Circulation in the vicinity of Mackenzie Canyon from a year-long mooring array

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lin, P., Pickart, R. S., Fissel, D., Ross, E., Kasper, J., Bahr, F., Torres, D. J., O'Brien, J., Borg, K., Melling, H., & Wiese, F. K. Circulation in the vicinity of Mackenzie Canyon from a year-long mooring array. Progress in Oceanography, 187, (2020): 102396, doi:10.1016/j.pocean.2020.102396.Data from a five-mooring array extending from the inner shelf to the continental slope in the vicinity of Mackenzie Canyon, Beaufort Sea are analyzed to elucidate the components of the boundary current system and their variability. The array, part of the Marine Arctic Ecosystem Study (MARES), was deployed from October 2016 to September 2017. Four distinct currents were identified: an eastward-directed flow adjacent to the coast; a westward-flowing, surface-intensified current centered on the outer-shelf; a bottom-intensified shelfbreak jet flowing to the east; and a recirculation at the base of the continental slope within the canyon. The shelf current transports −0.120.03 Sv in the mean and is primarily wind-driven. The response is modulated by the presence of ice, with little-to-no signal during periods of nearly-immobile ice cover and maximum response when there is partial ice cover. The shelfbreak jet transports 0.030.02 Sv in the mean, compared to 0.080.02 Sv measured upstream in the Alaskan Beaufort Sea over the same time period. The loss of transport is consistent with a previous energetics analysis and the lack of Pacific-origin summer water downstream. The recirculation in the canyon appears to be the result of local dynamics whereby a portion of the westward-flowing southern limb of the Beaufort Gyre is diverted up the canyon across isobaths. This interpretation is supported by the fact that the low-frequency variability of the recirculation is correlated with the wind-stress curl in the Canada Basin, which drives the Beaufort gyre.The authors are indebted to Fisheries and Oceans Canada for building the logistics for MARES into the at-sea missions of the Integrated Beaufort Observatory. We are grateful to the captain and crew of the CCGS Sir Wilfred Laurier for ably deploying and recovering the MARES array. Marshall Swartz assisted with the cruise preparation logistics. We thank the two anonymous reviewers for their input which helped improve the paper. This project was funded by the US Bureau of Ocean Energy Management (BOEM), on behalf of the National Ocean Partnership Program. The Canadian contribution was supported by the Environmental Studies Research Fund (ESRF Project 2014-02N). MARES publication 003

Modeling winter circulation under landfast ice : the interaction of winds with landfast ice

Author Posting. © American Geophysical Union, 2012. 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 117 (2012): C04006, doi:10.1029/2011JC007649.Idealized models and a simple vertically averaged vorticity equation illustrate the effects of an upwelling favorable wind and a spatially variable landfast ice cover on the circulation beneath landfast ice. For the case of no along-shore variations in ice, upwelling favorable winds seaward of the ice edge result in vortex squashing beneath the landfast ice leading to (1) large decreases in coastal and ice edge sea levels, (2) cross-shore sea level slopes and weak (<~.05 m s−1) under-ice currents flowing upwind, (3) strong downwind ice edge jets, and (4) offshore transport in the under-ice and bottom boundary layers of the landfast ice zone. The upwind under-ice current accelerates quickly within 2–4 days and then slows as cross-shore transport gradually decreases the cross-shore sea level slope. Near the ice edge, bottom boundary layer convergence produces ice edge upwelling. Cross-ice edge exchanges occur in the surface and above the bottom boundary layer and reduce the under-ice shelf volume by 15% in 10 days. Under-ice along-shore pressure gradients established by along- and cross-shore variations in ice width and/or under-ice friction alter this basic circulation pattern. For a landfast ice zone of finite width and length, upwelling-favorable winds blowing seaward of and transverse to the ice boundaries induce downwind flow beneath the ice and generate vorticity waves that propagate along-shore in the Kelvin wave direction. Our results imply that landfast ice dynamics, not included explicitly herein, can effectively convert the long-wavelength forcing of the wind into shorter-scale ocean motions beneath the landfast ice.J.K. was supported by the Prince William Sound Oil Spill Recovery Institute (OSRI), Alaska Sea Grant in cooperation with the Center for Global Change and the UAF Graduate School. Additional support was provided to J.K. and T.W. by the U.S. BOEMRE through the University of Alaska Coastal Marine Institute (Contract 1435-01-02-CA-85294) and by the Office of Naval Research through the National Oceanographic Partnership Program (grant N00014-07-1- 1040).2012-10-0

