Serving GODAE Data and Products to the Ocean Community

The Global Ocean Data Assimilation Experiment (GODAE [http:// www.godae.org]) has spanned a decade of rapid technological development. The ever-increasing volume and diversity of oceanographic data produced by in situ instruments, remote-sensing platforms, and computer simulations have driven the development of a number of innovative technologies that are essential for connecting scientists with the data that they need. This paper gives an overview of the technologies that have been developed and applied in the course of GODAE, which now provide users of oceanographic data with the capability to discover, evaluate, visualize, download, and analyze data from all over the world. The key to this capability is the ability to reduce the inherent complexity of oceanographic data by providing a consistent, harmonized view of the various data products. The challenges of data serving have been addressed over the last 10 years through the cooperative skills and energies of many individuals

Identification of an APC Variant in a Patient with Clinical Attenuated Familial Adenomatous Polyposis

Introduction. The objective of this case report is to discuss an unclassified germline variant of the adenomatous polyposis coli (APC) gene identified in an older patient with attenuated familial adenomatous polyposis syndrome (AFAP). Methods. We present a case report of a 66-year-old man diagnosed with AFAP. Colonoscopy found multiple polyps and invasive adenocarcinoma arising in the transverse colon. Samples were tested for mutations in the APC gene. Results. DNA sequencing of germline DNA identified a cytosine (C) to thymine (T) transition at nucleotide 1240, heterozygous. The C to T transition at codon 414 is predicted to convert an arginine residue to a cysteine that is possibly pathogenic. Analysis of the patient’s colon tumor DNA indicated that the tumor had lost the mutant variant allele and retained only the normal allele, suggesting that the variant may not be significant. Conclusions. The p.R414C variant has been described previously as a germline mutation of probable pathogenicity. This substitution should be considered an unclassified variant and possibly not pathogenic. These findings support the need for further genetic testing of tissue, as well as for developing a mechanism for testing all variants, as this could significantly impact the lives of patients and their family members

Fiducial Reference Measurements for Satellite Ocean Colour (FRM4SOC)

Earth observation data can help us understand and address some of the grand challenges and threats facing us today as a species and as a planet, for example climate change and its impacts and sustainable use of the Earth’s resources. However, in order to have confidence in earth observation data, measurements made at the surface of the Earth, with the intention of providing verification or validation of satellite-mounted sensor measurements, should be trustworthy and at least of the same high quality as those taken with the satellite sensors themselves. Metrology tells us that in order to be trustworthy, measurements should include an unbroken chain of SI-traceable calibrations and comparisons and full uncertainty budgets for each of the in situ sensors. Until now, this has not been the case for most satellite validation measurements. Therefore, within this context, the European Space Agency (ESA) funded a series of Fiducial Reference Measurements (FRM) projects targeting the validation of satellite data products of the atmosphere, land, and ocean, and setting the framework, standards, and protocols for future satellite validation efforts. The FRM4SOC project was structured to provide this support for evaluating and improving the state of the art in ocean colour radiometry (OCR) and satellite ocean colour validation through a series of comparisons under the auspices of the Committee on Earth Observation Satellites (CEOS). This followed the recommendations from the International Ocean Colour Coordinating Group’s white paper and supports the CEOS ocean colour virtual constellation. The main objective was to establish and maintain SI traceable ground-based FRM for satellite ocean colour and thus make a fundamental contribution to the European system for monitoring the Earth (Copernicus). This paper outlines the FRM4SOC project structure, objectives and methodology and highlights the main results and achievements of the project: (1) An international SI-traceable comparison of irradiance and radiance sources used for OCR calibration that set measurement, calibration and uncertainty estimation protocols and indicated good agreement between the participating calibration laboratories from around the world; (2) An international SI-traceable laboratory and outdoor comparison of radiometers used for satellite ocean colour validation that set OCR calibration and comparison protocols; (3) A major review and update to the protocols for taking irradiance and radiance field measurements for satellite ocean colour validation, with particular focus on aspects of data acquisition and processing that must be considered in the estimation of measurement uncertainty and guidelines for good practice; (4) A technical comparison of the main radiometers used globally for satellite ocean colour validation bringing radiometer manufacturers together around the same table for the first time to discuss instrument characterisation and its documentation, as needed for measurement uncertainty estimation; (5) Two major international side-by-side field intercomparisons of multiple ocean colour radiometers, one on the Atlantic Meridional Transect (AMT) oceanographic cruise, and the other on the Acqua Alta oceanographic tower in the Gulf of Venice; (6) Impact and promotion of FRM within the ocean colour community, including a scientific road map for the FRM-based future of satellite ocean colour validation and vicarious calibration (based on the findings of the FRM4SOC project, the consensus from two major international FRM4SOC workshops and previous literature, including the IOCCG white paper on in situ ocean colour radiometry)

Localization of a human T-cell-specific gene, RANTES (D17S136E), to chromosome 17q11.2-q12

