Showing papers by "United States Department of Energy published in 2003"
TL;DR: The Human Genome Project has been the first major foray of the biological and medical research communities into “big science” and many of the lessons learned will be applicable to future large-scale projects in biology.
Abstract: The Human Genome Project has been the first major foray of the biological and medical research communities into “big science.” In this Viewpoint, we present some of our experiences in organizing and managing such a complicated, publicly funded, international effort. We believe that many of the lessons we learned will be applicable to future large-scale projects in biology.
1,097 citations
TL;DR: The results demonstrate that in situ bioremediation of uranium-contaminated groundwater is feasible but suggest that the strategy should be optimized to better maintain long-term activity of Geobacter species.
Abstract: The potential for removing uranium from contaminated groundwater by stimulating the in situ activity of dissimilatory metal-reducing microorganisms was evaluated in a uranium-contaminated aquifer located in Rifle, Colo. Acetate (1 to 3 mM) was injected into the subsurface over a 3-month period via an injection gallery composed of 20 injection wells, which was installed upgradient from a series of 15 monitoring wells. U(VI) concentrations decreased in as little as 9 days after acetate injection was initiated, and within 50 days uranium had declined below the prescribed treatment level of 0.18 μM in some of the monitoring wells. Analysis of 16S ribosomal DNA (rDNA) sequences and phospholipid fatty acid profiles demonstrated that the initial loss of uranium from the groundwater was associated with an enrichment of Geobacter species in the treatment zone. Fe(II) in the groundwater also increased during this period, suggesting that U(VI) reduction was coincident with Fe(III) reduction. As the acetate injection continued over 50 days there was a loss of sulfate from the groundwater and an accumulation of sulfide and the composition of the microbial community changed. Organisms with 16S rDNA sequences most closely related to those of sulfate reducers became predominant, and Geobacter species became a minor component of the community. This apparent switch from Fe(III) reduction to sulfate reduction as the terminal electron accepting process for the oxidation of the injected acetate was associated with an increase in uranium concentration in the groundwater. These results demonstrate that in situ bioremediation of uranium-contaminated groundwater is feasible but suggest that the strategy should be optimized to better maintain long-term activity of Geobacter species.
906 citations
TL;DR: In this paper, a series of new mesoporous silica materials with MCM-41 type of structure containing a homogeneous layer of organic functional groups inside the pores was prepared using a co-condensation method under low surfactant concentration condition.
Abstract: A series of new mesoporous silica materials with MCM-41 type of structure containing a homogeneous layer of organic functional groups inside the pores was prepared using a co-condensation method under low surfactant concentration condition. This reproducible synthetic approach resulted in high surface coverage with several functional groups such as a primary amine, secondary amine, urea, isocyanate, vinyl, and nitrile. In addition, the presence of organoalkoxysilane precursors during the base catalyzed condensation greatly influenced the final particle shape. By changing the precursor or its concentration, the particle morphology was tuned to various shapes, including spheres, tubes, and rods of various dimensions. The synthetic procedures that gave rise to the specific particle morphologies were investigated and the mechanism responsible for shape control was postulated. The structure and functionality of these materials were characterized by field-emission scanning electron microscopy, transmission elec...
749 citations
TL;DR: One category of functional sequences postulated to lie in gene deserts is gene regulatory sequences, which are related to transcriptional regulation and regulation of transcriptional reprograming.
Abstract: Approximately 25% of the genome consists of gene-poor regions greater than 500 kb, termed gene deserts ([ 1 ][1]). These segments have been minimally explored, and their functional significance remains elusive. One category of functional sequences postulated to lie in gene deserts is gene regulatory
644 citations
TL;DR: This experimental verification of negative refraction of electromagnetic waves in a two-dimensional dielectric photonic crystal that has a periodically modulated positive permittivity and a permeability of unity is demonstrated.
