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At least 595 records · Page 33

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DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗

DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods: Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results: . Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions: PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗

DOE OSTI2019

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

Radiation detection system

A preamplifier circuit for processing a signal provided by a radiation detector includes a transimpedance amplifier coupled to receive a current signal from a detector and generate a voltage signal at its output. A second amplification stage has an input coupled to an output of the transimpedance amplifier for providing an amplified voltage signal. Detector electronics include a preamplifier circuit having a first and second transimpedance amplifier coupled to receive a current signal from a first and second location on a detector, respectively, and generate a first and second voltage signal at respective outputs. A second amplification stage has an input coupled to an output of the transimpedance amplifiers for amplifying the first and said second voltage signals to provide first and second amplified voltage signals. A differential output stage is coupled to the second amplification stage for receiving the first and second amplified voltage signals and providing a pair of outputs from each of the first and second amplified voltage signals. Read out circuitry has an input coupled to receive both of the pair of outputs, the read out circuitry having structure for processing each of the pair of outputs, and providing a single digital output having a time-stamp therefrom.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2015

Method and system for compact efficient laser architecture

A laser amplifier module having an enclosure includes an input window, a mirror optically coupled to the input window and disposed in a first plane, and a first amplifier head disposed along an optical amplification path adjacent a first end of the enclosure. The laser amplifier module also includes a second amplifier head disposed along the optical amplification path adjacent a second end of the enclosure and a cavity mirror disposed along the optical amplification path.

42 ENGINEERING↗

DOE OSTI2016

COMBINATION OF DENSITY AND ENERGY MODULATION IN MICROBUNCHING ANALYSIS

Microbunching instability (MBI) has been one of the most challenging issues in the transport of high-brightness electron beams for modern recirculating or energy recovery linac machines. Recently we have developed and implemented a Vlasov solver [1] to calculate the microbunching gain for an arbitrary beamline lattice, based on the extension of existing theoretical formulation [2-4] for the microbunching amplification from an initial density perturbation to the final density modulation. For more thorough analyses, in addition to the case of (initial) density to (final) density amplification, we extend in this paper the previous formulation to more general cases, including energy to density, density to energy and energy to energy amplifications for a recirculation machine. Such semi-analytical formulae are then incorporated into our Vlasov solver, and qualitative agreement is obtained when the semi-analytical Vlasov results are compared with particle tracking simulation using ELEGANT [5].

Tsai, Cheng Ying↗

DOE OSTI2019

Method and system for compact efficient laser architecture

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Method and system for compact efficient laser architecture

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Quantifying the Occurrence of Record Hot Years Through Normalized Warming Trends

Surface air temperature trends and extreme events are of global concern and they are related. Here we show that the occurrence of record hot years over different latitudes from 1960-2019 are more strongly correlated with the observational annual mean temperature trends normalized by internal variability. Compared with the raw trends showing Arctic amplification, the normalized trends show a tropical amplification over land. Two hot spots with more frequent occurrence of record hot years are identified: northern hemisphere ocean (versus land) and southern hemisphere tropical land (versus mid- and high-latitude lands). Ensemble mean results from 32 Earth system models agree with observations better than individual models, but they do not reproduce observed large differences in correlations across latitudes between normalized trends and record-breaking events over land versus ocean. Furthermore, our results enable the quantification of record hot year occurrence through normalized warming trends and provide new metrics for model evaluation and improvement.

58 GEOSCIENCES↗

DOE OSTI2015

Influence of seismicity on the Lusi mud eruption

Earthquakes trigger the eruption of mud and magmatic volcanoes and affect ongoing eruptive activity. One mechanism that could trigger an eruption is clay liquefaction. In this work we model the propagation of seismic waves beneath the Lusi mud eruption (East Java, Indonesia) using available seismic velocity and density models to assess the effect of subsurface structure on the amplification of incident seismic waves. We find that using an updated subsurface density and velocity structure, there is no significant amplification of incident seismic energy in the Upper Kalibeng Formation, the source of the erupting solids. Thus, the hypothesis that the Lusi eruption was triggered by clay liquefaction appears unlikely to be correct. Independent constraints from gas chemistry as well as analyses of drilling activities at the nearby Banjar-Panji 1 gas exploration well and an analysis of the effects of other earthquakes all favor a drilling trigger.

