Showing papers by "Argonne National Laboratory published in 2008"
TL;DR: A fully automated service for annotating bacterial and archaeal genomes that identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user.
Abstract: The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12–24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.
9,397 citations
TL;DR: The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes that is stable, extensible, and freely available to all researchers.
Abstract: Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers. A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats. The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis – the availability of high-performance computing for annotating the data. http://metagenomics.nmpdr.org
3,322 citations
TL;DR: Nanoalloys of Group 11 (Cu, Ag, Au) 865 5.1.5.2.
Abstract: 5.1. Nanoalloys of Group 11 (Cu, Ag, Au) 865 5.1.1. Cu−Ag 866 5.1.2. Cu−Au 867 5.1.3. Ag−Au 870 5.1.4. Cu−Ag−Au 872 5.2. Nanoalloys of Group 10 (Ni, Pd, Pt) 872 5.2.1. Ni−Pd 872 * To whom correspondence should be addressed. Phone: +39010 3536214. Fax:+39010 311066. E-mail: ferrando@fisica.unige.it. † Universita di Genova. ‡ Argonne National Laboratory. § University of Birmingham. | As of October 1, 2007, Chemical Sciences and Engineering Division. Volume 108, Number 3
3,114 citations
TL;DR: This work has shown that coherent oscillations of conduction electrons on a metal surface excited by electromagnetic radiation at a metal -dielectric interface can be associated with surface plasmons, which have potential applications in miniaturized optical devices, sensors, and photonic circuits.
Abstract: Surface plasmons (SPs) are coherent oscillations of conduction electrons on a metal surface excited by electromagnetic radiation at a metal -dielectric interface. The growing field of research on such light -metal interactions is known as ‘plasmonics’. 1-3 This branch of research has attracted much attention due to its potential applications in miniaturized optical devices, sensors, and photonic circuits as well as in medical diagnostics and therapeutics. 4-8
2,284 citations
TL;DR: It is shown that the choice of DNA sequences attached to the nanoparticle building blocks, the DNA linking molecules and the absence or presence of a non-bonding single-base flexor can be adjusted so that gold nanoparticles assemble into micrometre-sized face-centred-cubic or body- Centred- cubic crystal structures.
Abstract: It was first shown more than ten years ago that DNA oligonucleotides can be attached to gold nanoparticles rationally to direct the formation of larger assemblies. Since then, oligonucleotide-functionalized nanoparticles have been developed into powerful diagnostic tools for nucleic acids and proteins, and into intracellular probes and gene regulators. In contrast, the conceptually simple yet powerful idea that functionalized nanoparticles might serve as basic building blocks that can be rationally assembled through programmable base-pairing interactions into highly ordered macroscopic materials remains poorly developed. So far, the approach has mainly resulted in polymerization, with modest control over the placement of, the periodicity in, and the distance between particles within the assembled material. That is, most of the materials obtained thus far are best classified as amorphous polymers, although a few examples of colloidal crystal formation exist. Here, we demonstrate that DNA can be used to control the crystallization of nanoparticle-oligonucleotide conjugates to the extent that different DNA sequences guide the assembly of the same type of inorganic nanoparticle into different crystalline states. We show that the choice of DNA sequences attached to the nanoparticle building blocks, the DNA linking molecules and the absence or presence of a non-bonding single-base flexor can be adjusted so that gold nanoparticles assemble into micrometre-sized face-centred-cubic or body-centred-cubic crystal structures. Our findings thus clearly demonstrate that synthetically programmable colloidal crystallization is possible, and that a single-component system can be directed to form different structures.