Abstract: Materials that can bend light in the opposite direction to normal ('left-handed' materials) reverse the way in which refraction usually works — this negative refractive index is due to simultaneously negative permeability and permittivity1,2,3. Here we demonstrate negative refraction of electromagnetic waves in a two-dimensional dielectric photonic crystal that has a periodically modulated positive permittivity and a permeability of unity4,5,6. This experimental verification of negative refraction is a step towards the realization of a 'superlens' that will be able to focus features smaller than the wavelength of light.
635 citations
TL;DR: The utility of intraprimate sequence comparisons to discover common mammalian as well as primate-specific functional elements in the human genome, which are unattainable through the evaluation of more evolutionarily distant species are demonstrated.
Abstract: Nonhuman primates represent the most relevant model organisms to understand the biology of Homo sapiens. The recent divergence and associated overall sequence conservation between individual members of this taxon have nonetheless largely precluded the use of primates in comparative sequence studies. We used sequence comparisons of an extensive set of Old World and New World monkeys and hominoids to identify functional regions in the human genome. Analysis of these data enabled the discovery of primate-specific gene regulatory elements and the demarcation of the exons of multiple genes. Much of the information content of the comprehensive primate sequence comparisons could be captured with a small subset of phylogenetically close primates. These results demonstrate the utility of intraprimate sequence comparisons to discover common mammalian as well as primate-specific functional elements in the human genome, which are unattainable through the evaluation of more evolutionarily distant species.
556 citations
TL;DR: Results from animal experiments indicate that antioxidant nutrients, such as vitamin E and selenium compounds, are protective against lethality and other radiation effects but to a lesser degree than most synthetic protectors.
555 citations
TL;DR: In this article, an amine-grafted SBA-15 adhesively adsorbed CO2 as carbonates and bicarbonates with a total capacity of 200−400 μmol/g.
Abstract: CO2 adsorption/desorption on SBA-15 grafted with γ-(aminopropyl)triethoxysilane (APTS) has been studied by infrared spectroscopy coupled with temperature-programmed desorption. SBA-15, a mesoporous silica material with a uniform pore size of 21 nm and a surface area of 200−230 m2/g, provides an OH functional group for grafting of γ-(aminopropyl)triethoxysilane. The amine-grafted SBA-15 adsorbed CO2 as carbonates and bicarbonates with a total capacity of 200−400 μmol/g. The heat of CO2 desorption was determined to be 3.2−4.5 kJ/mol in the presence of H2O and 6.6−11.0 kJ/mol in the absence of H2O during temperature-programmed desorption. Repeated CO2 adsorption/desorption CO2 cycles shifted the desorption peak temperature downward and decreased the heat of CO2 adsorption.
399 citations
TL;DR: It is shown that Collembola, a wingless group traditionally considered as basal to all insects, appears instead to constitute a separate evolutionary lineage that branched much earlier than the separation of many crustaceans and insects and independently adapted to life on land.
Abstract: Recent morphological and molecular evidence has changed interpretations of arthropod phylogeny and evolution. Here we compare complete mitochondrial genomes to show that Collembola, a wingless group traditionally considered as basal to all insects, appears instead to constitute a separate evolutionary lineage that branched much earlier than the separation of many crustaceans and insects and independently adapted to life on land. Therefore, the taxon Hexapoda, as commonly defined to include all six-legged arthropods, is not monophyletic.
375 citations
TL;DR: In this article, solvent degradation from reversible chemical absorption using monoethanolamine (MEA) solvent was studied using degraded MEA samples from the IMC Chemicals Facility in Trona, California.
Abstract: One of the highest priorities in carbon sequestration science is the development of techniques for CO2 separation and capture, because it is expected to account for the majority of the total cost (∼75%). The most common currently used method of CO2 separation is reversible chemical absorption using monoethanolamine (MEA) solvent. In the current study, solvent degradation from this technique was studied using degraded MEA samples from the IMC Chemicals Facility in Trona, California. A major pathway to solvent degradation that had not been previously observed in laboratory experiments has been identified. This pathway, which is initiated by oxidation of the solvent, is a much more significant source of solvent degradation than the previously identified carbamate dimerization mechanism.
