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  • 1
    Publication Date: 2022-10-21
    Description: Presented at 2022 OCB Summer Workshop, Woods Hole, MA, 20 - 23, June 2022
    Description: An unparalleled data catalog of well-documented, interoperable oceanographic data and information, openly accessible to all end-users through an intuitive web-based interface for the purposes of advancing marine research, education, and policy. Conference Website: https://web.whoi.edu/ocb-workshop/
    Description: NSF #1924618
    Keywords: Data management
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 2
    Publication Date: 2022-10-21
    Description: Presented at Ocean Sciences, San Diego, 16-21, February 2020
    Description: BCO-DMO curates earth science data where models become increasingly important. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a publicly accessible earth science data repository created to curate, publicly serve (publish), and archive digital data and information from biological, chemical and biogeochemical research conducted in coastal, marine, great lakes and laboratory environments. Recently, more and more of the projects submitted to BCO-DMO represent modeling efforts which further increase our knowledge of chemical and biological properties within the ocean ecosystem. We feel the time is at hand for the scientific community to begin a concerted and holistic approach to the curation of code and software.
    Description: Award(s): NSF #1924618
    Keywords: Data management ; Open science ; Survey ; Research needs
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 3
    Publication Date: 2022-10-21
    Description: Presented at Ocean Sciences, San Diego, 16-21, February 2020
    Description: Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine biological, chemical, physical, and biogeochemical data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. Based upon community feedback, this infrastructure is undergoing evaluation and improvement to better meet oceanographic research needs. This poster will introduce the repository and describe some of the strategic enhancements coming to BCO-DMO, and presents an opportunity for you to provide feedback on enhancements yet to come. We invite you to think about your own research workflow of searching and accessing new data for research, and to provide your feedback through the poster’s interactive sections. Your input can help BCO-DMO improve its service to the research community.
    Description: Award(s): NSF #1924618
    Keywords: Data management ; Open science ; Survey ; Research needs
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 4
    Publication Date: 2022-10-21
    Description: Presented at Fall AGU (ESIP Data Helpdesk), New Orleans, 11-17, December 2021
    Description: BCO-DMO curates a database of research-ready data spanning the full range of marine ecosystem related measurements including in-situ and remotely sensed observations, experimental and model results, and synthesis products. We work closely with investigators to publish data and information from research projects supported by the National Science Foundation (NSF), as well as those supported by state, private, and other funding sources. BCO-DMO supports all phases of the data life cycle and ensures open access of well-curated project data and information. We employ F.A.I.R. Principles that comprise a set of values intended to guide data producers and publishers in establishing good data management practices that will enable effective reuse.
    Description: Award(s): NSF #1924618
    Keywords: Data management ; Open science ; Survey ; Research needs
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 5
    Publication Date: 2022-12-06
    Description: Deep learning can accurately represent sub‐grid‐scale convective processes in climate models, learning from high resolution simulations. However, deep learning methods usually lack interpretability due to large internal dimensionality, resulting in reduced trustworthiness in these methods. Here, we use Variational Encoder Decoder structures (VED), a non‐linear dimensionality reduction technique, to learn and understand convective processes in an aquaplanet superparameterized climate model simulation, where deep convective processes are simulated explicitly. We show that similar to previous deep learning studies based on feed‐forward neural nets, the VED is capable of learning and accurately reproducing convective processes. In contrast to past work, we show this can be achieved by compressing the original information into only five latent nodes. As a result, the VED can be used to understand convective processes and delineate modes of convection through the exploration of its latent dimensions. A close investigation of the latent space enables the identification of different convective regimes: (a) stable conditions are clearly distinguished from deep convection with low outgoing longwave radiation and strong precipitation; (b) high optically thin cirrus‐like clouds are separated from low optically thick cumulus clouds; and (c) shallow convective processes are associated with large‐scale moisture content and surface diabatic heating. Our results demonstrate that VEDs can accurately represent convective processes in climate models, while enabling interpretability and better understanding of sub‐grid‐scale physical processes, paving the way to increasingly interpretable machine learning parameterizations with promising generative properties.
