EPSRC Institutional Sponsorship 2012-13 – Loughborough University: final report

EPSRC Institutional Sponsorship 2012-13 – Loughborough University: final repor

Extracting and re-using research data from chemistry e-theses: the SPECTRa-T project

Scientific e-theses are data-rich resources, but much of the information they contain is not readily accessible. For chemistry, the SPECTRa-T project has addressed this problem by developing data-mining techniques to extract experimental data, creating RDF (Resource Description Framework) triples for exposure to sophisticated Semantic Web searches. We used OSCAR3, an Open Source chemistry text-mining tool, to parse and extract data from theses in PDF, and from theses in Office Open XML document format. Theses in PDF suffered data corruption and a loss of formatting that prevented the identification of chemical objects. Theses in .docx yielded semantically rich SciXML that enabled the additional extraction of associated data. Chemical objects were placed in a data repository, and RDF triples deposited in a triplestore. Data-mining from chemistry e-theses is both desirable and feasible; but the use of PDF, the de facto format standard for deposit in most repositories, prevents the optimal extraction of data for semantic querying. In order to facilitate this, we recommend that universities also require deposition of chemistry e-theses in an XML document format. Further work is required to clarify the complex IPR issues and ensure that they do not become an unwarranted barrier to data extraction and re-use

CMLLite: a design philosophy for CML.

CMLLite is a collection of definitions and processes which provide strong and flexible validation for a document in Chemical Markup Language (CML). It consists of an updated CML schema (schema3), conventions specifying rules in both human and machine-understandable forms and a validator available both online and offline to check conformance. This article explores the rationale behind the changes which have been made to the schema, explains how conventions interact and how they are designed, formulated, implemented and tested, and gives an overview of the validation service.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Intermediate scattering function and quantum recoil in non-Markovian quantum diffusion

Exact expressions are derived for the intermediate scattering function (ISF) of a quantum particle diffusing in a harmonic potential and linearly coupled to a harmonic bath. The results are valid for arbitrary strength and spectral density of the coupling. The general, exact non-Markovian result is expressed in terms of the classical velocity autocorrelation function, which represents an accumulated phase during a scattering event. The imaginary part of the exponent of the ISF is proportional to the accumulated phase, which is an antisymmetric function of the correlation time $t$. The expressions extend previous results given in the quantum Langevin framework where the classical response of the bath was taken as Markovian. For a special case of non-Markovian friction, where the friction kernel decays exponentially in time rather than instantaneously, we provide exact results relating to unconfined quantum diffusion, and identify general features that allow insight to be exported to more complex examples. The accumulated phase as a function of the t has a universal gradient at the origin, depending only on the mass of the diffusing system particle. At large t the accumulated phase reaches a constant limit that depends only on the classical diffusion coefficient and is therefore independent of the detailed memory properties of the friction kernel. Non-Markovian properties of the friction kernel are encoded in the details of how the accumulated phase switches from its $t\rightarrow -\infty$ to its $t\rightarrow -\infty$ limit, subject to the constraint of the universal gradient. When memory effects are significant, the transition from one limit to the other becomes non-monotonic, owing to oscillations in the classical velocity autocorrelation. The result is interpreted in terms of a solvent caging effect, in which slowly fluctuating bath modes create transient wells for the system particle.PT thanks the EPSRC for doctoral funding under the award reference 1363145, which enabled the majority of the present work

Reconstructing past forest composition and abundance by using archived Landsat and national forest inventory data

Effective modelling of forest susceptibility to defoliating insect outbreaks requires a better understanding of outbreak dynamics, which includes detailed knowledge of the pre- and post-outbreak forest status as well as subsequent feedback mechanisms. In this paper, we strive to fill the forest status need by combining archived Landsat sensor data (pre- and post-outbreak) with different formats and dates of the U.S. Forest Service’s Forest Inventory and Analysis (FIA) data (periodic [1970s, 1990s] and annual [2003–2006]). Specifically, we explore the utility of these FIA ground data for calibrating models of forest species and type abundance for mapping past forest composition in the Border Lakes Ecoregion (BLE) of Upper Midwest of the US. Model calibration results between Landsat reflectance and FIA ground data for both total forest basal area and balsam fir (Abies balsamea) relative basal area, a preferred host of the spruce budworm (SBW, Choristoneura fumiferana), were poor to moderate (R2adj 0.39 and 0.48, respectively). Results for aspen (Populous tremuloides) and spruce (Picea glauca and P. mariana) abundance yielded substantially better accuracies (R2adj 0.64 and 0.78; RMSE 15.56 and 10.65 m2 ha−1, respectively). Groupings of tree species into broadleaved and conifers substantially improved model calibration result (R2adj range: 0.72–0.91), except for the SBW host group (A. balsamea, P. glauca, and P. mariana). Periodic FIA ground data from the early 1990s generated stronger models compared to other FIA-Landsat date combinations tested. A paired t-test of abundance differences between undisturbed forest from the older 1977 and 1990 periodic inventories was significant (p-value \u3c 0.0001), suggesting possible effects of variable FIA sampling protocol or ground plot positional accuracy through time. However, a similar paired t-test of abundance difference between periodic FIA (1990) and annual FIA (2003–2006) was not significant (p-value = 0.249). We posit four potential factors that may have contributed to weak Landsat-FIA calibration results for species abundance: 1) variation in FIA subplot arrangement and sampling protocols through time, 2) variability in species abundance and heterogeneity among FIA sampling across adjacent Landsat orbital paths, 3) understory species (balsam fir) that are largely hidden from remote detection, and 4) cloud cover and orbital phase mismatches preventing capture of key forest phenology aids. While past and present FIA sampling protocols were not specifically designed for integration with 30-meter satellite sensor data, careful pairing of FIA ground data (past or present) with Landsat sensor data can facilitate reasonable estimates, of forest abundance for generalized forest types, and possibly forest species when heterogeneity is low. Nevertheless, we recommend that FIA subplot sampling protocols be augmented to include measurements of forest conditions that are more amenable to integration with 30-meter Landsat sensor data

Szegénység, társadalmi kirekesztés és társadalmi polarizáció, avagy: miért van szükség egy nemzetközi jóléti állam létrehozására

Az elmúlt, nagyjából ötven évben a konvencionális bölcsesség egyre csak azt szajkózta, hogy a gazdasági növekedés automatikusan csökkenti majd a szegénységet. Ez az álláspont nem tartható tovább. Az elkövetkező majd’ fél évszázad kilátásai szerint a világ legalapvetőbb problémája az lesz – s ebben teljes az egyetértés a nagy nemzetközi intézmények között, egyre inkább teszik magukévá ezt a véleményt az egyes kormányok is –, hogy a gazdagság és a szegénység egyre polarizáltabbnak mutatkozik meg, s hogy új prioritásokat kell kitűznünk magunk elé