Background
CT perfusion imaging (CTP) is used in the diagnostic workup of acute ischemic stroke (AIS). CTP may be performed within the angio suite using flat detector CT (FDCT) to help reduce patient ...management time.
Purpose
In order to significantly improve FDCT perfusion (FDCTP) imaging, data‐processing algorithms need to be able to compensate for the higher levels of noise, slow rotation speed, and a lower frame rate of current FDCT devices.
Methods
We performed a realistic simulation of FDCTP acquisition based on CTP data from seven subjects. We used the time separation technique (TST) as a model‐based approach for FDCTP data processing. We propose a novel dimension reduction in which we approximate the time attenuation curves by a linear combination of trigonometric functions. Our goal was to show that the TST can be used even without prior assumptions on the shape of the attenuation profiles.
Results
We first demonstrated that a trigonometric basis is suitable for dimension reduction of perfusion data. Using simulated FDCTP data, we have shown that a trigonometric basis in the TST provided better results than the classical straightforward processing even with additional noise. Average correlation coefficients of perfusion maps were improved for cerebral blood flow (CBF), cerebral blood volume, mean transit time (MTT) maps. In a moderate noise scenario, the average Pearson's coefficient for the CBF map was improved using the TST from 0.76 to 0.81. For the MTT map, it was improved from 0.37 to 0.45. Furthermore, we achieved a total processing time from the reconstruction of FDCTP data to the generation of perfusion maps of under 5 min.
Conclusions
In our study cohort, perfusion maps created from FDCTP data using the TST with a trigonometric basis showed equivalent perfusion deficits to classic CT perfusion maps. It follows, that this novel FDCTP technique has potential to provide fast and accurate FDCTP imaging for AIS patients.
In this paper we study the deformation of a body with a notch subject to an anti-plane state of stress within the context of a new class of elastic models. These models stem as approximations of ...constitutive response functions for an elastic body that is defined within the context of an implicit constitutive relation between the stress and the deformation gradient. Gum metal and many metallic alloys are described well by such constitutive relations. We consider the state of anti-plane stress of a body with a smoothened V-notch within the context of constitutive relations for the linearized strain in terms of a power-law for the stretch. The problem is solved numerically and the convergence and the stability of the solution is studied.
Primary cutaneous T-cell lymphomas (CTCL) affect the skin and tend to transform and spread. CTCL involves primarily the Mycosis fungoides (MF) and more aggressive Sezary syndrome (SS). Oncogenic ...microRNAs (miRs) are stable epigenetic inhibitors often deregulated in the tumour and detectable as biomarkers in non-cellular fractions of peripheral blood. The tumour-specific expression of miR-155, miR-203, and miR-205 was shown to correctly diagnose CTCL. We herein asked whether these microRNAs can be used as plasma biomarkers for clinical CTCL monitoring. Patients with CTCL (
= 10) and controls with non-malignant conditions (
= 11) repeatedly donated plasma samples every ca. five months. MicroRNAs were detected in the plasma samples by specifically-primed RT-PCR followed by multivariate analyses of the miR expression dynamics. We herein established the plasma miR-classifier for detecting CTCL based on the miR-155 upregulation and miR-203/miR-205 downregulation with 100% specificity and 94% sensitivity. The 3-miR-score in the consecutive samples coincided with the clinical outcome of MF and SS patients such as the therapy response or changes in the clinical stage or tumor size. Quantitation of the selected microRNAs in plasma is a specific and straightforward approach for evaluating CTCL outcome representing, thus, a valuable tool for CTCL diagnostics and therapy response monitoring.
The main purpose of this study is to investigate the efficacy and usefulness of a class of recently proposed models that could be reasonable candidates for describing the response of brittle elastic ...materials. The class of models that are considered allows for a non-linear relationship between the linearized elastic strain and the Cauchy stress, and this allows one to describe situations wherein the stress increases while the strain yet remains small. Thus one would be in a position to model the response of brittle elastic bodies in the neighborhood of the tips of cracks and notches. In this paper we study the behavior of such models in a plate with a V-notch subject to a state of anti-plane stress. This geometrical simplification enables us to characterize the governing equation for the problem by means of the Airy stress function, though the constitutive relation is a non-linear relation between the linearized strain and the stress. We study the problem numerically by appealing to the finite element method. We find that the numerical solutions are stable. We are able to provide some information regarding the nature of the solution near the tip of the V-notch. In particular we find stress concentration in the vicinity of the singularity.
Model-based reconstruction employing the time separation technique (TST) was found to improve dynamic perfusion imaging of the liver using C-arm cone-beam computed tomography (CBCT). To apply TST ...using prior knowledge extracted from CT perfusion data, the liver should be accurately segmented from the CT scans. Reconstructions of primary and model-based CBCT data need to be segmented for proper visualisation and interpretation of perfusion maps. This research proposes Turbolift learning, which trains a modified version of the multi-scale Attention UNet on different liver segmentation tasks serially, following the order of the trainings CT, CBCT, CBCT TST – making the previous trainings act as pre-training stages for the subsequent ones – addressing the problem of limited number of datasets for training. For the final task of liver segmentation from CBCT TST, the proposed method achieved an overall Dice scores of 0.874±0.031 and 0.905±0.007 in 6-fold and 4-fold cross-validation experiments, respectively — securing statistically significant improvements over the model, which was trained only for that task. Experiments revealed that Turbolift not only improves the overall performance of the model but also makes it robust against artefacts originating from the embolisation materials and truncation artefacts. Additionally, in-depth analyses confirmed the order of the segmentation tasks. This paper shows the potential of segmenting the liver from CT, CBCT, and CBCT TST, learning from the available limited training data, which can possibly be used in the future for the visualisation and evaluation of the perfusion maps for the treatment evaluation of liver diseases.
