Data management for NREL and beyond: a roadmap and recommendations

The SGS-LTER research site was established in 1980 by researchers at Colorado State University as part of a network of long-term research sites within the US LTER Network, supported by the National Science Foundation. Scientists within the Natural Resource Ecology Lab, Department of Forest and Rangeland Stewardship, Department of Soil and Crop Sciences, and Biology Department at CSU, California State Fullerton, USDA Agricultural Research Service, University of Northern Colorado, and the University of Wyoming, among others, have contributed to our understanding of the structure and functions of the shortgrass steppe and other diverse ecosystems across the network while maintaining a common mission and sharing expertise, data and infrastructure.Version 1.1 - June 2013.Includes bibliographical references.This report contains a summary of activities lead by Nicole Kaplan, RA, and Greg Newman, Research Scientist, and a strategy for managing data, which were supported by 2012 Program Development Funds at the Natural Resource Ecology Laboratory (NREL). We set out to describe current components, functions and expertise of the NREL cyber-infrastructure and inquire about current work and future needs for managing, archiving and providing access to data. The activities we coordinated included: (1) conducting a workshop, (2) arranging the Spring 2012 seminar series entitled Data Literacy: Bridging the Gap Between Science and Society, (3) contributing to over a dozen data management plans for NREL proposals, (4) providing database services to PHACE (a large collaborative project), and (5) attending conferences and workshops to obtain new ideas and build partnerships. The results of what we learned and accomplished include overall data management goals for NREL, a model for a data management system for NREL, requirements for a web-based data access and delivery system, policies for data sharing and attribution, training for undergraduate and graduate students, and scholarly work in Ecological Informatics (e.g. Chu et al. in press, Newman et al. 2011, Vanderbilt et al. 2009). Our work was presented at the NREL 2012 Annual Retreat and the presentation file is available upon request. Here, we present resources for NREL to plan and conduct data management as part of the research process. We propose a model that establishes a hierarchy of workspaces to support, preserve, and secure the flow of data from the private laboratory space of the Principal Investigator, to a web-based NREL Data Repository to disseminate data to the public and stakeholders. We detail how current cyber-infrastructure capabilities can be leveraged to meet needs within NREL for data management, facilitate research discovery and data re-use, and contribute to NREL excellence. Major benefits to managing, sharing and re-using data include increasing the competitiveness of NREL proposals, influencing expectations of funding agencies for data management, accelerating global change research (Wolkovich et al. 2012), and broadening scientific understanding and services to support decision-making (Dozier and Gail 2009). In addition, federal research sponsors are committed to increasing open access to data and are requiring data management plans from agencies and departments with over 100 million dollars in research and development expenditures (Holdren 2013 and e.g. The Fair Access to Science and Technology Research Act (FASTR).Supported by 2012 NREL Program Development Fund

Shortgrass Steppe LTER VI: examining ecosystem persistence and responses to global change, 2010-2014 proposal

Includes bibliographical references.The SGS-LTER research site was established in 1980 by researchers at Colorado State University as part of a network of long-term research sites within the US LTER Network, supported by the National Science Foundation. Scientists within the Natural Resource Ecology Lab, Department of Forest and Rangeland Stewardship, Department of Soil and Crop Sciences, and Biology Department at CSU, California State Fullerton, USDA Agricultural Research Service, University of Northern Colorado, and the University of Wyoming, among others, have contributed to our understanding of the structure and functions of the shortgrass steppe and other diverse ecosystems across the network while maintaining a common mission and sharing expertise, data and infrastructure.The Shortgrass Steppe Long-term Ecological Research (SGS-LTER) program focuses on how grassland ecosystems function and persist or change in the face of global change. Our conceptual framework asserts that climate, physiography, grazing, fire and landuse, operating over different spatial and temporal scales, are the dominant determinants of the structure, function, and persistence of the SGS. Using the shortgrass steppe (SGS) ecosystem of the North American Great Plains as a model, we seek to (1) identify the ecological attributes of grasslands that historically have resulted in their persistence and (2) understand these attributes in ways that will allow us to identify area of vulnerability and better forecast the future of grasslands in the face of global change. Given its geographic extent and history, the SGS encapsulates many of the features of a system driven by social-ecological interactions and the vulnerabilities of semiarid grasslands to global change. Our overarching question is: How will structure and function of the SGS respond to expected changes in climate, management, and land-use, and what will be the consequences

Data curation issues in transitioning a field science collection of long-term research data and artefacts from a local repository to an institutional repository

