Representation and use of chemistry in the global electronic age.

We present an overview of the current state of public semantic chemistry and propose new approaches at a strategic and a detailed level. We show by example how a model for a Chemical Semantic Web can be constructed using machine-processed data and information from journal articles.This manuscript addresses questions of robotic access to data and its automatic re-use, including the role of Open Access archival of data. This is a pre-refereed preprint allowed by the publisher's (Royal Soc. Chemistry) Green policy. The author's preferred manuscript is an HTML hyperdocument with ca. 20 links to images, some of which are JPEgs and some of which are SVG (scalable vector graphics) including animations. There are also links to molecules in CML, for which the Jmol viewer is recommended. We susgeest that readers who wish to see the full glory of the manuscript, download the Zipped version and unpack on their machine. We also supply a PDF and DOC (Word) version which obviously cannot show the animations, but which may be the best palce to start, particularly for those more interested in the text

Siberian snow forcing in a dynamically bias-corrected model

We investigate the effect of systematic model biases on teleconnections influencing the Northern Hemisphere wintertime circulation. We perform a two-step nudging and bias-correcting scheme for the dynamic variables of the ECHAM6 atmospheric model to reduce errors in the model climatology relative to ERA-Interim. One result is a significant increase in the strength of the Northern Hemisphere wintertime stratospheric polar vortex, reducing errors in the December–February mean zonal stratospheric winds by up to 75%. The bias corrections are applied to the full atmosphere or the stratosphere only. We compare the response of the bias-corrected and control runs to an increase in Siberian snow cover in October—a surface forcing that, in our experiments, weakens the stratospheric polar vortex from October to December. We find that despite large differences in the vortex strength the magnitude of the stratospheric weakening is similar among the different climatologies, with some differences in the timing and length of the response. Differences are more pronounced in the stratosphere–troposphere coupling, and the subsequent surface response. The snow forcing with the stratosphere-only bias corrections results in a stratospheric response that is comparable to control, yet with an enhanced surface response that extends into early January. The full-atmosphere bias correction’s snow response also has a comparable stratospheric response but a somewhat suppressed surface response. Despite these differences, our results show an overall small sensitivity of the Eurasian snow teleconnection to the background climatology

The relationship between protoporphyrin IX photobleaching during real-time dermatological methyl-aminolevulinate photodynamic therapy (MAL-PDT) and subsequent clinical outcome.

Journal Article"This is the peer reviewed version of the following article: Lasers in Surgery and Medicine 42:613–619 (2010), which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/lsm.20943/pdf. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."BACKGROUND AND OBJECTIVE: The relationship between protoporphyrin IX (PpIX) photobleaching and cellular damage during aminolevulinic (ALA) photodynamic therapy (PDT) has been studied at the cellular level. This study assessed the capability of a non-invasive fluorescence imaging system (Dyaderm, Biocam, Germany), to monitor changes in PpIX during real time methyl-aminolevulinate (MAL) PDT in dermatological lesions, and thus to act as a predictive tool in terms of observed clinical outcome post-treatment. MATERIALS AND METHODS: Patients attending Royal Cornwall Hospital (Truro, UK) for MAL-PDT to licensed lesions (actinic keratosis, Bowen's disease, and basal cell carcinoma) were monitored using the pre-validated non-invasive fluorescence imaging system. Patients were imaged at three distinct time points: prior to the application of MAL, after the 3 hours of MAL application and immediately following light irradiation. The fluorescence intensity of the images were analysed with image analysis software and the percentage change in fluorescence during light irradiation was related to the clinical outcome observed 3 months following treatment. In total 100 patients underwent at least one session of MAL-PDT. RESULTS: Significantly higher levels of change in PpIX fluorescence during light irradiation (P0.500) was observed in the total levels of PpIX recorded after MAL application in patients undergoing partial and complete clearance at 3 months. CONCLUSIONS: PpIX photobleaching is indicative of the level of cellular damage PDT treatment will induce and therefore the clinical outcome expected within patients. This study indicated the potential of the commercially available fluorescence imaging system investigated to predict treatment success at the time of light irradiation and in the future it may be possible to employ it to individualise treatment parameters to improve dermatological PDT efficacy/outcome

Monitoring the accumulation and dissipation of the photosensitizer protoporphyrin IX during standard dermatological methyl-aminolevulinate photodynamic therapy utilizing non-invasive fluorescence imaging and quantification

