Anomalous self-diffusion in the ferromagnetic Ising chain with Kawasaki dynamics

We investigate the motion of a tagged spin in a ferromagnetic Ising chain evolving under Kawasaki dynamics. At equilibrium, the displacement is Gaussian, with a variance growing as $A t^{1/2}$. The temperature dependence of the prefactor $A$ is derived exactly. At low temperature, where the static correlation length $\xi$ is large, the mean square displacement grows as $(t/\xi^2)^{2/3}$ in the coarsening regime, i.e., as a finite fraction of the mean square domain length. The case of totally asymmetric dynamics, where $(+)$ (resp. $(-)$) spins move only to the right (resp. to the left), is also considered. In the steady state, the displacement variance grows as $B t^{2/3}$. The temperature dependence of the prefactor $B$ is derived exactly, using the Kardar-Parisi-Zhang theory. At low temperature, the displacement variance grows as $t/\xi^2$ in the coarsening regime, again proportionally to the mean square domain length.Comment: 22 pages, 8 figures. A few minor changes and update

Berry phase, hyperorbits, and the Hofstadter spectrum: semiclassical dynamics in magnetic Bloch bands

We have derived a new set of semiclassical equations for electrons in magnetic Bloch bands. The velocity and energy of magnetic Bloch electrons are found to be modified by the Berry phase and magnetization. This semiclassical approach is used to study general electron transport in a DC or AC electric field. We also find a close connection between the cyclotron orbits in magnetic Bloch bands and the energy subbands in the Hofstadter spectrum. Based on this formalism, the pattern of band splitting, the distribution of Hall conduct- ivities, and the positions of energy subbands in the Hofstadter spectrum can be understood in a simple and unified picture.Comment: 26 pages, Revtex, 6 figures included, submitted to Phys.Rev.

Impact-based forecasting in South East Asia – what underlies impact perceptions?

The move towards impact-based forecasting presents a challenge for forecasters, who must combine information not just on what the weather might be, but also on what the weather might do. Yet different hazards and impacts are qualitatively distinct, meaning such information cannot be easily or straightforwardly integrated. The present study aimed to provide a way of characterising seemingly disparate impacts. In a collaboration between UK psychologists and partners from three meteorological organisations in Indonesia, Malaysia and the Philippines, the psychometric paradigm was employed to investigate how forecasters and stakeholders perceive weather-related impacts. Participants provided ratings of nine categories of impacts on a total of 10 characteristics, as well as providing an overall impact severity rating. Principal components analysis revealed differing component solutions across countries, which explained around 75% of the variance in perceptions. There were some similarities across all countries, with the characteristics ‘worry’ and ‘destructiveness’ loading positively together, as well as ‘likelihood of harm’ and ‘seriousness of harm’. We did not find strong evidence to indicate that forecasters and stakeholders perceive impacts in different ways. Our results highlight the complex nature of impact perceptions, which are characterised not just by objective factors such as impact scope and duration, but also subjective factors, such as worry and perceived severity

The Diffusion Region in Collisionless Magnetic Reconnection

A review of present understanding of the dissipation region in magnetic reconnection is presented. The review focuses on results of the thermal inertia-based dissipation mechanism but alternative mechanisms are mentioned as well. For the former process, a combination of analytical theory and numerical modeling is presented. Furthermore, a new relation between the electric field expressions for anti-parallel and guide field reconnection is developed

Riboflavin/UVA Collagen Cross-Linking-Induced Changes in Normal and Keratoconus Corneal Stroma

Purpose To determine the effect of Ultraviolet-A collagen cross-linking with hypo-osmolar and iso-osmolar riboflavin solutions on stromal collagen ultrastructure in normal and keratoconus ex vivo human corneas. Methods Using small-angle X-ray scattering, measurements of collagen D-periodicity, fibril diameter and interfibrillar spacing were made at 1 mm intervals across six normal post-mortem corneas (two above physiological hydration (swollen) and four below (unswollen)) and two post-transplant keratoconus corneal buttons (one swollen; one unswollen), before and after hypo-osmolar cross-linking. The same parameters were measured in three other unswollen normal corneas before and after iso-osmolar cross-linking and in three pairs of swollen normal corneas, in which only the left was cross-linked (with iso-osmolar riboflavin). Results Hypo-osmolar cross-linking resulted in an increase in corneal hydration in all corneas. In the keratoconus corneas and unswollen normal corneas, this was accompanied by an increase in collagen interfibrillar spacing (p<0.001); an increase in fibril diameter was also seen in two out of four unswollen normal corneas and one unswollen keratoconus cornea (p<0.001). Iso-osmolar cross-linking resulted in a decrease in tissue hydration in the swollen normal corneas only. Although there was no consistent treatment-induced change in hydration in the unswollen normal samples, iso-osmolar cross-linking of these corneas did result in a compaction of collagen fibrils and a reduced fibril diameter (p<0.001); these changes were not seen in the swollen normal corneas. Collagen D-periodicity was not affected by either treatment. Conclusion The observed structural changes following Ultraviolet-A cross-linking with hypo-osmolar or iso-osmolar riboflavin solutions are more likely a consequence of treatment-induced changes in tissue hydration rather than cross-linking

