Numerical investigation of the Arctic ice–ocean boundary layer and implications for air–sea gas fluxes

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ocean Science 13 (2017): 61-75, doi:10.5194/os-13-61-2017.In ice-covered regions it is challenging to determine constituent budgets – for heat and momentum, but also for biologically and climatically active gases like carbon dioxide and methane. The harsh environment and relative data scarcity make it difficult to characterize even the physical properties of the ocean surface. Here, we sought to evaluate if numerical model output helps us to better estimate the physical forcing that drives the air–sea gas exchange rate (k) in sea ice zones. We used the budget of radioactive 222Rn in the mixed layer to illustrate the effect that sea ice forcing has on gas budgets and air–sea gas exchange. Appropriate constraint of the 222Rn budget requires estimates of sea ice velocity, concentration, mixed-layer depth, and water velocities, as well as their evolution in time and space along the Lagrangian drift track of a mixed-layer water parcel. We used 36, 9 and 2 km horizontal resolution of regional Massachusetts Institute of Technology general circulation model (MITgcm) configuration with fine vertical spacing to evaluate the capability of the model to reproduce these parameters. We then compared the model results to existing field data including satellite, moorings and ice-tethered profilers. We found that mode sea ice coverage agrees with satellite-derived observation 88 to 98 % of the time when averaged over the Beaufort Gyre, and model sea ice speeds have 82 % correlation with observations. The model demonstrated the capacity to capture the broad trends in the mixed layer, although with a significant bias. Model water velocities showed only 29 % correlation with point-wise in situ data. This correlation remained low in all three model resolution simulations and we argued that is largely due to the quality of the input atmospheric forcing. Overall, we found that even the coarse-resolution model can make a modest contribution to gas exchange parameterization, by resolving the time variation of parameters that drive the 222Rn budget, including rate of mixed-layer change and sea ice forcings.Funding for this research was provided by the NSF Arctic Natural Sciences program through Award # 1203558

Identification of a BRCA2-Specific modifier locus at 6p24 related to breast cancer risk

Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer

Overview of the MOSAiC expedition: Physical oceanography

Arctic Ocean properties and processes are highly relevant to the regional and global coupled climate system, yet still scarcely observed, especially in winter. Team OCEAN conducted a full year of physical oceanography observations as part of the Multidisciplinary drifting Observatory for the Study of the Arctic Climate (MOSAiC), a drift with the Arctic sea ice from October 2019 to September 2020. An international team designed and implemented the program to characterize the Arctic Ocean system in unprecedented detail, from the seafloor to the air-sea ice-ocean interface, from sub-mesoscales to pan-Arctic. The oceanographic measurements were coordinated with the other teams to explore the ocean physics and linkages to the climate and ecosystem. This paper introduces the major components of the physical oceanography program and complements the other team overviews of the MOSAiC observational program. Team OCEAN’s sampling strategy was designed around hydrographic ship-, ice- and autonomous platform-based measurements to improve the understanding of regional circulation and mixing processes. Measurements were carried out both routinely, with a regular schedule, and in response to storms or opening leads. Here we present alongdrift time series of hydrographic properties, allowing insights into the seasonal and regional evolution of the water column from winter in the Laptev Sea to early summer in Fram Strait: freshening of the surface, deepening of the mixed layer, increase in temperature and salinity of the Atlantic Water. We also highlight the presence of Canada Basin deep water intrusions and a surface meltwater layer in leads. MOSAiC most likely was the most comprehensive program ever conducted over the ice-covered Arctic Ocean. While data analysis and interpretation are ongoing, the acquired datasets will support a wide range of physical oceanography and multi-disciplinary research. They will provide a significant foundation for assessing and advancing modeling capabilities in the Arctic Ocean

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Disseminated varicella-zoster virus in an immunocompetent adult

Varicella-zoster is the virus that causes varicella (chicken pox), herpes zoster (shingles), and rarely, severe disseminated disease including diffuse rash, encephalitis, hepatitis, and pneumonitis. Disseminated disease is most often seen in immunocompromised patients. We describe a case of disseminated zoster in an immunocompentent patient who had previously been immune to VZV. This case is also unusual in that his clinical presentation was most consistent with varicella while his laboratory data was most consistent with herpes zoster. For the purpose of rapid diagnosis and initiation of appropriate therapy, clinicians should be aware of these more atypical presentations of VZV infection

Disseminated varicella-zoster virus in an immunocompetent adult

Varicella-zoster is the virus that causes varicella (chicken pox), herpes zoster (shingles), and rarely, severe disseminated disease including diffuse rash, encephalitis, hepatitis, and pneumonitis. Disseminated disease is most often seen in immunocompromised patients. We describe a case of disseminated zoster in an immunocompentent patient who had previously been immune to VZV. This case is also unusual in that his clinical presentation was most consistent with varicella while his laboratory data was most consistent with herpes zoster. For the purpose of rapid diagnosis and initiation of appropriate therapy, clinicians should be aware of these more atypical presentations of VZV infection

Responses of oaks and tanoaks to the sudden oak death pathogen after 8 y of monitoring in two coastal California forests

Sudden oak death, caused by Phytophthora ramorum, is widely established in mesic forests of coastal central and northern California. In 2000, we placed 18 plots in two Marin County sites to monitor disease progression in coast live oaks (Quercus agrifolia), California black oaks (Q. kelloggii), and tanoaks (Lithocarpus densiflorus), the species that are most consistently killed by the pathogen in these areas. Through early 2008, the numbers of newly infected trees increased for all species. The infection rate for trees that were asymptomatic in 2000 was 5.0% y-1 for coast live oaks, 4.1% y-1 for black oaks and 10.0% y-1 for tanoaks. Mortality rates were 3.1% y-1 for coast live oaks, 2.4% y-1 for black oaks, and 5.4% y-1 for tanoaks. Mortality not attributed to P. ramorum was 0.54% y-1 for coast live oaks, and 0.75% y-1 for tanoaks. Weibull survival models of trees that were asymptomatic in 2000 provided overall median survival times of 13.7 y for coast live oaks, 13.8 y for black oaks, and 8.8 y for tanoaks. Survival of infected (bleeding) trees declined to 9.7 y for coast live oaks, 6.2 y for black oaks, and 5.8 y for tanoaks. Ambrosia beetle attacks on bleeding trees further reduced modeled survival times by 65-80%, reaffirming the earlier finding that beetle attacks on bleeding cankers considerably reduce survival. Across all plots, the modeled time for 90% of trees that were asymptomatic in 2000 to become infected is 36.5 y for coast live oaks and 15.4 y for tanoaks. There was a trend toward higher infection rates as tree diameter increased. Greater than 90% of living coast live oaks that failed during the study had extensive beetle tunneling at the site of the break. Disease intensity in coast live oaks at the plot level was positively associated with bay laurel (Umbellularia californica) basal area and negatively associated with Pacific madrone (Arbutus menziesii) basal area. This study demonstrates the use of survival modeling to characterize the effects of epidemic disease on different species and to project the future of forests infected with tree pathogens. © 2010 Elsevier B.V