Search results for "processing."
showing 10 items of 8323 documents
Imaging through scattering media by microstructured illumination
2016
We describe a method to image objects through scattering media based on microstructured illumination. A spatial light modulator is used to project a set of microstructured light patterns onto the sample. The image is retrieved computationally from the photocurrent fluctuations provided by a detector with no spatial structure. We review several optical setups developed in the last years with different illumination strategies and applied to different turbid media. In particular we introduce a new non-invasive optical system based on a reflection configuration. Our technique does not require coherent light, raster scanning, time-gated detection or a-priori calibration processes. Furthermore it…
Variance component analysis to assess protein quantification in biomarker discovery. Application to MALDI-TOF mass spectrometry.
2017
International audience; Controlling the technological variability on an analytical chain is critical for biomarker discovery. The sources of technological variability should be modeled, which calls for specific experimental design, signal processing, and statistical analysis. Furthermore, with unbalanced data, the various components of variability cannot be estimated with the sequential or adjusted sums of squares of usual software programs. We propose a novel approach to variance component analysis with application to the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) technology and use this approach for protein quantification by a classical signal processing algori…
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems
2016
This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of recordJorge González-Domínguez, Yongchao Liu, Juan Touriño, Bertil Schmidt; MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems, Bioinformatics, Volume 32, Issue 24, 15 December 2016, Pages 3826–3828, https://doi.org/10.1093/bioinformatics/btw558is available online at: https://doi.org/10.1093/bioinformatics/btw558 [Abstracts] MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-sca…
Towards Self-explanatory Ontology Visualization with Contextual Verbalization
2016
Ontologies are one of the core foundations of the Semantic Web. To participate in Semantic Web projects, domain experts need to be able to understand the ontologies involved. Visual notations can provide an overview of the ontology and help users to understand the connections among entities. However, the users first need to learn the visual notation before they can interpret it correctly. Controlled natural language representation would be readable right away and might be preferred in case of complex axioms, however, the structure of the ontology would remain less apparent. We propose to combine ontology visualizations with contextual ontology verbalizations of selected ontology (diagram) e…
Tandem affinity purification of histones, coupled to mass spectrometry, identifies associated proteins and new sites of post-translational modificati…
2015
Histones and their post-translational modifications contribute to regulating fundamental biological processes in all eukaryotic cells. We have applied a conventional tandem affinity purification strategy to histones H3 and H4 of the yeast Saccharomyces cerevisiae. Mass spectrometry analysis of the co-purified proteins revealed multiple associated proteins, including core histones, which indicates that tagged histones may be incorporated to the nucleosome particle. Among the many other co-isolated proteins there are histone chaperones, elements of chromatin remodeling, of nucleosome assembly/disassembly, and of histone modification complexes. The histone chaperone Rtt106p, two members of chr…
Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs
2017
Detecting higher-order epistatic interactions in Genome-Wide Association Studies (GWAS) remains a challenging task in the fields of genetic epidemiology and computer science. A number of algorithms have recently been proposed for epistasis discovery. However, they suffer from a high computational cost since statistical measures have to be evaluated for each possible combination of markers. Hence, many algorithms use additional filtering stages discarding potentially non-interacting markers in order to reduce the overall number of combinations to be examined. Among others, Mutual Information Clustering (MIC) is a common pre-processing filter for grouping markers into partitions using K-Means…
Characterisation of CDKL5 Transcript Isoforms in Human and Mouse.
2016
Mutations in the X-linked Cyclin-Dependent Kinase-Like 5 gene (CDKL5) cause early onset infantile spasms and subsequent severe developmental delay in affected children. Deleterious mutations have been reported to occur throughout the CDKL5 coding region. Several studies point to a complex CDKL5 gene structure in terms of exon usage and transcript expression. Improvements in molecular diagnosis and more extensive research into the neurobiology of CDKL5 and pathophysiology of CDKL5 disorders necessitate an updated analysis of the gene. In this study, we have analysed human and mouse CDKL5 transcript patterns both bioinformatically and experimentally. We have characterised the predominant brai…
Luminance Information Is Required for the Accurate Estimation of Contrast in Rapidly Changing Visual Contexts.
2020
Summary Visual perception scales with changes in the visual stimulus, or contrast, irrespective of background illumination. However, visual perception is challenged when adaptation is not fast enough to deal with sudden declines in overall illumination, for example, when gaze follows a moving object from bright sunlight into a shaded area. Here, we show that the visual system of the fly employs a solution by propagating a corrective luminance-sensitive signal. We use in vivo 2-photon imaging and behavioral analyses to demonstrate that distinct OFF-pathway inputs encode contrast and luminance. Predictions of contrast-sensitive neuronal responses show that contrast information alone cannot ex…
The impact of fermentation processes on the production, retention and bioavailability of carotenoids: An overview
2020
Abstract Background Carotenoids are isoprenoids compounds widely distributed in foods. A difference of carotenoids relative to other food bioactives is that some can be converted into compounds exhibiting vitamin A activity, which is essential for humans. Besides, they are more versatile as they are also natural pigments, antioxidants and can be involved in health-promoting actions. Lately, they are also attracting interest in relation to skin beauty. Their importance for different industry sector (foods, feeds, pharmaceutical, cosmetics) is therefore indisputable. Carotenoids can be obtained by different approaches including extraction from appropriate sources or synthesis. Scope and appro…
Primjena ekstrakta proteina sirutke u proizvodnji smrznutog mliječnog deserta
2018
The aim of this work was to substantiate the use of whey protein extract (WPE), a by-product of dairy industry, combined with different berry purees in the formulation of a whipped frozen dairy dessert (WFDD). After freezing, the swelling ability of WPE decreased significantly while at higher temperatures of the dispersion medium, the degree of swelling increased. A mixture containing 55±2 % WPE and 45±2 % milk presented a homogeneous consistency while the further processing did not improve the structure of the mixture. Final formulations of WFDD containing different berry purees (i.e. 10 % black¬currant puree, 25 % cherry puree, or 30 % strawberry puree) were proposed for which the nutriti…