Predicting chronic wasting disease in white-tailed deer at the county scale using machine learning.

Continued spread of chronic wasting disease (CWD) through wild cervid herds negatively impacts populations, erodes wildlife conservation, drains resource dollars, and challenges wildlife management agencies. Risk factors for CWD have been investigated at state scales, but a regional model to predict locations of new infections can guide increasingly efficient surveillance efforts. We predicted CWD incidence by county using CWD surveillance data depicting white-tailed deer (Odocoileus virginianus) in 16 eastern and midwestern US states. We predicted the binary outcome of CWD-status using four machine learning models, utilized five-fold cross-validation and grid search to pinpoint the best model, then compared model predictions against the subsequent year of surveillance data. Cross validation revealed that the Light Boosting Gradient model was the most reliable predictor given the regional data. The predictive model could be helpful for surveillance planning. Predictions of false positives emphasize areas that warrant targeted CWD surveillance because of similar conditions with counties known to harbor CWD. However, disagreements in positives and negatives between the CWD Prediction Web App predictions and the on-the-ground surveillance data one year later underscore the need for state wildlife agency professionals to use a layered modeling approach to ensure robust surveillance planning. The CWD Prediction Web App is at https://cwd-predict.streamlit.app/ .

Predicting the odds of chronic wasting disease with Habitat Risk software.

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in captive cervids in Colorado, United States (US) in 1967, but has since spread into free-ranging white-tailed deer (Odocoileus virginianus) across the US and Canada as well as to Scandinavia and South Korea. In some areas, the disease is considered endemic in wild deer populations, and governmental wildlife agencies have employed epidemiological models to understand long-term environmental risk. However, continued rapid spread of CWD into new regions of the continent has underscored the need for extension of these models into broader tools applicable for wide use by wildlife agencies. Additionally, efforts to semi-automate models will facilitate access of technical scientific methods to broader users. We introduce software (Habitat Risk) designed to link a previously published epidemiological model with spatially referenced environmental and disease testing data to enable agency personnel to make up-to-date, localized, data-driven predictions regarding the odds of CWD detection in surrounding areas after an outbreak is discovered. Habitat Risk requires pre-processing publicly available environmental datasets and standardization of disease testing (surveillance) data, after which an autonomous computational workflow terminates in a user interface that displays an interactive map of disease risk. We demonstrated the use of the Habitat Risk software with surveillance data of white-tailed deer from Tennessee, USA.

Split fertilizer nitrogen application with a cereal rye cover crop reduces tile nitrate loads in a corn-soybean rotation.

Splitting fertilizer nitrogen (N) applications and using cover crops are management strategies to reduce nitrate in tile drainage water. We investigated split fertilizer N applications to corn (Zea mays L.) on crop yields and tile nitrate loss in both corn and soybean (Glycine max L.) in rotation from 2016 through 2019. We evaluated the inclusion of cover crops in a split-N treatment. Fertilizer N treatments included 100% in the fall; 50% in the fall + 25% at planting + 25% at side-dress; 100% as spring preplant; 75% as spring preplant (reduced N rate); 50% as spring preplant + 50% at side-dress; and 50% as spring preplant + 50% at side-dress with a cover crop. We did not find significant differences between split and single full rate N application treatments for corn yields or tile nitrate loss; however, the reduced N rate treatment significantly decreased corn yield by 10%. Cumulative tile nitrate losses (over four seasons) ranged from 115 kg ha-1 for all of the N in the fall to 65 kg ha-1 for 50% as spring preplant + 50% at side-dress with a cover crop, a decrease of 43%. Tile nitrate loss responded similarly to (corn) N treatments under both corn and soybean, with 64% of the loss under corn and 36% under soybean. Our results suggest that decreasing the fertilizer N rate may impact corn yield more than nitrate loss, while split fertilizer N application with a cover crop has potential to reduce tile nitrate loss without decreasing crop yield.

Protecting human amnion and chorion matrices during processing: Performance enhancement in a diabetic mouse model and human co-culture system.

