Analysis of an ancient global warming event, the Paleocene-Eocene thermal maximum, under examination from ODP Holes 113-689B and 113-690B

Spatiotemporal patterns of carbonate dissolution provide a critical constraint on carbon input during an ancient (~55.5 Ma) global warming event known as the Paleocene-Eocene thermal maximum (PETM), yet the magnitude of lysocline shoaling in the Southern Ocean is poorly constrained due to limited spatial coverage in the circum-Antarctic region. This shortcoming is partially addressed by comparing patterns of carbonate sedimentation at the Site 690 PETM reference section to those herein reconstructed for nearby Site 689. Biochemostratigraphic correlation of the two records reveals that the first ~36 ka of the carbon isotope excursion (CIE) signaling PETM conditions is captured by the Site 689 section, while the remainder of the CIE interval and nearly all of the CIE recovery are missing due to a coring gap. A relatively expanded stratigraphy and higher carbonate content at mid-bathyal Site 689 indicate that dissolution was less severe than at Site 690. Thus, the bathymetric transect delimited by these two PETM records indicates that the lysocline shoaled above Site 689 (~1,100 m) while the calcite compensation depth remained below Site 690 (~1,900 m) in the Weddell Sea region. The ensuing recovery of carbonate sedimentation conforms to a bathymetric trend best explained by gradual lysocline deepening as negative feedback mechanisms neutralized ocean acidification. Further, biochemostratigraphic evidence indicates the tail end of the CIE recovery interval at both sites has been truncated by a hiatus most likely related to vigorous production and advection of intermediate waters.

Part of the global DOC versus AOU (dissolved organic carbon/apparent oxygen utilization) data compilation, Ross Sea

Dissolved and particulate organic matter was measured during six cruises to the southern Ross Sea. The cruises were conducted during late austral winter to autumn from 1994 to 1997 and included coverage of various stages of the seasonal phytoplankton bloom. The data from the various years are compiled into a representative seasonal cycle in order to assess general patterns of dissolved organic matter (DOM) and particulate organic matter (POM) dynamics in the southern Ross Sea. Dissolved organic carbon (DOC) and particulate organic carbon (POC) were at background concentrations of approximately 42 and 3 µM C, respectively, during the late winter conditions in October. As the spring phytoplankton bloom progressed, organic matter increased, and by January DOC and POC reached as high as 30 and 107 µM C, respectively, in excess of initial wintertime conditions. Stocks and concentrations of DOC and POC returned to near background values by autumn (April). Approximately 90% of the accumulated organic matter was partitioned into POM, with modest net accumulation of DOM stocks despite large net organic matter production and the dominance of Phaeocystis antarctica. Changes in NO3 concentration from wintertime values were used to calculate the equivalent biological drawdown of dissolved inorganic carbon (DICequiv). The fraction of DICequiv drawdown resulting in net DOC production was relatively constant (ca. 11%), despite large temporal and spatial variability in DICequiv drawdown. The C : N (molar ratio) of the seasonally produced DOM had a geometric mean of 6.2 and was nitrogen-rich compared to background DOM. The DOM stocks that accumulate in excess of deep refractory background stocks are often referred to as "semi-labile" DOM. The "semi-labile" pool in the Ross Sea turns over on timescales of about 6 months. As a result of the modest net DOM production and its lability, the role DOM plays in export to the deep sea is small in this region.

The CMCC Eddy-permitting Global Ocean Physical Reanalysis (C-GLORS v5, 1980-2014), links to NetCDF files

The CMCC Global Ocean Physical Reanalysis System (C-GLORS) is used to simulate the state of the ocean in the last decades. It consists of a variational data assimilation system (OceanVar), capable of assimilating all in-situ observations along with altimetry data, and a forecast step performed by the ocean model NEMO coupled with the LIM2 sea-ice model. KEY STRENGTHS: - Data are available for a large number of ocean parameters - An extensive validation has been conducted and is freely available - The reanalysis is performed at high resolution (1/4 degree) and spans the last 30 years KEY LIMITATIONS: - Quality may be discontinuos and depend on observation coverage - Uncertainty estimates are simply derived through verification skill scores

Global distributions of epipelagic macrozooplankton abundance and biomass - Gridded data product (NetCDF) - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