    Description: Plain Language Summary: Deep neural nets are hard to interpret due to their hundred thousand or million trainable parameters without further postprocessing. We demonstrate in this paper the usefulness of a network type that is designed to drastically reduce this high dimensional information in a lower‐dimensional space to enhance the interpretability of predictions compared to regular deep neural nets. Our approach is, on the one hand, able to reproduce small‐scale cloud related processes in the atmosphere learned from a physical model that simulates these processes skillfully. On the other hand, our network allows us to identify key features of different cloud types in the lower‐dimensional space. Additionally, the lower‐order manifold separates tropical samples from polar ones with a remarkable skill. Overall, our approach has the potential to boost our understanding of various complex processes in Earth System science.
    Description: Key Points: A Variational Encoder Decoder (VED) can predict sub‐grid‐scale thermodynamics from the coarse‐scale climate state. The VED's latent space can distinguish convective regimes, including shallow/deep/no convection. The VED's latent space reveals the main sources of convective predictability at different latitudes.
    Description: EC ERC HORIZON EUROPE European Research Council http://dx.doi.org/10.13039/100019180
    Description: Columbia sub‐award 1
    Description: Advanced Research Projects Agency - Energy http://dx.doi.org/10.13039/100006133
    Description: Deutsches Klimarechenzentrum http://dx.doi.org/10.13039/100018730
    Description: National Science Foundation Science and Technology Center Learning the Earth with Artificial intelligence and Physics
    Keywords: ddc:551.5 ; machine learning ; generative deep learning ; convection ; parameterization ; explainable artificial intelligence ; dimensionality reduction
    Language: English
    Type: doc-type:article
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  • 6
    Publication Date: 2022-10-31
    Description: Dataset: Share Your Thoughts
    Description: Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine biological, chemical, physical, and biogeochemical data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. Based upon community feedback, this infrastructure is undergoing evaluation and improvement to better meet oceanographic research needs. This poster will introduce the repository and describe some of the strategic enhancements coming to BCO-DMO, and presents an opportunity for you to provide feedback on enhancements yet to come. We invite you to think about your own research workflow of searching and accessing new data for research, and to provide your feedback through the poster’s interactive sections. Your input can help BCO-DMO improve its service to the research community. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/825238
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1924618
    Keywords: Data management. stakeholder needs ; Oceanography ; BCO-DMO ; Repository ; Community building
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 7
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in York, A., V., Frey, K. E., Jamali, S., & Das, S. B. Change points detected in decadal and seasonal trends of outlet glacier terminus positions across West Greenland. Remote Sensing, 12(21), (2020): 3651, doi:10.3390/rs12213651.
    Description: We investigated the change in terminus position between 1985 and 2015 of 17 marine-terminating glaciers that drain into Disko and Uummannaq Bays, West Greenland, by manually digitizing over 5000 individual frontal positions from over 1200 Landsat images. We find that 15 of 17 glacier termini retreated over the study period, with ~80% of this retreat occurring since 2000. Increased frequency of Landsat observations since 2000 allowed for further investigation of the seasonal variability in terminus position. We identified 10 actively retreating glaciers based on a significant positive relationship between glaciers with cumulative retreat 〉300 m since 2000 and their average annual amplitude (seasonal range) in terminus position. Finally, using the Detecting Breakpoints and Estimating Segments in Trend (DBEST) program, we investigated whether the 2000–2015 trends in terminus position were explained by the occurrence of change points (significant trend transitions). Based on the change point analysis, we found that nine of 10 glaciers identified as actively retreating also underwent two or three periods of change, during which their terminus positions were characterized by increases in cumulative retreat. Previous literature suggests potential relationships between our identified change dates with anomalous ocean conditions, such as low sea ice concentration and high sea surface temperatures, and our change durations with individual fjord geometry.
    Description: Partial support for this research was provided by NASA Earth and Space Science Fellowship Award NNX12AO01H and National Science Foundation Award 1205018 to K.F. S.J. was funded by Knut and Alice Wallenberg Grant 99007-RFh2018-2016.
    Keywords: Marine-terminating glacier ; Landsat ; Change point detection ; DBEST
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Brooks, T. W., Kroeger, K. D., Michael, H. A., & York, J. K. Oxygen-controlled recirculating seepage meter reveals extent of nitrogen transformation in discharging coastal groundwater at the aquifer-estuary interface. Limnology and Oceanography, 66, (2021): 3055-3069, https://doi.org/10.1002/lno.11858.
