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  • 1
    Publication Date: 2020-02-12
    Description: Background The proportion of conserved DNA sequences with no clear function is steadily growing in bioinformatics databases. Studies of sequence and structural homology have indicated that many uncharacterized protein domain sequences are variants of functionally described domains. If these variants promote an organism's ecological fitness, they are likely to be conserved in the genome of its progeny and the population at large. The genetic composition of microbial communities in their native ecosystems is accessible through metagenomics. We hypothesize the co-variation of protein domain sequences across metagenomes from similar ecosystems will provide insights into their potential roles and aid further investigation. Methodology/Principal findings We calculated the correlation of Pfam protein domain sequences across the Global Ocean Sampling metagenome collection, employing conservative detection and correlation thresholds to limit results to well-supported hits and associations. We then examined intercorrelations between domains of unknown function (DUFs) and domains involved in known metabolic pathways using network visualization and cluster-detection tools. We used a cautious “guilty-by-association” approach, referencing knowledge-level resources to identify and discuss associations that offer insight into DUF function. We observed numerous DUFs associated to photobiologically active domains and prevalent in the Cyanobacteria. Other clusters included DUFs associated with DNA maintenance and repair, inorganic nutrient metabolism, and sodium-translocating transport domains. We also observed a number of clusters reflecting known metabolic associations and cases that predicted functional reclassification of DUFs. Conclusion/Significance Critically examining domain covariation across metagenomic datasets can grant new perspectives on the roles and associations of DUFs in an ecological setting. Targeted attempts at DUF characterization in the laboratory or in silico may draw from these insights and opportunities to discover new associations and corroborate existing ones will arise as more large-scale metagenomic datasets emerge.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 2
    Publication Date: 2017-04-04
    Description: Global-scale variations in the climate system over the last half of the twentieth century. including long-term increases in global-mean near-surface temperatures. are consistent with concurrent human-induced emissions of radiatively active gases and aerosols. However, such consistency does not preclude the possible influence of other forcing agents, including internal modes of climate variability or unaccounted for aerosol effects. To test whether other unknown forcing agents may have contributed to multidecadal increases in global-mean near-surface temperatures from 1950 to 2000. data pertaining to observed changes in global-scale sea surface temperatures and observed changes in radiatively active atmospheric constituents are incorporated into numerical global climate models. Results indicate that the radiative forcing needed to produce the observed long-term trends in sea surface temperatures-and global-mean near-surface temperatures-is provided predominantly by known changes in greenhouse gases and aerosols. Further, results indicate that less than 10% of the long-term historical increase in global-mean near-surface temperatures over the last half of the twentieth century could have been the result of internal climate variability. In addition. they indicate that less than 25% of the total radiative forcing needed to produce the observed long-term trend in global-mean near-surface temperatures could have been provided by changes in net radiative forcing from unknown sources (either positive or negative). These results, which are derived from simple energy balance requirements. emphasize the important role humans have played in modifying the global climate over the last half of the twentieth century.
    Description: Published
    Description: 7163-7172
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: restricted
    Keywords: climate forcing ; temperature increase ; AGCM ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 3
    Publication Date: 2017-04-04
    Description: In this work the authors investigate possible changes in the distribution of heavy precipitation events under a warmer climate, using the results of a set of 20 climate models taking part in the Coupled Model Intercomparison Project phase 5 effort (CMIP5). Future changes are evaluated as the difference between the last four decades of the 21st and the 20th Century assuming the Representative Concentration Pathway RCP8.5 scenario. As a measure of the width of the right tail of the precipitation distribution, we use the difference between the 99th and the 90th percentiles. Despite a slight tendency to underestimate the observed heavy precipitation, the considered CMIP5 models well represent the observed patterns in terms of the ensemble average, during both summer and winter seasons for the 1997-2005 period. Future changes in average precipitation are consistentwith previous findings based on CMIP3 models. CMIP5 models show a projected increase for the end of the twenty-first century of the width of the right tail of the precipitation distribution, particularly pronounced over India, South East Asia, Indonesia and Central Africa during borealsummer, as well as over South America and southern Africa during boreal winter.