Macrozooplankton are an important link between higher and lower trophic levels in the oceans. They serve as the primary food for fish, reptiles, birds and mammals in some regions, and play a role in the export of carbon from the surface to the intermediate and deep ocean. Little, however, is known of their global distribution and biomass. Here we compiled a dataset of macrozooplankton abundance and biomass observations for the global ocean from a collection of four datasets. We harmonise the data to common units, calculate additional carbon biomass where possible, and bin the dataset in a global 1 x 1 degree grid. This dataset is part of a wider effort to provide a global picture of carbon biomass data for key plankton functional types, in particular to support the development of marine ecosystem models. Over 387 700 abundance data and 1330 carbon biomass data have been collected from pre-existing datasets. A further 34 938 abundance data were converted to carbon biomass data using species-specific length frequencies or using species-specific abundance to carbon biomass data. Depth-integrated values are used to calculate known epipelagic macrozooplankton biomass concentrations and global biomass. Global macrozooplankton biomass has a mean of 8.4 µg C l-1, median of 0.15 µg C l-1 and a standard deviation of 63.46 µg C l-1. The global annual average estimate of epipelagic macrozooplankton, based on the median value, is 0.02 Pg C. Biomass is highest in the tropics, decreasing in the sub-tropics and increasing slightly towards the poles. There are, however, limitations on the dataset; abundance observations have good coverage except in the South Pacific mid latitudes, but biomass observation coverage is only good at high latitudes. Biomass is restricted to data that is originally given in carbon or to data that can be converted from abundance to carbon. Carbon conversions from abundance are restricted in the most part by the lack of information on the size of the organism and/or the absence of taxonomic information. Distribution patterns of global macrozooplankton biomass and statistical information about biomass concentrations may be used to validate biogeochemical models and Plankton Functional Type models.

Global Ocean Colour for Carbon Cycle Research (full product set)

In 2005, the International Ocean Colour Coordinating Group (IOCCG) convened a working group to examine the state of the art in ocean colour data merging, which showed that the research techniques had matured sufficiently for creating long multi-sensor datasets (IOCCG, 2007). As a result, ESA initiated and funded the DUE GlobColour project (http://www.globcolour.info/) to develop a satellite based ocean colour data set to support global carbon-cycle research. It aims to satisfy the scientific requirement for a long (10+ year) time-series of consistently calibrated global ocean colour information with the best possible spatial coverage. This has been achieved by merging data from the three most capable sensors: SeaWiFS on GeoEye's Orbview-2 mission, MODIS on NASA's Aqua mission and MERIS on ESA's ENVISAT mission. In setting up the GlobColour project, three user organisations were invited to help. Their roles are to specify the detailed user requirements, act as a channel to the broader end user community and to provide feedback and assessment of the results. The International Ocean Carbon Coordination Project (IOCCP) based at UNESCO in Paris provides direct access to the carbon cycle modelling community's requirements and to the modellers themselves who will use the final products. The UK Met Office's National Centre for Ocean Forecasting (NCOF) in Exeter, UK, provides an understanding of the requirements of oceanography users, and the IOCCG bring their understanding of the global user needs and valuable advice on best practice within the ocean colour science community. The three year project kicked-off in November 2005 under the leadership of ACRI-ST (France). The first year was a feasibility demonstration phase that was successfully concluded at a user consultation workshop organised by the Laboratoire d'Océanographie de Villefranche, France, in December 2006. Error statistics and inter-sensor biases were quantified by comparison with insitu measurements from moored optical buoys and ship based campaigns, and used as an input to the merging. The second year was dedicated to the production of the time series. In total, more than 25 Tb of input (level 2) data have been ingested and 14 Tb of intermediate and output products created, with 4 Tb of data distributed to the user community. Quality control (QC) is provided through the Diagnostic Data Sets (DDS), which are extracted sub-areas covering locations of in-situ data collection or interesting oceanographic phenomena. This Full Product Set (FPS) covers global daily merged ocean colour products in the time period 1997-2006 and is also freely available for use by the worldwide science community at http://www.globcolour.info/data_access_full_prod_set.html. The GlobColour service distributes global daily, 8-day and monthly data sets at 4.6 km resolution for, chlorophyll-a concentration, normalised water-leaving radiances (412, 443, 490, 510, 531, 555 and 620 nm, 670, 681 and 709 nm), diffuse attenuation coefficient, coloured dissolved and detrital organic materials, total suspended matter or particulate backscattering coefficient, turbidity index, cloud fraction and quality indicators. Error statistics from the initial sensor characterisation are used as an input to the merging methods and propagate through the merging process to provide error estimates for the output merged products. These error estimates are a key component of GlobColour as they are invaluable to the users; particularly the modellers who need them in order to assimilate the ocean colour data into ocean simulations. An intensive phase of validation has been undertaken to assess the quality of the data set. In addition, inter-comparisons between the different merged datasets will help in further refining the techniques used. Both the final products and the quality assessment were presented at a second user consultation in Oslo on 20-22 November 2007 organised by the Norwegian Institute for Water Research (NIVA); presentations are available on the GlobColour WWW site. On request of the ESA Technical Officer for the GlobColour project, the FPS data set was mirrored in the PANGAEA data library.

