Towards Portable Large-Scale Image Processing with High-Performance Computing.

High-throughput, large-scale medical image computing demands tight integration of high-performance computing (HPC) infrastructure for data storage, job distribution, and image processing. The Vanderbilt University Institute for Imaging Science (VUIIS) Center for Computational Imaging (CCI) has constructed a large-scale image storage and processing infrastructure that is composed of (1) a large-scale image database using the eXtensible Neuroimaging Archive Toolkit (XNAT), (2) a content-aware job scheduling platform using the Distributed Automation for XNAT pipeline automation tool (DAX), and (3) a wide variety of encapsulated image processing pipelines called "spiders." The VUIIS CCI medical image data storage and processing infrastructure have housed and processed nearly half-million medical image volumes with Vanderbilt Advanced Computing Center for Research and Education (ACCRE), which is the HPC facility at the Vanderbilt University. The initial deployment was natively deployed (i.e., direct installations on a bare-metal server) within the ACCRE hardware and software environments, which lead to issues of portability and sustainability. First, it could be laborious to deploy the entire VUIIS CCI medical image data storage and processing infrastructure to another HPC center with varying hardware infrastructure, library availability, and software permission policies. Second, the spiders were not developed in an isolated manner, which has led to software dependency issues during system upgrades or remote software installation. To address such issues, herein, we describe recent innovations using containerization techniques with XNAT/DAX which are used to isolate the VUIIS CCI medical image data storage and processing infrastructure from the underlying hardware and software environments. The newly presented XNAT/DAX solution has the following new features: (1) multi-level portability from system level to the application level, (2) flexible and dynamic software development and expansion, and (3) scalable spider deployment compatible with HPC clusters and local workstations.

Transplanted sagebrush "wildlings" exhibit higher survival than greenhouse-grown tubelings yet both recruit new plants.

BACKGROUND: Land uses such as crop production, livestock grazing, mining, and urban development have contributed to degradation of drylands worldwide. Loss of big sagebrush (Artemisia tridentata) on disturbed drylands across the western U.S. has prompted massive efforts to re-establish this foundational species. There has been growing interest in avoiding the severe limitations experienced by plants at the seed and seedling stages by instead establishing plants from containerized greenhouse seedlings ("tubelings"). In some settings, a potential alternative approach is to transplant larger locally-collected plants ("wildlings"). We compared the establishment of mountain big sagebrush (A. tridentata ssp. vaseyana) from tubelings vs. wildlings in southeastern Idaho. A mix of native and non-native grass and forb species was drill-seeded in a pasture previously dominated by the introduced forage grass, smooth brome (Bromus inermis). We then established 80 m x 80 m treatment plots and planted sagebrush tubelings (n = 12 plots, 1200 plants) and wildlings (n = 12 plots, 1200 plants). We also established seeded plots (n = 12) and untreated control plots (n = 6) for long-term comparison. We tracked project expenses in order to calculate costs of using tubelings vs. wildlings as modified by probability of success. RESULTS: There was high (79%) tubeling and low (10%) wildling mortality within the first year. Three years post-planting, chance of survival for wildlings was significantly higher than that of tubelings (85% and 14% respectively). Despite high up-front costs of planting wildlings, high survival rates resulted in their being < 50% of the cost of tubelings on a per-surviving plant basis. Additionally, by the third year post-planting 34% of surviving tubelings and 95% of surviving wildlings showed evidence of reproduction (presence / absence of flowering stems), and the two types of plantings recruited new plants via seed (3.7 and 2.4 plants, respectively, per surviving tubeling/wildling). CONCLUSIONS: Our results indicate that larger plants with more developed root systems (wildlings) may be a promising avenue for increasing early establishment rates of sagebrush plants in restoration settings. Our results also illustrate the potential for tubelings and wildlings to improve restoration outcomes by "nucleating" the landscape via recruitment of new plants during ideal climate conditions.

An innovative tool for cost control under fragmented scenarios: The container freight index microinsurance.

With the impact of the COVID-19 pandemic, global container freights have increased dramatically since the second half of 2020, which has significantly hampered the booking activities of fragmented transportation space for small and medium-sized import and export enterprises (SMIEEs). To provide SMIEEs with an effective tool for controlling shipping costs, we propose the design principles of index microinsurance under fragmented scenarios and design the container freight index microinsurance (CFIM) based on a comprehensive analysis of the term, compensation and share structures. We further establish the pricing model for the CFIM and selection procedure for product optimization, and illustrate the framework with a case study based on the data of the China Containerized Freight Index Europe Service, which demonstrates the good performance of the designed product even under extreme market conditions. The design principles proposed can shed light on the innovation of index microinsurance product that meets fragmented needs and the newly designed CFIM, along with the pricing and optimization procedure, provides practitioners with useful tools for cost control.

The Stroke Neuro-Imaging Phenotype Repository: An Open Data Science Platform for Stroke Research.

