Lengthscales and Cooperativity in DNA Bubble Formation

It appears that thermally activated DNA bubbles of different sizes play central roles in important genetic processes. Here we show that the probability for the formation of such bubbles is regulated by the number of soft AT pairs in specific regions with lengths which at physiological temperatures are of the order of (but not equal to) the size of the bubble. The analysis is based on the Peyrard- Bishop-Dauxois model, whose equilibrium statistical properties have been accurately calculated here with a transfer integral approach

Dynamic and Static Excitations of a Classical Discrete Anisotropic Heisenberg Ferromagnetic Spin Chain

Using Jacobi elliptic function addition formulas and summation identities we obtain several static and moving periodic soliton solutions of a classical anisotropic, discrete Heisenberg spin chain with and without an external magnetic field. We predict the dispersion relations of these nonlinear excitations and contrast them with that of magnons and relate these findings to the materials realized by a discrete spin chain. As limiting cases, we discuss different forms of domain wall structures and their properties.Comment: Accepted for publication in Physica

Bubbles and denaturation in DNA

The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without the unwinding of the DNA double helix. Although these biological processes are driven by proteins, there might well be a relation between these biological openings and the spontaneous bubble formation due to thermal fluctuations. Mesoscopic models, like the Peyrard-Bishop-Dauxois model, have fairly accurately reproduced some experimental denaturation curves and the sharp phase transition in the thermodynamic limit. It is, hence, tempting to see whether these models could be used to predict the biological activity of DNA. In a previous study, we introduced a method that allows to obtain very accurate results on this subject, which showed that some previous claims in this direction, based on molecular dynamics studies, were premature. This could either imply that the present PBD should be improved or that biological activity can only be predicted in a more complex frame work that involves interactions with proteins and super helical stresses. In this article, we give detailed description of the statistical method introduced before. Moreover, for several DNA sequences, we give a thorough analysis of the bubble-statistics as function of position and bubble size and the so-called $l$-denaturation curves that can be measured experimentally. These show that some important experimental observations are missing in the present model. We discuss how the present model could be improved.Comment: 15 pages, 5 figures, published as Eur. Phys. J. E 20 : 421-434 AUG 200

Modulational and Parametric Instabilities of the Discrete Nonlinear Schr\"odinger Equation

We examine the modulational and parametric instabilities arising in a non-autonomous, discrete nonlinear Schr{\"o}dinger equation setting. The principal motivation for our study stems from the dynamics of Bose-Einstein condensates trapped in a deep optical lattice. We find that under periodic variations of the heights of the interwell barriers (or equivalently of the scattering length), additionally to the modulational instability, a window of parametric instability becomes available to the system. We explore this instability through multiple-scale analysis and identify it numerically. Its principal dynamical characteristic is that, typically, it develops over much larger times than the modulational instability, a feature that is qualitatively justified by comparison of the corresponding instability growth rates

45,X/46,XY Mosaicism Presenting With Isolated Unilateral Cryptorchidism and a Normal Blood Karyotype

Context: 45,X/46,XY mosaicism is a disorder of sex development leading to abnormal gonadal development and to unpredictable genital phenotype, growth, and pubertal development. / Case Description: A 2-year-old male presented with a right impalpable testis. Blood karyotype was 46,XY. A laparoscopy performed for right orchidopexy revealed a right streak gonad with Mullerian structures, whereas on the left side, a normal descended testis was present. The karyotype of the removed gonad was 45,X/46,XY. The child grew along the second centile, within the midparental height (MPH) range, until the time of puberty, when linear growth worsened due to a lack of a pubertal growth spurt, and growth hormone (GH) therapy was initiated. He developed spontaneous puberty (13 years of age) and showed normal pubertal progression. However, from the age of 15 years, he had low normal testosterone, raised follicle-stimulating hormone, and reduction of inhibin B, possibly suggestive of declining testicular function. His final height was −2.24 standard deviation score (SDS) (−2.4 SDS at GH start; MPH −1.6 SDS). / Conclusions: Our case describes a mild male phenotype associated with 45,X/46,XY mosaicism characterized by unilateral cryptorchidism, spontaneous onset of puberty, and normal blood karyotype. The case illustrates the difficulties inherent in making a diagnosis of 45,X/46,XY mosaicism when there is no genital ambiguity and makes the point that growth and testicular impairment may occur, mostly manifesting during adolescence. An early diagnosis is crucial to initiate careful monitoring for growth and pubertal disorders, increased tumor risk, and fertility issues commonly seen in these children

