Presentations and Papers
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This collection represents presentations made by members of the staff of the MBLWHOI Library or at the behest of the Library, and articles authored by members of the Library staff.
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ArticleComparison of annual biosynthetic calorie productions by phytoplankton in different southern Korean bays(Frontiers Media, 2024-07-29)We investigated assessments of calorie production and energy efficiencies of phytoplankton in Gwangyang, Jaran, and Geoje-Hansan bays in southern Korea, based on seasonal field measurements data for particulate organic carbon (POC), macromolecular compositions, calorie contents, and primary production. Our findings revealed that Geoje-Hansan Bay consistently exhibits higher POC concentrations compared to Gwangyang and Jaran bays, except during the summer season. The observed seasonal variations in POC concentrations and primary productions indicated distinct factors influencing POC distribution among the bays, which varies with the seasons. Macromolecular compositions displayed notable patterns, with Gwangyang Bay exhibiting pronounced seasonal variations, Jaran and Geoje-Hansan bays showing stable carbohydrate (CHO) dominance, and Gwangyang Bay displaying protein (PRT) dominance influenced by river-borne nutrients. Analysis of calorie content revealed that Geoje-Hansan Bay exhibited the highest calorie content, suggesting a more favorable physiological state of phytoplankton compared to Gwangyang and Jaran bays. Estimations of annual primary production and calorie production demonstrated regional variations, with Geoje-Hansan Bay having the highest values followed by Jaran Bay and Gwangyang Bay. These differences in primary production and calorie production reflect the diverse ecological conditions and nutrient availability specific to each bay. Interestingly, Gwangyang Bay demonstrated the highest energy efficiency, producing more calories per unit of carbon compared to the other two bays, potentially due to the influence of different dominant phytoplankton communities. This study enhances our understanding of ecosystem dynamics and ecological characteristics among the three bays, emphasizing the importance of considering seasonal variations and specific bay characteristics in investigating biogeochemical processes, energy flow, and ecosystem functioning. The findings contribute valuable insights for the sustainable management of coastal ecosystems and aquaculture practices.
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ArticleOrientation-independent-DIC imaging reveals that a transient rise in depletion attraction contributes to mitotic chromosome condensation(National Academy of Sciences, 2024-08-27)Genomic information must be faithfully transmitted into two daughter cells during mitosis. To ensure the transmission process, interphase chromatin is further condensed into mitotic chromosomes. Although protein factors like condensins and topoisomerase IIα are involved in the assembly of mitotic chromosomes, the physical bases of the condensation process remain unclear. Depletion attraction/macromolecular crowding, an effective attractive force that arises between large structures in crowded environments around chromosomes, may contribute to the condensation process. To approach this issue, we investigated the “chromosome milieu” during mitosis of living human cells using an orientation-independent-differential interference contrast module combined with a confocal laser scanning microscope, which is capable of precisely mapping optical path differences and estimating molecular densities. We found that the molecular density surrounding chromosomes increased with the progression from prophase to anaphase, concurring with chromosome condensation. However, the molecular density went down in telophase, when chromosome decondensation began. Changes in the molecular density around chromosomes by hypotonic or hypertonic treatment consistently altered the condensation levels of chromosomes. In vitro, native chromatin was converted into liquid droplets of chromatin in the presence of cations and a macromolecular crowder. Additional crowder made the chromatin droplets stiffer and more solid-like. These results suggest that a transient rise in depletion attraction, likely triggered by the relocation of macromolecules (proteins, RNAs, and others) via nuclear envelope breakdown and by a subsequent decrease in cell volumes, contributes to mitotic chromosome condensation, shedding light on a different aspect of the condensation mechanism in living human cells.
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ArticleProtocol for fluorescent live-cell staining of tardigrades(Elsevier, 2024-08-09)Tardigrades are microscopic organisms with exceptional resilience to environmental extremes. Most protocols to visualize the internal anatomy of tardigrades rely on fixation, hampering our understanding of dynamic changes to organelles and other subcellular components. Here, we provide protocols for staining live tardigrade adults and other postembryonic stages, facilitating real-time visualization of structures including lipid droplets, mitochondria, lysosomes, and DNA.
