When a DNA Triple helix melts: An analog of the Efimov state

The base sequences of DNA contain the genetic code and to decode it a double helical DNA has to open its base pairs. Recent studies have shown that one can use a third strand to identify the base sequences without opening the double helix but by forming a triple helix. It is predicted here that such a three chain system exhibits the unusual behaviour of the existence of a three chain bound state in the absence of any two being bound. This phenomenon is analogous to the Efimov state in three particle quantum mechanics. A scaling theory is used to justify the Efimov connection. Real space renormalization group (RG), and exact numerical calculations are used to validate the prediction of a biological Efimov effect.Comment: Replaced by the (almost) published version, except the word "curiouser

An efficient algorithm to perform local concerted movements of a chain molecule

The devising of efficient concerted rotation moves that modify only selected local portions of chain molecules is a long studied problem. Possible applications range from speeding the uncorrelated sampling of polymeric dense systems to loop reconstruction and structure refinement in protein modeling. Here, we propose and validate, on a few pedagogical examples, a novel numerical strategy that generalizes the notion of concerted rotation. The usage of the Denavit-Hartenberg parameters for chain description allows all possible choices for the subset of degrees of freedom to be modified in the move. They can be arbitrarily distributed along the chain and can be distanced between consecutive monomers as well. The efficiency of the methodology capitalizes on the inherent geometrical structure of the manifold defined by all chain configurations compatible with the fixed degrees of freedom. The chain portion to be moved is first opened along a direction chosen in the tangent space to the manifold, and then closed in the orthogonal space. As a consequence, in Monte Carlo simulations detailed balance is easily enforced without the need of using Jacobian reweighting. Moreover, the relative fluctuations of the degrees of freedom involved in the move can be easily tuned. We show different applications: the manifold of possible configurations is explored in a very efficient way for a protein fragment and for a cyclic molecule; the "local backbone volume", related to the volume spanned by the manifold, reproduces the mobility profile of all-α helical proteins; the refinement of small protein fragments with different secondary structures is addressed. The presented results suggest our methodology as a valuable exploration and sampling tool in the context of bio-molecular simulations

Continuum model for polymers with finite thickness

We consider the continuum limit of a recently-introduced model for discretized thick polymers, or tubes. We address both analytically and numerically how the polymer thickness influences the decay of tangent-tangent correlations and find how the persistence length scales with the thickness and the torsional rigidity of the tube centerline. At variance with the worm-like chain model, the phase diagram that we obtain for a continuous tube is richer; in particular, for a given polymer thickness there exists a threshold value for the centerline torsional rigidity separating a simple exponential decay of the tangent-tangent correlation from an oscillatory one.Comment: 8 pages, 4 figures. Accepted for publication in J. Phys.

Experience with the Platelia Candida ELISA for the diagnosis of invasive candidosis in neonatal patients

ABSTRACTThis preliminary study evaluated the use of the Platelia Candida antigen kit for the diagnosis of invasive candidosis in 70 of 184 pre-term infants admitted to a neonatal intensive care unit between March 2004 and March 2006. The frequency of confirmed candidaemia was 6.5%. The sensitivity and specificity of the assay were 94.4% and 94.2%, respectively, with a positive predictive value of 85% and a negative predictive value of 98%. These results suggest that the inclusion of regular serological surveillance for mannanaemia in some pre-term infants would complement blood cultures for the early detection of candidosis

The challenge of treatment in potential celiac disease

Potential celiac disease (PCD) is defined by the presence of positive serum antibodies, HLA-DQ2/DQ8 haplotypes, and a normal small intestinal mucosa (Marsh grade 0-1). This condition occurs in one-fifth of celiac disease (CD) patients and usually represents a clinical challenge. We reviewed genetic, histologic, and clinical features of this specific condition by performing a systematic search on MEDLINE, Embase, and Scholar database. Accordingly, we identified different genetic features in patients with PCD compared to the classical forms. Frequently, signs of inflammation (deposits of immunoglobulin A (IgA) and/or increased number of intraepithelial lymphocytes) can be clearly identify in the mucosa of PCD patients after an accurate histological assessment. Finally, the main challenge is represented by the treatment: the gluten-free diet should be considered only in the presence of gluten-dependent symptoms in both children and adults. What is known: (i) potential celiac disease (PCD) occurs in one-fifth of all celiac diseases (CD), and (ii) despite the absence of classical lesions, clear signs of inflammation are often detectable. What is new: (i) patients with PCD show different genetic features, and (ii) the presence of gluten-dependent symptoms is the main determinant to initiate the gluten-free diet, after a complete diagnostic work-up

