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The Chameleon project developed a unique experi- mental testbed by adapting a mainstream cloud implementation to the needs of systems research community and thereby demon- strated that clouds can be configured to serve as a platform for this type research. More recently, the CloudBank project embarked on a mission of providing a conduit to commercial clouds for the systems research community that eliminates much of the complexity and some of the cost of using them for research. This creates an opportunity to explore running systems experiments in a combined setting, spanning both research and commercial clouds. In this paper, we present an extension to Chameleon for constructing controlled experiments across its resources and commercial clouds accessible via CloudBank, present a case study of an experiment running across such combined resources, and discuss the impact of using a combined research platform. 

Bone is a unique biological composite material made up of a highly structured collagen mesh matrix and mineral deposits. Although mineral provides stiffness, collagen’s secondary organization provides a critical role in bone elasticity. Here, we performed polarimetric analysis of bone collagen fibers using second harmonic generation (SHG) imaging to evaluate lamella sheets and collagen fiber integrity in intact cranial bone. Our polarimetric data was fitted to a model accounting for diattenuation, polarization cross-talk, and birefringence. We compared our data to the fitted model and found no significant difference between our polarimetric observation and the representation of these scattering properties up to 70µm deep. We also observed a loss of resolution as we imaged up to 70µm deep into bone but a conservation of polarimetric response. Polarimetric SHG allows for the discrimination of collagen lamellar sheet structures in intact bone. Our work could allow for label-free identification of disease states and monitor the efficacy of therapies for bone disorders.

 

The Chameleon testbed is a case study in adapting the cloud paradigm for computer science research. In this paper, we explain how this adaptation was achieved, evaluate it from the perspective of supporting the most experiments for the most users, and make a case that utilizing mainstream technology in research testbeds can increase efficiency without compro- mising on functionality. We also highlight the opportunity inherent in the shared digital artifacts generated by testbeds and give an overview of the efforts we’ve made to develop it to foster reproducibility. 

More than 54 million Americans have or are at high risk of developing a metabolic bone disease; disorders of bone strength that leave individuals with fragile bones and disabilities. The gold standard to evaluate these diseases is dual energy x-ray absorptiometry, but this only measures mineral content. These diseases, however, impact collagen and mineral integrity which impede the bone’s ability to store hormones, proteoglycans, and glycoproteins imperative to homeostasis. We have established a second harmonic generation (SHG) polarimetric assay that describes bone collagen organization. To further our analysis, we propose multimodal optical evaluation of bone quality with third harmonic generation (THG) to measure osteocyte dendritic processes. This method of analysis could be used to evaluate the disease state of bone and response to therapy. 

Large scientific facilities are unique and complex infrastructures that have become fundamental instruments for enabling high quality, world-leading research to tackle scientific problems at unprecedented scales. Cyberinfrastructure (CI) is an essential component of these facilities, providing the user community with access to data, data products, and services with the potential to transform data into knowledge. However, the timely evolution of the CI available at large facilities is challenging and can result in science communities requirements not being fully satisfied. Furthermore, integrating CI across multiple facilities as part of a scientific workflow is hard, resulting in data silos. In this paper, we explore how science gateways can provide improved user experiences and services that may not be offered at large facility datacenters. Using a science gateway supported by the Science Gateway Community Institute, which provides subscription-based delivery of streamed data and data products from the NSF Ocean Observatories Initiative (OOI), we propose a system that enables streaming-based capabilities and workflows using data from large facilities, such as the OOI, in a scalable manner. We leverage data infrastructure building blocks, such as the Virtual Data Collaboratory, which provides data and comput- ing capabilities in the continuum to efficiently and collaboratively integrate multiple data-centric CIs, build data-driven workflows, and connect large facilities data sources with NSF-funded CI, such as XSEDE. We also introduce architectural solutions for running these workflows using dynamically provisioned federated CI.