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Researchers often have a difficult time defining meaningful thresholds for change. We sometimes identify subtle changes but what amount of change is beyond typical sources of variation? This is especially complicated when trying to understand new disease pathogenesis like the constellation of eye changes leading to Spaceflight-associated Neuro-ocular Syndrome (SANS). To support decision makers in defining minimal meaningful change, we used a Bayesian hierarchical model to estimate innate sources of variability such as natural day to day variation. Healthy subjects were recruited and imaged with MRI, OCT, and US on separate days and measured by several technicians. Models were developed specifying random effects for the sources of variation – between left and right eyes, within-individuals over time, between raters, and finally between individuals. This allowed us to find the posterior distribution for the total typical variation, within an eye, which we use to define a threshold where change beyond typical sources of variation is likely. This threshold is now used as our earliest indicator of systematic increase in Total Retinal Thickness (a precursor to optic disc edema).
Last year we presented techniques for the detection of fossils during robotic missions to Mars using both structural and chemical signatures[Storrie-Lombardi and Hoover, 2004]. Analyses included lossless compression of photographic images to estimate the relative complexity of a putative fossil compared to the rock matrix [Corsetti and Storrie-Lombardi, 2003] and elemental abundance distributions to provide mineralogical classification of the rock matrix [Storrie-Lombardi and Fisk, 2004]. We presented a classification strategy employing two exploratory classification algorithms (Principal Component Analysis and Hierarchical Cluster Analysis) and non-linear stochastic neural network to produce a Bayesian estimate of classification accuracy. We now present an extension of our previous experiments exploring putative fossil forms morphologically resembling cyanobacteria discovered in the Orgueil meteorite. Elemental abundances (C6, N7, O8, Na11, Mg12, Ai13, Si14, P15, S16, Cl17, K19, Ca20, Fe26) obtained for both extant cyanobacteria and fossil trilobites produce signatures readily distinguishing them from meteorite targets. When compared to elemental abundance signatures for extant cyanobacteria Orgueil structures exhibit decreased abundances for C6, N7, Na11, All3, P15, Cl17, K19, Ca20 and increases in Mg12, S16, Fe26. Diatoms and silicified portions of cyanobacterial sheaths exhibiting high levels of silicon and correspondingly low levels of carbon cluster more closely with terrestrial fossils than with extant cyanobacteria. Compression indices verify that variations in random and redundant textural patterns between perceived forms and the background matrix contribute significantly to morphological visual identification. The results provide a quantitative probabilistic methodology for discriminating putatitive fossils from the surrounding rock matrix and &om extant organisms using both structural and chemical information. The techniques described appear applicable to the geobiological analysis of meteoritic samples or in situ exploration of the Mars regolith. Keywords: cyanobacteria, microfossils, Mars, elemental abundances, complexity analysis, multifactor analysis, principal component analysis, hierarchical cluster analysis, artificial neural networks, paleo-biosignatures
We have previously outlined a strategy for the detection of fossils [Storrie-Lombardi and Hoover, 2004] and extant microbial life [Storrie-Lombaudi and Hoover, 20051 during robotic missions to Mars using co-registered structural and chemical signatures. Data inputs included image lossless compression indices to estimate relative textural complexity and elemental abundance distributions. Two exploratory classification algorithms (principal component analysis and hierarchical cluster analysis) provide an initial tentative classification of all targets. Nonlinear stochastic neural networks are then trained to produce a Bayesian estimate of algorithm classification accuracy. The strategy previously has been successful in distinguishing regions of biotic and abiotic alteration of basalt glass from unaltered samples. [Storrie-Lombardi and Fisk, 2004; Storrie-Lombardi and Fisk, 2004] Such investigations of abiotic versus biotic alteration of terrestrial mineralogy on Earth are compromised by .the difficulty finding mineralogy completely unaffected by the ubiquitous presence of microbial life on the planet. The renewed interest in lunar exploration offers an opportunity to investigate geological materials that may exhibit signs of aqueous alteration, but are highly unlikely to contain contaminating biological weathering signatures. We here present an extension of our earlier data set to include lunar dust samples obtained during the Apollo 17 mission. Apollo 17 landed in the Taurus-Littrow Valley in Mare Serenitatis. Most of the rock samples from this region of the lunar highlands are basalts comprised primarily of plagioclase and pyroxene and selected examples of orange and black volcanic glass. SEM images and elemental abundances (C6, N7, O8, Na11, Mg12, Al13, Si14, P15, S16, Cll7, K19, Ca20, Fe26) for a series of targets in the lunar dust samples are compared to the extant cyanobacteria, fossil trilobites, Orgueil meteorite, and terrestrial basalt targets previously discussed. The data set provides a first step in producing a quantitative probabilistic methodology for geobiological analysis of returned lunar samples or in situ exploration.
