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At least 55 records · Page 3

Improved high-throughput screening technique to rapidly isolate Chlamydomonas transformants expressing recombinant proteins

Abstract The single-celled eukaryotic green alga Chlamydomonas reinhardtii has long been a model system for developing genetic tools for algae, and is also considered a potential platform for the production of high-value recombinant proteins. Identifying transformants with high levels of recombinant protein expression has been a challenge in this organism, as random integration of transgenes into the nuclear genome leads to low frequency of cell lines with high gene expression. Here, we describe the design of an optimized vector for the expression of recombinant proteins in Chlamydomonas , that when transformed and screened using a dual antibiotic selection, followed by screening using fluorescence activated cell sorting (FACS), permits rapid identification and isolation of microalgal transformants with high expression of a recombinant protein. This process greatly reduces the time required for the screening process, and can produce large populations of recombinant algae transformants with between 60 and 100% of cells producing the recombinant protein of interest, in as little as 3 weeks, that can then be used for whole population sequencing or individual clone analysis. Utilizing this new vector and high-throughput screening (HTS) process resulted in an order of magnitude improvement over existing methods, which normally produced under 1% of algae transformants expressing the protein of interest. This process can be applied to other algal strains and recombinant proteins to enhance screening efficiency, thereby speeding up the discovery and development of algal-derived recombinant protein products. Key points • A protein expression vector using double-antibiotic resistance genes was designed • Double antibiotic selection causes fewer colonies with more positive for phenotype • Coupling the new vector with FACS improves microalgal screening efficiency > 60%

59 BASIC BIOLOGICAL SCIENCES↗

Time-Dependent Electric Bus and Charging Station Deployment Problem

Battery electric buses (BEBs) have gained popularity due to their emission-free and energy-efficient features. Many transit authorities worldwide have set goals to gradually replace their bus fleets with BEBs. Considering the potential decline in BEB battery and charger prices, this study proposes a time-dependent bus fleet transition model to determine the optimal bus fleet transition plan, which includes selecting the bus lines to be electrified, determining the timing and type of BEBs to be purchased, and deploying on-route fast chargers and depot chargers. The model is a bi-objective integer linear program that considers the trade-off between electrified transit mileages and bus electrification costs. A normalized normal constraint method is applied to solve the bi-objective optimization model. The effectiveness of the proposed model is tested using a real-world bus network. Additionally, sensitivity analyses are conducted to better understand the impact of different parameter values on the optimal solutions. Our proposed model can provide transit authorities with a powerful tool to make informed decisions about their BEB fleet replacement plans.

ADVANCED PROPULSION SYSTEMS↗

Comparison of multi-stage air treatment process divided by the same temperature and enthalpy difference

The multi-stage air treatment system has been proposed recently, and lower grade chilled/hot water could be used and energy efficiency could be improved. However, it has not been studied which division method of air treatment processes has higher energy efficiency. In this study, the model to calculate the energy consumption of multi-stage air treatment process is introduced, and the effects of two division methods, i.e. multi-stage air treatment process divided by the same temperature difference (ST method) or same enthalpy difference (SE method) between inlet and outlet at each stage, under 9 different air inlet parameters in the 2-stage and 3-stage air treatment processes are analysed and compared. The results show that (1) the system energy consumption of the SE method is generally lower than that of the ST method; (2) there is generally a larger energy consumption reduction rate of SE method when the air relative humidity is 70% compared to relative humidity of 50% and 90%; (3) the difference between ST method and SE method is not great, so both methods can be used for the design of multi-stage treatment system although SE method is normally recommended.

Wang, Wentao↗

Finite boundary effects on the spherical Rayleigh–Taylor instability between viscous fluids

For the Rayleigh–Taylor unstable arrangement of a viscous fluid sphere embedded in a finite viscous fluid spherical shell with a rigid boundary and a radially directed acceleration, a dispersion relation is developed from a linear stability analysis using the method of normal modes. [Formula: see text] is the radially directed acceleration at the interface. ρ i denotes the density, μ i is the viscosity, and R i is the radius, where i = 1 is the inner sphere and i = 2 is the outer sphere. The dispersion relation is a function of the following dimensionless variables: viscosity ratio [Formula: see text], density ratio [Formula: see text], spherical harmonic mode n, [Formula: see text], [Formula: see text], and the dimensionless growth rate [Formula: see text], where σ is the exponential growth rate. We show that the boundedness provided by the outer spherical shell has a strong influence on the instability behavior, which is reflected not only in the modulation of the growth rate but also in the selection of the most unstable modes that are physically possible. This outer boundary effect is quantified by the relative magnitude of the radius ratio H. We find that when H is close to unity, lower order harmonics are excluded from becoming the most unstable within a vast region of the parameter space. In other words, the effect of H has precedence over the other controlling parameters d, B, and a wide range of s in establishing what the lowest most unstable mode can be. When H ~ 1, low order harmonics can become the most unstable only for s >> 1. However, in the limit when s → ∞, we show that the most unstable mode is n = 1 and derive the dispersion relation in this limit. The exclusion of most unstable low order harmonics caused by a finite outer boundary is not realized when the outer boundary extends beyond a certain threshold length-scale in which case all modes are equally possible depending on the value of B.