The MUSE Extremely Deep Field: The cosmic web in emission at high redshift

We report the discovery of diffuse extended Lyα emission from redshift 3.1 to 4.5, tracing cosmic web filaments on scales of 2.5-4 cMpc. These structures have been observed in overdensities of Lyα emitters in the MUSE Extremely Deep Field, a 140 h deep MUSE observation located in the Hubble Ultra-Deep Field. Among the 22 overdense regions identified, five are likely to harbor very extended Lyα emission at high significance with an average surface brightness of 5  ×  10-20 erg s-1 cm-2 arcsec-2. Remarkably, 70% of the total Lyα luminosity from these filaments comes from beyond the circumgalactic medium of any identified Lyα emitter. Fluorescent Lyα emission powered by the cosmic UV background can only account for less than 34% of this emission at z  ≈  3 and for not more than 10% at higher redshift. We find that the bulk of this diffuse emission can be reproduced by the unresolved Lyα emission of a large population of ultra low-luminosity Lyα emitters (< 1040 erg s-1), provided that the faint end of the Lyα luminosity function is steep (α ⪅ -1.8), it extends down to luminosities lower than 1038 -  1037 erg s-1, and the clustering of these Lyα emitters is significant (filling factor < 1/6). If these Lyα emitters are powered by star formation, then this implies their luminosity function needs to extend down to star formation rates < 10-4M yr-1. These observations provide the first detection of the cosmic web in Lyα emission in typical filamentary environments and the first observational clue indicating the existence of a large population of ultra low-luminosity Lyα emitters at high redshift. © R. Bacon et al. 2021

Effects of THBS3, SPARC and SPP1 expression on biological behavior and survival in patients with osteosarcoma

BACKGROUND: Osteosarcoma is a very aggressive tumor with a propensity to metastasize and invade surrounding tissue. Identification of the molecular determinants of invasion and metastatic potential may guide the development of a rational strategy for devising specific therapies that target the pathways leading to osteosarcoma. METHODS: In this study, we used pathway-focused low density expression cDNA arrays to screen for candidate genes related to tumor progression. Expression patterns of the selected genes were validated by real time PCR on osteosarcoma patient tumor samples and correlated with clinical and pathological data. RESULTS: THBS3, SPARC and SPP1 were identified as genes differentially expressed in osteosarcoma. In particular, THBS3 was expressed at significantly high levels (p = 0.0001) in biopsies from patients with metastasis at diagnosis, which is a predictor of worse overall survival, event-free survival and relapse free survival at diagnosis. After chemotherapy, patients with tumors over-expressing THBS3 have worse relapse free survival. High SPARC expression was found in 51/55 (96.3%) osteosarcoma samples derived from 43 patients, and correlated with the worst event-free survival (p = 0.03) and relapse free survival (p = 0.07). Overexpression of SPP1 was found in 47 of 53 (89%) osteosarcomas correlating with better overall survival, event-free survival and relapse free survival at diagnosis. CONCLUSION: In this study three genes were identified with pattern of differential gene expression associated with a phenotypic role in metastasis and invasion. Interestingly all encode for proteins involved in extracellular remodeling suggesting potential roles in osteosarcoma progression. This is the first report on the THBS3 gene working as a stimulator of tumor progression. Higher levels of THBS3 maintain the capacity of angiogenesis. High levels of SPARC are not required for tumor progression but are necessary for tumor growth and maintenance. SPP1 is not necessary for tumor progression in osteosarcoma and may be associated with inflammatory response and bone remodeling, functioning as a good biomarker

A decade of remotely sensed observations highlight complex processes linked to coastal permafrost bluff erosion in the Arctic

