Flow-distributed spikes for Schnakenberg kinetics

This is the post-print version of the final published paper. The final publication is available at link.springer.com by following the link below. Copyright @ 2011 Springer-Verlag.We study a system of reaction–diffusion–convection equations which combine a reaction–diffusion system with Schnakenberg kinetics and the convective flow equations. It serves as a simple model for flow-distributed pattern formation. We show how the choice of boundary conditions and the size of the flow influence the positions of the emerging spiky patterns and give conditions when they are shifted to the right or to the left. Further, we analyze the shape and prove the stability of the spikes. This paper is the first providing a rigorous analysis of spiky patterns for reaction-diffusion systems coupled with convective flow. The importance of these results for biological applications, in particular the formation of left–right asymmetry in the mouse, is indicated.RGC of Hong Kon

Remote activation of host cell DNA synthesis in uninfected cells signalled by infected cells in advance of virus transmission.

Viruses modulate cellular processes and metabolism in diverse ways, but these are almost universally studied in the infected cell itself. Here, we study spatial organization of DNA synthesis during multiround transmission of herpes simplex virus (HSV) using pulse-labeling with ethynyl nucleotides and cycloaddition of azide fluorophores. We report a hitherto unknown and unexpected outcome of virus-host interaction. Consistent with the current understanding of the single-step growth cycle, HSV suppresses host DNA synthesis and promotes viral DNA synthesis in spatially segregated compartments within the cell. In striking contrast, during progressive rounds of infection initiated at a single cell, we observe that infection induces a clear and pronounced stimulation of cellular DNA replication in remote uninfected cells. This induced DNA synthesis was observed in hundreds of uninfected cells at the extended border, outside the perimeter of the progressing infection. Moreover, using pulse-chase analysis, we show that this activation is maintained, resulting in a propagating wave of host DNA synthesis continually in advance of infection. As the virus reaches and infects these activated cells, host DNA synthesis is then shut off and replaced with virus DNA synthesis. Using nonpropagating viruses or conditioned medium, we demonstrate a paracrine effector of uninfected cell DNA synthesis in remote cells continually in advance of infection. These findings have significant implications, likely with broad applicability, for our understanding of the ways in which virus infection manipulates cell processes not only in the infected cell itself but also now in remote uninfected cells, as well as of mechanisms governing host DNA synthesis. IMPORTANCE We show that during infection initiated by a single particle with progressive cell-cell virus transmission (i.e., the normal situation), HSV induces host DNA synthesis in uninfected cells, mediated by a virus-induced paracrine effector. The field has had no conception that this process occurs, and the work changes our interpretation of virus-host interaction during advancing infection and has implications for understanding controls of host DNA synthesis. Our findings demonstrate the utility of chemical biology techniques in analysis of infection processes, reveal distinct processes when infection is examined in multiround transmission versus single-step growth curves, and reveal a hitherto-unknown process in virus infection, likely relevant for other viruses (and other infectious agents) and for remote signaling of other processes, including transcription and protein synthesis

Seasonal, annual and decadal change in tadpole populations in tropical Australian streams

Abstract Declines due to fungal disease (chytridiomycosis) have affected many stream-dwelling frog species, especially in the tropics, leading to reduced abundance and diversity of their tadpoles. Studies in the Australian Wet Tropics have demonstrated that some frog species have declined or disappeared, while others have persisted. To assess the occurrence of stream-breeding frogs, we monitored tadpole populations of five frog species in Wet Tropics streams in the early 1990s (uplands, before chytridomycosis emergence), and in 2011-2013 (uplands and lowlands, after chytridiomycosis emergence), and investigated environmental factors that might influence tadpole abundance. Riffle-dwelling tadpoles of two frog species disappeared from the upland stream site during the 1990s, reflecting reported losses of adult populations. Tadpoles of one upland pool species initially declined but had recovered by 2011-2013. Samples from the lowlands in 2011 to 2013 indicated no similar loss. Chytridiomycosis was the likely cause of changes in tadpole abundances between the two survey periods, given its known occurrence and documented effects on adult frogs in these systems; however, we did not measure its prevalence in this study. Tadpole populations fluctuated seasonally, with abundances highest in spring and summer, reflecting the timing of frog reproduction. The most important biophysical influence on the assemblages that we measured was current velocity. Tadpole peak abundances suggest that they make a substantial contribution at the consumer level of food webs, and that their loss has altered food webs substantially in upland streams.</jats:p

Spotting the diffusion of New Psychoactive Substances over the Internet

Online availability and diffusion of New Psychoactive Substances (NPS) represent an emerging threat to healthcare systems. In this work, we analyse drugs forums, online shops, and Twitter. By mining the data from these sources, it is possible to understand the dynamics of drugs diffusion and their endorsement, as well as timely detecting new substances. We propose a set of visual analytics tools to support analysts in tackling NPS spreading and provide a better insight about drugs market and analysis

