Local and downstream relationships between Labrador Sea Water volume and North Atlantic meridional overturning circulation variability

While it has generally been understood that the production of Labrador Sea Water (LSW) impacts the Atlantic meridional overturning circulation (MOC), this relationship has not been explored extensively nor validated against observations. To explore this relationship, a suite of global ocean and ocean–sea-ice models forced by the same interannually-varying atmospheric dataset, varying in resolution from non-eddy-permitting to eddy-permitting (1°–1/4°), is analyzed to investigate the local and downstream relationships between LSW formation and the MOC on interannual to decadal time scales. While all models display a strong relationship between changes in the LSW volume and the MOC in the Labrador Sea, this relationship degrades considerably downstream of the Labrador Sea. In particular, there is no consistent pattern among the models in the North Atlantic subtropical basin over interannual to decadal time scales. Furthermore, the strong response of the MOC in the Labrador Sea to LSW volume changes in that basin may be biased by the overproduction of LSW in many models compared to observations. This analysis shows that changes in LSW volume in the Labrador Sea cannot be clearly and consistently linked to a coherent MOC response across latitudes over interannual to decadal time scales in ocean hindcast simulations of the last half-century. Similarly, no coherent relationships are identified between the MOC and the Labrador Sea mixed layer depth or the density of newly formed LSW across latitudes or across models over interannual to decadal time scales

Variability of the Atlantic meridional overturning circulation in CCSM4

Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 25 (2012): 5153–5172, doi:10.1175/JCLI-D-11-00463.1.Atlantic meridional overturning circulation (AMOC) variability is documented in the Community Climate System Model, version 4 (CCSM4) preindustrial control simulation that uses nominal 1° horizontal resolution in all its components. AMOC shows a broad spectrum of low-frequency variability covering the 50–200-yr range, contrasting sharply with the multidecadal variability seen in the T85 × 1 resolution CCSM3 present-day control simulation. Furthermore, the amplitude of variability is much reduced in CCSM4 compared to that of CCSM3. Similarities as well as differences in AMOC variability mechanisms between CCSM3 and CCSM4 are discussed. As in CCSM3, the CCSM4 AMOC variability is primarily driven by the positive density anomalies at the Labrador Sea (LS) deep-water formation site, peaking 2 yr prior to an AMOC maximum. All processes, including parameterized mesoscale and submesoscale eddies, play a role in the creation of salinity anomalies that dominate these density anomalies. High Nordic Sea densities do not necessarily lead to increased overflow transports because the overflow physics is governed by source and interior region density differences. Increased overflow transports do not lead to a higher AMOC either but instead appear to be a precursor to lower AMOC transports through enhanced stratification in LS. This has important implications for decadal prediction studies. The North Atlantic Oscillation (NAO) is significantly correlated with the positive boundary layer depth and density anomalies prior to an AMOC maximum. This suggests a role for NAO through setting the surface flux anomalies in LS and affecting the subpolar gyre circulation strength.The CCSM project is supported by NSF and the Office of Science (BER) of the U.S. Department of Energy. SGY and YOK were supported by the NOAA Climate Program Office under Climate Variability and Predictability Program Grants NA09OAR4310163 and NA10OAR4310202, respectively.2013-02-0

Mechanisms governing interannual variability of upper-ocean temperature in a global ocean hindcast simulation

Author Posting. © American Meteorological Society, 2007. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 37 (2007): 1918-1938, doi:10.1175/jpo3089.1.The interannual variability in upper-ocean (0–400 m) temperature and governing mechanisms for the period 1968–97 are quantified from a global ocean hindcast simulation driven by atmospheric reanalysis and satellite data products. The unconstrained simulation exhibits considerable skill in replicating the observed interannual variability in vertically integrated heat content estimated from hydrographic data and monthly satellite sea surface temperature and sea surface height data. Globally, the most significant interannual variability modes arise from El Niño–Southern Oscillation and the Indian Ocean zonal mode, with substantial extension beyond the Tropics into the midlatitudes. In the well-stratified Tropics and subtropics, net annual heat storage variability is driven predominately by the convergence of the advective heat transport, mostly reflecting velocity anomalies times the mean temperature field. Vertical velocity variability is caused by remote wind forcing, and subsurface temperature anomalies are governed mostly by isopycnal displacements (heave). The dynamics at mid- to high latitudes are qualitatively different and vary regionally. Interannual temperature variability is more coherent with depth because of deep winter mixing and variations in western boundary currents and the Antarctic Circumpolar Current that span the upper thermocline. Net annual heat storage variability is forced by a mixture of local air–sea heat fluxes and the convergence of the advective heat transport, the latter resulting from both velocity and temperature anomalies. Also, density-compensated temperature changes on isopycnal surfaces (spice) are quantitatively significant.This work was supported in part from NOAA Office of Global Programs ACCP Grant NA86GP0290, NSF Grant OCE96-33681, and the WHOI Ocean and Climate Change Institute