Global distributions of modern planktic foraminifera abundance and biomass - Gridded data product (NetCDF) - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

Planktic foraminifera are heterotrophic mesozooplankton of global marine abundance. The position of planktic foraminifers in the marine food web is different compared to other protozoans and ranges above the base of heterotrophic consumers. Being secondary producers with an omnivorous diet, which ranges from algae to small metazoans, planktic foraminifers are not limited to a single food source, and are assumed to occur at a balanced abundance displaying the overall marine biological productivity at a regional scale. We have calculated the assemblage carbon biomass from data on standing stocks between the sea surface and 2500 m water depth, based on 754 protein-biomass data of 21 planktic foraminifer species and morphotypes, produced with a newly developed method to analyze the protein biomass of single planktic foraminifer specimens. Samples include symbiont bearing and symbiont barren species, characteristic of surface and deep-water habitats. Conversion factors between individual protein-biomass and assemblage-biomass are calculated for test sizes between 72 and 845 µm (minimum diameter). The calculated assemblage biomass data presented here include 1057 sites and water depth intervals. Although the regional coverage of database is limited to the North Atlantic, Arabian Sea, Red Sea, and Caribbean, our data include a wide range of oligotrophic to eutrophic waters covering six orders of magnitude of assemblage biomass. A first order estimate of the global planktic foraminifer biomass from average standing stocks (>125 µm) ranges at 8.5-32.7 Tg C yr-1 (i.e. 0.008-0.033 Gt C yr-1), and might be more than three time as high including the entire fauna including neanic and juvenile individuals adding up to 25-100 Tg C yr-1. However, this is a first estimate of regional planktic-foraminifer assemblage-biomass (PFAB) extrapolated to the global scale, and future estimates based on larger data-sets might considerably deviate from the one presented here. This paper is supported by, and a contribution to the Marine Ecosystem Data project (MAREDAT).

An image segmentation based on a genetic algorithm for determining soil coverage by crop residues

Determination of the soil coverage by crop residues after ploughing is a fundamental element of Conservation Agriculture. This paper presents the application of genetic algorithms employed during the fine tuning of the segmentation process of a digital image with the aim of automatically quantifying the residue coverage. In other words, the objective is to achieve a segmentation that would permit the discrimination of the texture of the residue so that the output of the segmentation process is a binary image in which residue zones are isolated from the rest. The RGB images used come from a sample of images in which sections of terrain were photographed with a conventional camera positioned in zenith orientation atop a tripod. The images were taken outdoors under uncontrolled lighting conditions. Up to 92% similarity was achieved between the images obtained by the segmentation process proposed in this paper and the templates made by an elaborate manual tracing process. In addition to the proposed segmentation procedure and the fine tuning procedure that was developed, a global quantification of the soil coverage by residues for the sampled area was achieved that differed by only 0.85% from the quantification obtained using template images. Moreover, the proposed method does not depend on the type of residue present in the image. The study was conducted at the experimental farm “El Encín” in Alcalá de Henares (Madrid, Spain).

Towards definition of the global biotechnology value chain using cases from Australian biotechnology SMEs

The generic pharmaceutical value chain model has been employed to describe both the global pharmaceutical and biotechnology industries till now. This research investigates the organisational value chain in Australian biotechnology companies in order to assess the appropriateness of the pharmaceutical value chain to small-and medium-sized biotechnology companies. The main theme of the research is: Can a generic model of the organisational value chain be defined for the biotechnology industry? Emanating from the literature, two research propositions were developed. RP1: there are eight major definable elements/activities of the organisational value chain for the biotechnology industry. RP2: Coverage of the elements in the biotechnology value chain ranges from focused to broad. A multiple case study methodology was used to explore these propositions. To develop a number of case studies, data was collected from senior managers of small and medium Australian biotechnology companies using an interview instrument, as well as from publicly available documentation and through observation. The results were analysed using cross-case comparisons. The results showed that an aggregation of the value chains of each organisation can be reduced to these eight definable elements that constitute the biotechnology value chain: basic research, applied research, development, verification and validation, prototype development, clinical trials, manufacturing and marketing. However, the findings also indicate that these major elements of the value chain need to be further reduced into sub-activities or sub-tasks to cater for the unique differences between biotechnology companies. Generally, the findings were consistent with the literature. However, a wider sampling, including international biotechnology organisations should be studied. The major contribution of this research is in the development of a value chain model, including general sub-tasks, for the Australian biotechnology industry.

