1995, Spatial and temporal variability of late Neogene equatorial Pacific carbonate

High-resolution, continuous records of GRAPE wet bulk density (a carbonate proxy) from Ocean Drilling Program Leg 138 provide one the opportunity for a detailed study of eastern equatorial Pacific Ocean carbonate sedimentation during the last 6 m.y. The transect of sites drilled spans both latitude and longitude in the eastern equatorial Pacific from 90° to 110°W and from 5°S to 10°N. Two modes of variability are resolved through the use of Empirical Orthogonal Function (EOF) analysis. In the presence of large tectonic and climatic boundary condition changes over the last 6 m.y., the dominant mode of spatial variability in carbonate sedimentation is remarkably constant. The first mode accounts for over 50% of the variance in the data, and is consistent with forcing by equatorial divergence. This mode characterizes both carbonate concentration and carbonate mass accumulation rate time series. Variability in the first mode is highly coherent with insolation, indicating a strong linear relationship between equatorial Pacific car bonate sedimentation and Milankovitch variability. Frequency domain analysis indicates that the coupling to equatorial divergence in carbonate sedimentation is strongest in the precession band (19-23 k.y.) and weakest though present at lower frequencies. The second mode of variability has a consistent spatial pattern of east-west asymmetry over the past 4 m.y. only; prior to 4 Ma, a different mode of spatial variability may have been present, possibly suggesting influence by closure of the Isthmus of Panama or other tectonic changes. The second mode of variability may indicate influence by CaCO3 dissolution. The second mode of variability is not highly coherent with insolation. Comparison of the modes of carbonate variability to a 4 m.y. record of benthic δ 1 8 indicates that although overall correlation between carbonate and δ 1 8 is low, both modes of variability in carbonate sedimentation are coherent with δ 1 8 changes at some frequencies. The first mode of carbonate variability is coherent with Sites 846/849 δ 1 8 at the dominant insolation periods, and the second mode is coherent at 100 k.y. during the last 2 m.y. The coherence between carbonate sedimentation and δ 1 8 in both EOF modes suggests that multiple uncorrelated modes of variability operated within the climate system during the late Neogene

Leveraging OpenStack and Ceph for a Controlled-Access Data Cloud

While traditional HPC has and continues to satisfy most workflows, a new generation of researchers has emerged looking for sophisticated, scalable, on-demand, and self-service control of compute infrastructure in a cloud-like environment. Many also seek safe harbors to operate on or store sensitive and/or controlled-access data in a high capacity environment. To cater to these modern users, the Minnesota Supercomputing Institute designed and deployed Stratus, a locally-hosted cloud environment powered by the OpenStack platform, and backed by Ceph storage. The subscription-based service complements existing HPC systems by satisfying the following unmet needs of our users: a) on-demand availability of compute resources, b) long-running jobs (i.e., $> 30$ days), c) container-based computing with Docker, and d) adequate security controls to comply with controlled-access data requirements. This document provides an in-depth look at the design of Stratus with respect to security and compliance with the NIH's controlled-access data policy. Emphasis is placed on lessons learned while integrating OpenStack and Ceph features into a so-called "walled garden", and how those technologies influenced the security design. Many features of Stratus, including tiered secure storage with the introduction of a controlled-access data "cache", fault-tolerant live-migrations, and fully integrated two-factor authentication, depend on recent OpenStack and Ceph features.Comment: 7 pages, 5 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).

Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers

Halocline water modification and along slope advection at the Laptev Sea continental margin

A general pattern in water mass distribution and potential shelf–basin exchange is revealed at the Laptev Sea continental slope based on hydrochemical and stable oxygen isotope data from the summers 2005–2009. Despite considerable interannual variations, a frontal system can be inferred between shelf, continental slope and central Eurasian Basin waters in the upper 100 m of the water column along the continental slope. Net sea-ice melt is consistently found at the continental slope. However, the sea-ice meltwater signal is independent from the local retreat of the ice cover and appears to be advected from upwind locations. In addition to the along-slope frontal system at the continental shelf break, a strong gradient is identified on the Laptev Sea shelf between 122° E and 126° E with an eastward increase of riverine and sea-ice related brine water contents. These waters cross the shelf break at ~ 140° E and feed the low-salinity halocline water (LSHW, salinity S < 33) in the upper 50 m of the water column. High silicate concentrations in Laptev Sea bottom waters may lead to speculation about a link to the local silicate maximum found within the salinity range of ~ 33 to 34.5, typical for the Lower Halocline Water (LHW) at the continental slope. However brine signatures and nutrient ratios from the central Laptev Sea differ from those observed at the continental slope. Thus a significant contribution of Laptev Sea bottom waters to the LHW at the continental slope can be excluded. The silicate maximum within the LHW at the continental slope may be formed locally or at the outer Laptev Sea shelf. Similar to the advection of the sea-ice melt signal along the Laptev Sea continental slope, the nutrient signal at 50–70 m water depth within the LHW might also be fed by advection parallel to the slope. Thus, our analyses suggest that advective processes from upstream locations play a significant role in the halocline formation in the northern Laptev Sea