    Description: Published
    Description: 7902–7911
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: open
    Keywords: precipitation ; extreme events ; climate change ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 93 (2012): 1547–1566, doi:10.1175/BAMS-D-11-00201.1.
    Description: The Geostationary Coastal and Air Pollution Events (GEO-CAPE) mission was recommended by the National Research Council's (NRC's) Earth Science Decadal Survey to measure tropospheric trace gases and aerosols and coastal ocean phytoplankton, water quality, and biogeochemistry from geostationary orbit, providing continuous observations within the field of view. To fulfill the mandate and address the challenge put forth by the NRC, two GEO-CAPE Science Working Groups (SWGs), representing the atmospheric composition and ocean color disciplines, have developed realistic science objectives using input drawn from several community workshops. The GEO-CAPE mission will take advantage of this revolutionary advance in temporal frequency for both of these disciplines. Multiple observations per day are required to explore the physical, chemical, and dynamical processes that determine tropospheric composition and air quality over spatial scales ranging from urban to continental, and over temporal scales ranging from diurnal to seasonal. Likewise, high-frequency satellite observations are critical to studying and quantifying biological, chemical, and physical processes within the coastal ocean. These observations are to be achieved from a vantage point near 95°–100°W, providing a complete view of North America as well as the adjacent oceans. The SWGs have also endorsed the concept of phased implementation using commercial satellites to reduce mission risk and cost. GEO-CAPE will join the global constellation of geostationary atmospheric chemistry and coastal ocean color sensors planned to be in orbit in the 2020 time frame.
    Description: Funding for GEO-CAPE definition activities is provided by the Earth Science Division of the National Aeronautics and Space Administration.
    Description: 2013-04-01
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 17–28, doi:10.1175/JPO-D-11-0108.1.
    Description: Observational evidence is presented for transfer of energy from the internal tide to near-inertial motions near 29°N in the Pacific Ocean. The transfer is accomplished via parametric subharmonic instability (PSI), which involves interaction between a primary wave (the internal tide in this case) and two smaller-scale waves of nearly half the frequency. The internal tide at this location is a complex superposition of a low-mode waves propagating north from Hawaii and higher-mode waves generated at local seamounts, making application of PSI theory challenging. Nevertheless, a statistically significant phase locking is documented between the internal tide and upward- and downward-propagating near-inertial waves. The phase between those three waves is consistent with that expected from PSI theory. Calculated energy transfer rates from the tide to near-inertial motions are modest, consistent with local dissipation rate estimates. The conclusion is that while PSI does befall the tide near a critical latitude of 29°N, it does not do so catastrophically.
    Description: This work was sponsored by NSF OCE 04-25283.
    Description: 2013-07-01
    Keywords: Diapycnal mixing ; Internal waves ; Nonlinear dynamics
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e56393, doi:10.1371/journal.pone.0056393.
    Description: Evolutionary constraints which limit the forces produced during bell contractions of medusae affect the overall medusan morphospace such that jet propulsion is limited to only small medusae. Cubomedusae, which often possess large prolate bells and are thought to swim via jet propulsion, appear to violate the theoretical constraints which determine the medusan morphospace. To examine propulsion by cubomedusae, we quantified size related changes in wake dynamics, bell shape, swimming and turning kinematics of two species of cubomedusae, Chironex fleckeri and Chiropsella bronzie. During growth, these cubomedusae transitioned from using jet propulsion at smaller sizes to a rowing-jetting hybrid mode of propulsion at larger sizes. Simple modifications in the flexibility and kinematics of their velarium appeared to be sufficient to alter their propulsive mode. Turning occurs during both bell contraction and expansion and is achieved by generating asymmetric vortex structures during both stages of the swimming cycle. Swimming characteristics were considered in conjunction with the unique foraging strategy used by cubomedusae.
    Description: This work was supported by an ONR MURI award (N000140810654) and National Science Foundation grant OCE 0623508 to JHC, SPC, JOD. And the work was supported by the Roger Williams University Foundation to Promote Scholarship.
