Summary
A robust finite volume method for viscoelastic flow analysis on general unstructured meshes is developed. It is built upon a general‐purpose stabilization framework for high Weissenberg ...number flows. The numerical framework provides full combinatorial flexibility between different kinds of rheological models on the one hand, and effective stabilization methods on the other hand. A special emphasis is put on the velocity‐stress‐coupling on colocated computational grids. Using special face interpolation techniques, a semi‐implicit stress interpolation correction is proposed to correct the cell‐face interpolation of the stress in the divergence operator of the momentum balance. Investigating the entry‐flow problem of the 4:1 contraction benchmark, we demonstrate that the numerical methods are robust over a wide range of Weissenberg numbers and significantly alleviate the high Weissenberg number problem. The accuracy of the results is evaluated in a detailed mesh convergence study.
A robust finite volume method for viscoelastic flow analysis on general unstructured meshes is developed. The numerical framework provides full combinatorial flexibility between different kinds of rheological models on the one hand, and effective stabilization methods on the other hand. Investigating the entry‐flow problem of the 4:1 contraction benchmark, we demonstrate that the numerical methods are robust over a wide range of Weissenberg numbers and significantly alleviate the high Weissenberg number problem.
To determine whether changes in D(2) receptor availability are present in carriers of genetic mutations for primary dystonia.
Manifesting and nonmanifesting carriers of the DYT1 and DYT6 dystonia ...mutations were scanned with (11)C raclopride (RAC) and PET. Measures of D(2) receptor availability in the caudate nucleus and putamen were determined using an automated region-of-interest approach. Values from mutation carriers and healthy controls were compared using analysis of variance to assess the effects of genotype and phenotype. Additionally, voxel-based whole brain searches were conducted to detect group differences in extrastriatal regions.
Significant reductions in caudate and putamen D(2) receptor availability were evident in both groups of mutation carriers relative to healthy controls (p < 0.001). The changes were greater in DYT6 relative to DYT1 carriers (-38.0 +/- 3.0% vs -15.0 +/- 3.0%, p < 0.001). By contrast, there was no significant difference between manifesting and nonmanifesting carriers of either genotype. Voxel-based analysis confirmed these findings and additionally revealed reduced RAC binding in the ventrolateral thalamus of both groups of mutation carriers. As in the striatum, the thalamic binding reductions were more pronounced in DYT6 carriers and were not influenced by the presence of clinical manifestations.
Reduced D(2) receptor availability in carriers of dystonia genes is compatible with dysfunction or loss of D(2)-bearing neurons, increased synaptic dopamine levels, or both. These changes, which may be present to different degrees in the DYT1 and DYT6 genotypes, are likely to represent susceptibility factors for the development of clinical manifestations in mutation carriers.
A major data pre-processing step for large, multi-site studies is to handle site effects by harmonizing data, generating a dataset that enables more powerful analyses and more robust algorithms. ...There is a wide variety of data harmonization techniques, but there are few tools that streamline the process of harmonizing data, comparing across techniques, and benchmarking new techniques. In this paper, we introduce HArmonization BEnchmarking Tool (HABET), an open source tool for generating harmonized images and evaluating the performance of different harmonization algorithms. To demonstrate the capabilities of HABET, we harmonize diffusion MRI images from the Adolescent Brain and Cognitive Development (ABCD) study using two different approaches, and we compare their performance.
Selective concentration and anchoring of ionotropic receptors at the synapse is essential for neuronal signaling. Little is known about the molecules that mediate receptor clustering in the CNS. With ...use of the yeast two-hybrid system to screen a rat brain cDNA library and by in vitro binding assays, we have identified an interaction between NMDA receptor subunits 2A and 2B (NR2A and NR2B) and three distinct members of the PSD-95/SAP90 family of membrane-associated putative guanylate kinases. The interaction is mediated by binding of the C terminus of the NMDA receptor subunits to the first two PDZ (also known as GLGF or DHR) domains of PSD-95/SAP90, an abundant synaptic protein associated with the membrane cytoskeleton. PSD-95 is also known to bind and cluster Shaker-type voltage-gated K+ channels. Similarities between the C-termini of NR2 subunits and K+ channels suggest a common C-terminal binding motif for PDZ domains. These data suggest that PDZ domains can function as modules for protein-protein interactions. Members of the PSD-95 family might serve to anchor NMDA receptors to the submembrane cytoskeleton and aid in the assembly of signal transduction complexes at postsynaptic sites.
