Fluorescence Microscopy Imaging Denoising with Log-Euclidean Priors and Photobleaching Compensation

Fluorescent protein microscopy imaging is nowadays one of the most important tools in biomedical research. However, the resulting images present a low signal to noise ratio and a time intensity decay due to the photobleaching effect. This phenomenon is a consequence of the decreasing on the radiation emission efficiency of the tagging protein. This occurs because the fluorophore permanently loses its ability to fluoresce, due to photochemical reactions induced by the incident light. The Poisson multiplicative noise that corrupts these images, in addition with its quality degradation due to photobleaching, make long time biological observation processes very difficult. In this paper a denoising algorithm for Poisson data, where the photobleaching effect is explicitly taken into account, is described. The algorithm is designed in a Bayesian framework where the data fidelity term models the Poisson noise generation process as well as the exponential intensity decay caused by the photobleaching. The prior term is conceived with Gibbs priors and log-Euclidean potential functions, suitable to cope with the positivity constrained nature of the parameters to be estimated. Monte Carlo tests with synthetic data are presented to characterize the performance of the algorithm. One example with real data is included to illustrate its application.

A new control strategy with saturation effect compensation for an autonomous induction generator drivenby wide speed range turbines

This paper presents a variable speed autonomous squirrel cage generator excited by a current-controlled voltage source inverter to be used in stand-alone micro-hydro power plants. The paper proposes a system control strategy aiming to properly excite the machine as well as to achieve the load voltage control. A feed-forward control sets the appropriate generator flux by taking into account the actual speed and the desired load voltage. A load voltage control loop is used to adjust the generated active power in order to sustain the load voltage at a reference value. The control system is based on a rotor flux oriented vector control technique which takes into account the machine saturation effect. The proposed control strategy and the adopted system models were validated both by numerical simulation and by experimental results obtained from a laboratory prototype. Results covering the prototype start-up, as well as its steady-state and dynamical behavior are presented. (C) 2011 Elsevier Ltd. All rights reserved.

Convex Total Variation Denoising of Poisson Fluorescence Confocal Images With Anisotropic Filtering

Fluorescence confocal microscopy (FCM) is now one of the most important tools in biomedicine research. In fact, it makes it possible to accurately study the dynamic processes occurring inside the cell and its nucleus by following the motion of fluorescent molecules over time. Due to the small amount of acquired radiation and the huge optical and electronics amplification, the FCM images are usually corrupted by a severe type of Poisson noise. This noise may be even more damaging when very low intensity incident radiation is used to avoid phototoxicity. In this paper, a Bayesian algorithm is proposed to remove the Poisson intensity dependent noise corrupting the FCM image sequences. The observations are organized in a 3-D tensor where each plane is one of the images acquired along the time of a cell nucleus using the fluorescence loss in photobleaching (FLIP) technique. The method removes simultaneously the noise by considering different spatial and temporal correlations. This is accomplished by using an anisotropic 3-D filter that may be separately tuned in space and in time dimensions. Tests using synthetic and real data are described and presented to illustrate the application of the algorithm. A comparison with several state-of-the-art algorithms is also presented.

Detection of Change in Fluorescence Between Reactive Cyan and the Yellow Fluorophores Usinga-SiC:H Multilayer Transducers

Optical colour sensors based on multilayered a-SiC:H heterostructures can act as voltage controlled optical filters in the visible range. In this article we investigate the application of these structures for Fluorescence Resonance Energy Transfer (FRET) detection, The characteristics of a-SiC:H multilayered structure are studied both theoretically and experimentally in several wavelengths corresponding to different fluorophores. The tunable optical p-i'(a-SiC:H)-n/p-i(a-Si:H)-n heterostructures were produced by PECVD and tested for a proper fine tuning in the violet, cyan and yellow wavelengths. The devices were characterized through transmittance and spectral response measurements, under different electrical bias and frequencies. Violet, cyan and yellow signals were applied in simultaneous and results have shown that they can be recovered under suitable applied bias. A theoretical analysis supported by numerical simulation is presented.