74 ATOMIC AND MOLECULAR PHYSICS↗

Distributed Coordination of Networked Microgrids for Voltage Support in Bulk Power Grids

The increasing deployment of distributed energy resources (DERs) and microgrids (MGs) in power distribution systems has enabled the adjustment of reactive power consumption as seen at the substation, which can be used to provide voltage support for the bulk power system (BPS). Leveraging this new capability will provide greater resiliency to the power system as a whole. Here, the goal of this paper is to develop and compare three different algorithms, namely distributed optimal power flow, distributed consensus algorithm, and fully decentralized collaborative autonomy for unbalanced distribution systems for microgrid coordination. These algorithms use networked MGs to support the BPS voltage when a contingency at the bulk grid results in abnormally low voltages, which may be a precursor to voltage collapse. Our comparative analysis includes both qualitative and quantitative assessments of the three algorithms and a discussion of the trade-offs between the decentralized and distributed methods in normal and disrupted conditions. Each algorithm was evaluated on the modified IEEE 13-bus system and a real power distribution system at Chattanooga, Tennessee, that encompasses more than 4500 buses. Each algorithms excels differently and may be suited for different scenarios depending on the condition, operations, and priorities of the power and communication systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

A consensus protocol for the recovery of mercury methylation genes from metagenomes

Abstract Mercury (Hg) methylation genes ( hgcAB ) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal‐ash amended sediments, chlor‐alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg‐cycling microorganisms in aquatic and terrestrial ecosystems (Hg‐MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky‐coco”, a ready‐to‐use bioinformatic pipeline based on de novo single‐metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky‐coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗

The $^3$He+$^5$He$\rightarrow $ $\alpha $+$\alpha $ reaction below the Coulomb barrier via the Trojan Horse Method

For the first time in an application to nuclear astrophysics, a process induced by the unstable 5 He = ( 4 He-n) nucleus, the 3 He+ 5 He→2α reaction, has been studied through the Trojan Horse Method (THM). For that purpose, the quasi-free (QF) contribution of the 9 Be( 3 He,αα) 4 He reaction was selected at E 3 He =4 MeV incident energy. The reaction was studied in a kinematically complete experiment following a recent publication, where for the quasi free contribution the momentum distribution between α and 5 He particle cluster in the 9 Be nucleus in the ground state have been extracted. The angular distribution of the QF 3 He+ 5 He→2α reaction was measured at θ cm = 78°–115°. The energy dependence of the differential cross section of the 3 He+ 5 He→2α virtual reaction was extracted in the energy range E cm = 0–650 keV. In conclusion, the total cross section obtained from the Trojan-horse method was normalized to absolute cross sections from a theoretical calculation in the energy range E cm =300–620 keV.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Performance of Photovoltaic Systems Recorded by Open Solar Performance and Reliability Clearinghouse (oSPARC)

This article analyzes data from 2,200 photovoltaic systems collected through the Open Solar Performance and Reliability Clearinghouse (oSPARC, 2018) to draw conclusions about the measured performance of the systems, how it compares to expectations, and how wide the variation is. The systems range in size from 2 kW to 1,200 kW, with an average size of 229 kW, and were activated in oSPARC between March 13, 2007 and Dec. 16, 2016. Data regarding co-incident insolation and ambient temperature are provided through the oSPARC platform for the population of systems and summarized here. Results indicate that - after correcting for measured insolation, derating for temperature, and correcting for balance-of-system efficiency and degradation as a result of system age - the performance ratio of these 2,200 systems averages 91.7%. Adjusting for known parameters such as age and efficiency, the ratio would ideally be 100%. Thus, the 'underperformance' of this system sample is measured at 9.3% and suggests that as much as 9.3% could be recovered if the systems were caused to perform as expected through optimal operation and maintenance. Efforts to correlate the performance ratio with environmental conditions resulted in very low coefficients of regression, but the method already normalizes for actual site insolation and temperature, which are responsible for much of the site-specific variation. An exemption is air-quality nonattainment areas, where the measured performance of plants averages 86.9% and is consistently lower than the average of 95.9% in areas that are in compliance with air quality standards, likely because of particulate matter such as diesel soot exacerbating the soiling rate.