Author's post-print is subject to a Creative Commons Attribution Non-Commercial No Derivatives LicenseBACKGROUND: Dermatological methyl-aminolevulinate photodynamic therapy (MAL-PDT) is utilized to successfully treat dermatological conditions. This study monitored fluorescence changes attributed to the accumulation and destruction of the photosensitizer, protoporphyrin IX (PpIX), at several different stages during the first and second treatments of clinical dermatological MAL-PDT. METHODS: A commercially available, non-invasive, fluorescence imaging system (Dyaderm, Biocam, Germany) was utilized to monitor fluorescence changes during the first and second MAL-PDT treatments in seventy-five lesions. RESULTS: The clinical data indicated statistically significant increases in fluorescence within lesions following the application of MAL for both treatments (P<0.001 and P<0.01 respectively) and subsequent statistically significant decreases in fluorescence within the lesions following light irradiation for both treatments (P<0.001 and P<0.01 respectively) whilst normal skin fluorescence remained unaltered. Lesions receiving a second treatment accumulated and dissipated significantly less PpIX (P<0.05) than during the first treatment. No significant differences were noted in PpIX accumulation or dissipation during MAL-PDT when gender, age, lesion type and lesion surface area were considered. CONCLUSIONS: It can therefore be concluded that PpIX fluorescence imaging can be used in real-time to assess PpIX levels during dermatological PDT. Similar observations were recorded from the three currently licensed indications indicating that the standard 'one size fits all' protocol currently employed appears to allow adequate PpIX accumulation, which is subsequently fully utilized during light irradiation regardless of patient age, gender or lesion surface area

Optical carrier wave shocking: detection and dispersion

Carrier wave shocking is studied using the Pseudo-Spectral Spatial Domain (PSSD) technique. We describe the shock detection diagnostics necessary for this numerical study, and verify them against theoretical shocking predictions for the dispersionless case. These predictions show Carrier Envelope Phase (CEP) and pulse bandwidth sensitivity in the single-cycle regime. The flexible dispersion management offered by PSSD enables us to independently control the linear and nonlinear dispersion. Customized dispersion profiles allow us to analyze the development of both carrier self-steepening and shocks. The results exhibit a marked asymmetry between normal and anomalous dispersion, both in the limits of the shocking regime and in the (near) shocked pulse waveforms. Combining these insights, we offer some suggestions on how carrier shocking (or at least extreme self-steepening) might be realised experimentally.Comment: 9 page

Biological and physical forcing of carbonate chemistry in an upwelling filament off northwest Africa: Results from a Lagrangian study

The Mauritanian upwelling system is one of the most biologically productive regions of the world's oceans. Coastal upwelling transfers nutrients to the sun-lit surface ocean, thereby stimulating phytoplankton growth. Upwelling of deep waters also supplies dissolved inorganic carbon (DIC), high levels of which lead to low calcium carbonate saturation states in surface waters, with potentially adverse effects on marine calcifiers. In this study an upwelled filament off the coast of northwest Africa was followed using drifting buoys and sulphur hexafluoride to determine how the carbonate chemistry changed over time as a result of biological, physical and chemical processes. The initial pHtot in the mixed layer of the upwelled plume was 7.94 and the saturation states of calcite and aragonite were 3.4 and 2.2, respectively. As the plume moved offshore over a period of 9 days, biological uptake of DIC (37 ?mol kg?1) reduced pCO2 concentrations from 540 to 410 ?atm, thereby increasing pHtot to 8.05 and calcite and aragonite saturation states to 4.0 and 2.7 respectively. The increase (25 ?mol kg?1) in total alkalinity over the 9 day study period can be accounted for solely by the combined effects of nitrate uptake and processes that alter salinity (i.e., evaporation and mixing with other water masses). We found no evidence of significant alkalinity accumulation as a result of exudation of organic bases by primary producers. The ongoing expansion of oxygen minimum zones through global warming will likely further reduce the CaCO3 saturation of upwelled waters, amplifying any adverse consequences of ocean acidification on the ecosystem of the Mauritanian upwelling system

Quantifying the Subjective Brightness of Retroreflective Material Using Magnitude Estimations

Ten small patches of retroreflective material were evaluated using a method of magnitude estimation to quantify the effect of changing the coefficient of retroreflection (RA) on brightness perception. Seventeen undergraduates participated. The results show that brightness is tightly linked with RA. Brightness was influenced more by changes in lower RA than changes in higher RA and follows Steven’s power law for brightness. Practical and theoretical implications are discusse