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2022-05-25
    Description: This article is distributed under the terms of the Creative Commons Public Domain. The definitive version was published in PLoS ONE 8 (2013): e55273, doi:10.1371/journal.pone.0055273.
    Description: Georges Bank is a large, shallow feature separating the Gulf of Maine from the Atlantic Ocean. Previous studies demonstrated a strong tidal-mixing front during the warm season on the northern bank margin between thermally stratified water in the Gulf of Maine and mixed water on the bank. Tides transport warm water off the bank during flood tide and cool gulf water onto the bank during ebb tide. During 10 days in August 2009, we mapped frontal temperatures in five study areas along ~100 km of the bank margin. The seabed “frontal zone”, where temperature changed with frontal movment, experienced semidiurnal temperature maxima and minima. The tidal excursion of the frontal boundary between stratified and mixed water ranged 6 to 10 km. This “frontal boundary zone” was narrower than the frontal zone. Along transects perpendicular to the bank margin, seabed temperature change at individual sites ranged from 7.0°C in the frontal zone to 0.0°C in mixed bank water. At time series in frontal zone stations, changes during tidal cycles ranged from 1.2 to 6.1°C. The greatest rate of change (−2.48°C hr−1) occurred at mid-ebb. Geographic plots of seabed temperature change allowed the mapping of up to 8 subareas in each study area. The magnitude of temperature change in a subarea depended on its location in the frontal zone. Frontal movement had the greatest effect on seabed temperature in the 40 to 80 m depth interval. Subareas experiencing maximum temperature change in the frontal zone were not in the frontal boundary zone, but rather several km gulfward (off-bank) of the frontal boundary zone. These results provide a new ecological framework for examining the effect of tidally-driven temperature variability on the distribution, food resources, and reproductive success of benthic invertebrate and demersal fish species living in tidal front habitats.
    Description: This study was supported by salary funds from the regular annual salary budget from Northeast Fisheries Science Center (NEFSC) and United States Geological Survey Woods Hole Coastal and Marine Science Center (USGS WH C&MSC), respectively; ship time funds from the NEFSC annual budget for days-at-sea ship operations; equipment from the NEFSC and USGS WH C&MSC annual equipment budgets.
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 418–431, doi:10.1175/JPO-D-12-087.1.
    Description: The overflow of the dense water mass across the Greenland–Scotland Ridge (GSR) from the Nordic Seas drives the Atlantic meridional overturning circulation (AMOC). The Nordic Seas is a large basin with an enormous reservoir capacity. The volume of the dense water above the GSR sill depth in the Nordic Seas, according to previous estimates, is sufficient to supply decades of overflow transport. This large capacity buffers overflow’s responses to atmospheric variations and prevents an abrupt shutdown of the AMOC. In this study, the authors use a numerical and an analytical model to show that the effective reservoir capacity of the Nordic Seas is actually much smaller than what was estimated previously. Basin-scale oceanic circulation is nearly geostrophic and its streamlines are basically the same as the isobaths. The vast majority of the dense water is stored inside closed geostrophic contours in the deep basin and thus is not freely available to the overflow. The positive wind stress curl in the Nordic Seas forces a convergence of the dense water toward the deep basin and makes the interior water even more removed from the overflow-feeding boundary current. Eddies generated by the baroclinic instability help transport the interior water mass to the boundary current. But in absence of a robust renewal of deep water, the boundary current weakens rapidly and the eddy-generating mechanism becomes less effective. This study indicates that the Nordic Seas has a relatively small capacity as a dense water reservoir and thus the overflow transport is sensitive to climate changes.
    Description: This study has been supported by National Science Foundation (OCE0927017,ARC1107412).
    Description: 2013-08-01
    Keywords: Bottom currents ; Drainage flow ; Meridional overturning circulation ; Ocean dynamics ; Potential vorticity ; Topographic effects
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 283–300, doi:10.1175/JPO-D-11-0240.1.