58 GEOSCIENCES↗

DOE OSTI2014

Gaussian-type light bullet solutions of the (3+1)-dimensional Schrödinger equation with cubic and power-law nonlinearities in PT-symmetric potentials

Two kinds of Gaussian-type light bullet (LB) solutions of the (3+1)-dimensional Schrödinger equation with cubic and power-law nonlinearities in PT-symmetric potentials are analytically obtained. The phase switches, powers and transverse power-flow densities of these solutions in homogeneous media are studied. The linear stability analysis of these LB solutions and the direct numerical simulation indicate that LB solutions are stable below some thresholds for the imaginary part of PT-symmetric potentials in the defocusing cubic and focusing power-law nonlinear medium, while they are always unstable for all parameters in other media. Moreover, the broadened and compressed behaviors of LBs in the exponential periodic amplification system and diffraction decreasing system are discussed. Results indicate that LB is more stable for the sign-changing nonlinearity in the exponential periodic amplification system than for the non-sign-changing nonlinearity in the diffraction decreasing system at the same propagation distances.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2015

A spectral unaveraged algorithm for free electron laser simulations

We propose and discuss a numerical method to model electromagnetic emission from the oscillating relativistic charged particles and its coherent amplification. The developed technique is well suited for free electron laser simulations, but it may also be useful for a wider range of physical problems involving resonant field–particles interactions. The algorithm integrates the unaveraged coupled equations for the particles and the electromagnetic fields in a discrete spectral domain. Using this algorithm, it is possible to perform full three-dimensional or axisymmetric simulations of short-wavelength amplification. In this paper we describe the method, its implementation, and we present examples of free electron laser simulations comparing the results with the ones provided by commonly known free electron laser codes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2011

Multiplexed Electrochemical Immunoassay of Phosphorylated Proteins Based on Enzyme-Functionalized Gold Nanorod Labels and Electric Field-Driven Acceleration

A multiplexed electrochemical immunoassay integrating enzyme amplification and electric field-driven strategy was developed for fast and sensitive quantification of phosphorylated p53 at Ser392 (phospho-p53 392), Ser15 (phospho-p53 15), Ser46 (phospho-p53 46) and total p53 simultaneously. The disposable sensor array has four spatially separated working electrodes and each of them is modified with different capture antibody, which enables simultaneous immunoassay to be conducted without cross-talk between adjacent electrodes. The enhanced sensitivity was achieved by multi-enzymes amplification strategy using gold nanorods (AuNRs) as nanocarrier for co-immobilization of horseradish peroxidase (HRP) and detection antibody (Ab2) at high ratio of HRP/Ab2, which produced an amplified electrocatalytic response by the reduction of HRP oxidized thionine in the presence of hydrogen peroxide. The immunoreaction processes were accelerated by applying +0.4 V for 3 min and then -0.2 V for 1.5 min, thus the whole sandwich immunoreactions could be completed in less than 5 min. The disposable immunosensor array shows excellent promise for clinical screening of phosphorylated proteins and convenient point-of-care diagnostics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Axon-like active signal transmission

Any electrical signal propagating in a metallic conductor loses amplitude due to the natural resistance of the metal. Compensating for such losses presently requires repeatedly breaking the conductor and interposing amplifiers that consume and regenerate the signal. This century-old primitive severely constrains the design and performance of modern interconnect-dense chips. Here we present a fundamentally different primitive based on semi-stable edge of chaos (EOC), a long-theorized but experimentally elusive regime that underlies active (self-amplifying) transmission in biological axons. By electrically accessing the spin crossover in LaCoO 3 , we isolate semi-stable EOC, characterized by small-signal negative resistance and amplification of perturbations. In a metallic line atop a medium biased at EOC, a signal input at one end exits the other end amplified, without passing through a separate amplifying component. While superficially resembling superconductivity, active transmission offers controllably amplified time-varying small-signal propagation at normal temperature and pressure, but requires an electrically energized EOC medium. Operando thermal mapping reveals the mechanism of amplification—bias energy of the EOC medium, instead of fully dissipating as heat, is partly used to amplify signals in the metallic line, thereby enabling spatially continuous active transmission, which could transform the design and performance of complex electronic chips.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2012

