Crystal structure of a lipin/Pah phosphatidic acid phosphatase
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99 GENERAL AND MISCELLANEOUS↗
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Results for “activation function”
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Novel Amorphous Carbons for the Adsorption of Phosphate: Part I. Elucidation of Chemical Structure of N-Metal-Doped Chars
Due to phosphate’s necessity in agriculture and its danger to the environment, the development of adsorbents for its removal has been the subject of intensive research activity. Although the introduction of nitrogen functionality to chars and modification of biochar with metals have proven to change the character of the char structure, making it more active toward nutrients, there is no study regarding the doping of biochar with metals and nitrogen simultaneously for the adsorption of phosphates. This paper is the first of two in which we report the production, characterization, and evaluation of N-metal-doped biochars from cellulose for phosphate removal from liquid effluents. In this part, we describe the production and characterization of N-Ca-, N-Fe-, and N-Mg-doped biochars. The elemental composition and surface area of each of the materials produced is reported. Elemental and surface characterization of the chars are reported with the largest N content appearing at a temperature of 800 °C (12.5 wt %) and a maximum surface area for biochar produced at 900 °C (1314 m2/g). All of the adsorbents were visualized by scanning electron microscope (SEM), confirming that although there are some crystals on the surface of the biochar produced, most of the N, Mg, and Ca are part of the polyaromatic ring structure. Transmission electron microscope (TEM) images clearly show the formation of nanoclusters with the metals in the case of N-Fe and N-Ca biochars. The N-Mg biochars show a uniform distribution of the Mg through the carbon surface. X-ray photoelectron spectroscopy (XPS) studies of the biochars produced with metals and varying nitrogen levels clearly show Mg and Ca peaks shifting their position in the presence of N, suggesting the formation of stable structures between metals and N in the carbon polyaromatic ring system. To elucidate the nature of these structures, we conducted DFT-based calculations on different configurations of the nitrogenated structures. The calculated binding energy shifts were found to closely match the XPS experimental binding energy, confirming the likelihood of these structures in biochar. Finally, based on our experimental and modeling results, we hypothesize that an important fraction of the Mg and Ca is introduced to these biochars at the edges. Another fraction of Mg and Ca is in the form of phthalocyanine-like internal structures. More experimental studies are needed to confirm the formation of these very interesting structures and their potential use as adsorbents or catalysts.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Management and Climate Contributions to Satellite-Derived Active Fire Trends in the Contiguous United States
Fires in croplands, plantations, and rangelands contribute significantly to fire emissions in the United States, yet are often overshadowed by wildland fires in efforts to develop inventories or estimate responses to climate change. Here we quantified decadal trends, interannual variability, and seasonality of Terra Moderate Resolution Imaging Spectroradiometer (MODIS) observations of active fires (thermal anomalies) as a function of management type in the contiguous U.S. during 2001-2010. We used the Monitoring Trends in Burn Severity database to identify active fires within the perimeter of large wildland fires and land cover maps to identify active fires in croplands. A third class of fires defined as prescribed/other included all residual satellite active fire detections. Large wildland fires were the most variable of all three fire types and had no significant annual trend in the contiguous U.S. during 2001-2010. Active fires in croplands, in contrast, increased at a rate of 3.4 percent per year. Cropland and prescribed/other fire types combined were responsible for 77 percent of the total active fire detections within the U.S and were most abundant in the south and southeast. In the west, cropland active fires decreased at a rate of 5.9 percent per year, likely in response to intensive air quality policies. Potential evaporation was a dominant regulator of the interannual variability of large wildland fires, but had a weaker influence on the other two fire types. Our analysis suggests it may be possible to modify landscape fire emissions within the U.S. by influencing the way fires are used in managed ecosystems.
