Classification of Lakebed Geologic Substrate in Autonomously Collected Benthic Imagery Using Machine Learning

Mapping benthic habitats with bathymetric, acoustic, and spectral data requires georeferenced ground-truth information about habitat types and characteristics. New technologies like autonomous underwater vehicles (AUVs) collect tens of thousands of images per mission making image-based ground truthing particularly attractive. Two types of machine learning (ML) models, random forest (RF) and deep neural network (DNN), were tested to determine whether ML models could serve as an accurate substitute for manual classification of AUV images for substrate type interpretation. RF models were trained to predict substrate class as a function of texture, edge, and intensity metrics (i.e., features) calculated for each image. Models were tested using a manually classified image dataset with 9-, 6-, and 2-class schemes based on the Coastal and Marine Ecological Classification Standard (CMECS). Results suggest that both RF and DNN models achieve comparable accuracies, with the 9-class models being least accurate (~73–78%) and the 2-class models being the most accurate (~95–96%). However, the DNN models were more efficient to train and apply because they did not require feature estimation before training or classification. Integrating ML models into benthic habitat mapping process can improve our ability to efficiently and accurately ground-truth large areas of benthic habitat using AUV or similar images

Brain function early after stroke in relation to subsequent recovery.

This study aimed to characterize brain activation and perfusion early after stroke within cortical regions that would later change activation during recovery. Patients were studied serially after stroke (mean t1, = 16 days after stroke, t2 = 3.5 months later) using perfusion-weighted imaging and functional magnetic resonance imaging during finger movement. Controls (n = 7) showed no significant change in regional activation volumes over time. Among stroke patients (n = 8), however, recovery was accompanied by several patterns of functional magnetic resonance imaging change, with increased activation volumes over time in five patients and decreased in two. Most regions increasing activation over time were in the stroke hemisphere. Of the five patients showing increased activation over time, specific activation foci enlarged at t2 were already activated at t1 in four patients, and at least one focus growing from t1 to t2 was in a different arterial distribution from the infarct in all five patients. Perfusion of sensorimotor cortex at t1 was generally not reduced in the stroke hemisphere (94% of noninfarcted hemisphere). Improved clinical outcome was related to increased activation within sensory cortices of both brain sides, including bilateral secondary somatosensory areas. Early after stroke, cortical activation that will later increase in parallel with recovery is often already identifiable, can be remote from the vascular territory of the infarct, and is not likely hindered by reduced perfusion. The findings may be useful for restorative interventions introduced during the weeks after a stroke

Characterizing coal and mineral mines as a regional source of stress to stream fish assemblages

Mining impacts on stream systems have historically been studied over small spatial scales, yet investigations over large areas may be useful for characterizing mining as a regional source of stress to stream fishes. The associations between co-occurring stream fish assemblages and densities of various “classes” of mining occurring in the same catchments were tested using threshold analysis. Threshold analysis identifies the point at which fish assemblages change substantially from best available habitat conditions with increasing disturbance. As this occurred over large regions, species comprising fish assemblages were represented by various functional traits as well as other measures of interest to management (characterizing reproductive ecology and life history, habitat preferences, trophic ecology, assemblage diversity and evenness, tolerance to anthropogenic disturbance and state-recognized game species). We used two threshold detection methods: change-point analysis with indicator analysis and piecewise linear regression. We accepted only those thresholds that were highly statistically significant (p ≤ 0.01) for both techniques and overlapped within ≤ 5% error. We found consistent, wedge-shaped declines in multiple fish metrics with increasing levels of mining in catchments, suggesting mines are a regional source of disturbance. Threshold responses were consistent across the three ecoregions occurring at low mine densities. For 47.2% of the significant thresholds, a density of only ≤ 0.01 mines/km² caused a threshold response. In fact, at least 25% of streams in each of our three study ecoregions have mine densities in their catchments with the potential to affect fish assemblages. Compared to other anthropogenic impacts assessed over large areas (agriculture, impervious surface or urban land use), mining had a more pronounced and consistent impact on fish assemblages.Keywords: Game fishes, Rivers, Mining, Threshold analysis, Landscape influences, Fish functional trait

Fish Communities and Conservation of Aquatic Landscapes in Northeastern Mesoamerica.

Tropical river conservation is a global priority because these rivers support high biodiversity and rural livelihoods, and contribute to maintenance of marine ecosystems. A challenge to river conservation in tropical developing countries is the paucity of scientific information to assist with conservation planning at appropriate spatial scales. This research attempted to alleviate some of the information scarcity impeding conservation of rivers draining to the coast of Belize in northeastern Mesoamerica. This work drew on field and museum collections of freshwater fishes to: (1) investigate the influences of reach- and catchment-scale environmental conditions on fish communities; (2) document spatial and temporal patterns of spread of an invasive fish, African tilapia (Oreochromis spp.), and make recommendations for its control; and (3) design a freshwater protected areas network in a riverine context. Environmental characteristics across scales described a large portion of total fish assemblage variation (64%), and catchment-scale factors explained a greater percentage of total variance (25%) than reach-scale environment (14%). The high correlation between assemblage patterns and catchment-scale factors suggests that fish conservation efforts are most appropriately conceptualized at this scale. A reconstructed spatial chronology of tilapia spread suggested that the invading population experienced an initial lag period before advancing from its initial home range, and that Nile tilapia (O. niloticus) is now widely distributed in the coastal plain rivers of at least 9 of 29 drainage basins. The study revealed unintentional releases from aquaculture and flooding as the two most likely dispersal mechanisms, leading to recommendations focused on (1) prevention of tilapia spread to un-invaded systems, and (2) control of aquaculture activities. Riverine conservation areas comprising 11% of the study area that had high fish biodiversity and low human influence were identified using conservation planning software and species distribution models for 63 fishes. Management zones were specified to mitigate threats to conservation areas, protect fish movement corridors, and target basin management. Despite chronic information limitations, this work demonstrates how limited field data, interviews with resource users, and modeling can be used to create biologically realistic hypotheses about ecological reality that can serve as a starting point for conservation planning in rivers.Ph.D.Natural Resources and EnvironmentUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/62271/1/esselman_1.pd