1,366 citations
Michigan State University1, J. Craig Venter Institute2, National Institutes of Health3, Wellcome Trust Sanger Institute4, Plymouth Marine Laboratory5, University of Maryland, Baltimore6, University of Cambridge7, University of York8, United States Department of Energy9, Ghent University10, Pennsylvania State University11, Argonne National Laboratory12, University of California, San Diego13, Jacobs University Bremen14, University of Colorado Boulder15, National Science Foundation16, Edinburgh Napier University17, Boston Children's Hospital18, University of Georgia19, University of California, Berkeley20, Newcastle University21, Lawrence Berkeley National Laboratory22, University of California, Irvine23, University of Oxford24, Howard University25, Abertay University26, University of Manchester27, Technical University of Denmark28, University of Wyoming29, University of Pennsylvania30, University of New Mexico31
TL;DR: Here, the minimum information about a genome sequence (MIGS) specification is introduced with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange.
Abstract: With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.
1,097 citations
TL;DR: Multiwalled carbon nanotubes with a mean fracture strength >100 GPa are reported, which exceeds earlier observations by a factor of approximately three and are in excellent agreement with quantum-mechanical estimates for nanot tubes containing only an occasional vacancy defect, and are approximately 80% of the values expected for defect-free tubes.
Abstract: The excellent mechanical properties of carbon nanotubes are being exploited in a growing number of applications from ballistic armour to nanoelectronics. However, measurements of these properties have not achieved the values predicted by theory due to a combination of artifacts introduced during sample preparation and inadequate measurements. Here we report multiwalled carbon nanotubes with a mean fracture strength >100 GPa, which exceeds earlier observations by a factor of approximately three. These results are in excellent agreement with quantum-mechanical estimates for nanotubes containing only an occasional vacancy defect, and are ∼80% of the values expected for defect-free tubes. This performance is made possible by omitting chemical treatments from the sample preparation process, thus avoiding the formation of defects. High-resolution imaging was used to directly determine the number of fractured shells and the chirality of the outer shell. Electron irradiation at 200 keV for 10, 100 and 1,800 s led to improvements in the maximum sustainable loads by factors of 2.4, 7.9 and 11.6 compared with non-irradiated samples of similar diameter. This effect is attributed to crosslinking between the shells. Computer simulations also illustrate the effects of various irradiation-induced crosslinking defects on load sharing between the shells. The mechanical properties of carbon nanotubes rarely match the values predicted by theory owing to a combination of artefacts introduced during sample preparation and inadequate measurements. However, by avoiding chemical treatments and using high-resolution imaging, it is possible to obtain values of the mean fracture strength that exceed previous values by approximately a factor of three.
1,038 citations
TL;DR: In this article, the authors provide a detailed literature review and an assessment of results of the research and development work forming the current status of nanofluid technology for heat transfer applications.
Abstract: This study provides a detailed literature review and an assessment of results of the research and development work forming the current status of nanofluid technology for heat transfer applications. Nanofluid technology is a relatively new field, and as such, the supporting studies are not extensive. Specifically, experimental results were reviewed in this study regarding the enhancement of the thermal conductivity and convective heat transfer of nanofluids relative to conventional heat transfer fluids, and assessments were made as to the state-of-the-art of verified parametric trends and magnitudes. Pertinent parameters of particle volume concentration, particle material, particle size, particle shape, base fluid material, temperature, additive, and acidity were considered individually, and experimental results from multiple research groups were used together when assessing results. To this end, published research results from many studies were recast using a common parameter to facilitate comparisons of data among research groups and to identify thermal property and heat transfer trends. The current state of knowledge is presented as well as areas where the data are presently inconclusive or conflicting. Heat transfer enhancement for available nanofluids is shown to be in the 15-40% range, with a few situations resulting in orders of magnitude enhancement.
1,023 citations
San Diego State University1, University of South Florida2, Centre national de la recherche scientifique3, University of Georgia4, J. Craig Venter Institute5, Genome Institute of Singapore6, Argonne National Laboratory7, University of California, Santa Barbara8, University of Illinois at Urbana–Champaign9
TL;DR: The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.
Abstract: Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.
916 citations
TL;DR: In this article, the authors scrutinize the thin-film rotating disc electrode (TF-RDE) method for investigating the electrocatalytic activity of high surface area catalysts.
