The Jason II virtual control van system, data acquisition system, web-based event logger, and SeaNet

Scientific underwater remotely operated vehicles (ROVs) collect data from multiple video cameras and scientific instruments. This integrated information is often only available in an ROV control-van during operations. Although all the data is logged, it is difficult for scientists to re-create a combined display of this data and have the ability to review and access an entire cruise dataset easily. We introduce a methodology of taking continuous real-time information snapshots (infosnaps) during interesting events and at regular time intervals for complete data coverage. These infosnaps capture four simultaneous video sources, vehicle data, instrument data, and event data as entered by scientists. The infosnaps are automatically cataloged and immediately accessible and searchable via a web-browser. We developed, built, and deployed the Jason II Virtual Control Van system on seven Jason cruises. The system has captured over 50,000 control-van infosnaps, containing more than 200,000 images co-registered with vehicle telemetry and scientific instrument data. The Virtual Control Van is designed for both scientific collaboration and public/educational outreach. It has been integrated with the SeaNet system to provide remote on-shore access. The report describes the Jason II Virtual Control Van system and includes instructions for setting up the system in the field.Funding was provided by the W. M. Keck Foundation under Grant No. 991735

4DGeoBrowser : a web-based data browser and server for accessing and analyzing multi-disciplinary data

This report describes the 4DGeoBrowser software system. The GeoBrowser is a web-based application developed at the Woods Hole Oceanographic Institution by Steven Lerner and Andrew Maffei. It has been designed with the goal of creating, accessing, and analyzing repositories of oceanographic datasets that have been generated by investigators in differing scientific disciplines. Once the information is loaded onto a Geobrowser server the investigator-user is able to login to the website and use a set of data access and analysis tools to search, plot, and display this information. GeoBrowser servers are also capable of processing commands that are submitted remotely via HTTP URLs or email. Scientists are able to use this capability to make calls to the GeoBrowser server and generate click-able maps, tables of urls, and customized HTML pages. These can then be used to enhance websites associated with scientific projects. Examples of supporting scientific website functionality that includes time series plotting, data delivery by email, geo-spatial plotting of interdisciplinary data, map-based search capabilities and other functionality are presented in this report. The report includes examples of GeoBrowser application websites, a user manual, and a reference guide. In addition, the concept of Electronic Index Cards (EICs) is presented

An authoritative global database for active submarine hydrothermal vent fields

Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry, Geophysics, Geosystems 14 (2013): 4892–4905, doi:10.1002/2013GC004998.The InterRidge Vents Database is available online as the authoritative reference for locations of active submarine hydrothermal vent fields. Here we describe the revision of the database to an open source content management system and conduct a meta-analysis of the global distribution of known active vent fields. The number of known active vent fields has almost doubled in the past decade (521 as of year 2009), with about half visually confirmed and others inferred active from physical and chemical clues. Although previously known mainly from mid-ocean ridges (MORs), active vent fields at MORs now comprise only half of the total known, with about a quarter each now known at volcanic arcs and back-arc spreading centers. Discoveries in arc and back-arc settings resulted in an increase in known vent fields within exclusive economic zones, consequently reducing the proportion known in high seas to one third. The increase in known vent fields reflects a number of factors, including increased national and commercial interests in seafloor hydrothermal deposits as mineral resources. The purpose of the database now extends beyond academic research and education and into marine policy and management, with at least 18% of known vent fields in areas granted or pending applications for mineral prospecting and 8% in marine protected areas.For support to prepare this manuscript, we thank the National Science Foundation (OCE08-38923, GeoEd12-02977), the NOAA Vents (now Earth-Ocean Interactions) Program and the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) under NOAA Cooperative Agreement NA10OAR4320148, and WHOI.2014-05-1

Towards Linked Data for Oceanographic Science: The R2R Eventlogger Project, Controlled Vocabularies, and Ontologies at The MBLWHOI Library

