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Analisi di dati di espressione di microRNA e mRNA ottenute da cellule staminali ematopoietiche e loro progenie sia in topi wt che mutanti
No full textTesto in fase di caricamento.Completato€ 2.00
Inferring Gene Networks from gene-expression data
No full textCollana seminari interni 2012, Number 20120502.The network representation of cellular regulatory systems allows for application of mathematical tools to gain insights into the fundamental organisation of living entities. Gene Networks (GNs) are abstract models of gene communication with nodes representing the gene activities (gene expression levels, mRNA concentrations), and directed edges representing causal influences. Many techniques for constructing GNs from gene expression data have been proposed and the most popular techniques are based on ordinary differential equations or Bayesian networks. In this seminar, the general problem of reverse-engineering gene networks will be outlined, the report on latest advances in this area and comments on further directions to pursue will be explained
Fast and Robust Techniques for 3D/2D Registration and Blending of Photographs on Massive Point Clouds
No full textCollana seminari interni 2012, Number 20120314.We present a simple, fast and robust technique for semi-automatic 2D-3D registration capable to align a large set of unordered images to a massive point cloud with minimal human effort. Our method converts the hard to solve image-to-geometry registration problem in a Structure-from-Motion (SfM) plus a 3D-3D registration problem. We exploit a SfM framework that, starting just from the unordered image collection, computes an estimate of camera parameters and a sparse 3D geometry deriving from matched image features. We then coarsely register this model to the given 3D geometry by estimating a global scale and absolute orientation using minimal manual intervention. A specialized sparse bundle adjustment (SBA) step, exploiting the correspondence between the model deriving from image features and the fine input 3D geometry, is then used to refine intrinsic and extrinsic parameters of each camera. Output data is suitable for photo blending frameworks to produce seamless colored models. In this sense, we also present an efficient scalable streaming technique for mapping highly detailed color information on extremely dense point clouds. It does not require meshing or extensive processing of the input model, works on a coarsely spatially-reordered point stream and can adaptively refine point cloud geometry on the basis of image content. Seamless multi-band image blending is obtained by using GPU accelerated screenspace operators, which solve point set visibility, compute a per-pixel view-dependent weight and ensure a smooth weighting function over each input image. The proposed approach works independently on each image in a memory coherent manner, and can be easily extended to include further image quality estimators. The effectiveness of the method is demonstrated on a series of real-world Cultural Heritage datasets
Big Data processing with Hadoop
Full text linkCollana seminari interni 2012, Number 20120418.In this seminar, we explore the Hadoop MapReduce framework and its use to solve certain types of Big Data problems. These problems, characterized by their large data set sizes, are becoming more commonplace as data acquisition rates increase in many fields of study and business, luring people by the prospects of increased analysis sensitivity. However, by definition Big Data problems are not tractable when using commonly available software and computing systems, such as the desktop workstation. As a result, they require specialized solutions that are designed to handle large quantities of data and scale across large, possibly cheap, computing infrastructure. Hadoop provides relatively low cost access to such solutions by implementing distributed computation and robustness as integral features that, therefore, do not have to be reimplemented by the application developer. Moreover, in addition to its native Java API, it also provides a high-level Python API developed right here at CRS4. As a concrete example of a Big Data solution, we briefly look at the Seal suite of distributed tools for processing high-throughput DNA sequencing data, currently used by the CRS4 Sequencing and Genotyping Platform. Finally, we discuss how Hadoop may be applied to your own Big Data problems
Oral contraceptives modify DNA methylation and monocyte-derived macrophage function
Full text linkBackground: Fertile women may be encouraged to use contraception during clinical trials to avoid potential drug effects on fetuses. However, hormonal contraception interferes with pharmacokinetics and pharmacodynamics and modifies internal milieus. Macrophages depend on the milieu to which they are exposed. Therefore, we assessed whether macrophage function would be affected by the use of combined oral contraceptives (OCs) and if this influence depended on the androgenic or non-androgenic properties of progestin.
Methods: Healthy adult women were enrolled and stratified into two groups: women who did not use OCs (Fs) and women treated with OCs (FOCs). FOCs were further stratified as a function of androgenic (FOCA+) and non-androgenic (FOCA-) properties of progestins. Routine hematological, biochemical, inflammatory and endothelial dysfunction parameters were measured. Monocyte-derived macrophages (MDMs) were evaluated for the expression and activity of estrogen receptors and androgen receptors, and release of tumor necrosis factor α (TNFα) was measured from unstimulated and lipopolysaccharide-stimulated cells.
Results: As is already known, the use of OCs changed numerous parameters: the number of lymphocytes, iron levels, total iron-binding capacity of transferrin, triglycerides, high-density lipoprotein, total cholesterol, and C-reactive protein increased, while prothrombin time and alkaline phosphatase decreased. Hormonal levels also varied: cortisol was higher in FOCs, while luteinizing hormone, follicle-stimulating hormone, and testosterone were lower in FOCs. Asymmetric dimethylarginine, an index of endothelial function, was lower in FOC than in Fs, as were cysteine and bilirubin. The androgenic properties of progestins affected the activity of OCs: in particular, white blood cell count, hemoglobin, high-density lipoprotein and calcium were higher in FOCA- than in FOCA+, whereas percentage oxygen saturation and γ-glutamyl transpeptidase were lower in FOCA- than in FOCA+. Importantly, FOCs had a lower global DNA methylation, indicating that OC may have epigenetic effects on gene expression. OC did not modify the expression of androgen receptor but increased estrogen receptor α expression, more considerably in FOCA+, and decreased estrogen receptor β, more considerably in FOCA-. Importantly, the activation state of estrogen receptor β in FOCs was decreased, while estrogen receptor α was not active in either Fs or FOCs. Unstimulated MDMs obtained from FOCs showed higher release of TNFα in comparison with Fs. After lipopolysaccharide stimulation, the release of TNFα was significantly higher in Fs than in FOCs.
Conclusions: OC use induced many changes in hematological and plasmatic markers, modifying hormonal levels, endothelial function, inflammation index and some redox state parameters, producing a perturbation of the internal milieu that impacted macrophagic function. In fact, different levels of estrogen receptor expression and release of TNFα were observed in macrophages derived from OC users. Some of the above activities were linked to the androgenic properties of progestin. Even though it is not known whether these effects are reversible, the results indicate that to avoid potential skewing of results only a single type of OC should be used during a single clinical trial.Pubblicat
Creazione di un servizio di Bioinformatica e analisi dati per IZS
No full textTesto in fase di caricamento.Completato€ 10.00
Consultation and modelling/simulation of crystal of hydrogenated castor oil with and without modifiers
No full textTesto in fase di caricamento.Completato€ 21.00
Re-meshing strategies in CFD simulations of moving meshes
Full text linkMisc - august 2012.The presence of moving meshes when motions of fluids and solids are being simulated requires a good control of the cells topological deformations. The work done in getting the control of the mesh morphing techniques in Computational Fluid Dynamics (CFD) applications of fluid-structure interactions and rigid bodies motions is here presented. The effects of imposed rigid body motions on a fluid mesh surrounding a solid body are analysed and strategies for maintaining a reasonable quality mesh during its deformation are investigated and developed. Java programming is employed in order to automate the process of re-meshing when the mesh deformation is dangerously close to the degeneration
RATMAN RER 3D
No full textIl progetto ha come scopo l'estensione del framework del CRS4 (Visual
Computing) per lo streaming e la visualizzazione di terreni. Il sistema
rappresenta il core del framework di geoviewing regionale e, nel contesto di
questo progetto, viene trasferito alla regione Emilia-Romagna.Completato€ 125.00