348 citations
TL;DR: In this paper, the authors measured the permeability of hydrogen in bulk palladium membranes (approximately 1-mm thickness) at conditions of simultaneously elevated temperature (623-1173 K) and hydrogen pressure (0.1×106 to 2.76×106 ǫ).
TL;DR: Genome-wide sequence analysis in the invertebrate chordate, Ciona intestinalis, has provided a comprehensive picture of immune-related genes in an organism that occupies a key phylogenetic position in vertebrate evolution, suggesting that activating and inhibitory receptors have an MHC-independent function and an early evolutionary origin.
Abstract: Genome-wide sequence analysis in the invertebrate chordate, Ciona intestinalis, has provided a comprehensive picture of immune-related genes in an organism that occupies a key phylogenetic position in vertebrate evolution. The pivotal genes for adaptive immunity, such as the major histocompatibility complex (MHC) class I and II genes, T-cell receptors, or dimeric immunoglobulin molecules, have not been identified in the Ciona genome. Many genes involved in innate immunity have been identified, including complement components, Toll-like receptors, and the genes involved in intracellular signal transduction of immune responses, and show both expansion and unexpected diversity in comparison with the vertebrates. In addition, a number of genes were identified which predicted integral membrane proteins with extracellular C-type lectin or immunoglobulin domains and intracellular immunoreceptor tyrosine-based inhibitory motifs (ITIMs) and immunoreceptor tyrosine-based activation motifs (ITAMs) (plus their associated signal transduction molecules), suggesting that activating and inhibitory receptors have an MHC-independent function and an early evolutionary origin. A crucial component of vertebrate adaptive immunity is somatic diversification, and the recombination activating genes (RAG) and activation-induced cytidine deaminase (AID) genes responsible for the Generation of diversity are not present in Ciona. However, there are key V regions, the essential feature of an immunoglobulin superfamily VC1-like core, and possible proto-MHC regions scattered throughout the genome waiting for Godot.
TL;DR: In this article, a pressure-swing adsorption process, which uses zeolite 13X as an adsorbent to recover and sequester carbon dioxide from mixture gas (nitrogen and carbon dioxide), is investigated through dynamic simulation and optimization.
Abstract: A pressure-swing adsorption process, which uses zeolite 13X as an adsorbent to recover and sequester carbon dioxide from mixture gas (nitrogen and carbon dioxide), is investigated through dynamic simulation and optimization. The purpose of this paper is to improve the purity of each component by finding optimal values of decision variables with a given power constraint. Langmuir isotherm parameters are calculated from experimental data of zeolite 13X and a general mathematical model consisting of a set of partial differential and algebraic equations and solved in gPROMS. The method of centered finite differences is adopted for the discretization of the spatial domains, and a reduced space SQP method is used for the optimization. As a result, the optimal conditions at cyclic steady state are obtained.
TL;DR: In this article, the effects of anion type, C-2 hydrogen substitution, and alkyl chain length on the flammability, thermal stability, and phase change characteristics of 1,2,3-trialkylimidazolium room temperature ionic liquids were investigated.
TL;DR: The draft genome sequence and cDNA/EST database of the basal chordate Ciona intestinalis are searched to reveal the repertoire of homeodomain-containing transcription factors in the Ciona genome, which will be useful for future research on the development and evolution of chordates.