Juvenile survival in birds is difficult to estimate but this vital rate can be an important consideration for management decisions. We estimated juvenile survival of cooperatively breeding Florida Scrub-Jays (Aphelocoma coerulescens) in a landscape degraded by fire suppression and fragmentation using data from marked (n = 325) and unmarked juveniles (n = 1,306) with an integrated hierarchical Bayesian model. To assess the combined analyses, we also analyzed these datasets separately, with a Cormack-Jolly-Seber (CJS) model (marked) and young model (unmarked). Our data consisted of monthly censuses of territorial family groups from Florida Scrub-Jay populations in East Central Florida collected over a 22-yr period. Juvenile survival was estimated from July when young Florida Scrub-Jays begin developing independence to March when they become first year individuals and grouped according to the habitat quality class of their natal territory that were based on shrub height (with intermediate shrub heights being optimal and short and tall shrub heights being suboptimal) and the presence of sandy openings (the preferred open having many sandy openings; closed not having enough). Parameter estimates in the combined analysis were intermediate to the separate analyses. Notable differences among the separate analyses were that suboptimal habitat survival was lower in the unmarked analysis, the unmarked analysis showed a linear effect of time not seen in the marked analysis, and there was an effect of male breeder death in the marked but not unmarked analysis. The combined data analysis provided more inference than did either data set analyzed separately including juveniles in optimal-closed territories unexpectedly had higher survival than those in optimal-open, survival increased through time, and male breeder death had a negative effect on survival. This study suggests that optimal-closed habitat may play an important role in juvenile Florida Scrub-Jay survival perhaps by providing better cover from predators and warrants further investigation for management implications.
Topography affects abiotic conditions which can influence the structure, function, and dynamics of ecological communities. An increasing number of studies have demonstrated biological consequences of fine-scale topographic heterogeneity but we have a limited understanding of how We merged high-resolution (1 sq. meter) data on topography and canopy height derived from airborne lidar with ground-based data from 15 forest plots in Puerto Rico distributed along a precipitation gradient spanning ca. 800 to 3,500 mm yr(exp -1). Ground-based data included species composition, estimated above-ground biomass (AGB), and two key functional traits (wood density and leaf mass per area, LMA) that reflect resource-use strategies and a trade-off between hydraulic safety and hydraulic efficiency. We used hierarchical Bayesian models to evaluate how the interaction between topography climate is related to metrics of forest structure (i.e., canopy height and AGB), as well as taxonomic and functional alpha- and beta-diversity. Fine-scale topography (characterized with the topographic wetness index, TWI) significantly affected forest structure and the strength (and in some cases direction) of these effects varied across the precipitation gradient. In all plots, canopy height increased with topographic wetness but the effect was much stronger in dry compared to wet forest plots. In dry forest plots, topographically wetter microsites also had higher levels of AGB but in wet forest plots, topographically drier microsites had higher AGB. Fine-scale topography influenced functional composition but had only weak or non-significant effects on taxonomic and functional alpha- and beta-diversity. For instance, community-weighted wood density followed a similar pattern to AGB across plots. We also found a marginally significant association between variation of wood density and topographic heterogeneity that depended on climate context. Synthesis: The effects of fine-scale topographic heterogeneity on tropical forest structure and composition depend on the climate context. Our study demonstrates how a stronger integration of topographic heterogeneity across precipitation gradients could improve estimates of forest structure and biomass, and may provide insight to the ways that topography might mediate species responses to drought and climate change.
