The influence of land use and mobility policy on travel behavior : a comparative case study of Flanders and the Netherlands

Numerous transportation studies have indicated that the local built environment can have an important effect on travel behavior; people living in suburban neighborhoods travel more by car than people living in urban neighborhoods. In this paper, however, we will analyze whether the regional land use has an important influence on travel behavior by comparing two regions with a varying land-use pattern: Flanders (Belgium) and the Netherlands. The different land-use pattern seems to have influenced travel behavior in both regions. An active spatial planning policy in the Netherlands, clustering activities in urban surroundings, appears to have realized a sustainable travel behavior, as a substantial share of residents frequently walk, cycle or use public transportation. The rather passive spatial planning in Flanders, resulting in urban sprawl, seems to stimulate car use. The applied mobility policy also has an impact on the travel behavior and land use of the Flemings and the Dutch. Infrastructure is concentrated in Dutch urban environments, whereas Flanders has a more widespread network of infrastructure and cheap public transportation, resulting in a further increase of suburbanization

2D Mapping of pathological nuclei

The dynamics of genome regions are associated to the functional or dysfunctional behaviour of the human cell. In order to study these dynamics it is necessary to remove perturbations coming from movement and deformation of the nucleus, i.e. the container holding the genome. In literature models have been proposed to cope with the transformations corresponding to nuclear dynamics of healthy cells. However for pathological cells such as cancer cells, the nucleus deforms in an apparently random way, making the use of such models a non trivial task. In this paper we propose a mapping of the cell nucleus which is based on the minimization of telomere motion, i.e. the motion of the very ends of chromosomes

2013 REU Poster: Purification and Characterization of a Ferredoxin from Mycobacterium tuberculosis

Poster presentation at REU Summer's End Research Symposium, 2013, by REU participant Jonas A, de Oliveira, MassBay Community College - Sean Elliott group, Evan Judd lab mentorM. tuberculosis possesses a sulfite reductase (MtsirA) that is over-expressed when the bacteria is in its dormant stage of infection. MtSirA catalyzes the six-electron reduction of sulfite to sulfide. Previous kinetic studies of MtsirA have used methyl viologen (MV), a chemical reductant, as an electron donor. The goal of this work is to purify and characterize a ferredoxin from M. tuberculosis (MtFd) and determine if MtFd can act as an electron donor to mtSirA, with the ultimate goal of using it as a more physiologically relevant electron donor in kinetic studies of mtSirA. We have found that that MtFd purifies without a cluster and must be chemically reconstituted. MtFd likely contains a [4Fe-4S] cluster, and may be able to donate electrons to mtSirA.NSF-RE

Computational efficient segmentation of cell nuclei in 2D and 3D fluorescent micrographs

This paper proposes a new segmentation technique developed for the segmentation of cell nuclei in both 2D and 3D fluorescent micrographs. The proposed method can deal with both blurred edges as with touching nuclei. Using a dual scan line algorithm its both memory as computational efficient, making it interesting for the analysis of images coming from high throughput systems or the analysis of 3D microscopic images. Experiments show good results, i.e. recall of over 0.98

A computational efficient external energy for active contour segmentation using edge propagation

Active contours or snakes are widely used for segmentation and tracking. We propose a new active contour model, which converges reliably even when the initialization is far from the object of interest. The proposed segmentation technique uses an external energy function where the energy slowly decreases in the vicinity of an edge. This new energy function is calculated using an efficient dual scan line algorithm. The proposed energy function is tested on computational speed, its effect on the convergence speed of the active contour and the segmentation result. The proposed method gets similar segmentation results as the gradient vector flow active contours, but the energy function needs much less time to calculate

Quasar: A Programming Framework for Rapid Prototyping

We present a new programming framework, Quasar, which facilitates GPU programming. Our high-level programming language relieves the developer of all implementation details such that he can focus on the algorithm and the required accuracy. The proposed programming framework consists of a simple high-level programming language, an advanced compiler system, a runtime system and IDE. The Quasar language is a high level scripting language with an easy to learn syntax similar to python and MATLAB. This makes Quasar well suited for fast development and prototyping. A Quasar program is first processed by a front-end compiler that automatically detects serial and parallel loops that could be accelerated by heterogeneous hardware. In a second compilation phase, a number of back-end compilers processes the output of the front-end compiler, thus generating C++, OpenCL or CUDA code. Based on the generated code the runtime system can dynamically switch between CPU and GPU. This automatic scheduling at runtime is done by analyzing the load of all devices, the memory transfer cost and the complexity of the task. This way, the programmer is relieved from complicated implementation issues that are common for programming heterogeneous hardware. We validated the use of Quasar on a number of complex image processing and computer vision algorithms. These programs range from denoising to automated image segmentation applications. Using Quasar we get speed-up factors of 4 to over 60, depending on the application. All results were achieved using an NVIDIA GeForce M750

Mapping of cell nuclei based on contour warping

The dynamics of genome regions are associated to the functional or dysfunctional behaviour of the human cell. In order to study these dynamics it is necessary to remove all perturbations coming from movement and deformation of the nucleus, i.e. the container holding the genome. In literature models have been proposed to cope with the transformations corresponding to nuclear dynamics of healthy cells. However for pathological cells, the nucleus deforms in an apparently random way, making the use of such models a non trivial task. In this paper we propose a mapping of the cell nucleus which is based on the matching of the nuclear contours. The proposed method does not put constraints on the possible shapes nor on the possible deformations, making this method suited for the analysis of pathological nuclei

A fast external force field for parametric active contour segmentation

Active contours or snakes are widely used for segmentation and tracking. We propose a new active contour model, which converges reliably even when the initialization is far from the object of interest. The proposed segmentation technique uses an external energy function where the energy slowly decreases in the vicinity of an edge. Based on this energy a new external force field is defined. Both energy function and force field are calculated using an efficient dual scan line algorithm. The proposed force field is tested on computational speed, its effect on the convergence speed of the active contour and the segmentation result. The proposed method gets similar segmentation results as the gradient vector flow and vector field convolution active contours, but the force field needs significantly less time to calculate