https://www.uvm.edu/%7Egdrusche/Classes/GEOL%20295%20-%20Geomicrobiology/Khan%20et%20al.,%202004%20JEM%20-%20Remediation%20techniques%20overview.pdf

An overview and analysis of site remediation technologies

We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive procedure for finding read overlaps, a procedure for scoring overlaps that achieves high accuracy by correcting errors before assembly, read merger based on forward-reverse links, and detection of repeat contigs by forward-reverse link inconsistency. To test ARACHNE, we created simulated reads providing ∼10-fold coverage of the genomes of H. influenzae, S. cerevisiae, and D. melanogaster, as well as human chromosomes 21 and 22. The assemblies of these simulated reads yielded nearly complete coverage of the respective genomes, with a small number of contigs joined into a smaller number of supercontigs (or scaffolds). For example, analysis of the D. melanogaster genome yielded ∼98% coverage with an N50 contig length of 324 kb and an N50 supercontig length of 5143 kb. The assembly accuracy was high, although not perfect: small errors occurred at a frequency of roughly 1 per 1 Mb (typically, deletion of ∼1 kb in size), with a very small number of other misassemblies. The assembly was rapid: the Drosophila assembly required only 21 hours on a single 667 MHz processor and used 8.4 Gb of memory.

/pdf/arachne-a-whole-genome-shotgun-assembler-2hp3ckdckn.pdf

ARACHNE: A Whole-Genome Shotgun Assembler

Stable isotope fractionation analysis as a tool to monitor biodegradation in contaminated acquifers.

The advent of fast, relatively inexpensive (thus, widely available) microcomputers is transforming the way we analyze data in ecological and evolutionary research. Even more profound, however, are the associated changes in questions asked, empirical methods used, studies conducted, and interpretations offered. Now that an array of computation-intensive statistical methods is newly available for general use, it seems particularly important to assess their advantages and limitations, to note how they are currently being used, and then to consider implications for the future. I focus in this review on four related techniques known in the statistical and biological literature as randomization (or permutation) tests, Monte Carlo methods, bootstrapping, and the jackknife. I refer to them collectively as resampling methods, because each involves taking several-to-many samples from the original data set (randomization, bootstrap, jackknife) or from a stochastic process like the one believed to have generated the data set (Monte Carlo). Each of these methods is actually an extensive family of techniques and specific applications that cannot be thoroughly examined here; instead, I briefly characterize the focal methods and then survey the recent literature in ecology and evolution to identify the issues most frequently associated with these techniques. It emerges that resampling methods are well represented in

Resampling methods for computation-intensive data analysis in ecology and evolution

Tropospheric aqueous-phase chemistry: kinetics, mechanisms, and its coupling to a changing gas phase.

Overview of Natural Attenuation. Attenuation of Source Zones and Formation of Plumes. Abiotic Processes of Natural Attenuation. Overview of Intrinsic Bioremediation. Intrinsic Bioremediation of Petroleum Hydrocarbons. Intrinsic Bioremediation of Chlorinated Solvents. Evaluating Natural Attenuation. Modeling Natural Attenuation. Case Studies: Fuel Hydrocarbons. Case Studies: Chlorinated Solvents. Design of Long-Term Monitoring Programs. Appendices. Index.

Natural Attenuation of Fuels and Chlorinated Solvents in the Subsurface

Natural Attenuation of Fuels and Chlorinated Solvents in the Subsurface: Wiedemeier/Natural Attenuation of Fuels and Chlorinated Solvents in the Subsurface

Written for environmental scientists, engineers and others involved in the valuation and remediation of ground water, this book presents methods for dealing with the four major ground water issues facing us today: flow and contaminant transport processes, flow and transport modeling, field investigation methods, and ground water remediation. The authors explore methods for predicting rate and direction of flow in aquifer systems; review standard aquifer testing; discuss sources of ground water contamination, major contaminants, and nonaqueous phase liquids (NAPLs); and present detailed case studies.

Ground Water Contamination: Transport and Remediation

Performance and rebound of intensive source depletion technologies were evaluated at 59 chlorinated solvent sites where remediation targeted dense non–aqueous phase liquid (DNAPL) source zones. The four technologies included in the study are chemical oxidation, enhanced bioremediation, thermal treatment, and surfactant/cosolvent flushing. Performance was evaluated by examining temporal ground water concentration data before and after source remediation was performed. Results indicated that all four technologies have median concentration reductions of 88% or greater for the parent chlorinated volatile organic compound (CVOC). Approximately 75% of the source depletion projects were able to achieve a 70% reduction in parent compound concentrations. A median reduction in total CVOC concentrations (parent plus daughter compounds) of 72% was observed at 12 chemical oxidation sites and 62% at 21 enhanced bioremediation sites. Rebound was assessed at sites having at least 1 year of posttreatment data. Rebound occurrence was most prevalent at sites implementing chemical oxidation. At chemical oxidation sites where rebound was evaluated (n ¼ 7), the median parent CVOC concentration reduction was 90% immediately following treatment compared to 78% at the end of posttreatment monitoring (i.e., 1 to 5 years after treatment). For enhanced bioremediation sites where rebound was evaluated (n ¼ 10), median parent CVOC concentration reduction changed from 77% to 96% over the posttreatment monitoring period. Minimal concentration change was observed over the posttreatment monitoring period at surfactant/cosolvent sites (n ¼ 2) and thermal treatment sites (n ¼ 1) evaluated for rebound. Based on current data, none of the 59 source depletion projects was able to meet maximum contaminant levels throughout the treatment zone for all CVOCs.

http://www.eosremediation.com/download/Source%20Zones/Additional%20Source%20Zone%20Documents/McGuire%20et%20al.,%202006.pdf

Performance of DNAPL Source Depletion Technologies at 59 Chlorinated Solvent‐Impacted Sites

Chlorinated solvents such as trichloroethene (TCE) and tetrachloroethene (PCE) are widespread groundwater contaminants often released as dense nonaqueous phase liquids (DNAPLs). These contaminants ...

/pdf/chlorinated-ethene-source-remediation-lessons-learned-2p0zm3il16.pdf

Charles J. Newell

Papers

Natural Attenuation of Fuels and Chlorinated Solvents in the Subsurface

Natural Attenuation of Fuels and Chlorinated Solvents in the Subsurface: Wiedemeier/Natural Attenuation of Fuels and Chlorinated Solvents in the Subsurface

Ground Water Contamination: Transport and Remediation

Performance of DNAPL Source Depletion Technologies at 59 Chlorinated Solvent‐Impacted Sites

Chlorinated Ethene Source Remediation: Lessons Learned