Abstract: Homeobox-containing genes play crucial roles in various developmental processes, including body-plan specification, pattern formation and cell-type specification. The present study searched the draft genome sequence and cDNA/EST database of the basal chordate Ciona intestinalis to identify 83 homeobox-containing genes in this animal. This number of homeobox genes in the Ciona genome is smaller than that in the Caenorhabditis elegans, Drosophila melanogaster, human and mouse genomes. Of the 83 genes, 76 have possible human orthologues and 7 may be unique to Ciona. The ascidian homeobox genes were classified into 11 classes, including Hox class, NK class, Paired class, POU class, LIM class, TALE class, SIX class, Prox class, Cut class, ZFH class and HNF1 class, according to the classification scheme devised for known homeobox genes. As to the Hox cluster, the Ciona genome contains single copies of each of the paralogous groups, suggesting that there is a single Hox cluster, if any, but genes orthologous to Hox7, 8, 9 and 11 were not found in the genome. In addition, loss of genes had occurred independently in the Ciona lineage and was noticed in Gbx of the EHGbox subclass, Sax, NK3, Vax and vent of the NK class, Cart, Og9, Anf and Mix of the Paired class, POU-I, III, V and VI of the POU class, Lhx6/7 of the LIM class, TGIF of the TALE class, Cux and SATB of the Cut class, and ZFH1 of the ZFH class, which might have reduced the number of Ciona homeobox genes. Interestingly, one of the newly identified Ciona intestinalis genes and its vertebrate counterparts constitute a novel subclass of HNF1 class homeobox genes. Furthermore, evidence for the gene structures and expression of 54 of the 83 homeobox genes was provided by analysis of ESTs, suggesting that cDNAs for these 54 genes are available. The present data thus reveal the repertoire of homeodomain-containing transcription factors in the Ciona genome, which will be useful for future research on the development and evolution of chordates.
TL;DR: In this article, the authors give an overview of the different ways the wind resource at a site can be estimated, and the advantages and disadvantages of each of them are discussed in detail.
Abstract: This article gives an overview of the different ways the wind resource at a site can be estimated. Eight separate ways have been identified. Each of these will be described in some detail, and advantages and disadvantages of each of them will be discussed. Copyright © 2003 John Wiley & Sons, Ltd.
TL;DR: In this article, a review of passive methods used to improve the stability of low-emission combustors in stationary power gas turbines is presented, and Nyquist analysis is used to show how changing the time lag can be confounded by the presence of multiple acoustic modes.
Abstract: This paper summarizes passive methods used to improve the stability of low-emission combustors in stationary power gas turbines. Common passive methods are reviewed, including discussion of control model concepts, application of simple time-lag models, and a review of acoustic dampers. Applications of time-lag modie cations are presented, and limitations of this approach are discussed. Nyquist analysis is used to show how changing the time lag can be confounded by the presence of multiple acoustic modes. Experimental results demonstrating the frequency shifts predicted by Nyquist analysis are also shown. Stabilizing effects of distributed time lags are discussed, along with some e eld applications. A review of acousticdampers showsthat these devices are not widely applied in stationary engines compared to rocket or afterburner combustors, but have shown good results where applied. Nomenclature ¤ AB;C; D, = combustor sections and the acoustic E; F; G transfer matrices that represent these sections; elements of these 2 £2 matrices are identie ed using subscripts Ai;j where i D0;1 and j D0;1 c
TL;DR: In this paper, a volumetric gas adsorption of CO2, N 2, and O 2 on three natural zeolites, with different major cations, was conducted at 25 °C up to a pressure of 300 psi (2 10 6 Pa).
Abstract: Pressure swing adsorption (PSA) and temperature swing adsorption are potential techniques for removing CO2 from high-pressure fuel gas streams. Natural zeolites are suitable candidate sorbents for use in the PSA process. Studies of volumetric gas adsorption of CO2 ,N 2, and O2 on three natural zeolites, with different major cations, were conducted at 25 °C up to a pressure of 300 psi (2 10 6 Pa). Preferential adsorption of CO2 was observed with all three zeolites. The natural zeolite with the highest sodium content and highest surface area showed the highest CO2 adsorption capacity. Competitive gas adsorption studies also showed that the zeolite with the highest sodium content gave the best separation of CO2 from the gas mixtures. Contact time did not affect the extent of adsorption of the zeolites. Temperature-programmed desorption studies indicated that the majority of the physically adsorbed CO2 was desorbed at room temperature, while some strongly bound CO2 was desorbed at 115 °C.
