BCO-DMO Quick Guide

BCO-DMO, a repository funded by the National Science Foundation (NSF), supports the oceanographic research community’s data needs throughout the entire data life cycle. This guide describes the services available from BCO-DMO from proposal to preservation and highlights phases where researchers engage significantly with the office.Curating and providing open access to research data is a collaborative process. This process may be thought of as a life cycle with data passing through various phases. Each phase has its own associated actors, roles, and critical activities. Good data management practices are necessary for all phases, from proposal to preservation.NSF #143557

Towards Capturing Provenance of the Data Curation Process at Domain-specific Repositories

Presented at AGU Fall Meeting, American Geophysical Union, Washington, D.C., 10 – 14 Dec 2018Data repositories often transform submissions to improve understanding and reuse of data by researchers other than the original submitter. However, scientific workflows built by the data submitters often depend on the original data format. In some cases, this makes the repository’s final data product less useful to the submitter. As a result, these two workable but different versions of the data provide value to two disparate, non-interoperable research communities around what should be a single dataset. Data repositories could bridge these two communities by exposing provenance explaining the transform from original submission to final product. A subsequent benefit of this provenance would be the transparent value-add of domain repository data curation. To improve its data management process efficiency, the Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification defined by the Frictionless Data project (https://frictionlessdata.io). Recently, BCO-DMO has been using the Frictionless Data Package Pipelines Python library (https://github.com/frictionlessdata/datapackage-pipelines) to capture the data curation processing steps that transform original submissions to final data products. Because these processing steps are stored using a declarative language they can be converted to a structured provenance record using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). PROV-O abstracts the Frictionless Data elements of BCO-DMO’s workflow for capturing necessary curation provenance and enables interoperability with other external provenance sources and tools. Users who are familiar with PROV-O or the Frictionless Data Pipelines can use either record to reproduce the final data product in a machine-actionable way. While there may still be some curation steps that cannot be easily automated, this process is a step towards end-to-end reproducible transforms throughout the data curation process. In this presentation, BCO-DMO will demonstrate how Frictionless Data Package Pipelines can be used to capture data curation provenance from original submission to final data product exposing the concrete value-add of domain-specific repositories.NSF #143557

Biological & Chemical Oceanography Data Management Office : a domain-specific repository for oceanographic data from around the world [poster]

Presented at AGU Ocean Sciences, 11 - 16 February 2018, Portland, ORThe Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a domain-specific digital data repository that works with investigators funded under the National Science Foundation’s Division of Ocean Sciences and Office of Polar Programs to manage their data free of charge. Data managers work closely with investigators to satisfy their data sharing requirements and to develop comprehensive Data Management Plans, as well as to ensure that their data will be well described with extensive metadata creation. Additionally, BCO-DMO offers tools to find and reuse these high-quality data and metadata packages, and services such as DOI generation for publication and attribution. These resources are free for all to discover, access, and utilize. As a repository embedded in our research community, BCO-DMO is well positioned to offer knowledge and expertise from both domain trained data managers and the scientific community at large. BCO-DMO is currently home to more than 9000 datasets and 900 projects, all of which are or will be submitted for archive at the National Centers for Environmental Information (NCEI). Our data holdings continue to grow, and encompass a wide range of oceanographic research areas, including biological, chemical, physical, and ecological. These data represent cruises and experiments from around the world, and are managed using community best practices, standards, and technologies to ensure accuracy and promote re-use. BCO-DMO is a repository and tool for investigators, offering both ocean science data and resources for data dissemination and publication.NSF #143557

A Flat Photoionization Rate at 2<z<4.2: Evidence for a Stellar-Dominated UV Background and Against a Decline of Cosmic Star Formation Beyond z~3

We investigate the implications of our measurement of the Lyman-alpha forest opacity at redshifts 2<z<4.2 from a sample of 86 high-resolution quasar spectra for the evolution of the cosmic ultraviolet luminosity density and its sources. The derived hydrogen photoionization rate is remarkably flat over this redshift range, implying an increasing comoving ionizing emissivity with redshift. Because the quasar luminosity function is strongly peaked near z~2, star-forming galaxies likely dominate the ionizing emissivity at z>~3. Our measurement argues against a star formation rate density declining beyond z~3, in contrast with existing state-of-the-art determinations of the cosmic star formation history from direct galaxy counts. Stellar emission from galaxies therefore likely reionized the Universe.Comment: 5 pages, including 1 figure, published by Ap

Importance of the difference in surface pressures of the cell membrane in doxorubicin resistant cells that do not express Pgp and ABCG2

P-glycoprotein (Pgp) represents the archetypal mechanism of drug resistance. But Pgp alone cannot expel drugs. A small but growing body of works has demonstrated that the membrane biophysical properties are central to Pgp-mediated drug resistance. For example, a change in the membrane surface pressure is expected to support drug–Pgp interaction. An interesting aspect from these models is that under specific conditions, the membrane is predicted to take over Pgp concerning the mechanism of drug resistance especially when the surface pressure is high enough, at which point drugs remain physically blocked at the membrane level. However it remains to be determined experimentally whether the membrane itself could, on its own, affect drug entry into cells that have been selected by a low concentration of drug and that do not express transporters. We demonstrate here that in the case of the drug doxorubicin, alteration of the surface pressure of membrane leaflets drive drug resistance