Dynamic active contours for visual tracking Niethammer, M.; Tannenbaum, A.; Angenent, S.
IEEE transactions on automatic control,
04/2006, Letnik:
51, Številka:
4
Journal Article
Recenzirano
Odprti dostop
Visual tracking using active contours is usually set in a static framework. The active contour tracks the object of interest in a given frame of an image sequence. A subsequent prediction step ...ensures good initial placement for the next frame. This approach is unnatural; the curve evolution gets decoupled from the actual dynamics of the objects to be tracked. True dynamical approaches exist, all being marker particle based and thus prone to the shortcomings of such particle-based implementations. In particular, topological changes are not handled naturally in this framework. The now classical level set approach is tailored for evolutions of manifolds of codimension one. However, dynamic curve evolution is at least a codimension two problem. We propose an efficient, level set based approach for dynamic curve evolution, which addresses the artificial separation of segmentation and prediction while retaining all the desirable properties of the level set formulation. It is based on a new energy minimization functional which, for the first time, puts dynamics into the geodesic active contour framework.
Purpose
To evaluate feasibility of automatic software-based path proposals for CT-guided percutaneous biopsies.
Methods
Thirty-three patients (60
±
12 years) referred for CT-guided biopsy of focal ...liver lesions were consecutively included. Pre-interventional CT and dedicated software (FraunhoferMeVis Pathfinder) were used for (semi)automatic segmentation of relevant structures. The software subsequently generated three path proposals in downward quality for CT-guided biopsy. Proposed needle paths were compared with consensus proposal of two experts (comparable, less suitable, not feasible). In case of comparable results, equivalent approach to software-based path proposal was used. Quality of segmentation process was evaluated (Likert scale, 1
=
best, 6
=
worst), and time for processing was registered.
Results
All biopsies were performed successfully without complications. In 91 % one of the three automatic path proposals was rated comparable to experts’ proposal. None of the first proposals was rated not feasible, and 76 % were rated comparable to the experts’ proposal. 7 % automatic path proposals were rated not feasible, all being second choice (
n
=
1
) or third choice (
n
=
6
). In 79 %, segmentation at least was good. Average total time for establishing automatic path proposal was 42
±
9 s.
Conclusion
Automatic software-based path proposal for CT-guided liver biopsies in the majority provides path proposals that are easy to establish and comparable to experts’ insertion trajectories.
Abstract
Study question
Do hormonal treatments and initial cell number influence the formation of embryo-like structures (ELS) during their development in regard to size?
Summary answer
The chosen ...initial cell number for ELS-assembly seems to influence the ELS size only until day 4, while hormones affect embryo size throughout their development.
What is known already
The initial cell number is an important parameter for the development of ELS, which might help to better understand how embryos regulate their size. Previous studies on differently sized natural murine embryos revealed that an initial difference in size at the early stage is compensated until E6.75. Normal-size embryos experience an increased mitotic activity before E6.75, whereas larger sized embryos show an increased apoptotic activity, indicating an important control point of cell turnover by adapting mitotic activity and cell survival. Embryo development is strongly dependent on appropriate β-estradiol and progesterone levels.
Study design, size, duration
The first set of experiments interrogated the influence of initial cell number (two conditions) on the size of formed ELS during the first 3 days (D1–3). The second set included two different hormonal treatments and the two conditions of initial cell number (the same as in the first experiments) generating four different groups. For each day one Aggrewell (generating 1200 ELS/well) per condition was harvested. Experiments were repeated at least three times.
Participants/materials, setting, methods
ELS are generated by self-assembly in microwell-chamber plates combining embryonic stem cells, trophoblast stem cells and extraembryonic endoderm stem cells. Cells were cultured with and without addition of β-estradiol and progesterone, starting with different initial cell numbers (106 vs. 42 cells/ELS). ELS were harvested, stained, and at least 40 randomly picked ELS per condition were measured and statistically analyzed with Two-way ANOVA and Tukey’s multiple comparison test. Results show the average area ± SD.
