Adaptive sampling of transient environmental phenomena with autonomous mobile platforms

Submitted in partial fulfillment of the requirements for the degree of Master of Science in Aeronautics and Astronautics at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2019.In the environmental and earth sciences, hypotheses about transient phenomena have been universally investigated by collecting physical sample materials and performing ex situ analysis. Although the gold standard, logistical challenges limit the overall efficacy: the number of samples are limited to what can be stored and transported, human experts must be able to safely access or directly observe the target site, and time in the field and subsequently the laboratory, increases overall campaign expense. As a result, the temporal detail and spatial diversity in the samples may fail to capture insightful structure of the phenomenon of interest. The development of in situ instrumentation allows for near real-time analysis of physical phenomenon through observational strategies (e.g., optical), and in combination with unmanned mobile platforms, has considerably impacted field operations in the sciences. In practice, mobile platforms are either remotely operated or perform guided, supervised autonomous missions specified as navigation between humanselected waypoints. Missions like these are useful for gaining insight about a particular target site, but can be sample-sparse in scientifically valuable regions, particularly in complex or transient distributions. A skilled human expert and pilot can dynamically adjust mission trajectories based on sensor information. Encoding their insight onto a vehicle to enable adaptive sampling behaviors can broadly increase the utility of mobile platforms in the sciences. This thesis presents three field campaigns conducted with a human-piloted marine surface vehicle, the ChemYak, to study the greenhouse gases methane (CH4) and carbon dioxide (CO2) in estuaries, rivers, and the open ocean. These studies illustrate the utility of mobile surface platforms for environmental research, and highlight key challenges of studying transient phenomenon. This thesis then formalizes the maximum seek-and-sample (MSS) adaptive sampling problem, which requires a mobile vehicle to efficiently find and densely sample from the most scientifically valuable region in an a priori unknown, dynamic environment. The PLUMES algorithm — Plume Localization under Uncertainty using Maximum-ValuE information and Search—is subsequently presented, which addresses the MSS problem and overcomes key technical challenges with planning in natural environments. Theoretical performance guarantees are derived for PLUMES, and empirical performance is demonstrated against canonical uniform search and state-of-the-art baselines in simulation and field trials. Ultimately, this thesis examines the challenges of autonomous informative sampling in the environmental and earth sciences. In order to create useful systems that perform diverse scientific objectives in natural environments, approaches from robotics planning, field design, Bayesian optimization, machine learning, and the sciences must be drawn together. PLUMES captures the breadth and depth required to solve a specific objective within adaptive sampling, and this work as a whole highlights the potential for mobile technologies to perform intelligent autonomous science in the future

Observations of shallow methane bubble emissions from Cascadia Margin

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Michel, A. P. M., Preston, V. L., Fauria, K. E., & Nicholson, D. P. Observations of shallow methane bubble emissions from Cascadia Margin. Frontiers in Earth Science, 9, (2021): 613234, https://doi.org/10.3389/feart.2021.613234.Open questions exist about whether methane emitted from active seafloor seeps reaches the surface ocean to be subsequently ventilated to the atmosphere. Water depth variability, coupled with the transient nature of methane bubble plumes, adds complexity to examining these questions. Little data exist which trace methane transport from release at a seep into the water column. Here, we demonstrate a coupled technological approach for examining methane transport, combining multibeam sonar, a field-portable laser-based spectrometer, and the ChemYak, a robotic surface kayak, at two shallow (<75 m depth) seep sites on the Cascadia Margin. We demonstrate the presence of elevated methane (above the methane equilibration concentration with the atmosphere) throughout the water column. We observe areas of elevated dissolved methane at the surface, suggesting that at these shallow seep sites, methane is reaching the air-sea interface and is being emitted to the atmosphere.Funding for VP was provided by an NDSEG Fellowship. Funding for KF was provided by a WHOI Postdoctoral Scholar Fellowship. Ship time on the R/V Falkor was provided by the Schmidt Ocean Institute (FK180824)