Capturing Provenance of Data Curation at BCO-DMO

Presented at USGS Data Management Working Group, 9, November 2020At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easier for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.NSF #192461

Capturing Provenance of Data Curation at BCO-DMO

Presented at Data Curation Network, May 15, 2020At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easer for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.NSF #192461

Constraints on the Universal CIV Mass Density at z~6 from Early IR Spectra Obtained with the Magellan FIRE Spectrograph

We present a new determination of the intergalactic CIV mass density at 4.3 < z < 6.3. Our constraints are derived from high signal-to-noise spectra of seven quasars at z > 5.8 obtained with the newly commissioned FIRE spectrograph on the Magellan Baade telescope, coupled with six observations of northern objects taken from the literature. We confirm the presence of a downturn in the CIV abundance at =5.66 by a factor of 4.1 relative to its value at =4.96, as measured in the same sightlines. In the FIRE sample, a strong system previously reported in the literature as CIV at z=5.82 is re-identified as MgII at z=2.78, leading to a substantial downward revision in $\Omega_{CIV}$ for these prior studies. Additionally we confirm the presence of at least two systems with low-ionization CII, SiII, and OI absorption but relatively weak signal from CIV. The latter systems systems may be of interest if the downward trend in $\Omega_{CIV}$ at high redshift is driven in part by ionization effects.Comment: 14 pages, 6 figures, 2 tables. Submitted to Ap

RIP3, a kinase promoting necroptotic cell death, mediates adverse remodelling after myocardial infarction

Aims Programmed necrosis (necroptosis) represents a newly identified mechanism of cell death combining features of both apoptosis and necrosis. Like apoptosis, necroptosis is tightly regulated by distinct signalling pathways. A key regulatory role in programmed necrosis has been attributed to interactions of the receptor-interacting protein kinases, RIP1 and RIP3. However, the specific functional role of RIP3-dependent signalling and necroptosis in the heart is unknown. The aims of this study were thus to assess the significance of necroptosis and RIP3 in the context of myocardial ischaemia. Methods and results Immunoblots revealed strong expression of RIP3 in murine hearts, indicating potential functional significance of this protein in the myocardium. Consistent with a role in promoting necroptosis, adenoviral overexpression of RIP3 in neonatal rat cardiomyocytes and stimulation with TNF-α induced the formation of a complex of RIP1 and RIP3. Moreover, RIP3 overexpression was sufficient to induce necroptosis of cardiomyocytes. In vivo, cardiac expression of RIP3 was up-regulated upon myocardial infarction (MI). Conversely, mice deficient for RIP3 (RIP3−/−) showed a significantly better ejection fraction (45 ± 3.6 vs. 32 ± 4.4%, P < 0.05) and less hypertrophy in magnetic resonance imaging studies 30 days after experimental infarction due to left anterior descending coronary artery ligation. This was accompanied by a diminished inflammatory response of infarcted hearts and decreased generation of reactive oxygen species. Conclusion Here, we show that RIP3-dependent necroptosis modulates post-ischaemic adverse remodelling in a mouse model of MI. This novel signalling pathway may thus be an attractive target for future therapies that aim to limit the adverse consequences of myocardial ischaemi

Incident vertebral fractures and risk factors in the first three years following glucocorticoid initiation among pediatric patients with rheumatic disorders

Vertebral fractures are an important yet underrecognized manifestation of osteoporosis in children with chronic, glucocorticoid-treated illnesses. Our goal was to determine the incidence and clinical predictors of vertebral fractures in the 3 years following glucocorticoid initiation among pediatric patients with rheumatic disorders. Incident vertebral fractures were evaluated according to the Genant semiquantitative method on lateral radiographs at baseline and then annually in the 3 years following glucocorticoid initiation. Extended Cox models were used to assess the association between vertebral fractures and clinical risk predictors. A total of 134 children with rheumatic disorders were enrolled in the study (mean ± standard deviation (SD) age 9.9 ± 4.4 years; 65% girls). The unadjusted vertebral fracture incidence rate was 4.4 per 100 person-years, with a 3-year incidence proportion of 12.4%. The highest annual incidence occurred in the first year (6.0%; 95% confidence interval (CI) 2.9% to 11.7%). Almost one-half of the patients with fractures were asymptomatic. Every 0.5 mg/kg increase in average daily glucocorticoid (prednisone equivalents) dose was associated with a twofold increased fracture risk (hazard ratio (HR) 2.0; 95% CI 1.1 to 3.5). Other predictors of increased vertebral fracture risk included: (1) increases in disease severity scores between baseline and 12 months; (2) increases in body mass index Z-scores in the first 6 months of each 12-month period preceding the annual fracture assessment; and (3) decreases in lumbar spine bone mineral density Z-scores in the first 6 months of glucocorticoid therapy. As such, we observed that a clinically significant number of children with rheumatic disorders developed incident vertebral fractures in the 3 years following glucocorticoid initiation. Almost one-half of the children were asymptomatic and thereby would have been undiagnosed in the absence of radiographic monitoring. In addition, discrete clinical predictors of incident vertebral fractures were evident early in the course of glucocorticoid therapy