60 research outputs found
Quantitative Photo-acoustic Tomography with Partial Data
Photo-acoustic tomography is a newly developed hybrid imaging modality that
combines a high-resolution modality with a high-contrast modality. We analyze
the reconstruction of diffusion and absorption parameters in an elliptic
equation and improve an earlier result of Bal and Uhlmann to the partial date
case. We show that the reconstruction can be uniquely determined by the
knowledge of 4 internal data based on well-chosen partial boundary conditions.
Stability of this reconstruction is ensured if a convexity condition is
satisfied. Similar stability result is obtained without this geometric
constraint if 4n well-chosen partial boundary conditions are available, where
is the spatial dimension. The set of well-chosen boundary measurements is
characterized by some complex geometric optics (CGO) solutions vanishing on a
part of the boundary.Comment: arXiv admin note: text overlap with arXiv:0910.250
Neural networks-based regularization for large-scale medical image reconstruction
In this paper we present a generalized Deep Learning-based approach for solving ill-posed large-scale inverse problems occuring in medical image reconstruction. Recently, Deep Learning methods using iterative neural networks (NNs) and cascaded NNs have been reported to achieve state-of-the-art results with respect to various quantitative quality measures as PSNR, NRMSE and SSIM across different imaging modalities. However, the fact that these approaches employ the application of the forward and adjoint operators repeatedly in the network architecture requires the network to process the whole images or volumes at once, which for some applications is computationally infeasible. In this work, we follow a different reconstruction strategy by strictly separating the application of the NN, the regularization of the solution and the consistency with the measured data. The regularization is given in the form of an image prior obtained by the output of a previously trained NN which is used in a Tikhonov regularization framework. By doing so, more complex and sophisticated network architectures can be used for the removal of the artefacts or noise than it is usually the case in iterative NNs. Due to the large scale of the considered problems and the resulting computational complexity of the employed networks, the priors are obtained by processing the images or volumes as patches or slices. We evaluated the method for the cases of 3D cone-beam low dose CT and undersampled 2D radial cine MRI and compared it to a total variation-minimization-based reconstruction algorithm as well as to a method with regularization based on learned overcomplete dictionaries. The proposed method outperformed all the reported methods with respect to all chosen quantitative measures and further accelerates the regularization step in the reconstruction by several orders of magnitude
A series solution and a fast algorithm for the inversion of the spherical mean Radon transform
An explicit series solution is proposed for the inversion of the spherical
mean Radon transform. Such an inversion is required in problems of thermo- and
photo- acoustic tomography. Closed-form inversion formulae are currently known
only for the case when the centers of the integration spheres lie on a sphere
surrounding the support of the unknown function, or on certain unbounded
surfaces. Our approach results in an explicit series solution for any closed
measuring surface surrounding a region for which the eigenfunctions of the
Dirichlet Laplacian are explicitly known - such as, for example, cube, finite
cylinder, half-sphere etc. In addition, we present a fast reconstruction
algorithm applicable in the case when the detectors (the centers of the
integration spheres) lie on a surface of a cube. This algorithm reconsrtucts
3-D images thousands times faster than backprojection-type methods
Inverse Diffusion Theory of Photoacoustics
This paper analyzes the reconstruction of diffusion and absorption parameters
in an elliptic equation from knowledge of internal data. In the application of
photo-acoustics, the internal data are the amount of thermal energy deposited
by high frequency radiation propagating inside a domain of interest. These data
are obtained by solving an inverse wave equation, which is well-studied in the
literature. We show that knowledge of two internal data based on well-chosen
boundary conditions uniquely determines two constitutive parameters in
diffusion and Schroedinger equations. Stability of the reconstruction is
guaranteed under additional geometric constraints of strict convexity. No
geometric constraints are necessary when internal data for well-chosen
boundary conditions are available, where is spatial dimension. The set of
well-chosen boundary conditions is characterized in terms of appropriate
complex geometrical optics (CGO) solutions.Comment: 24 page
Uniqueness of reconstruction and an inversion procedure for thermoacoustic and photoacoustic tomography
The paper contains a simple approach to reconstruction in Thermoacoustic and
Photoacoustic Tomography. The technique works for any geometry of point
detectors placement and for variable sound speed satisfying a non-trapping
condition. A uniqueness of reconstruction result is also obtained
Sparse Regularization with Penalty Term
We consider the stable approximation of sparse solutions to non-linear
operator equations by means of Tikhonov regularization with a subquadratic
penalty term. Imposing certain assumptions, which for a linear operator are
equivalent to the standard range condition, we derive the usual convergence
rate of the regularized solutions in dependence of the noise
level . Particular emphasis lies on the case, where the true solution
is known to have a sparse representation in a given basis. In this case, if the
differential of the operator satisfies a certain injectivity condition, we can
show that the actual convergence rate improves up to .Comment: 15 page
Murine Gammaretrovirus Group G3 Was Not Found in Swedish Patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Fibromyalgia
