Advancing coastal ocean modelling, analysis, and prediction for the US Integrated Ocean Observing System

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here by permission of Taylor & Francis for personal use, not for redistribution. The definitive version was published in Journal of Operational Oceanography 10 (2017): 115-126, doi:10.1080/1755876X.2017.1322026.This paper outlines strategies that would advance coastal ocean modeling, analysis and prediction as a complement to the observing and data management activities of the coastal components of the U.S. Integrated Ocean Observing System (IOOS®) and the Global Ocean Observing System (GOOS). The views presented are the consensus of a group of U.S. based researchers with a cross-section of coastal oceanography and ocean modeling expertise and community representation drawn from Regional and U.S. Federal partners in IOOS. Priorities for research and development are suggested that would enhance the value of IOOS observations through model-based synthesis, deliver better model-based information products, and assist the design, evaluation and operation of the observing system itself. The proposed priorities are: model coupling, data assimilation, nearshore processes, cyberinfrastructure and model skill assessment, modeling for observing system design, evaluation and operation, ensemble prediction, and fast predictors. Approaches are suggested to accomplish substantial progress in a 3-8 year timeframe. In addition, the group proposes steps to promote collaboration between research and operations groups in Regional Associations, U.S. Federal Agencies, and the international ocean research community in general that would foster coordination on scientific and technical issues, and strengthen federal-academic partnerships benefiting IOOS stakeholders and end users.2018-05-2

From Ultracompact to Extended HII Regions. II: Cloud Gravity and Stellar Motion

The dynamical evolution of HII regions with and without stellar motion in dense, structured molecular clouds is studied. Clouds are modeled in hydrostatic equilibrium, with gaussian central cores and external halos that obey r**-2 and r**-3 density power laws. The cloud gravity is included as a time-independent, external force. Stellar velocities of 0, 2, 8, and 12 km/s are considered. When stellar motion is included, stars move from the central core to the edge of the cloud, producing transitions from ultracompact to extended HII regions as the stars move into lower density regions. The opposite behavior occurs when stars move toward the cloud cores. The main conclusion of our study is that ultracompact HII regions are pressure-confined entities while they remain embedded within dense cores. The confinement comes from ram and/or ambient pressures. The survival of ultracompact regions depends on the position of the star with respect to the core, the stellar life-time, and the core crossing time. Stars with velocities less than the cloud dispersion velocity can produce cometary shapes smaller than 0.1 pc at times of 20,000 yr or more. The sequence Ultracompact to Compact to Extended HII region shows a variety of unpredictable structures due to ionization-shock front instability. Some ultracompact HII regions with a core-halo morphology might be explained by self-blocking effects, when stars overtake and ionize leading, piled-up clumps of neutral gas. We use thermal energy to support the cloud against gravity; the results remain the same if other types of isotropic cloud support are used.Comment: 27 pages, 7 ps figures, 5 png figures; submitted to Astrophysical Journa

Wild to domestic and back again: the dynamics of fallow deer management in medieval England (c.11th-16th century AD)

This paper presents the results of the first comprehensive scientific study of the fallow deer, a non-native species whose medieval-period introduction to Britain transformed the cultural landscape. It brings together data from traditional zooarchaeological analyses with those derived from new ageing techniques as well as the results of a programme of radiocarbon dating, multi-element isotope studies and genetic analyses. These new data are here integrated with historical and landscape evidence to examine changing patterns of fallow deer translocation and management in medieval England between the 11th and 16th century AD

UV-driven Chemistry as a Signpost for Late-stage Planet Formation

The chemical reservoir within protoplanetary disks has a direct impact on planetary compositions and the potential for life. A long-lived carbon-and nitrogen-rich chemistry at cold temperatures (<=50K) is observed within cold and evolved planet-forming disks. This is evidenced by bright emission from small organic radicals in 1-10 Myr aged systems that would otherwise have frozen out onto grains within 1 Myr. We explain how the chemistry of a planet-forming disk evolves from a cosmic-ray/X-ray-dominated regime to an ultraviolet-dominated chemical equilibrium. This, in turn, will bring about a temporal transition in the chemical reservoir from which planets will accrete. This photochemical dominated gas phase chemistry develops as dust evolves via growth, settling and drift, and the small grain population is depleted from the disk atmosphere. A higher gas-to-dust mass ratio allows for deeper penetration of ultraviolet photons is coupled with a carbon-rich gas (C/O > 1) to form carbon-bearing radicals and ions. This further results in gas phase formation of organic molecules, which then would be accreted by any actively forming planets present in the evolved disk.Comment: Accepted to Nature Astronomy, Published Dec 8th 202

Phosphorothioate backbone modifications of nucleotide-based drugs are potent platelet activators