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ArticleSea level modulation of Atlantic nitrogen fixation over glacial cycles(American Geophysical Union, 2024-08-09)N2 fixation in low-latitude surface waters dominates the input of fixed nitrogen (N) to the global ocean, sustaining ocean fertility. In the Caribbean Sea, higher foraminifera-bound (FB-)δ15N indicates a decline in N2 fixation during ice ages, but its cause and broader implications are unclear. Here, we report three additional Atlantic FB-δ15N records, from the subtropical North and South Atlantic gyres (MSM58-50 and DSDP Site 516) and the equatorial Atlantic (ODP Site 662). Similar glacial and interglacial δ15N in the equatorial Atlantic suggests a stable δ15N for the nitrate below the gyre thermoclines. The North Atlantic record shows a FB-δ15N rise during the ice ages, resembling a previously published FB-δ15N record from the South China Sea. The commonality among the FB-δ15N records is that they resemble sea level-driven variation in regional shelf area, with high FB-δ15N (inferred reduction in N2 fixation) during periods of low shelf area. The South China Sea shows the largest δ15N signal, the subtropical North Atlantic shows less, and the South Atlantic shows the least, the same ordering as the ice age reductions in continental shelf area in the different regions. Reduced shelf sedimentary denitrification would have increased the nitrogen-to-phosphorus ratio of the nutrient supply to open ocean surface waters, leading to decreased N2 fixation and thus higher gyre thermocline nitrate δ15N, explaining the higher FB-δ15N of peak ice ages. These observations identify shelf sediment denitrification as an important regional driver of modern N2 fixation and imply strong basin-scale coupling of fixed nitrogen losses and inputs.
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ArticleInvestigation of suspected Holocene fault scarp near Montréal, Québec:tThe first paleoseismic trench in eastern Canada(Seismica, 2024-07-25)Québec has experienced historical damaging earthquakes in several seismic zones (eg 1732 M5.8 Montréal, 1663 M7 Charlevoix, 1935 M6.2 Témiscamingue). Despite a high seismicity rate, no surface-rupturing faults have been discovered due to a combination of dense vegetation cover, recent glaciation, sparse earthquake records, and low regional strain rates. We manually searched lidar-derived digital elevation models (DEMs) of the region to search for potential post-glacial surface-rupturing faults across southern Québec and identified a scarp ~50km north of Montréal. We performed three geophysical surveys (ground penetrating radar, depth estimates from ambient seismic noise, and refraction seismology) that revealed a buried scarp, confirmed with a <1 m-deep hand-dug test pit. These observations convinced us to excavate the first paleoseismic trench in Quebec to test for the presence of a surface-rupturing fault in July 2023. We found a glacial diamict containing no signs of syn- or post-glacial deformation. In this paper, we present the observations that led to the identification of a scarp and hypothesized faulting. We highlight the importance of trenching to confirm recent fault scarps in challenging environments. We hope our study can be used to optimize future paleoseismic research in the province of Quebec and similar intracratonic glaciated landscapes.
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ArticleSustaining hydrothermal circulation with gravity relevant to ocean worlds(American Geophysical Union, 2024-06-24)Some ocean worlds may sustain active, seafloor hydrothermal systems, but the characteristics and controls on fluid-heat transport in these systems are not well understood. We developed three-dimensional numerical simulations, using a ridge-flank hydrothermal system on Earth as a reference, to test the influence of ocean world gravity on fluid and heat transport. Simulations represented the upper ∼4–5 km below the seafloor and explored ranges of: heat input at the base, aquifer thickness, depth, and permeability, and gravity values appropriate for Earth, Europa, and Enceladus. We tested when a hydrothermal siphon could be sustained and quantified consequent circulation temperatures, flow rates, and advective heat output. Calculations illustrate a trade-off in energy between the reduction of buoyancy at lower gravity, which tends to reduce the primary forces driving fluid circulation, and the concomitant reduction in secondary convection, which consumes available energy. When a siphon was sustained under lower gravity, circulation temperatures tended to increase modestly (which should lead to more extensive geochemical reactions), whereas mass flow rates and advective heat output tended to be reduced. Deeper subseafloor circulation resulted in higher temperatures and flow rates, with a deeper, thin aquifer being more efficient in removing heat from the rocky interior. Water-rock ratios were lower when gravity was lower, as was the efficiency of heat extraction, whereas the time required to circulate the volume of an ocean-world's ocean through the seafloor increased. This may help to explain how small ocean worlds could sustain hydrothermal circulation for a long time despite limited heat sources.
