HydroShare GIS: Visualizing Spatial Data in the Cloud

Cloud-based data management systems are more conducive to collaborative efforts when they are integrated with cloud-computing tools that interact with their stored data. HydroShare, a web based data management system for climate and water data, has implemented an Application Programming Interface and a web application platform deployed using Tethys Platform to encourage the development of apps that interact with its data. HydroShare GIS is the result of one such development effort to provide cloud-based visualization of spatial data stored in HydroShare. It functions by accessing the spatial metadata contained within the HydroShare resource data model and overlaying datasets as layers within the OpenLayers JavaScript library. Data are passed from the app’s server to a GeoServer data server and shared as web mapping service layers. Thus, users can easily build map projects from data sources registered in HydroShare and save them back to HydroShare as map project resources, which can both be shared with others and re-opened in HydroShare GIS. This paper will describe the design of the HydroShare GIS app and the cyber-infrastructure that supports it, and evaluate its efficacy as a web based mapping tool

Quantitative Methods for Comparing Different Polyline Stream Network Models

Abstract Two techniques for exploring relative horizontal accuracy of complex linear spatial features are described and sample source code (pseudo code) is presented for this purpose. The first technique, relative sinuosity, is presented as a measure of the complexity or detail of a polyline network in comparison to a reference network. We term the second technique longitudinal root mean squared error (LRMSE) and present it as a means for quantitatively assessing the horizontal variance between two polyline data sets representing digitize

Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'

<p>Abstract</p> <p>Background</p> <p>Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of '<it>Candidatus </it>Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content.</p> <p>Results</p> <p>To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of '<it>Cand</it>. P. ubique' by targeting our search to long intergenic regions (IGRs) with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc.) shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from '<it>Cand</it>. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely <it>cis</it>-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data.</p> <p>Conclusion</p> <p>This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.</p

Kepler constraints on planets near hot Jupiters

We present the results of a search for planetary companions orbiting near hot Jupiter planet candidates (Jupiter-size candidates with orbital periods near 3 d) identified in the Kepler data through its sixth quarter of science operations. Special emphasis is given to companions between the 2∶1 interior and exterior mean-motion resonances. A photometric transit search excludes companions with sizes ranging from roughly two-thirds to five times the size of the Earth, depending upon the noise properties of the target star. A search for dynamically induced deviations from a constant period (transit timing variations) also shows no significant signals. In contrast, comparison studies of warm Jupiters (with slightly larger orbits) and hot Neptune-size candidates do exhibit signatures of additional companions with these same tests. These differences between hot Jupiters and other planetary systems denote a distinctly different formation or dynamical history

HydroShare – A Case Study of the Application of Modern Software Engineering to a Large Distributed Federally-Funded Scientific Software Development Project

HydroShare is an online collaborative system under development to support the open sharing of hydrologic data, analytical tools, and computer models. With HydroShare, scientists can easily discover, access, and analyze hydrologic data and thereby enhance the production and reproducibility of hydrologic scientific results. HydroShare also takes advantage of emerging social media functionality to enable users to enhance information about and collaboration around hydrologic data and models. HydroShare is being developed by an interdisciplinary collaborative team of domain scientists, university software developers, and professional software engineers from ten institutions located across the United States. While the combination of non–co-located, diverse stakeholders presents communication and management challenges, the interdisciplinary nature of the team is integral to the project’s goal of improving scientific software development and capabilities in academia. This chapter describes the challenges faced and lessons learned with the development of HydroShare, as well as the approach to software development that the HydroShare team adopted on the basis of the lessons learned. The chapter closes with recommendations for the application of modern software engineering techniques to large, collaborative, scientific software development projects, similar to the National Science Foundation (NSF)–funded HydroShare, in order to promote the successful application of the approach described herein by other teams for other projects

Cost Analysis of Single-Level Lumbar Fusions

Study Design: Cost analysis of a retrospectively identified cohort of patients who had undergone primary single-level lumbar fusion at a single institution's orthopedic or neurosurgery department. Objective: The purpose of this article is to analyze the determinants of direct costs for single-level lumbar fusions and identify potential areas for cost reduction. Methods: Adult patients who underwent primary single-level lumbar fusion from fiscal years 2008 to 2012 were identified via administrative and departmental databases and were eligible for inclusion. Patients were excluded if they underwent multiple surgeries, had previous surgery at the same anatomic region, underwent corpectomy, kyphectomy, disc replacement, surgery for tumor or infection, or had incomplete cost data. Demographic data, surgical data, and direct cost data in the categories of supplies, services, room and care, and pharmacy, was collected for each patient. Results: The cohort included 532 patients. Direct costs ranged from $8286 to$73 727 (median = $21 781; mean =$22 890 +/- $6323). Surgical approach was an important determinant of cost. The mean direct cost was highest for the circumferential approach and lowest for posterior instrumented spinal fusions without an interbody cage. The difference in mean direct cost between transforaminal lumbar interbody fusions, anterior lumbar interbody fusions, and lateral transpsoas fusions was not statistically significant. Surgical supplies accounted for 44% of direct costs. Spinal implants were the primary component of supply costs (84.9%). Services accounted for 38% of direct costs and were highly dependent on operative time. Comorbidities were an important contributor to variance in the cost of care as evidenced by high variance in pharmacy costs and length of stay related to their management. Conclusion: The costs of spinal surgeries are highly variable. Important cost drivers in our analysis included surgical approach, implants, operating room time, and length of hospital stay. Areas of high cost and high variance offer potential targets for cost savings and quality improvements.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Dural tears in adult deformity surgery: Incidence, risk factors, and outcomes

Study Design: Retrospective cohort study. Objectives: Describe the rate of dural tears (DTs) in adult spinal deformity (ASD) surgery. Describe the risk factors for DT and the impact of this complication on clinical outcomes. Methods: Patients with ASD undergoing surgery between 2008 and 2014 were separated into DT and non-DT cohorts; demographics, operative details, radiographic, and clinical outcomes were compared. Statistical analysis included Results: A total of 564 patients were identified. The rate of DT was 10.8% (n = 61). Patients with DT were older (61.1 vs 56.5 years, Conclusions: The rate of DT was 10.8% in an ASD cohort. This is similar to rates of DT reported following surgery for degenerative pathology. A history of prior spine surgery, decompression, interbody fusion, and osteotomies are all associated with an increased risk of DT, but decompression is the only independent risk factor for DT

Toward Open and Reproducible Environmental Modeling by Integrating Online Data Repositories, Computational Environments, and Model Application Programming Interfaces

Cyberinfrastructure needs to be advanced to enable open and reproducible environmental modeling research. Recent efforts toward this goal have focused on advancing online repositories for data and model sharing, online computational environments along with containerization technology and notebooks for capturing reproducible computational studies, and Application Programming Interfaces (APIs) for simulation models to foster intuitive programmatic control. The objective of this research is to show how these efforts can be integrated to support reproducible environmental modeling. We present first the high-level concept and general approach for integrating these three components. We then present one possible implementation that integrates HydroShare (an online repository), CUAHSI JupyterHub and CyberGIS-Jupyter for Water (computational environments), and pySUMMA (a model API) to support open and reproducible hydrologic modeling. We apply the example implementation for a hydrologic modeling use case to demonstrate how the approach can advance reproducible environmental modeling through the seamless integration of cyberinfrastructure services