    Description: Nutrient loads delivered to estuaries via submarine groundwater discharge (SGD) play an important role in the nitrogen (N) budget and eutrophication status. However, accurate and reliable quantification of the chemical flux across the final decimeters and centimeters at the sediment–estuary interface remains a challenge, because there is significant potential for biogeochemical alteration due to contrasting conditions in the coastal aquifer and surface sediment. Here, a novel, oxygen- and light-regulated ultrasonic seepage meter, and a standard seepage meter, were used to measure SGD and calculate N species fluxes across the sediment–estuary interface. Coupling the measurements to an endmember approach based on subsurface N concentrations and an assumption of conservative transport enabled estimation of the extent of transformation occurring in discharging groundwater within the benthic zone. Biogeochemical transformation within reactive estuarine surface sediment was a dominant driver in modifying the N flux carried upward by SGD, and resulted in a similar percentage of N removal (~ 42–52%) as did transformations occurring deeper within the coastal aquifer salinity mixing zone (~ 42–47%). Seasonal shifts in the relative importance of biogeochemical processes including denitrification, nitrification, dissimilatory nitrate reduction, and assimilation altered the composition of the flux to estuarine surface water, which was dominated by ammonium in June and by nitrate in August, despite the endmember-based observation that fixed N in discharging groundwater was strongly dominated by nitrate. This may have important ramifications for the ecology and management of estuaries, since past N loading estimates have generally assumed conservative transport from the nearshore aquifer to estuary.
    Description: This work was supported by an award from Delaware Sea Grant (award No. NA100AR4170084 to J.K.Y. and K.D.K.), and by the USGS Coastal and Marine Hazards and Resources Program.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 9
    Publication Date: 2022-05-27
    Description: ZooSCAN images of zooplankton collected during OAPS MOCNESS tows during R/V Oceanus cruise OC473 in the Northwestern Atlantic in 2011 and R/V New Horizon cruise NH1208 in the Northeastern Pacific in 2012. Day and night stations were sampled between 0 to 1000m depths from 35 to 50 N in the northwest Atlantic in 2011, and from 35 and 50N along CLIVAR line P17N in 2012. Some chaetognaths and all pteropods were removed prior to imaging in association with the original OAPS and ancillary projects.
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1041068 NSF Division of Ocean Sciences (NSF OCE) OCE-1829318 NSF Division of Ocean Sciences (NSF OCE) OCE-1948162
    Description: 2024-06-01
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 10
    Publication Date: 2022-09-22
    Description: Pleurotomariida have the longest fossil record among living gastropods and are diverse and abundant in the middle and upper Palaeozoic. Its traditional classification is based on adult shell characters. The early shell morphology has been largely unknown. We describe exceptionally well‐preserved Pleurotomariida from the Pennsylvanian marine shales of Texas, Oklahoma, Kansas and Ohio. In total, 38 species representing 19 genera are described, including 10 new species, one new genus and one new subgenus: Eirlysella buckhornensis gen. et sp. nov., Shansiella (Oklahomaella) globilineata subgen. et sp. nov., Phymatopleura girtyi, Phymatopleura conica, Worthenia (Yochelsonospira) kuesi, Dictyotomaria turrisbabel, Paragoniozona yanceyi, Spiroscala shwedagoniformis, Peruvispira oklahomaensis, Baylea tenera. Replacement names are Paragoniozona ornata nom. nov. (for Pleurotomaria aspera Girty), Spiroscala quasipulchra nom. nov. (for Euconospira pulchra Batten). The early ontogenetic shells including protoconchs and early teleoconchs are reported in detail for the first time for most taxa. Most species have a protoconch of one whorl as that of living Vetigastropoda. Planktotrophic protoconchs (multi‐whorled larval shells with sinusigera) are reported for Platyzona and Peruvispira; they are therefore placed in the family Goniasmatidae (Caenogastropoda). Repaired shell scars were found in juvenile Pleurotomariida specimens (c. 1 mm), suggesting exposure to predation from an early stage of ontogeny. Pleurotomariida are strongly dominant in surface samples of the Finis Shale (Texas) but in bulk samples using fine mesh‐sizes, dominance is much less pronounced, indicating a change in clade proportion depending on sampling method. The taxonomic richness and abundance of Pleurotomariida seen in these Carboniferous shales have not been reported from post‐Triassic formations.
    Description: The Deutsche Forschungsgemeinschaft (DFG) http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:564
    Language: English
    Type: doc-type:article
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