cumulative distribution functions (CDF) were calculated based on the histogram distributions. Comparing these CDFs, the transformation function can be determined. Application of this transformation function not only improves the visual similarity of matching slices it can also be used for further quantitative analysis.
Conference paper
(2016)
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Shengnan Liu, Jeroen Eggermont, Ron Wolterbeek, Boudewijn P.F. Lelieveldy, J Dijkstra
Intravascular optical coherence tomography (IVOCT) is an intravascular imaging modality which enables the visualization arterial structures at the micro-structural level. The interpretations of these structures is mainly on the basis of relative image intensities. However, even for homogeneous tissue light intensities can differ. In this study the incident light intensity is modeled to be related to the catheter position. Two factors, the distance between catheter and inner lumen wall as well as the incident angle of the light upon the lumen wall, are considered. A three-level hierarchical model is constructed to statistically validate this model to include the potential effect of different pullbacks and/or frame numbers. The model is solved using 169 images out of 9 pull-backs recorded with a St.Jude Medical IVOCT system. F-tests results indicate that both the distance and the incident angle contribute to the model statistically significantly with p < 0.001. Based on the results from the statistical analysis, a potential compensation method is introduced to normalize the IVOCT intensities for the catheter position effects and small shadows
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Intravascular optical coherence tomography (IVOCT) is an intravascular imaging modality which enables the visualization arterial structures at the micro-structural level. The interpretations of these structures is mainly on the basis of relative image intensities. However, even for homogeneous tissue light intensities can differ. In this study the incident light intensity is modeled to be related to the catheter position. Two factors, the distance between catheter and inner lumen wall as well as the incident angle of the light upon the lumen wall, are considered. A three-level hierarchical model is constructed to statistically validate this model to include the potential effect of different pullbacks and/or frame numbers. The model is solved using 169 images out of 9 pull-backs recorded with a St.Jude Medical IVOCT system. F-tests results indicate that both the distance and the incident angle contribute to the model statistically significantly with p < 0.001. Based on the results from the statistical analysis, a potential compensation method is introduced to normalize the IVOCT intensities for the catheter position effects and small shadows