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Draft genome sequence of Therminicola potens strain JR

Description: 'Thermincola potens' strain JR is one of the first Gram-positive dissimilatory metal-reducing bacteria (DMRB) for which there is a complete genome sequence. Consistent with the physiology of this organism, preliminary annotation revealed an abundance of multiheme c-type cytochromes that are putatively associated with the periplasm and cell surface in a Gram-positive bacterium. Here we report the complete genome sequence of strain JR.
Date: July 1, 2010
Creator: Byrne-Bailey, K.G.; Wrighton, K.C.; Melnyk, R.A.; Agbo, P.; Hazen, T.C. & Coates, J.D.
Partner: UNT Libraries Government Documents Department

Delineating the major KREEP-bearing terranes on the moon with global measurements of absolute thorium abundances

Description: The Lunar Prospector (LP) Gamma-Ray Spectrometer (GRS) has been used to map the global composition of thorium on the lunar surface. Previous LP results of relative thorium abundances demonstrated that thorium is highly concentrated in and around the nearside western maria and less so in the South Pole Aitken (SPA) basin. Using new detector modeling results and a larger data set, the authors present here a global map of absolute thorium abundances on a 2{degree} by 2{degree} equal-area pixel scale. Because thorium is a tracer of KREEP-rich material, these data provide fundamental information regarding the locations and importance of terranes that are rich in KREEP bearing materials.
Date: March 1, 1999
Creator: Lawrence, D.J.; Feldman, W.C.; Barraclough, B.L.; Elphic, R.C.; Prettyman, T.H.; Binder, A.B. et al.
Partner: UNT Libraries Government Documents Department


Description: Determining columnar water vapor is a fundamental problem in remote sensing. This measurement is important both for understanding atmospheric variability and also from removing atmospheric effects from remotely sensed data. Therefore discovering a reliable and if possible automated method for determining water vapor column abundance is important. There are two standard methods for determining precipitable water vapor during the daytime from multi-spectral data. The first method is the Continuum Interpolated Band Ratio (CIBR) (see for example King et al. 1996). This method assumes a baseline and measures the depth of a water vapor feature as compared to this baseline. The second method is the Atmospheric Pre-corrected Differential Absorption technique (APDA) (see Schlaepfer et al. 1998); this method accounts for the path radiance contribution to the top of atmosphere radiance measurement which is increasingly important at lower and lower reflectance values. We have also developed two methods of modifying CIBR. We use a simple curve fitting procedure to account for and remove any systematic errors due to low reflectance while still preserving the random spread of the CIBR values as a function of surface reflectance. We also have developed a two-dimensional look-up table for CIBR; CIBR using this technique is a function of both water vapor (as with all CIBR techniques) and surface reflectance. Here we use data recently acquired with the Multi-spectral Thermal Imager spacecraft (MTI) to compare these four methods of determining columnar water vapor content.
Date: March 1, 2001
Creator: HIRSCH, K. & AL, ET
Partner: UNT Libraries Government Documents Department


Description: Atomic Mass Evaluations have had a major impact on the values of the atomic weights for the twenty mononuclidic elements plus two elements, Thorium and Protactinium, which have no stable nuclides but a characteristic terrestrial isotopic composition. This paper reviews the history of the atomic weight values of these elements in the years, since the reference mass standard changed from {sup 16}O to {sup 12}C. There is a problem for Thorium, which is considered to have an abundance value of 100%, but is not treated as such in the Standard Atomic Weights' Table. Recommendations for handling the Standard Atomic Weight values for 2001 are presented.
Date: June 29, 2001
Creator: HOLDEN, N.E.
Partner: UNT Libraries Government Documents Department

Determination of mineral abundances in samples from the Exploratory Studies Facility, Yucca Mountain, Nevada, using x-ray diffraction

Description: Tuff samples collected from the Exploratory Studies Facility (ESF) were X-rayed to estimate relative mineral abundances. X-ray analysis was performed on sub-samples of specimens collected from both the Single Heater Test (SHT) and Drift Scale Heater Test (MT) that were used for thermomechanical measurements, as well as samples collected from cores retrieved from boreholes in the Drift Scale Test Area. The abundance of minerals that could affect the behavior of the host rock at repository relevant temperatures is of particular interest. These minerals include cristobalite, which undergoes a phase transition and volume change at elevated temperature (-250 {degree}C), and smectite and clinoptilolite that can dehydrate at elevated temperature with accompanying volume reduction. In addition, the spatial distribution of Si02 polymorphs and secondary minerals may provide evidence for deducing past fluid pathways. The mineral abundances tabulated here include data reported previously in three milestone reports but reanalyzed, as well as previously unreported data.
Date: January 13, 1998
Creator: Roberts, S. & Viani, B.
Partner: UNT Libraries Government Documents Department

