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Field-grown transgenic switchgras (Panicum virgatum L.) with altered lignin does not affect soil chemistry, microbiology, and carbon storage potential

Description: This article describes a study to evaluate effects of two independent lines of caffeic acid O-methyltransferase (COMT) downregulated switchgrass plants on soils in terms of chemistry, microbiolgy, and carbon cycling when grown in the field.
Date: September 22, 2016
Creator: DeBruyn, Jennifer M.; Bevard, David A.; Essington, Michael E.; McKnight, Julie Y.; Schaeffer, Sean M.; Baxter, Holly L. et al.
Partner: UNT College of Arts and Sciences

Mesoscopic structure conditions the emergence of cooperation on social networks

Description: We study the evolutionary Prisoner's Dilemma on two social networks substrates obtained from actual relational data. We find very different cooperation levels on each of them that cannot be easily understood in terms of global statistical properties of both networks. We claim that the result can be understood at the mesoscopic scale, by studying the community structure of the networks. We explain the dependence of the cooperation level on the temptation parameter in terms of the internal structure of the communities and their interconnections. We then test our results on community-structured, specifically designed artificial networks, finding a good agreement with the observations in both real substrates. Our results support the conclusion that studies of evolutionary games on model networks and their interpretation in terms of global properties may not be sufficient to study specific, real social systems. Further, the study allows us to define new quantitative parameters that summarize the mesoscopic structure of any network. In addition, the community perspective may be helpful to interpret the origin and behavior of existing networks as well as to design structures that show resilient cooperative behavior.
Date: December 1, 2008
Creator: Lozano, S.; Arenas, A. & Sanchez, A.
Partner: UNT Libraries Government Documents Department

Mapping the evolution of scientific ideas

Description: Despite the apparent conceptual boundaries of scientific fields, a formal description for their evolution is lacking. Here we describe a novel approach to study the dynamics and evolution of scientific fields using a network-based analysis. We build an idea network consisting of American Physical Society PACS numbers as nodes representing scientific concepts. Two PACS numbers are linked if there exist publications that reference them simultaneously. We locate scientific fields using Cfinder, an overlapping community finding algorithm, and describe the time evolution of these fields using a community evolution method over the course of 1985-2006. The communities we identify map to known scientific fields, and their age strongly depends on t.heir size, impact and activity. Our analysis further suggests that communities that redefine themselves by merging and creating new groups of ideas tend to have more fitness as measured by the impact per paper, and hence communities with a higher fitness tend to be short-lived. The described approach to quantify the evolution of ideas may be relevant in making predictions about the future of science and how to guide its development.
Date: January 1, 2009
Creator: Roberts, David; Herrera, Mark & Gulbahce, Natali
Partner: UNT Libraries Government Documents Department

Of Institutions, Initiatives, and the Importance of Regional Academic Communities: Building NYCDH

Description: Video recording of a presentation at the 2016 Digital Frontiers Annual Conference. In this presentation, Kimon Keramidas and Alex Gil discuss how the New York City Digital Humanities group enables a wide variety of communities of practice, and the importance of regional communities in facilitating the growth of new academic fields, such as digital humanities.
Date: September 22, 2016
Creator: Keramidas, Kimon & Gil, Alex
Partner: UNT Libraries

U.S. Department of Energy (DOE) Technical Assistance to Beichuan Reconstruction: Creating and Designing Low- to Zero-carbon Communities in New Beichuan, Sichuan Province

Description: Beichuan county, located in north of Sichuan Province, was the most severely damaged township in last May's Sichuan earthquake. Reconstruction of a new Beichuan is a high-profiled project by the governments. In addition to constructing structurally-sound, quake-safe buildings in the new development, rebuilding Beichuan presents an opportunity for constructing new low- to zero-carbon communities in the region. In fact, building up greener communities in the reconstruction has become a top priority for the county, which, at an estimated 7 square km, is expected to have 50,000 residents in 2015 and 70,000 in 2020. The recent focus of construction projects is on the east side of the river, while land on its west bank will be reserved for development in the mid- to long-term. In the near term, a number of new public buildings are scheduled to be constructed starting in November 2009. As indicated by the deputy county chief, Mr. He Wang, the construction timeframe is unusually tight. Many buildings, although in various stages of planning and design, will be constructed starting in November 2009. Timely expert advice on design improvement and planning considerations will benefit the integration of energy efficiency and environmental benign elements in Beichuan's reconstruction, and will help promoting integrated development of green communities with low- to zero-carbon emission from the region.
Date: October 29, 2009
Creator: Xu, Tengfang; Wang, Chuang; Hong, Tianzhen & Levine, Mark
Partner: UNT Libraries Government Documents Department