    Description: Motivated by the recent interest in ocean energetics, the widespread use of horizontal eddy viscosity in models, and the promise of high horizontal resolution data from the planned wide-swath satellite altimeter, this paper explores the impacts of horizontal eddy viscosity and horizontal grid resolution on geostrophic turbulence, with a particular focus on spectral kinetic energy fluxes Π(K) computed in the isotropic wavenumber (K) domain. The paper utilizes idealized two-layer quasigeostrophic (QG) models, realistic high-resolution ocean general circulation models, and present-generation gridded satellite altimeter data. Adding horizontal eddy viscosity to the QG model results in a forward cascade at smaller scales, in apparent agreement with results from present-generation altimetry. Eddy viscosity is taken to roughly represent coupling of mesoscale eddies to internal waves or to submesoscale eddies. Filtering the output of either the QG or realistic models before computing Π(K) also greatly increases the forward cascade. Such filtering mimics the smoothing inherent in the construction of present-generation gridded altimeter data. It is therefore difficult to say whether the forward cascades seen in present-generation altimeter data are due to real physics (represented here by eddy viscosity) or to insufficient horizontal resolution. The inverse cascade at larger scales remains in the models even after filtering, suggesting that its existence in the models and in altimeter data is robust. However, the magnitude of the inverse cascade is affected by filtering, suggesting that the wide-swath altimeter will allow a more accurate determination of the inverse cascade at larger scales as well as providing important constraints on smaller-scale dynamics.
    Description: BKA received support from Office of Naval Research Grant N00014-11-1-0487, National Science Foundation (NSF) Grants OCE-0924481 and OCE- 09607820, and University of Michigan startup funds. KLP acknowledges support from Woods Hole Oceanographic Institution bridge support funds. RBS acknowledges support from NSF grants OCE-0960834 and OCE-0851457, a contract with the National Oceanography Centre, Southampton, and a NASA subcontract to Boston University. JFS and JGR were supported by the projects ‘‘Global and remote littoral forcing in global ocean models’’ and ‘‘Agesotrophic vorticity dynamics of the ocean,’’ respectively, both sponsored by the Office of Naval Research under program element 601153N.
    Description: 2013-08-01
    Keywords: Eddies ; Nonlinear dynamics ; Ocean dynamics ; Satellite observations ; Ocean models
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2022-05-25
    Description: Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 43 (2013): 744–765, doi:10.1175/JPO-D-12-067.1.
    Description: This study investigates the coherence between ocean bottom pressure signals at the Rapid Climate Change programme (RAPID) West Atlantic Variability Experiment (WAVE) array on the western North Atlantic continental slope, including the Woods Hole Oceanographic Institution Line W. Highly coherent pressure signals propagate southwestward along the slope, at speeds in excess of 128 m s−1, consistent with expectations of barotropic Kelvin-like waves. Coherent signals are also evidenced in the smaller pressure differences relative to 1000-m depth, which are expected to be associated with depth-dependent basinwide meridional transport variations or an overturning circulation. These signals are coherent and almost in phase for all time scales from 3.6 years down to 3 months. Coherence is still seen at shorter time scales for which group delay estimates are consistent with a propagation speed of about 1 m s−1 over 990 km of continental slope but with large error bounds on the speed. This is roughly consistent with expectations for propagation of coastally trapped waves, though somewhat slower than expected. A comparison with both Eulerian currents and Lagrangian float measurements shows that the coherence is inconsistent with a propagation of signals by advection, except possibly on time scales longer than 6 months.
    Description: This work was funded by the U.K. Natural Environment Research Council. Sofia Olhede was supported by EPSRC Grant EP/I005250/1. Initial observations at StationW(2001–04) were made possible by a grant from the G. Unger Vetlesen Foundation and support from the Woods Hole Oceanographic Institution. Since 2004, the Line W program has been supported by the U.S. National Science Foundation with supplemental contribution from WHOIs Ocean and Climate Change Institute.
    Description: 2013-10-01
    Keywords: Atlantic Ocean ; Boundary currents ; Meridional overturning circulation ; Pressure ; Waves, oceanic ; In situ oceanic observations
    Repository Name: Woods Hole Open Access Server
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