887 citations
Karolinska Institutet1, University of Oxford2, University of Toronto3, Centre national de la recherche scientifique4, University of California, Berkeley5, Los Alamos National Laboratory6, Tsinghua University7, University of Science and Technology of China8, Weizmann Institute of Science9, Scripps Research Institute10, Novartis11, Argonne National Laboratory12, Yeshiva University13, Brookhaven National Laboratory14, Rutgers University15, Case Western Reserve University16, University of California, San Francisco17, Columbia University18, Max Delbrück Center for Molecular Medicine19, New York University20
TL;DR: This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators.
Abstract: In selecting a method to produce a recombinant protein, a researcher is faced with a bewildering array of choices as to where to start. To facilitate decision-making, we describe a consensus 'what to try first' strategy based on our collective analysis of the expression and purification of over 10,000 different proteins. This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators.
TL;DR: This work shows that even a pure compound, in this case lead titanate, can display a morphotropic phase boundary under pressure, and finds that complex microstructures or compositions are not necessary to obtain strong piezoelectricity.
Abstract: A piezoelectric material is one that generates a voltage in response to a mechanical strain (and vice versa). The most useful piezoelectric materials display a transition region in their composition phase diagrams, known as a morphotropic phase boundary, where the crystal structure changes abruptly and the electromechanical properties are maximal. As a result, modern piezoelectric materials for technological applications are usually complex, engineered, solid solutions, which complicates their manufacture as well as introducing complexity in the study of the microscopic origins of their properties. Here we show that even a pure compound, in this case lead titanate, can display a morphotropic phase boundary under pressure. The results are consistent with first-principles theoretical predictions, but show a richer phase diagram than anticipated; moreover, the predicted electromechanical coupling at the transition is larger than any known. Our results show that the high electromechanical coupling in solid solutions with lead titanate is due to tuning of the high-pressure morphotropic phase boundary in pure lead titanate to ambient pressure. We also find that complex microstructures or compositions are not necessary to obtain strong piezoelectricity. This opens the door to the possible discovery of high-performance, pure-compound electromechanical materials, which could greatly decrease costs and expand the utility of piezoelectric materials.
TL;DR: The energy spectrum of cosmic rays above 2.5 x 10;{18} eV, derived from 20,000 events recorded at the Pierre Auger Observatory, is described and the hypothesis of a single power law is rejected with a significance greater than 6 standard deviations.
Abstract: The energy spectrum of cosmic rays above 2.5 x 10;{18} eV, derived from 20,000 events recorded at the Pierre Auger Observatory, is described. The spectral index gamma of the particle flux, J proportional, variantE;{-gamma}, at energies between 4 x 10;{18} eV and 4 x 10;{19} eV is 2.69+/-0.02(stat)+/-0.06(syst), steepening to 4.2+/-0.4(stat)+/-0.06(syst) at higher energies. The hypothesis of a single power law is rejected with a significance greater than 6 standard deviations. The data are consistent with the prediction by Greisen and by Zatsepin and Kuz'min.
TL;DR: In this article, the synthesis, structural and electrochemical characterization of xLi2MnO3·(1 − x)LiMn0.33Ni0.233Co0.333O2 electrodes over a wide compositional range is explored.
Abstract: Lithium- and manganese-rich layered electrode materials, represented by the general formula xLi2MnO3·(1 − x)LiMO2 in which M is Mn, Ni, and Co, are of interest for both high-power and high-capacity lithium ion cells. In this paper, the synthesis, structural and electrochemical characterization of xLi2MnO3·(1 − x)LiMn0.333Ni0.333Co0.333O2 electrodes over a wide compositional range (0 ≤ x ≤ 0.7) is explored. Changes that occur to the compositional, structural, and electrochemical properties of the electrodes as a function of x and the importance of using a relatively high manganese content and a high charging potential (>4.4 V) to generate high capacity (>200 mAh/g) electrodes are highlighted. Particular attention is given to the electrode composition 0.3Li2MnO3·0.7LiMn0.333Ni0.333Co0.333O2 (x = 0.3) which, if completely delithiated during charge, yields Mn0.533Ni0.233Co0.233O2, in which the manganese ions are tetravalent and, when fully discharged, LiMn0.533Ni0.233Co0.233O2, in which the average manganese ...
