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NASA's Ice, Cloud, and land Elevation Satellite-2 (ICESat-2) carries a laser altimeter that fires 10,000 pulses per second towards Earth and records the travel time of individual photons to measure the elevation of the surface below. The volume of data produced by ICESat-2, nearly a TB per day, presents significant challenges for users wishing to efficiently explore the dataset. NASA's National Snow and Ice Data Center (NSIDC) Distributed Active Archive Center (DAAC), which is responsible for archiving and distributing ICESat-2 data, provides search and subsetting services on mission data products, but providing interactive data discovery and visualization tools needed to assess data coverage and quality in a given area of interest is outside of NSIDC's mandate. The OpenAltimetry project, a NASA-funded collaboration between NSIDC, UNAVCO and the University of California San Diego, has developed a web-based cyberinfrastructure platform that allows users to locate, visualize, and download ICESat-2 surface elevation data and photon clouds for any location on Earth, on demand. OpenAltimetry also provides access to elevations and waveforms for ICESat (the predecessor mission to ICESat-2). In addition, OpenAltimetry enables data access via APIs, opening opportunities for rapid access, experimentation, and computation via third party applications like Jupyter notebooks. OpenAltimetry emphasizes ease-of-use for new users and rapid access to entire altimetry datasets for experts and has been successful in meeting the needs of different user groups. In this paper we describe the principles that guided the design and development of the OpenAltimetry platform and provide a high-level overview of the cyberinfrastructure components of the system.

AbstractNASA’s Ice, Cloud, and land Elevation Satellite-2 (ICESat-2) carries a laser altimeter that fires 10,000 pulses per second towards Earth and records the travel time of individual photons to measure the elevation of the surface below. The volume of data produced by ICESat-2, nearly a TB per day, presents significant challenges for users wishing to efficiently explore the dataset. NASA’s National Snow and Ice Data Center (NSIDC) Distributed Active Archive Center (DAAC), which is responsible for archiving and distributing ICESat-2 data, provides search and subsetting services on mission data products, but providing interactive data discovery and visualization tools needed to assess data coverage and quality in a given area of interest is outside of NSIDC’s mandate. The OpenAltimetry project, a NASA-funded collaboration between NSIDC, UNAVCO and the University of California San Diego, has developed a web-based cyberinfrastructure platform that allows users to locate, visualize, and download ICESat-2 surface elevation data and photon clouds for any location on Earth, on demand. OpenAltimetry also provides access to elevations and waveforms for ICESat (the predecessor mission to ICESat-2). In addition, OpenAltimetry enables data access via APIs, opening opportunities for rapid access, experimentation, and computation via third party applications like Jupyter notebooks. OpenAltimetry emphasizes ease-of-use for new users and rapid access to entire altimetry datasets for experts and has been successful in meeting the needs of different user groups. In this paper we describe the principles that guided the design and development of the OpenAltimetry platform and provide a high-level overview of the cyberinfrastructure components of the system.

Intraoperative diagnosis is essential for providing safe and effective care during cancer surgery1. The existing workflow for intraoperative diagnosis based on hematoxylin and eosin staining of processed tissue is time, resource and labor intensive2,3. Moreover, interpretation of intraoperative histologic images is dependent on a contracting, unevenly distributed, pathology workforce4. In the present study, we report a parallel workflow that combines stimulated Raman histology (SRH)5-7, a label-free optical imaging method and deep convolutional neural networks (CNNs) to predict diagnosis at the bedside in near real-time in an automated fashion. Specifically, our CNNs, trained on over 2.5 million SRH images, predict brain tumor diagnosis in the operating room in under 150 s, an order of magnitude faster than conventional techniques (for example, 20-30 min)2. In a multicenter, prospective clinical trial (n = 278), we demonstrated that CNN-based diagnosis of SRH images was noninferior to pathologist-based interpretation of conventional histologic images (overall accuracy, 94.6% versus 93.9%). Our CNNs learned a hierarchy of recognizable histologic feature representations to classify the major histopathologic classes of brain tumors. In addition, we implemented a semantic segmentation method to identify tumor-infiltrated diagnostic regions within SRH images. These results demonstrate how intraoperative cancer diagnosis can be streamlined, creating a complementary pathway for tissue diagnosis that is independent of a traditional pathology laboratory.

Although the quality of weather forecasts in the polar regions is improving, forecast skill there still lags behind lower latitudes. So far there have been relatively few efforts to evaluate processes in numerical weather prediction systems using in situ and remote sensing datasets from meteorological observatories in the terrestrial Arctic and Antarctic compared to the mid-latitudes. Progress has been limited both by the heterogeneous nature of observatory and forecast data and by limited availability of the parameters needed to perform process-oriented evaluation in multi-model forecast archives. The Year of Polar Prediction (YOPP) site Model Inter-comparison Project (YOPPsiteMIP) is addressing this gap by producing merged observatory data files (MODFs) and merged model data files (MMDFs), bringing together observations and forecast data at polar meteorological observatories in a format designed to facilitate process-oriented evaluation. An evaluation of forecast performance was performed at seven Arctic sites, focussing on the first YOPP Special Observing Period in the Northern Hemisphere (NH-SOP1) in February and March 2018. It demonstrated that although the characteristics of forecast skill vary between the different sites and systems, an underestimation in boundary layer temperature variability across models, which goes hand in hand with an inability to capture cold extremes, is a common issue at several sites. It is found that many models tend to underestimate the sensitivity of the 2 m air temperature (T2m) and the surface skin temperature to variations in radiative forcing, and the reasons for this are discussed. [ABSTRACT FROM AUTHOR]