Eroding permafrost coasts are likely indicators and integrators of changes in the Arctic System as they are susceptible to the combined effects of declining sea ice extent, increases in open water duration, more frequent and impactful storms, sea-level rise, and warming permafrost. However, few observation sites in the Arctic have yet to link decadal-scale erosion rates with changing environmental conditions due to temporal data gaps. This study increases the temporal fidelity of coastal permafrost bluff observations using near-annual high spatial resolution (<1 m) satellite imagery acquired between 2008–2017 for a 9 km segment of coastline at Drew Point, Beaufort Sea coast, Alaska. Our results show that mean annual erosion for the 2007–2016 decade was 17.2 m yr−1, which is 2.5 times faster than historic rates, indicating that bluff erosion at this site is likely responding to changes in the Arctic System. In spite of a sustained increase in decadal-scale mean annual erosion rates, mean open water season erosion varied from 6.7 m yr−1 in 2010 to more than 22.0 m yr−1 in 2007, 2012, and 2016. This variability provided a range of coastal responses through which we explored the different roles of potential environmental drivers. The lack of significant correlations between mean open water season erosion and the environmental variables compiled in this study indicates that we may not be adequately capturing the environmental forcing factors, that the system is conditioned by long-term transient effects or extreme weather events rather than annual variability, or that other not yet considered factors may be responsible for the increased erosion occurring at Drew Point. Our results highlight an increase in erosion at Drew Point in the 21st century as well as the complexities associated with unraveling the factors responsible for changing coastal permafrost bluffs in the Arctic

Multiple Histone Methyl and Acetyltransferase Complex Components Bind the HLA-DRA Gene

Major histocompatibility complex class II (MHC-II) genes are fundamental components that contribute to adaptive immune responses. While characterization of the chromatin features at the core promoter region of these genes has been studied, the scope of histone modifications and the modifying factors responsible for activation of these genes are less well defined. Using the MHC-II gene HLA-DRA as a model, the extent and distribution of major histone modifications associated with active expression were defined in interferon-γ induced epithelial cells, B cells, and B-cell mutants for MHC-II expression. With active transcription, nucleosome density around the proximal regulatory region was diminished and histone acetylation and methylation modifications were distributed throughout the gene in distinct patterns that were dependent on the modification examined. Irrespective of the location, the majority of these modifications were dependent on the binding of either the X-box binding factor RFX or the class II transactivator (CIITA) to the proximal regulatory region. Importantly, once established, the modifications were stable through multiple cell divisions after the activating stimulus was removed, suggesting that activation of this system resulted in an epigenetic state. A dual crosslinking chromatin immunoprecipitation method was used to detect histone modifying protein components that interacted across the gene. Components of the MLL methyltransferase and GCN5 acetyltransferase complexes were identified. Some MLL complex components were found to be CIITA independent, including MLL1, ASH2L and RbBP5. Likewise, GCN5 containing acetyltransferase complex components belonging to the ATAC and STAGA complexes were also identified. These results suggest that multiple complexes are either used or are assembled as the gene is activated for expression. Together the results define and illustrate a complex network of histone modifying proteins and multisubunit complexes participating in MHC-II transcription

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, management, and analysis. In this perspective, we present AnVIL, describe its ecosystem and interoperability with other platforms, and highlight how this platform and associated initiatives contribute to improved genomic data sharing efforts. The AnVIL is a federated cloud platform designed to manage and store genomics and related data, enable population-scale analysis, and facilitate collaboration through the sharing of data, code, and analysis results. By inverting the traditional model of data sharing, the AnVIL eliminates the need for data movement while also adding security measures for active threat detection and monitoring and provides scalable, shared computing resources for any researcher. We describe the core data management and analysis components of the AnVIL, which currently consists of Terra, Gen3, Galaxy, RStudio/Bioconductor, Dockstore, and Jupyter, and describe several flagship genomics datasets available within the AnVIL. We continue to extend and innovate the AnVIL ecosystem by implementing new capabilities, including mechanisms for interoperability and responsible data sharing, while streamlining access management. The AnVIL opens many new opportunities for analysis, collaboration, and data sharing that are needed to drive research and to make discoveries through the joint analysis of hundreds of thousands to millions of genomes along with associated clinical and molecular data types

CIRCULATION AND WATER PROPERTY VARIATIONS IN THE NEARSHORE ALASKAN BEAUFORT SEA (1999 – 2007)