TL;DR: In this paper, the authors highlight the basic physical understanding and experimental techniques that will enable a new generation of applications in nano-optics and highlight some of the key advances in each of these areas.
Abstract: The rapid emergence of nanoplasmonics as a novel technology has been driven by recent progress in the fabrication, characterization, and understanding of metal-nanoparticle systems. In this review, we highlight some of the key advances in each of these areas. We emphasize the basic physical understanding and experimental techniques that will enable a new generation of applications in nano-optics.
TL;DR: The microwave sample shows a selectivity of approximately 30 for CO2 over CH4, which is among the highest selectivities reported for this separation, and the applicability of IAST to this system was demonstrated by performing GCMC simulations for both single-component and mixture adsorption.
Abstract: The adsorption of CO2 and CH4 in a mixed-ligand metal−organic framework (MOF) Zn2(NDC)2(DPNI) [NDC = 2,6-naphthalenedicarboxylate, DPNI = N,N′-di-(4-pyridyl)-1,4,5,8-naphthalene tetracarboxydiimide] was investigated using volumetric adsorption measurements and grand canonical Monte Carlo (GCMC) simulations. The MOF was synthesized by two routes: first at 80 °C for two days with conventional heating, and second at 120 °C for 1 h using microwave heating. The two as-synthesized samples exhibit very similar powder X-ray diffraction patterns, but the evacuated samples show differences in nitrogen uptake. From the single-component CO2 and CH4 isotherms, mixture adsorption was predicted using the ideal adsorbed solution theory (IAST). The microwave sample shows a selectivity of ∼30 for CO2 over CH4, which is among the highest selectivities reported for this separation. The applicability of IAST to this system was demonstrated by performing GCMC simulations for both single-component and mixture adsorption.
TL;DR: In this article, a power-law distribution of on-and off-times observed in colloidal semiconductor quantum dots, nanorods, nanowires and some organic dyes is discussed.
Abstract: Virtually all known fluorophores exhibit mysterious episodes of emission intermittency. A remarkable feature of the phenomenon is a power-law distribution of on- and off-times observed in colloidal semiconductor quantum dots, nanorods, nanowires and some organic dyes. For nanoparticles, the resulting power law extends over an extraordinarily wide dynamic range: nine orders of magnitude in probability density and five to six orders of magnitude in time. Exponents hover about the ubiquitous value of -3/2. Dark states routinely last for tens of seconds—practically forever on quantum mechanical timescales. Despite such infinite states of darkness, the dots miraculously recover and start emitting again. Although the underlying mechanism responsible for this phenomenon remains a mystery and many questions persist, we argue that substantial theoretical progress has been made.
TL;DR: In this paper, the Pierre Auger Observatory data was used to confirm the anisotropy of the arrival direction of the highest-energy cosmic rays with the highest energy, which are correlated with the positions of relatively nearby active galactic nuclei (AGN) at a confidence level of more than 99%.
TL;DR: Inelastic neutron scattering observations of a magnetic resonance below Tc in Ba0.6K0.4Fe2As2 are reported, a phase-sensitive measurement demonstrating that the superconducting energy gap has unconventional symmetry in the iron arsenide superconductors.