14 SOLAR ENERGY↗

Cooling rate and dendrite spacing control in direct metal deposition printed Cu-Fe alloys

Over the last several decades, additive manufacturing (AM) has been primarily used for rapid prototyping or to create novel geometries that would be difficult or impossible to create by normal manufacturing methods. More recently, research has been focused on expanding the list of materials that can be made through additive manufacturing, opening a greater range of material properties for this manufacturing method. Due to the unusual conditions during AM, including the high cooling rates and voxel by voxel method of production, AM parts often have anisotropic material microstructures and properties. In this investigation, the laser power, composition, and nozzle head speed during direct metal deposition of copper-iron alloys was varied to understand how the grain structure within the printed parts could be changed and controlled. The resulting dendrite spacing was measured and compared to calculated cooling rates from Gaussian beams on flat plates under similar material and laser properties, which resulted in a cooling rate to dendrite spacing relationship following an inverse square root, as is found in other dendritic systems [Young and Kerkwood, Metall. Trans. A 6, 197–205 (1975)]. Thus, it is demonstrated that in the Cu-Fe system, dendrite spacing can be controlled through manipulation of printing parameters.

36 MATERIALS SCIENCE↗

Capturing the interactions between ice sheets, sea level and the solid Earth on a range of timescales: a new “time window” algorithm

Retreat and advance of ice sheets perturb the gravitational field, solid surface and rotation of the Earth, leading to spatially variable sea-level changes over a range of timescales $\textit{O}$ (10 0–6 years), which in turn feed back onto ice-sheet dynamics. Coupled ice-sheet–sea-level models have been developed to capture the interactive processes between ice sheets, sea level and the solid Earth, but it is computationally challenging to capture short-term interactions $\textit{O}$ (10 0–2 years) precisely within longer $\textit{O}$ (10 3–6 years) simulations. The standard forward sea-level modelling algorithm assigns a uniform temporal resolution in the sea-level model, causing a quadratic increase in total CPU time with the total number of input ice history steps, which increases with either the length or temporal resolution of the simulation. In this study, we introduce a new “time window” algorithm for 1D pseudo-spectral sea-level models based on the normal mode method that enables users to define the temporal resolution at which the ice loading history is captured during different time intervals before the current simulation time. Utilizing the time window, we assign a fine temporal resolution $\textit{O}$ (10 0–2 years) for the period of ongoing and recent history of surface ice and ocean loading changes and a coarser temporal resolution $\textit{O}$ (10 3–6 years) for earlier periods in the simulation. This reduces the total CPU time and memory required per model time step while maintaining the precision of the model results. We explore the sensitivity of sea-level model results to the model temporal resolution and show how this sensitivity feeds back onto ice-sheet dynamics in coupled modelling. We apply the new algorithm to simulate sea-level changes in response to global ice-sheet evolution over two glacial cycles and the rapid collapse of marine sectors of the West Antarctic Ice Sheet in the coming centuries and provide appropriate time window profiles for each application. The time window algorithm reduces the total CPU time by ~ 50 % in each of these examples and changes the trend of the total CPU time increase from quadratic to linear. This improvement would increase with longer simulations than those considered here. Our algorithm also allows for coupling time intervals of annual temporal scale for coupled ice-sheet–sea-level modelling of regions such as West Antarctica that are characterized by rapid solid Earth response to ice changes due to the thin lithosphere and low mantle viscosities.

59 BASIC BIOLOGICAL SCIENCES↗

Solving high-dimensional inverse problems using amortized likelihood-free inference with noisy and incomplete data

Here, we present a likelihood-free probabilistic inversion method based on normalizing flows for high-dimensional inverse problems. The proposed method is composed of two complementary networks: a summary network for data compression and an inference network for parameter estimation. The summary network encodes raw observations into a fixed-size vector of summary features, while the inference network generates samples of the approximate posterior distribution of the model parameters based on these summary features. The posterior samples are produced in a deep generative fashion by sampling from a latent Gaussian distribution and passing these samples through an invertible transformation. We construct this invertible transformation by sequentially alternating conditional invertible neural network and conditional neural spline flow layers. The summary and inference networks are trained simultaneously. We apply the proposed method to an inversion problem in groundwater hydrology to estimate the posterior distribution of the log-conductivity field conditioned on spatially sparse time-series observations of the system’s hydraulic head responses. The conductivity field is represented with 706 degrees of freedom in the considered problem. Comparison with the likelihood-based iterative ensemble smoother PEST-IES method demonstrates that the proposed method accurately estimates the parameter posterior distribution and the observations’ predictive posterior distribution at a fraction of the inference time of PEST-IES.