Possible origins of a time-resolved frequency shift in Raman plasma amplifiers

Raman amplification is a resonant process in which the energy of a long pump pulse is transferred to a short seed pulse by a plasma wave. There has been a significant effort to identify a window in parameter space within which the interaction is expected to be highly efficient and not degraded by competing instabilities or excessive damping. However, experimental results have thus far failed to approach the theoretical limits. Recent amplified signal spectra display a characteristic blue shift, which evolves within the seed pulse duration and suggests that the mechanism responsible for this shift is also limiting amplification in these experiments. We present the evidence and explore different hypotheses for the origins of the shift-namely localization in density minima along the axis of laser propagation induced by an ion acoustic wave that could arise from the Langmuir decay instability, filamentation which could also modulate the plasma density but in the plane transverse to laser propagation, particle trapping, and additional ionization induced by the amplified seed field.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2014

Nondegenerate parametric generation of 2.2-mJ, few-cycle 2.05-μm pulses using a mixed phase matching scheme

We describe the production of 2.2-mJ, ∼6 optical-cycle-long mid-infrared laser pulses with a carrier wavelength of 2.05 μm in a two-stage β-BaB{sub 2}O{sub 4} nondegenerate optical parametric amplifier design with a mixed phase matching scheme, which is pumped by a standard Ti:sapphire chirped-pulse amplification system. It is demonstrated that relatively high pulse energies, short pulse durations, high stability, and excellent beam profiles can be obtained using this simple approach, even without the use of optical parametric chirped-pulse amplification.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2014

Optical switching and photoluminescence in erbium-implanted vanadium dioxide thin films

Vanadium dioxide (VO{sub 2}) is under intensive consideration for optical switching due to its reversible phase transition, which features a drastic and rapid shift in infrared reflectivity. Classified as an insulator–to–metal transition, the phase transition in VO{sub 2} can be induced thermally, electrically, and optically. When induced optically, the transition can occur on sub-picosecond time scales. It is interesting to dope VO{sub 2} with erbium ions (Er{sup 3+}) and observe their combined properties. The first excited-state luminescence of Er{sup 3+} lies within the wavelength window of minimal transmission-loss in silicon and has been widely utilized for signal amplification and generation in silicon photonics. The incorporation of Er{sup 3+} into VO{sub 2} could therefore result in a novel photonic material capable of simultaneous optical switching and amplification. In this work, we investigate the optical switching and photoluminescence in Er-implanted VO{sub 2} thin films. Thermally driven optical switching is demonstrated in the Er-implanted VO{sub 2} by infrared reflectometry. Photoluminescence is observed in the thin films annealed at ∼800 °C or above. In addition, Raman spectroscopy and a statistical analysis of switching hysteresis are carried out to assess the effects of the ion implantation on the VO{sub 2} thin films. We conclude that Er-implanted VO{sub 2} can function as an optical switch and amplifier, but with reduced switching quality compared to pure VO{sub 2}.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2014

Wave–current interaction in the presence of a three-dimensional bathymetry: Deep water wave focusing in opposing current conditions

Large scale experiments were carried out in the Ocean Engineering Basin FIRST, France. A tri-dimensional bathymetry consisting of two symmetrical submerged mounds was displayed on the flat bed on both sides of the basin. Regular waves of frequency corresponding to deep water conditions above the bathymetry were generated in opposing current conditions. A strong tri-dimensional behaviour is observed for the wave amplitude, leading to a strong focusing (up to twice the incident amplitude) of the wave energy towards the central deeper zone. This amplification cannot be ascribed to the increase of the current intensity in the main wave direction, nor to a current gradient normally to the wave direction. A wave phase gradient, normal to its main direction, is observed up-wave (or downstream) the mounds. This phase lag depends on the wave amplitude, it is the higher for the moderate amplitude case. The experimental data are compared with calculations of a refraction-diffraction model assuming a depth-averaged current. If the model qualitatively predicts the wave amplification in the centerline of the basin, discrepancies are observed in the vicinity of the depth changes. The observed mean current vertical profile shape is then supposed to play a significant role in the wave focusing, especially near the steep slopes down-stream the mounds. In addition, the waves are found to modify substantially both horizontal and vertical current fields.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