Abstract: The discovery of a new family of superconductors containing layers of iron arsenide, the iron oxypnictides, has stimulated much interest, largely because they combine promisingly high transition temperatures with a mechanism of superconductivity rather similar to that of that the high-temperature copper oxide superconductors. In both the iron arsenides and the copper oxides, superconductivity arises when an antiferromagnetically ordered phase is suppressed by chemical doping. A universal feature of the copper oxide superconductors is the existence of a resonant magnetic excitation that is predicted to occur when the superconducting energy gap has opposite sign on different parts of the Fermi surface. Now inelastic neutron scattering observations of the iron arsenide Ba0.6K0.4Fe2As2 reveal a magnetic resonance below Tc in Ba0.6K0.4Fe2As2, demonstrating that the superconducting energy gap in these materials has unconventional symmetry. A new family of superconductors containing layers of iron arsenide has attracted considerable interest because of their high transition temperatures and similarities with the high-Tc copper oxide superconductors. This paper reports inelastic neutron scattering observations of a magnetic resonance below Tc in Ba0.6K0.4Fe2As2, demonstrating that the superconducting energy gap has unconventional symmetry. A new family of superconductors containing layers of iron arsenide1,2,3 has attracted considerable interest because of their high transition temperatures (Tc), some of which are >50 K, and because of similarities with the high-Tc copper oxide superconductors. In both the iron arsenides and the copper oxides, superconductivity arises when an antiferromagnetically ordered phase has been suppressed by chemical doping4. A universal feature of the copper oxide superconductors is the existence of a resonant magnetic excitation, localized in both energy and wavevector, within the superconducting phase5,6,7,8,9. This resonance, which has also been observed in several heavy-fermion superconductors10,11,12, is predicted to occur when the sign of the superconducting energy gap takes opposite values on different parts of the Fermi surface13, an unusual gap symmetry which implies that the electron pairing interaction is repulsive at short range14. Angle-resolved photoelectron spectroscopy shows no evidence of gap anisotropy in the iron arsenides, but such measurements are insensitive to the phase of the gap on separate parts of the Fermi surface15. Here we report inelastic neutron scattering observations of a magnetic resonance below Tc in Ba0.6K0.4Fe2As2, a phase-sensitive measurement demonstrating that the superconducting energy gap has unconventional symmetry in the iron arsenide superconductors.
TL;DR: This group contribution method is demonstrated to be capable of estimating Delta(r)G'(o) and Delta(f)G (o) for the majority of the biochemical compounds and reactions found in the iJR904 and iAF1260 genome-scale metabolic models of Escherichia coli and in the Kyoto Encyclopedia of Genes and Genomes and University of Minnesota Biocatalysis and Biodegradation Database.
07 Dec 2008
TL;DR: The results show that for Montage, a workflow with short job runtimes, the virtual environment can provide good compute time performance but it can suffer from resource scheduling delays and widearea communications.
Abstract: This paper explores the use of cloud computing for scientific workflows, focusing on a widely used astronomy application-Montage. The approach is to evaluate from the point of view of a scientific workflow the tradeoffs between running in a local environment, if such is available, and running in a virtual environment via remote, wide-area network resource access. Our results show that for Montage, a workflow with short job runtimes, the virtual environment can provide good compute time performance but it can suffer from resource scheduling delays and widearea communications.
University of Zurich1, University of Notre Dame2, CERN3, Brookhaven National Laboratory4, Durham University5, University of Hamburg6, Max Planck Society7, Autonomous University of Madrid8, University of Victoria9, Technische Universität München10, University of Cagliari11, Instituto Superior Técnico12, University of British Columbia13, University of Valencia14, International School for Advanced Studies15, University of Warsaw16, University of Lyon17, Yale University18, University of Manchester19, University of Pisa20, RWTH Aachen University21, University of Wisconsin-Madison22, University of Sussex23, University of Tokyo24, Argonne National Laboratory25, Helsinki Institute of Physics26, University of Oregon27, University of Zagreb28, KEK29, University of Southampton30, Paul Scherrer Institute31, Petersburg Nuclear Physics Institute32, University of California33, University of Paris34, University of Rome Tor Vergata35, Bulgarian Academy of Sciences36, University of Salento37, Boston University38, University of Würzburg39, International Centre for Theoretical Physics40, University of Murcia41, University of Michigan42, Indian Institute of Science43
TL;DR: In this article, the authors discuss the theoretical, phenomenological and experimental issues related to flavor phenomena in the charged lepton sector and in flavor conserving CP-violating processes.