Satellite-derived↗
Adaptive, Active Learning, and Multifidelity Monte Carlo Methods in the MOOSE Stochastic Tools Module
MOOSE is an open-source computational platform for constructing multi-physics models and executing them in a massively parallel fashion. It has a stochastic tools module (STM) for forward/inverse uncertainty quantification (UQ) and surrogate modeling. This presentation details some recent developments to the STM with respect to the implementation of adaptive, active learning, and multifidelity Monte Carlo methods for forward UQ of computational models. Specifically, the adaptive Monte Carlo methods include Markov Chain Monte Carlo (MCMC)-driven algorithms like adaptive importance sampling and parallelized subset simulation for statistical QoI estimation, rare events analysis, and stochastic gradient-free optimization. The active learning methods include Gaussian Process (GP) surrogates and their training via Adam optimization, design of acquisition functions, and integration with samplers like Monte Carlo, adaptive importance, and parallelized subset simulation. These active learning methods are also designed to work in a batch mode, wherein, the required calls to the full computational model are executed in parallel whenever a user-specified batch size is met. The multifidelity methods in STM are broadly divided into two categories: hierarchical, where a defined hierarchy exists among the low-fidelity models, and peer, where all the low-fidelity models are treated equally. A GP surrogate is used to learn the differences between the low- and high-fidelity models in both multifidelity categories, and acquisition functions from the active learning classes are used to decide whether to rely on a low-fidelity model or call the expensive high-fidelity model. Alongside the software description and usage, applications are also presented to nuclear engineering computational models including a TRISO nuclear fuel particle, a reactor pressure vessel, and a heat-pipe microreactor.
97 MATHEMATICS AND COMPUTING↗
Skeletal muscle satellite cells
Evidence now suggests that satellite cells constitute a class of myogenic cells that differ distinctly from other embryonic myoblasts. Satellite cells arise from somites and first appear as a distinct myoblast type well before birth. Satellite cells from different muscles cannot be functionally distinguished from one another and are able to provide nuclei to all fibers without regard to phenotype. Thus, it is difficult to ascribe any significant function to establishing or stabilizing fiber type, even during regeneration. Within a muscle, satellite cells exhibit marked heterogeneity with respect to their proliferative behavior. The satellite cell population on a fiber can be partitioned into those that function as stem cells and those which are readily available for fusion. Recent studies have shown that the cells are not simply spindle shaped, but are very diverse in their morphology and have multiple branches emanating from the poles of the cells. This finding is consistent with other studies indicating that the cells have the capacity for extensive migration within, and perhaps between, muscles. Complexity of cell shape usually reflects increased cytoplasmic volume and organelles including a well developed Golgi, and is usually associated with growing postnatal muscle or muscles undergoing some form of induced adaptive change or repair. The appearance of activated satellite cells suggests some function of the cells in the adaptive process through elaboration and secretion of a product. Significant advances have been made in determining the potential secretion products that satellite cells make. The manner in which satellite cell proliferative and fusion behavior is controlled has also been studied. There seems to be little doubt that cellcell coupling is not how satellite cells and myofibers communicate. Rather satellite cell regulation is through a number of potential growth factors that arise from a number of sources. Critical to the understanding of this form of control is to determine which of the many growth factors that can alter satellite cell behavior in vitro are at work in vivo. Little work has been done to determine what controls are at work after a regeneration response has been initiated. It seems likely that, after injury, growth factors are liberated through proteolytic activity and initiate an activation process whereby cells enter into a proliferative phase. After myofibers are formed, it also seems likely that satellite cell behavior is regulated through diffusible factors arising from the fibers rather than continuous control by circulating factors.(ABSTRACT TRUNCATED AT 400 WORDS).
NASA Program Space Biology↗
Unveiling Synergetic Photocatalytic Activity from Heterometallic Ti/Ce Clusters
Titanium-oxo clusters, with their robust structure and suitable optical and electronic properties, have been widely investigated as photocatalysts. Heterometallic Ti/M-oxo clusters provide additional tunability and functionality, which enable systematic structure-activity investigations to elucidate reaction mechanisms and improve catalyst de-sign. Incorporating cerium into Ti-oxo clusters can provide additional redox (Ce IV /Ce III ) and oxygen harvesting ability, but to date only limited number of structurally defined titanium-cerium (Ti/Ce) clusters have been reported due to their synthetic challenges. Herein, we report the synthesis and photocatalytic properties of two structurally defined Ti/Ce-oxo clusters, Ti 8 Ce 2 (BA) 16 and Ti 9 Ce 4 (BA) 20 , as well as a TiCe-BA cluster with a calculated formula of Ti 20 Ce 9 O 36 (BA) 42 . Photocatalytic study of these clusters demonstrates that the amount of Ce 3+ species greatly impacts its photocatalytic oxidation performance, and their superior photocatalytic reactivity towards aerobic alcohol oxidation can be contributed to the synergistic effects of the multiple radical species generated upon light absorption. Furthermore, this work represents a significant milestone in the construction of stable Ti/Ce-oxo clusters, enriching the current library of known heterometallic Ti/M-oxo clusters, and providing a series of crystalline materials with great promise of photo-luminescence and photovoltaic chemistry.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Technical Capability Level 2 Unmanned Aircraft System Traffic Management (UTM) Flight Demonstration: Description and Analysis
NASA's UAS Traffic Management (UTM) project concluded its second flight demonstration activity in late October 2016. This activity demonstrated the capabilities and functionality incorporated into its Technical Capability Level 2 (TCL2) concept, which envisions future operations that are low density, capable of being performed over sparsely populated areas, and allow for a concurrent mix of longer duration, beyond visual-line-of-sight flights and shorter flights within visual-line-of-sight (VLOS). To incorporate these features into a flight demonstration, a scenario-based approach was taken to address different aspects of the TCL2 environment and to meet defined objectives. This paper will describe elements of how the flight activity was conducted and present analyses regarding UTM operations, system messages, and alerting as they pertained to meeting the demonstration objectives and shedding light on research questions and lessons learned.NASA was able to successfully demonstrate complex UTMoperations in a TCL 2 environment in collaboration withindustry partners and the Reno-Stead Airport UAS test range.A scenario-based approach to the demonstration provided arelevant means through which the key elements and objectivesof the test could be captured. Although issues were identifiedthrough the testing and feedback of test participants, theoverall results were in line with the overall UTM objective ofsafely enabling large-scale UAS operations in low altitudeairspace.
Homola, Jeffrey↗
A time dependent anatomically detailed model of cardiac conduction
In order to understand the determinants of transitions in cardiac electrical activity from normal patterns to dysrhythmias such as ventricular fibrillation, we are constructing an anatomically and physiologically detailed finite element simulation of myocardial electrical propagation. A healthy human heart embedded in paraffin was sectioned to provide a detailed anatomical substrate for model calculations. The simulation of propagation includes anisotropy in conduction velocity due to fiber orientation as well as gradients in conduction velocities, absolute and relative refractory periods, action potential duration and electrotonic influence of nearest neighbors. The model also includes changes in the behaviour of myocardial tissue as a function of the past local activity. With this model, we can examine the significance of fiber orientation and time dependence of local propagation parameters on dysrhythmogenesis.
Computer Simulation↗
Uncrewed Lunar Surface Operations and Support Activities
This presentation summarizes the contents of the uncrewed lunar surface operations and support activities paper. It outlines the functions, features, and capabilities that support sustained human and robotic surface operations. It summarizes the complexities associated with the development and operation of autonomous systems and discusses a simulation tool for integrated surface operations planning.
Lunar↗
Low-Activity Waste Melter Process (LMP) System Design Description (Rev. 4)
This system design description (SDD) defines the technical, functional, and performance requirements of the low-activity waste (LAW) melter process system (LMP). This document details the waste treatment requirements, environmental compliance requirements, and authorization basis requirements of the LMP system as they are currently known and understood. This SDD describes the process and functional design requirements of the LMP, including the following: 1) Services and utility requirements, operating materials and supplies, and other external interfaces; 2) Operations limits and design bases; 3) Other criteria and requirements pertinent to the design of the LMP system; 4) Boundaries, system interfaces, and functional description of the LMP system. The LMP system is composed of two LAW melters of the same design with the contingency to add the third. Also included in the LMP system are the pour spouts, which are positioned under the melter discharge chambers of each melter, and the container level detectors. The boundaries, system interfaces, and functional description of the LMP system are provided in Section 2.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Functional characterization of diverse type I-F CRISPR-associated transposons
CRISPR-Cas systems generally provide adaptive immunity in prokaryotes through RNA-guided degradation of foreign genetic elements like bacteriophages and plasmids. Recently, however, transposon-encoded and nuclease-deficient CRISPR-Cas systems were characterized and shown to be co-opted by Tn7-like transposons for CRISPR RNA-guided DNA transposition. As a genome engineering tool, these CRISPR-Cas systems and their associated transposon proteins can be deployed for programmable, site-specific integration of sizable cargo DNA, circumventing the need for DNA cleavage and homology-directed repair involving endogenous repair machinery. Here, we selected a diverse set of type I-F3 CRISPR-associated transposon systems derived from Gammaproteobacteria, predicted all components essential for transposition activity, and deployed them for functionality testing within Escherichia coli. Our results demonstrate that these systems possess a significant range of integration efficiencies with regards to temperature, transposon size, and flexible PAM requirements. Additionally, our findings support the categorization of these systems into functional compatibility groups for efficient and orthogonal RNA-guided DNA integration. This work expands the CRISPR-based toolbox with new CRISPR RNA-guided DNA integrases that can be applied to complex and extensive genome engineering efforts.
59 BASIC BIOLOGICAL SCIENCES↗
Structures of TGF-β with betaglycan and signaling receptors reveal mechanisms of complex assembly and signaling
Abstract Betaglycan (BG) is a transmembrane co-receptor of the transforming growth factor-β (TGF-β) family of signaling ligands. It is essential for embryonic development, tissue homeostasis and fertility in adults. It functions by enabling binding of the three TGF-β isoforms to their signaling receptors and is additionally required for inhibin A (InhA) activity. Despite its requirement for the functions of TGF-βs and InhA in vivo, structural information explaining BG ligand selectivity and its mechanism of action is lacking. Here, we determine the structure of TGF-β bound both to BG and the signaling receptors, TGFBR1 and TGFBR2. We identify key regions responsible for ligand engagement, which has revealed binding interfaces that differ from those described for the closely related co-receptor of the TGF-β family, endoglin, thus demonstrating remarkable evolutionary adaptation to enable ligand selectivity. Finally, we provide a structural explanation for the hand-off mechanism underlying TGF-β signal potentiation.
Science & Technology - Other Topics↗
Studies of Neutron and Proton Nuclear Activation in Low-Earth Orbit 2
The study of neutron and proton nuclear activation in low-Earth orbit reported in NASA CR-162051 has been continued with increasing emphasis given to primary and secondary neutron activation. The previously reported activation due to protons has been modified to include: (1) flux attenuation caused by all inelastic reactions; (2) the modification of the proton flux distribution caused by sample covering material; and (3) the activation of the sample as a function of the distance into the sample from the surface of incidence. A method has been developed for including the effects on the activation of the finite width and length of the samples. The reactant product spectra produced by proton-induced reactions has been studied. Cross sections needed for neutron induced reactions leading to long-lived (half-life 1 day) radioisotopes have been identified and, in some cases, compiled.
Laird, C. E.↗
Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its [4Fe-4S] cluster cofactor and active site required for DNA repair
Abstract MUTYH is a clinically important DNA glycosylase that thwarts mutations by initiating base-excision repair at 8-oxoguanine (OG):A lesions. The roles for its [4Fe-4S] cofactor in DNA repair remain enigmatic. Functional profiling of cancer-associated variants near the [4Fe-4S] cofactor reveals that most variations abrogate both retention of the cofactor and enzyme activity. Surprisingly, R241Q and N238S retained the metal cluster and bound substrate DNA tightly, but were completely inactive. We determine the crystal structure of human MUTYH bound to a transition state mimic and this shows that Arg241 and Asn238 build an H-bond network connecting the [4Fe-4S] cluster to the catalytic Asp236 that mediates base excision. The structure of the bacterial MutY variant R149Q, along with molecular dynamics simulations of the human enzyme, support a model in which the cofactor functions to position and activate the catalytic Asp. These results suggest that allosteric cross-talk between the DNA binding [4Fe-4S] cofactor and the base excision site of MUTYH regulate its DNA repair function.
Science & Technology - Other Topics↗
Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model
The brain produces diverse functions, from perceiving sounds to producing arm reaches, through the collective activity of populations of many neurons. Determining if and how the features of these exogenous variables (e.g., sound frequency, reach angle) are reflected in population neural activity is important for understanding how the brain operates. Often, high-dimensional neural population activity is confined to low-dimensional latent spaces. However, many current methods fail to extract latent spaces that are clearly structured by exogenous variables. This has contributed to a debate about whether or not brains should be thought of as dynamical systems or representational systems. Here, we developed a new latent process Bayesian regression framework, the orthogonal stochastic linear mixing model (OSLMM) which introduces an orthogonality constraint amongst time-varying mixture coefficients, and provide Markov chain Monte Carlo inference procedures. We demonstrate superior performance of OSLMM on latent trajectory recovery in synthetic experiments and show superior computational efficiency and prediction performance on several real-world benchmark data sets. We primarily focus on demonstrating the utility of OSLMM in two neural data sets: μ ECoG recordings from rat auditory cortex during presentation of pure tones and multi-single unit recordings form monkey motor cortex during complex arm reaching. We show that OSLMM achieves superior or comparable predictive accuracy of neural data and decoding of external variables (e.g., reach velocity). Most importantly, in both experimental contexts, we demonstrate that OSLMM latent trajectories directly reflect features of the sounds and reaches, demonstrating that neural dynamics are structured by neural representations. Together, these results demonstrate that OSLMM will be useful for the analysis of diverse, large-scale biological time-series datasets.
59 BASIC BIOLOGICAL SCIENCES↗
Active microwave sensor technology, chapter 5
The relationship between surface properties and echo characteristics, as determined by radar technology, is discussed; echo enhancement to reduce measurement uncertainty was included. Feasibility data, suggested baseline functional descriptions of various types of active microwave sensors, and examples of existing radar techniques are summarized. Data manage and measurement processes are also covered.
Source record↗
Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity
We report the biochemical, structural, and functional characterization of the protein coded by gene PA4880 in the P. aeruginosa PAO1 genome. The PA4880 gene had been annotated as coding a probable bacterioferritin. Our structural work shows that the product of gene PA4880 is a protein that adopts the Dps subunit fold, which oligomerizes into a 12-mer quaternary structure. Unlike Dps, however, the ferroxidase di-iron centers and iron coordinating ligands are buried within each subunit, in a manner identical to that observed in the ferroxidase center of P. aeruginosa bacterioferritin. Since these structural characteristics correspond to Dps-like proteins, we term the protein as P. aeruginosa Dps-like, or Pa DpsL. The ferroxidase centers in Pa DpsL catalyze the oxidation of Fe 2+ utilizing O 2 or H 2 O 2 as oxidant, and the resultant Fe 3+ is compartmentalized in the interior cavity. Interestingly, incubating Pa DpsL with plasmid DNA results in efficient nicking of the DNA and at higher concentrations of Pa DpsL the DNA is linearized and eventually degraded. The nickase and endonuclease activities suggest that Pa DpsL, in addition to participating in the defense of P. aeruginosa cells against iron-induced toxicity, may also participate in the innate immune mechanisms consisting of restriction endonucleases and cognate methyl transferases.
59 BASIC BIOLOGICAL SCIENCES↗
Origin of Electrochemical Activation Leading to Enhanced Cycling Stability of Li‐ and Mn‐Rich Cathodes
Electrochemical activation is a critical step for optimal functioning of Li- and Mn-rich (LMR) cathodes, yet the underlying mechanism for such activation remains elusive. Here, by using scanning/transmission electron microscopy (S/TEM) combined with the associated energy-dispersive x-ray spectroscopy (EDS) and electron energy-loss spectroscopy (EELS), we decipher the origin of the activation enhanced electrochemical properties. We reveal that activation induces the formation of a spinel-like phase within the C2/m domains of the LMR cathode, where the transition-metal ions partially occupy both the tetrahedral (8a) and octahedral (16c) sites of the $Fd\bar{3}m$ spinel lattice, distinguishing the spinel-like phase from the conventional high-voltage spinel. Systematic varying the cycling voltage reveals a critical activation voltage above which this spinel-like phase forms, while lower voltages preserve the layered bulk structure. As the spinel-like phase is a stable structure for electrochemical cycling, the present findings provide direct mechanistic insight into the voltage-dependent activation process and explain how the C2/m to spinel-like transformation upon activation contributes to the electrochemical performance of LMR cathodes, providing guidance for the rational design of Li-rich cathodes with enhanced cycling durability.
Li-rich and Mn-rich cathode↗