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

Persistent organic pollutants in ocean sediments from the North Pacific to the Arctic Ocean

Concentrations of polychlorinated biphenyls (PCBs), organochlorine pesticides (OC pesticides), and polybrominated diphenyl ethers (PBDEs) are reported in surficial sediments sampled along cruise transects from the Bering Sea to the central Arctic Ocean. OCs and PCBs all had significantly higher concentrations in the relatively shallow water (500 m) of the Bering Sea and Arctic Ocean (e.g., Canada Basin ΣPCB 149 ± 102 pg g−1 dw). Concentrations were similar to, or slightly lower than, studies from the 1990s, indicating a lack of a declining trend. PBDEs (excluding BDE-209) displayed very low concentrations (e.g., range of median values, 3.5–6.6 pg/g dw). In the shelf areas, the sediments comprised similar proportions of silt and clay, whereas the deep basin sediments were dominated by clay, with a lower total organic carbon (TOC) content. While significant positive correlations were observed between persistent organic pollutant (POP) concentrations and TOC (Pearson correlation, r = 0.66–0.75, p <0.05), the lack of strong correlations, combined with differing chemical profiles between the sediments and technical formulations (and/or marine surface waters), indicate substantial chemical processing during transfer to the benthic environment. Marked differences in sedimentation rates between the shallow and deeper water regions are apparent (the ∼5 cm-depth grab samples collected here representing ∼100 years of accumulation for the shelf sediments and ∼1000 years for the deeper ocean regions), which may bias any comparisons. Nonetheless, the sediments of the shallower coastal arctic seas appear to serve as significant repositories for POPs deposited from surface waters

Accumulation of perfluoroalkyl compounds in Tibetan mountain snow:temporal patterns from 1980 to 2010

The use of snow and ice cores as recorders of environmental contamination is particularly relevant for per- and polyfluoroalky substances (PFASs) given their production history, differing source regions and varied mechanisms driving their global distribution. In a unique study perfluoroalkyl acids (PFAAs) were analyzed in dated snow-cores obtained from high mountain glaciers on the Tibetan Plateau (TP). One snow core was obtained from the Mt Muztagata glacier (accumulation period of 1980–1999), located in western Tibet and a second core from Mt. Zuoqiupo (accumulation period: 1996–2007) located in southeastern Tibet, with fresh surface snow collected near Lake Namco in 2010 (southern Tibet). The higher concentrations of ∑PFAAs were observed in the older Mt Muztagata core and dominated by perfluorooctanesulfonic acid (PFOS) (61.4–346 pg/L) and perfluorooctanoic acid (PFOA) (40.8–243 pg/L), whereas in the Mt Zuoqiupu core the concentrations were lower (e.g., PFOA: 37.8–183 pg/L) with PFOS below detection limits. These differences in PFAA concentrations and composition profile likely reflect the upwind sources affecting the respective sites (e.g., European/central Asian sources for Mt Muztagata and India sources for Mt Zuoqiupu). Perfluorobutanoic acid (PFBA) dominated the recent surface snowpack of Lake Namco which is mainly associated with India sources where the shorter chain volatile PFASs precursors predominate. The use of snow cores in different parts of Tibet provides useful recorders to examine the influence of different PFASs source regions and reflect changing PFAS production/use in the Northern Hemisphere

Proline-Rich Homeodomain protein (PRH/HHEX) is a suppressor of breast tumour growth

Breast tumours progress from hyperplasia to ductal carcinoma in situ (DCIS) and invasive breast carcinoma (IBC). PRH/HHEX (Proline Rich Homeodomain/Haematopoietically expressed homeobox) is a transcription factor that displays both tumour suppressor and oncogenic activity in different disease contexts however, the role of PRH in breast cancer is poorly understood. Here we show that nuclear localisation of the PRH protein is decreased in DCIS and IBC compared to normal breast. Our previous work has shown that PRH phosphorylation by protein kinase CK2 prevents PRH from binding to DNA and regulating the transcription of multiple genes encoding growth factors and growth factor receptors. Here we show that transcriptionally inactive phosphorylated PRH is elevated in DCIS and IBC compared to normal breast. To determine the consequences of PRH loss of function in breast cancer cells we generated inducible PRH depletion in MCF-7 cells. We show that PRH depletion results in increased MCF-7 cell proliferation in part at least due to increased vascular endothelial growth factor signaling. Moreover we demonstrate that PRH depletion increases the formation of breast cancer cells with cancer stem cell-like properties. Finally, and in keeping with these findings, we show that PRH over-expression inhibits the growth of mammary tumours in mice. Collectively these data indicate that PRH plays a tumour suppressive role in the breast and they provide an explanation for the finding that low PRH mRNA levels are associated with a poor prognosis in breast cancer

