Aspects of Discrete Breathers and New Directions

We describe results concerning the existence proofs of Discrete Breathers (DBs) in the two classes of dynamical systems with optical linear phonons and with acoustic linear phonons. A standard approach is by continuation of DBs from an anticontinuous limit. A new approach, which is purely variational, is presented. We also review some numerical results on intraband DBs in random nonlinear systems. Some non-conventional physical applications of DBs are suggested. One of them is understanding slow relaxation properties of glassy materials. Another one concerns energy focusing and transport in biomolecules by targeted energy transfer of DBs. A similar theory could be used for describing targeted charge transfer of nonlinear electrons (polarons) and, more generally, for targeted transfer of several excitations (e.g. Davydov soliton).Comment: to appear in the Proceedings of NATO Advanced Research Workshop "Nonlinearity and Disorder: Theory and Applications", Tashkent,Uzbekistan,October 1-6, 200

Five mucosal transcripts of interest in ulcerative colitis identified by quantitative real-time PCR: a prospective study

<p>Abstract</p> <p>Background</p> <p>The cause and pathophysiology of ulcerative colitis are both mainly unknown. We have previously used whole-genome microarray technique on biopsies obtained from patients with ulcerative colitis to identifiy 5 changed mucosal transcripts. The aim of this study was to compare mucosal expressions of these five transcripts in ulcerative colitis patients vs. controls, along with the transcript expression in relation to the clinical ulcerative colitis status.</p> <p>Methods</p> <p>Colonic mucosal specimens from rectum and caecum were taken at ambulatory colonoscopy from ulcerative colitis patients (<it>n </it>= 49) with defined inflammatory activity and disease extension, and from controls (<it>n </it>= 67) without inflammatory bowel disease. The five mucosal transcripts aldolase B, elafin, MST-1, simNIPhom and SLC6A14 were analyzed using quantitative real-time PCR.</p> <p>Results</p> <p>Significant transcript differences in the rectal mucosa for all five transcripts were demonstrated in ulcerative colitis patients compared to controls. The grade of transcript expression was related to the clinical disease activity.</p> <p>Conclusion</p> <p>The five gene transcripts were changed in patients with ulcerative colitis, and were related to the disease activity. The known biological function of some of the transcripts may contribute to the inflammatory features and indicate a possible role of microbes in ulcerative colitis. The findings may also contribute to our pathophysiological understanding of ulcerative colitis.</p

Rate theory of acceleration of the defect annealing driven by discrete breathers

Novel mechanisms of defect annealing in solids are discussed, which are based on the large amplitude anharmonic lattice vibrations, a.k.a. intrinsic localized modes or discrete breathers (DBs). A model for amplification of defect annealing rate in Ge by low energy plasma-generated DBs is proposed, in which, based on recent atomistic modelling, it is assumed that DBs can excite atoms around defects rather strongly, giving them energy $\gg k_BT$ for $\sim$100 oscillation periods. This is shown to result in the amplification of the annealing rates proportional to the DB flux, i.e. to the flux of ions (or energetic atoms) impinging at the Ge surface from inductively coupled plasma (ICP)Comment: 18 pages, 11 figures. arXiv admin note: text overlap with arXiv:1406.394

Discrete breathers in ϕ4\phi^4 and related models

We touch upon the wide topic of discrete breather formation with a special emphasis on the the $\phi^4$ model. We start by introducing the model and discussing some of the application areas/motivational aspects of exploring time periodic, spatially localized structures, such as the discrete breathers. Our main emphasis is on the existence, and especially on the stability features of such solutions. We explore their spectral stability numerically, as well as in special limits (such as the vicinity of the so-called anti-continuum limit of vanishing coupling) analytically. We also provide and explore a simple, yet powerful stability criterion involving the sign of the derivative of the energy vs. frequency dependence of such solutions. We then turn our attention to nonlinear stability, bringing forth the importance of a topological notion, namely the Krein signature. Furthermore, we briefly touch upon linearly and nonlinearly unstable dynamics of such states. Some special aspects/extensions of such structures are only touched upon, including moving breathers and dissipative variations of the model and some possibilities for future work are highlighted

Quantum dynamics in strong fluctuating fields

A large number of multifaceted quantum transport processes in molecular systems and physical nanosystems can be treated in terms of quantum relaxation processes which couple to one or several fluctuating environments. A thermal equilibrium environment can conveniently be modelled by a thermal bath of harmonic oscillators. An archetype situation provides a two-state dissipative quantum dynamics, commonly known under the label of a spin-boson dynamics. An interesting and nontrivial physical situation emerges, however, when the quantum dynamics evolves far away from thermal equilibrium. This occurs, for example, when a charge transferring medium possesses nonequilibrium degrees of freedom, or when a strong time-dependent control field is applied externally. Accordingly, certain parameters of underlying quantum subsystem acquire stochastic character. Herein, we review the general theoretical framework which is based on the method of projector operators, yielding the quantum master equations for systems that are exposed to strong external fields. This allows one to investigate on a common basis the influence of nonequilibrium fluctuations and periodic electrical fields on quantum transport processes. Most importantly, such strong fluctuating fields induce a whole variety of nonlinear and nonequilibrium phenomena. A characteristic feature of such dynamics is the absence of thermal (quantum) detailed balance.Comment: review article, Advances in Physics (2005), in pres