The construction of solar energy facilities can have positive or negative impacts on biodiversity depending on siting and associated land use transitions. We identified drivers of solar siting and quantified patterns of buildout in states surrounding the Chesapeake Bay watershed – a biodiversity hotspot with numerous ecosystem services. Using a convolutional neural network, we mapped the footprints of ground-mounted solar arrays present in satellite imagery annually from 2017 to 2021 in Delaware, Maryland, Pennsylvania, New York, Virginia, and West Virginia. As of 2021, we identified 958 solar arrays covering 52.3 km2 built primarily on previously cultivated land, while avoiding natural landcover. We fit a binomial-Weibull model to these solar timeseries data in a hierarchical, Bayesian framework to quantify the relationship between geospatial covariates and rate of solar development. Solar array construction rate increased in cultivated areas, areas of lower agricultural suitability, lower slope, lower forest cover, lower biodiversity protection, and greater distances from roads. We also estimated changes in the rate of solar construction over time and found differences among states: acceleration in Virginia and deceleration in New York. We used parameter estimates to map the relative likelihood of future solar development across the study area. This methodology can be used to anticipate where solar is likely to be built in different landscapes and how these patterns align with conservation goals. Around the Chesapeake Bay watershed, the selection of lower quality agricultural areas for solar energy minimizes removal of important habitat and provides opportunities for native plant and pollinator restoration.
Stars like our sun (initial masses between 0.8 to 8 solar masses) end their lives as swollen red giants surrounded by cool extended atmospheres. The nuclear reactions in their cores create carbon, nitrogen and oxygen, which are transported by convection to the outer envelope of the stellar atmosphere. As the star finally collapses to become a white dwarf, this envelope is expelled from the star to form a planetary nebula (PN) rich in organic molecules. The physics, dynamics, and chemistry of these nebulae are poorly understood and have implications not only for our understanding of the stellar life cycle but also for organic astrochemistry and the creation of prebiotic molecules in interstellar space. We are working toward generating three-dimensional models of planetary nebulae (PNe), which include the size, orientation, shape, expansion rate and mass distribution of the nebula. Such a reconstruction of a PN is a challenging problem for several reasons. First, the data consist of images obtained over time from the Hubble Space Telescope (HST) and spectra obtained from Kitt Peak National Observatory (KPNO) and Cerro Tololo Inter-American Observatory (CTIO). These images are of course taken from a single viewpoint in space, which amounts to a very challenging tomographic reconstruction. Second, the fact that we have two disparate and orthogonal data types requires that we utilize a method that allows these data to be used together to obtain a solution. To address these first two challenges we employ Bayesian model estimation using a parameterized physical model that incorporates much prior information about the known physics of the PN. In our previous works we have found that the forward problem of the comprehensive model is extremely time consuming. To address this challenge, we explore the use of a set of hierarchical models, which allow us to estimate increasingly more detailed sets of model parameters. These hierarchical models of increasing complexity are akin to scientific theories of increasing sophistication, with each new model/theory being a refinement of a previous one by either incorporating additional prior information or by introducing a new set of parameters to model an entirely new phenomenon. We apply these models to both a simulated and a real ellipsoidal PN to initially estimate the position, angular size, and orientation of the nebula as a two-dimensional object and use these estimates to later examine its three-dimensional properties. The efficiency/accuracy tradeoffs of the techniques are studied to determine the advantages and disadvantages of employing a set of hierarchical models over a single comprehensive model.