A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval

Characterizing the DNA-binding specificities of transcription factors is a key problem in computational biology that has been addressed by multiple algorithms. These usually take as input sequences that are putatively bound by the same factor and output one or more DNA motifs. A common practice is to apply several such algorithms simultaneously to improve coverage at the price of redundancy. In interpreting such results, two tasks are crucial: clustering of redundant motifs, and attributing the motifs to transcription factors by retrieval of similar motifs from previously characterized motif libraries. Both tasks inherently involve motif comparison. Here we present a novel method for comparing and merging motifs, based on Bayesian probabilistic principles. This method takes into account both the similarity in positional nucleotide distributions of the two motifs and their dissimilarity to the background distribution. We demonstrate the use of the new comparison method as a basis for motif clustering and retrieval procedures, and compare it to several commonly used alternatives. Our results show that the new method outperforms other available methods in accuracy and sensitivity. We incorporated the resulting motif clustering and retrieval procedures in a large-scale automated pipeline for analyzing DNA motifs. This pipeline integrates the results of various DNA motif discovery algorithms and automatically merges redundant motifs from multiple training sets into a coherent annotated library of motifs. Application of this pipeline to recent genome-wide transcription factor location data in S. cerevisiae successfully identified DNA motifs in a manner that is as good as semi-automated analysis reported in the literature. Moreover, we show how this analysis elucidates the mechanisms of condition-specific preferences of transcription factors

How might acupuncture work? A systematic review of physiologic rationales from clinical trials

BACKGROUND: Scientific interest in acupuncture has led numerous investigators to conduct clinical trials to test the efficacy of acupuncture for various conditions, but the mechanisms underlying acupuncture are poorly understood. METHODS: The author conducted a PubMed search to obtain a fair sample of acupuncture clinical trials published in English in 2005. Each article was reviewed for a physiologic rationale, as well as study objectives and outcomes, experimental and control interventions, country of origin, funding sources and journal type. RESULTS: Seventy-nine acupuncture clinical trials were identified. Twenty-six studies (33%) offered no physiologic rationale. Fifty-three studies (67%) posited a physiologic basis for acupuncture: 33 (62% of 53) proposed neurochemical mechanisms, 2 (4%) segmental nervous system effects, 6 (11%) autonomic nervous system regulation, 3 (6%) local effects, 5 (9%) effects on brain function and 5 (9%) other effects. No rationale was proposed for stroke; otherwise having a rationale was not associated with objective, positive or negative findings, means of intervention, country of origin, funding source or journal type. The dominant explanation for how acupuncture might work involves neurochemical responses and is not reported to be dependent on treatment objective, specific points, means or method of stimulation. CONCLUSION: Many acupuncture trials fail to offer a meaningful rationale, but proposing a rationale can help investigators to develop and test a causal hypothesis, choose an appropriate control and rule out placebo effects. Acupuncture may stimulate self-regulatory processes independent of the treatment objective, points, means or methods used; this would account for acupuncture's reported benefits in so many disparate pathologic conditions

Linking genes to literature: text mining, information extraction, and retrieval applications for biology

Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the final interpretation and communication of the results. The biological literature also constitutes the main information source for manual literature curation used by expert-curated databases. Following the increasing popularity of web-based applications for analyzing biological data, new text-mining and information extraction strategies are being implemented. These systems exploit existing regularities in natural language to extract biologically relevant information from electronic texts automatically. The aim of the BioCreative challenge is to promote the development of such tools and to provide insight into their performance. This review presents a general introduction to the main characteristics and applications of currently available text-mining systems for life sciences in terms of the following: the type of biological information demands being addressed; the level of information granularity of both user queries and results; and the features and methods commonly exploited by these applications. The current trend in biomedical text mining points toward an increasing diversification in terms of application types and techniques, together with integration of domain-specific resources such as ontologies. Additional descriptions of some of the systems discussed here are available on the internet