Calcium carbonate global LGM Burial rate data

Global databases of calcium carbonate concentrations and mass accumulation rates in Holocene and last glacial maximum sediments were used to estimate the deep-sea sedimentary calcium carbonate burial rate during these two time intervals. Sparse calcite mass accumulation rate data were extrapolated across regions of varying calcium carbonate concentration using a gridded map of calcium carbonate concentrations and the assumption that accumulation of noncarbonate material is uncorrelated with calcite concentration within some geographical region. Mean noncarbonate accumulation rates were estimated within each of nine regions, determined by the distribution and nature of the accumulation rate data. For core-top sediments the regions of reasonable data coverage encompass 67% of the high-calcite (>75%) sediments globally, and within these regions we estimate an accumulation rate of 55.9 ± 3.6 x 10**11 mol/yr. The same regions cover 48% of glacial high-CaCO3 sediments (the smaller fraction is due to a shift of calcite deposition to the poorly sampled South Pacific) and total 44.1 ± 6.0 x 10**11 mol/yr. Projecting both estimates to 100 % coverage yields accumulation estimates of 8.3 x 10**12 mol/yr today and 9.2 x 10**12 mol/yr during glacial time. This is little better than a guess given the incomplete data coverage, but it suggests that glacial deep sea calcite burial rate was probably not considerably faster than today in spite of a presumed decrease in shallow water burial during glacial time.

Seawater carbonate chemistry, and Lithophyllum sp. and Feldmannia spp. coverage and dry weight during experiments, 2009

Climate-driven change represents the cumulative effect of global through local-scale conditions, and understanding their manifestation at local scales can empower local management. Change in the dominance of habitats is often the product of local nutrient pollution that occurs at relatively local scales (i.e. catchment scale), a critical scale of management at which global impacts will manifest. We tested whether forecasted global-scale change [elevated carbon dioxide (CO2) and subsequent ocean acidification] and local stressors (elevated nutrients) can combine to accelerate the expansion of filamentous turfs at the expense of calcifying algae (kelp understorey). Our results not only support this model of future change, but also highlight the synergistic effects of future CO2 and nutrient concentrations on the abundance of turfs. These results suggest that global and local stressors need to be assessed in meaningful combinations so that the anticipated effects of climate change do not create the false impression that, however complex, climate change will produce smaller effects than reality. These findings empower local managers because they show that policies of reducing local stressors (e.g. nutrient pollution) can reduce the effects of global stressors not under their governance (e.g. ocean acidification). The connection between research and government policy provides an example whereby knowledge (and decision making) across local through global scales provides solutions to some of the most vexing challenges for attaining social goals of sustainability, biological conservation and economic development.

Estimates of global, regional, and national incidence, prevalence, and mortality of HIV, 1980-2015 : the Global Burden of Disease Study 2015

Background Timely assessment of the burden of HIV/AIDS is essential for policy setting and programme evaluation. In this report from the Global Burden of Disease Study 2015 (GBD 2015), we provide national estimates of levels and trends of HIV/AIDS incidence, prevalence, coverage of antiretroviral therapy (ART), and mortality for 195 countries and territories from 1980 to 2015. Methods For countries without high-quality vital registration data, we estimated prevalence and incidence with data from antenatal care clinics and population-based seroprevalence surveys, and with assumptions by age and sex on initial CD4 distribution at infection, CD4 progression rates (probability of progression from higher to lower CD4 cell-count category), on and off antiretroviral therapy (ART) mortality, and mortality from all other causes. Our estimation strategy links the GBD 2015 assessment of all-cause mortality and estimation of incidence and prevalence so that for each draw from the uncertainty distribution all assumptions used in each step are internally consistent. We estimated incidence, prevalence, and death with GBD versions of the Estimation and Projection Package (EPP) and Spectrum software originally developed by the Joint United Nations Programme on HIV/AIDS (UNAIDS). We used an open-source version of EPP and recoded Spectrum for speed, and used updated assumptions from systematic reviews of the literature and GBD demographic data. For countries with high-quality vital registration data, we developed the cohort incidence bias adjustment model to estimate HIV incidence and prevalence largely from the number of deaths caused by HIV recorded in cause-of-death statistics. We corrected these statistics for garbage coding and HIV misclassifi cation. Findings Global HIV incidence reached its peak in 1997, at 3·3 million new infections (95% uncertainty interval [UI] 3·1–3·4 million). Annual incidence has stayed relatively constant at about 2·6 million per year (range 2·5–2·8 million) since 2005, after a period of fast decline between 1997 and 2005. The number of people living with HIV/AIDS has been steadily increasing and reached 38·8 million (95% UI 37·6–40·4 million) in 2015. At the same time, HIV/AIDS mortality has been declining at a steady pace, from a peak of 1·8 million deaths (95% UI 1·7–1·9 million) in 2005, to 1·2 million deaths (1·1–1·3 million) in 2015. We recorded substantial heterogeneity in the levels and trends of HIV/AIDS across countries. Although many countries have experienced decreases in HIV/AIDS mortality and in annual new infections, other countries have had slowdowns or increases in rates of change in annual new infections. Interpretation Scale-up of ART and prevention of mother-to-child transmission has been one of the great successes of global health in the past two decades. However, in the past decade, progress in reducing new infections has been slow, development assistance for health devoted to HIV has stagnated, and resources for health in low-income countries have grown slowly. Achievement of the new ambitious goals for HIV enshrined in Sustainable Development Goal 3 and the 90-90-90 UNAIDS targets will be challenging, and will need continued eff orts from governments and international agencies in the next 15 years to end AIDS by 2030.