Objective: Research vessels coordinated by the United States University-National Oceanographic Laboratory System (US-UNOLS) collect data which are considered important oceanographic science research products. The NSF-funded Rolling Deck to Repository (R2R) project aims to improve access to these data and diminish barriers to their use. One aspect of the R2R project has been to develop a shipboard scientific event logging system, Eventlogger, which incorporates best practice guidelines, controlled vocabularies, a cruise metadata schema, and a scientific event log. Eventlogger facilitates the eventual ingestion of datasets into oceanographic data repositories for subsequent integration and synthesis by investigators. The careful use of controlled vocabularies and ontologies is an important feature of this system, as the use of internationally-informed, consensus-driven controlled vocabularies will make data sets more interoperable, discoverable and reusable. Methods: The R2R Eventlogger project is led by Woods Hole Oceanographic Institution (WHOI), and the management of the controlled vocabularies is led by the Data Librarian in the Marine Biological Laboratory/Woods Hole Oceanographic Institution (MBLWHOI) Library. The first target vocabulary has been one for oceanographic instruments. Management of this vocabulary has thus far consisted of reconciling project vocabulary terms with the more widely used community vocabularies served by the NERC Vocabulary Server v2.0 (NVS2.0): terms included in the SeaDataNet Device Catalogue (L22) and the SeaDataNet Device Category vocabularies (L05). Rather than adopt existing community terms, it is more often the case that local terms are mapped by the Data Managers in the NSF-funded Biological and Chemical Oceanographic Data Management Office (BCO-DMO) to community terms, which preserves any important information and meaning investigators impart through the process of assigning these local terms, and has less impact on researchers. New terms, those that cannot be mapped to the existing community vocabularies (often custom, or modified instruments), are submitted for review to the SeaVOX governance process for addition to the community vocabularies. These vocabularies and their mappings are an important part of the aforementioned Eventlogger system. Before a research cruise, investigators configure the instruments they intend to use for their science activities. The instruments available for selection are provided by the MBLWHOI Data Librarian, who curates UNOLS ship-specific lists of standard shipboard instruments using terms for instruments from the R2R Eventlogger Project Vocabulary. Nonstandard shipboard instruments a researcher or investigator wishes to use can also be added, and these instrument terms will eventually be inducted into the R2R Eventlogger Project Vocabulary. Results: Eventlogger is currently being tested across the UNOLS fleet. A large submission of suggested instrument terms to the SeaDataNet community listserv is currently in progress. New tools for facilitating the management, mapping, and use of these controlled vocabularies are being developed, and new projects with eager partners are envisioned. Ideas for future controlled vocabularies for the ocean science community include: Cruise IDs, Persons, and Ships. Conclusions: The promotion and use of controlled vocabularies and ontologies will pave the way for linked data in oceanographic science. By mapping local terms to authoritative and community-accepted terms, links are created whereby related data sets can be better discovered, and utilized. Librarians have an established history of working with controlled vocabularies and metadata. Libraries, have and will continue to, serve as centers for information discovery as well as a natural home for the management of standards

Toward cyberinfrastructure to facilitate collaboration and reproducibility for marine integrated ecosystem assessments

Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Earth Science Informatics 10 (2017): 85-97, doi:10.1007/s12145-016-0280-4.There is a growing need for cyberinfrastructure to support science-based decision making in management of natural resources. In particular, our motivation was to aid the development of cyberinfrastructure for Integrated Ecosystem Assessments (IEAs) for marine ecosystems. The IEA process involves analysis of natural and socio-economic information based on diverse and disparate sources of data, requiring collaboration among scientists of many disciplines and communication with other stakeholders. Here we describe our bottom-up approach to developing cyberinfrastructure through a collaborative process engaging a small group of domain and computer scientists and software engineers. We report on a use case evaluated for an Ecosystem Status Report, a multi-disciplinary report inclusive of Earth, life, and social sciences, for the Northeast U.S. Continental Shelf Large Marine Ecosystem. Ultimately, we focused on sharing workflows as a component of the cyberinfrastructure to facilitate collaboration and reproducibility. We developed and deployed a software environment to generate a portion of the Report, retaining traceability of derived datasets including indicators of climate forcing, physical pressures, and ecosystem states. Our solution for sharing workflows and delivering reproducible documents includes IPython (now Jupyter) Notebooks. We describe technical and social challenges that we encountered in the use case and the importance of training to aid the adoption of best practices and new technologies by domain scientists. We consider the larger challenges for developing end-to-end cyberinfrastructure that engages other participants and stakeholders in the IEA process.Support for this research was provided by the U. S. National Science Foundation #0955649 with additional support to SB by the Investment in Science Fund at Woods Hole Oceanographic Institution

Shallow Water ’06 : a joint acoustic propagation/nonlinear internal wave physics experiment

Author Posting. © Oceanography Society, 2007. This article is posted here by permission of Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 20, 4 (2007): 156-167.Since the end of the Cold War, the US Navy has had an increasing interest in continental shelves and slopes as operational areas. To work in such areas requires a good understanding of ocean acoustics, coastal physical oceanography, and, in the modern era, autonomous underwater vehicle (AUV) operations

Acoustic and oceanographic observations and configuration information for the WHOI moorings from the SW06 experiment

