Identifying and training deep learning neural networks on biomedical-related datasets.

This manuscript describes the development of a resources module that is part of a learning platform named 'NIGMS Sandbox for Cloud-based Learning' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module delivers learning materials on implementing deep learning algorithms for biomedical image data in an interactive format that uses appropriate cloud resources for data access and analyses. Biomedical-related datasets are widely used in both research and clinical settings, but the ability for professionally trained clinicians and researchers to interpret datasets becomes difficult as the size and breadth of these datasets increases. Artificial intelligence, and specifically deep learning neural networks, have recently become an important tool in novel biomedical research. However, use is limited due to their computational requirements and confusion regarding different neural network architectures. The goal of this learning module is to introduce types of deep learning neural networks and cover practices that are commonly used in biomedical research. This module is subdivided into four submodules that cover classification, augmentation, segmentation and regression. Each complementary submodule was written on the Google Cloud Platform and contains detailed code and explanations, as well as quizzes and challenges to facilitate user training. Overall, the goal of this learning module is to enable users to identify and integrate the correct type of neural network with their data while highlighting the ease-of-use of cloud computing for implementing neural networks. This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.

Energy-Efficient Ultrasonic Water Level Detection System with Dual-Target Monitoring.

This study presents a developed ultrasonic water level detection (UWLD) system with an energy-efficient design and dual-target monitoring. The water level monitoring system with a non-contact sensor is one of the suitable methods since it is not directly exposed to water. In addition, a web-based monitoring system using a cloud computing platform is a well-known technique to provide real-time water level monitoring. However, the long-term stable operation of remotely communicating units is an issue for real-time water level monitoring. Therefore, this paper proposes a UWLD unit using a low-power consumption design for renewable energy harvesting (e.g., solar) by controlling the unit with dual microcontrollers (MCUs) to improve the energy efficiency of the system. In addition, dual targeting to the pavement and streamside is uniquely designed to monitor both the urban inundation and stream overflow. The real-time water level monitoring data obtained from the proposed UWLD system is analyzed with water level changing rate (WLCR) and water level index. The quantified WLCR and water level index with various sampling rates present a different sensitivity to heavy rain.

Cloud-based serverless computing enables accelerated monte carlo simulations for nuclear medicine imaging.

Objective.This study investigates the potential of cloud-based serverless computing to accelerate Monte Carlo (MC) simulations for nuclear medicine imaging tasks. MC simulations can pose a high computational burden-even when executed on modern multi-core computing servers. Cloud computing allows simulation tasks to be highly parallelized and considerably accelerated.Approach.We investigate the computational performance of a cloud-based serverless MC simulation of radioactive decays for positron emission tomography imaging using Amazon Web Service (AWS) Lambda serverless computing platform for the first time in scientific literature. We provide a comparison of the computational performance of AWS to a modern on-premises multi-thread reconstruction server by measuring the execution times of the processes using between105and2·1010simulated decays. We deployed two popular MC simulation frameworks-SimSET and GATE-within the AWS computing environment. Containerized application images were used as a basis for an AWS Lambda function, and local (non-cloud) scripts were used to orchestrate the deployment of simulations. The task was broken down into smaller parallel runs, and launched on concurrently running AWS Lambda instances, and the results were postprocessed and downloaded via the Simple Storage Service.Main results.Our implementation of cloud-based MC simulations with SimSET outperforms local server-based computations by more than an order of magnitude. However, the GATE implementation creates more and larger output file sizes and reveals that the internet connection speed can become the primary bottleneck for data transfers. Simulating 109decays using SimSET is possible within 5 min and accrues computation costs of about $10 on AWS, whereas GATE would have to run in batches for more than 100 min at considerably higher costs.Significance.Adopting cloud-based serverless computing architecture in medical imaging research facilities can considerably improve processing times and overall workflow efficiency, with future research exploring additional enhancements through optimized configurations and computational methods.

Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance.

Introduction: The SARS-CoV-2 pandemic represented a formidable scientific and technological challenge to public health due to its rapid spread and evolution. To meet these challenges and to characterize the virus over time, the State of California established the California SARS-CoV-2 Whole Genome Sequencing (WGS) Initiative, or "California COVIDNet". This initiative constituted an unprecedented multi-sector collaborative effort to achieve large-scale genomic surveillance of SARS-CoV-2 across California to monitor the spread of variants within the state, to detect new and emerging variants, and to characterize outbreaks in congregate, workplace, and other settings. Methods: California COVIDNet consists of 50 laboratory partners that include public health laboratories, private clinical diagnostic laboratories, and academic sequencing facilities as well as expert advisors, scientists, consultants, and contractors. Data management, sample sourcing and processing, and computational infrastructure were major challenges that had to be resolved in the midst of the pandemic chaos in order to conduct SARS-CoV-2 genomic surveillance. Data management, storage, and analytics needs were addressed with both conventional database applications and newer cloud-based data solutions, which also fulfilled computational requirements. Results: Representative and randomly selected samples were sourced from state-sponsored community testing sites. Since March of 2021, California COVIDNet partners have contributed more than 450,000 SARS-CoV-2 genomes sequenced from remnant samples from both molecular and antigen tests. Combined with genomes from CDC-contracted WGS labs, there are currently nearly 800,000 genomes from all 61 local health jurisdictions (LHJs) in California in the COVIDNet sequence database. More than 5% of all reported positive tests in the state have been sequenced, with similar rates of sequencing across 5 major geographic regions in the state. Discussion: Implementation of California COVIDNet revealed challenges and limitations in the public health system. These were overcome by engaging in novel partnerships that established a successful genomic surveillance program which provided valuable data to inform the COVID-19 public health response in California. Significantly, California COVIDNet has provided a foundational data framework and computational infrastructure needed to respond to future public health crises.

Metrix Matrix: A Cloud-Based System for Tracking Non-Relative Value Unit Value-Added Work Metrics.

PURPOSE: In the era of value-based medicine, it will become increasingly important for radiologists to provide metrics that demonstrate their value beyond clinical productivity. In this article the authors describe their institution's development of an easy-to-use system for tracking value-added but non-relative value unit (RVU)-based activities. METHODS: Metrix Matrix is an efficient cloud-based system for tracking value-added work. A password-protected home page contains links to web-based forms created using Google Forms, with collected data populating Google Sheets spreadsheets. Value-added work metrics selected for tracking included interdisciplinary conferences, hospital committee meetings, consulting on nonbilled outside studies, and practice-based quality improvement. Over a period of 4 months, value-added work data were collected for all clinical attending faculty members in a university-based radiology department (n = 39). Time required for data entry was analyzed for 2 faculty members over the same time period. RESULTS: Thirty-nine faculty members (equivalent to 36.4 full-time equivalents) reported a total of 1,223.5 hours of value-added work time (VAWT). A formula was used to calculate "value-added RVUs" (vRVUs) from VAWT. VAWT amounted to 5,793.6 vRVUs or 6.0% of total work performed (vRVUs plus work RVUs [wRVUs]). Were vRVUs considered equivalent to wRVUs for staffing purposes, this would require an additional 2.3 full-time equivalents, on the basis of average wRVU calculations. Mean data entry time was 56.1 seconds per day per faculty member. CONCLUSIONS: As health care reimbursement evolves with an emphasis on value-based medicine, it is imperative that radiologists demonstrate the value they add to patient care beyond wRVUs. This free and easy-to-use cloud-based system allows the efficient quantification of value-added work activities.