Automatic generation of alignments for 3D QSAR analyses

Many 3D QSAR methods require the alignment of the molecules in a dataset, which can require a fair amount of manual effort in deciding upon a rational basis for the superposition. This paper describes the use of FBSS, a pro-ram for field-based similarity searching in chemical databases, for generating such alignments automatically. The CoMFA and CoMSIA experiments with several literature datasets show that the QSAR models resulting from the FBSS alignments are broadly comparable in predictive performance with the models resulting from manual alignments

Linking Nutrient Transport to Soil Physical Processes During Freeze/Thaw Events to Promote Wintertime Manure Management, Nutrient Use Efficiency, and Surface Water Quality.

The application of dairy manure to the landscape during winter is a longstanding practice for farms in the Midwestern United States and other temperate regions. Practical motivations behind winter spreading include affordability, availability of time, and the reduced risk of compaction from farm equipment on frozen soils. Wintertime manure applications, however, coincide with environmental conditions that are prone to runoff and accelerate nutrient losses from agricultural fields. Understanding the nutrient dynamics in response to winter-applied manure is especially important to Wisconsin, a leading state in dairy production, where up to 75% of annual runoff volumes occur on frozen and thawing soils. The high potential for winter runoff, hence nutrient transport, has prompted revisions to winter manure regulations, yet little conclusive data exist to guide these changing standards

Temperature and Manure Placement in a Snowpack Affect Nutrient Release from Dairy Manure During Snowmelt

Agricultural nutrient management is an issue due to N and P losses from fields and water quality degradation. Better information is needed on the risk of nutrient loss in runoff from dairy manure applied in winter. We investigated the effect of temperature on nutrient release from liquid and semisolid manure to water, and of manure quantity and placement within a snowpack on nutrient release to melting snow. Temperature did not affect manure P and NH4–N release during water extraction. Manure P release, but not NH4–N release, was significantly influenced by the water/manure solids extraction ratio. During snowmelt, manure P release was not significantly affected by manure placement in the snowpack, and the rate of P release decreased as application rate increased. Water extraction data can reliably estimate P release from manure during snowmelt; however, snowmelt water interaction with manure of greater solids content and subsequent P release appears incomplete compared with liquid manures. Manure NH4–N released during snowmelt was statistically the same regardless of application rate. For the semisolid manure, NH4–N released during snowmelt increased with the depth of snow covering it, most likely due to reduced NH3 volatilization. For the liquid manure, there was no effect of manure placement within the snowpack on NH4–N released during snowmelt. Water extraction data can also reliably estimate manure NH4–N release during snowmelt as long as NH3 volatilization is accounted for with liquid manures for all placements in a snowpack and semisolid manures applied on top of snow

Dynamics of Measured and Simulated Dissolved Phosphorus in Runoff from Winter-Applied Dairy Manure

Agricultural P loss from fields is an issue due to water quality degradation. Better information is needed on the P loss in runoff from dairy manure applied in winter and the ability to reliably simulate P loss by computer models. We monitored P in runoff during two winters from chisel-tilled and no-till field plots that had liquid dairy manure applied in December or January. Runoff total P was dominated by nondissolved forms when soils were bare and unfrozen. Runoff from snow-covered, frozen soils had much less sediment and sediment-related P, and much more dissolved P. Transport of manure solids was greatest when manure was applied on top of snow and runoff shortly after application was caused by snowmelt. Dissolved P concentrations in runoff were greater when manure was applied on top of snow because manure liquid remained in the snowpack and allowed more P to be available for loss. Dissolved runoff P also increased as the amount of rain or snowmelt that became runoff (runoff ratio) increased. The SurPhos manure P runoff model reliably simulated these processes to provide realistic predictions of dissolved P in runoff from surface manure. Overall, for liquid dairy manure applied in winter, dissolved P concentrations in runoff can be decreased if manure is applied onto bare, unfrozen soil, or if runoff ratio can be reduced, perhaps through greater soil surface roughness from fall tillage. Both management approaches will allow more manure P to infiltrate into soil and less move in runoff. SurPhos is a tool that can reliably evaluate P loss for different management and policy scenarios for winter manure application

Quantifying the Impact of Seasonal and Short-term Manure Application Decisions on Phosphorus Loss in Surface Runoff

Agricultural phosphorus (P) management is a research and policy issue due to P loss from fields and water quality degradation. Better information is needed on the risk of P loss from dairy manure applied in winter or when runoff is imminent. We used the SurPhos computer model and 108 site–years of weather and runoff data to assess the impact of these two practices on dissolved P loss. Model results showed that winter manure application can increase P loss by 2.5 to 3.6 times compared with non-winter applications, with the amount increasing as the average runoff from a field increases. Increased P loss is true for manure applied any time from late November through early March, with a maximum P loss from application in late January and early February. Shifting manure application to fields with less runoff can reduce P loss by 3.4 to 7.5 times. Delaying manure application when runoff is imminent can reduce P loss any time of the year, and sometimes quite significantly, but the number of times that application delays will reduce P loss is limited to only 3 to 9% of possible spreading days, and average P loss may be reduced by only 15% for winter-applied manure and 6% for non-winter-applied manure. Overall, long-term strategies of shifting manure applications to low runoff seasons and fields can potentially reduce dissolved P loss in runoff much more compared with near-term, tactical application decisions of avoiding manure application when runoff is imminent

Multicentric validation of proteomic biomarkers in urine specific for diabetic nephropathy

Background: Urine proteome analysis is rapidly emerging as a tool for diagnosis and prognosis in disease states. For diagnosis of diabetic nephropathy (DN), urinary proteome analysis was successfully applied in a pilot study. The validity of the previously established proteomic biomarkers with respect to the diagnostic and prognostic potential was assessed on a separate set of patients recruited at three different European centers. In this case-control study of 148 Caucasian patients with diabetes mellitus type 2 and duration >= 5 years, cases of DN were defined as albuminuria >300 mg/d and diabetic retinopathy (n = 66). Controls were matched for gender and diabetes duration (n = 82). Methodology/Principal Findings: Proteome analysis was performed blinded using high-resolution capillary electrophoresis coupled with mass spectrometry (CE-MS). Data were evaluated employing the previously developed model for DN. Upon unblinding, the model for DN showed 93.8% sensitivity and 91.4% specificity, with an AUC of 0.948 (95% CI 0.898-0.978). Of 65 previously identified peptides, 60 were significantly different between cases and controls of this study. In <10% of cases and controls classification by proteome analysis not entirely resulted in the expected clinical outcome. Analysis of patient's subsequent clinical course revealed later progression to DN in some of the false positive classified DN control patients. Conclusions: These data provide the first independent confirmation that profiling of the urinary proteome by CE-MS can adequately identify subjects with DN, supporting the generalizability of this approach. The data further establish urinary collagen fragments as biomarkers for diabetes-induced renal damage that may serve as earlier and more specific biomarkers than the currently used urinary albumin