Abstract: This chapter of the report of the “Flavor in the era of the LHC” Workshop discusses the theoretical, phenomenological and experimental issues related to flavor phenomena in the charged lepton sector and in flavor conserving CP-violating processes. We review the current experimental limits and the main theoretical models for the flavor structure of fundamental particles. We analyze the phenomenological consequences of the available data, setting constraints on explicit models beyond the standard model, presenting benchmarks for the discovery potential of forthcoming measurements both at the LHC and at low energy, and exploring options for possible future experiments.
TL;DR: This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities – if the challenges of elucidating the functions of so many never-seen-before gene families are overcome.
Abstract: Background: Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities. Methodology/Principal Findings: We present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92%) versus ribosomal RNA. Analysis of corresponding metagenomes confirms much higher levels of assembly in the metatranscriptomic samples and a far higher yield of large gene families with .100 members, ,91% of which were novel. Conclusions/Significance: This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities – if we can overcome the challenges of elucidating the functions of so many never-seen-before gene families.
TL;DR: It is found that heavy water is a more structured liquid than light water, and the OH Bond length in H2O is approximately 3% longer than the OD bond length in D2O, a much larger change than current predictions.
Abstract: The structures of heavy and light water at ambient conditions are investigated with the combined techniques of x-ray diffraction, neutron diffraction, and computer simulation. It is found that heavy water is a more structured liquid than light water. We find the OH bond length in H2O is approximately 3% longer than the OD bond length in D2O. This is a much larger change than current predictions. Corresponding to this, the hydrogen bond in light water is approximately 4% shorter than in heavy water, while the intermolecular HH distance is approximately 2% longer.
TL;DR: In this article, a quark model is applied to the spectrum of baryons containing heavy quarks, and the model gives masses for the known heavy quark that are in agreement with experiment, but for the doubly-charmed baryon Ξcc, the model prediction is too heavy.
Abstract: A quark model is applied to the spectrum of baryons containing heavy quarks. The model gives masses for the known heavy baryons that are in agreement with experiment, but for the doubly-charmed baryon Ξcc, the model prediction is too heavy. Mixing between the ΞQ and Ξ′Q states is examined and is found to be small for the lowest lying states. In contrast with this, mixing between the Ξbc and Ξ′bc states is found to be large, and the implication of this mixing for properties of these states is briefly discussed. We also examine heavy-quark spin-symmetry multiplets, and find that many states in the model can be placed in such multiplets. We compare our predictions with those of a number of other authors.
TL;DR: A new dedicated high-resolution high-throughput powder diffraction beamline has been built, fully commissioned, and opened to general users at the Advanced Photon Source.
Abstract: A new dedicated high-resolution high-throughput powder diffraction beamline has been built, fully commissioned, and opened to general users at the Advanced Photon Source. The optical design and commissioning results are presented. Beamline performance was examined using a mixture of the NIST Si and Al2O3 standard reference materials, as well as the LaB6 line-shape standard. Instrumental resolution as high as 1.7×10−4 (ΔQ∕Q) was observed.
TL;DR: The data disfavor two alternative explanations for the disappearance of neutrinos in flight: namely, neutrino decays into lighter particles and quantum decoherence of neutRinos, at the 3.7 and 5.7 standard-deviation levels, respectively.
Abstract: This Letter reports new results from the MINOS experiment based on a two-year exposure to muon neutrinos from the Fermilab NuMI beam. Our data are consistent with quantum-mechanical oscillations of neutrino flavor with mass splitting |Δm^2|=(2.43±0.13)×10^-3 eV^2 (68% C.L.) and mixing angle sin^2(2θ)>0.90 (90% C.L.). Our data disfavor two alternative explanations for the disappearance of neutrinos in flight: namely, neutrino decays into lighter particles and quantum decoherence of neutrinos, at the 3.7 and 5.7 standard-deviation levels, respectively.