An assessment of the Arctic Ocean in a suite of interannual CORE-II simulations. Part III: Hydrography and fluxes

In this paper we compare the simulated Arctic Ocean in 15 global ocean–sea ice models in the framework of the Coordinated Ocean-ice Reference Experiments, phase II (CORE-II). Most of these models are the ocean and sea-ice components of the coupled climate models used in the Coupled Model Intercomparison Project Phase 5 (CMIP5) experiments. We mainly focus on the hydrography of the Arctic interior, the state of Atlantic Water layer and heat and volume transports at the gateways of the Davis Strait, the Bering Strait, the Fram Strait and the Barents Sea Opening. We found that there is a large spread in temperature in the Arctic Ocean between the models, and generally large differences compared to the observed temperature at intermediate depths. Warm bias models have a strong temperature anomaly of inflow of the Atlantic Water entering the Arctic Ocean through the Fram Strait. Another process that is not represented accurately in the CORE-II models is the formation of cold and dense water, originating on the eastern shelves. In the cold bias models, excessive cold water forms in the Barents Sea and spreads into the Arctic Ocean through the St. Anna Through. There is a large spread in the simulated mean heat and volume transports through the Fram Strait and the Barents Sea Opening. The models agree more on the decadal variability, to a large degree dictated by the common atmospheric forcing. We conclude that the CORE-II model study helps us to understand the crucial biases in the Arctic Ocean. The current coarse resolution state-of-the-art ocean models need to be improved in accurate representation of the Atlantic Water inflow into the Arctic and density currents coming from the shelves

North Atlantic simulations in Coordinated Ocean-ice Reference Experiments phase II (CORE-II). Part I: Mean states

Simulation characteristics from eighteen global ocean–sea-ice coupled models are presented with a focus on the mean Atlantic meridional overturning circulation (AMOC) and other related fields in the North Atlantic. These experiments use inter-annually varying atmospheric forcing data sets for the 60-year period from 1948 to 2007 and are performed as contributions to the second phase of the Coordinated Ocean-ice Reference Experiments (CORE-II). The protocol for conducting such CORE-II experiments is summarized. Despite using the same atmospheric forcing, the solutions show significant differences. As most models also differ from available observations, biases in the Labrador Sea region in upper-ocean potential temperature and salinity distributions, mixed layer depths, and sea-ice cover are identified as contributors to differences in AMOC. These differences in the solutions do not suggest an obvious grouping of the models based on their ocean model lineage, their vertical coordinate representations, or surface salinity restoring strengths. Thus, the solution differences among the models are attributed primarily to use of different subgrid scale parameterizations and parameter choices as well as to differences in vertical and horizontal grid resolutions in the ocean models. Use of a wide variety of sea-ice models with diverse snow and sea-ice albedo treatments also contributes to these differences. Based on the diagnostics considered, the majority of the models appear suitable for use in studies involving the North Atlantic, but some models require dedicated development effort

Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families.