HUD PowerSaver Pilot Loan Program

Description: The U.S. Department of Housing and Urban Development (HUD) recently announced the creation of a pilot loan program for home energy improvements. The PowerSaver loan program is a new, energy-focused variant of the Title I Property Improvement Loan Insurance Program (Title I Program) and is planned for introduction in early 2011. The PowerSaver pilot will provide lender insurance for secured and unsecured loans up to $25,000 to single family homeowners. These loans will specifically target residential energy efficiency and renewable energy improvements. HUD estimates the two-year pilot will fund approximately 24,000 loans worth up to $300 million; the program is not capped. The Federal Housing Administration (FHA), HUD's mortgage insurance unit, will provide up to $25 million in grants as incentives to participating lenders. FHA is seeking lenders in communities with existing programs for promoting residential energy upgrades.
Date: December 10, 2010
Creator: Zimring, Mark & Hoffman, Ian
Partner: UNT Libraries Government Documents Department

MILLIMETER-SCALE GENETIC GRADIENTS AND COMMUNITY-LEVEL MOLECULAR CONVERGENCE IN A HYPERSALINE MICROBIAL MAT

Description: To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter-scale genetic gradients that are consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near identical and acid-shifted isoelectric point profiles due to a molecular convergence of amino acid usage indicating that hypersalinity enforces an overriding selective pressure on the mat community.
Date: April 30, 2008
Creator: Fenner, Marsha W; Kunin, Victor; Raes, Jeroen; Harris, J. Kirk; Spear, John R.; Walker, Jeffrey J. et al.
Partner: UNT Libraries Government Documents Department

Effect of size heterogeneity on community identification in complex networks

Description: Identifying community structure can be a potent tool in the analysis and understanding of the structure of complex networks. Up to now, methods for evaluating the performance of identification algorithms use ad-hoc networks with communities of equal size. We show that inhomogeneities in community sizes can and do affect the performance of algorithms considerably, and propose an alternative method which takes these factors into account. Furthermore, we propose a simple modification of the algorithm proposed by Newman for community detection (Phys. Rev. E 69 066133) which treats communities of different sizes on an equal footing, and show that it outperforms the original algorithm while retaining its speed.
Date: January 1, 2008
Creator: Danon, L.; Diaz-Guilera, A. & Arenas, A.
Partner: UNT Libraries Government Documents Department

Accurate phylogenetic classification of DNA fragments based onsequence composition

Description: Metagenome studies have retrieved vast amounts of sequenceout of a variety of environments, leading to novel discoveries and greatinsights into the uncultured microbial world. Except for very simplecommunities, diversity makes sequence assembly and analysis a verychallenging problem. To understand the structure a 5 nd function ofmicrobial communities, a taxonomic characterization of the obtainedsequence fragments is highly desirable, yet currently limited mostly tothose sequences that contain phylogenetic marker genes. We show that forclades at the rank of domain down to genus, sequence composition allowsthe very accurate phylogenetic 10 characterization of genomic sequence.We developed a composition-based classifier, PhyloPythia, for de novophylogenetic sequence characterization and have trained it on adata setof 340 genomes. By extensive evaluation experiments we show that themethodis accurate across all taxonomic ranks considered, even forsequences that originate fromnovel organisms and are as short as 1kb.Application to two metagenome datasets 15 obtained from samples ofphosphorus-removing sludge showed that the method allows the accurateclassification at genus level of most sequence fragments from thedominant populations, while at the same time correctly characterizingeven larger parts of the samples at higher taxonomic levels.
Date: May 1, 2006
Creator: McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis; Hugenholtz, Philip & Rigoutsos, Isidore
Partner: UNT Libraries Government Documents Department

Microbial co-habitation and lateral gene transfer: what transposases can tell us

Description: Determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change over time. In this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with? All currently sequenced microbial genomes were surveyed to identify pairs of taxa that share a transposase that is likely to have been acquired through lateral gene transfer. A microbial interaction network including almost 800 organisms was then derived from these connections. Although the majority of the connections are between closely related organisms with the same or overlapping habitat assignments, numerous examples were found of cross-habitat and cross-phylum connections. We present a large-scale study of the distributions of transposases across phylogeny and habitat, and find a significant correlation between habitat and transposase connections. We observed cases where phylogenetic boundaries are traversed, especially when organisms share habitats; this suggests that the potential exists for genetic material to move laterally between diverse groups via bridging connections. The results presented here also suggest that the complex dynamics of microbial ecology may be traceable in the microbial genomes.
Date: March 1, 2009
Creator: Hooper, Sean D.; Mavromatis, Konstantinos & Kyrpides, Nikos C.
Partner: UNT Libraries Government Documents Department

Genome Sequence Databases (Overview): Sequencing and Assembly

Description: From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.
Date: January 1, 2009
Creator: Lapidus, Alla L.
Partner: UNT Libraries Government Documents Department