Clustering of tau-immunoreactive pathology in chronic traumatic encephalopathy

Chronic traumatic encephalopathy (CTE) is a neurodegenerative disorder which may result from repetitive brain injury. A variety of tau-immunoreactive pathologies are present, including neurofibrillary tangles (NFT), neuropil threads (NT), dot-like grains (DLG), astrocytic tangles (AT), and occasional neuritic plaques (NP). In tauopathies, cellular inclusions in the cortex are clustered within specific laminae, the clusters being regularly distributed parallel to the pia mater. To determine whether a similar spatial pattern is present in CTE, clustering of the tau-immunoreactive pathology was studied in the cortex, hippocampus, and dentate gyrus in 11 cases of CTE and 7 cases of Alzheimer’s disease neuropathologic change (ADNC) without CTE. In CTE: (1) all aspects of tau-immunoreactive pathology were clustered and the clusters were frequently regularly distributed parallel to the tissue boundary, (2) clustering was similar in two CTE cases with minimal co-pathology compared with cases with associated ADNC or TDP-43 proteinopathy, (3) in a proportion of cortical gyri, estimated cluster size was similar to that of cell columns of the cortico-cortical pathways, and (4) clusters of the tau-immunoreactive pathology were infrequently spatially correlated with blood vessels. The NFT and NP in ADNC without CTE were less frequently randomly or uniformly distributed and more frequently in defined clusters than in CTE. Hence, the spatial pattern of the tau-immunoreactive pathology observed in CTE is typical of the tauopathies but with some distinct differences compared to ADNC alone. The spread of pathogenic tau along anatomical pathways could be a factor in the pathogenesis of the disease

Axiomatic and tableau-based reasoning for Kt(H,R)

We introduce a tense logic, called Kt(H, R), arising from logics for spatial reasoning. Kt(H, R) is a multi-modal logic with two modalities and their converses defined with respect to a pre-order and a relation stable over this pre-order. We show Kt(H,R) is decidable, it has the effective finite model property and reasoning in Kt(H,R) is PSPACE-complete. Two complete Hilbert-style axiomatisations are given. The main focus of the paper is tableau-based reasoning. Our aim is to gain insight into the numerous possibilities of defining tableau calculi and their properties. We present several labelled tableau calculi for Kt(H,R) in which the theory rules range from accommodating correspondence properties closely, to accommodating Hilbert axioms closely. The calculi provide the basis for decision procedures that have been imple- mented and tested on modal and intuitionistic problems

A Bi-Intuitionistic Modal Logic: Foundations and Automation

The paper introduces a bi-intuitionistic modal logic, called BISKT, with two adjoint pairs of tense operators. The semantics of BISKT is defined using Kripke models in which the set of worlds carries a pre-order relation as well as an accessibility relation, and the two relations are linked by a stability condition. A special case of these models arises from graphs in which the worlds are interpreted as nodes and edges of graphs, and formulae represent subgraphs. The pre-order is the incidence structure of the graphs. We present a comprehensive study of the logic, giving decidability, complexity and correspondence results. We also show the logic has the effective finite model property. We present a sound, complete and terminating tableau calculus for the logic and use the MetTeL system to explore implementations of different versions of the calculus. An experimental evaluation gave good results for satisfiable problems using predecessor blocking

The bright optical afterglow of the nearby gamma-ray burst of 29 March 2003

Many past studies of cosmological gamma-ray bursts (GRBs) have been limited because of the large distance to typical GRBs, resulting in faint afterglows. There has long been a recognition that a nearby GRB would shed light on the origin of these mysterious cosmic explosions, as well as the physics of their fireballs. However, GRBs nearer than z=0.2 are extremely rare, with an estimated rate of localisation of one every decade. Here, we report the discovery of bright optical afterglow emission from GRB 030329. Our prompt dissemination and the brilliance of the afterglow resulted in extensive followup (more than 65 telescopes) from radio through X-ray bands, as well as measurement of the redshift, z=0.169. The gamma-ray and afterglow properties of GRB 030329 are similar to those of cosmological GRBs (after accounting for the small distance), making this the nearest known cosmological GRB. Observations have already securely identified the progenitor as a massive star that exploded as a supernova, and we anticipate futher revelations of the GRB phenomenon from studies of this source.Comment: 13 pages, 4 figures. Original tex

Feasibility of Photofrin II as a radiosensitizing agent in solid tumors - Preliminary results

Background: Photofrin II has been demonstrated to serve as a specific and selective radiosensitizing agent in in vitro and in vivo tumor models. We aimed to investigate the feasibility of a clinical application of Photofrin II. Material and Methods: 12 patients were included in the study (7 unresectable solid tumors of the pelvic region, 3 malignant gliomas, 1 recurrent oropharyngeal cancer, 1 recurrent adenocarcinoma of the sphenoid sinus). The dose of ionizing irradiation was 30-50.4 Gy; a boost irradiation of 14 Gy was added for the pelvic region. All patients were intravenously injected with 1 mg/kg Photofrin II 24 h prior to the commencement of radiotherapy. Magnetic resonance imaging (MRI) controls and in some cases positron emission tomography (PET) were performed in short intervals. The mean follow-up was 12.9 months. Results: No major adverse events were noted. Minor adverse events consisted of mild diarrhea, nausea and skin reactions. A complete remission was observed in 4/12 patients. A reduction in local tumor volume of > 45% was achieved in 4/12 patients. Stable disease was observed in 4/12 patients. 1 patient showed local disease progression after 5 months. Conclusion: The early follow-up results are encouraging regarding the feasibility of the application of Photofrin II as a radiosensitizing agent