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At least 1,783 records · Page 99
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

SU-F-I-49: Vendor-Independent, Model-Based Iterative Reconstruction On a Rotating Grid with Coordinate-Descent Optimization for CT Imaging Investigations

Purpose: Iterative reconstruction methods show promise for improving image quality and lowering the dose in helical CT. We aim to develop a novel model-based reconstruction method that offers potential for dose reduction with reasonable computation speed and storage requirements for vendor-independent reconstruction from clinical data on a normal desktop computer. Methods: In 2012, Xu proposed reconstructing on rotating slices to exploit helical symmetry and reduce the storage requirements for the CT system matrix. Inspired by this concept, we have developed a novel reconstruction method incorporating the stored-system-matrix approach together with iterative coordinate-descent (ICD) optimization. A penalized-least-squares objective function with a quadratic penalty term is solved analytically voxel-by-voxel, sequentially iterating along the axial direction first, followed by the transaxial direction. 8 in-plane (transaxial) neighbors are used for the ICD algorithm. The forward problem is modeled via a unique approach that combines the principle of Joseph’s method with trilinear B-spline interpolation to enable accurate reconstruction with low storage requirements. Iterations are accelerated with multi-CPU OpenMP libraries. For preliminary evaluations, we reconstructed (1) a simulated 3D ellipse phantom and (2) an ACR accreditation phantom dataset exported from a clinical scanner (Definition AS, Siemens Healthcare). Image quality was evaluated in the resolution module. Results: Image quality was excellent for the ellipse phantom. For the ACR phantom, image quality was comparable to clinical reconstructions and reconstructions using open-source FreeCT-wFBP software. Also, we did not observe any deleterious impact associated with the utilization of rotating slices. The system matrix storage requirement was only 4.5GB, and reconstruction time was 50 seconds per iteration. Conclusion: Our reconstruction method shows potential for furthering research in low-dose helical CT, in particular as part of our ongoing development of an acquisition/reconstruction pipeline for generating images under a wide range of conditions. Our algorithm will be made available open-source as “FreeCT-ICD”. NIH U01 CA181156; Disclosures (McNitt-Gray): Institutional research agreement, Siemens Healthcare; Past recipient, research grant support, Siemens Healthcare; Consultant, Toshiba America Medical Systems; Consultant, Samsung Electronics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Designing polymeric membranes with coordination chemistry for high-precision ion separations

State-of-the-art polymeric membranes are unable to perform the high-precision ion separations needed for technologies essential to a circular economy and clean energy future. Coordinative interactions are a mechanism to increase sorption of a target species into a membrane, but the effects of these interactions on membrane permeability and selectivity are poorly understood. We use a multilayered polymer membrane to assess how ion-membrane binding energies affect membrane permeability of similarly sized cations: Cu 2+ , Ni 2+ , Zn 2+ , Co 2+ , and Mg 2+ . We report that metals with higher binding energy to iminodiacetate groups of the polymer more selectively permeate through the membrane in multisalt solutions than single-salt solutions. In contrast, weaker binding species are precluded from diffusing into the polymer membrane, which leads to passage proportional to binding energy and independent of membrane thickness. Our findings demonstrate that selectivity of polymeric membranes can markedly increase by tailoring ion-membrane binding energy and minimizing membrane thickness.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Xylanolytic metabolism is regulated by coordination of transcription factors XynR and XylR in extremely thermophilic Caldicellulosiruptorales

