Developing an open data portal for the ESA climate change initiative

We introduce the rationale for, and architecture of, the European Space Agency Climate Change Initiative (CCI) Open Data Portal (http://cci.esa.int/data/). The Open Data Portal hosts a set of richly diverse datasets – 13 “Essential Climate Variables” – from the CCI programme in a consistent and harmonised form and to provides a single point of access for the (>100 TB) data for broad dissemination to an international user community. These data have been produced by a range of different institutions and vary across both scientific and spatio-temporal characteristics. This heterogeneity of the data together with the range of services to be supported presented significant technical challenges. An iterative development methodology was key to tackling these challenges: the system developed exploits a workflow which takes data that conforms to the CCI data specification, ingests it into a managed archive and uses both manual and automatically generated metadata to support data discovery, browse, and delivery services. It utilises both Earth System Grid Federation (ESGF) data nodes and the Open Geospatial Consortium Catalogue Service for the Web (OGC-CSW) interface, serving data into both the ESGF and the Global Earth Observation System of Systems (GEOSS). A key part of the system is a new vocabulary server, populated with CCI specific terms and relationships which integrates OGC-CSW and ESGF search services together, developed as part of a dialogue between domain scientists and linked data specialists. These services have enabled the development of a unified user interface for graphical search and visualisation – the CCI Open Data Portal Web Presence

Hypovitaminosis D among rheumatology outpatients in clinical practice.

OBJECTIVES: A role for vitamin D in the pathogenesis of autoimmune and inflammatory diseases is emerging. We undertook an audit of 25-hydroxyvitamin D (25OHD) investigation and treatment in rheumatology outpatients. METHODS: Serum 25OHD requests were matched to electronic medical records from rheumatology and metabolic bone clinics (April 2006-March 2007). Data were analysed separately for two groups, 'Documented osteoporosis/osteopaenia' (Group 1) and 'General rheumatology outpatients' (Group 2, sub-divided by diagnosis). Hypovitaminosis D was defined by 25OHD levels <50 nmol/l. Values were compared with healthy adults to calculate geometric z-scores. RESULTS: A total of 263 patients were included (Group 1, n = 122; Group 2, n = 141) with an overall median 25OHD of 44 nmol/l. The 25OHD level among general rheumatology patients (median 39 nmol/l, mean z score -1.2, was statistically significantly lower than among osteoporotic/osteopaenic patients (median 49 nmol/l, mean z score of -0.9, p < 0.05 for the difference). 25OHD was lower in inflammatory arthritis and chronic pain/fibromyalgia than in other groups. Prescribing was recorded in 100 in Group 1 (of whom 95% were prescribed calcium/800 IU cholecalciferol) and 83 in Group 2 (91% calcium/800 IU). Only 31% of the patients with 25OHD <50 nmol/l would have been identified using general guidelines for screening patients at 'high risk' of hypovitaminosis D. CONCLUSIONS: Improved guidelines for managing hypovitaminosis D in rheumatology patients are needed. We found a high prevalence of hypovitaminosis D among secondary care patients in rheumatology and widespread supplementation with 800 IU cholecalciferol. Substantially reduced levels of serum 25OHD were identified among patients with inflammatory arthritis and chronic pain

Energy levels in polarization superlattices: a comparison of continuum strain models

A theoretical model for the energy levels in polarization superlattices is presented. The model includes the effect of strain on the local polarization-induced electric fields and the subsequent effect on the energy levels. Two continuum strain models are contrasted. One is the standard strain model derived from Hooke's law that is typically used to calculate energy levels in polarization superlattices and quantum wells. The other is a fully-coupled strain model derived from the thermodynamic equation of state for piezoelectric materials. The latter is more complete and applicable to strongly piezoelectric materials where corrections to the standard model are significant. The underlying theory has been applied to AlGaN/GaN superlattices and quantum wells. It is found that the fully-coupled strain model yields very different electric fields from the standard model. The calculated intersubband transition energies are shifted by approximately 5 -- 19 meV, depending on the structure. Thus from a device standpoint, the effect of applying the fully-coupled model produces a very measurable shift in the peak wavelength. This result has implications for the design of AlGaN/GaN optical switches.Comment: Revtex

Donor ionization in size controlled silicon nanocrystals: The transition from defect passivation to free electron generation

We studied the photoluminescence spectra of silicon and phosphorus co-implanted silica thin films on (100) silicon substrates as a function of isothermal annealing time. The rapid phase segregation, formation, and growth dynamics of intrinsic silicon nanocrystals are observed, in the first 600 s of rapid thermal processing, using dark field mode X-TEM. For short annealing times, when the nanocrystal size distribution exhibits a relatively small mean diameter, formation in the presence of phosphorus yields an increase in the luminescence intensity and a blue shift in the emission peak compared with intrinsic nanocrystals. As the mean size increases with annealing time, this enhancement rapidly diminishes and the peak energy shifts further to the red than the intrinsic nanocrystals. These results indicate the existence of competing pathways for the donor electron, which depends strongly on the nanocrystal size. In samples containing a large density of relatively small nanocrystals, the tendency of phosphorus to accumulate at the nanocrystal-oxide interface means that ionization results in a passivation of dangling bond (Pb -centre) type defects, through a charge compensation mechanism. As the size distribution evolves with isothermal annealing, the density of large nanocrystals increases at the expense of smaller nanocrystals, through an Ostwald ripening mechanism, and the majority of phosphorus atoms occupy substitutional lattice sites within the nanocrystals. As a consequence of the smaller band-gap, ionization of phosphorus donors at these sites increases the free carrier concentration and opens up an efficient, non-radiative de-excitation route for photo-generated electrons via Auger recombination. This effect is exacerbated by an enhanced diffusion in phosphorus doped glasses, which accelerates silicon nanocrystal growth