Simulation of the Magnetic Induction Vector of a Magnetic Core to be Used in FFC NMR Relaxometry

This paper is a contribution for the assessment and comparison of magnet properties based on magnetic field characteristics particularly concerning the magnetic induction uniformity in the air gaps. For this aim, a solver was developed and implemented to determine the magnetic field of a magnetic core to be used in Fast Field Cycling (FFC) Nuclear Magnetic Resonance (NMR) relaxometry. The electromagnetic field computation is based on a 2D finite-element method (FEM) using both the scalar and the vector potential formulation. Results for the magnetic field lines and the magnetic induction vector in the air gap are presented. The target magnetic induction is 0.2 T, which is a typical requirement of the FFC NMR technique, which can be achieved with a magnetic core based on permanent magnets or coils. In addition, this application requires high magnetic induction uniformity. To achieve this goal, a solution including superconducting pieces is analyzed. Results are compared with a different FEM program.

Detection of Change in Fluorescence Between Reactive Cyan and the Yellow Fluorophores Using a-SiC:H Multilayer Transducers

The transducer consists of a semiconductor device based on two stacked -i-n heterostructures that were designed to detect the emissions of the fluorescence resonance energy transfer between fluorophores in the cyan (470 nm) and yellow (588 nm) range of the spectrum. This research represents a preliminary study on the use of such wavelength-sensitive devices as photodetectors for this kind of application. The device was characterized through optoelectronic measurements concerning spectral response measurements under different electrical and optical biasing conditions. To simulate the fluorescence resonance energy transfer (FRET) pairs, a chromatic time-dependent combination of cyan and yellow wavelengths was applied to the device. The generated photocurrent was measured under reverse and forward bias to read out the output photocurrent signal. A different wavelength-biasing light was also superimposed. Results show that under reverse bias, the photocurrent signal presents four separate levels, each one assigned to the different wavelength combinations of the FRET pairs. If a blue background is superimposed, the yellow channel is enhanced and the cyan suppressed, while under red irradiation, the opposite behavior occurs. So, under suitable biasing light, the transducer is able to detect separately the cyan and yellow fluorescence pairs. An electrical model, supported by a numerical simulation, supports the transduction mechanism of the device.

Differential expression of the eukaryotic release factor 3 (eRF3/GSPT1) according to gastric cancer histological types

Background: There are now several lines of evidence to suggest that protein synthesis and translation factors are involved in the regulation of cell proliferation and cancer development. Aims: To investigate gene expression patterns of eukaryotic releasing factor 3 (eRF3) in gastric cancer. Methods: RNA was prepared from 25 gastric tumour biopsies and adjacent non-neoplastic mucosa. Real time TaqMan reverse transcription polymerase chain reaction (RT-PCR) was performed to measure the relative gene expression levels. DNA was isolated from tumour and normal tissues and gene dosage was determined by a quantitative real time PCR using SYBR Green dye. Results: Different histological types of gastric tumours were analysed and nine of the 25 tumours revealed eRF3/GSPT1 overexpression; moreover, eight of the 12 intestinal type carcinomas analysed overexpressed the gene, whereas eRF3/GSPT1 was overexpressed in only one of the 10 diffuse type carcinomas (Kruskal-Wallis Test; p , 0.05). No correlation was found between ploidy and transcript expression levels of eRF3/GSPT1. Overexpression of eRF3/GSPT1 was not associated with increased translation rates because the upregulation of eRF3/GSPT1 did not correlate with increased eRF1 levels. Conclusions: Overexpression of eRF3/GSPT1 in intestinal type gastric tumours may lead to an increase in the translation efficiency of specific oncogenic transcripts. Alternatively, eRF3/GSPT1 may be involved in tumorigenesis as a result of its non-translational roles, namely (dis)regulating the cell cycle, apoptosis, or transcription.