TL;DR: In this article, the authors used electron paramagnetic resonance (EPR) spectroscopy to study the local structures of surface/interfacial Cu2+ sites using a sensitive paramagnetic probe.
Abstract: Coupled CuO−TiO2 nanocomposite photocatalysts were prepared by a deposition precipitation method and were characterized with a variety of techniques. Electron paramagnetic resonance (EPR) spectroscopy was employed to study the local structures of surface/interfacial Cu2+ sites using Cu2+ as a sensitive paramagnetic probe. The addition of bulk CuO to TiO2 led to decreased photocatalytic efficiency in the degradation of methylene blue. However, doping with a very small amount of CuO (0.1 wt % copper loading) significantly enhanced the photocatalytic activity of TiO2. EPR study of the TiO2 surface revealed the presence of both highly dispersed CuO clusters and substitutional Cu2+ sites (Ti−O−Cu linkages) at 0.1 wt % copper loading. The data suggest that the Ti−O−Cu linkages contributed to the improved photooxidative activity of the 0.1% CuO−TiO2 nanocomposite. In contrast, at higher loadings the bulk form of CuO created charge recombination centers lowering the photoactivity of the composites.
TL;DR: A wider survey of whole grain speciation of white and brown rice samples from numerous sources showed that brown rice had a higher proportion of inorganic arsenic present than white rice, and the percentage of DMA present in the grain increased along with total grain arsenic.
Abstract: Synchrotron-based X-ray fluorescence (S-XRF) was utilized to locate arsenic (As) in polished (white) and unpolished (brown) rice grains from the United States, China, and Bangladesh. In white rice As was generally dispersed throughout the grain, the bulk of which constitutes the endosperm. In brown rice As was found to be preferentially localized at the surface, in the region corresponding to the pericarp and aleurone layer. Copper, iron, manganese, and zinc localization followed that of arsenic in brown rice, while the location for cadmium and nickel was distinctly different, showing relatively even distribution throughout the endosperm. The localization of As in the outer grain of brown rice was confirmed by laser ablation ICP-MS. Arsenic speciation of all grains using spatially resolved X-ray absorption near edge structure (micro-XANES) and bulk extraction followed by anion exchange HPLC-ICP-MS revealed the presence of mainly inorganic As and dimethylarsinic acid (DMA). However, the two techniques indicated different proportions of inorganic:organic As species. A wider survey of whole grain speciation of white (n=39) and brown (n=45) rice samples from numerous sources (field collected, supermarket survey, and pot trials) showed that brown rice had a higher proportion of inorganic arsenic present than white rice. Furthermore, the percentage of DMA present in the grain increased along with total grain arsenic.
Kent State University1, Tel Aviv University2, Massachusetts Institute of Technology3, California State University, Los Angeles4, University of Glasgow5, Argonne National Laboratory6, Prince Mohammad bin Fahd University7, Syracuse University8, University of Maryland, College Park9, Florida International University10, Thomas Jefferson National Accelerator Facility11, Seoul National University12, University of Virginia13, Rutgers University14, Kharkov Institute of Physics and Technology15, College of William & Mary16, Old Dominion University17, University of Saskatchewan18, University of Massachusetts Amherst19, University of Kentucky20, Norfolk State University21, Temple University22, Yerevan Physics Institute23, University of Ljubljana24, University of Illinois at Urbana–Champaign25
TL;DR: Scattering experiments show that in carbon-12 the neutron-proton pairs are nearly 20 times as prevalent as proton- Proton pairs and, by inference, neutron-neutron pairs, which has implications for understanding cold dense nuclear systems such as neutron stars.
Abstract: The protons and neutrons in a nucleus can form strongly correlated nucleon pairs. Scattering experiments, in which a proton is knocked out of the nucleus with high-momentum transfer and high missing momentum, show that in carbon-12 the neutron-proton pairs are nearly 20 times as prevalent as proton-proton pairs and, by inference, neutron-neutron pairs. This difference between the types of pairs is due to the nature of the strong force and has implications for understanding cold dense nuclear systems such as neutron stars.