BACKGROUND: The recent report of gammaretroviruses of probable murine origin in humans, called xenotropic murine retrovirus related virus (XMRV) and human murine leukemia virus related virus (HMRV), necessitated a bioinformatic search for this virus in genomes of the mouse and other vertebrates, and by PCR in humans. RESULTS: Three major groups of murine endogenous gammaretroviruses were identified. The third group encompassed both exogenous and endogenous Murine Leukemia Viruses (MLVs), and most XMRV/HMRV sequences reported from patients suffering from myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Two sensitive real-time PCRs for this group were developed. The predicted and observed amplification range for these and three published XMRV/HMRV PCRs demonstrated conspicuous differences between some of them, partly explainable by a recombinatorial origin of XMRV. Three reverse transcription real-time PCRs (RTQPCRs), directed against conserved and not overlapping stretches of env, gag and integrase (INT) sequences of XMRV/HMRV were used on human samples. White blood cells from 78 patients suffering from ME/CFS, of which 30 patients also fulfilled the diagnostic criteria for fibromyalgia (ME/CFS/FM) and in 7 patients with fibromyalgia (FM) only, all from the Gothenburg area of Sweden. As controls we analyzed 168 sera from Uppsala blood donors. We controlled for presence and amplifiability of nucleic acid and for mouse DNA contamination. To score as positive, a sample had to react with several of the XMRV/HMRV PCRs. None of the samples gave PCR reactions which fulfilled the positivity criteria. CONCLUSIONS: XMRV/HMRV like proviruses occur in the third murine gammaretrovirus group, characterized here. PCRs developed by us, and others, approximately cover this group, except for the INT RTQPCR, which is rather strictly XMRV specific. Using such PCRs, XMRV/HMRV could not be detected in PBMC and plasma samples from Swedish patients suffering from ME/CFS/FM, and in sera from Swedish blood donors
Molecular Insights into Reprogramming-Initiation Events Mediated by the OSKM Gene Regulatory Network
Somatic cells can be reprogrammed to induced pluripotent stem cells by over-expression of OCT4, SOX2, KLF4 and c-MYC (OSKM). With the aim of unveiling the early mechanisms underlying the induction of pluripotency, we have analyzed transcriptional profiles at 24, 48 and 72 hours post-transduction of OSKM into human foreskin fibroblasts. Experiments confirmed that upon viral transduction, the immediate response is innate immunity, which induces free radical generation, oxidative DNA damage, p53 activation, senescence, and apoptosis, ultimately leading to a reduction in the reprogramming efficiency. Conversely, nucleofection of OSKM plasmids does not elicit the same cellular stress, suggesting viral response as an early reprogramming roadblock. Additional initiation events include the activation of surface markers associated with pluripotency and the suppression of epithelial-to-mesenchymal transition. Furthermore, reconstruction of an OSKM interaction network highlights intermediate path nodes as candidates for improvement intervention. Overall, the results suggest three strategies to improve reprogramming efficiency employing: 1) anti-inflammatory modulation of innate immune response, 2) pre-selection of cells expressing pluripotency-associated surface antigens, 3) activation of specific interaction paths that amplify the pluripotency signal
Inhibition of Src kinase activity attenuates amyloid associated microgliosis in a murine model of Alzheimer’s disease
<p>Abstract</p> <p>Background</p> <p>Microglial activation is an important histologic characteristic of the pathology of Alzheimer’s disease (AD). One hypothesis is that amyloid beta (Aβ) peptide serves as a specific stimulus for tyrosine kinase-based microglial activation leading to pro-inflammatory changes that contribute to disease. Therefore, inhibiting Aβ stimulation of microglia may prove to be an important therapeutic strategy for AD.</p> <p>Methods</p> <p>Primary murine microglia cultures and the murine microglia cell line, BV2, were used for stimulation with fibrillar Aβ1-42. The non-receptor tyrosine kinase inhibitor, dasatinib, was used to treat the cells to determine whether Src family kinase activity was required for the Aβ stimulated signaling response and subsequent increase in TNFα secretion using Western blot analysis and enzyme-linked immunosorbent assay (ELISA), respectively. A histologic longitudinal analysis was performed using an AD transgenic mouse model, APP/PS1, to determine an age at which microglial protein tyrosine kinase levels increased in order to administer dasatinib via mini osmotic pump diffusion. Effects of dasatinib administration on microglial and astroglial activation, protein phosphotyrosine levels, active Src kinase levels, Aβ plaque deposition, and spatial working memory were assessed via immunohistochemistry, Western blot, and T maze analysis.</p> <p>Results</p> <p>Aβ fibrils stimulated primary murine microglia via a tyrosine kinase pathway involving Src kinase that was attenuated by dasatinib. Dasatinib administration to APP/PS1 mice decreased protein phosphotyrosine, active Src, reactive microglia, and TNFα levels in the hippocampus and temporal cortex. The drug had no effect on GFAP levels, Aβ plaque load, or the related tyrosine kinase, Lyn. These anti-inflammatory changes correlated with improved performance on the T maze test in dasatinib infused animals compared to control animals.</p> <p>Conclusions</p> <p>These data suggest that amyloid dependent microgliosis may be Src kinase dependent <it>in vitro</it> and <it>in vivo.</it> This study defines a role for Src kinase in the microgliosis characteristic of diseased brains and suggests that particular tyrosine kinase inhibition may be a valid anti-inflammatory approach to disease. Dasatinib is an FDA-approved drug for treating chronic myeloid leukemia cancer with a reported ability to cross the blood-brain barrier. Therefore, this suggests a novel use for this drug as well as similar acting molecules.</p
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