Stars like our sun (initial masses between 0.8 to 8 solar masses) end their lives as swollen red giants surrounded by cool extended atmospheres. The nuclear reactions in their cores create carbon, nitrogen and oxygen, which are transported by convection to the outer envelope of the stellar atmosphere. As the star finally collapses to become a white dwarf, this envelope is expelled from the star to form a planetary nebula (PN) rich in organic molecules. The physics, dynamics, and chemistry of these nebulae are poorly understood and have implications not only for our understanding of the stellar life cycle but also for organic astrochemistry and the creation of prebiotic molecules in interstellar space. We are working toward generating three-dimensional models of planetary nebulae (PNe), which include the size, orientation, shape, expansion rate and mass distribution of the nebula. Such a reconstruction of a PN is a challenging problem for several reasons. First, the data consist of images obtained over time from the Hubble Space Telescope (HST) and spectra obtained from Kitt Peak National Observatory (KPNO) and Cerro Tololo Inter-American Observatory (CTIO). These images are of course taken from a single viewpoint in space, which amounts to a very challenging tomographic reconstruction. Second, the fact that we have two disparate and orthogonal data types requires that we utilize a method that allows these data to be used together to obtain a solution. To address these first two challenges we employ Bayesian model estimation using a parameterized physical model that incorporates much prior information about the known physics of the PN. In our previous works we have found that the forward problem of the comprehensive model is extremely time consuming. To address this challenge, we explore the use of a set of hierarchical models, which allow us to estimate increasingly more detailed sets of model parameters. These hierarchical models of increasing complexity are akin to scientific theories of increasing sophistication, with each new model/theory being a refinement of a previous one by either incorporating additional prior information or by introducing a new set of parameters to model an entirely new phenomenon. We apply these models to both a simulated and a real ellipsoidal PN to initially estimate the position, angular size, and orientation of the nebula as a two-dimensional object and use these estimates to later examine its three-dimensional properties. The efficiency/accuracy tradeoffs of the techniques are studied to determine the advantages and disadvantages of employing a set of hierarchical models over a single comprehensive model.
The behavior of complex aerospace systems is governed by numerous parameters. For safety analysis it is important to understand how the system behaves with respect to these parameter values. In particular, understanding the boundaries between safe and unsafe regions is of major importance. In this paper, we describe a hierarchical Bayesian statistical modeling approach for the online detection and characterization of such boundaries. Our method for classification with active learning uses a particle filter-based model and a boundary-aware metric for best performance. From a library of candidate shapes incorporated with domain expert knowledge, the location and parameters of the boundaries are estimated using advanced Bayesian modeling techniques. The results of our boundary analysis are then provided in a form understandable by the domain expert. We illustrate our approach using a simulation model of a NASA neuro-adaptive flight control system, as well as a system for the detection of separation violations in the terminal airspace.
Atmospheric Carbon Monoxide (CO) is a pollutant gas of which the US congress has mandated regular monitoring, and satellite sensors can be used to retrieve regional concentrations of CO over several vertical layers. However, CO at cloudy locations cannot be observed and have to be estimated from the observed data set, resulting in an interpolation problem. The current state-of-the-art solution is to combine prior information, computed by a deterministic physical model, with observations. However, the deterministic model may introduce uncertainties that do not derive from the data. While sharing certain features with the physical model, this paper presents a Bayesian hierarchical model for interpolating CO on a 3-dimensional spatial grid, across time. To our knowledge such a model has not been considered before. The model is applied to a hypothetical air-quality monitoring scenario, and is compared to existing interpolation methods. The results provide motivation for the use of the statistical model for regional to local applications.
Fecundity, the number of young produced by a breeding pair during a breeding season, is a primary component in evolutionary and ecological theory and applications. Fecundity can be influenced by many environmental factors and requires long-term study due to the range of variation in ecosystem dynamics. Fecundity data often include a large proportion of zeros when many pairs fail to produce any young during a breeding season due to nest failure or when all young die independently after fledging. We conducted color banding and monthly censuses of Florida scrub-jays (Aphelocoma coerulescens) across 31 years, 15 populations, and 761 territories along central Florida’s Atlantic coast. We quantified how fecundity (juveniles/pair-year) was influenced by habitat quality, presence/absence of nonbreeders, population density, breeder experience, and rainfall, with a zero-inflated Bayesian hierarchical model including both a Bernoulli (e.g., brood success) and a Poisson (counts of young) submodel, and random effects for year, population, and territory. The results identified the importance of increasing “strong” quality habitat, which was a mid-successional state related to fire frequency and extent, because strong territories, and the proportion of strong territories in the overall population, influenced fecundity of breeding pairs. Populations subject to supplementary feeding also had greater fecundity. Territory size, population density, breeder experience, and rainfall surprisingly had no or small effects. Different mechanisms appeared to cause annual variation in fecundity, as estimates of random effects were not correlated between the success and count submodels. The increased fecundity for pairs with nonbreeders, compared to pairs without, identified empirical research needed to understand how the proportion of low-quality habitats influences population recovery and sustainability, because dispersal into low-quality habitats can drain nonbreeders from strong territories and decrease overall fecundity. We also describe how long term study resulted in reversals in our understanding because of complications involving habitat quality, sociobiology, and population density.
