Identification of possible differences in coding and non coding fragments of DNA sequences by using the method of the Recurrence Quantification Analysis

Starting with the results of Li et al. in 1992 there is valuable interest in finding long range correlations in DNA sequences since it raises questions about the role of introns and intron-containing genes. In the present paper we studied two sequences that are the human T-cell receptor alpha/delta locus, Gen-Bank name HUMTCRADCV, a noncoding chromosomal fragment of M = 97630 bases (composed of less than 10% of coding regions), and the Escherichia Coli K12, Gen-Bank name ECO110K, a genomic fragment with M = 111401 bases consisting of mostly coding regions and containing more that 80% of coding regions. We attributed the value (+1) to the purines and the value (-1) to the pirimidines and to such reconstructed random walk we applied the method of the Recurrence Quantification Analysis(RQA) that was introduced by Zbilut and Webber in 1994. By using dimension D=1 and Embedded Dimensions D=3 and D=5, we obtain some indicative results. Also by a simple eye examination of the reconstructed maps, the differences between coding and non coding regions are evident and impressive and consist in the presence in noncoding regions of long patches of the same colour that are absent in the coding sequence. At first sight this suggests a simple explanation to the concept of „long-range‟ correlation. On the quantitative plane, we used the %Rec., the %Det., the Ratio, the Entropy, the %Lam., and the Lmax that, as explained in detail in the text, represent the basic variables of RQA. The significant result that we have here is that both Lmax and Laminarity exhibit very large values in HUMTCRADCV and actually different in values respect to ECO110K where such variables assume more modest values. Therefore we suggest that there is the observed difference between HUMTCRADCV and ECO110K. The claimed higher long-range correlations of introns respect to exons from many authors may be explained here in reasonof such found higher values of Lmax and of Laminarity in HUMTCRADCV respect to ECO110K

Modeling invasion patterns in the glioblastoma battlefield

Glioblastoma is the most aggressive tumor of the central nervous system, due to its great infiltration capacity. Understanding the mechanisms that regulate the Glioblastoma invasion front is a major challenge with preeminent potential clinical relevances. In the infiltration front, the key features of tumor dynamics relate to biochemical and biomechanical aspects, which result in the extension of cellular protrusions known as tumor microtubes. The coordination of metalloproteases expression, extracellular matrix degradation, and integrin activity emerges as a leading mechanism that facilitates Glioblastoma expansion and infiltration in uncontaminated brain regions. We propose a novel multidisciplinary approach, based on in vivo experiments in Drosophila and mathematical models, that describes the dynamics of active and inactive integrins in relation to matrix metalloprotease concentration and tumor density at the Glioblastoma invasion front. The mathematical model is based on a non-linear system of evolution equations in which the mechanisms leading chemotaxis, haptotaxis, and front dynamics compete with the movement induced by the saturated flux in porous media. This approach is able to capture the relative influences of the involved agents and reproduce the formation of patterns, which drive tumor front evolution. These patterns have the value of providing biomarker information that is related to the direction of the dynamical evolution of the front and based on static measures of proteins in several tumor samples. Furthermore, we consider in our model biomechanical elements, like the tissue porosity, as indicators of the healthy tissue resistance to tumor progression

Chemo-enzymatic synthesis of new resveratrol-related dimers containing the benzo[b]furan framework and evaluation of their radical scavenger activities

The chemo-enzymatic synthesis and the evaluation of radical scavenger performance of resveratrolrelated dimers with antioxidative power have been investigated. The dimeric compounds, containing the benzo[b]furan framework, were prepared via an oxidative dimerization catalyzed by a laccase from Trametes versicolor, followed by a treatment with the organic oxidant DDQ. This methodology can be useful for the synthesis of various 2,3-diarylbenzo[b]furans derivates, a class of compound that exhibits a wide range of biological activities

Case Report: Generalized Mutual Information (GMI) Analysis of Sensory Motor Rhythm in a Subject Affected by Facioscapulohumeral Muscular Dystrophy after Ken Ware Treatment

In this case report we study the dynamics of the SMR band in a subject affected from Facioscapulohumeral Muscular Dystrophy and subjected to Ken Ware Neuro Physics treatment. We use the Generalized Mutual Information (GMI) to analyze in detail the SMR band at rest during the treatment. Brain dynamics responds to a chaotic-deterministic regime with a complex behaviour that constantly self-rearranges and self-organizes such dynamics in function of the outside requirements. We demonstrate that the SMR chaotic dynamics responds directly to such regime and that also decreasing in EEG during muscular activity really increases its ability of self-arrangement and self-organization in brain. The proposed novel method of the GMI is arranged by us so that it may be used in several cases of clinical interest. In the case of muscular dystrophy here examined, GMI enables us to quantify with accuracy the improvement that the subject realizes during such treatment

Laser tracker kinematic error model formulation and subsequent verification under real working conditions

A kinematic model of the Laser Tracker (LT) based on the Denavit-Hartenberg method has been developed. In this model, error matrices have been included with error parameters for linear and rotary joints. The calibration method is based on the measurement of a mesh of reflectors measured by a LT from different positions. Error parameters are calculated knowing that distances between every pair of reflectors is the same regardless the LT position. The absence of nominal data prevents us from knowing the calibration behaviour and its suitability. Although synthetic data tests show a good accuracy improvement, it is not possible to know if this will work with under real working conditions. An experiment has been made to check the calibration procedure. A set of 17 reflectors have been placed on a Coordinate Measuring Machine (CMM) and have been measured by a LT from 5 different positions. Reflector positions have also been measured with the CMM to calculate the initial errors. With LT measurements we calculate the error parameters. LT measurements are recalculated considering the kinematic error model and compared with the CMM measurements to get the residual error. Two errors have been calculated; distances error between reflectors and their position error compared with CMM data

Developing novel non-hydroxamate histone deacetylase inhibitors: the chelidamic warhead

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