A large and ever-growing body of geophysical information is measured in campaigns and at specialized observatories as a part of scientific expeditions and experiments. These collections of observed data include many essential climate variables (as defined by the Global Climate Observing System) but are often distinguished by a wide range of additional non-routine measurements that are designed to not only document the state of the environment but also the drivers that contribute to that state. These field data are used not only to further understand environmental processes through observation-based studies but also to provide baseline data to test model performance and to codify understanding to improve predictive capabilities. To address the considerable barriers and difficulty in utilizing these diverse and complex data for observation–model research, the Merged Observatory Data File (MODF) concept has been developed. A MODF combines measurements from multiple instruments into a single file that complies with well-established data format and metadata practices and has been designed to parallel the development of corresponding Merged Model Data Files (MMDFs). Using the MODF and MMDF protocols will facilitate the evolution of model intercomparison projects into model intercomparison and improvement projects by putting observation and model data "on the same page" in a timely manner. The MODF concept was developed especially for weather forecast model studies in the Arctic. The surprisingly complex process of implementing MODFs in that context refined the concept itself. Thus, this article explains the concept of MODFs by providing details on the issues that were revealed and resolved during that first specific implementation. Detailed instructions are provided on how to make MODFs, and this article can be considered a MODF creation manual. [ABSTRACT FROM AUTHOR]

Studies on surgical site infection (SSI) in adult neurosurgery have presented all subtypes of SSIs as the general 'SSI'. Given that SSIs constitute a broad range of infections, we hypothesized that clinical outcomes and management vary based on SSI subtype. A retrospective analysis of all neurosurgical SSI from 2012–2019 was conducted at a tertiary care institution. SSI subtypes were categorized as deep and superficial incisional SSI, brain, dural or spinal abscesses, meningitis or ventriculitis, and osteomyelitis. 9620 craniotomy, shunt, and fusion procedures were studied. 147 procedures (1.5%) resulted in postoperative SSI. 87 (59.2%) of these were associated with craniotomy, 36 (24.5%) with spinal fusion, and 24 (16.3%) with ventricular shunting. Compared with superficial incisional primary SSI, rates of reoperation to treat SSI were highest for deep incisional primary SSI (91.2% vs 38.9% for superficial, p < 0.001) and second-highest for intracranial SSI (90.9% vs 38.9%, p = 0.0001). Postoperative meningitis was associated with the highest mortality rate (14.9%). Compared with superficial incisional SSI, the rate of readmission for intracranial SSI was highest (57.6% vs 16.7%, p = 0.022). Deep incisional and organ space SSI demonstrate a greater association with morbidity relative to superficial incisional SSI. Future studies should assess subtypes of SSI given these differences. [ABSTRACT FROM AUTHOR]

Although the quality of weather forecasts in the polar regions is improving, forecast skill there still lags the lower latitudes. So far there have been relatively few efforts to evaluate processes in Numerical Weather Prediction systems using in-situ and remote sensing datasets from meteorological observatories in the terrestrial Arctic and Antarctic, compared to the mid-latitudes. Progress has been limited both by the heterogeneous nature of observatory and forecast data but also by limited availability of the parameters needed to perform process-oriented evaluation in multi-model forecast archives. The YOPP site Model Inter-comparison Project (YOPPsiteMIP) is addressing this gap by producing Merged Observatory Data Files (MODFs) and Merged Model Data Files (MMDFs), bringing together observations and forecast data at polar meteorological observatories in a format designed to facilitate process-oriented evaluation. An evaluation of forecast performance was performed at seven Arctic sites, focussing on the first YOPP Special Observing Period in the Northern Hemisphere (SOP1), February and March 2018. It demonstrated that although the characteristics of forecast skill vary between the different sites and systems, an underestimation in boundary layer temperature variance across models, which goes hand in hand with an inability to capture cold extremes, is a common issue at several sites. Diagnostic analysis using surface fluxes suggests that this is at least partly related to insufficient thermal representation of the land-surface in the models, which all use a single layer snow model. [ABSTRACT FROM AUTHOR]

A large and ever-growing body of geophysical information is measured on campaigns and at specialized observatories as a part of scientific expeditions/experiments. These collections of observed data include many essential climate variables (as defined by the World Meteorological Organization), but are often distinguished by a wide range of additional non-routine measurements that are designed to not only document the state of the environment, but also the drivers that contribute to that state. These field data are not only used to further understand the environmental processes through observation-based studies, but also to provide baseline data to test model performance and to codify understanding to improve predictive capabilities. To address the considerable barriers and difficulty in utilizing these diverse and complex data for observation-model research, the Merged Observatory Data File (MODF) concept has been developed. The MODF combines measurements from multiple instruments into a single file that complies with well-established data format and metadata practices and has been designed to parallel development of corresponding Merged Model Data Files (MMDFs). Using MODF and MMDF protocols will facilitate the evolution of Model Intercomparison Projects into Model Intercomparison and Improvement Projects by putting observation and model data 'on the same page' in a timely manner. The MODF concept was developed especially for weather forecast model studies in the Arctic. The surprisingly complex process of implementing MODFs in that context refined the concept itself. Thus this article explains the concept of MODFs by providing details on the issues that were revealed and resolved during this first specific implementation. Detailed instructions are provided on how to make MODFs, and this article can thus be considered a MODF creation manual. [ABSTRACT FROM AUTHOR]