Six years of current meter and water property data were collected year-round (1999 – 2007) from the landfast ice zone of the nearshore Alaskan Beaufort Sea (ABS). The data show large seasonal differences in the circulation that is defined by the set-up and breakup of the landfast ice. During the open water season (July – mid-October) mid-depth currents often exceed 20 cm-s-1, whereas during the landfast ice season (mid-October – June) these currents are generally \u3c10 cm-s-1. Tidal currents are feeble (\u3c3 cm-s-1) year-round and probably do not play a dynamically significant role on the inner shelf. Most (\u3e90%) of the current variability is in the along-shore direction year-round. In general the mean currents are not statistically different from zero over the whole record or in individual seasons. Open water currents are significantly correlated with the local winds, but currents beneath the landfast ice are not. Calculations conducted over both seasons suggest along-shore sea-level gradients are about 10-6, with the magnitude of these gradients being only slightly larger during the open water season than during the landfast ice season. These gradients are presumably set-up by the winds during the open water season, but their origin during the landfast ice season is unknown. However, preliminary model studies indicate that spatial variations in the underice friction coefficient are capable of establishing along-shore pressure gradients of this magnitude. During the open water season upwelling-favorable winds force westward flows that are strongly sheared in the vertical and with maximum currents at the surface. In contrast, downwelling favorable winds are weakly sheared in the vertical. The asymmetric current structure is presumed due to differences in stratification; strongly stratified during upwelling (westward) winds and weakly stratified during downwelling (eastward) winds. Cross-shore flows are generally small (~3 cm s-1) compared to along-shore currents. However, cross-shore flows of ~10 cm-s-1 were observed during the landfast ice season when the spring freshet resulted in an offshore spreading of a buoyant plume beneath the landfast ice. Although measured cross-shore flows are generally small, satellite imagery suggests that frontal instabilities associated with low-salinity nearshore plumes can transport inner shelf waters offshore to the Beaufort shelfbreak during the open water season. Observations from elsewhere in the Arctic suggest that cross-shore current speeds associated with instabilities can be as large as 30 cm s-1. Our results suggest that oil spilled beneath the landfast ice will stay within the vicinity of the oil spill source as current speeds will rarely exceed the threshold velocity required to transport an oil slick once it has attained its equilibrium thickness. We find that an underice oil spill has a 90% probability of remaining within 20 km of its origin over a 12-day period. Because of the broad spatial coherence in the flow field (~100 km in along-shore extent), underice currents could be monitored at one point and transmitted real-time to cleanup crews in the event of an underice spill. This information would verify the current speeds and whether oil would stay in the vicinity of the spill. Oil spilled during the open water season could be rapidly dispersed over great distances (~200 km in 12 days) in both the along- and cross-shore directions, however. Water properties also vary seasonally in response to ice formation and melting, the spring freshet, and wind-mixing. Salinities increase and temperatures decrease throughout the winter due to freezing and brine expulsion from sea-ice. During the spring freshet, the inner shelf is strongly stratified and remains so until the ice retreats and downwelling winds mix the water column. The annual suspended sediment cycle, based on transmissivity measurements, suggests rapid deposition of river borne sediments beneath the landfast ice during the spring freshet, with re-suspension and transport occurring throughout the open water season depending upon storm frequency. Re-suspension and transport is also vigorous during the formation of landfast ice and we conclude that much sediment is incorporated into the ice matrix at this time of the year. Ice-incorporated sediments are either transported with the ice or returned to the water column during melting the following summer. There are several important issues that we believe need to be addressed in the future. Modeling of the landfast ice zone requires an understanding of the role that ice-water friction plays in this region. Measurements of the spatially and temporally varying underice topography are critical to understanding the dynamics of this shelf. Second, the source and magnitude of the along-shore pressure gradients responsible for the underice currents needs to be determined. Third, it is not clear if the findings based on current measurements made in water depths ≤17 m apply to deeper portions of the landfast ice zone. Hence the cross-shore coherence in the underice circulation field needs to be determined. Fourth, the introduction of freshwater creates stratification that can lead to an asymmetric current response to wind-forcing during the open water season. Observations on the thermohaline structure of the Beaufort shelf are needed in order to understand and model the circulation field during the open water season. Cross-shore salinity fronts, established by river runoff, can become unstable and cause energetic cross-shelf flows capable of carrying pollutants far offshore. The dynamics and kinematics of these features need study. Fifth, sediments can adsorb pollutants and be incorporated into the ice along with oil; hence we recommend that consideration be given to the potential role that ice plays in the transport of sediments and pollutants on this shelf