We report here the localization of the gene for a human T-cell-specific molecule, designated RANTES, to human chromosome region 17q11.2-q12 by in situ hybridization and analysis of somatic cell hybrids using a cDNA probe to the gene. We have recently shown that this gene, which encodes a small, secreted, putative lymphokine, is a member of a larger gene family some of whose members reside on chromosome 4 but most of whose members have not to date been mapped. A secondary hybridization peak was noted on the region of human chromosome 5q31-q34, which may represent the location of other members of the gene family. Interestingly, this latter region overlaps with the location of an extended linked cluster of growth factor and receptor genes, some of which may be coregulated with members of the RANTES gene family.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/28717/1/0000538.pd

An operational analysis of Lake Surface Water Temperature

Operational analyses of Lake Surface Water Temperature (LSWT) have many potential uses including improvement of numerical weather prediction (NWP) models on regional scales. In November 2011, LSWT was included in the Met Office Operational Sea Surface Temperature and Ice Analysis (OSTIA) product, for 248 lakes globally. The OSTIA analysis procedure, which has been optimised for oceans, has also been used for the lakes in this first version of the product. Infra-red satellite observations of lakes and in situ measurements are assimilated. The satellite observations are based on retrievals optimised for Sea Surface Temperature (SST) which, although they may introduce inaccuracies into the LSWT data, are currently the only near-real-time information available. The LSWT analysis has a global root mean square difference of 1.31 K and a mean difference of 0.65 K (including a cool skin effect of 0.2 K) compared to independent data from the ESA ARC-Lake project for a 3-month period (June to August 2009). It is demonstrated that the OSTIA LSWT is an improvement over the use of climatology to capture the day-to-day variation in global lake surface temperatures

Field Intercomparison of Radiometer Measurements for Ocean Colour Validation

A field intercomparison was conducted at the Acqua Alta Oceanographic Tower (AAOT) in the northern Adriatic Sea, from 9 to 19 July 2018 to assess differences in the accuracy of in- and above-water radiometer measurements used for the validation of ocean colour products. Ten measurement systems were compared. Prior to the intercomparison, the absolute radiometric calibration of all sensors was carried out using the same standards and methods at the same reference laboratory. Measurements were performed under clear sky conditions, relatively low sun zenith angles, moderately low sea state and on the same deployment platform and frame (except in-water systems). The weighted average of five above-water measurements was used as baseline reference for comparisons. For downwelling irradiance (), there was generally good agreement between sensors with differences of <6% for most of the sensors over the spectral range 400 nm–665 nm. One sensor exhibited a systematic bias, of up to 11%, due to poor cosine response. For sky radiance () the spectrally averaged difference between optical systems was <2.5% with a root mean square error (RMS) <0.01 mWm−2 nm−1 sr−1. For total above-water upwelling radiance (), the difference was <3.5% with an RMS <0.009 mWm−2 nm−1 sr−1. For remote-sensing reflectance (), the differences between above-water TriOS RAMSES were <3.5% and <2.5% at 443 and 560 nm, respectively, and were <7.5% for some systems at 665 nm. Seabird HyperSAS sensors were on average within 3.5% at 443 nm, 1% at 560 nm, and 3% at 665 nm. The differences between the weighted mean of the above-water and in-water systems was <15.8% across visible bands. A sensitivity analysis showed that accounted for the largest fraction of the variance in , which suggests that minimizing the errors arising from this measurement is the most important variable in reducing the inter-group differences in . The differences may also be due, in part, to using five of the above-water systems as a reference. To avoid this, in situ normalized water-leaving radiance () was therefore compared to AERONET-OC SeaPRiSM as an alternative reference measurement. For the TriOS-RAMSES and Seabird-Hyperspectral Surface Acquisition System (HyperSAS) sensors the differences were similar across the visible spectra with 4.7% and 4.9%, respectively. The difference between SeaPRiSM and two in-water systems at blue, green and red bands was 11.8%. This was partly due to temporal and spatial differences in sampling between the in-water and above-water systems and possibly due to uncertainties in instrument self-shading for one of the in-water measurements

The inv dup (15) or idic (15) syndrome (Tetrasomy 15q)

The inv dup(15) or idic(15) syndrome displays distinctive clinical findings represented by early central hypotonia, developmental delay and intellectual disability, epilepsy, and autistic behaviour. Incidence at birth is estimated at 1 in 30,000 with a sex ratio of almost 1:1. Developmental delay and intellectual disability affect all individuals with inv dup(15) and are usually moderate to profound. Expressive language is absent or very poor and often echolalic. Comprehension is very limited and contextual. Intention to communicate is absent or very limited. The distinct behavioral disorder shown by children and adolescents has been widely described as autistic or autistic-like. Epilepsy with a wide variety of seizure types can occur in these individuals, with onset between 6 months and 9 years. Various EEG abnormalities have been described. Muscle hypotonia is observed in almost all individuals, associated, in most of them, with joint hyperextensibility and drooling. Facial dysmorphic features are absent or subtle, and major malformations are rare. Feeding difficulties are reported in the newborn period