TL;DR: An overview of the different methods used today for predicting the power output from wind farms on the 1-2 day time horizon is given in this article, where the authors describe the general set-up of such prediction systems and also give examples of their performance.
Abstract: This article gives an overview of the different methods used today for predicting the power output from wind farms on the 1–2 day time horizon It describes the general set-up of such prediction systems and also gives examples of their performance Copyright © 2003 John Wiley & Sons, Ltd
TL;DR: In this paper, a set of new techniques with significantly improved accuracy and precision has been developed and qualified for isotope ratio measurements of nuclear material using thermal ionization mass spectrometry (TIMS).
TL;DR: In this article, a molecular model for the adsorption of CO2, N2, H2, and their mixtures in dehydrated zeolite Na-4A is presented.
Abstract: We present a molecular model for the adsorption of CO2, N2, H2, and their mixtures in dehydrated zeolite Na-4A. The interatomic potentials for this model were developed by comparing the results of grand canonical Monte Carlo (GCMC) simulations of single-component adsorption at room temperature with experimental measurements. GCMC simulation is also used to assess the adsorption selectivity of CO2/N2 and CO2/H2 mixtures, as a function of temperature and gas-phase composition. At room temperature, Na-4A is strongly selective for CO2 over both N2 and H2, although this selectivity decreases slightly as the gas-phase pressure increases. Ideal adsorbed solution theory is shown to give accurate predictions of the adsorption selectivity at low CO2 partial pressures, provided that a functional form that accurately describes the CO2 single-component isotherm is used. The adsorption properties of CO2/N2 mixtures in Na-4A are compared to the same mixtures in silicalite.
TL;DR: Exposures to doses of radiation of 1–10 Gy, defined in this workshop as moderate-dose radiation, may occur during the course of radiation therapy or as the result of radiation accidents or nuclear/radiological terrorism alone or in conjunction with bioterrorism.
Abstract: Coleman, C. N., Blakely, W. F., Fike, J. R., MacVittie, T. J., Metting, N. F., Mitchell, J. B., Moulder, J. E., Preston, R. J., Seed, T. M., Stone, H. B., Tofilon, P. J. and Wong, R. S. L. Molecular and Cellular Biology of Moderate-Dose (1–10 Gy) Radiation and Potential Mechanisms of Radiation Protection: Report of a Workshop at Bethesda, Maryland, December 17–18, 2001. Radiat. Res. 159, 812–834 (2003). Exposures to doses of radiation of 1–10 Gy, defined in this workshop as moderate-dose radiation, may occur during the course of radiation therapy or as the result of radiation accidents or nuclear/radiological terrorism alone or in conjunction with bioterrorism. The resulting radiation injuries would be due to a series of molecular, cellular, tissue and whole-animal processes. To address the status of research on these issues, a broad-based workshop was convened. The specific recommendations were: (1) Research: Identify the key molecular, cellular and tissue pathways that lead from the initial mol...
Patent•
31 Oct 2003TL;DR: A number of materials with the composition Li 1+x Ni α Mn β Co γ M′ δ O 2−z F z (M′=Mg,Zn,Al,Ga,B,Zr,Ti) for use with rechargeable batteries are presented in this article.
Abstract: A number of materials with the composition Li 1+x Ni α Mn β Co γ M′ δ O 2−z F z (M′=Mg,Zn,Al,Ga,B,Zr,Ti) for use with rechargeable batteries, wherein x is between about 0 and 0.3, α is between about 0.2 and 0.6, β is between about 0.2 and 0.6, γ is between about 0 and 0.3, δ is between about 0 and 0.15, and z is between about 0 and 0.2. Adding the above metal and fluorine dopants affects capacity, impedance, and stability of the layered oxide structure during electrochemical cycling.
TL;DR: In this paper, a simulation of premixed ozone (O 3 ) decomposition in a bubbling fluidized bed using the multiphase CFD code MFIX was conducted. And the grid-independent results were in very good agreement with reported experimental data on total conversion over a range of fluidization velocities and initial bed heights.