ABSTRACT Global transcription factors (TFs) control metabolic processes in bacteria to efficiently utilize available carbon. The orderCaldicellulosiruptoraleshas drawn interest due to the ability of its members to degrade components of lignocellulosic biomass. Regulatory reconstruction ofAnaerocellum (f. Caldicellulosiruptor) besciiidentified two major global transcription factors for xylan utilization, XynR and XylR, and the corresponding putative transcription factor binding sites. Recombinant versions of XynR (LacI family) and XylR (ROK family) were subjected to fluorescence polarization (FP) and biolayer interferometry (BLI) analysis to confirm the predicted binding sites. Four XynR sites and two XylR sites were validated, accounting for 20 of 26 genes regulated by XynR and six of seven genes regulated by XylR. Bioinformatic analysis of the individual genes controlled by the two regulators showed an inter-dependent scheme for xylan conversion; the transport of xylooligosaccharides (XOS) is dependent on XylR, while enzymes responsible for hydrolysis are controlled by both regulators. For xylose catabolism by the xylose isomerase-xylulose kinase pathway, regulation is also split, with XylR controlling xylose isomerase and XynR controlling xylokinase. The XynR/XylR regulator pair withinA. besciiis conserved in all sequenced species ofCaldicellulosiruptorales, suggesting similarities in regulating linear xylan conversion. In other xylanolytic thermophiles, XylR homologs control xylan degradation, compared to just 6 out of 26 genes forA. bescii. These results show that two separate regulatory schemes (dual repression) are coordinated byA. besciito effectively regulate the hemicellulose inventory and xylan catabolism. IMPORTANCE To take full advantage of extreme thermophiles as platform metabolic engineering microorganisms, the tools for genetic manipulation must be further developed, and strategies that exploit a better understanding of metabolic regulation need to be discerned.Anaerocellum bescii, the most studied of the extremely thermophilic fermentative anaerobic bacteria that can utilize microcrystalline cellulose, can degrade microcrystalline cellulose and hemicellulose and has been metabolically engineered to convert the resulting sugars to products such as ethanol and acetone. For xylan, in particular, two major global transcription factors (TFs), XynR and XylR, play a role in sugar metabolism, although their predicted regulatory interdependence from bioinformatics analysis has not been elucidated experimentally. Here, fluorescence polarization (FP) and biolayer interferometry (BLI) were used to explore this issue to support metabolic engineering efforts aimed at improving carbohydrate processing to industrial chemicals.

Biotechnology & Applied Microbiology↗
DOE OSTI2017

InvS Coordinates Expression of PrgH and FimZ and Is Required for Invasion of Epithelial Cells by Salmonella enterica serovar Typhimurium

ABSTRACT Deep sequencing has revolutionized our understanding of the bacterial RNA world and has facilitated the identification of 280 small RNAs (sRNAs) in Salmonella . Despite the suspicions that sRNAs may play important roles in Salmonella pathogenesis, the functions of most sRNAs remain unknown. To advance our understanding of RNA biology in Salmonella virulence, we searched for sRNAs required for bacterial invasion into nonphagocytic cells. After screening 75 sRNAs, we discovered that the ablation of InvS caused a significant decrease of Salmonella invasion into epithelial cells. A proteomic analysis showed that InvS modulated the levels of several type III secreted Salmonella proteins. The level of PrgH, a type III secretion apparatus protein, was significantly lower in the absence of InvS, consistent with the known roles of PrgH in effector secretion and bacterial invasion. We discovered that InvS modulates fimZ expression and hence flagellar gene expression and motility. We propose that InvS coordinates the increase of PrgH and decrease in FimZ that promote efficient Salmonella invasion into nonphagocytic cells. IMPORTANCE Salmonellosis continues to be the most common foodborne infection reported by the CDC in the United States. Central to Salmonella pathogenesis is the ability to invade nonphagocytic cells and to replicate inside host cells. Invasion genes are known to be regulated by protein transcriptional networks, but little is known about the role played by small RNAs (sRNAs) in this process. We have identified a novel sRNA, InvS, that is involved in Salmonella invasion. Our result will likely provide an opportunity to better understand the fundamental question of how Salmonella regulates invasion gene expression and may inform strategies for therapeutic intervention.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2020

Coordinating and Assisting Research at the SARS-CoV-2/Microbiome Nexus

Although the COVID-19 pandemic is caused by a single virus, the rest of the human microbiome appears to be involved in the disease and could influence vaccine responses while offering opportunities for microbiome-directed therapeutics. The newly formed Microbiome Centers Consortium (MCC) surveyed its membership and identified four ways to leverage the strengths and experience of microbiome centers in the response to the COVID-19 pandemic. To meet these needs, the MCC will provide a platform to coordinate clinical and environmental research, assist with practical obstacles, and help communicate the connections between the microbiome and COVID-19. We ask that microbiome researchers join us in these efforts to address the ongoing pandemic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Novosphingobium aromaticivorans LigR coordinates transcription of genes involved in metabolism of multiple types of aromatics