Recent evidence suggests that protecting human amnion and chorion matrices (HACM) during processing enhances the performance of HACM for wound repair and tissue regeneration. We utilised a diabetic (db/db) delayed wound healing mouse model. Treatment of db/db full-thickness excisional wounds with HACM, processed with a polyampholyte preservative accentuated the proliferative phase of wound healing that decreased the time necessary to heal wounds. Polyampholyte protection improved the preservation of growth factors and cytokines during room temperature storage following E-beam sterilisation and improved its function in wound healing applications. Our findings indicate protected HACM tissue up-regulated MIP2, NF-kB, TNF-α, KI-67, and Arg1 (0.6-fold to 1.5-fold) but those changes were not statistically significant. Immunofluorescent assessment identifying cell activity illustrated an induction of the proliferative phase of wound healing and a switch from an inflammatory macrophage phenotype (M1) to a pro-regenerative macrophage phenotype (M2a). Genomic profiling of 282 genes was performed using Nanostring from co-cultures of human macrophages and fibroblasts. The polyampholyte + HACM-treated group, compared with the HACM or polyampholyte alone groups, had a statistically significant up-regulation (32-368 fold) of 12 genes primarily involved in macrophage plasticity including CLC7, CD209, CD36, HSD11B1, ICAM1, IL1RN, IL3RA, ITGAX, LSP1, and PLXDC2 (adj. p-value < 0.05). The polyampholyte alone group demonstrated statistically significant down-regulation of four genes ADRA2, COL7A1, CSF3, and PTGS2 (adj. p < 0.05). The HACM alone group up-regulated four genes ATG14, CXCL11, DNMT3A, and THBD, but the results were not statistically significant. Biomechanical measurements indicated that wounds treated with polyampholyte-protected HACM had more tensile integrity compared with wounds treated with HACM alone. These findings indicate that better protection of HACM during processing stabilises the HACM matrix, which may lead to improved wound healing outcomes.

Using movement to inform conservation corridor design for Mojave desert tortoise.

BACKGROUND: Preserving corridors for movement and gene flow among populations can assist in the recovery of threatened and endangered species. As human activity continues to fragment habitats, characterizing natural corridors is important in establishing and maintaining connectivity corridors within the anthropogenic development matrix. The Mojave desert tortoise (Gopherus agassizii) is a threatened species occupying a variety of habitats in the Mojave and Colorado Deserts. Desert tortoises have been referred to as corridor-dwellers, and understanding how they move within suitable habitat can be crucial to defining corridors that will sustain sufficient gene flow to maintain connections among populations amidst the increases in human development. METHODS: To elucidate how tortoises traverse available habitat and interact with potentially inhospitable terrain and human infrastructure, we used GPS dataloggers to document fine-scale movement of individuals and estimate home ranges at ten study sites along the California/Nevada border. Our sites encompass a variety of habitats, including mountain passes that serve as important natural corridors connecting neighboring valleys, and are impacted by a variety of linear anthropogenic features. We used path selection functions to quantify tortoise movements and develop resistance surfaces based on landscape characteristics including natural features, anthropogenic alterations, and estimated home ranges with autocorrelated kernel density methods. Using the best supported path selection models and estimated home ranges, we determined characteristics of known natural corridors and compared them to mitigation corridors (remnant habitat patches) that have been integrated into land management decisions in the Ivanpah Valley. RESULTS: Tortoises avoided areas of high slope and low perennial vegetation cover, avoided moving near low-density roads, and traveled along linear barriers (fences and flood control berms). CONCLUSIONS: We found that mitigation corridors designated between solar facilities should be wide enough to retain home ranges and maintain function. Differences in home range size and movement resistance between our two natural mountain pass corridors align with differences in genetic connectivity, suggesting that not all natural corridors provide the same functionality. Furthermore, creation of mitigation corridors with fences may have unintended consequences and may function differently than natural corridors. Understanding characteristics of corridors with different functionality will help future managers ensure that connectivity is maintained among Mojave desert tortoise populations.

Insights into pancreatic ß cell energy metabolism using rodent ß cell models.

Background: Mitochondrial diabetes is primarily caused by ß-cell failure, a cell type whose unique properties are important in pathogenesis. Methods: By reducing glucose, we induced energetic stress in two rodent ß-cell models to assess effects on cellular function. Results: Culturing rat insulin-secreting INS-1 cells in low glucose conditions caused a rapid reduction in whole cell respiration, associated with elevated mitochondrial reactive oxygen species production, and an altered glucose-stimulated insulin secretion profile. Prolonged exposure to reduced glucose directly impaired mitochondrial function and reduced autophagy. Conclusions: Insulinoma cell lines have a very different bioenergetic profile to many other cell lines and provide a useful model of mechanisms affecting ß-cell mitochondrial function.

Riverine Response of Sulfate to Declining Atmospheric Sulfur Deposition in Agricultural Watersheds.