The SGS-LTER research site was established in 1980 by researchers at Colorado State University as part of a network of long-term research sites within the US LTER Network, supported by the National Science Foundation. Scientists within the Natural Resource Ecology Lab, Department of Forest and Rangeland Stewardship, Department of Soil and Crop Sciences, and Biology Department at CSU, California State Fullerton, USDA Agricultural Research Service, University of Northern Colorado, and the University of Wyoming, among others, have contributed to our understanding of the structure and functions of the shortgrass steppe and other diverse ecosystems across the network while maintaining a common mission and sharing expertise, data and infrastructure.Transition a local 32 year project, the Shortgrass Steppe Long-Term Ecological Research (SGS-LTER), with over 100 data packages and related digital artefacts, to an Institutional Repository (IR) at Colorado State University (CSU) Libraries to ensure persistent, reliable, and interoperable access to our collection of scientific data. Our collaborative team envisions being part of a larger information environment, which enables sharing of knowledge and data - a web of repositories. Poster presented at the 9th International Digital Curation Conference held in San Francisco, California on February 25, 2014. Refereed.This work is supported by NSF Grant Number DEB-0823405, Colorado State University, and the UIUC Data Curation Education at Research Centers (DCERC IMLS Award #RE-02-10-0004-10)

Managing scientific research data: data packaging and organizing materials for curation

The SGS-LTER research site was established in 1980 by researchers at Colorado State University as part of a network of long-term research sites within the US LTER Network, supported by the National Science Foundation. Scientists within the Natural Resource Ecology Lab, Department of Forest and Rangeland Stewardship, Department of Soil and Crop Sciences, and Biology Department at CSU, California State Fullerton, USDA Agricultural Research Service, University of Northern Colorado, and the University of Wyoming, among others, have contributed to our understanding of the structure and functions of the shortgrass steppe and other diverse ecosystems across the network while maintaining a common mission and sharing expertise, data and infrastructure.Presentation held at the Front Range Data Librarian Meeting on June 16, 2014 at CSU Libraries and Natural Resource Ecology Laboratory in Fort Collins, Colorado.NSF Grant DEB-1027319

Through the looking glass: what do we see, what have we learned, what can we share? Information management at the Shortgrass Steppe Long Term Ecological Research site

The SGS-LTER research site was established in 1980 by researchers at Colorado State University as part of a network of long-term research sites within the US LTER Network, supported by the National Science Foundation. Scientists within the Natural Resource Ecology Lab, Department of Forest and Rangeland Stewardship, Department of Soil and Crop Sciences, and Biology Department at CSU, California State Fullerton, USDA Agricultural Research Service, University of Northern Colorado, and the University of Wyoming, among others, have contributed to our understanding of the structure and functions of the shortgrass steppe and other diverse ecosystems across the network while maintaining a common mission and sharing expertise, data and infrastructure.This poster displays the development of a successful information management system at a Long Term Ecological Research (LTER) site that has a rich history of data collection and management. Over sixty years of data from three separate projects are incorporated into the Shortgrass Steppe (SGS) LTER information management system and databases. People with different strengths and expertise ranging from clerical administrator, programmer, to ecologist, have filled the role of Information Manager (IM) at the SGS-LTER. Today the information management needs of the SGS are provided by a team of IMs with various levels of expertise in a wide variety of domains from information technology administration to education and outreach. It is critical for IMs at any long-term research site to understand how information and data were managed in the past and what recent changes have been added to the system, in order to effectively implement a management plan for the future. We are able to evaluate the effectiveness of different approaches to information management and have a commitment to share our successes with the information management community

Proteomic, biomechanical and functional analyses define neutrophil heterogeneity in systemic lupus erythematosus

