Assessment of the National Wind Coordinating Collaborative: Addressing Environmental and Siting Issues Associated with Wind Energy Development

The National Wind Coordinating Collaborative (NWCC) is a consensus-based stakeholder group comprised of representatives from the utility, wind industry, environmental, consumer, regulatory, power marketer, agricultural, tribal, economic development, and state and federal government sectors. The purpose of the NWCC is to support the development of an environmentally, economically, and politically sustainable commercial market for wind power (NWCC 2010). The NWCC has been funded by the U.S. Department of Energy (DOE) since its inception in 1994. In order to evaluate the impact of the work of the NWCC and how this work aligns with DOE’s strategic priorities, DOE tasked Pacific Northwest National Laboratory (PNNL) to conduct a series of informal interviews with a small sample of those involved with NWCC

CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures

We present CATHEDRAL, an iterative protocol for determining the location of previously observed protein folds in novel multidomain protein structures. CATHEDRAL builds on the features of a fast secondary-structure–based method (using graph theory) to locate known folds within a multidomain context and a residue-based, double-dynamic programming algorithm, which is used to align members of the target fold groups against the query protein structure to identify the closest relative and assign domain boundaries. To increase the fidelity of the assignments, a support vector machine is used to provide an optimal scoring scheme. Once a domain is verified, it is excised, and the search protocol is repeated in an iterative fashion until all recognisable domains have been identified. We have performed an initial benchmark of CATHEDRAL against other publicly available structure comparison methods using a consensus dataset of domains derived from the CATH and SCOP domain classifications. CATHEDRAL shows superior performance in fold recognition and alignment accuracy when compared with many equivalent methods. If a novel multidomain structure contains a known fold, CATHEDRAL will locate it in 90% of cases, with <1% false positives. For nearly 80% of assigned domains in a manually validated test set, the boundaries were correctly delineated within a tolerance of ten residues. For the remaining cases, previously classified domains were very remotely related to the query chain so that embellishments to the core of the fold caused significant differences in domain sizes and manual refinement of the boundaries was necessary. To put this performance in context, a well-established sequence method based on hidden Markov models was only able to detect 65% of domains, with 33% of the subsequent boundaries assigned within ten residues. Since, on average, 50% of newly determined protein structures contain more than one domain unit, and typically 90% or more of these domains are already classified in CATH, CATHEDRAL will considerably facilitate the automation of protein structure classification

Trait Correlations in the Genomics Era

© 2017 Elsevier Ltd Thinking about the evolutionary causes and consequences of trait correlations has been dominated by quantitative genetics theory that is focused on hypothetical loci. Since this theory was initially developed, technology has enabled the identification of specific genetic variants that contribute to trait correlations. Here, we review studies of the genetic basis of trait correlations to ask: What has this new information taught us? We find that causal variants can be pleiotropic and/or linked in different ways, indicating that pleiotropy and linkage are not alternative genetic mechanisms. Further, many trait correlations have a polygenic basis, suggesting that both pleiotropy and linkage likely contribute. We discuss implications of these findings for the evolutionary causes and consequences of trait correlations

The Dissociation of Vibrationally Excited CH3OSO Radicals and Their Photolytic Precurson, Methoxysulfinyl Chloride

I developed a synthesis of an unstable molecule that undergoes cleavage when exposed to light. Laurie Butler, in her lab at the University of Chicago, studied the rate of decay/bond dissociation for this molecule. It serves as a model for bond dissociation processes that occur with pollutant molecules in the upper atmosphere. --author-supplied descriptio

Archeological Impact Evaluations and Surveys in the Texas Department of Transportation\u27s Corpus Christi, Laredo, Pharr, and San Antonio Districts 2003-2005

This document constitutes the final report of work done by Prewitt and Associates, Inc. (PAI), under a contract from the Texas Department of Transportation (TxDOT) to provide archeological services in four TxDOT districts—Corpus Christi, Laredo, Pharr, and San Antonio. Under this contract, PAI completed Impact Evaluations and Surveys to assist TxDOT in meeting the requirements of their Memorandum of Understanding with the Texas Historical Commission and a Programmatic Agreement between the Advisory Council on Historic Preservation, the Federal Highway Administration, the Texas Historical Commission, and TxDOT. The contract began on March 17, 2003, and the last work authorization was issued on February 17, 2005. During those two years, fieldwork was done under 33 work authorizations. The 33 work authorizations consisted of 53 Impact Evaluations, 33 Surveys, and 2 Surveys with Geoarcheological Evaluation. Combined, these work authorizations entailed efforts at 47 bridge replacements, 4 bridge rehabilitation projects, 2 locations where new bridges will be built, 20 road rehabilitation or widening projects (many also involving bridge replacements or upgrades), 1 interstate highway rest area replacement, 3 drainage improvement projects, 2 curve realignment projects, 3 projects involving construction of new roads, 1 project involving construction of a railroad grade separation, 1 pedestrian bridge construction project, 1 project involving construction of a water taxi landing, 1 project involving construction of a hike-and-bike trail, 1 project involving modification of a highway interchange, and 1 project involving documentation of an archeological site disturbed by placement of a buried utility line. During completion of these work authorizations, 26 newly discovered or previously recorded archeological sites were investigated, although in the case of 9 previously recorded sites, no archeological remains were observed in the areas that will be impacted by the proposed Transportation Activities. Three of the Impact Evaluations led to recommendations that survey could be needed before construction, in some cases depending on whether new right of way would be required. The other 50 Impact Evaluations resulted in recommendations that no survey be required before construction based on the limited potential for sites with good integrity. Thirteen of the Surveys investigated a total of 3 newly recorded and 12 previously recorded sites. Of these 15 sites, 1 was considered eligible for listing in the National Register of Historic Places and designation as a State Archeological Landmark, and 1 was recommended as needing testing to assess eligibility. The other 33 Surveys either did not find any archeological sites, or they investigated sites that could be assessed as ineligible for National Register listing and State Archeological Landmark designation using the survey data. The records and artifacts generated by the project are curated at the Texas Archeological Research Laboratory