conditional invertible neural network↗

Normalizing flows for domain adaptation when identifying Λ hyperon events

Here this study focuses on the application of a normalizing flow as a method of domain adaptation when classifying physics data. Normalizing flows offer a way to transform data points between two different distributions. The present study investigates a novel method of transforming latent representations of physics data to a normal distribution and then to a physics distribution again. The final distribution models a simulated distribution. After being transformed, the data can be classified by a neural network trained on labeled simulation data. The present study succeeds in training two normalizing flows that can transform between data (or simulation) and a Gaussian distribution.

47 OTHER INSTRUMENTATION↗

Star Formation Histories from Spectral Energy Distributions and Color–magnitude Diagrams Agree: Evidence for Synchronized Star Formation in Local Volume Dwarf Galaxies over the Past 3 Gyr

Star formation histories (SFHs) reveal physical processes that influence how galaxies form their stellar mass. We compare the SFHs of a sample of 36 nearby (D ≲ 4 Mpc) dwarf galaxies from the ACS Nearby Galaxy Survey Treasury (ANGST), inferred from the color–magnitude diagrams (CMDs) of individually resolved stars in these galaxies, with those reconstructed by broadband spectral energy distribution (SED) fitting using the dense basis SED-fitting code. When comparing individual SFHs, we introduce metrics for evaluating SFH reconstruction techniques. For both the SED and CMD methods, the median normalized SFH of galaxies in the sample shows a period of quiescence at lookback times of 3–6 Gyr followed by rejuvenated star formation over the past 3 Gyr that remains active until the present day. To determine if these represent special epochs of star formation in the D <4 Mpc portion of the Local Volume, we break this ANGST dwarf galaxy sample into subsets based on specific star formation rate and spatial location. Modulo offsets between the methods of about 1 Gyr, all subsets show significant decreases and increases in their median normalized SFHs at the same epochs, and the majority of the individual galaxy SFHs are consistent with these trends. These results motivate further study of potential synchronized star formation quiescence and rejuvenation in the Local Volume as well as development of a hybrid method of SFH reconstruction that combines CMDs and SEDs, which have complementary systematics.

79 ASTRONOMY AND ASTROPHYSICS↗

Bay Area Regional Energy: Network Integrated Commercial Retrofits (BRICR) Project. Final Report

The BRICR project applied large-scale building energy modeling concepts with the aim of reducing the cost of energy efficiency targeting, design, and project development, and measurement of energy savings for energy efficiency programs implemented by local governments that serve small and medium commercial buildings (SMB). The project leveraged the services and resources of existing local government energy programs serving disadvantaged and hard-to-reach SMB customers. In contrast to programs run by utilities, local government programs generally do not have direct access to energy billing records for an entire class of customers in a geographic area, which prior research demonstrated useful for large-scale building energy model baseline development and calibration. , However, local governments are rich in public records that offer important clues about physical attributes and uses that, along with behavior, determine energy use. Relying only on public records, BRICR demonstrated development of credible baseline energy models for 3,792 office, retail, and hotel buildings. Publicly disclosed annual energy use data from a local energy benchmarking program and anonymized data from the Building Performance Database, the nation’s largest dataset about energy-related characteristics of buildings, were utilized to validate and calibrate energy models via an innovative method comparing distributions of energy intensity by fuel type for portfolios of buildings of similar size, vintage, and use. Portfolio calibration does not provide certainty that an energy model fits an individual building; the method is useful when billing data is not accessible – a common situation for researchers, energy service providers and ESCOs, local governments, and any party other than a utility. A software component was developed, the BRICR gem, which automates simulation when relevant data is added or edited by the user to a file saved in the standardized BuildingSync XML schema for energy audit data. The component was demonstrated as a simplified means to generate a mass of energy models corresponding to public records containing basic attributes such as building scale, location, use, year built, and aspect ratio in combination with building energy code prototype data corresponding to use and vintage. The component was also demonstrated as a simplified means to automate energy simulation when attributes are revised; the intention was to enable iterative improvement of the baseline model and energy savings estimates for common energy conservation measures as users revise relevant attributes based on their observations. In the context of institutional change and uncertainty for the participating local government energy programs, 13 whole building retrofits were completed. Impacts were measured by applying the CalTRACK2.0 methods to standardize measurement of normalized metered energy consumption. The GRIDMeter methods of stratified sampling and individual load shape analysis were applied to adjust for impacts of the effect of COVID-19 on retrofitted buildings in the context of all local buildings of similar size and use. Excluding impacts of the pandemic, retrofitted buildings demonstrated between 1.6% and 25.1% reduction in energy use. The project contributed use cases and feedback that helped inform evolution of the software tools and data formats that were combined for the first time in the BRICR project.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