Pesticides contaminated dust exposure, risk diagnosis and exposure markers in occupational and residential settings of Lahore, Pakistan

There are few studies documenting the dust loaded with pesticides as a potential non-dietary exposure source for occupational worker and populations living near agricultural farms and pesticides formulation plants. In present study we have evaluated the pesticide concentration in dust from potential sites and relevant health risk from dust ingestion. Furthermore, the effect of currently used pesticides was investigated on blood and urine parameters of subjects: farmer, factory worker, urban resident and rural resident and controlled subjects with presumably different levels of exposure. The urinary metabolites (TCPY and IMPY) were quantified as biomarkers of exposure to chlorpyrifos and diazinon in relation with biomarkers of effect including BuChE, LH, FSH, testosterone and oxidative stress. Results showed that chlorpyrifos and diazinon were present in higher concentration in dust and posed a high health risk to exposed subjects. The mean SOD value was high among the farmer (3048 U/g Hb) followed by factory worker (1677.6U/g Hb). The urinary biomarkers – TCPY and IMPY- were found higher in exposed subjects as compared to control. Furthermore, testosterone was found in higher concentration in factory worker than control (12.63 ng/ml vs 4.61 ng/ml respectively). A decreased BuChE activity was noticed in occupational group and significant differences were observed in control verses exposed subjects. The PCA analysis evidenced the impact of pesticides on exposure biomarkers and male reproductive hormones. The study suggests that dust contaminated with pesticides engenders significant health risk particularly related to the nervous and endocrine system, not only for occupational workers exposed to direct ingestion but also for nearby residential community. Succinctly putting: Pesticides loaded dust in the city of Lahore, being a high priority concern for the government of Pakistan, demands to be addressed

FAMILIAL DYSALBUMINAEMIC HYPERTHYROXINEMIA INTERFERES WITH CURRENT FREE THYROID HORMONE IMMUNOASSAY METHODS

Familial dysalbuminaemic hyperthyroxinemia (FDH), most commonly due to an Arginine to Histidine mutation at residue 218 (R218H) in the albumin gene, causes artefactual elevation of free thyroid hormones in euthyroid individuals. We have evaluated the susceptibility of most current free thyroid hormone immunoassay methods used in the UK, Europe and Far East to interference by R218H FDH. Methods: Different, one- and two-step immunoassay methods were tested, measuring Free T4 (FT4) and Free T3 (FT3) in 37 individuals with genetically-proven R218H FDH. Results: With the exception of Ortho VITROS, FT4 measurements were raised in all assays, with greatest to lowest susceptibility to interference being Beckman ACCESS &gt; Roche ELECSYS &gt; FUJIREBIO Lumipulse &gt; Siemens CENTAUR &gt; Abbott ARCHITECT &gt; Perkin-Elmer DELFIA. Five different assays recorded high FT3 levels, with the Siemens CENTAUR method measuring high FT3 values in up to 30% of cases. However, depending on the assay method, FT4 measurements were unexpectedly normal in some, genetically-confirmed, affected relatives of index FDH cases. Conclusions: All FT4 immunoassays evaluated are prone to interference by R218H FDH, with their varying susceptibility not being related to assay architecture but likely due to differing assay conditions or buffer composition. Added susceptibility of many FT3 assays to measurement interference, resulting in high FT4 and FT3 with non-suppressed TSH levels, raises the possibility of R218H FDH being misdiagnosed as Resistance to Thyroid Hormone beta or TSH-secreting pituitary tumour, potentially leading to unnecessary investigation and inappropriate treatment.Research is supported by funding from the Wellcome Trust (210755/Z/18/Z to KC) and NIHR Cambridge Biomedical Research Centre (CM, MG, KC)

Hyperthyroxinemia and Hypercortisolemia due to Familial Dysalbuminemia.