Nucleotide-based drug candidates such as antisense oligonucleotides, aptamers, immunoreceptor-activating nucleotides, or (anti)microRNAs hold great therapeutic promise for many human diseases. Phosphorothioate (PS) backbone modification of nucleotide-based drugs is common practice to protect these promising drug candidates from rapid degradation by plasma and intracellular nucleases. Effects of the changes in physicochemical properties associated with PS modification on platelets have not been elucidated so far. Here we report the unexpected binding of PS-modified oligonucleotides to platelets eliciting strong platelet activation, signaling, reactive oxygen species generation, adhesion, spreading, aggregation, and thrombus formation in vitro and in vivo. Mechanistically, the platelet-specific receptor glycoprotein VI (GPVI) mediates these platelet-activating effects. Notably, platelets from GPVI function-deficient patients do not exhibit binding of PS-modified oligonucleotides, and platelet activation is fully abolished. Our data demonstrate a novel, unexpected, PS backbone-dependent, platelet-activating effect of nucleotide-based drug candidates mediated by GPVI. This unforeseen effect should be considered in the ongoing development programs for the broad range of upcoming and promising DNA/RNA therapeutics

MEMORY AND COGNITIVE ABILITIES IN UNIVERSITY PROFESSORS:

Professors from the University of California at Berkeley were administered a 90-min test battery of cognitive performance that included measures of reaction time, paired-associate learning, working memory, and prose recall. Age effects among the professors were observed on tests of reaction time, paired-associate memory, and some aspects of working memory. Age effects were not observed on measures of proactive interference and prose recall, though age-related declines are generally observed in standard groups of elderly individuals. The findings suggest that age-related decrements in certain cognitive functions may be mitigated in intelligent, cognitively active individualsPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72229/1/j.1467-9280.1995.tb00510.x.pd

The \u3cem\u3eChlamydomonas\u3c/em\u3e Genome Reveals the Evolution of Key Animal and Plant Functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella

Molecules with ALMA at Planet-forming Scales (MAPS). VI. Distribution of the small organics HCN, C2H, and H2CO

Funding: I.C. was supported by NASA through the NASA Hubble Fellowship grant HST-HF2-51405.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555. C.W. acknowledges financial support from the University of Leeds, STFC, and UKRI (grant Nos. ST/R000549/1, ST/T000287/1, and MR/T040726/1). J.D.I. acknowledges support from the Science and Technology Facilities Council of the United Kingdom (STFC) under ST/T000287/1.Small organic molecules, such as C2H, HCN, and H2CO, are tracers of the C, N, and O budget in protoplanetary disks. We present high-angular-resolution (10-50 au) observations of C2H, HCN, and H2CO lines in five protoplanetary disks from the Molecules with ALMA at Planet-forming Scales (MAPS) ALMA Large Program. We derive column density and excitation temperature profiles for HCN and C2H, and find that the HCN emission arises in a temperate (20-30 K) layer in the disk, while C2H is present in relatively warmer (20-60 K) layers. In the case of HD 163296, we find a decrease in column density for HCN and C2H inside one of the dust gaps near ~83 au, where a planet has been proposed to be located. We derive H2CO column density profiles assuming temperatures between 20 and 50 K, and find slightly higher column densities in the colder disks around T Tauri stars than around Herbig Ae stars. The H2CO column densities rise near the location of the CO snowline and/or millimeter dust edge, suggesting an efficient release of H2CO ices in the outer disk. Finally, we find that the inner 50 au of these disks are rich in organic species, with abundances relative to water that are similar to cometary values. Comets could therefore deliver water and key organics to future planets in these disks, similar to what might have happened here on Earth. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement.Publisher PDFPeer reviewe

Molecules with ALMA at Planet-forming Scales (MAPS). VIII. CO gap in AS 209-gas depletion or chemical processing?

Funding: I.C. was supported by NASA through the NASA Hubble Fellowship grant HST-HF2-51405.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555. J.D.I. acknowledges support from the Science and Technology Facilities Council of the United Kingdom (STFC) under ST/T000287/1. C.W. acknowledges financial support from the University of Leeds, SFTC, and UKRI (grant Nos. ST/R000549/1, ST/T000287/1, and MR/T040726/1).Emission substructures in gas and dust are common in protoplanetary disks. Such substructures can be linked to planet formation or planets themselves. We explore the observed gas substructures in AS 209 using thermochemical modeling with RAC2D and high-spatial-resolution data from the Molecules with ALMA at Planet-forming Scales (MAPS) program. The observations of C18O J = 2-1 emission exhibit a strong depression at 88 au overlapping with the positions of multiple gaps in millimeter dust continuum emission. We find that the observed CO column density is consistent with either gas surface-density perturbations or chemical processing, while C2H column density traces changes in the C/O ratio rather than the H2 gas surface density. However, the presence of a massive planet (>0.2 MJup) would be required to account for this level of gas depression, which conflicts with constraints set by the dust emission and the pressure profile measured by gas kinematics. Based on our models, we infer that a local decrease of CO abundance is required to explain the observed structure in CO, dominating over a possible gap-carving planet present and its effect on the H2 surface density. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement.Publisher PDFPeer reviewe