BACKGROUND: Genetic variants are likely to contribute to a portion of prostate cancer risk. Full elucidation of the genetic etiology of prostate cancer is difficult because of incomplete penetrance and genetic and phenotypic heterogeneity. Current evidence suggests that genetic linkage to prostate cancer has been found on several chromosomes including the X; however, identification of causative genes has been elusive. METHODS: Parametric and non-parametric linkage analyses were performed using 26 microsatellite markers in each of 11 groups of multiple-case prostate cancer families from the International Consortium for Prostate Cancer Genetics (ICPCG). Meta-analyses of the resultant family-specific linkage statistics across the entire 1,323 families and in several predefined subsets were then performed. RESULTS: Meta-analyses of linkage statistics resulted in a maximum parametric heterogeneity lod score (HLOD) of 1.28, and an allele-sharing lod score (LOD) of 2.0 in favor of linkage to Xq27-q28 at 138 cM. In subset analyses, families with average age at onset less than 65 years exhibited a maximum HLOD of 1.8 (at 138 cM) versus a maximum regional HLOD of only 0.32 in families with average age at onset of 65 years or older. Surprisingly, the subset of families with only 2-3 affected men and some evidence of male-to-male transmission of prostate cancer gave the strongest evidence of linkage to the region (HLOD = 3.24, 134 cM). For this subset, the HLOD was slightly increased (HLOD = 3.47 at 134 cM) when families used in the original published report of linkage to Xq27-28 were excluded. CONCLUSIONS: Although there was not strong support for linkage to the Xq27-28 region in the complete set of families, the subset of families with earlier age at onset exhibited more evidence of linkage than families with later onset of disease. A subset of families with 2-3 affected individuals and with some evidence of male to male disease transmission showed stronger linkage signals. Our results suggest that the genetic basis for prostate cancer in our families is much more complex than a single susceptibility locus on the X chromosome, and that future explorations of the Xq27-28 region should focus on the subset of families identified here with the strongest evidence of linkage to this region.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

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation

Although genome-wide association studies have identified over 100 risk loci that explain ∼33% of familial risk for prostate cancer (PrCa), their functional effects on risk remain largely unknown. Here we use genotype data from 59,089 men of European and African American ancestries combined with cell-type-specific epigenetic data to build a genomic atlas of single-nucleotide polymorphism (SNP) heritability in PrCa. We find significant differences in heritability between variants in prostate-relevant epigenetic marks defined in normal versus tumour tissue as well as between tissue and cell lines. The majority of SNP heritability lies in regions marked by H3k27 acetylation in prostate adenoc7arcinoma cell line (LNCaP) or by DNaseI hypersensitive sites in cancer cell lines. We find a high degree of similarity between European and African American ancestries suggesting a similar genetic architecture from common variation underlying PrCa risk. Our findings showcase the power of integrating functional annotation with genetic data to understand the genetic basis of PrCa

JRA55-based repeat year forcing datasets for driving ocean-sea-ice models

JRA55-do, the new atmospheric dataset for driving ocean-sea-ice models based on the Japanese 55-year atmospheric reanalysis (JRA-55), has been recently proffered for use in future ocean-sea-ice hindcast simulations, including those under the Ocean Model Intercomparison Project (OMIP) umbrella, thereby replacing the Coordinated Ocean-ice Reference Experiments (CORE) interannual forcing dataset. The JRA55-do dataset contains numerous and substantial improvements over the existing CORE dataset, including refined resolution, self-consistency of forcing fields, and duration. However, one feature of CORE, that is not available in JRA55- do, is the "Normal Year Forcing" (CORE-NYF), a single repeating annual cycle of all forcing fields necessary to run an ocean-sea-ice model without imposed interannual variability. Here, we propose a process for obtaining and evaluating "Repeat Year Forcing" (RYF) datasets based on the JRA55-do dataset for driving ocean-sea-ice models. This process involves the identification of 12-month periods (not necessarily a single calendar year) that are most neutral in terms of major climate modes of variability. Three candidate periods are identified and evaluated with three global ocean-sea-ice models. We find that the largest differences between the simulations arise from model biases, indicating the ultimate choice of the candidate repeat year is not critical. By referencing to the respective CORE-NYF simulations (in an attempt to account for model bias), we find the differences between the three RYF periods to be generally consistent across the models, except for an anthropogenic warming signal for later candidate years. Based on the analysis presented here, we find all three candidate periods to be suitable for use as RYF datasets, subject to application, and we recommend the period from 1st May 1990 to 30th April 1991 to be the best available RYF dataset for driving ocean-sea-ice models.COSIMA is supported by an Australian Research Council Linkage Project (LP160100073). KDS was supported by the Australian Government Department of the Environment through the National Environmental Science Program (NESP). MRI contribution to this study was supported by Meteorological Research Institute, Japan and JSPS, Japan KAKENHI Grant Number 15H03726. NCAR contribution to this study by the US National Oceanic and Atmospheric Administration (NOAA) Climate Program Office Climate Variability and Predictability Program. NCAR is a major facility sponsored by the US National Science Foundation (NSF) under Cooperative Agreement 1852977. Analysis was performed with the resources of the National Computational Infrastructure (Canberra, Australia), which is supported by the Australian Commonwealth Government