Synorogenic evolution of large-scale drainage patterns: Isotope paleohydrology of sequential Laramide basins

In the past decade, we and others have compiled an extensive dataset of O, C and Sr isotope stratigraphies from sedimentary basins throughout the Paleogene North American Cordillera. In this study, we present new results from the Piceance Creek Basin of northwest Colorado, which record the evolving hydrology of the Eocene Green River Lake system. We then place the new data in the context of the broader Cordilleran dataset and summarize implications for understanding the synorogenic evolution of large-scale drainage patterns. The combined data reflect (1) a period of throughgoing foreland rivers heading in the Sevier fold-and-thrust belt and flowing east, (2) ponding of freshwater lakes in the foredeep as Laramide uplifts blocked drainage, (3) hydrologic closure that led to both intensive evaporation in the terminal sink of the Piceance Creek Basin and integration of catchments over length-scales \u3e1000 km, (4) infilling of basin accommodation by southward migrating magmatism in distal catchments, leading to the freshening and demise of intraforeland lakes that also stepped south over time

A Study of the Diverse T Dwarf Population Revealed by WISE

We report the discovery of 87 new T dwarfs uncovered with the Wide-field Infrared Survey Explorer (WISE) and 3 brown dwarfs with extremely red near-infrared colors that exhibit characteristics of both L and T dwarfs. Two of the new T dwarfs are likely binaries with L7 ± 1 primaries and mid-type T secondaries. In addition, our follow-up program has confirmed 10 previously identified T dwarfs and 4 photometrically selected L and T dwarf candidates in the literature. This sample, along with the previous WISE discoveries, triples the number of known brown dwarfs with spectral types later than T5. Using the WISE All-Sky Source Catalog we present updated color-color and color-type diagrams for all the WISE-discovered T and Y dwarfs. Near-infrared spectra of the new discoveries are presented along with spectral classifications. To accommodate later T dwarfs we have modified the integrated flux method of determining spectral indices to instead use the median flux. Furthermore, a newly defined J-narrow index differentiates the early-type Y dwarfs from late-type T dwarfs based on the J-band continuum slope. The K/J indices for this expanded sample show that 32% of late-type T dwarfs have suppressed K-band flux and are blue relative to the spectral standards, while only 11% are redder than the standards. Comparison of the Y/J and K/J index to models suggests diverse atmospheric conditions and supports the possible re-emergence of clouds after the L/T transition. We also discuss peculiar brown dwarfs and candidates that were found not to be substellar, including two young stellar objects and two active galactic nuclei. The substantial increase in the number of known late-type T dwarfs provides a population that will be used to test models of cold atmospheres and star formation. The coolest WISE-discovered brown dwarfs are the closest of their type and will remain the only sample of their kind for many years to come

Evidence for Direct Roles of Two Additional Factors, SECp43 and Soluble Liver Antigen, in the Selenoprotein Synthesis Machinery