Graphene under hydrostatic pressure

In-situ high pressure Raman spectroscopy is used to study monolayer, bilayer and few-layer graphene samples supported on silicon in a diamond anvil cell to 3.5 GPa. The results show that monolayer graphene adheres to the silicon substrate under compressive stress. A clear trend in this behaviour as a function of graphene sample thickness is observed. We also study unsupported graphene samples in a diamond anvil cell to 8 GPa, and show that the properties of graphene under compression are intrinsically similar to graphite. Our results demonstrate the differing effects of uniaxial and biaxial strain on the electronic bandstructure.Comment: Accepted in Physical Review B with minor change

The CMS Tracker Readout Front End Driver

The Front End Driver, FED, is a 9U 400mm VME64x card designed for reading out the Compact Muon Solenoid, CMS, silicon tracker signals transmitted by the APV25 analogue pipeline Application Specific Integrated Circuits. The FED receives the signals via 96 optical fibers at a total input rate of 3.4 GB/sec. The signals are digitized and processed by applying algorithms for pedestal and common mode noise subtraction. Algorithms that search for clusters of hits are used to further reduce the input rate. Only the cluster data along with trigger information of the event are transmitted to the CMS data acquisition system using the S-LINK64 protocol at a maximum rate of 400 MB/sec. All data processing algorithms on the FED are executed in large on-board Field Programmable Gate Arrays. Results on the design, performance, testing and quality control of the FED are presented and discussed

Mendelian randomization study of B-type natriuretic peptide and type 2 diabetes: evidence of causal association from population studies

&lt;p&gt;Background: Genetic and epidemiological evidence suggests an inverse association between B-type natriuretic peptide (BNP) levels in blood and risk of type 2 diabetes (T2D), but the prospective association of BNP with T2D is uncertain, and it is unclear whether the association is confounded.&lt;/p&gt; &lt;p&gt;Methods and Findings: We analysed the association between levels of the N-terminal fragment of pro-BNP (NT-pro-BNP) in blood and risk of incident T2D in a prospective case-cohort study and genotyped the variant rs198389 within the BNP locus in three T2D case-control studies. We combined our results with existing data in a meta-analysis of 11 case-control studies. Using a Mendelian randomization approach, we compared the observed association between rs198389 and T2D to that expected from the NT-pro-BNP level to T2D association and the NT-pro-BNP difference per C allele of rs198389. In participants of our case-cohort study who were free of T2D and cardiovascular disease at baseline, we observed a 21% (95% CI 3%-36%) decreased risk of incident T2D per one standard deviation (SD) higher log-transformed NT-pro-BNP levels in analysis adjusted for age, sex, body mass index, systolic blood pressure, smoking, family history of T2D, history of hypertension, and levels of triglycerides, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol. The association between rs198389 and T2D observed in case-control studies (odds ratio = 0.94 per C allele, 95% CI 0.91-0.97) was similar to that expected (0.96, 0.93-0.98) based on the pooled estimate for the log-NT-pro-BNP level to T2D association derived from a meta-analysis of our study and published data (hazard ratio = 0.82 per SD, 0.74-0.90) and the difference in NT-pro-BNP levels (0.22 SD, 0.15-0.29) per C allele of rs198389. No significant associations were observed between the rs198389 genotype and potential confounders.&lt;/p&gt; &lt;p&gt;Conclusions: Our results provide evidence for a potential causal role of the BNP system in the aetiology of T2D. Further studies are needed to investigate the mechanisms underlying this association and possibilities for preventive interventions.&lt;/p&gt

A novel albumin gene mutation (R222I) in familial dysalbuminemic hyperthyroxinemia

Context: Familial dysalbuminemic hyperthyroxinemia, characterized by abnormal circulating albuminwith increased T4 affinity, causes artefactual elevation of free T4 concentrations in euthyroid individuals. Objective: Four unrelated index cases with discordant thyroid function tests in different assay platforms were investigated. Design and Results: Laboratory biochemical assessment, radiolabeled T4 binding studies, and ALB sequencing were undertaken. 125I-T4 binding to both serum and albumin in affected individuals was markedly increased, comparable with known familial dysalbuminemic hyperthyroxinemia cases. Sequencing showed heterozygosity for a novel ALB mutation (arginine to isoleucine at codon 222, R222I) in all four cases and segregation of the genetic defect with abnormal biochemical phenotype in one family. Molecular modeling indicates that arginine 222 is located within a high-affinity T4 binding site in albumin, with substitution by isoleucine, which has a smaller side chain predicted to reduce steric hindrance, thereby facilitating T 4 and rT3 binding. When tested in current immunoassays, serum free T4 values from R222I heterozygotes were more measurably abnormal in one-step vs two-step assay architectures. Total rT3 measurements were also abnormally elevated. Conclusions: A novel mutation (R222I) in the ALB gene mediates dominantly inherited dysalbuminemic hyperthyroxinemia. Susceptibility of current free T4 immunoassays to interference by this mutant albumin suggests likely future identification of individuals with this variant binding protein