Practical Considerations in Cloud Utilization for the Science Gateway nanoHUB.org

nanoHUB.org is arguably the largest online nanotechnology user facility in the world. Just between July 2010 and June 2011 it served 177,823 users. 10,477 users ran 393,648 simulation jobs on a variety of computational resources ranging from HUBzero-based virtual execution hosts for rapid, interactive runs as well as grid-based resources for computationally-intense runs. We believe that as such our users experience a fully operational scientific “cloud”-based infrastructure even though it is not using “standard” computational cloud infrastructures such as EC2. In this paper we explore the use of standard computational cloud-based resources to determine whether they can deliver satisfactory outcomes for our users without requiring high personnel costs for configuration. In a science gateway environment, the assignment of jobs to the appropriate computational resource is not trivial. Resource availability, wait time, time to completion, and likelihood of job success must all be considered in order to transparently deliver an acceptable level of service to our users. In this paper, we present preliminary results examining the benefits and drawbacks of utilizing standard computational cloud resources as one potential venue for nanoHUB computational runs. In summary we find that cloud resources performed competitively with other grid resources in terms of wait time, CPU usage, and success in a multiple job submission strategy

Hunting Bubbles Falkor Cruise 2019

The Hunting Bubbles Cruise took place in August-September 2018 on the R/V Falkor (cruise ID 180824). Ship time was provided by the Schmidt Ocean Institute. This cruise investigated transport of methane from seeps located on the Cascadia Margin. Data archived at the WHOAS repository supplements additional data from this cruise available at the R2R rolling deck to repository and at MGDS: Marine Geoscience Data System

Discovering hydrothermalism from afar: in situ methane instrumentation and change-point detection for decision-making

Seafloor hydrothermalism plays a critical role in fundamental interactions between geochemical and biological processes in the deep ocean. A significant number of hydrothermal vents are hypothesized to exist, but many of these remain undiscovered due in part to the difficulty of detecting hydrothermalism using standard sensors on rosettes towed in the water column or robotic platforms performing surveys. Here, we use in situ methane sensors to complement standard sensing technology for hydrothermalism discovery and compare sensing equipment on a towed rosette and autonomous underwater vehicle (AUV) during a 17 km long transect in the Northern Guaymas Basin. This transect spatially intersected with a known hydrothermally active venting site. These data show that methane signaled possible hydrothermal activity 1.5-3 km laterally (100-150m vertically) from a known vent. Methane as a signal for hydrothermalism performed similarly to standard turbidity sensors (plume detection 2.2-3.3 km from reference source), and more sensitively and clearly than temperature, salinity, and oxygen instruments which readily respond to physical mixing in background seawater. We additionally introduce change-point detection algorithms---streaming cross-correlation and regime identification---as a means of real-time hydrothermalism discovery and discuss related data monitoring technologies that could be used in planning, executing, and monitoring explorative surveys for hydrothermalism.NSF OCE OTIC: #1842053 Woods Hole Oceanographic Institution: Innovative Technology Award NOAA Ocean Exploration: #NA18OAR0110354 Schmidt Marine Technology Partners: #G-21-62431 NASA: #NNX17AB31G NSF OCE: #0838107 Gordon and Betty Moore Foundation: #9208 NDSEG: Graduate Fellowship MIT Martin Family Society of Fellows: Graduate Fellowship Microsoft: Graduate Research Fellowship DOE/National Nuclear Security Administration: #DE-NA000392 MIT EAPS: Houghton Fun

Health-status outcomes with invasive or conservative care in coronary disease

BACKGROUND In the ISCHEMIA trial, an invasive strategy with angiographic assessment and revascularization did not reduce clinical events among patients with stable ischemic heart disease and moderate or severe ischemia. A secondary objective of the trial was to assess angina-related health status among these patients. METHODS We assessed angina-related symptoms, function, and quality of life with the Seattle Angina Questionnaire (SAQ) at randomization, at months 1.5, 3, and 6, and every 6 months thereafter in participants who had been randomly assigned to an invasive treatment strategy (2295 participants) or a conservative strategy (2322). Mixed-effects cumulative probability models within a Bayesian framework were used to estimate differences between the treatment groups. The primary outcome of this health-status analysis was the SAQ summary score (scores range from 0 to 100, with higher scores indicating better health status). All analyses were performed in the overall population and according to baseline angina frequency. RESULTS At baseline, 35% of patients reported having no angina in the previous month. SAQ summary scores increased in both treatment groups, with increases at 3, 12, and 36 months that were 4.1 points (95% credible interval, 3.2 to 5.0), 4.2 points (95% credible interval, 3.3 to 5.1), and 2.9 points (95% credible interval, 2.2 to 3.7) higher with the invasive strategy than with the conservative strategy. Differences were larger among participants who had more frequent angina at baseline (8.5 vs. 0.1 points at 3 months and 5.3 vs. 1.2 points at 36 months among participants with daily or weekly angina as compared with no angina). CONCLUSIONS In the overall trial population with moderate or severe ischemia, which included 35% of participants without angina at baseline, patients randomly assigned to the invasive strategy had greater improvement in angina-related health status than those assigned to the conservative strategy. The modest mean differences favoring the invasive strategy in the overall group reflected minimal differences among asymptomatic patients and larger differences among patients who had had angina at baseline