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PresentationMBLWHOI Library’s Institutional Repository – WHOAS: DSpace 7.2 migration(Woods Hole Oceanographic Institution, 2022-12-01)The MBLWHOI Library’s Institutional Repository (IR) is a DSpace repository. We are migrating from version 5.6 to 7.2. This presentation will demonstrate new DSpace 7 features in our repository, while discussing our story and our takeaways from our migration.
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PresentationChoosing open access licensing when publishing(Woods Hole Oceanographic Institution, 2020-10-21)When filling out the publication agreement forms for a manuscript to be published what license should I choose? Studies continue to show favorable impact of Open Access on the scholarly literature through increased dissemination and re-use.
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PresentationMBLWHOI Library’s institutional repository stewardship responsibility(Woods Hole Oceanographic Institution, 2020-12-03)The MBLWHOI Library’s Institutional Repository (IR) is a CoreTrustSeal certified repository. We chose to go through this process to demonstrate our commitment to quality stewardship and to be a trusted option for our researchers facing funder and publisher requirements that data be accessible, and more recently, also citable with a DOI. The Library always recommends that researchers deposit data in an appropriate subject or community repository, but there are many cases where the dataset needing a DOI does not fit that scenario. The ability to quickly and easily deposit data in a certified repository is a value added service for our users. Some funders now mandate the data must be deposited in a FAIR repository. Being a CoreTrustSeal certified repository ensures that the MBLWHOI Library’s Institutional Repository practices FAIR principles. This lighting talk will show the steps we went through to become certified, some of the hurdles and benefits, as well our current status as an application reviewer. This process enabled us to review our internal process and procedures and re-examine any outdated practices. It shined a light on places we could improve our documentation and more clearly state our policies. The importance of demonstrating our commitment to quality and the Library’s continued efforts with the repository to remain on the forefront of technology with linked open data, schema.org, etc.
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PresentationData Science Training Camp at Woods Hole Oceanographic Institution: Syllabus and slide presentations in 2020(Woods Hole Oceanographic Institution, 2020-08-21)With data and software increasingly recognized as scholarly research products, and aiming towards open science and reproducibility, it is imperative for today's oceanographers to learn foundational practices and skills for data management and research computing, as well as practices specific to the ocean sciences. This educational package was developed as a data science training camp for graduate students and professionals in the ocean sciences and implemented at the Woods Hole Oceanographic Institution (WHOI) in 2019 and 2020. Here we provide materials for the 2020 camp which was delivered in-person during two afternoons (total of 8 hours), with two modules per afternoon. We aimed for ~40 participants per camp, with disciplines spanning Earth and life sciences and engineering. Disciplines at each table were mixed on the first afternoon but similar on the second afternoon. Contents of this package include the syllabus and slide presentations for each of the four modules: 1 "Good enough practices in scientific computing," 2 Data management, 3 Software development and research computing, and 4 Best practices in the ocean sciences. The 3rd module is split into two parts. We also include a poster presented at the 2020 Ocean Science Meeting, which has some results from pre- and post-surveys. Funding: The camp was funded by WHOI Academic Programs Office through a Doherty Chair in Education Award, with additional support from WHOI Ocean Informatics Working Group, WHOI Information Services, MBLWHOI Library, the NSF-funded Biological and Chemical Oceanography Data Management Office (BCO-DMO), and an NSF-funded XSEDE Jetstream Education Allocation TG-OCE190011. We also utilized resources from the NSF-funded Pangeo project.