A 23-year-old man and his grandmother with hyperthyroxinemia and hypercortisolemia were heterozygous for an ALB mutation (p. Arg218Pro), known to cause familial dysalbuminemic hyperthyroxinemia (FDH). However, serum-free cortisol levels in these individuals were normal and total cortisol concentrations fell markedly after depletion of albumin from their serum. We conclude that binding of steroid as well as iodothyronines to mutant albumin causes raised circulating cortisol as well as thyroid hormones in euthyroid euadrenal individuals with R218P FDH, with potential for misdiagnosis, unnecessary investigation, and inappropriate treatment.Wellcome Trust NIHR Cambridge Biomedical Research Centr

Assessing residual status and spatial variation of current-use pesticides under the influence of environmental factors in major cash crop growing areas of Pakistan

The status of seven currently used pesticides were assessed under the influence of soil parameters in surface soils of cash crop growing areas of Pakistan. Chlorpyrifos occurred in highest mean concentration (1.18 mg kg−1). Selected pesticides exhibited higher affinity towards both organic carbon and black carbon fractions. The δ13C stable carbon isotopic fraction of inorganic carbon was also used as a tracer and disclosed high retention of total organic carbon in Swat and Swabi sites. Statistical analysis revealed that carbon storage was primarily influenced by altitude and temperature. Soil clay mineral oxides of aluminum and iron positively correlated with organic carbon and selected pesticides (chlorpyrifos and cyprodinil). Soil to plant bio-concentration ratios predicted heightened uptake of azinfos and diazinon in major cash crop bio mass. Occupational risk via soil ingestion expressed no significant threat to the farmer community

Volatile per- and polyfluoroalkyl compounds in the remote atmosphere of the western Antarctic Peninsula: an indirect source of perfluoroalkyl acids to Antarctic waters

Volatile per– and polyfluoroalkyl compounds were measured in air in the vicinity of the Western Antarctic Peninsula during February 2009 (Austral summer). The 6:2, 8:2 and 10:2 fluorotelomer alcohols (FTOHs) were the most abundant compounds with 8:2 and 10:2 FTOH concentrations averaging 9.9 and 7.4 pgm –3 respectively, followed by the shorter chain (C4) compounds of methyl perfluorobutane sulfonamide (MeFBSA) and sulfonamidoethanol (MeFBSE) with average concentrations of 3 to 4 pgm–3. Methyl/ethyl fluorooctane sulfonamides and sulfonamidoethanols (FOSA/Es) were <1 pgm–3 in all air samples (n = 8). The concentrations of FTOHs and FOSAs were in good agreement with a previous study (2007) that measured these chemicals in the background atmosphere of the Southern Ocean, although the levels of the MeFBSA/E were found to be 10–fold higher and possibly indicative of the increased use of these chemicals. Air mass back trajectories revealed that air mass movement was from the Antarctic landmass or from the Southern Ocean, the latter in keeping with the prevailing direction of the Antarctic Circulation Current. Those samples corresponding to air passing over the Antarctic Peninsula did not show notable differences in chemical concentrations or profile indicating that the scientific bases located on or near the Peninsula did not appear to influence PFC levels in the regional atmosphere.Given the lack of air mass incursions from the north (i.e. from the South American continent) then the levels measured here are representative of background concentrations around Antarctica. However,the relatively high levels of MeFBSE were surprising given the reported reactivity of this chemical and short atmospheric residence time. It is likely that this compound, alongside MeFBSA, is providing a source of C2–C4 perfluoroalkyl acids(PFAs)to Antarctic surface waters. We recommend that long–term air monitoring be established in Antarctica for volatile PFCs and possibly accompanied by deposition monitoring for the PFAs