Automatic variable selection in ecological niche modeling: A case study using Cassin's Sparrow (Peucaea cassinii).

MERRA/Max provides a feature selection approach to dimensionality reduction that enables direct use of global climate model outputs in ecological niche modeling. The system accomplishes this reduction through a Monte Carlo optimization in which many independent MaxEnt runs, operating on a species occurrence file and a small set of randomly selected variables in a large collection of variables, converge on an estimate of the top contributing predictors in the larger collection. These top predictors can be viewed as potential candidates in the variable selection step of the ecological niche modeling process. MERRA/Max's Monte Carlo algorithm operates on files stored in the underlying filesystem, making it scalable to large data sets. Its software components can run as parallel processes in a high-performance cloud computing environment to yield near real-time performance. In tests using Cassin's Sparrow (Peucaea cassinii) as the target species, MERRA/Max selected a set of predictors from Worldclim's Bioclim collection of 19 environmental variables that have been shown to be important determinants of the species' bioclimatic niche. It also selected biologically and ecologically plausible predictors from a more diverse set of 86 environmental variables derived from NASA's Modern-Era Retrospective Analysis for Research and Applications Version 2 (MERRA-2) reanalysis, an output product of the Goddard Earth Observing System Version 5 (GEOS-5) modeling system. We believe these results point to a technological approach that could expand the use global climate model outputs in ecological niche modeling, foster exploratory experimentation with otherwise difficult-to-use climate data sets, streamline the modeling process, and, eventually, enable automated bioclimatic modeling as a practical, readily accessible, low-cost, commercial cloud service.

Toward a Monte Carlo approach to selecting climate variables in MaxEnt.

MaxEnt is an important aid in understanding the influence of climate change on species distributions. There is growing interest in using IPCC-class global climate model outputs as environmental predictors in this work. These models provide realistic, global representations of the climate system, projections for hundreds of variables (including Essential Climate Variables), and combine observations from an array of satellite, airborne, and in-situ sensors. Unfortunately, direct use of this important class of data in MaxEnt modeling has been limited by the large size of climate model output collections and the fact that MaxEnt can only operate on a relatively small set of predictors stored in a computer's main memory. In this study, we demonstrate the feasibility of a Monte Carlo method that overcomes this limitation by finding a useful subset of predictors in a larger, externally-stored collection of environmental variables in a reasonable amount of time. Our proposed solution takes an ensemble approach wherein many MaxEnt runs, each drawing on a small random subset of variables, converges on a global estimate of the top contributing subset of variables in the larger collection. In preliminary tests, the Monte Carlo approach selected a consistent set of top six variables within 540 runs, with the four most contributory variables of the top six accounting for approximately 93% of overall permutation importance in a final model. These results suggest that a Monte Carlo approach could offer a viable means of screening environmental predictors prior to final model construction that is amenable to parallelization and scalable to very large data sets. This points to the possibility of near-real-time multiprocessor implementations that could enable broader and more exploratory use of global climate model outputs in environmental niche modeling and aid in the discovery of viable predictors.

Airway smooth muscle hypertrophy and hyperplasia in asthma.

RATIONALE: Increased thickness of the airway smooth muscle (ASM) layer in asthma may result from hyperplasia or hypertrophy of muscle cells or increased extracellular matrix (ECM). OBJECTIVES: To relate ASM hypertrophy, ASM hyperplasia, and deposition of ECM to the severity and duration of asthma. METHODS: Airways from control subjects (n = 51) and from cases of nonfatal (n = 49) and fatal (n = 55) asthma were examined postmortem. Mean ASM cell volume (V(C)), the number of ASM cells per length of airway (N(L)), and the volume fraction of extracellular matrix (f(ECM)) within the ASM layer were estimated. Comparisons between subject groups were made on the basis of general linear regression models. MEASUREMENTS AND MAIN RESULTS: Mean V(C) was increased in the large airways of cases of nonfatal asthma (P = 0.015) and fatal asthma (P < 0.001) compared with control subjects. N(L) was similar in nonfatal cases and control subjects but increased in large (P < 0.001), medium (P < 0.001), and small (P = 0.034) airways of cases of fatal asthma compared with control subjects and with nonfatal cases (large and medium airways, P ≤ 0.003). The f(ECM) was similar in cases of asthma and control subjects. Duration of asthma was associated with a small increase in N(L). CONCLUSIONS: Hypertrophy of ASM cells occurs in the large airways in both nonfatal and fatal cases of asthma, but hyperplasia of ASM cells is present in the large and small airways in fatal asthma cases only. Both are associated with an absolute increase in ECM. Duration of asthma has little or no effect on ASM hypertrophy or hyperplasia or f(ECM).