Overcoming Information Limitations for the Prescription of an Environmental Flow Regime for a Central American River

Hydropower dam construction is expanding rapidly in Central America because of the increasing demand for electricity. Although hydropower can provide a low-carbon source of energy, dams can also degrade socially valued riverine and riparian ecosystems and the services they provide. Such degradation can be partially mitigated by the release of environmental flows below dams. However, environmental flows have been applied infrequently to dams in Central America, partly because of the lack of information on the ecological, social, and economic aspects of rivers. This paper presents a case study of how resource and information limitations were addressed in the development of environmental flow recommendations for the Patuca River in Honduras below a proposed hydroelectric dam. To develop flow recommendations, we applied a multistep process that included hydrological analysis and modeling, the collection of traditional ecological knowledge (TEK) during field trips, expert consultation, and environmental flow workshops for scientists, water managers, and community members. The final environmental flow recommendation specifies flow ranges for different components of river hydrology, including low flows for each month, high-flow pulses, and floods, in dry, normal, and wet years. The TEK collected from local and indigenous riverine communities was particularly important for forming hypotheses about flow-dependent ecological and social factors that may be vulnerable to disruption from dam-modified river flows. We show that our recommended environmental flows would have a minimal impact on the dam's potential to generate electricity. In light of rapid hydropower development in Central America, we suggest that environmental flows are important at the local scale, but that an integrated landscape perspective is ultimately needed to pursue hydropower development in a manner that is as ecologically sustainable as possible

Using Multiscale Environmental and Spatial Analyses to Understand Natural and Anthropogenic Influence on Fish Communities in Four Canadian Rivers

Science-based conservation of riverine fishes can be best targeted with specific information about spatial-ecological controls on the community, including anthropogenic stressors. Because anthropogenic stressors can originate at multiple spatial scales, we investigated the influence of natural and anthropogenic variables summarized within the reach, valley, and catchment on fish community composition along four river mainstems in Ontario, Canada. We used Redundancy Analyses (RDA) to explore models with multi- and single-scale variables on fish community composition. We used partial RDAs to differentiate the relative effects of variable types in multiscale models and to determine if spatial variables explained additional variation in fish community composition. Catchment variables accounted for the majority of explained variation in fish community composition in three of the four rivers, but instream habitat variables accounted for considerable variability in fish community composition in the two rivers that are highly fragmented by dams or naturally occurring rapids. Natural and human-derived fragmentation in rivers may reduce the influence of catchment controls, disrupt longitudinal gradients, and increase the influence of local instream habitat. Environmental variables that explained fish distribution had longitudinal or patchy spatial pattern within rivers, but spatial variables representing impediments to fish dispersal and proximity to receiving waterbodies failed to explain additional variation in fish community composition

Brain function early after stroke in relation to subsequent recovery.

This study aimed to characterize brain activation and perfusion early after stroke within cortical regions that would later change activation during recovery. Patients were studied serially after stroke (mean t1, = 16 days after stroke, t2 = 3.5 months later) using perfusion-weighted imaging and functional magnetic resonance imaging during finger movement. Controls (n = 7) showed no significant change in regional activation volumes over time. Among stroke patients (n = 8), however, recovery was accompanied by several patterns of functional magnetic resonance imaging change, with increased activation volumes over time in five patients and decreased in two. Most regions increasing activation over time were in the stroke hemisphere. Of the five patients showing increased activation over time, specific activation foci enlarged at t2 were already activated at t1 in four patients, and at least one focus growing from t1 to t2 was in a different arterial distribution from the infarct in all five patients. Perfusion of sensorimotor cortex at t1 was generally not reduced in the stroke hemisphere (94% of noninfarcted hemisphere). Improved clinical outcome was related to increased activation within sensory cortices of both brain sides, including bilateral secondary somatosensory areas. Early after stroke, cortical activation that will later increase in parallel with recovery is often already identifiable, can be remote from the vascular territory of the infarct, and is not likely hindered by reduced perfusion. The findings may be useful for restorative interventions introduced during the weeks after a stroke

Landscape Drivers and Social Dynamics Shaping Microbial Contamination Risk in Three Maya Communities in Southern Belize, Central America

Land transformation can have cascading effects on hydrology, water quality, and human users of water resources, with serious implications for human health. An interdisciplinary analysis is presented, whereby remote-sensing data of changing land use and cover are related to surface hydrology and microbial contamination in domestic use areas of three indigenous Maya communities in Belize, Central America. We asked whether a departure from traditional land-use patterns toward intensified use led to consequences for hydrology and microbial contamination of drinking water, and investigated how social factors in the three study communities may act to ameliorate human health risks associated with water contamination. We showed that a departure from traditional land use to more intensive cultivation and grazing led to significantly increased surface water runoff, and intensified microbial contamination of surface water sources sometimes used for drinking. Results further suggested that groundwater contamination was widespread regardless of land cover, due to the widespread presence of pit latrines, pigs, and cows on the landscape, and that human users were consistently subject to health risks from potential pathogens as a result. Given that both surface and groundwater resources were found to be contaminated, it is important that water distribution systems (piped water from tanks; shallow and deep wells) be monitored for Escherichia coli and treated when necessary to reduce or eliminate contaminants and protect public health. Results of interviews suggested that strengthened capacity within the communities to monitor and treat centralized drinking water sources and increase water treatment at the point of use could lead to reduced risk to water consumers