Aromatic compounds are a ubiquitous and diverse family of chemicals with functions as biomolecules, natural products, industrial chemicals, and pollutants. Novosphingobium aromaticivorans DSM 12444 uses multiple inducible pathways to catabolize H-, G-, and S-type aromatics that contain zero, one, or two methoxy groups, respectively. Here, we obtain a systems-level view of the transcriptional control of its aromatic metabolic pathways. Several in vitro analyses found that a N. aromaticivorans homolog of the Sphingobium lignivorans SYK-6 transcription factor LigR bound genomic DNA upstream of genes involved in metabolism of multiple aromatic types. We found that a ΔLigR mutant had growth defects on all three types of aromatics as sole carbon sources. Transcriptomic analysis revealed that LigR was required to increase expression of gene products that function in metabolism of all three aromatic types. We also found that, in media containing both glucose and an aromatic carbon source, the ΔLigR mutant directed intermediates through alternative aromatic metabolic pathways. Protein-DNA binding assays showed that N. aromaticivorans LigR binds immediately upstream of promoters of genes involved in aromatic metabolism. We found that N. aromaticivorans LigR coordinates the expression of enzymes that function in the catabolism of H-, G-, and S-type aromatics, and that there are differences in the role of LigR in N. aromaticivorans and S. lignivorans. A comparative genomic analysis predicted that LigR homologs and the aromatic-metabolizing genes that it directly regulates are often co-localized in the genomes of Sphingomonadales, but often not found in this arrangement in many other known aromatic metabolizing bacteria.

Aromatic Compound Degradation↗
DOE OSTI2011

Structure and magnetic properties of heterometallic coordination carboxylate polymers with cobalt and lithium atoms

Reactions between lithium pivalate and cobalt coordination polymers [Co{sub 5}(OH{sub 2})(OH)(Piv){sub 9})L{sup 1}){sub 4}]{sub n} (I) and [Co{sub 2}(OH{sub 2})(Piv){sub 4}(L{sup 2}){sub 2}]{sub n} (II), where Piv-is the pivalate anion, L{sup 1} is pyrazine, and L{sup 2} is pyrimidine, result in new heterometallic polymers {l_brace}[Li{sub 2}Co{sub 2}(Piv){sub 6}(L{sup 1}){sub 2}]{sub 2}MeCN{r_brace}{sub n} (III), {l_brace}[Li{sub 2}Co{sub 2}(Piv){sub 6}(L{sup 2})]{sub 0.5}MeCN{r_brace}{sub n} (IV), and [Li{sub 2}Co{sub 2}(Piv){sub 6}(L{sup 2}){sub 2}]{sub n} (V). The resulting compounds contain tetra-nuclear {l_brace}Li{sub 2}Co{sub 2}(Piv){sub 6}{r_brace} fragments connected by neutral bridging ligands (pyrazine or pyrimidine) into layer structures. Crystal structures III-V are determined, and the magnetic properties of III and IV are studied.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Synthesis and physicochemical characterization of a porous coordination polymer of Sn-Cu xylarate: The structure of [Sn{sub 4}Cu{sub 8.5}(HL){sub 2}(L){sub 4}O{sub 2}(OH)(H{sub 2}O){sub 12.5}] {center_dot} 17.2H{sub 2}O

A porous coordination polymer of Sn-Cu xylarate [Sn{sub 4}Cu{sub 8.5}(HL){sub 2}(L){sub 4}O{sub 2}(OH)(H{sub 2}O){sub 12.5}] {center_dot} 17.2H{sub 2}O (H{sub 5}L is xylaric acid) is synthesized for the first time and characterized by chemical analysis, IR spectroscopy, and X-ray diffraction. Centrosymmetric heterometallic fragments [Sn{sub 4}Cu{sub 6}(HL){sub 2}(L){sub 4}O{sub 2}(H{sub 2}O){sub 6}] (A) including copper Cu1-3 and tin Sn1,2 atoms are distinguished in the structure. The Cu4(OH){sub 0.5}(H{sub 2}O){sub 2.5} bridges connect A units into chains running along the c axis, and the Cu5(OH)(H{sub 2}O) bridges connect A fragments into layers perpendicular to the c axis. The Cu4,5 atoms form a framework whose voids accommodate the crystallization water molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Crystal and molecular structure of the coordination compounds of Er{sup 3+} with 1-(methoxydiphenylphosphoryl)-2-diphenylphosphorylbenzene [ErL{sub 2}{sup 1}(NO{sub 3}){sub 2}]{sub 2}[Er(NO{sub 3}){sub 2}(H{sub 2}O){sub 5}]{sub 0.333}(NO{sub 3}){sub 2.333} · 2.833H{sub 2}O and its ethyl substituted derivative [ErL{sub 2}{sup 2}(NO{sub 3}){sub 2}][Er(NO{sub 3}){sub 5}]{sub 0.5} · 0.5H{sub 2}O