•This research proposes Turbolift learning which trains a modified version of the multi-scale Attention UNet on different liver segmentation tasks serially.•Making the previous trainings act as pre-training stages for the subsequent ones — CT, CBCT, CBCT TST.•Addressing the problem of limited number of datasets for training using the stage-wise training strategy.•For the final task of liver segmentation from CBCT TST, the proposed method achieved an overall Dice scores of 0.874±0.031 and 0.905±0.007 in 6-fold and 4-fold cross-validation experiments.•Turbolift not only improves the overall performance of the model but also makes it robust against artefacts originating from the embolisation materials and truncation artefacts.
The mechanisms by which myelodysplastic syndrome (MDS) cells resist the effects of hypomethylating agents (HMA) are currently the subject of intensive research. A better understanding of mechanisms ...by which the MDS cell becomes to tolerate HMA and progresses to acute myeloid leukemia (AML) requires the development of new cellular models. From MDS/AML cell lines we developed a model of 5-azacytidine (AZA) resistance whose stability was validated by a transplantation approach into immunocompromised mice. When investigating mRNA expression and DNA variants of the AZA resistant phenotype we observed deregulation of several cancer-related pathways including the phosphatidylinosito-3 kinase signaling. We have further shown that these pathways can be modulated by specific inhibitors that, while blocking the proliferation of AZA resistant cells, are unable to increase their sensitivity to AZA. Our data reveal a set of molecular mechanisms that can be targeted to expand therapeutic options during progression on AZA therapy.
The imitation switch nuclear ATPase Smarca5 (Snf2h) is one of the most conserved chromatin remodeling factors. It exists in a variety of oligosubunit complexes that move DNA with respect to the ...histone octamer to generate regularly spaced nucleosomal arrays. Smarca5 interacts with different accessory proteins and represents a molecular motor for DNA replication, repair, and transcription. We deleted Smarca5 at the onset of definitive hematopoiesis (Vav1‐iCre) and observed that animals die during late fetal development due to anemia. Hematopoietic stem and progenitor cells accumulated but their maturation toward erythroid and myeloid lineages was inhibited. Proerythroblasts were dysplastic while basophilic erythroblasts were blocked in G2/M and depleted. Smarca5 deficiency led to increased p53 levels, its activation at two residues, one associated with DNA damage (S15Ph°s) second with CBP/p300 (K376Ac), and finally activation of the p53 targets. We also deleted Smarca5 in committed erythroid cells (Epor‐iCre) and observed that animals were anemic postnatally. Furthermore, 4‐hydroxytamoxifen‐mediated deletion of Smarca5 in the ex vivo cultures confirmed its requirement for erythroid cell proliferation. Thus, Smarca5 plays indispensable roles during early hematopoiesis and erythropoiesis. Stem Cells 2017;35:1614–1623
Smarca5 requirement during mouse hematopoietic development. Hematopoietic stem cells (HSCs) lacking Smarca5 temporarily activate proliferation followed by G2/M arrest during erythroid and myeloid differentiation leading to fatal anemia with tetraploid erythroblasts and p53 activation. Erythroid‐specific deletion of Smarca5 resulted in milder phenotypes: anemia and tetraploidy.
Krylov subspace methods are considered a standard tool to solve large systems of linear algebraic equations in many scientific disciplines such as image restoration or solving partial differential ...equations in mechanics of continuum. In the context of computer tomography however, the mostly used algebraic reconstruction techniques are based on classical iterative schemes. In this work we present software package that implements fully 3D cone beam projection operator and uses Krylov subspace methods, namely CGLS and LSQR to solve related tomographic reconstruction problems. It also implements basic preconditioning strategies. On the example of the cone beam CT reconstruction of 3D Shepp-Logan phantom we show that the speed of convergence of the CGLS clearly outperforms PSIRT algorithm. Therefore Krylov subspace methods present an interesting option for the reconstruction of large 3D cone beam CT problems.
In this paper, we introduce a new class of projectors for 3D cone beam tomographic reconstruction. We find analytical formulas for the relationship between the voxel volume projected onto a given ...detector pixel and its contribution to the extinction value detected on that pixel. Using this approach, we construct a near-exact projector and backprojector that can be used especially for algebraic reconstruction techniques. We have implemented this cutting voxel projector and a less accurate, speed-optimized version of it together with two established projectors, a ray tracing projector based on Siddon's algorithm and a TT footprint projector. We show that the cutting voxel projector achieves, especially for large cone beam angles, noticeably higher accuracy than the TT projector. Moreover, our implementation of the relaxed version of the cutting voxel projector is significantly faster than current footprint projector implementations. We further show that Siddon's algorithm with comparable accuracy would be much slower than the cutting voxel projector. All algorithms are implemented within an open source framework for algebraic reconstruction in OpenCL 1.2 and C++ and are optimized for GPU computation. They are published as open-source software under the GNU GPL 3 license, see https://github.com/kulvait/KCT_cbct.
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