Modeling the fate and transport of agricultural pollutants and their environmental impact on surface and subsurface water quality

This dissertation describes the modeling efforts that devoted to understand the fate and transport processes of agricultural chemicals (pesticides and fertilizers) in aquatic environments and their impacts on surface and subsurface water quality. The main tasks were to develop and apply a two-dimensional (2D) reservoir toxic model for the fate and transport of toxic substances and to evaluate a field-scale non- point source model, the Erosion Productivity Impact Calculator (EPIC), as a tool for agricultural policy analysis;The 2D toxic model was developed using finite difference method to the laterally integrated hydrodynamics, mass transport, and transformation equations. It was applied to the Shasta Reservoir, California to investigate the effects of reservoir flow regime on the persistence and behavior of a spilled toxicant, methyl isothiocyanate (MITC). The results demonstrated that flow regime can substantially affect the persistence and transport of contaminant in the late stage of the spill. The model was also tested using field data, atrazine [2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine], collected from the Saylorville Reservoir, Iowa. Time-variable half-life of atrazine was estimated using a mass balance concept in the reservoir. The half-life varied monthly from 2 to 58 days depending upon environmental conditions (i.e., sunlight, temperature, and microorganisms). The 2D model accurately simulated the temporal and spatial variations of atrazine concentrations in the reservoir;The EPIC model was tested at two field sites in Iowa. It is concluded that standard curve number values should be adequately reduced to represent the impacts of residue cover on the partition of precipitation between surface runoff and infiltration. The results showed that EPIC is sensitive to variations in tillage and cropping practices and can be used to estimate environmental indicators in response to different management systems. However, clear discrepancies occurred between some model estimates and corresponding measured values, e.g., under-prediction of peak flows and nitrogen losses during storm events. Two potential sources of these errors include: (1) the lack of a preferential flow component, and (2) nitrogen transformation routines that may not adequately reflect all of the processes that occur in the field. EPIC showed a limited capability to reproduce tillage and crop rotation effects on crop yield

Evaluation of EPIC for Assessing Tile Flow and Nitrogen Losses for Alternative Agricultural Management Systems

The Erosion Productivity Impact Calculator (EPIC) model has been successfully applied for agricultural policy analyses for more than a decade. EPIC has been tested and validated under a wide range of conditions; however, there is an ongoing need to further test the model to improve its prediction capabilities. In this study, EPIC was calibrated and validated using 3 years (1990–1992) of data collected from a field site near Nashua, Iowa. The model’s performance was evaluated by assessing its ability to replicate the effects of various tillage and crop rotation systems on subsurface tile flow, nitrate–nitrogen (NO3–N) loss with tile flow, and crop yield. Predicted annual average tile flows and nitrate losses in the tile flows were generally within 10% of measured values; the major exceptions were errors of 19.3% and 58.3% predicted for tile flow and nitrate loss for a no–tilled corn–soybean rotation system. Comparisons of monthly predictions with measured values resulted in r2 values between 0.67 and 0.89 for the tile flows and 0.60 to 0.83 for the associated nitrate losses in the tile flows. Paired t–tests that accounted for tillage and crop rotation effects on tile flow and nitrate losses showed that EPIC was in agreement with observed values in 11 out of 14 comparisons. However, EPIC showed a limited capability to reproduce tillage and crop rotation effects on crop yield, similar to results found in several previous studies. Further testing of EPIC is needed to refine and improve the model’s performance under conditions similar to those at the Nashua site

Estrogen Antagonist and Development of Macular Hole

To describe the clinical and optical coherence tomography (OCT) features of a macular hole (MH) or its precursor lesion in patients treated with systemic antiestrogen agents. We reviewed the medical history of the patient, ophthalmic examination, and both fundus and OCT findings. Three female patients receiving antiestrogen therapy sought treatment for visual disturbance. All of the patients showed foveal cystic changes with outer retinal defect upon OCT. Visual improvement was achieved through surgery for the treatment of MH in two patients. Antiestrogen therapy may result in MH or its precursor lesion, in addition to perifoveal refractile deposits. OCT examination would be helpful for early detection in such cases

Increased Releasability of Skin Mast Cells after Exercise in Patients with Exercise-induced Asthma

The role of lung mast cells in exercise-induced asthma (EIA) is controversial. To investigate whether the skin mast cell releasability is increased after exercise in EIA, 49 young atopic men with or without asthma took part in a free-running test for 6 min and were given skin prick tests using morphine, a mast cell secretagogue, before and after the exercise. The mean diameters of the wheal induced by morphine in patients with EIA were not significantly different from those in patients without EIA before exercise, although the baseline lung function was significantly lower and the airway hyperresponsiveness, the peripheral blood eosinophil count, and the size of the wheal in response to Dermatophagoides pteronyssinus were significantly higher in patients with EIA. However, the differences of the morphine-induced wheal diameter between patients with EIA and those without EIA became significant at 120 min after exercise (p<0.05), while the responses to histamine were not significantly different. These results suggest that exercise increases the releasability of skin mast cells in EIA patients whose asthma/allergy are relatively severe

Intraosseous Nerve Sheath Tumors in the Jaws

Although the head and neck region is recognized as the most common location for peripheral nerve sheath tumors, central involvement, particularly in the jaw bones, is quite unusual. Neurofibroma is one of the most common nerve sheath tumors occurring in the soft tissue and generally appears in neurofibromatosis 1 (NF1 or von Recklinghausen's disease). Malignant peripheral nerve sheath tumors (MPNSTs) are uncommon sarcomas that almost always arise in the soft tissue. Here, we report four cases of intraosseous peripheral nerve sheath tumors occurring in the jaw bones and compare the clinical, radiologic, and pathologic findings in order to make a differential diagnosis

Prevalence and detection of low-allele-fraction variants in clinical cancer samples

Accurate detection of genomic alterations using high-throughput sequencing is an essential component of precision cancer medicine. We characterize the variant allele fractions (VAFs) of somatic single nucleotide variants and indels across 5095 clinical samples profiled using a custom panel, CancerSCAN. Our results demonstrate that a significant fraction of clinically actionable variants have low VAFs, often due to low tumor purity and treatment-induced mutations. The percentages of mutations under 5% VAF across hotspots in EGFR, KRAS, PIK3CA, and BRAF are 16%, 11%, 12%, and 10%, respectively, with 24% for EGFR T790M and 17% for PIK3CA E545. For clinical relevance, we describe two patients for whom targeted therapy achieved remission despite low VAF mutations. We also characterize the read depths necessary to achieve sensitivity and specificity comparable to current laboratory assays. These results show that capturing low VAF mutations at hotspots by sufficient sequencing coverage and carefully tuned algorithms is imperative for a clinical assay