GalaxyFlow: upsampling hydrodynamical simulations for realistic mock stellar catalogues

ABSTRACT Cosmological N-body simulations of galaxies operate at the level of ‘star particles’ with a mass resolution on the scale of thousands of solar masses. Turning these simulations into stellar mock catalogues requires ‘upsampling’ the star particles into individual stars following the same phase-space density. In this paper, we introduce two new upsampling methods. First, we describe GalaxyFlow, a sophisticated upsampling method that utilizes normalizing flows to both estimate the stellar phase-space density and sample from it. Secondly, we improve on existing upsamplers based on adaptive kernel density estimation (KDE), using maximum likelihood estimation to fine-tune the bandwidth for such algorithms in a way that improves both the density estimation accuracy and upsampling results. We demonstrate our upsampling techniques on a neighbourhood of the Solar location in two simulated galaxies: Auriga 6 and h277. Both yield smooth stellar distributions that closely resemble the stellar densities seen in the Gaia DR3 catalogue. Furthermore, we introduce a novel multimodel classifier test to compare the accuracy of different upsampling methods quantitatively. This test confirms that GalaxyFlow more accurately estimates the density of the underlying star particles than methods based on KDE, at the cost of being more computationally intensive.

Lim, Sung Hak (ORCID:0000000330981092)↗

The Reservoir Temperature Estimator (RTEst): A multicomponent geothermometry tool

The Reservoir Temperature Estimator (RTEst) is a multicomponent geothermometry tool for estimating reservoir geochemical parameters including reservoir temperature, CO 2 fugacity, mass of water lost or gained, and a reaction factor. It estimates these parameters and their associated uncertainties by minimizing an objective function that is the weighted sum of squares of the saturation indices of a user-selected set of minerals believed to be equilibrated with the reservoir fluid. RTEst accomplishes these estimates by combining the geochemical modeling capabilities of The Geochemist’s Workbench® with the optimization/parameter estimation resources of PEST®. An included interface aids the user in selecting plausible mineral phases to comprise the objective function and calculates their weighting factors. The working principles of RTEst are described and its efficacy is illustrated by presenting results of its application to various geothermal fields with known conditions. These examples show RTEst can account for the alteration of ascending reservoir fluid by mineral (calcite) re-equilibration with changes in temperature, reconstruct waters with CO 2 loss, correct for the deficit of water and other volatiles (CO 2,gas , H 2 S gas ) from boiling, and determine the amount of mixing of thermal and non-thermal waters. RTEst can use data with basis species below detection limit, missing, or unreliable either by assuming equilibrium with a controlling mineral (fixed-analyte method) or by treating the analyte concentration as an optimization parameter. The inverse of variance weighting method included in RTEst provides more representative results than either the normalization or unit weighting methods. Finally, the ability of RTEst to calculate reservoir temperatures, gas fugacity, and mixing fractions demonstrates its usefulness as a tool for evaluating geothermal systems.

15 GEOTHERMAL ENERGY↗

Unique features and emerging in vitro models of human placental development

Abstract Background The placenta is an essential organ for the normal development of mammalian fetuses. Most of our knowledge on the molecular mechanisms of placental development has come from the analyses of mice, especially histopathological examination of knockout mice. Choriocarcinoma and immortalized cell lines have also been used for basic research on the human placenta. However, these cells are quite different from normal trophoblast cells. Methods In this review, we first provide an overview of mouse and human placental development with particular focus on the differences in the anatomy, transcription factor networks, and epigenetic characteristics between these species. Next, we discuss pregnancy complications associated with abnormal placentation. Finally, we introduce emerging in vitro models to study the human placenta, including human trophoblast stem (TS) cells, trophoblast and endometrium organoids, and artificial embryos. Main findings The placental structure and development differ greatly between humans and mice. The recent establishment of human TS cells and trophoblast and endometrial organoids enhances our understanding of the mechanisms underlying human placental development. Conclusion These in vitro models will greatly advance our understanding of human placental development and potentially contribute to the elucidation of the causes of infertility and other pregnancy complications.

Shibata, Shun↗