On the String Consensus Problem and the Manhattan Sequence Consensus Problem

In the Manhattan Sequence Consensus problem (MSC problem) we are given $k$ integer sequences, each of length $l$, and we are to find an integer sequence $x$ of length $l$ (called a consensus sequence), such that the maximum Manhattan distance of $x$ from each of the input sequences is minimized. For binary sequences Manhattan distance coincides with Hamming distance, hence in this case the string consensus problem (also called string center problem or closest string problem) is a special case of MSC. Our main result is a practically efficient $O(l)$-time algorithm solving MSC for $k\le 5$ sequences. Practicality of our algorithms has been verified experimentally. It improves upon the quadratic algorithm by Amir et al.\ (SPIRE 2012) for string consensus problem for $k=5$ binary strings. Similarly as in Amir's algorithm we use a column-based framework. We replace the implied general integer linear programming by its easy special cases, due to combinatorial properties of the MSC for $k\le 5$. We also show that for a general parameter $k$ any instance can be reduced in linear time to a kernel of size $k!$, so the problem is fixed-parameter tractable. Nevertheless, for $k\ge 4$ this is still too large for any naive solution to be feasible in practice.Comment: accepted to SPIRE 201

Phylogenetic Incongruence in E. coli O104: Understanding the Evolutionary Relationships of Emerging Pathogens in the Face of Homologous Recombination

Escherichia coli O104:H4 was identified as an emerging pathogen during the spring and summer of 2011 and was responsible for a widespread outbreak that resulted in the deaths of 50 people and sickened over 4075. Traditional phenotypic and genotypic assays, such as serotyping, pulsed field gel electrophoresis (PFGE), and multilocus sequence typing (MLST), permit identification and classification of bacterial pathogens, but cannot accurately resolve relationships among genotypically similar but pathotypically different isolates. To understand the evolutionary origins of E. coli O104:H4, we sequenced two strains isolated in Ontario, Canada. One was epidemiologically linked to the 2011 outbreak, and the second, unrelated isolate, was obtained in 2010. MLST analysis indicated that both isolates are of the same sequence type (ST678), but whole-genome sequencing revealed differences in chromosomal and plasmid content. Through comprehensive phylogenetic analysis of five O104:H4 ST678 genomes, we identified 167 genes in three gene clusters that have undergone homologous recombination with distantly related E. coli strains. These recombination events have resulted in unexpectedly high sequence diversity within the same sequence type. Failure to recognize or adjust for homologous recombination can result in phylogenetic incongruence. Understanding the extent of homologous recombination among different strains of the same sequence type may explain the pathotypic differences between the ON2010 and ON2011 strains and help shed new light on the emergence of this new pathogen

Archeological Impact Evaluations and Surveys in the Texas Department of Transportation\u27s Abilene, Austin, Brownwood, Bryan, Fort Worth, Waco, and Yoakum Districts, 2001-2003

This document constitutes the final report of work done by Prewitt and Associates, Inc. (PAI), under a contract from the Texas Department of Transportation (TxDOT) to provide archeological services in seven TxDOT districts—Abilene, Austin, Brownwood, Bryan, Fort Worth, Waco, and Yoakum. Under this contract, PAI completed Impact Evaluations and Surveys to assist TxDOT in meeting the requirements of their Memorandum of Understanding with the Texas Historical Commission and a Programmatic Agreement among the Advisory Council on Historic Preservation, the Federal Highway Administration, the Texas Historical Commission, and TxDOT. The contract began on 21 September 2001, and the last work authorization was issued on 15 September 2003. During those two years, fieldwork was done under 96 work authorizations. The 97 work authorizations consisted of 94 Impact Evaluations, 74 Surveys, and 14 Surveys with Geoarcheological Evaluation. Combined, these work authorizations entailed efforts at 128 bridge replacements, 40 road realignments or widening projects (many also involving bridge replacements), 5 new road construction projects, 4 hike-and-bike trail construction projects, 4 rest area construction projects, 3 projects involving upgrades to 9 existing bridges or culverts, 2 projects where new borrow pits are planned, 2 projects involving relocation of historic bridges to public parks, 1 project involving construction of 2 new bridges, 1 project involving replacement of an interstate highway interchange, and 1 project involving establishment of a wetland mitigation area. During completion of these work authorizations, 43 newly discovered or previously recorded archeological sites were investigated, although in the case of 14 previously recorded sites, no archeological remains were observed in the areas that will be affected by the proposed Transportation Activities. Twenty-three of the Impact Evaluations led to recommendations that survey could be needed before construction, in some cases depending on whether new right of way would be required. Based on the limited potential for sites with good integrity, the other 71 Impact Evaluations resulted in recommendations that no survey be required before construction. Twenty-two of the Surveys investigated a total of 17 newly recorded and 9 previously recorded sites. Of these 26 sites, 6 were recommended for testing to assess eligibility for listing in the National Register of Historic Places and designation as State Archeological Landmarks. The other 82 Surveys either did not find any archeological sites or investigated sites that could be assessed as ineligible for National Register listing and State Archeological Landmark designation using the survey data. All artifacts collected and records generated by projects done under this contract are curated at the Texas Archeological Research Laboratory (TARL), The University of Texas at Austin. Artifacts were collected from four sites. Those from 41GM3 are from state-owned lands and thus are curated in a held-in-trust status at TARL. The artifacts from 41BU51, 41BU54, and 41LE325 are from private lands and are curated in a non-held-in-trust status