The coordination compounds of Er{sup 3+} with 1-(methoxydiphenylphosphoryl)-2-diphenylphosphorylbenzene [ErL{sub 2}{sup 1}(NO{sub 3}){sub 2}]{sub 2}[Er(NO{sub 3}){sub 2}(H{sub 2}O){sub 5}]{sub 0.333}(NO{sub 3}){sub 2.333} · 2.833H{sub 2}O (I) and its ethyl substituted derivative [ErL{sub 2}{sup 2}(NO{sub 3}){sub 2}][Er(NO{sub 3}){sub 5}]{sub 0.5} · 0.5H{sub 2}O (II) are synthesized and their crystal structures are studied. I and II contain [ErL{sub 2}(NO{sub 3}){sub 2}]{sup +} complex cations of identical composition and close structure. The eight-vertex polyhedron of the Er atom in the shape of a distorted octahedron with two split trans vertices is formed by the O atoms of the phosphoryl groups of L ligands and nitrate anions. L ligands close nine-membered metallocycles. The structures contain spacious channels which are populated differently, namely, by disordered [Er(NO{sub 3}){sub 2}(H{sub 2}O){sub 5}]{sup +} complex cations, NO{sub 3}{sup −} anions, and crystallization water molecules in I and disordered [Er(NO{sub 3}){sub 5}]{sup 2−} complex anions and crystallization water molecules in II. The IR spectra of I and II are studied.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Synthesis and crystal structure of a novel Mn(II) coordination polymer with 3-(4-(1H-benzo[d]imidazol-1-yl)-4-methoxyphenyl)-1-phenylprop-2-en-1-one ligands

3-(4-(1H-Benzo[d]imidazol-1-yl)-4-methoxyphenyl)-1-phenylprop-2-en-1-one (L{sup 1}, 1) and its Mn(II) complex, [Mn(L{sup 1}){sub 2}(SCN){sub 2}]{sub ∞} (2), were synthesized and characterized by elemental analyses, IR spectroscopy and single-crystal X-ray diffraction. The Mn(II) ion in 2 is six-coordinated to four nitrogen atoms of two L{sup 1} ligands, two SCN-ligands, and two oxygen atoms of other two L{sup 1} ligands to form a distorted octahedral geometry. Therefore, each L{sup 1} links Mn ions through the O and N atoms to generate 2D sheet structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Two new coordination polymers based on tartaric acid ligand: Syntheses, crystal structure and thermal stability

Two new coordination polymers [Cd{sub 3}(D-Tar){sub 3}]{sub n} (1) and [Pb(meso-Tar)]{sub n} (2) (H{sub 2}Tar = tartaric acid) have been synthesized by hydrothermal reaction and characterized by single crystal X-ray diffraction analysis and IR spectra. 1 crystallizes in the C222{sub 1} chiral space group and shows a 3D (4,4)-connected net with the (4.6.8{sup 4}){sub 4}(4.6{sup 2}.8{sup 2}.10)(4.6{sup 2}.8{sup 3})(4.6{sup 3}.8{sup 2})(4.6{sup 3}.8{sup 2}){sub 4}(4.8{sup 5}){sub 2} topology. 2 possesses a 3D (4,4)-connected net with the (4{sup 3}.6{sup 2}.8) topology. In addition, the thermogravimetric analyses (TGA) results for polymers are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Crystal Growth and Structural Characterization of a Thiocyanato-Bridged Copper(I/II) Mixed-Valence Coordination Polymer

A new mixed-valence coordination polymer [Cu{sub 3}(SCN){sub 4}(DMSO){sub 2}]{sub n} (SCN{sup –} = thiocyanato and DMSO = dimethyl sulfoxide) was prepared and characterized by single crystal X-ray diffraction method. The in situ formation of thiocyanate during the synthesis induces reduction of a part of Cu(II) to Cu(I). The three-dimensional structure of the binuclear thiocyanato bridged compound provided an example of pseudohalide materials containing two different environments for both copper centers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

The First Seven-Coordinated Triiodo Complex of Rhenium(III)

The reaction of cis-[ReO{sub 2}I(PPh{sub 3}){sub 2}] with tert-butyl isocyanide in benzene led to the isolation of the complex [ReI{sub 3}(CN-t-Bu){sub 3}(PPh{sub 3})] (1). The complex is unusual since it contains bulky ligands with large cone angles, i.e. three iodides, three isocyanides with tert-butyl groups and a triphenylphosphine as ligands in a seven-coordinate geometry around the rhenium(III) metal ion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Synthesis and Crystal Structure of a Four-coordinated Cobalt Complex with 1-Methylbenzimidazole