Astronomical objects known as planetary nebulae (PNe) consist of a shell of gas expelled by an aging medium-sized star as it makes its transition from a red giant to a white dwarf. In many cases this gas shell can be approximately described as a prolate ellipsoid. Knowledge of the physics of ionization processes in this gaseous shell enables us to construct a model in three dimensions (3D) called the Ionization-Bounded Prolate Ellipsoidal Shell model (IBPES model). Using this model we can generate synthetic nebular images, which can be used in conjunction with Hubble Space Telescope (HST) images of actual PNe to perform Bayesian model estimation. Since the IBPES model is characterized by thirteen parameters, model estimation requires the search of a 13-dimensional parameter space. The 'curse of dimensionality,' compounded by a computationally intense forward problem, makes forward searches extremely time-consuming and frequently causes them to become trapped in local solutions. We find that both the speed and of the search can be improved by judiciously reducing the dimensionality of the search space. Our basic approach employs a hierarchy of models of increasing complexity that converges to the IBPES model. Earlier studies establish that a hierarchical sequence converges more quickly, and to a better solution, than a search relying only on the most complex model. Here we report results for a hierarchy of five models. The first three models treat the nebula as a 2D image, while the last two models explore its characteristics as a 3D object and enable us to characterize the physics of the nebula. This five-model hierarchy is applied to HST images of ellipsoidal PNe to estimate their geometric properties and gas density profiles.
This paper demonstrates the use of two Bayesian statistical models to analyze single-event sonic boom exposure and human annoyance data from community response surveys. Each model is fit to data from a NASA pilot study.Unlike many community noise surveys, this study used a panel sample to collect multiple observations per participant instead of a single observation. Thus, a multilevel (also known as hierarchical or mixed-effects) model is used to account for the within-subject correlation in the panel sample data. This paper describes a multilevel logistic regression model and a multilevel ordinal regression model. The paper also proposes a method for calculating a summary dose-response curve from the multilevel models that represents the population. The two models’ summary dose-response curves are visually similar. However, their estimates differ when calculating the noise dose at a fixed percent highly annoyed.
This document is motivated by likely needs of the Quesst mission community response tests, which will culminate in data collection and estimation of dose-response regression relationships for consideration by domestic and international aviation regulators. Furthermore, basic research questions evaluating interactions between rates of community annoyance, dose levels, and indicators of the presence of rattle, vibration, and startle hinge on hypothesis testing in the context of regression models. For a variety of reasons, noise doses may be known only imprecisely and may not reflect the actual level experienced by responding subjects. These differences between true dose and estimated dose, be they systematic or random, constitute covariate measurement error. Available statistics literature speaks to the impacts of measurement error on regression models, both in terms of bias in estimated coefficients and predicted values, and in terms of the loss of statistical power for hypothesis testing. Given the particulars of a categorical annoyance response variable and a continuous noise dose predictor variable subject to measurement error during testing, the emphasis of this report is on findings and methods pertinent to generalized linear (and mixed) models likely to be employed during the Quesst mission community tests. We reach the following conclusions: 1. Of four reviewed methods, structural Bayesian measurement error models and simulation extrapolation (SIMEX) may be the most readily applicable to Quesst mission community noise study objectives. 2. If warranted, a linear measurement model can help model systematic sources of measurement error that the classical measurement error does not. 3. For its ready implementation and small additional input requirements, simulation extrapolation may be ideally suited for addressing secondary research questions involving interactions between annoyance, noise dose, and other factors through hypothesis testing. 4. For their flexibility and ability to propagate uncertainty, structural Bayesian hierarchical models have great appeal for mission purposes; some care may be needed in developing appropriate probability models describing actual noise exposure during testing. An annotated bibliography logs additional papers and resources that may be of value to analysts in other projects and disciplines.