Time filter

Source Type

Pairo E.,Institute of BioEngineering of Catalonia
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference | Year: 2011

MEET is an R package that integrates a set of algorithms for the detection of transcription factor binding sites (TFBS). The MEET R package includes five motif searching algorithms: MEME/MAST(Multiple Expectation-Maximization for Motif Elicitation), Q-residuals, MDscan (Motif Discovery scan), ITEME (Information Theory Elements for Motif Estimation) and MATCH. In addition MEET allows the user to work with different alignment algorithms: MUSCLE (Multiple Sequence Comparison by Log-Expectation), ClustalW and MEME. The package can work in two modes, training and detection. The training mode allows the user to choose the best parameters of a detector. Once the parameters are chosen, the detection mode allows to analyze a genome looking for binding sites. Both modes can combine the different alignment and detection methods, offering multiple possibilities. Combining the alignments and the detection algorithms makes possible the comparison between detection models at the same level, without having to care about the differences produced during the alignment process. The MEET R package can be downloaded from http://sisbio.recerca.upc.edu/R/MEET_1.0. tar.gz. Source

Perrault C.M.,McGill University | Perrault C.M.,Institute of BioEngineering of Catalonia | Qasaimeh M.A.,McGill University | Brastaviceanu T.,McGill University | And 3 more authors.
Review of Scientific Instruments | Year: 2010

The microfluidic probe (MFP) consists of a flat, blunt tip with two apertures for the injection and reaspiration of a microjet into a solution-thus hydrodynamically confining the microjet-and is operated atop an inverted microscope that enables live imaging. By scanning across a surface, the microjet can be used for surface processing with the capability of both depositing and removing material; as it operates under immersed conditions, sensitive biological materials and living cells can be processed. During scanning, the MFP is kept immobile and centered over the objective of the inverted microscope, a few micrometers above a substrate that is displaced by moving the microscope stage and that is flushed continuously with the microjet. For consistent and reproducible surface processing, the gap between the MFP and the substrate, the MFP's alignment, the scanning speed, the injection and aspiration flow rates, and the image capture need all to be controlled and synchronized. Here, we present an automated MFP station that integrates all of these functionalities and automates the key operational parameters. A custom software program is used to control an independent motorized Z stage for adjusting the gap, a motorized microscope stage for scanning the substrate, up to 16 syringe pumps for injecting and aspirating fluids, and an inverted fluorescence microscope equipped with a charge-coupled device camera. The parallelism between the MFP and the substrate is adjusted using manual goniometer at the beginning of the experiment. The alignment of the injection and aspiration apertures along the scanning axis is performed using a newly designed MFP screw holder. We illustrate the integrated MFP station by the programmed, automated patterning of fluorescently labeled biotin on a streptavidin-coated surface. © 2010 American Institute of Physics. Source

Salleras M.,University of California at Irvine | Carmona M.,University of Barcelona | Marco S.,University of Barcelona | Marco S.,Institute of BioEngineering of Catalonia
IEEE Transactions on Advanced Packaging | Year: 2010

An analysis of accuracy of time-constant spectrum extraction from thermal transients has been performed. Numerical calculations based on analytical models and finite element method simulations have been used in order to obtain the thermal transients. Simple geometries have been used such that analytical expressions for their time-constant spectrums are known. Results show that a large error in the time-constant spectrum is obtained for very small rms error (< 1 mK) in the thermal transient. The estimation problem is ill-conditioned. Moreover, the differential structure function shows a low accuracy identifying stacked structures. The initial part of the differential structure function shows numerical oscillations and the final part has an asymptotic behavior to infinity that has been identified as an artifact related to errors in the time-constant spectrum estimation. Peak identification from the differential structure function heavily depends on an accurate determination of the time-constant spectrum. The limited spectral resolution and dynamic range of the differential structure function are a direct consequence of the time-constant spectrum imprecision. © 2006 IEEE. Source

Perez-Balaguer A.,Hospital General Universitari dAlacant | Perez-Balaguer A.,Institute of BioEngineering of Catalonia | Ortiz-Martinez F.,Hospital General Universitari dAlacant | Garcia-Martinez A.,Hospital General Universitari dAlacant | And 4 more authors.
Breast Cancer Research and Treatment | Year: 2015

The FOXA family of transcription factors regulates chromatin structure and gene expression especially during embryonic development. In normal breast tissue FOXA1 acts throughout mammary development; whereas in breast carcinoma its expression promotes luminal phenotype and correlates with good prognosis. However, the role of FOXA2 has not been previously studied in breast cancer. Our purpose was to analyze the expression of FOXA2 in breast cancer cells, to explore its role in breast cancer stem cells, and to correlate its mRNA expression with clinicopathological features and outcome in a series of patients diagnosed with breast carcinoma. We analyzed FOXA2 mRNA expression in a retrospective cohort of 230 breast cancer patients and in cell lines. We also knocked down FOXA2 mRNA expression by siRNA to determine the impact on cell proliferation and mammospheres formation using a cancer stem cells culture assay. In vitro studies demonstrated higher FOXA2 mRNA expression in Triple-Negative/Basal-like cells. Further, when it was knocked down, cells decreased proliferation and its capability of forming mammospheres. Similarly, FOXA2 mRNA expression was detected in 10 % (23/230) of the tumors, especially in Triple-Negative/Basal-like phenotype (p < 0.001, Fisher’s test). Patients whose tumors expressed FOXA2 had increased relapses (59 vs. 79 %, p = 0.024, log-rank test) that revealed an independent prognostic value (HR = 3.29, C.I.95 % = 1.45–7.45, p = 0.004, Cox regression). Our results suggest that FOXA2 promotes cell proliferation, maintains cancer stem cells, favors the development of Triple-Negative/Basal-like tumors, and is associated with increase relapses. © 2015, Springer Science+Business Media New York. Source

Crassous J.J.,Lund University | Casal-Dujat L.,Lund University | Medebach M.,Lund University | Obiols-Rabasa M.,Lund University | And 8 more authors.
Langmuir | Year: 2013

We use a combination of different scattering techniques and rheology to highlight the link between structure and dynamics of dense aqueous suspensions of soft repulsive colloids in the vicinity of a glass transition. Three different latex formulations with an increasing amount of the hydrophilic component resulting in either purely electrostatically or electrosterically stabilized suspensions are investigated. From the analysis of the static structure factor measured by small-angle X-ray scattering, we derive an effective volume fraction that includes contributions from interparticle interactions. We further investigate the dynamics of the suspensions using 3D cross-correlation dynamic light scattering (3DDLS) and rheology. We analyze the data using an effective hard sphere model and in particular compare the linear viscoelasticity and flow behavior to the predictions of mode coupling theory, which accounts for a purely kinetic glass transition determined by the equilibrium structure factor. We demonstrate that seemingly very different colloidal systems exhibit the same generic behavior when the effects from interparticle interactions are incorporated using an effective volume fraction description. © 2013 American Chemical Society. Source

Discover hidden collaborations