Proteomics: Technology and Applications

Description: This meeting took place at the Keystone, Colorado resort from March 25-30, 2003. It was attended by 206 participants, of which 35 were students; 39% of attendees submitted abstracts. The meeting had 30% returning attendees and 70% new attendees. The group of speakers was composed of internationally recruited junior and senior experts in their respective fields. The group included representatives from academia and the private sector, highlights the convergence of proteomics efforts in the two sectors. The completion of the genome sequences of a large number of prokaryotic and eukaryotic species has catalyzed new research approaches to study the structure, function and control of biological processes. They are characterized by the systematic and in many cases quantitative analysis of all the molecules of a particular type expressed by a cell or tissue. The systematic analysis of proteins has been terms ''proteomics''. In an initial phase, most of the proteomics efforts were focused on large-scale protein identification. More recently, the objectives and technologies of proteomics have been diversified and expanded. Current proteomics research attempts to systematically and, where applicable, quantitatively determine the many properties of proteins and their biological function, including: protein abundance, state of modification, specific activity, interaction with other biomolecules, half-life, subcelluar location, structure and more. Significant current challenges include the development of suitable technologies to determine these properties on a proteome-wide scale, the interpretation of the large amounts of data obtained, and the integration of different types of data into a coherent model describing a biological process. The scientific program of the meeting intended to provide an up-to-date overview of the breadth of proteomics research and of emerging and mature technologies. Special emphasis was placed on discussing how proteomics technologies intersect with biological and clinical research. This was accomplished by bringing together leading experts from the different areas ...
Date: March 25, 2003
Creator: Aebersold, Ruedi
Partner: UNT Libraries Government Documents Department


Description: A small number of type I supernovae exhibit well defined peculiarities. In particular some type I supernovae do not have the characteristic 6150 {angstrom} feature and some do not have the 1.2 {micro}m absorption. It is noted that all SN which lack the infrared absorption also lack the 6150 {angstrom} feature which is attributed to Si II. It is proposed that these supernovae constitute a single sub-class and that Si could be responsible for the strong unidentified infrared absorption which is characteristic of classical SNI. Si I has a dense array of strong lines in the near infrared so this ion could be responsible for the dominant features of SNIa IR behaviour. If this hypothesis is vindicated by subsequent observations or by calculation of synthetic spectra then it is most likely that the difference between ordinary supernovae and these peculiar ones is the abundance of Si.
Date: November 1, 1985
Creator: Graham, J.R.
Partner: UNT Libraries Government Documents Department

Measuring solar abundances

Description: This is the rapporteur paper of Working Group 2 on Measuring Solar Abundances. The working group presented and discussed the different observations and methods for obtaining the elemental and isotopic composition of the Sun, and critically reviewed their results and the accuracies thereof. Furthermore, a few important yet unanswered questions were identified, and the potential of future missions to provide answers was assessed.
Date: January 1, 2001
Creator: Reisenfeld, D. B. (Daniel B.); Von Steiger, R. (Rudolf); Vial, J.-C. (Jean-Claude); Bochsler, P.; Chaussidon, M.; Cohen, C. M. S. et al.
Partner: UNT Libraries Government Documents Department

Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

Description: Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by patterns in mutation, suggesting thatselection which causes their conservation is not always verystrong.
Date: February 21, 2007
Creator: Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S. & Dubchak, Inna
Partner: UNT Libraries Government Documents Department

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

Description: Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield greater than two orders of magnitude more sensitivity than traditional PCR-cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCRbased community structure profiling methods. We tested the effect of amplicon length and primer pair on estimates of species richness number of species and evenness relative abundance of species by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1-V2 or V8 regions, using amplicons ranging n length from 352 to 1443 bp. Our results demonstrate that both amplicon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities.
Date: December 1, 2009
Creator: Engelbrektson, Anna; Kunin, Victor; Wrighton, Kelly C.; Zvenigorodsky, Natasha; Chen, Feng; Ochman, Howard et al.
Partner: UNT Libraries Government Documents Department

Literature survey of isotopic abundance data for 1987-1989

Description: I have compiled all of the data on isotopic abundance measurements and their variation in nature for the time period since the last General Assembly. Most of the data deals with the variations in the abundances as given by per mil deviations from some standard. As such, they are not of major interest to the Atomic Weights Commission. However, there were some measurements which are of general interest in this list.
Date: August 9, 1989
Creator: Holden, N.E. (Brookhaven National Lab., Upton, NY (USA))
Partner: UNT Libraries Government Documents Department

Feasibility of eddy current measurement of ferrite content in stainless steel welds