Wig-1, a novel regulator of N-Myc mRNA and N-Myc-driven tumor growth

Wig-1 is a transcriptional target of the p53 tumor suppressor and encodes an mRNA stability-regulating protein. We show here that Wig-1 knockdown causes a dramatic inhibition of N-Myc expression and triggers differentiation in neuroblastoma cells carrying amplified N-Myc. Transient Wig-1 knockdown significantly delays development of N-Myc-driven tumors in mice. We also show that N-Myc expression is induced upon moderate p53-activating stress, suggesting a role of the p53-Wig-1-N-Myc axis in promoting cell cycle re-entry upon p53-induced cell cycle arrest and DNA repair. Moreover, our findings raise possibilities for the improved treatment of poor prognosis neuroblastomas that carry amplified N-Myc

Central nervous system rather than immune cell-derived BDNF mediates axonal protective effects early in autoimmune demyelination

Brain-derived neurotrophic factor (BDNF) is involved in neuronal and glial development and survival. While neurons and astrocytes are its main cellular source in the central nervous system (CNS), bioactive BDNF is also expressed in immune cells and in lesions of multiple sclerosis and its animal model experimental autoimmune encephalomyelitis (EAE). Previous data revealed that BDNF exerts neuroprotective effects in myelin oligodendrocyte glycoprotein-induced EAE. Using a conditional knock-out model with inducible deletion of BDNF, we here show that clinical symptoms and structural damage are increased when BDNF is absent during the initiation phase of clinical EAE. In contrast, deletion of BDNF later in the disease course of EAE did not result in significant changes, either in the disease course or in axonal integrity. Bone marrow chimeras revealed that the deletion of BDNF in the CNS alone, with no deletion of BDNF in the infiltrating immune cells, was sufficient for the observed effects. Finally, the therapeutic effect of glatiramer acetate, a well-characterized disease-modifying drug with the potential to modulate BDNF expression, was partially reversed in mice in which BDNF was deleted shortly before the onset of disease. In summary, our data argue for an early window of therapeutic opportunity where modulation of BDNF may exert neuroprotective effects in experimental autoimmune demyelination

The Adjuvanticity of an O. volvulus-Derived rOv-ASP-1 Protein in Mice Using Sequential Vaccinations and in Non-Human Primates

Adjuvants potentiate antigen-specific protective immune responses and can be key elements promoting vaccine effectiveness. We previously reported that the Onchocerca volvulus recombinant protein rOv-ASP-1 can induce activation and maturation of naïve human DCs and therefore could be used as an innate adjuvant to promote balanced Th1 and Th2 responses to bystander vaccine antigens in mice. With a few vaccine antigens, it also promoted a Th1-biased response based on pronounced induction of Th1-associated IgG2a and IgG2b antibody responses and the upregulated production of Th1 cytokines, including IL-2, IFN-γ, TNF-α and IL-6. However, because it is a protein, the rOv-ASP-1 adjuvant may also induce anti-self-antibodies. Therefore, it was important to verify that the host responses to self will not affect the adjuvanticity of rOv-ASP-1 when it is used in subsequent vaccinations with the same or different vaccine antigens. In this study, we have established rOv-ASP-1's adjuvanticity in mice during the course of two sequential vaccinations using two vaccine model systems: the receptor-binding domain (RBD) of SARS-CoV spike protein and a commercial influenza virus hemagglutinin (HA) vaccine comprised of three virus strains. Moreover, the adjuvanticity of rOv-ASP-1 was retained with an efficacy similar to that obtained when it was used for a first vaccination, even though a high level of anti-rOv-ASP-1 antibodies was present in the sera of mice before the administration of the second vaccine. To further demonstrate its utility as an adjuvant for human use, we also immunized non-human primates (NHPs) with RBD plus rOv-ASP-1 and showed that rOv-ASP-1 could induce high titres of functional and protective anti-RBD antibody responses in NHPs. Notably, the rOv-ASP-1 adjuvant did not induce high titer antibodies against self in NHPs. Thus, the present study provided a sound scientific foundation for future strategies in the development of this novel protein adjuvant

Automated Discovery of Food Webs from Ecological Data Using Logic-Based Machine Learning

Networks of trophic links (food webs) are used to describe and understand mechanistic routes for translocation of energy (biomass) between species. However, a relatively low proportion of ecosystems have been studied using food web approaches due to difficulties in making observations on large numbers of species. In this paper we demonstrate that Machine Learning of food webs, using a logic-based approach called A/ILP, can generate plausible and testable food webs from field sample data. Our example data come from a national-scale Vortis suction sampling of invertebrates from arable fields in Great Britain. We found that 45 invertebrate species or taxa, representing approximately 25% of the sample and about 74% of the invertebrate individuals included in the learning, were hypothesized to be linked. As might be expected, detritivore Collembola were consistently the most important prey. Generalist and omnivorous carabid beetles were hypothesized to be the dominant predators of the system. We were, however, surprised by the importance of carabid larvae suggested by the machine learning as predators of a wide variety of prey. High probability links were hypothesized for widespread, potentially destabilizing, intra-guild predation; predictions that could be experimentally tested. Many of the high probability links in the model have already been observed or suggested for this system, supporting our contention that A/ILP learning can produce plausible food webs from sample data, independent of our preconceptions about “who eats whom.” Well-characterised links in the literature correspond with links ascribed with high probability through A/ILP. We believe that this very general Machine Learning approach has great power and could be used to extend and test our current theories of agricultural ecosystem dynamics and function. In particular, we believe it could be used to support the development of a wider theory of ecosystem responses to environmental change