Search results for "Deconvolution"
showing 10 items of 82 documents
Assessment of tumor-infiltrating TCRV γ 9V δ 2 γδ lymphocyte abundance by deconvolution of human cancers microarrays
2017
Most human blood γδ cells are cytolytic TCRVγ9Vδ2+lymphocytes with antitumor activity. They are currently investigated in several clinical trials of cancer immunotherapy but so far, their tumor infiltration has not been systematically explored across human cancers. Novel algorithms allowing the deconvolution of bulk tumor transcriptomes to find the relative proportions of infiltrating leucocytes, such as CIBERSORT, should be appropriate for this aim but in practice they fail to accurately recognize γδ T lymphocytes. Here, by implementing machine learning from microarray data, we first improved the computational identification of blood-derived TCRVγ9Vδ2+γδ lymphocytes and then appl…
Two simple criteria to estimate an objective's performance when imaging in non design tissue clearing solutions
2019
Tissue clearing techniques are undergoing a renaissance motivated by the need to image fluorescent neurons, and other cells, deep in the sample without physical sectioning. Optical transparency is achieved by equilibrating tissues with high refractive index (RI) solutions. When the microscope objective is not perfectly matched to the RI of the cleared sample, aberrations are introduced. We present two simple-to-calculate numerical criteria predicting: (i) the degradation in image quality (brightness and resolution) from optimal conditions of any clearing solution/objective combination; (ii) which objective, among several available, achieves the highest resolution in a given medium. We deriv…
Dissection of DLBCL microenvironment provides a gene expression-based predictor of survival applicable to formalin-fixed paraffin-embedded tissue
2018
Abstract Background Gene expression profiling (GEP) studies recognized a prognostic role for tumor microenvironment (TME) in diffuse large B-cell lymphoma (DLBCL), but the routinely adoption of prognostic stromal signatures remains limited. Patients and methods Here, we applied the computational method CIBERSORT to generate a 1028-gene matrix incorporating signatures of 17 immune and stromal cytotypes. Then, we carried out a deconvolution on publicly available GEP data of 482 untreated DLBCLs to reveal associations between clinical outcomes and proportions of putative tumor-infiltrating cell types. Forty-five genes related to peculiar prognostic cytotypes were selected and their expression …
Deconvolution of the cellular origin in hepatocellular carcinoma: Hepatocytes take the center stage.
2016
The expression of biliary/progenitor markers by hepatocellular carcinoma (HCC) is often associated with poor prognosis and stem cell-like behaviors of tumor cells. Hepatocellular adenomas (HCA) also often express biliary/progenitor markers and frequently act as precursor lesions for HCC. However, the cell of origin of HCA and HCC that expresses these markers still remains unclear. Therefore, to evaluate if mature hepatocytes give rise to HCA and HCC tumors, and to understand the molecular pathways involved in tumorigenesis, we lineage-labeled hepatocytes by injecting adeno-associated virus (AAV) containing thyroxine-binding globulin (TBG) promoter driven-Cre into RosaYFP mice. Yellow fluore…
Assessing the Contribution of Relative Macrophage Frequencies to Subcutaneous Adipose Tissue
2021
Background: Macrophages play an important role in regulating adipose tissue function, while their frequencies in adipose tissue vary between individuals. Adipose tissue infiltration by high frequencies of macrophages has been linked to changes in adipokine levels and low-grade inflammation, frequently associated with the progression of obesity. The objective of this project was to assess the contribution of relative macrophage frequencies to the overall subcutaneous adipose tissue gene expression using publicly available datasets.Methods: Seven publicly available microarray gene expression datasets from human subcutaneous adipose tissue biopsies (n = 519) were used together with TissueDecod…
Optimisation of chromatographic resolution using objective functions including both time and spectral information.
2014
The optimisation of the resolution in high-performance liquid chromatography is traditionally performed attending only to the time information. However, even in the optimal conditions, some peak pairs may remain unresolved. Such incomplete resolution can be still accomplished by deconvolution, which can be carried out with more guarantees of success by including spectral information. In this work, two-way chromatographic objective functions (COFs) that incorporate both time and spectral information were tested, based on the peak purity (analyte peak fraction free of overlapping) and the multivariate selectivity (figure of merit derived from the net analyte signal) concepts. These COFs are s…
Calculation of the surface concentration of Zn(I) from the anodic voltammetric peak of zinc combined with the QCM results
2004
Deconvolution of voltammograms of anodic dissolution of zinc has proved to be possible through the electrochemical quartz crystal microbalance data and the F(dm/dQ) function. This deconvolution allows to calculate the surface concentration of Zn(I) and to obtain an estimation for the kinetic constant of the second single-electron transfer. Keywords: Zinc anodic dissolution, EQCM, Surface concentration, Deconvolution and kinetic constant
Deconvolution procedure of the UV-vis spectra. A powerful tool for the estimation of the binding of a model drug to specific solubilisation loci of b…
2015
UV-vis-spectra evolution of Nile Red loaded into Tween 20 micelles with pH and [Tween 20] have been analysed in a non-conventional manner by exploiting the deconvolution method. The number of buried sub-bands has been found to depend on both pH and bio-surfactant concentration, whose positions have been associated to Nile Red confined in aqueous solution and in the three micellar solubilisation sites. For the first time, by using an extended classical two-pseudo-phases-model, the robust treatment of the spectrophotometric data allows the estimation of Nile Red binding constant to the available loci. Hosting capability towards Nile Red is exalted by the pH enhancement. Comparison between bin…
Blind deconvolution using TV regularization and Bregman iteration
2005
In this paper we formulate a new time dependent model for blind deconvolution based on a constrained variational model that uses the sum of the total variation norms of the signal and the kernel as a regularizing functional. We incorporate mass conservation and the nonnegativity of the kernel and the signal as additional constraints. We apply the idea of Bregman iterative regularization, first used for image restoration by Osher and colleagues [S.J. Osher, M. Burger, D. Goldfarb, J.J. Xu, and W. Yin, An iterated regularization method for total variation based on image restoration, UCLA CAM Report, 04-13, (2004)]. to recover finer scales. We also present an analytical study of the model disc…
Free-depths reconstruction with synthetic impulse response in integral imaging
2015
Integral Imaging provides spatial and angular information of three-dimensional (3D) objects, which can be used both for 3D display and for computational post-processing purposes. In order to recover the depth information from an integral image, several algorithms have been developed. In this paper, we propose a new free depth synthesis and reconstruction method based on the two-dimensional (2D) deconvolution between the integral image and a simplified version of the periodic impulse response function (IRF) of the system. The period of the IRF depends directly on the axial position within the object space. Then, we can retrieve the depth information by performing the deconvolution with compu…