Empagliflozin in Patients with Chronic Kidney Disease

Background The effects of empagliflozin in patients with chronic kidney disease who are at risk for disease progression are not well understood. The EMPA-KIDNEY trial was designed to assess the effects of treatment with empagliflozin in a broad range of such patients. Methods We enrolled patients with chronic kidney disease who had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m(2) of body-surface area, or who had an eGFR of at least 45 but less than 90 ml per minute per 1.73 m(2) with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Patients were randomly assigned to receive empagliflozin (10 mg once daily) or matching placebo. The primary outcome was a composite of progression of kidney disease (defined as end-stage kidney disease, a sustained decrease in eGFR to &lt; 10 ml per minute per 1.73 m(2), a sustained decrease in eGFR of &amp; GE;40% from baseline, or death from renal causes) or death from cardiovascular causes. Results A total of 6609 patients underwent randomization. During a median of 2.0 years of follow-up, progression of kidney disease or death from cardiovascular causes occurred in 432 of 3304 patients (13.1%) in the empagliflozin group and in 558 of 3305 patients (16.9%) in the placebo group (hazard ratio, 0.72; 95% confidence interval [CI], 0.64 to 0.82; P &lt; 0.001). Results were consistent among patients with or without diabetes and across subgroups defined according to eGFR ranges. The rate of hospitalization from any cause was lower in the empagliflozin group than in the placebo group (hazard ratio, 0.86; 95% CI, 0.78 to 0.95; P=0.003), but there were no significant between-group differences with respect to the composite outcome of hospitalization for heart failure or death from cardiovascular causes (which occurred in 4.0% in the empagliflozin group and 4.6% in the placebo group) or death from any cause (in 4.5% and 5.1%, respectively). The rates of serious adverse events were similar in the two groups. Conclusions Among a wide range of patients with chronic kidney disease who were at risk for disease progression, empagliflozin therapy led to a lower risk of progression of kidney disease or death from cardiovascular causes than placebo

Initial invasive or conservative strategy for stable coronary disease

BACKGROUND Among patients with stable coronary disease and moderate or severe ischemia, whether clinical outcomes are better in those who receive an invasive intervention plus medical therapy than in those who receive medical therapy alone is uncertain. METHODS We randomly assigned 5179 patients with moderate or severe ischemia to an initial invasive strategy (angiography and revascularization when feasible) and medical therapy or to an initial conservative strategy of medical therapy alone and angiography if medical therapy failed. The primary outcome was a composite of death from cardiovascular causes, myocardial infarction, or hospitalization for unstable angina, heart failure, or resuscitated cardiac arrest. A key secondary outcome was death from cardiovascular causes or myocardial infarction. RESULTS Over a median of 3.2 years, 318 primary outcome events occurred in the invasive-strategy group and 352 occurred in the conservative-strategy group. At 6 months, the cumulative event rate was 5.3% in the invasive-strategy group and 3.4% in the conservative-strategy group (difference, 1.9 percentage points; 95% confidence interval [CI], 0.8 to 3.0); at 5 years, the cumulative event rate was 16.4% and 18.2%, respectively (difference, 121.8 percentage points; 95% CI, 124.7 to 1.0). Results were similar with respect to the key secondary outcome. The incidence of the primary outcome was sensitive to the definition of myocardial infarction; a secondary analysis yielded more procedural myocardial infarctions of uncertain clinical importance. There were 145 deaths in the invasive-strategy group and 144 deaths in the conservative-strategy group (hazard ratio, 1.05; 95% CI, 0.83 to 1.32). CONCLUSIONS Among patients with stable coronary disease and moderate or severe ischemia, we did not find evidence that an initial invasive strategy, as compared with an initial conservative strategy, reduced the risk of ischemic cardiovascular events or death from any cause over a median of 3.2 years. The trial findings were sensitive to the definition of myocardial infarction that was used

Analysis of Outcomes in Ischemic vs Nonischemic Cardiomyopathy in Patients With Atrial Fibrillation A Report From the GARFIELD-AF Registry

IMPORTANCE Congestive heart failure (CHF) is commonly associated with nonvalvular atrial fibrillation (AF), and their combination may affect treatment strategies and outcomes