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Still ImageMBLWHOI Library Banner( 2019-09)
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Working PaperMBLWHOI LIBRARY Recommendation for Webinar Series( 2018-12-14)This report was completed for a graduate level class at Syracuse University entitled IST 613 Library Planning, Marketing, and Assessment. This report was completed in partnership with Lisa Raymond and Jennifer Walton, Co-Directors of the MBLWHOI Library in Woods Hole, Massachusetts. The following report delivers information on the existing value and impact areas of the library including an analysis of the existing stakeholders, services, and resources. The MBLWHOI Library is a vital resource to the five science institutions located in Woods Hole, Massachusetts, as it provides both strong core and specialized services to assist patrons in furthering their endeavors in discovery, education, and research; however, communicating the value and impact of the library and its specialized services to its busy user community can be challenging. Bridging this gap is how the recommendation of the monthly lunch and learn webinar series was developed. The lunch and learn webinar series will not only help the library to share its specialized services and resources with its community, but it will also allow the library to meet and expand a good number of the goals listed within its Strategic Plan for 2018. A focus on identifying user needs via assessment will be key to creating a webinar series that is both relevant and inviting to the library’s community. By using webinar services that are provided at no cost by the institutions, the library can reinforce communication with its users, while also ensuring that the library budget remains primarily focused on resources, such as journal articles, that are of great importance to library patrons. Strengths for the recommendation stem from dedicated library staff, evidence of user needs for instruction on specialized services, as well as the library’s strong core values of furthering the education and research projects within the Woods Hole community. Marketing of the webinar series via flyers, social media, and email newsletters will refresh the library’s presence on campus, thus helping it to meet its goal of being viewed by the community as the primary knowledge resource on campus. The increased communication efforts will be tailored to various audience types by using key messages for each user group, as well as ensuring that the communication initiated by the library is brief, informative, and timely. Assessing the webinar series will be essential, and the continued success of the program will rest on the library’s ability to identify strengths and weaknesses in the series, as well as user need areas. User surveys, focus groups, informal conversations, and library statistics will all be collected and used as assessment tools. Assessment of the webinar series will help the library to ensure that the series’ outcomes and strategic plan goals are being met. Available library staff time and library budget will determine the ability of the library to implement the webinar series; however, the benefits of implementing the webinar series will not only create a platform for the increased exchange of knowledge between the library and its users, but it will also bring renewed focus to the library that will allow for the library to maximize the value and impact they are able to bestow on their user community.
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PresentationAdvancing Open Source, Linked Data Solutions for Cross-Repository Discovery and Collaboration( 2016-05)The MBLWHOI Library collaborated in multi-year NSF EarthCube funded projects, applying semantic technologies to enable knowledge discovery, sharing, and integration
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PresentationUsing linked open data to search across geoscience repositories [poster]( 2017-10)The MBLWHOI Library collaborated in multi-year NSF EarthCube funded projects, applying semantic technologies to enable knowledge discovery, sharing, and integration
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PresentationLeveraging the GeoLink Knowledge Base for Cruise Information(Federation of Earth Science Information Partners, 2016-12-21)Open Linked Data (LOD) is providing an excellent opportunity for repositories, libraries, and archives to expand the use of their holdings and advance the work of researchers. The implementation of the GeoLink Knowledgebase has created an exciting LOD framework for organizations specializing in Earth Sciences. As an NSF EarthCube Building Block, GeoLink brings together several powerful data sources, such as BCO-DMO, Rolling Deck to Repository (R2R), Data One, IEDA, IODP, and LTER, with publication providers such as the MBLWHOI Library’s Woods Hole Open Access Server (WHOAS), ESIP, and AGU. While publishing to the GeoLink knowledgebase offers a great way to make collections and metadata more findable and relevant, becoming a linked data publisher is not the only way to engage with linked data or the GeoLink project. Any repository can use simple, easily customizable code developed by members of the GeoLink team to add live GeoLink content to a page based on the item's metadata, leveraging GeoLink’s powerful framework for searching across repositories, organizations, and disciplines.
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PresentationGetting Started with Data Management & DMPTool at WHOI( 2017-01-25)Introduction to DMP Tool for WHOI staff given on January 26th, 2017. Presentation adapted from https://dmptool.org/promote#slides.