Integrated Omics for the global mapping of biomolecules in LDL

Circulating low density lipoproteins (LDL) are thought to play a crucial role in the onset and development of atherosclerosis, though the detailed molecular mechanisms responsible for their biological effects remain controversial. The complexity of biomolecules (lipids, glycans and protein) and structural features (isoforms and chemical modifications) found in LDL particles hampers the complete understanding of the mechanism underlying its atherogenicity. For this reason the screening of LDL for features discriminative of a particular pathology in search of biomarkers is of high importance. Three major biomolecule classes (lipids, protein and glycans) in LDL particles were screened using mass spectrometry coupled to liquid chromatography. Dual-polarity screening resulted in good lipidome coverage, identifying over 300 lipid species from 12 lipid sub-classes. Multivariate analysis was used to investigate potential discriminators in the individual lipid sub-classes for different study groups (age, gender, pathology). Additionally, the high protein sequence coverage of ApoB-100 routinely achieved (≥70%) assisted in the search for protein modifications correlating to aging and pathology. The large size and complexity of the datasets required the use of chemometric methods (Partial Least Square-Discriminant Analysis, PLS-DA) for their analysis and for the identification of ions that discriminate between study groups. The peptide profile from enzymatically digested ApoB-100 can be correlated with the high structural complexity of lipids associated with ApoB-100 using exploratory data analysis. In addition, using targeted scanning modes, glycosylation sites within neutral and acidic sugar residues in ApoB-100 are also being explored. Together or individually, knowledge of the profiles and modifications of the major biomolecules in LDL particles will contribute towards an in-depth understanding, will help to map the structural features that contribute to the atherogenicity of LDL, and may allow identification of reliable, pathology-specific biomarkers. This research was supported by a Marie Curie Intra-European Fellowship within the 7th European Community Framework Program (IEF 255076). Work of A. Rudnitskaya was supported by Portuguese Science and Technology Foundation, through the European Social Fund (ESF) and "Programa Operacional Potencial Humano - POPH".

DNI Measurements in the South of Portugal: Long Term Results through Direct Comparison with Global and Diffuse Radiation Measurements and Existing Time Series

The present work describes the measurement effort for direct normal irradiance (DNI) evaluation in the sunny south of Portugal, with a network of eight radiation measurement stations in several locations (including Évora) providing a good coverage of the region. This new initiative for DNI measurement will still need many years (typically 10 or more) to produce a time series which can claim having long term statistical value. This problem can, however, be temporarily mitigated by measuring DNI at the same time as GHI and DHI, in a place where long term series dating back, already exist for those two. It so happens that a long term series (20 years) of global and diffuse solar irradiation exists for the location Évora. So the expectation is to establish correlations with the goal of attributing at least some long term statistical significance to the short and recent DNI series. The paper describes the setup of the measuring stations and presents the preliminary measurements obtained. It further presents the first correlations of monthly averages between normal beam (DNI), global and diffuse radiation. It then uses these correlations, admittedly without acceptable statistical significance (short series of less than one year of measured data), to exemplify how to get a prediction of long term DNI for Évora. This preliminary obtained value is compared to that predicted by the commercial data from Meteonorm.