Modeling the permeability evolution of microcracked rocks from elastic wave velocity inversion at elevated isostatic pressure

[1] A key consequence of the presence of microcracks within rock is their significant influence upon elastic anisotropy and transport properties. Here two rock types (a basalt and a granite) with contrasting microstructures, dominated by microcracks, have been investigated using an advanced experimental arrangement capable of measuring porosity, P wave velocity, S wave velocity, and permeability contemporaneously at effective pressures up to 100 MPa. Using the Kachanov (1994) noninteractive effective medium theory, the measured elastic wave velocities are inverted using a least squares fit, permitting the recovery of the evolution of crack density and aspect ratio with increasing isostatic pressure. Overall, the agreement between measured and predicted velocities is good, with average error less than 0.05 km/s. At larger scales and above the percolation threshold, macroscopic fluid flow also depends on the crack density and aspect ratio. Using the permeability model of Guéguen and Dienes (1989) and the crack density and aspect ratio recovered from the elastic wave velocity inversion, we successfully predict the evolution of permeability with pressure for direct comparison with the laboratory measurements. We also calculate the evolution of the crack porosity with increasing isostatic pressure, on the basis of the calculated crack density, and compare this directly with the experimentally measured porosity. These combined experimental and modeling results illustrate the importance of understanding the details of how rock microstructures change in response to an external stimulus when predicting the simultaneous evolution of rock physical properties

The tyrosine kinase receptor c-met, its cognate ligand HGF and the tyrosine kinase receptor trasducers STAT3, PI3K and RHO in thyroid nodules associated with Hashimoto's thyroiditis: an immunohisto-chemical characterization

Hepatocyte growth factor (HGF) exerts proliferative activities in thyrocytes upon binding to its tyrosine kinase receptor c-met and is also expressed in benign thyroid nodules as well as in Hashimoto's thyroiditis (HT)

Modeling the permeability evolution of microcracked rocks from elastic wave velocity inversion at elevated isostatic pressure

[1] A key consequence of the presence of microcracks within rock is their significant influence upon elastic anisotropy and transport properties. Here two rock types (a basalt and a granite) with contrasting microstructures, dominated by microcracks, have been investigated using an advanced experimental arrangement capable of measuring porosity, P wave velocity, S wave velocity, and permeability contemporaneously at effective pressures up to 100 MPa. Using the Kachanov (1994) noninteractive effective medium theory, the measured elastic wave velocities are inverted using a least squares fit, permitting the recovery of the evolution of crack density and aspect ratio with increasing isostatic pressure. Overall, the agreement between measured and predicted velocities is good, with average error less than 0.05 km/s. At larger scales and above the percolation threshold, macroscopic fluid flow also depends on the crack density and aspect ratio. Using the permeability model of Guéguen and Dienes (1989) and the crack density and aspect ratio recovered from the elastic wave velocity inversion, we successfully predict the evolution of permeability with pressure for direct comparison with the laboratory measurements. We also calculate the evolution of the crack porosity with increasing isostatic pressure, on the basis of the calculated crack density, and compare this directly with the experimentally measured porosity. These combined experimental and modeling results illustrate the importance of understanding the details of how rock microstructures change in response to an external stimulus when predicting the simultaneous evolution of rock physical properties

A numerical approach to copolymers at selective interfaces

We consider a model of a random copolymer at a selective interface which undergoes a localization/delocalization transition. In spite of the several rigorous results available for this model, the theoretical characterization of the phase transition has remained elusive and there is still no agreement about several important issues, for example the behavior of the polymer near the phase transition line. From a rigorous viewpoint non coinciding upper and lower bounds on the critical line are known. In this paper we combine numerical computations with rigorous arguments to get to a better understanding of the phase diagram. Our main results include: - Various numerical observations that suggest that the critical line lies strictly in between the two bounds. - A rigorous statistical test based on concentration inequalities and super-additivity, for determining whether a given point of the phase diagram is in the localized phase. This is applied in particular to show that, with a very low level of error, the lower bound does not coincide with the critical line. - An analysis of the precise asymptotic behavior of the partition function in the delocalized phase, with particular attention to the effect of rare atypical stretches in the disorder sequence and on whether or not in the delocalized regime the polymer path has a Brownian scaling. - A new proof of the lower bound on the critical line. This proof relies on a characterization of the localized regime which is more appealing for interpreting the numerical data.Comment: accepted for publication on J. Stat. Phy