Pattern Forming Dynamical Instabilities of Bose-Einstein Condensates: A Short Review

In this short topical review, we revisit a number of works on the pattern-forming dynamical instabilities of Bose-Einstein condensates in one- and two-dimensional settings. In particular, we illustrate the trapping conditions that allow the reduction of the three-dimensional, mean field description of the condensates (through the Gross-Pitaevskii equation) to such lower dimensional settings, as well as to lattice settings. We then go on to study the modulational instability in one dimension and the snaking/transverse instability in two dimensions as typical examples of long-wavelength perturbations that can destabilize the condensates and lead to the formation of patterns of coherent structures in them. Trains of solitons in one-dimension and vortex arrays in two-dimensions are prototypical examples of the resulting nonlinear waveforms, upon which we briefly touch at the end of this review.Comment: 28 pages, 9 figures, publishe

Epidemiology of interstitial lung diseases in Greece

SummaryIntroductionFew data are available on the epidemiology of interstitial lung diseases (ILDs), especially after the current classification of idiopathic interstitial pneumonias. The aim of this study is to provide data on the epidemiology of ILDs in Greece, under the ATS/ERS international consensus.MethodsDepartments of Pneumonology were contacted and asked to complete a questionnaire for every case of ILD that was alive on 2004 as well as for every new case from 1st January 2004 to 31st December 2004. Questions on the patients' demographic data, the exact diagnosis and the procedures used to establish the diagnosis were included. Centers covering about 60% of the Greek population have been analyzed.ResultsA total of 967 cases have been registered. The estimated prevalence of ILDs is 17.3 cases per 100,000 inhabitants. The estimated annual incidence of ILDs is 4.63 new cases per 100,000 inhabitants. The most frequent disease is sarcoidosis (34.1%), followed in decreasing order by idiopathic pulmonary fibrosis (19.5%), ILD associated with collagen vascular diseases (12.4%), cryptogenic organizing pneumonia (5.3%), histiocytosis (3.8%), and hypersensitivity pneumonitis (2.6%). Unclassified ILD or not otherwise specified accounted for the 8.5% of prevalent cases.ConclusionsThese data suggest that sarcoidosis and idiopathic pulmonary fibrosis are the most frequent ILDs in our population. In comparison with the few previous reports, interesting dissimilarities have been observed

The role of mobility in the dynamics of the COVID-19 epidemic in Andalusia

Metapopulation models have been a popular tool for the study of epidemic spread over a network of highly populated nodes (cities, provinces, countries) and have been extensively used in the context of the ongoing COVID-19 pandemic. In the present work, we revisit such a model, bearing a particular case example in mind, namely that of the region of Andalusia in Spain during the period of the summer-fall of 2020 (i.e., between the first and second pandemic waves). Our aim is to consider the possibility of incorporation of mobility across the province nodes focusing on mobile-phone time dependent data, but also discussing the comparison for our case example with a gravity model, as well as with the dynamics in the absence of mobility. Our main finding is that mobility is key towards a quantitative understanding of the emergence of the second wave of the pandemic and that the most accurate way to capture it involves dynamic (rather than static) inclusion of time-dependent mobility matrices based on cell-phone data. Alternatives bearing no mobility are unable to capture the trends revealed by the data in the context of the metapopulation model considered herein