Main results and the role of chance
The results show a continuous increase in the size of ELS during the first three days of cultivation, with significant lower values (on D1-D3) when ELS were assembled from 42 initial cells (D1: 224.1±87.7 μm²; D3: 674.0± 84.4 μm²) compared to ELS formed with 106 initial cells (D1: 467.1±224.1 μm²; D3: 1275.0±348.0 μm²). Onward on the course of self-assembly, ELS with 42 initial cells were still smaller on D4 (1465.7±657.6 μm²) compared to ELS formed with 106 initial cells (2028.6±522.4 μm²). However, these differences could not be measured on D5 (106 initial cells: 1892.2±603.7 μm²; 42 initial cells: 1855±448.5 μm²), D6 (106 initial cells: 2143.3±622.1 μm²; 42 initial cells: 1788.4±585.5 μm²) and D7 (106 initial cells: 2146.7±628.1 μm²; 42 initial cells: 2319.5±778.8 μm²). Differences between the conditions with and without hormonal treatments (HT) could also be detected especially when ELS were generated with 42 cells: on D4 ELS with HT (1730.4±852.4 μm²) were significantly larger than without hormones (1201.2±462.9 μm²). In contrast, on D7 HT influenced the size of ELS distinctly depending on the initial cell number (42 cells: 1989.2±558.3 μm² with HT vs. 2649.7±999.4 μm² without HT; 106 cells: 2334.9±770.2μm² with HT vs. 1958.6±486.1 μm² without HT).
Limitations, reasons for caution
An even cell distribution is crucial for reproducible ELS-formation. Unfortunately, the used techniques for cell seeding led to an uneven distribution within the microwells. Moreover, different orientation of ELS during the size assessment might be an additional reason for the high variance of ELS size within one condition.
Wider implications of the findings: Even if the results seem to be in accordance with the observations made with natural embryos regarding compensation of size until E6.75, additional experiments need to be conducted. Further investigations should be carried out by testing different culture formats to obtain a more even cell distribution during the cultivation.
Trial registration number
Not applicable
Color centers with long-lived spins are established platforms for quantum sensing and quantum information applications. Color centers exist in different charge states, each of them with distinct ...optical and spin properties. Application to quantum technology requires the capability to access and stabilize charge states for each specific task. Here, we investigate charge state manipulation of individual silicon vacancies in silicon carbide, a system which has recently shown a unique combination of long spin coherence time and ultrastable spin-selective optical transitions. In particular, we demonstrate charge state switching through the bias applied to the color center in an integrated silicon carbide optoelectronic device. We show that the electronic environment defined by the doping profile and the distribution of other defects in the device plays a key role for charge state control. Our experimental results and numerical modeling evidence that control of these complex interactions can, under certain conditions, enhance the photon emission rate. These findings open the way for deterministic control over the charge state of spin-active color centers for quantum technology and provide novel techniques for monitoring doping profiles and voltage sensing in microscopic devices.
In computed tomography (CT), selection of a convolution kernel determines the tradeoff between image sharpness and pixel noise. For certain clinical applications it is desirable to have two or more ...sets of images with different settings. So far, this typically requires reconstruction of several sets of images. We present an alternative approach using default reconstruction of sharp images and online filtering in the spatial domain allowing modification of the sharpness-noise tradeoff in real time. A suitable smoothing filter function in the frequency domain is the ratio of smooth and original (sharp) kernel. Efficient implementation can be achieved by a Fourier transform of this ratio to the spatial domain. Separating the two-dimensional spatial filtering into two subsequent one-dimensional filtering stages in the x and y directions using a Gaussian approximation for the convolution kernel further reduces computational complexity. Due to efficient implementation, interactive modification of the filter settings becomes possible, which can completely replace the variety of different reconstruction kernels.
Ultrasound spectroscopy Aylward, S. R.; McCormick, M.; Kang, H. J. ...
2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI),
04/2016, Letnik:
2016
Conference Proceeding, Journal Article
Odprti dostop
We introduce the concept of "Ultrasound Spectroscopy". The premise of ultrasound spectroscopy is that by acquiring ultrasound RF data at multiple power and frequency settings, a rich set of features ...can be extracted from that RF data and used to characterize the underlying tissues. This is beneficial for a variety of problems, such as accurate tissue classification, application-specific image generation, and numerous other quantitative tasks. These capabilities are particularly relevant to point-of-care ultrasound (POCUS) applications, where operator experience with ultrasound may be limited. Instead of displaying B-mode images, a POCUS application using ultrasound spectroscopy can, for example, automatically detect internal abdominal bleeding. In this paper, we present ex vivo tissue phantom studies to demonstrate the accuracy of ultrasound spectroscopy over previous approaches. Our studies suggest that ultrasound spectroscopy provides exceptional accuracy and informative features for classifying blood versus other tissues across image locations and body habitus.
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