http://hdl.handle.net/1957/25639 2013-05-22T11:27:54Z 2013-05-22T11:27:54Z Bradford, David F. Stanley, Kerri A. Tallent, Nita G. Sparling, Donald W. Nash, Maliha S. Knapp, Roland A. McConnell, Laura L. Simonich, Staci L. Massey http://hdl.handle.net/1957/38317 2013-04-24T17:08:13Z 2013-03-01T00:00:00Z

Temporal and spatial variation of atmospherically deposited organic contaminants at high elevation in Yosemite National Park, California, USA Bradford, David F.; Stanley, Kerri A.; Tallent, Nita G.; Sparling, Donald W.; Nash, Maliha S.; Knapp, Roland A.; McConnell, Laura L.; Simonich, Staci L. Massey Contaminants used at low elevation, such as pesticides on crops, can be transported tens of kilometers and deposited in adjacent mountains in many parts of the world. Atmospherically deposited organic contaminants in the Sierra Nevada Mountains of California, USA, have exceeded some thresholds of concern, but the spatial and temporal distributions of contaminants in the mountains are not well known. The authors sampled shallow-water sediment and tadpoles (Pseudacris sierra) for pesticides, polycyclic aromatic hydrocarbons (PAHs), and polychlorinated biphenyls in four high-elevation sites in Yosemite National Park in the central Sierra Nevada twice during the summers of 2006, 2007, and 2008. Both historic- and current-use pesticides showed a striking pattern of lower concentrations in both sediment and tadpoles in Yosemite than was observed previously in Sequoia–Kings Canyon National Parks in the southern Sierra Nevada. By contrast, PAH concentrations in sediment were generally greater in Yosemite than in Sequoia–Kings Canyon. The authors suggest that pesticide concentrations tend to be greater in Sequoia–Kings Canyon because of a longer air flow path over agricultural lands for this park along with greater pesticide use near this park. Concentrations for DDT-related compounds in some sediment samples exceeded guidelines or critical thresholds in both parks. A general pattern of difference between Yosemite and Sequoia–Kings Canyon was not evident for total tadpole cholinesterase activity, an indicator of harmful exposure to organophosphorus and carbamate pesticides. Variability of chemical concentrations among sites, between sampling periods within each year, and among years, contributed significantly to total variation, although the relative contributions differed between sediment and tadpoles. This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by John Wiley & Sons, Inc. and can be found at: http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291552-8618. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.

2013-03-01T00:00:00Z Larkin, Andrew Siddens, Lisbeth K. Krueger, Sharon K. Tilton, Susan C. Waters, Katrina M. Williams, David E. Baird, William M. http://hdl.handle.net/1957/38298 2013-04-23T16:55:50Z 2012-12-20T00:00:00Z

Application of a fuzzy neural network model in predicting polycyclic aromatic hydrocarbon-mediated perturbations of the Cyp1b1 transcriptional regulatory network in mouse skin Larkin, Andrew; Siddens, Lisbeth K.; Krueger, Sharon K.; Tilton, Susan C.; Waters, Katrina M.; Williams, David E.; Baird, William M. Polycyclic aromatic hydrocarbons (PAHs) are present in the environment as complex mixtures with components that have diverse carcinogenic potencies and mostly unknown interactive effects. Non-additive PAH interactions have been observed in regulation of cytochrome P450 (CYP) gene expression in the CYP1 family. To better understand and predict biological effects of complex mixtures, such as environmental PAHs, an 11 gene input-1 gene output fuzzy neural network (FNN) was developed for predicting PAH-mediated perturbations of dermal Cyp1b1 transcription in mice. Input values were generalized using fuzzy logic into low, medium, and high fuzzy subsets, and sorted using k-means clustering to create Mamdani logic functions for predicting Cyp1b1 mRNA expression. Model testing was performed with data from microarray analysis of skin samples from FVB/N mice treated with toluene (vehicle control), dibenzo[def,p]chrysene (DBC), benzo[a]pyrene (BaP), or 1 of 3 combinations of diesel particulate extract (DPE), coal tar extract (CTE) and cigarette smoke condensate (CSC) using leave-one-out cross-validation. Predictions were within 1 log₂ fold change unit of microarray data, with the exception of the DBC treatment group, where the unexpected down-regulation of Cyp1b1 expression was predicted but did not reach statistical significance on the microarrays. Adding CTE to DPE was predicted to increase Cyp1b1 expression, whereas adding CSC to CTE and DPE was predicted to have no effect, in agreement with microarray results. The aryl hydrocarbon receptor repressor (Ahrr) was determined to be the most significant input variable for model predictions using back-propagation and normalization of FNN weights. (C) 2012 Elsevier Inc. All rights reserved. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.elsevier.com/.

2012-12-20T00:00:00Z Chiaia-Hernandez, Aurea C. Banta-Green, Caleb J. Field, Jennifer A. http://hdl.handle.net/1957/37975 2013-04-03T00:57:49Z 2011-11-01T00:00:00Z

Interpreting Methamphetamine Levels in a High-Use Community Chiaia-Hernandez, Aurea C.; Banta-Green, Caleb J.; Field, Jennifer A. Illicit drug use is a largely hidden phenomenon and population measures are notoriously problematic. Reliable and valid data for local, regional and national public health and other interventions are needed. To address this information we examined temporal trends within and across weeks in methamphetamine (MA) in a single location in order to inform a sampling plan for understanding long-term trends in MA use based on sampling raw influent to waste water treatment plants. The measured concentrations in wastewater are used to estimate the total mass of MA consumed MA rather than the number of doses due to the uncertainty surrounding methamphetamine purity, mass of MA per dose, and the number of doses used per day. Results from a region with high levels of MA use indicate that MA levels do not differ significantly between weekdays and weekends (p=0.1), consistent with a predominately regular, daily use pattern use. The potential contribution of legal sales of d- and l-MA to the mass of MA consumed within the community was estimated to range from 3-8%. Limitations and uncertainties associated with estimating the mass of MA consumption include small contributions of prescription and over-the-counter drugs that are metabolized to MA as well as measurement and sampling variability. This is the author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Springer and can be found at: http://link.springer.com/journal/11356.

2011-11-01T00:00:00Z Thomas, Dennis G. Gaheen, Sharon Harper, Stacey L. Fritts, Martin Klaessig, Fred Hahn-Dantona, Elizabeth Paik, David Pan, Sue Stafford, Grace A. Freund, Elaine T. Klemm, Juli D. Baker, Nathan A. http://hdl.handle.net/1957/37919 2013-04-01T17:57:10Z 2013-01-14T00:00:00Z

ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format Thomas, Dennis G.; Gaheen, Sharon; Harper, Stacey L.; Fritts, Martin; Klaessig, Fred; Hahn-Dantona, Elizabeth; Paik, David; Pan, Sue; Stafford, Grace A.; Freund, Elaine T.; Klemm, Juli D.; Baker, Nathan A. Background and motivation: The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials. Results: We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata. Conclusion: The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by BioMed Central Ltd. and can be found at: http://www.biomedcentral.com/.

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