Differential expression of CDC25 phosphatases splice variants in human breast cancer cells

Background: CDC25 phosphatases control cell cycle progression by activating cyclin dependent kinases. The three CDC25 isoforms encoding genes are submitted to alternative splicing events which generate at least two variants for CDC25A and five for both CDC25B and CDC25C. An over-expression of CDC25 was reported in several types of cancer, including breast cancer, and is often associated with a poor prognosis. Nevertheless, most of the previous studies did not address the expression of CDC25 splice variants. Here, we evaluated CDC25 spliced transcripts expression in anti-cancerous drug-sensitive and resistant breast cancer cell lines in order to identify potential breast cancer biomarkers. Methods: CDC25 splice variants mRNA levels were evaluated by semi-quantitative RT-PCR and by an original real-time RT-PCR assay. Results: CDC25 spliced transcripts are differentially expres-sed in the breast cancer cell lines studied. An up-regulation of CDC25A2 variant and an increase of the CDC25C5/C1 ratio are associated to the multidrug-resistance in VCREMS and DOXOR breast cancer cells, compared to their sensitive counterpart cell line MCF-7. Additionally, CDC25B2 tran-script is exclusively over-expressed in VCREMS resistant cells and could therefore be involved in the development of certain type of drug resistance. Conclusions: CDC25 splice variants could represent interesting potential breast cancer prognostic biomarkers.

Differential expression of GSPT1 GGCn alleles in cancer

The human eukaryotic release factor 3a (eRF3a), encoded by the G1 to S phase transition 1 gene (GSPT1; alias eRF3a), is upregulated in various human cancers. GSPT1 contains a GGCn polymorphism in exon 1, encoding a polyglycine expansion in the N-terminal of the protein. The longer allele, GGC12, was previously shown to be associated to cancer. The GGC12 allele was present in 2.2% of colorectal cancer patients but was absent in Crohn disease patients and in the control group. Real-time quantitative RT-PCR analysis showed that the GGC12 allele was present at up to 10-fold higher transcription levels than the GGC10 allele (P < 0.001). No GSPT1 amplifications were detected, and there was no correlation between the length of the alleles and methylation levels of the CpG sites inside the GGC expansion. Using flow cytometry, we compared the levels of apoptosis and proliferation rates between cell lines with different genotypes, but detected no significant differences. Finally, we used a cytokinesis-block micronucleus assay to evaluate the frequency of micronuclei in the same cell lines. Cell lines with the longer alleles had higher frequencies of micronuclei in binucleated cells, which is probably a result of defects in mitotic spindle formation. Altogether, these findings indicate that GSPT1 should be considered a potential proto-oncogene.

A class of singular first order differential equations with applications in reaction-diffusion

Agências Financiadoras: FCT e MIUR

Optimization of magneto-electro-elastic composite structures using differential evolution

Magneto-electro-elastic structures are built from materials that provide them the ability to convert in an interchangeable way, magnetic, electric and mechanical forms of energy. This characteristic can therefore provide an adaptive behaviour to a general configuration elastic structure, being commonly used in association with any type of composite material in an embedded or surface mounted mode, or by considering the usage of multiphase materials that enable achieving different magneto-electro-elastic properties. In a first stage of this work, a few cases studies will be considered to enable the validation of the model considered and the influence of the coupling characteristics of this type of adaptive structures. After that we consider the application of a recent computational intelligence technique, the differential evolution, in a deflection profile minimization problem. Studies on the influence of optimization parameters associated to the problem considered will be performed as well as the adoption of an adaptive scheme for the perturbation factor. Results are also compared with those obtained using an enhanced particle swarm optimization technique. (C) 2013 Elsevier Ltd. All rights reserved.

Supervisory control of a variable speed wind turbine with doubly fed induction generator

This paper is on an onshore variable speed wind turbine with doubly fed induction generator and under supervisory control. The control architecture is equipped with an event-based supervisor for the supervision level and fuzzy proportional integral or discrete adaptive linear quadratic as proposed controllers for the execution level. The supervisory control assesses the operational state of the variable speed wind turbine and sends the state to the execution level. Controllers operation are in the full load region to extract energy at full power from the wind while ensuring safety conditions required to inject the energy into the electric grid. A comparison between the simulations of the proposed controllers with the inclusion of the supervisory control on the variable speed wind turbine benchmark model is presented to assess advantages of these controls. (C) 2015 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).