Selenocysteine (Sec) is inserted into selenoproteins co-translationally with the help of various cis- and trans-acting factors. The specific mechanisms of Sec biosynthesis and insertion into protein in eukaryotic cells, however, are not known. Two proteins, SECp43 and the soluble liver antigen (SLA), were previously reported to interact with tRNA [Ser]Sec, but their functions remained elusive. Herein, we report that knockdown of SECp43 in NIH3T3 or TCMK-1 cells using RNA interference technology resulted in a reduction in the level of methylation at the 2’-hydroxylribosyl moiety in the wobble position (Um34) of Sec tRNA [Ser]Sec, and consequently reduced glutathione peroxidase 1 expression. Double knockdown of SECp43 and SLA resulted in decreased selenoprotein expression. SECp43 formed a complex with Sec tRNA [Ser]Sec and SLA, and the targeted removal of one of these proteins affected the binding of the other to Sec tRNA [Ser]Sec. SECp43 was located primarily in the nucleus, whereas SLA was found in the cytoplasm. Co-transfection of both proteins resulted in the nuclear translocation of SLA suggesting that SECp43 may also promote shuttling of SLA and Sec tRNA [Ser]Sec between different cellular compartments. Taken together, these data establish the role of SECp43 and SLA in selenoprotein biosynthesis through interaction with tRNA [Ser]Sec in a multiprotein complex. The data also reveal a role of SECp43 in regulation of selenoprotein expression by affecting the synthesis of Um34 on tRNA[ [Ser]Sec and the intracellular location of SLA

Reduced admixture of North Atlantic Deep Water to the deep central South Pacific during the last two glacial periods

Key Points: • Little deep water circulation changes in the past 240,000 years in the central South Pacific • Reduced North Atlantic Deep Water admixture during glacials to the Southern Ocean • South Pacific lithogenic material mainly sourced from SE Australia and South New Zealand The South Pacific is a sensitive location for the variability of the global oceanic thermohaline circulation given that deep waters from the Atlantic Ocean, the Southern Ocean, and the Pacific basin are exchanged. Here we reconstruct the deep-water circulation of the central South Pacific for the last two glacial cycles (from 240,000 years ago to the Holocene) based on radiogenic neodymium (Nd) and lead (Pb) isotope records complemented by benthic stable carbon data obtained from two sediment cores located on the flanks of the East Pacific Rise. The records show small but consistent glacial/interglacial changes in all three isotopic systems with interglacial average values of -5.8 and 18.757 for εNd and 206Pb/204Pb, respectively, whereas glacial averages are -5.3 and 18.744. Comparison of this variability of Circumpolar Deep Water (CDW) to previously published records along the pathway of the global thermohaline circulation is consistent with reduced admixture of North Atlantic Deep Water (NADW) to CDW during cold stages. The absolute values and amplitudes of the benthic δ13C variations are essentially indistinguishable from other records of the Southern Hemisphere and confirm that the low central South Pacific sedimentation rates did not result in a significant reduction of the amplitude of any of the measured proxies. In addition, the combined detrital Nd and strontium (87Sr/86Sr) isotope signatures imply that Australian and New Zealand dust has remained the principal contributor of lithogenic material to the central South Pacific

A Study of the Diverse T Dwarf Population Revealed by WISE

We report the discovery of 87 new T dwarfs uncovered with the Wide-field Infrared Survey Explorer (WISE) and three brown dwarfs with extremely red near-infrared colors that exhibit characteristics of both L and T dwarfs. Two of the new T dwarfs are likely binaries with L7+/-1 primaries and mid-type T secondaries. In addition, our follow-up program has confirmed 10 previously identified T dwarfs and four photometrically-selected L and T dwarf candidates in the literature. This sample, along with the previous WISE discoveries, triples the number of known brown dwarfs with spectral types later than T5. Using the WISE All-Sky Source Catalog we present updated color-color and color-type diagrams for all the WISE-discovered T and Y dwarfs. Near-infrared spectra of the new discoveries are presented, along with spectral classifications. To accommodate later T dwarfs we have modified the integrated flux method of determining spectral indices to instead use the median flux. Furthermore, a newly defined J-narrow index differentiates the early-type Y dwarfs from late-type T dwarfs based on the J-band continuum slope. The K/J indices for this expanded sample show that 32% of late-type T dwarfs have suppressed K-band flux and are blue relative to the spectral standards, while only 11% are redder than the standards. Comparison of the Y/J and K/J index to models suggests diverse atmospheric conditions and supports the possible re-emergence of clouds after the L/T transition. We also discuss peculiar brown dwarfs and candidates that were found not to be substellar, including two Young Stellar Objects and two Active Galactic Nuclei. The coolest WISE-discovered brown dwarfs are the closest of their type and will remain the only sample of their kind for many years to come.Comment: Accepted to ApJS on 15 January 2013; 99 pages in preprint format, 30 figures, 12 table