Biases in the air-sea flux of CO2 resulting from ocean surface temperature gradients

Author Posting. © American Geophysical Union, 2004. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 109 (2004): C08S08, doi:10.1029/2003JC001800.The difference in the fugacities of CO2 across the diffusive sublayer at the ocean surface is the driving force behind the air-sea flux of CO2. Bulk seawater fugacity is normally measured several meters below the surface, while the fugacity at the water surface, assumed to be in equilibrium with the atmosphere, is measured several meters above the surface. Implied in these measurements is that the fugacity values are the same as those across the diffusive boundary layer. However, temperature gradients exist at the interface due to molecular transfer processes, resulting in a cool surface temperature, known as the skin effect. A warm layer from solar radiation can also result in a heterogeneous temperature profile within the upper few meters of the ocean. Here we describe measurements carried out during a 14-day study in the equatorial Pacific Ocean (GasEx-2001) aimed at estimating the gradients of CO2 near the surface and resulting flux anomalies. The fugacity measurements were corrected for temperature effects using data from the ship's thermosalinograph, a high-resolution profiler (SkinDeEP), an infrared radiometer (CIRIMS), and several point measurements at different depths on various platforms. Results from SkinDeEP show that the largest cool skin and warm layer biases occur at low winds, with maximum biases of −4% and +4%, respectively. Time series ship data show an average CO2 flux cool skin retardation of about 2%. Ship and drifter data show significant CO2 flux enhancement due to the warm layer, with maximums occurring in the afternoon. Temperature measurements were compared to predictions based on available cool skin parameterizations to predict the skin-bulk temperature difference, along with a warm layer model.This material is based upon work supported by the NSF under grant OCE-9986724, and by NOAA/OGP grant GC00-226

The resolution sensitivity of the Asian summer monsoon and its inter-model comparison between MRI-AGCM and MetUM

In this study, we compare the resolution sensitivity of the Asian Summer Monsoon (ASM) in two Atmospheric General Circulation Models (AGCMs): the MRI-AGCM and the MetUM. We analyze the MetUM at three different resolutions, N96 (approximately 200-km mesh on the equator), N216 (90-km mesh) and N512 (40-km mesh), and the MRI-AGCM at TL95 (approximately 180-km mesh on the equator), TL319 (60-km mesh), and TL959 (20-km mesh). The MRI-AGCM and the MetUM both show decreasing precipitation over the western Pacific with increasing resolution, but their precipitation responses differ over the Indian Ocean. In MRI-AGCM, a large precipitation increase appears off the equator (5–20°N). In MetUM, this off-equatorial precipitation increase is less significant and precipitation decreases over the equator. Moisture budget analysis demonstrates that a changing in moisture flux convergence at higher resolution is related to the precipitation response. Orographic effects, intra-seasonal variability and the representation of the meridional thermal gradient are explored as possible causes of the resolution sensitivity. Both high-resolution AGCMs (TL959 and N512) can represent steep topography, which anchors the rainfall pattern over south Asia and the Maritime Continent. In MRI-AGCM, representation of low pressure systems in TL959 also contributes to the rainfall pattern. Furthermore, the seasonal evolution of the meridional thermal gradient appears to be more accurate at higher resolution, particularly in the MRI-AGCM. These findings emphasize that the impact of resolution is only robust across the two AGCMs for some features of the ASM, and highlights the importance of multi-model studies of GCM resolution sensitivity

The role of horizontal resolution in simulating drivers of the global hydrological cycle

The role of atmospheric general circulation model (AGCM) horizontal resolution in representing the global energy budget and hydrological cycle is assessed, with the aim of improving the understanding of model uncertainties in simulating the hydrological cycle. We use two AGCMs from the UK Met Office Hadley Centre: HadGEM1-A at resolutions ranging from 270 to 60 km, and HadGEM3-A ranging from 135 to 25 km. The models exhibit a stable hydrological cycle, although too intense compared to reanalyses and observations. This over-intensity is explained by excess surface shortwave radiation, a common error in general circulation models (GCMs). This result is insensitive to resolution. However, as resolution is increased, precipitation decreases over the ocean and increases over the land. This is associated with an increase in atmospheric moisture transport from ocean to land, which changes the partitioning of moisture fluxes that contribute to precipitation over land from less local to more non-local moisture sources. The results start to converge at 60-km resolution, which underlines the excessive reliance of the mean hydrological cycle on physical parametrization (local unresolved processes) versus model dynamics (large-scale resolved processes) in coarser HadGEM1 and HadGEM3 GCMs. This finding may be valid for other GCMs, showing the necessity to analyze other chains of GCMs that may become available in the future with such a range of horizontal resolutions. Our finding supports the hypothesis that heterogeneity in model parametrization is one of the underlying causes of model disagreement in the Coupled Model Intercomparison Project (CMIP) exercises