Sulfur received extensive study as an input to terrestrial ecosystems from acidic deposition during the 1980s. With declining S deposition inputs across the eastern United States, there have been many studies evaluating ecosystem response, with the exception of agricultural watersheds. We used long-term (22 and 18 yr) sulfate concentration data from two rivers and recent (6 yr) data from a third river to better understand cycling and transport of S in agricultural, tile-drained watersheds. Sulfate concentrations and yields steadily declined in the Embarras (from ∼10 to 6 mg S L) and Kaskaskia rivers (from 7 to 3.5 mg S L) during the sampling period, with an overall -23.1 and -12.8 kg S ha yr balance for the two watersheds. There was evidence of deep groundwater inputs of sulfate in the Salt Fork watershed, with a much smaller input to the Embarras and none to the Kaskaskia. Tiles in the watersheds had low sulfate concentrations (<10 mg S L), similar to the Kaskaskia River, unless the field had received some form of S fertilizer. A multiple regression model of runoff (cm) and S deposition explained much of the variation in Embarras River sulfate ( = 0.86 and 0.80 for concentrations and yields; = 46). Although atmospheric deposition was much less than outputs (grain harvest + stream export of sulfate), riverine transport of sulfate reflected the decline in inputs. Watershed S balances suggest a small annual depletion of soil organic S pools, and S fertilization will likely be needed at some future date to maintain crop yields.

Chloride Sources and Losses in Two Tile-Drained Agricultural Watersheds.

Chloride is a relatively unreactive plant nutrient that has long been used as a biogeochemical tracer but also can be a pollutant causing aquatic biology impacts when concentrations are high, typically from rock salt applications used for deicing roads. Chloride inputs to watersheds are most often from atmospheric deposition, road salt, or agricultural fertilizer, although studies on agricultural watersheds with large fertilizer inputs are few. We used long-term (21 and 17 yr) chloride water quality data in two rivers of east-central Illinois to better understand chloride biogeochemistry in two agricultural watersheds (Embarras and Kaskaskia), the former with a larger urban land use and both with extensive tile drainage. During our sampling period, the average chloride concentration was 23.7 and 20.9 mg L in the Embarras and Kaskaskia Rivers, respectively. Annual fluxes of chloride were 72.5 and 61.2 kg ha yr in the Embarras and Kaskaskia watersheds, respectively. In both watersheds, fertilizer chloride was the dominant input (∼49 kg ha yr), with road salt likely the other major source (23.2 and 7.2 kg ha yr for the Embarras and Kaskaskia watersheds, respectively). Combining our monitoring data with earlier published data on the Embarras River showed an increase in chloride concentrations as potash use increased in Illinois during the 1960s and 1970s with a lag of about 2 to 6 yr to changes in potash inputs based on a multiple-regression model. In these agricultural watersheds, riverine chloride responds relatively quickly to potash fertilization as a result of tile-drainage.

Role of arthropod communities in bioenergy crop litter decomposition†.

The extensive land use conversion expected to occur to meet demands for bioenergy feedstock production will likely have widespread impacts on agroecosystem biodiversity and ecosystem services, including carbon sequestration. Although arthropod detritivores are known to contribute to litter decomposition and thus energy flow and nutrient cycling in many plant communities, their importance in bioenergy feedstock communities has not yet been assessed. We undertook an experimental study quantifying rates of litter mass loss and nutrient cycling in the presence and absence of these organisms in three bioenergy feedstock crops-miscanthus (Miscanthus x giganteus), switchgrass (Panicum virgatum), and a planted prairie community. Overall arthropod abundance and litter decomposition rates were similar in all three communities. Despite effective reduction of arthropods in experimental plots via insecticide application, litter decomposition rates, inorganic nitrogen leaching, and carbon-nitrogen ratios did not differ significantly between control (with arthropods) and treatment (without arthropods) plots in any of the three community types. Our findings suggest that changes in arthropod faunal composition associated with widespread adoption of bioenergy feedstock crops may not be associated with profoundly altered arthropod-mediated litter decomposition and nutrient release.

Reduced nitrogen losses after conversion of row crop agriculture to perennial biofuel crops.