This document describes data, sensors, and other useful information pertaining to the moorings that were deployed from the R/V Knorr from July 24th to August 4th, 2006 in support of the SW06 experiment. The SW06 experiment was a large, multi-disciplinary effort performed 100 miles east of the New Jersey coast. A total of 62 acoustic and oceanographic moorings were deployed and recovered. The moorings were deployed in a “T” geometry to create an along-shelf path along the 80 meter isobath and an across-shelf path starting at 600 meters depth and going shoreward to a depth of 60 meters. A cluster of moorings was placed at the intersection of the two paths to create a dense sensor-populated area to measure a 3-dimensional physical oceanography. Environmental moorings were deployed along both along-shelf and across-shelf paths to measure the physical oceanography along those paths. Moorings with acoustic sources were placed at the outer ends of the “T” to propagate various signals along these paths. Five single hydrophone receivers were positioned on the across shelf path and a vertical and horizontal hydrophone array was positioned at the intersection of the “T” to get receptions from all the acoustics assets that were used during SW06.Funding was provided by the Office of Naval Research under Contract No. N00014-04-1014

Jaguar Densities across Human-Dominated Landscapes in Colombia: The Contribution of Unprotected Areas to Long Term Conservation

Large carnivores such as jaguars (Panthera onca) are species of conservation concern because they are suffering population declines and are keystone species in their ecosystems. Their large area requirements imply that unprotected and ever-increasing agricultural regions can be important habitats as they allow connectivity and dispersal among core protected areas. Yet information on jaguar densities across unprotected landscapes it is still scarce and crucially needed to assist management and range-wide conservation strategies. Our study provides the first jaguar density estimates of Colombia in agricultural regions which included cattle ranching, the main land use in the country, and oil palm cultivation, an increasing land use across the Neotropics. We used camera trapping across two agricultural landscapes located in the Magdalena River valley and in the Colombian llanos (47–53 stations respectively; >2000 trap nights at both sites) and classic and spatially explicit capture-recapture models with the sex of individuals as a covariate. Density estimates were 2.52±0.46–3.15±1.08 adults/100 km2 in the Magdalena valley, whereas 1.12±0.13–2.19±0.99 adults/100 km2 in the Colombian llanos, depending on analysis used. We suggest that jaguars are able to live across unprotected human-use areas and co-exist with agricultural landscapes including oil-palm plantations if natural areas and riparian habitats persist in the landscape and hunting of both jaguar and prey is limited. In the face of an expanding agriculture across the tropics we recommend land-use planning, adequate incentives, regulations, and good agricultural practices for range-wide jaguar connectivity and survival

A high fat diet increases mitochondrial fatty acid oxidation and uncoupling to decrease efficiency in rat heart

Elevated levels of cardiac mitochondrial uncoupling protein 3 (UCP3) and decreased cardiac efficiency (hydraulic power/oxygen consumption) with abnormal cardiac function occur in obese, diabetic mice. To determine whether cardiac mitochondrial uncoupling occurs in non-genetic obesity, we fed rats a high fat diet (55% kcal from fat) or standard laboratory chow (7% kcal from fat) for 3 weeks, after which we measured cardiac function in vivo using cine MRI, efficiency in isolated working hearts and respiration rates and ADP/O ratios in isolated interfibrillar mitochondria; also, measured were medium chain acyl-CoA dehydrogenase (MCAD) and citrate synthase activities plus uncoupling protein 3 (UCP3), mitochondrial thioesterase 1 (MTE-1), adenine nucleotide translocase (ANT) and ATP synthase protein levels. We found that in vivo cardiac function was the same for all rats, yet oxygen consumption was 19% higher in high fat-fed rat hearts, therefore, efficiency was 21% lower than in controls. We found that mitochondrial fatty acid oxidation rates were 25% higher, and MCAD activity was 23% higher, in hearts from rats fed the high fat diet when compared with controls. Mitochondria from high fat-fed rat hearts had lower ADP/O ratios than controls, indicating increased respiratory uncoupling, which was ameliorated by GDP, a UCP3 inhibitor. Mitochondrial UCP3 and MTE-1 levels were both increased by 20% in high fat-fed rat hearts when compared with controls, with no significant change in ATP synthase or ANT levels, or citrate synthase activity. We conclude that increased cardiac oxygen utilisation, and thereby decreased cardiac efficiency, occurs in non-genetic obesity, which is associated with increased mitochondrial uncoupling due to elevated UCP3 and MTE-1 levels

Detection chain and electronic readout of the QUBIC instrument

The Q and U Bolometric Interferometer for Cosmology (QUBIC) Technical Demonstrator (TD) aiming to shows the feasibility of the combination of interferometry and bolometric detection. The electronic readout system is based on an array of 128 NbSi Transition Edge Sensors cooled at 350mK readout with 128 SQUIDs at 1K controlled and amplified by an Application Specific Integrated Circuit at 40K. This readout design allows a 128:1 Time Domain Multiplexing. We report the design and the performance of the detection chain in this paper. The technological demonstrator unwent a campaign of test in the lab. Evaluation of the QUBIC bolometers and readout electronics includes the measurement of I-V curves, time constant and the Noise Equivalent Power. Currently the mean Noise Equivalent Power is ~ 2 x 10⁻¹⁶ W/√Hz