Toward Interoperable Mesh, Geometry and Field Components for PDE Simulation Development

Description: Mesh-based PDE simulation codes are becoming increasingly sophisticated and rely on advanced meshing and discretization tools. Unfortunately, it is still difficult to interchange or interoperate tools developed by different communities to experiment with various technologies or to develop new capabilities. To address these difficulties, we have developed component interfaces designed to support the information flow of mesh-based PDE simulations. We describe this information flow and discuss typical roles and services provided by the geometry, mesh, and field components of the simulation. Based on this delineation for the roles of each component, we give a high-level description of the abstract data model and set of interfaces developed by the Department of Energy's Interoperable Tools for Advanced Petascale Simulation (ITAPS) center. These common interfaces are critical to our interoperability goal, and we give examples of several services based upon these interfaces including mesh adaptation and mesh improvement.
Date: July 11, 2005
Creator: Chand, K K; Diachin, L F; Li, X; Ollivier-Gooch, C; Seol, E S; Shephard, M et al.
Partner: UNT Libraries Government Documents Department

Reconnaissance of Benthic Invertebrates from Tributary Streams of the Yampa and North Platte River Basins, Northwestern Colorado

Description: From purpose and scope: The study was designed to describe and quantify the benthic invertebrate communities in selected streams in coal mining areas. A secondary purpose was to compare the results with other data collected prior to this study and to assess possible changes in water quality reflected in the composition of the benthic invertebrate community.
Date: 1983
Creator: Britton, Linda J.
Partner: UNT Libraries Government Documents Department

Accumulation of Radioactivity in Columbia River Fish in the Vicinity of the Hanford Works

Description: Abstract: The data obtained from the radioassay of fish collected in vicinity of the Hanford Works between April, 1948 and June, 1950 are presented. Most of the radioactivity in the fish resulted from the concentration of p32 in the scales, bone, and certain visceral organs. The level of activity density in the fish was influenced by size, feeding habits and metabolic rate in addition to the activity density of the water. Changes in operation of nuclear reactors have resulted in progressive increases in activity densities of fish from one year to the next. The levels of radioactivity are not sufficiently high to be hazardous to either the fish or persons eating them.
Date: July 1, 1952
Creator: Olson, P. A. & Foster, Richard F.
Partner: UNT Libraries Government Documents Department

A Study Of The Perception Of Cataloging Quality Among Catalogers In Academic Libraries

Description: This study explores the concept of "quality" in library cataloging and examines the perception of quality cataloging among catalogers who work in academic libraries. An examination of the concept of "quality cataloging" in library science literature revealed that even though there is some general agreement on how this concept is defined, the level of detail and focus of these definitions often vary. These various perceptions were dissected in order to develop a framework for evaluating quality cataloging definitions; this framework was used to evaluate study participants' definitions of quality cataloging. Studying cataloger perceptions of quality cataloging is important because it is catalogers (particularly original catalogers) who are largely responsible for what is included in bibliographic records. Survey participants (n = 296) provided their personal definition of quality cataloging as well as their opinions on their department's cataloging, their influence upon their department's policies and procedures, and the specific data that should be included in a quality bibliographic record. Interview participants (n = 20) provided insight on how their opinions of quality cataloging were formed and the influences that shaped these opinions.
Date: December 2011
Creator: Snow, Karen
Partner: UNT Libraries

[Pottery workshop]

Description: Photograph of the Kiyomizu Pottery Community in Kyoto, Japan. A small workshop is visible in the foreground. Three workers sit and paint bowls while others walk around and observe. Rows of bowls and dishes line the back wall.
Date: 1978
Creator: Gough, Ray
Partner: UNT College of Visual Arts + Design

[Clay sculpture]

Description: Photograph of a the yard at the Kiyomizu Pottery Community in Kyoto, Japan. A clay sculpture is visible in the foreground in front of piles of wood. A chain link fence is visible in the background. Numerous people wait behind the fence.
Date: 1978
Creator: Gough, Ray
Partner: UNT College of Visual Arts + Design

[Community building]

Description: Photograph of the Kiyomizu Pottery Community building in Kyoto, Japan. The side of the building is visible in the foreground. Tree branches and a bush intersect the foreground. A concrete lantern and a white scroll are visible outside of the building.
Date: 1978
Creator: Gough, Ray
Partner: UNT College of Visual Arts + Design

[Kiyomizu Pottery Community]

Description: Photograph of the Kiyomizu Pottery Community in Kyoto, Japan. A workshop is visible in the foreground. A man faces the camera. He sits behind a shelf filled with white bowls. Another worker is visible in the background in front of a row of windows.
Date: 1978
Creator: Gough, Ray
Partner: UNT College of Visual Arts + Design