Funder: NHLI FoundationFunder: NIHR Imperial Biomedical Research Centre; FundRef: http://dx.doi.org/10.13039/501100013342Funder: National Heart Lung and Blood InstituteFunder: Medical Research Council; FundRef: http://dx.doi.org/10.13039/501100000265Funder: National Institute of Biomedical Imaging and Bioengineering; FundRef: http://dx.doi.org/10.13039/100000070Funder: Gates Cambridge ScholarshipFunder: NIH/OXCAM FellowshipObjectives: Low-density granulocytes (LDGs) are a distinct subset of proinflammatory and vasculopathic neutrophils expanded in systemic lupus erythematosus (SLE). Neutrophil trafficking and immune function are intimately linked to cellular biophysical properties. This study used proteomic, biomechanical and functional analyses to further define neutrophil heterogeneity in the context of SLE. Methods: Proteomic/phosphoproteomic analyses were performed in healthy control (HC) normal density neutrophils (NDNs), SLE NDNs and autologous SLE LDGs. The biophysical properties of these neutrophil subsets were analysed by real-time deformability cytometry and lattice light-sheet microscopy. A two-dimensional endothelial flow system and a three-dimensional microfluidic microvasculature mimetic (MMM) were used to decouple the contributions of cell surface mediators and biophysical properties to neutrophil trafficking, respectively. Results: Proteomic and phosphoproteomic differences were detected between HC and SLE neutrophils and between SLE NDNs and LDGs. Increased abundance of type 1 interferon-regulated proteins and differential phosphorylation of proteins associated with cytoskeletal organisation were identified in SLE LDGs relative to SLE NDNs. The cell surface of SLE LDGs was rougher than in SLE and HC NDNs, suggesting membrane perturbances. While SLE LDGs did not display increased binding to endothelial cells in the two-dimensional assay, they were increasingly retained/trapped in the narrow channels of the lung MMM. Conclusions: Modulation of the neutrophil proteome and distinct changes in biophysical properties are observed alongside differences in neutrophil trafficking. SLE LDGs may be increasingly retained in microvasculature networks, which has important pathogenic implications in the context of lupus organ damage and small vessel vasculopathy

As in Real Estate, Location Matters: Cellular Expression of Complement Varies Between Macular and Peripheral Regions of the Retina and Supporting Tissues.

The cellular events that dictate the initiation of the complement pathway in ocular degeneration, such as age-related macular degeneration (AMD), is poorly understood. Using gene expression analysis (single cell and bulk), mass spectrometry, and immunohistochemistry, we dissected the role of multiple retinal and choroidal cell types in determining the complement homeostasis. Our scRNA-seq data show that the cellular response to early AMD is more robust in the choroid, particularly in fibroblasts, pericytes and endothelial cells. In late AMD, complement changes were more prominent in the retina especially with the expression of the classical pathway initiators. Notably, we found a spatial preference for these differences. Overall, this study provides insights into the heterogeneity of cellular responses for complement expression and the cooperation of neighboring cells to complete the pathway in healthy and AMD eyes. Further, our findings provide new cellular targets for therapies directed at complement

Complex Interactions between GSK3 and aPKC in Drosophila Embryonic Epithelial Morphogenesis

Generally, epithelial cells must organize in three dimensions to form functional tissue sheets. Here we investigate one such sheet, the Drosophila embryonic epidermis, and the morphogenetic processes organizing cells within it. We report that epidermal morphogenesis requires the proper distribution of the apical polarity determinant aPKC. Specifically, we find roles for the kinases GSK3 and aPKC in cellular alignment, asymmetric protein distribution, and adhesion during the development of this polarized tissue. Finally, we propose a model explaining how regulation of aPKC protein levels can reorganize both adhesion and the cytoskeleton

Bodyweight Perceptions among Texas Women: The Effects of Religion, Race/Ethnicity, and Citizenship Status

Despite previous work exploring linkages between religious participation and health, little research has looked at the role of religion in affecting bodyweight perceptions. Using the theoretical model developed by Levin et al. (Sociol Q 36(1):157–173, 1995) on the multidimensionality of religious participation, we develop several hypotheses and test them by using data from the 2004 Survey of Texas Adults. We estimate multinomial logistic regression models to determine the relative risk of women perceiving themselves as overweight. Results indicate that religious attendance lowers risk of women perceiving themselves as very overweight. Citizenship status was an important factor for Latinas, with noncitizens being less likely to see themselves as overweight. We also test interaction effects between religion and race. Religious attendance and prayer have a moderating effect among Latina non-citizens so that among these women, attendance and prayer intensify perceptions of feeling less overweight when compared to their white counterparts. Among African American women, the effect of increased church attendance leads to perceptions of being overweight. Prayer is also a correlate of overweight perceptions but only among African American women. We close with a discussion that highlights key implications from our findings, note study limitations, and several promising avenues for future research

Long-term ecological research on Colorado Shortgrass Steppe

The SGS-LTER research site was established in 1980 by researchers at Colorado State University as part of a network of long-term research sites within the US LTER Network, supported by the National Science Foundation. Scientists within the Natural Resource Ecology Lab, Department of Forest and Rangeland Stewardship, Department of Soil and Crop Sciences, and Biology Department at CSU, California State Fullerton, USDA Agricultural Research Service, University of Northern Colorado, and the University of Wyoming, among others, have contributed to our understanding of the structure and functions of the shortgrass steppe and other diverse ecosystems across the network while maintaining a common mission and sharing expertise, data and infrastructure.Poster presented at the LTER All Scientists Meeting held in Estes Park, CO on September 10-13, 2012