Stroke is one of the leading causes of death and disability worldwide. Reducing this disease burden through drug discovery and evaluation of stroke patient outcomes requires broader characterization of stroke pathophysiology, yet the underlying biologic and genetic factors contributing to outcomes are largely unknown. Remedying this critical knowledge gap requires deeper phenotyping, including large-scale integration of demographic, clinical, genomic, and imaging features. Such big data approaches will be facilitated by developing and running processing pipelines to extract stroke-related phenotypes at large scale. Millions of stroke patients undergo routine brain imaging each year, capturing a rich set of data on stroke-related injury and outcomes. The Stroke Neuroimaging Phenotype Repository (SNIPR) was developed as a multi-center centralized imaging repository of clinical computed tomography (CT) and magnetic resonance imaging (MRI) scans from stroke patients worldwide, based on the open source XNAT imaging informatics platform. The aims of this repository are to: (i) store, manage, process, and facilitate sharing of high-value stroke imaging data sets, (ii) implement containerized automated computational methods to extract image characteristics and disease-specific features from contributed images, (iii) facilitate integration of imaging, genomic, and clinical data to perform large-scale analysis of complications after stroke; and (iv) develop SNIPR as a collaborative platform aimed at both data scientists and clinical investigators. Currently, SNIPR hosts research projects encompassing ischemic and hemorrhagic stroke, with data from 2,246 subjects, and 6,149 imaging sessions from Washington University's clinical image archive as well as contributions from collaborators in different countries, including Finland, Poland, and Spain. Moreover, we have extended the XNAT data model to include relevant clinical features, including subject demographics, stroke severity (NIH Stroke Scale), stroke subtype (using TOAST classification), and outcome [modified Rankin Scale (mRS)]. Image processing pipelines are deployed on SNIPR using containerized modules, which facilitate replicability at a large scale. The first such pipeline identifies axial brain CT scans from DICOM header data and image data using a meta deep learning scan classifier, registers serial scans to an atlas, segments tissue compartments, and calculates CSF volume. The resulting volume can be used to quantify the progression of cerebral edema after ischemic stroke. SNIPR thus enables the development and validation of pipelines to automatically extract imaging phenotypes and couple them with clinical data with the overarching aim of enabling a broad understanding of stroke progression and outcomes.

Evaluation of systemic neonicotinoid insecticides for the management of the Asian citrus psyllid Diaphorina citri on containerized citrus.

BACKGROUND: Studies were conducted to evaluate uptake and retention of three systemic neonicotinoid insecticides, dinotefuran, imidacloprid and thiamethoxam, in potted citrus nursery plants treated at standard label rates. Infestation of these plants placed at a field site with moderate levels of Asian citrus psyllid (ACP) was monitored for 14 weeks following treatments, and insecticide residues in leaf tissue were quantified using enzyme-linked immunosorbent assay (ELISA). Bioassays were conducted using leaves harvested on various dates post-treatment to compare the efficacies of residues against adult ACP. RESULTS: Residues of the three neonicotinoids were detected in leaf tissues within 1 week after treatment. Peak concentrations established at 1 week for imidacloprid and dinotefuran and at 2 weeks for thiamethoxam. Imidacloprid and thiamethoxam outperformed the control and dinotefuran treatments at protecting trees from infestations by ACP eggs and nymphs. For a given insecticide concentration in leaf tissue, thiamethoxam induced the highest mortality of the three insecticides, and dinotefuran was the least toxic. CONCLUSION: If the time needed to achieve effective thresholds of a systemic neonicotinoid is known, treatments at production facilities could be scheduled that would minimize unnecessary post-treatment holding periods and ensure maximum retention of effective concentrations after the plants have shipped to retail outlets. The rapid uptake of the insecticides and retention at effective concentrations in containerized citrus suggest that the current 30 day post-treatment shipping restriction from production facilities to retail outlets outside of quarantine could be shortened to 14 days. Thiamethoxam should be added to the list of approved nursery treatments. © 2016 Society of Chemical Industry.

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Excessive use of peat may cause some environmental problems. To alleviate the negative effect, an experiment was conducted with the mushroom residue compost to replace peat in Larix principis-rupprechtii containerized transplant production, and the proportion of mushroom residue compost was 0% (T0, control), 15% (T1), 18.75% (T2), 25% (T3), 37.50% (T4), 50% (T5), 56.25% (T6) and 60% (T7), respectively. The physical and chemical features of the substrates and its effect on the vegetative growth and nutrient accumulation of L. principis-rupprechtii containerized transplants were studied. The results showed when the proportion of mushroom residue compost in the substrate accounted for 50% or less, there was no significant difference in the transplant height, diameter, and biomass compared with the control, and the nutrient concentration in T2, T4, T5 treatments was significantly higher than in T0. The pH value was sub-acidic to neutral which was suitable to the transplant growth. When the compost proportion accounted for more than 50%, the pH value was altered to alkali and was not suitable to the transplant growth. When the proportion of mushroom residue compost accounted for 15%, the plant grew best, and the height, diameter, and total biomass got the highest. Therefore, using mushroom residue compost to replace peat in L. principis-rupprechtii containerized transplants cultivation was feasible and the maximum replacement ratio could reach 50%. The high quality transplants could be obtained when the compost replacement ratio was 15%.