Current biofuel feedstock crops such as corn lead to large environmental losses of N through nitrate leaching and NO emissions; second-generation cellulosic crops have the potential to reduce these N losses. We measured N losses and cycling in establishing miscanthus (), switchgrass ( L. fertilized with 56 kg N ha yr), and mixed prairie, along with a corn ( L.)-corn-soybean [ (L.) Merr.] rotation (corn fertilized at 168-202 kg N ha). Nitrous oxide emissions, soil N mineralization, mid-profile nitrate leaching, and tile flow and nitrate concentrations were measured. Perennial crops quickly reduced nitrate leaching at a 50-cm soil depth as well as concentrations and loads from the tile systems (year 1 tile nitrate concentrations of 10-15 mg N L declined significantly by year 4 in all perennial crops to <0.6 mg N L, with losses of <0.8 kg N ha yr). Nitrous oxide emissions were 2.2 to 7.7 kg N ha yr in the corn-corn-soybean rotation but were <1.0 kg N ha yr by year 4 in the perennial crops. Overall N balances (atmospheric deposition + fertilization + soybean N fixation - harvest, leaching losses, and NO emissions) were positive for corn and soybean (22 kg N ha yr) as well as switchgrass (9.7 kg N ha yr) but were -18 and -29 kg N ha yr for prairie and miscanthus, respectively. Our results demonstrate rapid tightening of the N cycle as perennial biofuel crops established on a rich Mollisol soil.

Miscanthus and switchgrass production in central Illinois: impacts on hydrology and inorganic nitrogen leaching.

Biomass crops are being promoted as environmentally favorable alternatives to fossil fuels or ethanol production from maize (Zea mays L.), particularly across the Corn Belt of the United States. However, there are few if any empirical studies on inorganic N leaching losses from perennial grasses that are harvested on an annual basis, nor has there been empirical evaluation of the hydrologic consequences of perennial cropping systems. Here we report on the results of 4 yr of field measurements of soil moisture and inorganic N leaching from a conventional maize-soybean [Glycine max (L.) Merr.] system and two unfertilized perennial grasses harvested in winter for biomass: Miscanthus x giganteus and switchgrass (Panicum virgatum cv. Cave-in-Rock). All crops were grown on fertile Mollisols in east-central Illinois. Inorganic N leaching was measured with ion exchange resin lysimeters placed 50 cm below the soil surface. Maize--soybean nitrate leaching averaged 40.4 kg N ha(-1) yr(-1), whereas switchgrass and Miscanthus had values of 1.4 and 3.0 kg N ha(-1) yr(-1), respectively. Soil moisture monitoring (to a depth of 90 cm) indicated that both perennial grasses dried the soil out earlier in the growing season compared with maize-soybean. Later in the growing season, soil moisture under switchgrass tended to be greater than maize-soybean or Miscanthus, whereas the soil under Miscanthus was consistently drier than under maize--soybean. Water budget calculations indicated that evapotranspiration from Miscanthus was about 104 mm yr(-1) greater than under maize-soybean, which could reduce annual drainage water flows by 32% in central Illinois. Drainage water is a primary source of surface water flows in the region, and the impact ofextensive Miscanthus production on surface water supplies and aquatic ecosystems deserves further investigation.

Assessment of chlorophyll-a as a criterion for establishing nutrient standards in the streams and rivers of Illinois.

Nutrient enrichment is a frequently cited cause for biotic impairment of streams and rivers in the USA. Efforts are underway to develop nutrient standards in many states, but defensible nutrient standards require an empirical relationship between nitrogen (N) or phosphorus (P) concentrations and some criterion that relates nutrient levels to the attainment of designated uses. Algal biomass, measured as chlorophyll-a (chl-a), is a commonly proposed criterion, yet nutrient-chl-a relationships have not been well documented in Illinois at a state-wide scale. We used state-wide surveys of >100 stream and river sites to assess the applicability of chl-a as a criterion for establishing nutrient standards for Illinois. Among all sites, the median total P and total N concentrations were 0.185 and 5.6 mg L(-1), respectively, during high-discharge conditions. During low-discharge conditions, median total P concentration was 0.168 mg L(-1), with 25% of sites having a total P of > or =0.326 mg L(-1). Across the state, 90% of the sites had sestonic chl-a values of < or =35 microg L(-1), and watershed area was the best predictor of sestonic chl-a. During low discharge there was a significant correlation between sestonic chl-a and total P for those sites that had canopy cover < or =25% and total P of < or =0.2 mg L(-1). Results suggest sestonic chl-a may be an appropriate criterion for the larger rivers in Illinois but is inappropriate for small rivers and streams. Coarse substrate to support benthic chl-a occurred in <50% of the sites we examined; a study using artificial substrates did not reveal a relationship between chl-a accrual and N or P concentrations. For many streams and rivers in Illinois, nutrients may not be the limiting factor for algal biomass due to the generally high nutrient concentrations and the effects of other factors, such as substrate conditions and turbidity.