A four-coordinated complex, L{sub 2}Co(NCO){sub 2}, (L = 1-methylbenzimidazole) has been synthesized and characterized by IR spectroscopy, elemental analyses, and single crystal X-ray diffraction. The crystal is monoclinic, a = 14.522(2) Å, b = 14.610(2) Å, c = 8.6850(13) Å, β = 92.037(3)°, Z = 4, sp. gr. P2{sub 1}/c. Bond lengths Co–N(L) are equal to 2.0165(16) and 2.0174(15) Å, Co–O(NCO) are 1.944(2) and 1.945(2) Å. Intermolecular C–H···O, C–H···N, and C–H···π interactions link the molecules into three-dimensional networks in the crystal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Investigation of the Cosmic Rays Flux Anisotropy at High Energies (10{sup 15}–10{sup 17} eV) by Means of Muon Bundles Registered with the Coordinate-Tracking Detector DECOR

First results of the analysis of cosmic ray anisotropy from muon bundles recorded in the coordinate tracking detector DECOR of the Experimental Complex NEVOD during the 2013–2017 measurement series are discussed. Two event samples differing in the multiplicity of muons, selection conditions, and ranges of the zenith and azimuth angles are analyzed. Estimates of the anisotropy parameters of the flux of primary cosmic rays with energies of 10{sup 1}5–10{sup 1}7 eV are presented.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Two-Stage Conversion of Silicon to Nanostructured Carbon by the Method of Coordinated Atomic Substitution

Abstract—: A fundamentally new method of obtaining epitaxial layers of nanostructured carbon on silicon substrates has been considered. Epitaxial growth in the case of seemingly incompatible lattices has been achieved by converting the crystal by the method of coordinated substitution of atoms, in which the overall structure of the bonds between the atoms is not destroyed. In the first stage of conversion, the first half of the silicon atoms are concertedly replaced by the carbon atoms due to the reaction of silicon with CO gas, during which an epitaxial layer of SiC–3C cubic silicon carbide is obtained. In the second stage of conversion, the remaining half of silicon atoms is concertedly replaced by carbon atoms due to the reaction of SiC with CF{sub 4} gas. Carbon structures with different properties from nanodiamonds to nanotubes and carbon nanoonions have been obtained depending on the orientation of the silicon surface, pressure of the reagent gas, and temperature and growth time. A key feature of this method is that the substrate orders the resulting structures using the original chemical bonds between the atoms in silicon. The term “concertedly” means that new chemical bonds are formed simultaneously and concertedly with the destruction of old bonds. Data on electron diffraction and analysis of Raman and ellipsometric spectra of the obtained samples of nanostructured carbon on silicon substrates have been presented. Two competing growth mechanisms have been discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Interfacing of a Coordinate-Sensitive Detector Based on Charge-Coupled Devices for Recording Ions with a Portable Static Mass Spectrograph

An IDS 2030 IonCCD coordinate-sensitive detector (Analytical/CMS Field Products) is interfaced with a small-sized mass spectrograph developed at the Ioffe Physical Technical Institute, Russian Academy of Sciences. The measurement data obtained with the mass spectrograph using an IonCCD detector and a Magnum-5901-37029PS channel secondary electron multiplier (Photonics USA Inc., United States) are compared. The results of measurements are discussed, and the prospects for using the IonCCD coupled with a microchannel plate are assessed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Generalizable coordination of large multiscale workflows: challenges and learnings at scale

The advancement of machine learning techniques and the heterogeneous architectures of most current supercomputers are propelling the demand for large multiscale simulations that can automatically and autonomously couple diverse components and map them to relevant resources to solve complex problems at multiple scales. Nevertheless, despite the recent progress in workflow technologies, current capabilities are limited to coupling two scales. In the first-ever demonstration of using three scales of resolution, we present a scalable and generalizable framework that couples pairs of models using machine learning and in situ feedback. We expand upon the massively parallel Multiscale Machine-Learned Modeling Infrastructure (MuMMI), a recent, award-winning workflow, and generalize the framework beyond its original design. We discuss the challenges and learnings in executing a massive multiscale simulation campaign that utilized over 600,000 node hours on Summit and achieved more than 98% GPU occupancy for more than 83% of the time. We present innovations to enable several orders of magnitude scaling, including simultaneously coordinating 24,000 jobs, and managing several TBs of new data per day and over a billion files in total. Finally, we describe the generalizability of our framework and, with an upcoming open-source release, discuss how the presented framework may be used for new applications.

Bhatia, Harsh↗