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PresentationOpen Access : the Power of One (or, how one individual moved an institution toward adopting an open access policy)( 2016-10-25)A presentation and discussion on the ongoing process to elevate open access in Woods Hole, sponsored by the MBLWHOI Library in observance of International Open Access week. Presented 25 October 2016 at the Smith Lab, Woods Hole Oceanographic Institution, Woods Hole, MA
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PreprintKey components of data publishing : using current best practices to develop a reference model for data publishing( 2015-12-04)Availability of workflows for data publishing could have an enormous impact on researchers, research practices and publishing paradigms, as well as on funding strategies and career and research evaluations. We present the generic components of such workflows in order to provide a reference model for these stakeholders. Methods: The RDA-WDS Data Publishing Workflows group set out to study the current data publishing workflow landscape across disciplines and institutions. A diverse set of workflows were examined to identify common components and standard practices, including basic self-publishing services, institutional data repositories, long term projects, curated data repositories, and joint data journal and repository arrangements. Results: The results of this examination have been used to derive a data publishing reference model comprised of generic components. From an assessment of the current data publishing landscape, we highlight important gaps and challenges to consider, especially when dealing with more complex workflows and their integration into wider community frameworks. Conclusions: It is clear that the data publishing landscape is varied and dynamic, and that there are important gaps and challenges. The different components of a data publishing system need to work, to the greatest extent possible, in a seamless and integrated way. We therefore advocate the implementation of existing standards for repositories and all parts of the data publishing process, and the development of new standards where necessary. Effective and trustworthy data publishing should be embedded in documented workflows. As more research communities seek to publish the data associated with their research, they can build on one or more of the components identified in this reference model.
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BookOcean data publication cookbook(UNESCO, 2013)Executive summary: This “Cookbook” has been written for data managers and librarians who are interested in assigning a permanent identifier to a dataset for the purposes of publishing that dataset online and for the citation of that dataset within the scientific literature. A formal publishing process adds value to the dataset for the data originators as well as for future users of the data. Value may be added by providing an indication of the scientific quality and importance of the dataset (as measured through a process of peer review), and by ensuring that the dataset is complete, frozen and has enough supporting metadata and other information to allow it to be used by others. Publishing a dataset also implies a commitment to persistence of the data and allows data producers to obtain academic credit for their work in creating the datasets. One form of persistent identifier is the Digital Object Identifier (DOI). A DOI is a character string (a "digital identifier") used to provide a unique identity of an object such as an electronic document. Metadata about the object is stored in association with the DOI name and this metadata may include a location where the object can be found. The DOI for a document is permanent, whereas its location and other metadata may change. Referring to an online document by its DOI provides more stable linking than simply referring to it by its URL, because if its URL changes, the publisher need only update the metadata for the DOI to link to the new URL. A DOI may be obtained for a variety of objects, including documents, data files and images. The assignment of DOIs to peer-reviewed journal articles has become commonplace. This cookbook provides a step-by-step guide to the data publication process and showcases some best practices for data publication.
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PresentationNo Repository is an Island: Putting the WHOAS community repository in a geoscience context [poster](E-Science Symposium, University of Massachusetts Medical School, 2016-04-06)The MBLWHOI Library is partner in the NSF-funded EarthCube building block, GeoLink, whose goal is to push the boundaries of semantic technology in cross-repository discovery within the geosciences field. GeoLink has created ontology design patterns that link together: the MBLWHOI Library’s Woods Hole Open Access Server (WHOAS); data repositories, including Rolling Deck to Repository (R2R), Biological and Chemical Oceanography Data Management Office (BCO-DMO), Integrated Earth Data Applications (IEDA), Long-Term Ecological Research Network (LTER), DataONE and the International Ocean Discovery Program (IODP); the National Science Foundation (NSF) funded awards; and American Geophysical Union (AGU) conference presentations. The Library created WHOAS, a DSpace repository, more than 10 years ago. As part of the GeoLink project we have been collaborating with @mire, a leader in open source DSpace development to develop modular code that can be integrated into other DSpace installations to improve LOD functionality. Our DSpace goals are to provide a built-in SPARQL endpoint for easy access to the data, implement editable authority concepts with URIs, and be able to integrate concepts from other authoritative sources using SPARQL queries. There is a second layer that takes dc-based DSpace triples and constructs triples based on GeoLink patterns which describes the data in a geoscience context. This provides flexibility and serves as a model for organizations contributing data to multiple LOD communities. This code is freely available to the 1700 registered DSpace repositories worldwide.