Abstract: Recent advances in dense, multiphase, computational fluid dynamics (CFD) have allowed accurate simulation of the gas and particle motion in bubbling and circulating fluidized beds. Since fluidized-bed reactors are used for many chemical processes, a simulation must also be able to accurately couple chemical reactions to bed hydrodynamics. The catalytic decomposition of ozone (O 3 ) often has been used to study experimentally the contacting behavior of catalytic reactors. Simulations of laboratory-scale experiments of premixed O 3 decomposition in a bubbling fluidized bed using the multiphase CFD code MFIX were conducted. The grid-independent results are in very good agreement with reported experimental data on total conversion over a range of fluidization velocities and initial bed heights. This confirms the ability of multiphase hydrodynamic models to capture quantitatively the effect of hydrodynamics on chemical reactions in a bubbling fluidized bed.
TL;DR: These values are targets that can be considered in plant breeding programmes aimed at maximizing carbon or energy retention from photosynthate and analyses of (minimum) metabolic costs of responding to environmental change or pest attack involving increased lignin biosynthesis.
TL;DR: In this article, the authors present the test results and analysis of the power and capacity fade resulting from the cycle-life testing using PNGV (now referred to as FreedomCAR) test protocols at 25 and 45°C of 18650-size Li-ion batteries developed by the US Department of Energy sponsored Advanced Technology Development (ATD) Program.
TL;DR: The present analysis provides an insight into the basic set of bHLH genes that the last common ancestor of ascidian and vertebrates had, and will provide important background information for future studies using ascidians as a model system for vertebrate development.
Abstract: The basic helix-loop-helix (bHLH) proteins are transcription factors that play important roles in many biological processes, including the development of various animals. We identified 46 genes encoding bHLH proteins in the draft genome sequence of the basal chordate Ciona intestinalis. These 46 genes represent an almost complete set of bHLH genes in this animal. This number is comparable to 39 and 58 bHLH genes in those of Caenorhabditis elegans and Drosophila melanogaster but is much smaller than the 125 in the human genome. Genes that encode NeuroD, Beta3, Oligo, SCL, NSCL, SRC, Clock and Bmal were not found in the Ciona genome. We could also identify groucho and CBP orthologues in the Ciona genome. In addition, the comparison between the numbers of orthologous human and Ciona bHLH factors reveals the simplicity of the Ciona genome, in accordance with its phylogenetic position within chordates. The present analysis provides an insight into the basic set of bHLH genes that the last common ancestor of ascidians and vertebrates had, and will provide important background information for future studies using ascidians as a model system for vertebrate development.
TL;DR: In an attempt to maximize the uptake of methane during methane hydrate formation, the addition of sodium dodecyl sulfate provided methane uptake of over 97% of the theoretical maximum uptake as discussed by the authors.
TL;DR: In this article, a ship-mounted sodar was used to measure wind turbine wakes in an offshore wind farm in Denmark, where the wake magnitude and vertical extent were determined by measuring the wind speed profile behind an operating turbine, then shutting down the turbine and measuring the freestream wind profile.
Abstract: A ship-mounted sodar was used to measure wind turbine wakes in an offshore wind farm in Denmark. The wake magnitude and vertical extent were determined by measuring the wind speed profile behind an operating turbine, then shutting down the turbine and measuring the freestream wind profile. These measurements were compared with meteorological measurements on two offshore and one coastal mast at the same site. The main purposes of the experiment were to evaluate the utility of sodar for determining wind speed profiles offshore and to provide the first offshore wake measurements with varying distance from a wind turbine. Over the course of a week, 36 experiments were conducted in total. After quality control of the data (mainly to exclude rain periods), 13 turbine-on, turbine-off pairs were analyzed to provide the velocity deficit at hub height as a function of the distance from the turbine. The results are presented in the context of wake measurements at other coastal locations. The velocity defici...