Current-eddy interaction in the Agulhas Return Current region from the seismic oceanography perspective

Interleaving in the Agulhas Return Current (ARC) frontal region is commonly manifested in the form of thermohaline intrusions, as sub-tropical and sub-polar water masses of similar density meet. In Jan/Feb 2012, the Naval Research Laboratory and collaborators carried out a field experiment in which seismic and traditional hydrographic observations were acquired to examine frontal zone mixing processes. The high lateral resolution (10 m) of the seismic observations allowed fine-scale lateral tracking of thermal intrusions, which were corroborated with simultaneous XBT casts. Between seismic deployments both salinity and temperature data were acquired via CTD, Underway-CTD and microstructure profiles. This study focuses on analyzing seismic reflection data in a particular E-W transect where the northward flowing ARC interacted with the southward flowing portion of a large anticyclonic eddy. Strong reflectors were most prominent at the edge of a hyperbolic zone formed between the eddy and ARC, where sub-polar waters interacted with waters of sub-tropical origin on either side. Reflectors were shallow within the hyperbolic zone and extended to 1200 m below the ARC. The nature of the observed reflectors will be determined from comparison of seismic reflection and derived ∂T/∂z fields, and XBT and TS profiles from the available hydrographic data

Seismic oceanography imaging of thermal intrusions in strong frontal regions

The Naval Research Laboratory and collaborating partners carried out two dedicated seismic oceanography field experiments in two very different strong frontal regions. ADRIASEISMIC took seismic oceanography measurements at the confluence of North Adriatic Dense Water advected along the Western Adriatic Current and Modified Levantine Intermediate Water advected around the topographic rim of the Southern Adriatic basin. ARC12 took seismic oceanography measurements in and around the Agulhas Return Current as it curved northwards past the Agulhas Plateau and interacted with a large anticyclone that had collided with the current. Despite one study focused on coastal boundary currents and the other focused on a major Western Boundary Current extension, the complex horizontal structures seen through seismic imaging are tied to the processes of thermal intrusions and interleaving in both systems. Seismic Oceanography provides a unique capability of tracking the fine-scale horizontal extent of these intrusions

Energetics in Delaware Bay: Comparison of two box models with observations

A corrected version of an unstratified box model of potential energy anomaly , initially developed by Garvine and Whitney (2006), and a new two-layer box model that allows for stratified and well-mixed conditions are applied to Delaware Bay. The models are applied for the Garvine and Whitney (2006) 1988-1994 study period and in Spring 2003; however, only model results of potential energy anomaly from the latter period are compared to in situ observations obtained outside the bay mouth. Unstratified model results for the two study periods reveal that the river discharge (Ω1) is the largest potential energy anomaly contributor. This term is closely followed (but with opposite sign) by the coastal current efflux term (Ω2). For the two-layer model the largest contributor is the dense inflow term (Ω6). The wind term (Ω5) is the second largest, followed by the tide (Ω3), river discharge (Ω1) and coastal current terms. In both models the solar heat flux term (Ω4) makes the smallest contribution to ϕ. The available one-month comparison of model results to observations renders statistically insignificant correlation coefficients for both models. We speculate dynamical differences between conditions at the estuary mouth and the instrument location on the nearby shelf contribute to the model-observation mismatch. Other statistics, such as the root mean square error indicate that the unstratified model performs better than the two-layer model for the observation period. The latter model is, however, able to depict the importance of tides and winds in the computation of potential energy anomaly and is able to detect the response of ϕ due to strong wind events. While there is no clear model choice for the Delaware Bay, the unstratified model may be entirely inappropriate for highly stratified estuaries

Spring 2009 water mass distribution, mixing and transport in the southern Adriatic after a low production of winter dense waters

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High-Resolution Sampling of a Broad Marine Life Size Spectrum Reveals Differing Size- and Composition-Based Associations With Physical Oceanographic Structure

Observing multiple size classes of organisms, along with oceanographic properties and water mass origins, can improve our understanding of the drivers of aggregations, yet acquiring these measurements remains a fundamental challenge in biological oceanography. By deploying multiple biological sampling systems, from conventional bottle and net sampling to in situ imaging and acoustics, we describe the spatial patterns of different size classes of marine organisms (several microns to ∼10 cm) in relation to local and regional (m to km) physical oceanographic conditions on the Delaware continental shelf. The imaging and acoustic systems deployed included (in ascending order of target organism size) an imaging flow cytometer (CytoSense), a digital holographic imaging system (HOLOCAM), an In Situ Ichthyoplankton Imaging System (ISIIS, 2 cameras with different pixel resolutions), and multi-frequency acoustics (SIMRAD, 18 and 38 kHz). Spatial patterns generated by the different systems showed size-dependent aggregations and differing connections to horizontal and vertical salinity and temperature gradients that would not have been detected with traditional station-based sampling (∼9-km resolution). A direct comparison of the two ISIIS cameras showed composition and spatial patchiness changes that depended on the organism size, morphology, and camera pixel resolution. Large zooplankton near the surface, primarily composed of appendicularians and gelatinous organisms, tended to be more abundant offshore near the shelf break. This region was also associated with high phytoplankton biomass and higher overall organism abundances in the ISIIS, acoustics, and targeted net sampling. In contrast, the inshore region was dominated by hard-bodied zooplankton and had relatively low acoustic backscatter. The nets showed a community dominated by copepods, but they also showed high relative abundances of soft-bodied organisms in the offshore region where these organisms were quantified by the ISIIS. The HOLOCAM detected dense patches of ciliates that were too small to be captured in the nets or ISIIS imagery. This near-simultaneous deployment of different systems enables the description of the spatial patterns of different organism size classes, their spatial relation to potential prey and predators, and their association with specific oceanographic conditions. These datasets can also be used to evaluate the efficacy of sampling techniques, ultimately aiding in the design of efficient, hypothesis-driven sampling programs that incorporate these complementary technologies

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin