Genetic mapping of complement system proteins for islet autoimmunity in children with high risk of T1D
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Life Sciences & Biomedicine - Other Topics↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Making Common Fund data more findable: catalyzing a data ecosystem
The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes of Health Common Fund without requiring that data owners move, reformat, or rehost those data. This system is centered on a catalog that integrates detailed descriptions of biomedical datasets from individual Common Fund Programs’ Data Coordination Centers (DCCs) into a uniform metadata model that can then be indexed and searched from a centralized portal. This Crosscut Metadata Model (C2M2) supports the wide variety of data types and metadata terms used by individual DCCs and can readily describe nearly all forms of biomedical research data. We detail its use to ingest and index data from 11 DCCs.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Proteome-wide association study and functional validation identify novel protein markers for pancreatic ductal adenocarcinoma
Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy, largely due to the paucity of reliable biomarkers for early detection and therapeutic targeting. Existing blood protein biomarkers for PDAC often suffer from replicability issues, arising from inherent limitations such as unmeasured confounding factors in conventional epidemiologic study designs. To circumvent these limitations, we use genetic instruments to identify proteins with genetically predicted levels to be associated with PDAC risk. Leveraging genome and plasma proteome data from the INTERVAL study, we established and validated models to predict protein levels using genetic variants. By examining 8,275 PDAC cases and 6,723 controls, we identified 40 associated proteins, of which 16 are novel. Functionally validating these candidates by focusing on 2 selected novel protein-encoding genes, GOLM1 and B4GALT1, we demonstrated their pivotal roles in driving PDAC cell proliferation, migration, and invasion. Furthermore, we also identified potential drug repurposing opportunities for treating PDAC.
60 APPLIED LIFE SCIENCES↗
iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
Background: Scientists have amassed a wealth of microbiome datasets, making it possible to study microbes in biotic and abiotic systems on a population or planetary scale; however, this potential has not been fully realized given that the tools, datasets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community. Findings: The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation–supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API, which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP). Conclusions: iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform.
59 BASIC BIOLOGICAL SCIENCES↗
Models, Databases, and Simulation Tools Needed for the Realization of Integrated Computational Materials Engineering. Proceedings of the Symposium Held at Materials Science and Technology 2010
Topics covered include: An Annotative Review of Multiscale Modeling and its Application to Scales Inherent in the Field of ICME; and A Multiscale, Nonlinear, Modeling Framework Enabling the Design and Analysis of Composite Materials and Structures.
Arnold, Steven M.↗
Molecular coupling competing with defects within insulator of the magnetic tunnel junction-based molecular spintronics devices
Nearly 70 years old dream of incorporating molecule as the device element is still challenged by competing defects in almost every experimentally tested molecular device approach. This paper focuses on the magnetic tunnel junction (MTJ) based molecular spintronics device (MTJMSD) method. An MTJMSD utilizes a tunnel barrier to ensure a robust and mass-producible physical gap between two ferromagnetic electrodes. MTJMSD approach may benefit from MTJ's industrial practices; however, the MTJMSD approach still needs to overcome additional challenges arising from the inclusion of magnetic molecules in conjunction with competing defects. Molecular device channels are covalently bonded between two ferromagnets across the insulating barrier. An insulating barrier may possess a variety of potential defects arising during the fabrication or operational phase. This paper describes an experimental and theoretical study of molecular coupling between ferromagnets in the presence of the competing coupling via an insulating tunnel barrier. We discuss the experimental observations of hillocks and pinhole-type defects producing inter-layer coupling that compete with molecular device elements. We performed theoretical simulations to encompass a wide range of competition between molecules and defects. Monte Carlo Simulation (MCS) was used for investigating the defect-induced inter-layer coupling on MTJMSD. Our research may help understand and design molecular spintronics devices utilizing various insulating spacers such as aluminum oxide (AlOx) and magnesium oxide (MgO) on a wide range of metal electrodes. This paper intends to provide practical insights for researchers intending to investigate the molecular device properties via the MTJMSD approach and do not have a background in magnetic tunnel junction fabrication.
36 MATERIALS SCIENCE↗
van der Waals Correction to the Physisorption of Graphene on Metal Surfaces
Adsorption is a scientifically and technologically important interfacial phenomenon, which however presents challenges to conventional density functional theory (DFT) due to the long-range van der Waals (vdW) interactions. We have developed a model of long-range vdW correction for physisorption of graphene (G) on metals with the Lifshitz–Zaremba–Kohn second-order perturbation theory, by incorporating dipole- and quadrupole-surface interactions and screening effects. The physisorption energies calculated by the model between graphene and eight metal surfaces (Al, Ni, Co, Pd, Pt, Cu, Ag, and Au), and the adsorption energies for the same G/metal structures from self-consistent DFT PBE (Perdew–Burke–Ernzerhof) calculations, are obtained in a range of distances between G and the metal surfaces. The sum of these two parts is the total adsorption energy as a function of the distance, from which the equilibrium distance and the binding energy are determined simultaneously. The results show high accuracy, with the mean absolute error (MAE) of binding energy of 7 meV and the MAE of equilibrium distance of 0.2 Å, significantly improving upon other vdW methods. Here, the PBE + vdW binding energy curves give better fits to the random phase approximation curves around the equilibrium distances than do the curves of other methods considered here. The higher-order quadrupole-surface correction is important and accounts for about 30% of the total vdW correction.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Distinct magneto-Raman signatures of spin-flip phase transitions in CrI 3
The discovery of 2-dimensional (2D) materials, such as CrI 3 , that retain magnetic ordering at monolayer thickness has resulted in a surge of both pure and applied research in 2D magnetism. Here, we report a magneto-Raman spectroscopy study on multilayered CrI 3 , focusing on two additional features in the spectra that appear below the magnetic ordering temperature and were previously assigned to high frequency magnons. Instead, we conclude these modes are actually zone-folded phonons. We observe a striking evolution of the Raman spectra with increasing magnetic field applied perpendicular to the atomic layers in which clear, sudden changes in intensities of the modes are attributed to the interlayer ordering changing from antiferromagnetic to ferromagnetic at a critical magnetic field. Our work highlights the sensitivity of the Raman modes to weak interlayer spin ordering in CrI 3 .
47 OTHER INSTRUMENTATION↗
Identifying critical features of iron phosphate particle for lithium preference
One-dimensional (1D) olivine iron phosphate (FePO 4 ) is widely proposed for electrochemical lithium (Li) extraction from dilute water sources, however, significant variations in Li selectivity were observed for particles with different physical attributes. Understanding how particle features influence Li and sodium (Na) co-intercalation is crucial for system design and enhancing Li selectivity. Here, we investigate a series of FePO 4 particles with various features and revealed the importance of harnessing kinetic and chemo-mechanical barrier difference between lithiation and sodiation to promote selectivity. The thermodynamic preference of FePO 4 provides baseline of selectivity while the particle features are critical to induce different kinetic pathways and barriers, resulting in different Li to Na selectivity from 6.2 × 10 2 to 2.3 × 10 4 . Importantly, we categorize the FePO 4 particles into two groups based on their distinctly paired phase evolutions upon lithiation and sodiation, and generate quantitative correlation maps among Li preference, morphological features, and electrochemical properties. By selecting FePO 4 particles with specific features, we demonstrate fast (636 mA/g) Li extraction from a high Li source (1: 100 Li to Na) with (96.6 ± 0.2)% purity, and high selectivity (2.3 × 10 4 ) from a low Li source (1: 1000 Li to Na) with (95.8 ± 0.3)% purity in a single step.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins
Zinc acquisition from limited environments is critical for bacterial survival and pathogenesis. AztD has been identified as a periplasmic or cell surface zinc-binding protein in numerous bacterial species. In Paracoccus denitrificans , AztD can transfer zinc directly to AztC, the solute binding protein for a zinc-specific ATP-binding cassette transporter system, suggesting a role in zinc acquisition and homeostasis. Here, we present the first cry stal structures of AztD from P. denitrificans and tbe human pathogen Citrobacter koseri , revealing a beta-propeller fold and two high-affinity zinc-binding sites that are highly conserved among AztD homologs. These structures combined with transfer assays using WT and mutant proteins provide rare insight into the mechanism of direct zinc transfer from one protein to another. Given the importance of zinc import to bacterial pathogenesis, these insights may prove valuable to the development of zinc transfer inhibitors as antibiotics.
59 BASIC BIOLOGICAL SCIENCES↗
Effects of presenilin-1 familial Alzheimer’s disease mutations on γ-secretase activation for cleavage of amyloid precursor protein
Presenilin-1 (PS1) is the catalytic subunit of γ-secretase which cleaves within the transmembrane domain of over 150 peptide substrates. Dominant missense mutations in PS1 cause early-onset familial Alzheimer’s disease (FAD); however, the exact pathogenic mechanism remains unknown. Here we combined Gaussian accelerated molecular dynamics (GaMD) simulations and biochemical experiments to determine the effects of six representative PS1 FAD mutations (P117L, I143T, L166P, G384A, L435F, and L286V) on the enzyme-substrate interactions between γ-secretase and amyloid precursor protein (APP). Biochemical experiments showed that all six PS1 FAD mutations rendered γ-secretase less active for the endoproteolytic (ε) cleavage of APP. Distinct low-energy conformational states were identified from the free energy profiles of wildtype and PS1 FAD-mutant γ-secretase. The P117L and L286V FAD mutants could still sample the “Active” state for substrate cleavage, but with noticeably reduced conformational space compared with the wildtype. The other mutants hardly visited the “Active” state. The PS1 FAD mutants were found to reduce γ-secretase proteolytic activity by hindering APP residue L49 from proper orientation in the active site and/or disrupting the distance between the catalytic aspartates. Therefore, our findings provide mechanistic insights into how PS1 FAD mutations affect structural dynamics and enzyme-substrate interactions of γ-secretase and APP.
60 APPLIED LIFE SCIENCES↗
High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates
Abstract The ability to perform sophisticated, high-throughput optogenetic experiments has been greatly enhanced by recent open-source illumination devices that allow independent programming of light patterns in single wells of microwell plates. However, there is currently a lack of instrumentation to monitor such experiments in real time, necessitating repeated transfers of the samples to stand-alone analytical instruments, thus limiting the types of experiments that could be performed. Here we address this gap with the development of the optoPlateReader (oPR), an open-source, solid-state, compact device that allows automated optogenetic stimulation and spectroscopy in each well of a 96-well plate. The oPR integrates an optoPlate illumination module with a module called the optoReader, an array of 96 photodiodes and LEDs that allows 96 parallel light measurements. The oPR was optimized for stimulation with blue light and for measurements of optical density and fluorescence. After calibration of all device components, we used the oPR to measure growth and to induce and measure fluorescent protein expression in E. coli . We further demonstrated how the optical read/write capabilities of the oPR permit computer-in-the-loop feedback control, where the current state of the sample can be used to adjust the optical stimulation parameters of the sample according to pre-defined feedback algorithms. The oPR will thus help realize an untapped potential for optogenetic experiments by enabling automated reading, writing, and feedback in microwell plates through open-source hardware that is accessible, customizable, and inexpensive.
59 BASIC BIOLOGICAL SCIENCES↗
Topology on a new facet of bismuth
Bismuth-based materials have been instrumental in the development of topological physics, even though bulk bismuth itself has been long thought to be topologically trivial. A recent study has, however, shown that bismuth is in fact a higher-order topological insulator featuring one-dimensional (1D) topological hinge states protected by threefold rotational and inversion symmetries. In this paper, we uncover another hidden facet of the band topology of bismuth by showing that bismuth is also a first-order topological crystalline insulator protected by a twofold rotational symmetry. As a result, its ( 1 1 ¯ 0 ) surface exhibits a pair of gapless Dirac surface states. Remarkably, these surface Dirac cones are “unpinned” in the sense that they are not restricted to locate at specific k points in the ( 1 1 ¯ 0 ) surface Brillouin zone. These unpinned 2D Dirac surface states could be probed directly via various spectroscopic techniques. Our analysis also reveals the presence of a distinct, previously uncharacterized set of 1D topological hinge states protected by the twofold rotational symmetry. Our study thus provides a comprehensive understanding of the topological band structure of bismuth.
36 MATERIALS SCIENCE↗
Formation and surface-stabilizing contributions to bare nanoemulsions created with negligible surface charge
The stabilization of nanoemulsions, nanosized oil droplets dispersed in water, is commonly achieved through the addition of surfactants and polymers. However, nanoemulsions in the absence of emulsifiers have been observed to acquire a significant negative charge at their surface, which ultimately contributes to their stability. While the source of this negative charge is disputed to this day, its presence is taken as an inherent property of the aqueous–hydrophobic interface. This report provides a look at the molecular structure and bonding characteristics of bare aqueous–hydrophobic nanoemulsion interfaces. We report the creation of bare nanoemulsions with near zero surface charge, which are marginally stable for several days. The process of creating these low-charge nanoemulsions (LCNEs) required rigorous cleaning procedures and proper solvent storage conditions. Using vibrational sum-frequency scattering spectroscopy, we measure the structure and bonding of the interfacial aqueous and hydrophobic phases. The surfaces of these LCNE samples possess a measurable free OH vibration, not found in previous studies and indicative of a clean interface. Tuning the nanoemulsion charge through addition of anionic surfactants, modeling potential surface-active contaminants, we observe the free OH to disappear and a reorientation of the interfacial hydrophobic molecules at micromolar surfactant concentrations. Notably, the free OH vibration provides evidence for stronger dispersion interactions between water molecules and the hydrophobic phase at the LCNE surface compared with similar planar water–alkane interfaces. We propose the stronger bonding interactions, in addition to an ordered interfacial aqueous layer, contribute to the delayed droplet coalescence and subsequent phase separation.
59 BASIC BIOLOGICAL SCIENCES↗
Giant impacts stochastically change the internal pressures of terrestrial planets
Pressure is a key parameter in the physics and chemistry of planet formation and evolution. Previous studies have erroneously assumed that internal pressures monotonically increase with the mass of a body. Using smoothed particle hydrodynamics and potential field method calculations, we demonstrate that the hot, rapidly rotating bodies produced by giant impacts can have much lower internal pressures than cool, slowly rotating planets of the same mass. Pressures subsequently increase because of thermal and rotational evolution of the body. Using the Moon-forming impact as an example, we show that the internal pressures after the collision could have been less than half that in present-day Earth. The current pressure profile was not established until Earth cooled and the Moon receded, a process that may take up to tens of millions of years. Our work defines a new paradigm for pressure evolution during accretion of terrestrial planets: stochastic changes driven by impacts.
79 ASTRONOMY AND ASTROPHYSICS↗
Topology control of human fibroblast cells monolayer by liquid crystal elastomer
Eukaryotic cells in living tissues form dynamic patterns with spatially varying orientational order that affects important physiological processes such as apoptosis and cell migration. The challenge is how to impart a predesigned map of orientational order onto a growing tissue. Here, we demonstrate an approach to produce cell monolayers of human dermal fibroblasts with predesigned orientational patterns and topological defects using a photoaligned liquid crystal elastomer (LCE) that swells anisotropically in an aqueous medium. The patterns inscribed into the LCE are replicated by the tissue monolayer and cause a strong spatial variation of cells phenotype, their surface density, and number density fluctuations. Unbinding dynamics of defect pairs intrinsic to active matter is suppressed by anisotropic surface anchoring allowing the estimation of the elastic characteristics of the tissues. The demonstrated patterned LCE approach has potential to control the collective behavior of cells in living tissues, cell differentiation, and tissue morphogenesis.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Visualization Techniques in Space and Atmospheric Sciences
Unprecedented volumes of data will be generated by research programs that investigate the Earth as a system and the origin of the universe, which will in turn require analysis and interpretation that will lead to meaningful scientific insight. Providing a widely distributed research community with the ability to access, manipulate, analyze, and visualize these complex, multidimensional data sets depends on a wide range of computer science and technology topics. Data storage and compression, data base management, computational methods and algorithms, artificial intelligence, telecommunications, and high-resolution display are just a few of the topics addressed. A unifying theme throughout the papers with regards to advanced data handling and visualization is the need for interactivity, speed, user-friendliness, and extensibility.
Szuszczewicz, E. P.↗
Excursions in technology policy
This technical report presents a summary of three distinct projects: (1) Measuring economic benefits; (2) Evaluating the SBIR program; and (3) A model for evaluating changes in support for science and technology. the first project deals with the Technology Applications Group (TAG) at NASA Langley Research Center. The mission of TAG is to assist firms interested in commercializing technologies. TAG is a relatively new group as is the emphasis on technology commercialization for NASA. One problem faced by TAG and similar groups at other centers is measuring their effectiveness. The first project this summer, a paper entitled, 'Measuring the Economic Benefits of Technology Transfer from a National Laboratory: A Primer,' focused on this measurement problem. We found that the existing studies of the impact of technology transfer on the economy were conceptually flawed. The 'primer' outlines the appropriate theoretical framework for measuring the economic benefits of technology transfer. The second project discusses, one of the programs of TAG, the Small Business Innovation Research (SBIR) program. This program has led to over 400 contracts with Small Business since its inception in 1985. The program has never been evaluated. Crucial questions such as those about the extent of commercial successes from the contracts need to be answered. This summer we designed and implemented a performance evaluation survey instrument. The analysis of the data will take place in the fall. The discussion of the third project focuses on a model for evaluating changes in support for science and technology. At present several powerful forces are combining to change the environment for science and technology policy. The end of the cold war eliminated the rationale for federal support for many projects. The new- found Congressional conviction to balance the budget without tax increases combined with demographic changes which automatically increase spending for some politically popular programs will make it difficult to find funding for science and technology. Also, the two political parties have very different conceptions of the appropriate future for research and development spending. All these changes create the potential for serious, perhaps unintended, consequences for the economic future of the country. In a paper entitled, 'A Conceptual Framework for Evaluating the Impact of Changes in Federal Support for Science and Technology,' we introduce a model to evaluate the effects of changes in federal spending for science and technology. This paper both provides a way of organizing informed discussions and points out important research topics for science and technology policy.
Archibald, Robert B.↗