Description: A phase-sensitive eddy current system was used to measure the presence of ferrite in an austenitic stainless steel matrix. Measurements were made on pressed powder specimens and on a weld in Type 304L stainless steel. The data obtained showed that small amounts of ferrite, on the order of 1 to 3%, could easily be detected. Variation in ferrite with position within the weld was also detected with good reproducibility. Absolute values for the ferrite content were not obtained as accurate standards for calibration were not available. (auth)
Date: December 17, 1973
Creator: Lassahn, G. D. & Moment, R. L.
Partner: UNT Libraries Government Documents Department

Age estimates of stratospheric air

Description: It is shown that careful consideration of /sup 32/P//sup 7/Be ratios (both isotopes being generated in the atmosphere by cosmic radiation) not only yields information on the stratospheric or tropospheric origin of air masses. These ratios may also be used to determine the residence time in the stratosphere of tropospheric air that underwent upward transport through the tropopause and re-entered the troposphere at a later date. (auth)
Date: August 1, 1973
Creator: Reiter, E.R.
Partner: UNT Libraries Government Documents Department

Transcriptional Profiling Using the Flowthrough Genosensor

Description: A Cooperative Research and Development Agreement (CRADA) between Lockheed Martin Energy Research Corporation (Contractor) and Gene Logic, Inc., (Participant) was carried out to evaluate the technical feasibility study of the application of the flowthrough genosensor for gene expression (transcriptional) profiling, over the current industry practice of using flat surface hybridization arrays to monitor the relative abundance of individual mRNA species in a cell. Various parameters, including substrate preparation, flow rates, hybridization conditions and sample concentrations, were evaluated on the flowthrough genosensor. The superiority of the flowthrough genosensor, in terms of hybridization rate and sensitivity were established.
Date: September 27, 1999
Creator: Doktycz, M.J.
Partner: UNT Libraries Government Documents Department

Assessment of Nonnative Invasive Plants in the DOE Oak Ridge National Environmental Research Park

Description: The Department of Energy (DOE) National Environmental Research Park at Oak Ridge, Tennessee, is composed of second-growth forest stands characteristic of much of the eastern deciduous forest of the Ridge and Valley Province of Tennessee. Human use of natural ecosystems in this region has facilitated the establishment of at least 167 nonnative, invasive plant species on the Research Park. Our objective was to assess the distribution, abundance, impact, and potential for control of the 18 most abundant invasive species on the Research Park. In 2000, field surveys were conducted of 16 management areas on the Research Park (14 Natural Areas, 1 Reference Area, and Walker Branch Watershed) and the Research Park as a whole to acquire qualitative and quantitative data on the distribution and abundance of these taxa. Data from the surveys were used to rank the relative importance of these species using the ''Alien Plant Ranking System, Version 5.1'' developed by the U.S. Geological Survey. Microstegium (Microstegium vimineum) was ranked highest, or most problematic, for the entire Research Park because of its potential impact on natural systems, its tendency to become a management problem, and how difficult it is to control. Microstegium was present in 12 of the 16 individual sites surveyed; when present, it consistently ranked as the most problematic invasive species, particularly in terms of its potential impact on natural systems. Japanese honeysuckle (Lonicera japonica) and Chinese privet (Ligustrum sinense) were the second- and third-most problematic plant species on the Research Park; these two species were present in 12 and 9 of the 16 sites surveyed, respectively, and often ranked second- or third-most problematic. Other nonnative, invasive species, in decreasing rank order, included kudzu (Pueraria montma), multiflora rose (Rosa multiflora), Chinese lespedeza (Lespedeza cuneara), and other species representing a variety of life forms and growth forms. Results ...
Date: November 5, 2002
Creator: Drake, S.J.
Partner: UNT Libraries Government Documents Department

The discovery of fullerenes in the 1.85 billion-year-old Sudbury meteorite crater

Description: Fullerenes (C{sub 60}, C{sub 70}) have been identified by laser time-of-flight and electron-ionization mass spectroscopy in rock samples (black tuff in the Onaping formation) from the crater. They were likely synthesized within the impact plume from carbon contained in the meteorite. The isotopic ratios suggest {sup 13}C enrichment. They are associated with sulfur which may have protected them. This is the largest known deposit of naturally occurring fullerenes.
Date: February 1, 1996
Creator: Becker, L.; Bada, J.L.; Winans, R.E.; Hunt, J.E.; Bunch, T.E. & French, B.M.
Partner: UNT Libraries Government Documents Department

Isotope tracers of organic carbon during artificial recharge

Description: This project developed an analytical technique for measuring the isotope abundance for 14C and 13C in total organic carbon (TOC) in order to test whether these measurements can trace TOC interaction with sedimentary material at the bottom of rivers and lakes, soils, and subsurface aquifer rocks.
Date: February 9, 1998
Creator: Davisson, M.L.
Partner: UNT Libraries Government Documents Department